The Basics of General, Organic, and Biological Chemistry

1

What Is Chemistry?

What Is Chemistry?

🧭 Overview

🧠 One-sentence thesis

Chemistry is the central science that studies matter and its changes, using the scientific method to generate testable explanations about the natural universe.

📌 Key points (3–5)

  • What chemistry studies: matter—what it consists of, its properties, and how it changes.
  • Why chemistry is central: chemical principles are essential for understanding other sciences like biology, geology, and medicine.
  • How science works: through the scientific method—proposing hypotheses, testing them through experiments, and refining them based on results.
  • Common confusion: hypothesis vs. theory—a hypothesis is a testable idea, while a theory is a general statement describing a large set of observations and represents the highest level of scientific understanding.
  • Chemistry's connections: chemistry overlaps with other fields (biochemistry, geochemistry) because the physical universe is interconnected.

🔬 Defining chemistry and its scope

🔬 What chemistry is

Chemistry is the study of matter—what it consists of, what its properties are, and how it changes.

  • Chemistry describes real-world processes: cooking food, striking a match, shampooing hair.
  • Example: describing the ingredients in a cake and how they change when baked is chemistry.
  • It focuses on physical, observable phenomena, not abstract concepts.

🌍 What matter is

Matter is anything that has mass and takes up space—that is, anything that is physically real.

  • Some matter is obvious (a book), some less so (air).
  • Matter vs. non-matter distinction:
    • Matter: a baby, the Empire State Building, air, stars
    • Not matter: ideas, emotions, love
  • Don't confuse: just because something is invisible (like air) doesn't mean it isn't matter.

🔗 Chemistry as the central science

  • Chemistry lies at the center of many scientific fields because chemical principles are essential for understanding other sciences.
  • The excerpt emphasizes that chemistry "pervades your life" and is fundamental to understanding the natural world.
  • Chemical processes are "continuously at work all around us."

🌐 Science and its branches

🌐 What science is

Science is the process by which we learn about the natural universe by observing, testing, and then generating models that explain our observations.

  • Science is a process, not just a body of knowledge.
  • It focuses on the natural universe—things that are physically real and observable.
  • Mathematics is described as "the language of science" used to communicate ideas.

🌳 How scientific fields relate

The excerpt describes science as divided into many branches, but with significant overlap:

FieldWhat it studies
ChemistryMatter
BiologyLiving things
GeologyRocks and the earth
BiochemistryOverlap of biology and chemistry
GeochemistryOverlap of geology and chemistry
  • Don't confuse: fields are divided for convenience, but the natural universe is interconnected, so overlap is common.
  • Example: some scientists work in both biology and chemistry, creating the field of biochemistry.

🚫 What is not science

The excerpt implies that not all fields of study are science:

  • Science studies "some aspect of the natural universe."
  • Fields like sculpture, politics, or astrology are not branches of science because they don't study the natural universe through observation and testing.
  • Example: astronomy (study of stars and planets) is science; astrology (predicting human events from star positions) is not.

🔍 The scientific method

🔍 Overview of the method

The scientific method is an organized procedure for learning answers to questions.

  • It provides a systematic way to investigate questions about the natural world.
  • The steps may not always be as clear-cut in real practice, but most scientific work follows this general outline.

📝 Step 1: Propose a hypothesis

A hypothesis is a testable idea to try to answer a question or explain how the natural universe works.

  • A scientist generates a hypothesis to answer a specific question.
  • Example question from the excerpt: "Why do birds fly toward Earth's equator during the cold months?"
  • Don't confuse hypothesis with theory (see below).

🧪 Step 2: Test the hypothesis

  • A scientist devises and carries out experiments to evaluate the hypothesis.
  • Possible outcomes:
    • If the hypothesis passes the test → it may be a proper answer
    • If it does not pass → it may not be a good answer

🔄 Step 3: Refine the hypothesis if necessary

  • Based on experimental results, a scientist may modify the hypothesis and test again.
  • Sometimes results show the original hypothesis is completely wrong, requiring a new hypothesis.
  • This iterative process reflects that science is self-correcting.

⚖️ Hypothesis vs. theory

Critical distinction to avoid confusion:

TermDefinitionLevel of certainty
HypothesisA testable ideaStarting point for investigation
TheoryA general statement describing a large set of observations and dataHighest level of scientific understanding
  • Don't confuse: when someone says "I have a theory that excess salt causes high blood pressure," they really have a hypothesis, not a theory.
  • A theory represents extensive testing and validation across many observations.

📜 Historical context: Alchemy

📜 Alchemy as chemistry's predecessor

  • Modern chemistry developed in the 1600s and 1700s based on principles considered valid today.
  • Before that, the study of matter was called alchemy, practiced mainly in China, Arabia, Egypt, and Europe.

🔮 How alchemy differed from chemistry

  • Alchemy was "mystical and secretive" rather than systematic and open.
  • Alchemists believed all matter was composed of four basic elements: fire, water, earth, and air.
  • They thought changing the proportions of these elements could transform substances.
  • Major goals:
    • Transmute common metals into gold
    • Synthesize the philosopher's stone (for long life or immortality)

🔒 Secrecy vs. communication

  • Alchemists used symbols to represent substances, but not to communicate ideas (as modern chemists do).
  • Purpose was to "maintain the secrecy of alchemical knowledge, keeping others from sharing in it."
  • Despite secrecy, alchemy was respected as a serious scholarly endeavor in its time.
  • Example: Isaac Newton, the great mathematician and physicist, was also an alchemist.
2

The Classification of Matter

The Classification of Matter

🧭 Overview

🧠 One-sentence thesis

Matter can be systematically classified by its properties (physical vs. chemical), composition (element, compound, or mixture), and phase (solid, liquid, or gas), allowing chemists to describe and understand all materials in the universe.

📌 Key points (3–5)

  • Two types of properties: physical properties describe matter's characteristics (size, shape, color), while chemical properties describe how matter changes chemically (e.g., flammability).
  • Three composition categories: elements cannot be broken down further, compounds contain multiple elements and can be broken down, and mixtures contain multiple substances that keep their identities.
  • Common confusion: homogeneous vs. heterogeneous mixtures—homogeneous mixtures (solutions) act like single substances, while heterogeneous mixtures show obvious separate components.
  • Three phases: solids have definite shape and volume, liquids have definite volume but take container shape, gases expand to fill containers.
  • Phase changes: substances can transition between phases (melting, boiling, freezing, etc.) when conditions like temperature change.

🔬 Properties of Matter

🔬 Physical properties

Physical properties: characteristics that describe matter, such as size, shape, color, and mass.

  • These describe what matter is or looks like, not how it changes.
  • They are observable features you can measure or detect without changing the substance's chemical identity.
  • Example: the color of a metal, the mass of a sample, or the shape of a crystal.

⚗️ Chemical properties

Chemical properties: characteristics that describe how matter changes its chemical structure or composition.

  • These describe what matter does when it undergoes chemical reactions.
  • The excerpt gives flammability (ability to burn) as the key example—burning changes the chemical composition.
  • Don't confuse: observing a chemical property usually requires changing the substance, while physical properties can be observed without chemical change.

🧱 Composition Categories

🧱 Elements

Element: a substance that cannot be broken down into chemically simpler components.

  • The most basic chemical building blocks.
  • The excerpt notes about 118 elements exist in the known universe.
  • Example: aluminum (used in soda cans) and oxygen.
  • The smallest part that maintains an element's identity is an atom.

🔗 Compounds

Compound: a substance that can be broken down into chemically simpler components (because it has more than one element).

  • Made of two or more elements combined chemically.
  • The excerpt notes tens of millions of different compounds have been identified.
  • Example: water is composed of hydrogen and oxygen elements.
  • The smallest part that maintains a compound's identity is a molecule (atoms attached together behaving as a unit).

🥗 Mixtures

Mixture: a material composed of two or more substances where individual substances maintain their chemical identities.

  • Unlike compounds, the components don't chemically combine—they just coexist.
  • Two types exist: heterogeneous and homogeneous.

🔀 Types of Mixtures

🔀 Heterogeneous mixtures

Heterogeneous mixtures: obvious combinations of two or more substances.

  • You can see the different components.
  • Example: a mixture of sand and water, or soil (composed of small pieces of various materials).
  • The components remain visibly separate.

💧 Homogeneous mixtures (solutions)

Homogeneous mixtures (or solutions): mixtures with a consistent composition throughout that act like a single substance.

  • The components are so intimately combined you cannot distinguish them.
  • Example: sugar dissolved in water, saltwater, air (nitrogen and oxygen), or steel (a solid solution/metal alloy).
  • Don't confuse with compounds: in solutions, substances maintain their chemical identities; in compounds, elements chemically bond to form something new.

🌡️ Phases and Phase Changes

🧊 The three phases

PhaseShapeVolumeBehavior
SolidDefiniteDefiniteMaintains fixed form
LiquidTakes container shapeDefiniteFlows but has fixed volume
GasTakes container shapeExpands to fill containerNeither definite shape nor volume
  • Example: water exists in all three phases—ice (solid), water (liquid), and steam (gas).

🔄 Phase changes

Phase change: a physical process in which a substance goes from one phase to another.

  • Typically caused by varying temperature (and less commonly, pressure).
  • Common phase changes include:
    • Solid to liquid: melting or fusion
    • Liquid to gas: boiling or evaporation
    • Liquid to solid: solidification or freezing
    • Gas to liquid: condensation
    • Solid to gas: sublimation
    • Gas to solid: deposition
  • Example: when liquid water boils to make gaseous water (steam), it undergoes a phase change.

🔬 Scales of Observation

🔭 Macroscopic vs. microscopic viewpoints

  • Macroscopic view: working with large numbers of atoms or molecules at a time—what we observe in everyday life.
  • Microscopic view: describing chemical events at the level of individual atoms or molecules.
  • The excerpt notes atoms are extremely tiny—217 million iron atoms would be needed to make a line 1 inch long.
  • Scientists use both viewpoints: we see bulk matter macroscopically, but understand it through microscopic particle behavior.

🧪 Substance definition

Substance: any sample of matter that has the same physical and chemical properties throughout the sample.

  • By definition, any single substance is pure (the word "pure" is sometimes added but not necessary).
  • There are two types: elements and compounds.
  • Don't confuse substances with mixtures: substances are uniform in composition and properties; mixtures contain multiple substances.
3

Measurements

Measurements

🧭 Overview

🧠 One-sentence thesis

A proper measurement in chemistry requires both a number (how many or how much) and a unit (the scale of measurement), and without both parts the quantity cannot be communicated correctly.

📌 Key points (3–5)

  • What a quantity is: an amount of something that consists of two parts—a number and a unit.
  • Why both parts matter: the number tells "how many/much" and the unit tells "what scale"; missing either part makes the measurement incomplete.
  • Common confusion: stating only a number (e.g., "12") without a unit leaves ambiguity—12 miles? 12 kilometers? 12 yards?
  • Real-world importance: proper quantities are crucial in medicine (dosages), everyday tasks (following instructions), and all scientific measurements.

📏 What makes a proper quantity

📏 The two required components

Quantity: an amount of something that consists of a number and a unit.

  • Number: tells us how many or how much of something.
  • Unit: tells us the scale of measurement being used.
  • Both parts must be included together to express a quantity properly.

❌ What happens without both parts

  • If someone answers "12" when asked about distance, you cannot know whether they mean 12 miles, 12 kilometers, 12 furlongs, or 12 yards.
  • The measurement is incomplete and cannot be properly communicated.
  • Example: A classmate says the homework is "twenty"—this could mean problem #20 or 20 problems total.

🔢 Identifying numbers and units

🔢 Simple quantities

Examples from the excerpt show how to break down quantities:

QuantityNumberUnit
one dozen eggsonedozen eggs
2.54 centimeters2.54centimeter
a box of pencils1 (implied)box of pencils
88 meters per second88meters per second

🔗 Compound units

  • Some units combine two measurements together.
  • Example: "88 meters per second" has a number (88) and a compound unit (meters and seconds combined).
  • Other examples: miles per hour, degrees Fahrenheit.

💊 Why measurements matter in practice

💊 Medical dosages

Dosage (or dose): the specific amount of a medicine known to be therapeutic for an ailment in a patient of a certain size.

  • Dosages are described by units of mass (grams or milligrams).
  • The amount must be precise: too little won't work; too much can cause harmful side effects.
  • Example: levothyroxine sodium tablets are available in 11 different doses ranging from 25 micrograms to 300 micrograms.

👨‍⚕️ Professional responsibility

  • Doctors must prescribe the correct dosage.
  • Pharmacists must provide the correct medicine at the prescribed dosage.
  • Proper quantities (numbers + units) are crucial for patient health and safety.

☕ Everyday measurements

  • Following instructions requires measurements: "4 cups of water and 3 scoops of coffee."
  • Medical checkups involve measurements: temperature, height, weight, blood pressure.
  • Chemists measure properties of matter and express them as quantities.
4

Expressing Numbers: Scientific Notation

Expressing Numbers: Scientific Notation

🧭 Overview

🧠 One-sentence thesis

Scientific notation provides a compact system for expressing extremely large or small numbers by rewriting them as a simple number multiplied by 10 raised to an appropriate power.

📌 Key points (3–5)

  • Why scientific notation exists: numbers with many zeros are cumbersome to work with, so scientists use a compact system based on powers of 10.
  • The convention: write a single nonzero first digit, a decimal point, the rest of the digits (excluding trailing zeros), then multiply by 10 raised to the necessary power.
  • Positive vs negative powers: numbers greater than 1 use positive powers; numbers less than 1 use negative powers.
  • Common confusion: the power equals the number of places the decimal moves—positive when moving left (large numbers), negative when moving right (small numbers).
  • Reversibility: converting from scientific to standard notation reverses the process by moving the decimal point in the opposite direction.

🔢 What scientific notation is and why it matters

🔢 The basic idea

Scientific notation: a system for expressing very large or very small numbers in a compact manner using powers of 10.

  • Instead of writing many zeros, rewrite the number as a simple figure multiplied by 10 raised to an exponent (also called a power).
  • Example: 1,500,000 miles can be thought of as 1.5 times 1 million, and 1 million equals 10 × 10 × 10 × 10 × 10 × 10, or 10 to the sixth power.
  • Therefore 1,500,000 = 1.5 × 10⁶.

🎯 Why it's useful

  • Real-world quantities can be enormous (e.g., 5,000,000,000,000 red blood cells in a liter of blood) or tiny (e.g., iron atom diameter of 0.000000014 inches).
  • Numbers with many zeros are cumbersome to write and prone to error.
  • Scientific notation is more convenient than listing a large number of zeros.

📏 The convention and how to apply it

📏 Standard format rules

The convention requires:

  • A single nonzero first digit
  • A decimal point
  • The rest of the digits (excluding any trailing zeros)
  • A multiplication sign
  • 10 raised to the power necessary to reproduce the original number

Example: although 1,500,000 could be written as 15. × 10⁵, the convention is to have only one digit before the decimal point, so 1.5 × 10⁶ is correct.

➡️ Converting large numbers (positive powers)

  • Move the decimal point to the left until it follows the first digit.
  • The power of 10 equals the number of places you moved the decimal.
  • The resulting number being multiplied must be between 1 and 10.
Original numberDecimal movesScientific notation
67,000,000,00010 places left6.7 × 10¹⁰
1,6893 places left1.689 × 10³
12.61 place left1.26 × 10¹

⬅️ Converting small numbers (negative powers)

  • For numbers with magnitude less than 1, use a negative power.
  • Move the decimal point to the right to follow the first nonzero digit.
  • The negative power indicates the number of places moved to the right.

Example: 0.006 can be expressed as 6 divided by 1,000, which equals 6 × 10⁻³.

Original numberDecimal movesScientific notation
0.0000065676 places right6.567 × 10⁻⁶
−0.00040044 places right−4.004 × 10⁻⁴
0.00000000000012313 places right1.23 × 10⁻¹³

Don't confuse: the negative sign on the number itself does not affect how the rules of scientific notation are applied; it's separate from the sign of the power.

🔄 Converting back to standard notation

🔄 Reversing the process

To change scientific notation back to standard notation, move the decimal point in the opposite direction.

➡️ Positive powers (move right)

  • Move the decimal point to the right by the number of places indicated by the power.
  • Add zeros to the end if necessary to produce a number of the proper magnitude.

Example: 5.27 × 10⁴ becomes 52,700 (decimal moved 4 places right).

⬅️ Negative powers (move left)

  • Move the decimal point to the left by the number of places indicated by the power.
  • Add zeros as needed.

Example: 6.22 × 10⁻² becomes 0.0622 (decimal moved 2 places left).

🧮 Key patterns to remember

🧮 The magnitude rule

MagnitudePower signExample
Greater than 1Positive power5,230,000 = 5.23 × 10⁶
Less than 1Negative power0.000064 = 6.4 × 10⁻⁴

🧮 Powers of 10 reference

For large numbers:

  • 10⁰ = 1
  • 10¹ = 10
  • 10² = 100
  • 10³ = 1,000
  • 10⁴ = 10,000

For small numbers:

  • 10⁻¹ = 1/10
  • 10⁻² = 1/100
  • 10⁻³ = 1/1,000
  • 10⁻⁴ = 1/10,000
  • 10⁻⁵ = 1/100,000

⚠️ Calculator note

Many calculators handle scientific notation, but the method for entering it differs by model. Learning to enter scientific notation properly is essential; incorrect entry will produce wrong final answers in calculations.

5

Expressing Numbers: Significant Figures

Expressing Numbers: Significant Figures

🧭 Overview

🧠 One-sentence thesis

Significant figures communicate the precision of a measurement by including all known digits plus the first estimated digit, and specific rules govern how to preserve this precision when performing calculations.

📌 Key points (3–5)

  • What significant figures represent: all digits known with certainty plus the first uncertain (estimated) digit in a measurement.
  • Why they matter: they prevent reporting false precision beyond what the measuring instrument can actually determine.
  • Rules for identifying significant figures: nonzero digits are always significant; zeros may or may not be significant depending on their position.
  • Common confusion: trailing zeros—they are significant only if the number has a decimal point (1,500 has two sig figs; 1,500.00 has six).
  • Calculation rules differ: addition/subtraction limits by decimal position; multiplication/division limits by count of significant figures.

🔍 What significant figures mean

🔍 Definition and purpose

Significant figures: all the digits known with certainty and the first uncertain, or estimated, digit.

  • A measurement reflects the precision of the measuring instrument.
  • The last digit reported is always an estimate based on the finest marking available.
  • It makes no sense to report digits beyond the first uncertain one.
  • Example: A meterstick marked in millimeters can measure to the nearest millimeter, with the next decimal place estimated; reporting more digits would falsely suggest greater precision.

📏 Why the last digit is estimated

  • Measuring instruments have limits—marks indicate certain values, but between marks you must estimate.
  • If a table measures 1,357 mm, the digits 1, 3, and 5 are certain (read directly from marks), and the 7 is estimated.
  • Reporting 1,357.0 or 1,357.00 would wrongly imply the instrument could measure to tenths or hundredths of a millimeter.

🚫 Zeros as placeholders

  • Zeros are used to position significant figures correctly.
  • Not all zeros are significant—some only serve to place other digits in the correct decimal position.
  • Example: In 0.000458, the first four zeros are not significant; they only position the digits 4, 5, and 8.

📐 Rules for identifying significant figures

✅ Rule 1: All nonzero digits are significant

  • Any digit from 1 to 9 is always significant.
  • Example: In 1,357, all four digits are significant.

✅ Rule 2: Captive (embedded) zeros are significant

  • Zeros between nonzero digits are always significant.
  • Example: In 405, all three digits are significant (the zero is between 4 and 5).

❌ Rule 3: Leading zeros are not significant

  • Leading zeros appear at the beginning of a decimal number less than 1.
  • They are never significant; they only position the decimal point.
  • Example: In 0.000458, the first four digits (0.000) are leading zeros and not significant; this number has three significant figures (4, 5, 8).

⚠️ Rule 4: Trailing zeros depend on the decimal point

  • Trailing zeros are zeros at the end of a number.
  • Without a decimal point: trailing zeros are not significant.
    • Example: 1,500 has two significant figures (the two trailing zeros are not significant).
  • With a decimal point: all trailing zeros are significant.
    • Example: 1,500.00 has six significant figures (all digits, including trailing zeros, are significant).
  • Don't confuse: The presence or absence of a decimal point completely changes whether trailing zeros count.
NumberDecimal point?Significant figuresExplanation
1,500No2Trailing zeros not significant
1,500.00Yes6All digits including trailing zeros significant
6,798,000No4Three trailing zeros not significant
6,000,798.00Yes9All digits significant

🧮 Calculation rules for significant figures

➕ Addition and subtraction: align by decimal position

  • Rule: Stack numbers with decimal points aligned, then limit the answer to the rightmost column where all numbers have significant figures.
  • The answer's precision is limited by the least precise measurement (the one with the fewest decimal places).
  • Example: Adding numbers with values in the tenths, hundredths, and thousandths places—if one number only goes to the tenths place, the answer must be limited to the tenths place.
  • After identifying the rightmost significant column, drop all digits to the right and round appropriately.

✖️ Multiplication and division: count significant figures

  • Rule: Count the significant figures in each number, then limit the answer to the lowest count.
  • The answer cannot be more precise than the least precise input.
  • Example: Multiplying a number with four significant figures by a number with three significant figures—the answer must have three significant figures.
  • After calculation, round the result to match the lowest count of significant figures from the inputs.

🔄 Rounding rules

  • If the first dropped digit is 5 or higher: round up.
  • If the first dropped digit is lower than 5: do not round up.
  • Example: Dropping digits after 1,459.08—the first dropped digit (hundredths place) is 8, so round up the tenths place from 0 to 1, giving 1,459.1.
  • Example: If the result is 4,094.1 and you need four significant figures, the first dropped digit is 1 (less than 5), so do not round up; the answer is 4,094.

🔬 Scientific notation removes ambiguity

  • Scientific notation explicitly shows all significant figures in the leading number.
  • Example: 450 with two significant figures is written as 4.5 × 10 to the power 2.
  • Example: 450.0 with four significant figures is written as 4.500 × 10 to the power 2.
  • All significant figures are listed explicitly, eliminating confusion about trailing zeros.

⚠️ Important reminders

🖩 Calculators do not understand significant figures

  • Calculators display many digits, often far beyond the precision of the input data.
  • Example: Dividing 125 by 307 gives 0.4071661238… on a calculator, but if both inputs have only three significant figures, reporting all those digits is meaningless.
  • You must apply the rules: the calculator cannot determine the appropriate number of significant figures—only the user can.

🎯 Why significant figures matter

  • They properly communicate the precision and reliability of measurements.
  • Reporting too many digits suggests false precision; reporting too few loses information.
  • Significant figures ensure that calculated results reflect the limitations of the original measurements.
6

The International System of Units

The International System of Units

🧭 Overview

🧠 One-sentence thesis

The International System of Units (SI) provides a standardized measurement framework for scientists worldwide, built from seven base units that can be combined with prefixes and mathematical operations to express any quantity needed in chemistry and other sciences.

📌 Key points (3–5)

  • Why SI exists: to enable efficient communication among scientists around the world through standardized units.
  • Seven base units: SI has seven fundamental units; chemistry primarily uses five (mole, kilogram, meter, second, kelvin).
  • Prefix system: prefixes multiply or divide base units by powers of 10, creating convenient sizes (e.g., kilo- = 1,000×, milli- = 1/1,000×).
  • Derived units: combinations of base units (multiplied or divided) create units for other quantities like volume (m³), energy (joules), and density (g/cm³).
  • Common confusion: don't confuse base units with derived units—base units are fundamental, while derived units are mathematical combinations of base units.

📏 Base units and the SI foundation

📏 What are base units

Base (or basic) units are the fundamental units of SI.

  • SI defines exactly seven base units by international convention.
  • Each base unit measures one fundamental property (length, mass, time, etc.).
  • The size of each base unit is defined by international standards—for example, the kilogram is defined by a special metal cylinder kept in France.

🧪 The five base units chemistry uses

PropertyUnitAbbreviation
Amountmolemol
Masskilogramkg
Lengthmeterm
Timeseconds
TemperaturekelvinK
  • The degree Celsius (°C) is also commonly used for temperature.
  • Relationship: K = °C + 273
  • Note: The kilogram itself already contains a prefix (kilo-) combined with the gram.

🌍 Why SI matters globally

  • Many countries have adopted SI units for everyday use.
  • The United States is one of the few countries that has not fully adopted SI for everyday measurements.
  • The United States uses the English system (inches, feet, miles, gallons, pounds) for many quantities.
  • Scientists worldwide use SI to communicate efficiently regardless of their country's everyday measurement system.

🔢 The prefix system

🔢 How prefixes work

  • Prefixes attach to base units to create units that are larger or smaller by powers of 10.
  • Some prefixes create multiples: 1 kilogram = 1,000 grams; 1 megameter = 1,000,000 meters.
  • Other prefixes create fractions: 1 centimeter = 1/100 meter; 1 millimeter = 1/1,000 meter; 1 microgram = 1/1,000,000 gram.
  • The combination of a prefix abbreviation with a base unit abbreviation gives the abbreviation for the modified unit (e.g., kg for kilogram).

📊 Common SI prefixes

PrefixAbbreviationMultiplicative FactorScientific Notation
giga-G1,000,000,000×10⁹×
mega-M1,000,000×10⁶×
kilo-k1,000×10³×
deca-D10×10¹×
deci-d1/10×10⁻¹×
centi-c1/100×10⁻²×
milli-m1/1,000×10⁻³×
micro-μ1/1,000,000×10⁻⁶×
nano-n1/1,000,000,000×10⁻⁹×

Note: μ is the Greek lowercase letter for m, pronounced "myoo."

🎯 Why prefixes are convenient

  • Base unit sizes are not always convenient for all measurements.
  • Example: A meter is too large for describing human hair width.
  • Instead of reporting hair diameter as 0.00012 m or 1.2 × 10⁻⁴ m, you can use a smaller unit with a prefix.
  • Prefixes let you express the same quantity in a more readable form.

🧩 Derived units

🧩 What derived units are

Derived units are combinations of SI base units.

  • Units can be multiplied and divided, just as numbers can.
  • Derived units are built by mathematical operations on base units.
  • Don't confuse: base units are fundamental and defined by convention; derived units are constructed from base units through multiplication or division.

📦 Volume

Volume is the amount of space that a given substance occupies and is defined geometrically as length × width × height.

  • Each distance is expressed in meters, so volume has the derived unit m × m × m = m³ (cubic meters).
  • A cubic meter is rather large, so scientists typically use 1/1,000 of a cubic meter.
  • This unit has its own name: the liter (L).
  • A liter is a little larger than 1 US quart.
  • A liter is also 1,000 cm³.
  • By definition, 1 mL = 1 cm³ (1 milliliter equals 1 cubic centimeter).

⚡ Energy

Energy is the ability to perform work, such as moving a box from one side of a room to the other.

  • Energy has a derived unit of kg·m²/s² (the dot implies multiplication).
  • This combination is redefined as a joule (J) because the full form is cumbersome.
  • An older unit, the calorie (cal), is also widely used.
  • Conversion: 4.184 J = 1 cal.
  • All chemical processes occur with a simultaneous change in energy.

Food energy context:

  • The food industry uses the kilocalorie and calls it the Calorie (capital C).
  • 1 Calorie = 1,000 calories (lowercase c).
  • Average daily energy requirement: about 2,000–2,500 Calories = 2,000,000–2,500,000 calories.
  • If energy intake equals energy expenditure, body weight remains stable; excess intake leads to weight gain (stored as fat); deficit leads to weight loss.

🏋️ Density

Density is defined as the mass of an object divided by its volume; it describes the amount of matter contained in a given amount of space.

  • Formula: density = mass / volume
  • Units of density: units of mass divided by units of volume.
  • Common density units: g/cm³ or g/mL (for solids and liquids), g/L (for gases), kg/m³.

Examples from the excerpt:

  • Water: about 1.00 g/cm³
  • Mercury: 13.6 g/mL (over 13 times as dense as water—contains over 13 times the amount of matter in the same space)
  • Air at room temperature: about 1.3 g/L

Sample calculation:

  • A 25.3 cm³ bone sample has a mass of 27.8 g.
  • Density = 27.8 g / 25.3 cm³ = 1.10 g/cm³

🔄 How units follow math rules

  • Units follow the same mathematical rules as numbers.
  • Units can be multiplied: 2 cm × 2 cm = 4 cm² (area).
  • Units can be divided: mass / volume = density.
  • Example: mL × (g/mL) = g (the mL cancels out).

🌐 Approximate equivalents

🌐 SI to English conversions

SI UnitApproximate English Equivalent
1 m≈ 39.36 in. ≈ 3.28 ft ≈ 1.09 yd
1 cm≈ 2.54 in.
1 km≈ 0.62 mi
1 kg≈ 2.20 lb
1 lb≈ 454 g
1 L≈ 1.06 qt
1 qt≈ 0.946 L
  • These conversions help relate SI units to the English system still used in the United States for everyday measurements.
7

Converting Units

Converting Units

🧭 Overview

🧠 One-sentence thesis

Unit conversion is a systematic technique using conversion factors to change measurements from one unit to another while preserving the quantity's value and correctly tracking significant figures.

📌 Key points (3–5)

  • What a conversion factor is: a fraction with equivalent quantities in numerator and denominator but expressed in different units, which equals 1.
  • How to set up conversions: multiply the original quantity by a conversion factor arranged so the old unit cancels and the new unit appears.
  • Exact vs. measured numbers: prefix-based conversions (like kg to g) use exact numbers that don't affect significant figures, but conversions from measurements (like density) do.
  • Common confusion: which conversion factor to use—always place the unit you want to cancel in the denominator so it cancels algebraically with the numerator.
  • Multi-step conversions: complex conversions can be done step-by-step or combined into one calculation; both methods yield the same answer if done correctly.

🔧 What conversion factors are and why they work

🔧 Definition and structure

Conversion factor: a fraction that has equivalent quantities in the numerator and the denominator but expressed in different units.

  • Because the numerator and denominator represent the same quantity (just in different units), the fraction equals 1.
  • Multiplying by a conversion factor is the same as multiplying by 1, so it doesn't change the actual value—only the units.
  • Example: 100 cm = 1 m, so both 100 cm / 1 m and 1 m / 100 cm are valid conversion factors that equal 1.

⚖️ Why multiplying by 1 preserves the quantity

  • The excerpt emphasizes that dividing both sides of an equation by the same quantity (number and unit) maintains equality.
  • When the same quantity appears in numerator and denominator, the fraction equals 1.
  • This is the mathematical foundation: you're not changing the measurement, only its expression.

🎯 How to perform unit conversions

🎯 The basic procedure

The general process is:

quantity (in old units) × conversion factor = quantity (in new units)

Steps:

  1. Write the quantity you are given.
  2. Multiply by a conversion factor.
  3. Arrange the conversion factor so the original unit cancels.
  4. Perform the calculation.
  5. Report the answer with correct significant figures.

🔄 Choosing the correct conversion factor orientation

  • Key rule: construct the conversion factor so the original unit cancels out.
  • The unit you want to eliminate must appear in the denominator of the conversion factor (so it cancels with the numerator of your starting quantity).
  • The unit you want to introduce should be in the numerator of the conversion factor.

Don't confuse: If you use the conversion factor upside-down, the units won't cancel properly and you'll get a meaningless result.

Example from the excerpt: converting 3.55 m to cm

  • Correct: 3.55 m × (100 cm / 1 m) = 355 cm — meters cancel
  • Wrong: 3.55 m × (1 m / 100 cm) = 0.0355 m²/cm — units don't cancel correctly

📐 Canceling units algebraically

  • Units follow the same mathematical rules as numbers.
  • When the same unit appears in both numerator and denominator, it cancels.
  • Example: (3.55 m / 1) × (100 cm / 1 m) — the "m" cancels, leaving only "cm"

🔢 Significant figures in conversions

🔢 Exact numbers vs. measured numbers

Exact numbers: defined or counted numbers, not measured numbers, and can be considered as having an infinite number of significant figures.

TypeExamplesEffect on sig figs
Exact (prefix-based)1 kg = 1,000 g; 1 m = 100 cmDo NOT limit significant figures
Exact (counted)16 students in a classroomDo NOT limit significant figures
MeasuredDensity values from measurementDO limit significant figures
  • Numbers in conversion factors based on prefix definitions (kilo-, milli-, etc.) are exact by definition.
  • These exact numbers are not considered when determining significant figures in the final answer.
  • Conversion factors from measurements or approximations have limited significant figures and must be considered.

📏 Applying sig fig rules

  • For conversions using exact factors: the original measurement's significant figures determine the answer's precision.
  • Example from excerpt: 4.7 L has 2 sig figs; converting to mL using the exact factor 1,000 mL/L gives 4,700 mL, reported as 4,700 mL (2 sig figs).
  • Normal multiplication/division rules apply when conversion factors contain measured values.

🔗 Special conversions and multi-step problems

🔗 Using density as a conversion factor

  • Density relates mass and volume, so it can convert between them.
  • Example: mercury has density 13.6 g/mL, meaning 13.6 g mercury = 1 mL mercury.
  • Two possible conversion factors: 13.6 g / 1 mL or 1 mL / 13.6 g
  • Choose based on which unit you need to cancel.

Scenario: What is the mass of 16 mL of mercury?

  • Use 13.6 g / 1 mL so mL cancels: 16 mL × (13.6 g / 1 mL) = 217.6 g
  • Round to 220 g (2 sig figs, limited by the 16 mL measurement)

Scenario: What is the volume of 0.750 g of mercury?

  • Use 1 mL / 13.6 g so g cancels: 0.750 g × (1 mL / 13.6 g) = 0.0551 mL

🪜 Multi-step conversions

  • Sometimes you need more than one conversion to reach the desired unit.
  • Two approaches: convert step-by-step, or combine all conversions in one expression.
  • Both methods are acceptable and should give the same answer.

Step-by-step approach:

  1. Convert to the base unit first (e.g., km → m)
  2. Then convert from base unit to final unit (e.g., m → mm)

Combined approach:

  • Chain multiple conversion factors together in one calculation
  • Example: 54.7 km × (1,000 m / 1 km) × (1,000 mm / 1 m) = 5.47 × 10⁷ mm

Important: Apply significant figure rules only after the final step when combining conversions.

🧮 Scientific notation in conversions

  • Large or small results should be expressed in scientific notation.
  • Example: 54,700,000 mm is written as 5.47 × 10⁷ mm
  • The excerpt shows this is standard practice for very large or very small converted values.

🏥 Practical applications

💊 Medical and health contexts

The excerpt provides several real-world scenarios:

  • Nursing: A nurse with 50 mg aspirin tablets who must administer 0.2 g needs to know 0.2 g = 200 mg, so 4 tablets are needed.
  • Body measurements: Bone density (0.95–1.05 g/cm³ for healthy individuals; below 0.6–0.7 g/cm³ indicates osteoporosis)
  • Urine analysis: Density of urine provides health clues (normal specific gravity: 1.002 to 1.028)
  • Body fat: Overall body density correlates with body fat percentage (fat is less dense than muscle)

🔬 Why the formal procedure matters

  • Simple conversions might be done mentally, but the formal method works for all problems.
  • The excerpt emphasizes: "In later studies, the conversion problems you will encounter will not always be so simple."
  • Mastering the conversion factor technique prepares you for complex, multi-step problems.
8

The Elements

The Elements

🧭 Overview

🧠 One-sentence thesis

Elements are the fundamental chemical building blocks of matter that cannot be broken down into simpler substances, and each element is represented by a unique chemical symbol for convenient use in chemistry.

📌 Key points (3–5)

  • What an element is: a substance that cannot be broken down into simpler chemical substances; about 118 elements are known today (90 naturally occurring, ~30 created by technology).
  • Abundance varies widely: hydrogen dominates the universe (~90% of atoms), but Earth's crust is mostly oxygen (46.1%) and silicon (28.5%); the human body concentrates certain rare elements like carbon.
  • Chemical symbols: each element has a one- or two-letter abbreviation (first letter capitalized, second lowercase) derived from its name or earlier Latin name.
  • Common confusion: element abundance in the human body vs. Earth's crust—the body concentrates elements based on availability in assimilable forms (e.g., carbon from food, not air), not just crustal abundance.
  • Atomic theory foundation: all elements are composed of atoms, the smallest units that maintain an element's identity; some elements exist as individual atoms, others as diatomic molecules.

🌍 Abundance of elements

🌌 Universe vs. Earth

LocationMost abundant elementSecond most abundantKey difference
UniverseHydrogen (~90% of atoms)Helium (most of remaining 10%)All other elements are trace amounts
Earth's crustOxygen (46.1% by mass)Silicon (28.5%)Hydrogen is only 0.14%
  • The situation on Earth is "rather different" from the universe as a whole.
  • Oxygen dominates Earth's crust, mostly in combination with other elements.

🧬 Human body composition

The relative amounts of elements in the body have less to do with their abundances on Earth than with their availability in a form we can assimilate.

  • Oxygen is highest in both Earth's crust and the human body.
  • Carbon is the second-highest element in the body (23%) but is relatively rare on Earth (part of the 0.174% "other" in crustal composition).
  • How the body concentrates rare elements: we obtain elements from accessible sources—oxygen and hydrogen from air and water, carbon and nitrogen from food (not from atmospheric CO₂ or N₂).

🔬 Phosphorus bottleneck example

  • Phosphorus makes up 1.1% of the human body but only 0.105% of Earth's crust.
  • It is essential for bones, teeth, and all living cells, but there is no convenient environmental source like CO₂ for carbon.
  • Why it matters: phosphorus availability limits the amount of life Earth can sustain.
  • Example: phosphorus-containing detergents in the 1950s increased algae growth in lakes → bacteria consumed dead algae → oxygen dropped → fish died (eutrophication). Modern detergents often omit phosphorus to prevent this.
  • Don't confuse: abundance in the body with abundance in the environment; availability matters more than total crustal percentage.

🔤 Chemical symbols

🔤 What they are and why they're used

Each element name is abbreviated as a one- or two-letter chemical symbol.

  • Element names can be cumbersome to write in full, especially in compound names.
  • Convention: first letter is capitalized, second letter (if present) is lowercase.
  • Example: Bromine → Br, Calcium → Ca, Gold → Au.

🏛️ Origin of symbols

  • Usually the first letter of the element's name, plus another letter from the name.
  • Some symbols derive from earlier (mostly Latin) names and may not match the English name.
ElementSymbolOrigin
GoldAuLatin aurum
SilverAgLatin argentum
IronFeLatin ferrum
LeadPbLatin plumbum
TinSnLatin stannum
SodiumNaLatin natrium
PotassiumKLatin kalium
MercuryHgLatin hydrargyrum
TungstenWGerman wolfram
  • Don't confuse: CO (carbon monoxide, a compound) with Co (cobalt, an element); the second letter must be lowercase for a single element symbol.

🌐 Names in other languages

  • Element names in other languages are often close to their Latin names.
  • Example: gold is oro in Spanish, or in French (compare Latin aurum); silver is argent in French (compare argentum).

⚛️ Atomic theory

⚛️ What the modern atomic theory states

The modern atomic theory, proposed about 1803 by the English chemist John Dalton, is a fundamental concept that states that all elements are composed of atoms.

  • Atom definition: the smallest part of an element that maintains the identity of that element.
  • Individual atoms are extremely small: the largest atom has a diameter of only about 5.4 × 10⁻¹⁰ meters.
  • Example: it takes over 18 million of the largest atoms, lined up side by side, to equal the width of a little finger (about 1 cm).

🧪 How elements exist

  • Most elements: exist as individual atoms in their pure form.
    • Example: a macroscopic chunk of iron metal is composed, microscopically, of individual atoms.
  • Some elements: exist as groups of atoms called molecules.

🔗 Diatomic molecules

Several important elements exist as two-atom combinations and are called diatomic molecules.

  • Represented by the element symbol with a subscript 2 (e.g., H₂, O₂).
  • The seven diatomic elements: hydrogen (H₂), oxygen (O₂), nitrogen (N₂), fluorine (F₂), chlorine (Cl₂), bromine (Br₂), and iodine (I₂).

📜 Historical context

  • The concept of atoms is very old: Greek philosophers Leucippus and Democritus introduced atomic concepts in the fifth century BC.
  • The word atom comes from Greek atomos, meaning "indivisible" or "uncuttable."
  • What made Dalton's theory "modern": he had experimental evidence (formulas of simple chemicals, behavior of gases) and used the scientific method, not just philosophical discussion.
  • Don't confuse: ancient atomic philosophy (speculative) with modern atomic theory (evidence-based).
9

Atomic Theory

Atomic Theory

🧭 Overview

🧠 One-sentence thesis

The modern atomic theory establishes that all matter is composed of atoms—the smallest parts of an element that maintain that element's identity—and this theory is supported by experimental evidence rather than just philosophical speculation.

📌 Key points (3–5)

  • What atoms are: the smallest parts of an element that maintain the identity of that element; extremely small (largest atom ≈ 5.4 × 10⁻¹⁰ m diameter).
  • The fundamental concept: all elements are composed of atoms.
  • How elements exist: most elements exist as individual atoms, but some exist as diatomic molecules (two-atom combinations).
  • Common confusion: ancient Greek atomic concepts vs. modern atomic theory—Dalton's version is "modern" because it rests on experimental evidence (formulas, gas behavior), not just philosophical discussion.
  • Key diatomic elements: hydrogen (H₂), oxygen (O₂), nitrogen (N₂), fluorine (F₂), chlorine (Cl₂), bromine (Br₂), and iodine (I₂).

🔬 What atoms are and their scale

🔬 Definition of an atom

Atom: the smallest part of an element that maintains the identity of that element.

  • Atoms are the ultimate building blocks of all matter.
  • They are not just "small pieces"; they are the smallest pieces that still preserve what makes an element that element.

📏 Size of atoms

  • Individual atoms are extremely small.
  • Even the largest atom has an approximate diameter of only 5.4 × 10⁻¹⁰ meters.
  • Example: it takes over 18 million of these atoms, lined up side by side, to equal the width of your little finger (about 1 cm).
  • This scale emphasizes that atoms are far beyond everyday human perception.

🧪 How elements exist in nature

🧪 Individual atoms vs. molecules

Most elements in their pure form exist as individual atoms.

  • Example: a macroscopic chunk of iron metal is composed, microscopically, of individual atoms.
  • However, some elements exist as groups of atoms called molecules.

🔗 Diatomic molecules

Diatomic molecule: a two-atom grouping that behaves as a single chemical entity.

  • Several important elements exist as two-atom combinations.
  • In representing a diatomic molecule, we use the symbol of the element and include the subscript 2 to indicate that two atoms of that element are joined together.

📋 The seven diatomic elements

The elements that exist as diatomic molecules are:

ElementSymbol
HydrogenH₂
OxygenO₂
NitrogenN₂
FluorineF₂
ChlorineCl₂
BromineBr₂
IodineI₂

Don't confuse: helium exists as individual He atoms, but hydrogen exists as H₂ molecules in its elemental form. Similarly, calcium exists as individual Ca atoms, but chlorine exists as Cl₂ molecules.

🏛️ Historical context: ancient vs. modern atomic theory

🏛️ Ancient Greek origins

  • The Greek philosophers Leucippus and Democritus originally introduced atomic concepts in the fifth century BC.
  • The word "atom" comes from the Greek word "atomos," which means "indivisible" or "uncuttable."
  • However, this was purely philosophical discussion without experimental support.

🔬 Why Dalton's theory is "modern"

Dalton's ideas are called the modern atomic theory because:

  • Dalton had experimental evidence that the ancient Greek philosophers didn't have.
  • His evidence included the formulas of simple chemicals and the behavior of gases.
  • In the 150 years or so before Dalton, natural philosophy had been maturing into modern science, and the scientific method was being used to study nature.
  • When Dalton announced his theory, he was proposing a fundamental theory to describe many previous observations of the natural world, not just participating in philosophical discussion.

👤 John Dalton

  • John Dalton was an English scientist who enunciated the modern atomic theory.
  • He used the scientific method and experimental evidence to support his claims.

🎯 Core takeaways

🎯 The modern atomic theory statement

The modern atomic theory states that all matter is composed of atoms.

  • This is the fundamental concept that unifies chemistry.
  • It means every element, every compound, every material substance is ultimately built from atoms.

🎯 Atoms as building blocks

  • Atoms are the ultimate building blocks of all matter.
  • They establish the concepts of how matter is composed at the most fundamental level.
  • Understanding atoms is essential for understanding chemistry and the natural world.
10

The Structure of Atoms

The Structure of Atoms

🧭 Overview

🧠 One-sentence thesis

Atoms are composed of three subatomic particles—protons and neutrons concentrated in a central nucleus, with electrons orbiting in the surrounding space—which explains why atoms are mostly empty space despite having measurable mass.

📌 Key points (3–5)

  • Three subatomic particles: protons (positive charge, large mass), neutrons (no charge, large mass), and electrons (negative charge, tiny mass).
  • Arrangement: protons and neutrons are grouped in the nucleus; electrons orbit outside the nucleus.
  • Mass vs. volume: most of an atom's mass is in the nucleus, but most of an atom's volume is empty space occupied by electron orbits.
  • Common confusion: the planetary model (electrons in fixed circular orbits) is overly simplistic—electrons actually form fuzzy clouds around the nucleus, not discrete orbits.
  • Experimental evidence: Rutherford's metal-foil experiments (1909–1911) showed that most alpha particles pass straight through atoms, proving atoms are mostly empty space with a dense central nucleus.

⚛️ The three subatomic particles

🔬 Discovery and properties

The three particles were discovered over time:

  • Electron (1897): identified first.
  • Proton (by 1920): experimental evidence confirmed its existence.
  • Neutron (1932): evidence established the third particle.

⚡ Charge and mass characteristics

ParticleSymbolChargeMass (kg)Relative mass (proton = 1)
Protonp⁺+1 (positive)1.673 × 10⁻²⁷1
Neutronn⁰0 (neutral)1.675 × 10⁻²⁷1
Electrone⁻−1 (negative)9.109 × 10⁻³¹0.00055

Key contrasts:

  • Protons and neutrons have nearly the same mass (about 2,000 times greater than an electron).
  • Protons and electrons have the same amount of charge, but opposite signs.
  • Neutrons have no electrical charge.

🧲 How charges interact

  • Opposite charges attract each other; like charges repel.
  • Protons (positive) attract electrons (negative), and vice versa.
  • This attraction explains why electrons stay near the nucleus.

🎯 Rutherford's nucleus model

🧪 The Geiger-Marsden experiment (1909–1911)

Ernest Rutherford, Hans Geiger, and Ernest Marsden performed experiments to probe atomic structure:

  • Setup: aimed a beam of positively charged alpha particles (combinations of two protons and two neutrons) at very thin metal foil (gold or platinum).
  • Detection: used a scintillator (glows when hit) or unexposed film to track where particles ended up after hitting the foil.

🎲 Unexpected results

  • Most particles traveled straight through the foil.
  • Some particles were deflected to one side.
  • A few particles were deflected back toward the source.

Rutherford remarked: "It was almost as incredible as if you fired a 15-inch shell at a piece of tissue paper and it came back and hit you."

🏛️ The nuclear model explanation

Nucleus: the central region of an atom that contains protons and neutrons.

Rutherford proposed:

  • Protons and neutrons are concentrated in a tiny, dense nucleus.
  • Electrons orbit outside the nucleus, attracted by the positive charge.
  • Most of the atom's mass is in the nucleus.
  • Most of the atom's size (volume) is empty space where electrons orbit.

Why the results make sense:

  • Most alpha particles go straight through because atoms are mostly empty space.
  • A few particles are deflected because they pass near the positive nucleus and are repelled.
  • Very few ricochet back because they hit the dense nucleus head-on.

Don't confuse: The nucleus is much smaller than depicted in diagrams—it is tiny compared to the overall atom size.

🌌 From planetary model to modern understanding

🪐 The planetary model

Rutherford called his description the "planetary model":

  • Electrons orbit the nucleus like planets orbit the sun.
  • This replaced the earlier "plum pudding model" (electrons floating aimlessly in a "pudding" of positive charge).

☁️ Modern refinement

The planetary model is overly simplistic:

  • Electrons do not occupy specific, circular orbits.
  • Instead, electrons form fuzzy clouds around the nucleus.
  • A better description: electrons occupy regions of space (probability clouds), not discrete paths.

Example: In a hydrogen atom, the darker the color or the more crowded the dots in a diagram, the higher the probability that an electron will be at that point. The nucleus is at the center, but the electron's exact position is not fixed.

🔄 Why the distinction matters

  • The planetary model suggests fixed, predictable paths.
  • The modern model reflects that we can only describe where electrons are likely to be, not where they are at any exact moment.

📦 Structure summary

🧱 How atoms are arranged

  • Nucleus (center): contains protons and neutrons; accounts for most of the atom's mass.
  • Electron cloud (surrounding space): electrons orbit about the nucleus; accounts for most of the atom's size.
  • Overall charge: if an atom is electrically neutral, the number of protons equals the number of electrons (opposite charges cancel out).

🔍 Key takeaways from the excerpt

  • Atoms can be broken down into subatomic particles (contradicting Dalton's original idea that atoms are indivisible).
  • The nucleus is extremely small compared to the atom's total volume.
  • Electrons are attracted to the nucleus but occupy a large region of space around it.
  • The structure explains both the mass distribution (concentrated in the nucleus) and the volume (mostly empty space).
11

Nuclei of Atoms

Nuclei of Atoms

🧭 Overview

🧠 One-sentence thesis

The atomic number (number of protons) defines an element's identity, while isotopes of the same element differ only in their number of neutrons, and together protons and neutrons determine an atom's mass number.

📌 Key points (3–5)

  • Atomic number defines the element: every atom of a particular element has the same number of protons; different elements have different numbers of protons.
  • Neutral atoms have equal protons and electrons: the number of electrons equals the number of protons when an atom is electrically neutral, canceling out opposite charges.
  • Isotopes are variants of the same element: atoms of the same element can have different numbers of neutrons, creating isotopes with different masses.
  • Mass number = protons + neutrons: the mass number is the sum of protons and neutrons in the nucleus, allowing you to calculate neutrons by subtracting atomic number from mass number.
  • Common confusion: atomic number vs. mass number—atomic number identifies the element (protons only), while mass number describes a specific isotope (protons + neutrons).

🔢 Atomic number and element identity

🔢 What atomic number means

Atomic number: the number of protons in the nucleus of an atom.

  • Experiments with X-rays in the 1910s showed that all atoms of the same element have the same number of protons.
  • Different elements have different numbers of protons.
  • The atomic number is characteristic of a particular element—it defines what element an atom is.
  • Example: hydrogen has atomic number 1 (1 proton); helium has atomic number 2 (2 protons). A nucleus with 2 protons cannot be hydrogen; it must be helium.

⚡ Electrons in neutral atoms

  • For an electrically neutral atom, the number of electrons equals the number of protons.
  • Equal numbers of opposite charges cancel out, producing a neutral atom.
  • Therefore, the atomic number also tells you the number of electrons in a neutral atom.
  • Don't confuse: later, elements may gain or lose electrons, making atoms no longer neutral; in those cases, electron count differs from proton count.

🧬 Isotopes and neutron variation

🧬 What isotopes are

Isotopes: atoms of the same element that have different numbers of neutrons.

  • Initially scientists thought neutron number was also characteristic of an element, but this turned out to be incorrect.
  • Atoms of the same element can have different numbers of neutrons.
  • Example: 99% of carbon atoms on Earth have 6 neutrons and 6 protons; about 1% have 7 neutrons. Naturally occurring carbon is actually a mixture of isotopes.

🔬 Hydrogen isotopes as an example

The excerpt highlights hydrogen isotopes to illustrate variation:

IsotopeProtonsNeutronsNotes
Most hydrogen10Single proton only
Deuterium11About 1 in 10,000 hydrogen nuclei
Tritium12Extremely rare
  • All three are hydrogen (same atomic number), but they differ in neutron count and therefore mass.

📝 Minor change to Dalton's theory

  • Dalton thought all atoms of the same element were exactly the same.
  • The discovery of isotopes required a correction: most elements exist as mixtures of isotopes.
  • Currently over 3,500 isotopes are known for all the elements.

⚖️ Mass number and isotope notation

⚖️ What mass number means

Mass number: the sum of the numbers of protons and neutrons in the nucleus of an atom.

  • Mass number is not the same as atomic number.
  • To find the number of neutrons: subtract the atomic number from the mass number.
  • Formula in words: neutrons = mass number minus atomic number.

🏷️ How to write isotopes

Scientists use efficient notation to specify isotopes:

  • Superscript-subscript notation: mass number as superscript on the left, atomic number as subscript on the left of the element symbol.
  • Example: ²⁶₅₆Fe (written as 26 on bottom, 56 on top, then Fe) indicates iron with atomic number 26 and mass number 56.
  • Calculating neutrons: 56 − 26 = 30 neutrons.
  • Simplified notation: often only the superscript is shown (e.g., ¹³C or ²³⁵U), since each element has a unique atomic number.
  • Word notation: isotopes may also be written as "carbon-13" or "uranium-235."

🧮 Working with isotope symbols

Example from the excerpt:

  • ¹⁷₃₅Cl: 17 protons (atomic number), 35 − 17 = 18 neutrons.
  • ⁵³₁₂₇I: 53 protons, 127 − 53 = 74 neutrons.

Don't confuse: the subscript (atomic number) is often omitted because it's redundant—the element symbol already tells you the atomic number.

📊 Summary of key relationships

ConceptWhat it tells youHow to use it
Atomic numberNumber of protons; defines the elementLook up in periodic table; also equals electrons in neutral atom
Mass numberProtons + neutrons in a specific isotopeSubtract atomic number to find neutrons
IsotopesSame element, different neutron countsSame atomic number, different mass numbers
Neutral atomElectrically balancedProtons = electrons

🎯 Why these concepts matter

  • The atomic number is fundamental: it defines what element you have.
  • Isotopes explain why atoms of the same element can have different masses.
  • Mass number allows you to specify exactly which isotope you're discussing.
  • Understanding the relationship between protons, neutrons, and electrons is essential for describing any atom accurately.
12

Atomic Masses

Atomic Masses

🧭 Overview

🧠 One-sentence thesis

Atomic mass is a weighted average of all naturally occurring isotopes of an element, measured in atomic mass units (u), where 1 u equals one-twelfth the mass of a carbon-12 atom.

📌 Key points (3–5)

  • What atomic mass is: a weighted average of an element's isotope masses, based on natural abundance of each isotope.
  • The atomic mass unit (u): defined as 1/12th the mass of a carbon-12 atom; 1 u = 1.661 × 10⁻²⁴ grams.
  • How to calculate: multiply each isotope's mass by its natural abundance (as a decimal), then sum the results.
  • Common confusion: atomic mass is not the mass of a single atom—it's an average across all naturally occurring isotopes of that element.
  • Why it matters: atomic mass allows conversion between atomic-scale measurements and macroscopic grams, essential for chemistry calculations.

⚖️ What atomic mass means

⚖️ Weighted average definition

Atomic mass: an average of an element's atomic masses, weighted by the natural abundance of each isotope of that element.

  • It is not the mass of one specific atom; it reflects the mix of isotopes found in nature.
  • Different isotopes have different masses, so the average must account for how common each isotope is.
  • Example: Boron exists as 19.9% boron-10 and 80.1% boron-11 in nature, so the atomic mass reflects mostly boron-11.

🔢 The atomic mass unit (u)

1 u = 1/12 the mass of a carbon-12 atom.

  • This standard reference point makes atomic masses easy to compare.
  • Conversion to grams: 1 u = 1.661 × 10⁻²⁴ grams.
  • Don't confuse: the atomic mass unit is a defined standard, not an arbitrary choice—it's anchored to carbon-12.

🧮 How to calculate atomic mass

🧮 The weighted average formula

The excerpt shows the calculation for boron:

  • Boron-10: 10.0 u, abundance 19.9% (0.199 as a decimal)
  • Boron-11: 11.0 u, abundance 80.1% (0.801 as a decimal)
  • Calculation: (0.199 × 10.0 u) + (0.801 × 11.0 u) = 10.8 u

Steps:

  1. Convert each isotope's natural abundance percentage to a decimal.
  2. Multiply each isotope's mass by its decimal abundance.
  3. Add all the products together.

🌍 Real-world example: carbon

  • Carbon exists as about 99% carbon-12 and about 1% carbon-13 on Earth.
  • The weighted average mass is 12.01 u (slightly above 12 u because of the small contribution from carbon-13).
  • This shows why atomic masses are rarely whole numbers—they reflect the isotope mix.

🔬 Converting to grams

🔬 From atomic mass units to grams

The excerpt provides a worked example for carbon:

  • Carbon's atomic mass: 12.01 u
  • Conversion: 12.01 u × (1.661 × 10⁻²⁴ g / 1 u) = 1.995 × 10⁻²³ grams
  • This is an extremely small mass, illustrating how tiny individual atoms are.

📏 Why this conversion matters

  • Atomic mass units are convenient for comparing atoms to each other.
  • Grams are needed for laboratory measurements and real-world chemistry.
  • The conversion factor (1 u = 1.661 × 10⁻²⁴ g) bridges the atomic scale and the macroscopic scale.

🔑 Key takeaway from the excerpt

🔑 Mass basis

The excerpt emphasizes:

Atoms have a mass that is based largely on the number of protons and neutrons in their nucleus.

  • Electrons contribute negligibly to atomic mass because they are so light.
  • The atomic mass reflects the nucleus (protons + neutrons), averaged across isotopes.
  • Example exercises in the excerpt ask students to find atomic masses from tables, convert to grams, and compare masses of different numbers of atoms—all reinforcing the practical use of atomic mass.
13

Arrangements of Electrons

Arrangements of Electrons

🧭 Overview

🧠 One-sentence thesis

Electrons in atoms are organized into shells and subshells with specific energy levels and capacities, and the electrons in the outermost shell (valence electrons) determine how atoms interact chemically.

📌 Key points (3–5)

  • Quantum mechanics governs electron behavior: electrons can only have certain specific energies (quantized) and are organized into shells and subshells.
  • Shells and subshells have fixed capacities: s subshells hold up to 2 electrons, p holds 6, d holds 10, and f holds 14.
  • Electron configurations describe electron arrangement: a shorthand notation (e.g., 1s² 2s² 2p⁶) shows which shells and subshells electrons occupy.
  • Common confusion—core vs. valence electrons: valence electrons are in the highest-numbered shell and determine chemical behavior; core electrons are in lower-numbered shells.
  • Filling order matters: subshells fill in a specific sequence, and sometimes a higher-numbered shell begins filling before a lower-numbered shell is complete (e.g., 4s fills before 3d).

⚛️ Quantum mechanics and electron organization

⚛️ What quantum mechanics tells us about electrons

Quantum mechanics: the modern theory of electron behavior.

The theory makes four key statements about electrons in atoms:

  • Electrons can only have certain specific energies—their energies are quantized (having a fixed value).
  • Electrons are organized into shells (groupings of electrons within an atom), with higher-energy shells generally farther from the nucleus on average.
  • Shells do not have fixed distances from the nucleus, but higher-energy electrons spend more time farther away.
  • Shells are divided into subshells (groupings of electrons within a shell).

🏗️ Shell and subshell structure

Shell numberSubshells presentMaximum electrons per subshell
1s onlys: 2
2s, ps: 2, p: 6
3s, p, ds: 2, p: 6, d: 10
4+s, p, d, fs: 2, p: 6, d: 10, f: 14
  • The first shell has only an s subshell.
  • The second shell has s and p subshells.
  • The third shell has s, p, and d subshells.
  • Subshells are labeled with the letters s, p, d, and f in order.

📝 Electron configurations

📝 What electron configurations show

Electron configuration: a shorthand description of the arrangement of electrons in an atom.

  • Combines shell number + subshell letter + superscript for number of electrons.
  • Example: 1s¹ means one electron in the s subshell of the first shell.
  • Spoken as "one-ess-one."

🔢 How to write electron configurations

The excerpt provides a step-by-step filling pattern:

  • Hydrogen (1 electron): 1s¹
  • Helium (2 electrons): 1s² (the 1s subshell is now full)
  • Lithium (3 electrons): 1s² 2s¹ (the third electron must go into the second shell because s subshells hold maximum 2 electrons)
  • Beryllium (4 electrons): 1s² 2s²
  • Boron through neon (5–10 electrons): electrons begin filling the 2p subshell
    • B: 1s² 2s² 2p¹
    • C: 1s² 2s² 2p²
    • N: 1s² 2s² 2p³
    • O: 1s² 2s² 2p⁴
    • F: 1s² 2s² 2p⁵
    • Ne: 1s² 2s² 2p⁶

Example from the excerpt: A neutral phosphorus atom has 15 electrons, so its electron configuration is 1s² 2s² 2p⁶ 3s² 3p³.

⚠️ Unusual filling order

  • After the 3p subshell is filled, a curious thing happens: the 4s subshell begins to fill before the 3d subshell does.
  • The exact ordering of subshells becomes more complicated after argon (18 electrons).
  • Don't confuse: higher shell numbers don't always fill in strict numerical order.

🎯 Valence and core electrons

🎯 What valence electrons are

Valence shell electrons (or valence electrons): the electrons in the highest-numbered shell, or valence shell.

Core electrons: the electrons in lower-numbered shells.

  • Chemistry results from interactions between the outermost shells of electrons on different atoms.
  • It is convenient to separate electrons into these two groups.

🔍 How to identify valence vs. core electrons

Example from the excerpt: A carbon atom has electron configuration 1s² 2s² 2p².

  • The highest-numbered shell is shell 2.
  • Valence electrons: 2s² 2p² = 4 valence electrons.
  • Core electrons: 1s² = 2 core electrons.

Example: Neutral phosphorus (1s² 2s² 2p⁶ 3s² 3p³):

  • Highest-numbered shell is the third shell (3s² 3p³).
  • Total valence electrons: 2 + 3 = 5.
  • Core electrons: the 10 remaining electrons from the first and second shells.

💡 Why the distinction matters

  • The excerpt states that chemistry results from interactions between the outermost shells of electrons on different atoms.
  • Valence electrons determine chemical behavior; core electrons do not participate in typical chemical reactions.

📊 Summary of key rules

ConceptRule
Subshell capacitys: 2, p: 6, d: 10, f: 14
Shell structureShell 1: s only; Shell 2: s, p; Shell 3: s, p, d; Shell 4+: s, p, d, f
Filling orderGenerally follows shell number, but exceptions exist (e.g., 4s before 3d)
Valence electronsElectrons in the highest-numbered shell
Core electronsAll electrons in lower-numbered shells
14

The Periodic Table

The Periodic Table

🧭 Overview

🧠 One-sentence thesis

The periodic table organizes elements by atomic number and groups them by similar chemical properties, which arise from shared valence electron configurations and show predictable trends in atomic size and behavior.

📌 Key points (3–5)

  • Historical organization: Elements were first grouped by atomic mass and similar chemical properties; Mendeleev's version predicted undiscovered elements successfully.
  • Structure reflects electron filling: The table's shape mirrors the order in which electron subshells fill, and elements in the same column share the same valence shell electron configuration.
  • Groups vs periods: Columns (groups/families) contain elements with similar properties; rows (periods) vary in length and represent different electron shell numbers.
  • Common confusion: Atomic radius trends—radius increases going down a column (more shells) but decreases going across a period (stronger nuclear pull on the same shell).
  • Classification by properties: Elements are categorized as metals, nonmetals, or semimetals based on physical and chemical characteristics.

📜 Historical development

📜 Early organization efforts

  • In the 19th century, scientists noticed that certain sets of elements had similar chemical properties.
  • Example: Chlorine, bromine, and iodine all react with sodium to make similar compounds; lithium, sodium, and potassium all react with oxygen similarly.

🔬 Mendeleev's breakthrough

  • Julius Lothar Meyer (1864) organized elements by atomic mass and grouped them by chemical properties.
  • Dmitri Mendeleev organized all known elements according to similar properties and left gaps for undiscovered elements.
  • His bold predictions about the properties of missing elements were later confirmed, gaining favor for his version.
  • Note: Mendeleev had to list some elements out of atomic mass order to group them with elements having similar properties.

🔄 Why "periodic"

Periodic table: a chart of elements that groups the elements by some of their properties.

  • Certain properties repeat on a regular basis throughout the table—they are periodic.
  • The table became known as the periodic table because of this regular repetition of properties.

🏗️ Structure and organization

🏗️ Basic arrangement

  • Elements are listed in order of atomic number (not atomic mass).
  • Most periodic tables provide additional data (such as atomic mass) in a box containing each element's symbol.

📊 Groups (columns)

Groups (or families): a column of elements on the periodic table.

  • Elements with similar chemical properties are grouped in vertical columns.
  • Groups are both numbered and named:
Group nameLocationExamples
Alkali metalsFirst columnLithium, sodium, potassium, rubidium, cesium, francium
Alkaline earth metalsSecond columnMagnesium, calcium, barium
HalogensNext-to-last columnFluorine, chlorine, bromine, iodine
Noble gasesLast columnHelium, neon, argon, radon
  • Note: "Halogen" comes from Greek for "salt maker" because these elements combine with other elements to form salts.

📏 Periods (rows)

Period: a row of elements on the periodic table.

  • Periods have different lengths:
    • First period: only 2 elements (hydrogen and helium)
    • Second and third periods: 8 elements each
    • Fourth and fifth periods: 18 elements each
    • Later periods: so long that segments are removed and placed beneath the main body of the table

🔬 Element classifications

🔬 Metals, nonmetals, and semimetals

TypePropertiesLocation
MetalShiny, typically silvery, excellent conductor of electricity and heat, malleable (beaten into thin sheets), ductile (drawn into thin wires)Left three-fourths of the periodic table
NonmetalTypically dull, poor conductor of electricity and heat, brittle when solidUpper right-hand corner (except hydrogen)
Semimetal (metalloid)Properties intermediate between metals and nonmetalsAdjacent to the bold line in the right-hand portion

🎯 Special sections

Main group elements: an element in the first two or the last six columns on the periodic table.

Transition metals: an element between the main group elements on the periodic table.

Inner transition metals: an element in the two rows beneath the main body on the periodic table (also called lanthanide and actinide elements).

  • The first two columns on the left and the last six columns on the right are main group elements.
  • The ten-column block between these contains the transition metals.
  • The two rows beneath the main body contain the inner transition metals (lanthanide metals and actinide metals).

⚛️ Electron configuration connection

⚛️ Why similar properties occur

  • The shape of the periodic table reflects the filling of subshells with electrons.
  • Starting with the first period and going left to right, the table reproduces the order of filling of electron subshells in atoms.
  • Crucial observation: Elements in the same column share the same valence shell electron configuration.

🔑 Valence electrons determine chemistry

  • Chemistry is largely the result of interactions between the valence electrons of different atoms.
  • Atoms with the same valence shell electron configuration have similar chemistry.
  • Example: All elements in the first column have a single s electron in their valence shells (configuration: ns¹, where n represents the shell number).
  • Example: Alkaline earth metals (second column) have valence configuration ns².
  • Example: Carbon's column has valence configuration ns² np².

🧮 Using the pattern

  • The variable n represents the number of the valence electron shell.
  • Each group can be described by its valence shell electron configuration.
  • This pattern explains why elements in the same column behave similarly chemically.

📐 Atomic radius trends

📐 What atomic radius means

Atomic radius: the approximate size of an atom.

📉 Trend going down a column (increasing)

  • As you go down a column, the atomic radius increases.
  • Reason: Higher shell numbers mean electrons are farther from the nucleus.
  • The size of an atom is generally determined by the number of the valence electron shell.
  • Example: Bismuth (Bi) atoms are larger than nitrogen (N) atoms because Bi is below N and has electrons in higher-numbered shells.

📈 Trend going across a period (decreasing)

  • As you go across a period (left to right), the atomic radius decreases.
  • Reason: Electrons are being added to the same valence shell, but more protons are being added to the nucleus.
  • The increasing positive charge attracts electrons more strongly, pulling them closer to the nucleus.
  • Example: Magnesium (Mg) atoms are larger than chlorine (Cl) atoms because both are in period 3, but Cl lies farther to the right.

🔄 Don't confuse

  • Down a column = more shells = larger atoms
  • Across a period = same shell but stronger nuclear pull = smaller atoms
  • These two trends work in opposite directions and can be used to compare any two elements on the table.
15

Two Types of Bonding

Two Types of Bonding

🧭 Overview

🧠 One-sentence thesis

Atoms form chemical bonds to achieve a stable eight-electron outer shell (the octet rule), either by transferring electrons to create ionic bonds or by sharing electrons to create covalent bonds.

📌 Key points (3–5)

  • The octet rule: atoms are especially stable when they have eight electrons in their outermost shell, which drives bond formation.
  • Two pathways to an octet: atoms can transfer electrons (forming ionic bonds) or share electrons (forming covalent bonds).
  • Ionic bonds form from charge attraction: atoms that lose electrons become positively charged ions, atoms that gain electrons become negatively charged ions, and opposite charges attract.
  • Common confusion: not all atoms follow the octet rule—small atoms like hydrogen, helium, and lithium follow a "duet rule" (two electrons in the outermost shell).
  • Why atoms bond: noble gases (helium, neon, argon, etc.) rarely form compounds because they already have stable electron configurations, showing that stability drives bonding.

🔬 Why atoms form bonds

🔬 The stability clue from noble gases

  • Noble gas elements (helium, neon, argon, krypton, xenon, radon) occupy the rightmost column of the periodic table.
  • These elements do not form compounds easily, suggesting they are especially stable as lone atoms.
  • All noble gases except helium have eight valence electrons in their outermost shell.
  • This observation led chemists to conclude that eight electrons in the outer shell is a particularly stable arrangement.

🎯 The octet rule

Octet rule: the concept that atoms tend to have eight electrons in their valence electron shell.

  • Atoms that do not have an octet of valence electrons will seek to obtain one.
  • This rule is a key to understanding why compounds form.
  • The drive to achieve an octet explains why atoms make chemical bonds rather than remaining as individual atoms.

⚠️ Exception: the duet rule

  • Small atoms (hydrogen, helium, lithium) have a first shell that becomes the outermost shell.
  • This shell holds only two electrons, not eight.
  • These atoms satisfy a "duet rule" rather than the octet rule.
  • Don't confuse: the octet rule applies to most atoms, but the smallest atoms follow a different pattern.

⚡ Ionic bonding: electron transfer

⚡ How ionic bonds form

Chemical bond: a very strong attraction between two atoms, formed when electrons in different atoms interact to make an arrangement that is more stable than when the atoms are apart.

Ionic bond: an attraction between oppositely charged ions.

  • One way to obtain an octet is by transferring electrons between atoms until all atoms have octets.
  • Some atoms lose electrons, others gain electrons.
  • There is no overall change in the number of electrons, but individual atoms acquire a nonzero electric charge.

🔋 Formation of ions

Ions: charged atoms.

  • Atoms that lose electrons become positively charged.
  • Atoms that gain electrons become negatively charged.
  • Opposite charges attract (while like charges repel).
  • These oppositely charged ions attract each other, forming ionic bonds.

🧂 Ionic compounds

Ionic compounds: compounds formed with ionic bonds.

  • The compounds resulting from ionic bonding are called ionic compounds.
  • Example from the excerpt: Table salt consists of sodium and chlorine, but the compound has properties completely different from either elemental sodium (a chemically reactive metal) or elemental chlorine (a poisonous, green gas).

💡 Which atoms lose vs. gain electrons

  • Atoms with only a few valence electrons are more likely to lose them.
  • Atoms with nearly eight valence electrons are more likely to gain the remaining electrons.

Example: Sodium atom

  • A sodium atom has one valence electron.
  • It is more likely to lose that single electron than to gain seven electrons.
  • When it loses one electron, it becomes an ion with a net positive charge:
    • Sodium atom: 11 protons (11+), 11 electrons (11−), 0 overall charge
    • Sodium ion: 11 protons (11+), 10 electrons (10−), +1 overall charge

Example: Fluorine atom

  • A fluorine atom has seven valence electrons.
  • It is more likely to gain one electron than to lose seven electrons to obtain an octet.

🚫 Why ionic compounds need opposite charges

  • An ionic compound is unlikely to consist of two positively charged ions because positive charges repel each other.
  • Similarly, an ionic compound is unlikely to consist of two negatively charged ions because negative charges also repel each other.
  • Only oppositely charged ions attract strongly enough to form stable ionic bonds.

🔗 Covalent bonding: electron sharing

🔗 The second pathway to an octet

Covalent bond: the bond made by electron sharing.

  • The second way for an atom to obtain an octet is by sharing electrons with another atom.
  • These shared electrons simultaneously occupy the outermost shell of more than one atom.
  • Covalent bonding and covalent compounds are noted as the subject of a later chapter (not detailed in this excerpt).

📊 Comparison of bonding types

Bonding typeHow octet is achievedWhat formsKey mechanism
IonicTransfer of electronsOppositely charged ionsAttraction between opposite charges
CovalentSharing of electronsShared electron pairsElectrons occupy multiple atoms' outer shells
16

Ions

Ions

🧭 Overview

🧠 One-sentence thesis

Atoms form ions by losing or gaining electrons to achieve a stable octet, creating positively charged cations or negatively charged anions that combine through electrostatic attraction to form ionic compounds.

📌 Key points (3–5)

  • Two types of ions: cations (positively charged, formed when atoms lose electrons) and anions (negatively charged, formed when atoms gain electrons).
  • The octet rule drives ion formation: atoms lose or gain electrons to achieve eight electrons in their outermost shell.
  • Periodic table patterns: elements in the same column form ions with the same charge (e.g., alkali metals form 1+ ions, halogens form 1− ions).
  • Common confusion: the number of electrons lost or gained depends on which path requires fewer changes—atoms with few valence electrons lose them; atoms with nearly eight gain electrons.
  • Lewis diagrams simplify visualization: dots around element symbols show valence electrons and illustrate electron transfer between atoms.

⚛️ What ions are and how they form

⚛️ Cations: positively charged ions

Cations: positively charged ions formed when atoms lose electrons.

  • Most atoms do not naturally have eight electrons in their valence shell.
  • Atoms with three or fewer valence electrons tend to lose those electrons.
  • When electrons are lost, fewer negative charges remain to balance the positive protons in the nucleus, resulting in a net positive charge.
  • Most metals become cations when forming ionic compounds.
  • Example: A sodium atom loses its one valence electron to become Na⁺, the sodium ion.

⚛️ Anions: negatively charged ions

Anions: negatively charged ions formed when atoms gain electrons.

  • Atoms with nearly eight valence electrons can gain additional electrons to complete an octet.
  • When electrons are gained, the atom now has more electrons than protons, creating a net negative charge.
  • Most nonmetals become anions when forming ionic compounds.
  • Example: A chlorine atom gains one electron to become Cl⁻, the chloride ion (note the suffix changes from -ine to -ide).

⚡ Electrostatic attraction creates compounds

  • Oppositely charged ions attract each other.
  • This attraction holds cations and anions together to form ionic compounds.
  • The compound is electrically neutral overall—the number of electrons lost equals the number gained.
  • Example: In sodium chloride, one sodium atom loses one electron and one chlorine atom gains one electron, with no leftover electrons.

🔄 The electron transfer process

🔄 Achieving the octet

  • The octet rule: atoms tend to gain, lose, or share electrons to have eight electrons in their outermost shell.
  • Atoms choose the path requiring the fewest changes.
  • Sodium (one valence electron) loses one electron rather than gaining seven.
  • Chlorine (seven valence electrons) gains one electron rather than losing seven.

🔄 Electron configurations before and after

  • Sodium atom electron configuration: 1s² 2s² 2p⁶ 3s¹
  • After losing one electron, Na⁺ has configuration 1s² 2s² 2p⁶ (the second shell now becomes the outermost shell with eight electrons).
  • Chlorine atom electron configuration: 1s² 2s² 2p⁶ 3s² 3p⁵
  • After gaining one electron, Cl⁻ has a complete octet in its outermost shell.

🔄 Multiple atom transfers

  • Some ionic compounds require electron transfer between more than one atom.
  • The ratio of cations to anions adjusts to balance charges.
  • Example: Magnesium bromide (MgBr₂) forms when one magnesium atom (loses two electrons) combines with two bromine atoms (each gains one electron).

📊 Periodic table patterns

📊 Predicting ion charges by position

Periodic table groupTypical ion chargeExamples
First column (alkali metals)1+Na⁺, Li⁺, K⁺
Second column (alkaline earth metals)2+Mg²⁺, Ca²⁺, Ba²⁺
Next-to-last column (halogens)1−Cl⁻, Br⁻, I⁻, F⁻
Third-to-last column2−S²⁻, O²⁻
  • Elements in the same vertical column (group) form ions with the same charge because they have the same number of valence electrons.
  • The periodic table becomes a tool for remembering ion charges.
  • Convention: write the number first, then the sign (Ba²⁺, not Ba⁺²).

📊 Transition metals are different

  • Transition metals can form ions with multiple different charges.
  • There is no simple pattern for transition metal ion charges.
  • Don't confuse: main group elements follow predictable patterns; transition metals do not.

🖊️ Lewis diagrams

🖊️ What Lewis diagrams show

Lewis diagrams (or Lewis electron dot diagrams): representations that show valence electrons as dots around the chemical symbol of an atom.

  • Named after Gilbert N. Lewis, an American chemist.
  • Show only valence electrons, not all electrons.
  • Use up to eight dots around the element symbol (maximum two dots per side).
  • Each dot represents one valence electron.

🖊️ Advantages over electron shell diagrams

  1. They show only valence electrons (the ones that matter for bonding).
  2. They are simpler—dots instead of circles with electrons inside.
  3. They clearly illustrate electron transfer between atoms.

🖊️ Drawing electron transfer

  • Start with Lewis diagrams of neutral atoms showing their valence electrons.
  • Show arrows indicating electron transfer from one atom to another.
  • The resulting ions are shown with their charges.
  • In the final formula representation, the dots are omitted.
  • Example: Lithium (one dot) transfers its electron to bromine (seven dots) to form Li⁺ and Br⁻, which combine as LiBr.

🖊️ Counting valence electrons

  • For main group elements, the number of valence electrons equals the group number at the top of the periodic table.
  • It does not matter which sides the dots are placed on, as long as no side has more than two dots.
17

Formulas for Ionic Compounds

Formulas for Ionic Compounds

🧭 Overview

🧠 One-sentence thesis

Ionic compound formulas represent the lowest whole-number ratio of ions needed to balance total positive and negative charges, following specific conventions for writing and recognizing these compounds.

📌 Key points (3–5)

  • What a chemical formula shows: the elements in a compound and their ratios, not individual particles but a continuous crystal lattice.
  • The balancing rule: total positive charge must always equal total negative charge; determine how many of each ion is needed to achieve this balance.
  • Writing conventions: cation (usually metal) comes first, anion (usually nonmetal) second; charges are not written; use lowest whole-number ratios; subscripts indicate multiple ions.
  • Common confusion: polyatomic ions vs. diatomic elements—MgCl₂ contains two separate chloride ions, not a Cl₂ molecule; when multiple polyatomic ions are needed, enclose the entire ion formula in parentheses with the subscript outside.
  • How to recognize ionic compounds: look for metal + nonmetal combinations, or recognize polyatomic ion formulas within the compound.

🔬 What chemical formulas represent

🧱 Crystal structure, not individual units

Chemical formula: a concise list of the elements in a compound and the ratios of these elements.

  • Ionic compounds exist as three-dimensional arrays called crystals, with alternating positive and negative ions.
  • There are no individual "particles" like separate NaCl units; instead, a continuous lattice exists.
  • Each ion is surrounded by ions of opposite charge, not exclusively paired with any single ion.
  • Example: A sodium chloride crystal is a collection of alternating sodium and chloride ions in a regular pattern.

📐 Formula unit concept

Formula unit: a set of oppositely charged ions that compose an ionic compound.

  • Although no single ion pairs exclusively with another, we use the ratio expressed in lowest whole numbers to describe the compound.
  • A macroscopic sample contains myriads of these ratio units.
  • Example: NaCl represents a 1:1 ratio of sodium to chloride ions, even though the crystal is a continuous array.

⚖️ The charge-balancing rule

⚖️ Total positive equals total negative

  • The fundamental rule: the total positive charge must equal the total negative charge.
  • This rule is based on the fact that matter is overall electrically neutral.
  • Determine how many of each ion is needed to balance charges.

🔢 Working out ion ratios

Ion pairChargesRatio neededFormulaWhy
Li⁺ and Br⁻1+ and 1−1:1LiBrOne of each balances
Mg²⁺ and O²⁻2+ and 2−1:1MgOEqual charges balance in 1:1
Mg²⁺ and Cl⁻2+ and 1−1:2MgCl₂Two chloride ions needed to balance one magnesium
Na⁺ and S²⁻1+ and 2−2:1Na₂STwo sodium ions needed to balance one sulfur
Al³⁺ and F⁻3+ and 1−1:3AlF₃Three fluoride ions needed to balance one aluminum
Fe³⁺ and O²⁻3+ and 2−2:3Fe₂O₃Least common multiple is 6: two iron (6+) and three oxygen (6−)
  • Don't confuse: Mg₂Cl₄ has balanced charges in a 1:2 ratio, but it is not the lowest whole-number ratio—MgCl₂ is correct.

📝 Writing conventions

📝 Order and notation rules

  1. Cation first, anion second: because most metals form cations and most nonmetals form anions, the metal is typically listed first.
  2. No charges written: even though the species are ions, not neutral atoms, charges are omitted from the formula.
  3. Subscripts for multiples: when more than one ion of a type is needed, use a numerical subscript (e.g., MgCl₂).
  4. No subscript "1": by convention, assume only one atom if no subscript is present; do not write "1" as a subscript.
  5. Lowest whole-number ratio: always use the simplest ratio.

🔤 Reading subscripts correctly

  • The subscript applies to the element immediately before it.
  • Example: In MgCl₂, the "2" means two chloride ions, not a Cl₂ molecule.
  • Don't confuse: Cl₂ in this context is not diatomic elemental chlorine; it represents two separate chloride ions.

🔗 Polyatomic ions

🔗 What polyatomic ions are

Polyatomic ions: ions that consist of groups of atoms bonded together with an overall electric charge.

  • These ions contain more than one atom.
  • They have characteristic formulas, names, and charges that must be memorized.
  • Example: NO₃⁻ is the nitrate ion (one nitrogen, three oxygen atoms, overall 1− charge).

🔗 Common polyatomic ions (partial list from excerpt)

NameFormulaCharge
AmmoniumNH₄⁺1+
NitrateNO₃⁻1−
SulfateSO₄²⁻2−
CarbonateCO₃²⁻2−
PhosphatePO₄³⁻3−
HydroxideOH⁻1−

📦 Parentheses rule for polyatomic ions

  • If more than one polyatomic ion is needed to balance charge, enclose the entire formula for the polyatomic ion in parentheses.
  • Place the numerical subscript outside the parentheses to show it applies to the entire ion.
  • Example: Ba(NO₃)₂ means one barium ion and two nitrate ions.
  • Example: Ca(NO₃)₂—calcium ions have 2+ charge, nitrate ions have 1− charge, so two nitrate ions are needed.

🔍 Recognizing ionic compounds

🔍 Two recognition methods

Method 1: Metal + nonmetal

  • Compounds between metal and nonmetal elements are usually ionic.
  • Example: CaBr₂ contains calcium (group 2A metal) and bromine (group 7A nonmetal), so it is ionic.
  • Contrast: NO₂ contains two nonmetals (nitrogen from group 5A, oxygen from group 6A), so it is not ionic—it is covalent.
  • Don't confuse: NO₂ with no charge specified is not the nitrite ion; it is a different type of compound.

Method 2: Recognize polyatomic ions

  • If you recognize a polyatomic ion formula within a compound, the compound is ionic.
  • Example: Ba(NO₃)₂—recognizing "NO₃" as the nitrate ion (NO₃⁻) is a clue that Ba is the Ba²⁺ ion.
  • The 2+ charge on barium balances the overall 2− charge from two nitrate ions.
  • Remember: the convention for ionic formulas is not to include the ionic charge in the written formula.

🔍 Practice examples from excerpt

CompoundIonic or not?Reason
Na₂OIonicSodium (metal) + oxygen (nonmetal)
PCl₃Not ionicBoth phosphorus and chlorine are nonmetals
NH₄ClIonicContains ammonium ion (NH₄⁺), a polyatomic ion
OF₂Not ionicBoth oxygen and fluorine are nonmetals

📊 Additional context: Blood and seawater comparison

📊 Similar but different compositions

  • Science has long recognized that blood and seawater have similar compositions—both have ionic compounds dissolved in them.
  • Many scientists think the first life forms on Earth arose in the oceans, which may explain the similarity.
  • However, a closer look shows they are quite different in concentration and ion types.

📊 Key differences

  • Salt concentration: Blood approximates 0.9% sodium chloride; seawater is principally 3% sodium chloride (over three times the concentration).
  • Hydrogen carbonate ions (HCO₃⁻): far more abundant in blood than seawater; crucial for controlling acid-base properties of blood.
  • Hydrogen phosphate ions (HPO₄²⁻ and H₂PO₄⁻): very low in seawater but present in higher amounts in blood, where they also affect acid-base properties.
  • Sulfate ion (SO₄²⁻): present in seawater but not in significant amounts in blood.
  • Most other ions (Na⁺, Cl⁻, Mg²⁺, K⁺, Ca²⁺) are more abundant in seawater than in blood.
18

Ionic Nomenclature

Ionic Nomenclature

🧭 Overview

🧠 One-sentence thesis

Ionic compounds are named systematically by combining the names of their cation and anion, with special rules for metals that can form ions of different charges.

📌 Key points (3–5)

  • Nomenclature is systematic: the formal study of naming chemical compounds follows specific rules.
  • Cation naming: monatomic cations use the element name + "ion"; metals with multiple charges need either Stock system (roman numerals) or common system (-ic/-ous suffixes).
  • Anion naming: monatomic anions use the element stem + "-ide ion"; polyatomic ions have their own characteristic names.
  • Common confusion: distinguishing Fe²⁺ from Fe³⁺—two different charges make two different compounds with unique properties, so each needs a distinct name.
  • Compound naming order: cation name first, then anion name, dropping the word "ion" from both.

🏷️ Naming individual ions

🏷️ Monatomic cations

The name of a monatomic cation is simply the name of the element followed by the word "ion."

  • Na⁺ is the sodium ion, Al³⁺ is the aluminum ion, Ca²⁺ is the calcium ion.
  • This straightforward rule works when the element forms only one common positive ion.
  • Example: Sodium forms only a 1+ ion, so "sodium ion" is unambiguous—no need to specify the charge.

⚡ Cations with multiple charges

Some elements lose different numbers of electrons, producing ions of different charges. Iron can form Fe²⁺ or Fe³⁺; each makes a different compound with unique physical and chemical properties when combined with the same anion.

Two naming systems exist:

SystemHow it worksExample (Fe²⁺ / Fe³⁺)
Stock system (modern)Roman numeral in parentheses after element name + "ion"iron(II) ion / iron(III) ion
Common system (older, still used in health sciences)Stem + suffix (-ous for lower charge, -ic for higher charge)ferrous ion / ferric ion
  • The Stock system is used only for elements that form more than one common positive ion.
  • Don't confuse: the -ic suffix represents the greater charge, -ous represents the lower charge.
  • In many cases, the stem comes from the Latin name of the element (e.g., iron → ferr-, copper → cupr-, tin → stann-, lead → plumb-, chromium → chrom-, gold → aur-).

🔻 Monatomic anions

The name of a monatomic anion consists of the stem of the element name, the suffix "-ide," and then the word "ion."

  • Cl⁻ is the chloride ion, O²⁻ is the oxide ion, Se²⁻ is the selenide ion.
  • Other examples: F⁻ (fluoride ion), Br⁻ (bromide ion), I⁻ (iodide ion), S²⁻ (sulfide ion), P³⁻ (phosphide ion), N³⁻ (nitride ion).

🔷 Polyatomic ions

Polyatomic ions have their own characteristic names (from earlier tables in the text).

  • Examples mentioned: SO₃²⁻ (sulfite ion), NH₄⁺ (ammonium ion), SO₄²⁻ (sulfate ion), PO₄³⁻ (phosphate ion), HCO₃⁻ (hydrogen carbonate or bicarbonate ion), NO₃⁻ (nitrate ion), Cr₂O₇²⁻ (dichromate ion), CrO₄²⁻ (chromate ion), OH⁻ (hydroxide ion), CO₃²⁻ (carbonate ion).
  • Note: some polyatomic ion names include prefixes like "di-" (e.g., dichromate).

🧪 Naming ionic compounds

🧪 The basic rule

Place the name of the cation first, followed by the name of the anion, and drop the word "ion" from both parts.

  • Example: Ba(NO₃)₂ is named barium nitrate.
  • The compound's name does not indicate the number of ions (e.g., "two nitrate ions for every barium ion").
  • You must determine the relative numbers by balancing positive and negative charges.

🔍 Determining cation charge from formula

If the cation can have more than one possible charge, first determine the charge from the formula before naming.

  • Example: FeCl₂ has two Cl⁻ ions (each 1− charge), so the iron ion must be Fe²⁺ → iron(II) chloride or ferrous chloride.
  • Example: FeCl₃ has three Cl⁻ ions, so the iron ion must be Fe³⁺ → iron(III) chloride or ferric chloride.
  • Don't confuse: these are two different compounds with different properties, so they need different names.

📋 Naming examples

  • Ca₃(PO₄)₂ → calcium phosphate
  • (NH₄)₂Cr₂O₇ → ammonium dichromate (the prefix "di-" is part of the anion name)
  • KCl → potassium chloride
  • CuCl → copper(I) chloride or cuprous chloride
  • SnF₂ → tin(II) fluoride or stannous fluoride

🗺️ Step-by-step process

The excerpt provides a guide (Figure 3.7):

  1. Identify the cation and anion.
  2. Name the cation (use Stock or common system if the metal has multiple charges).
  3. Name the anion.
  4. Combine: cation name + anion name, dropping "ion" from both.
  5. Do not use numerical prefixes to indicate the number of ions.

🔑 Key distinctions

🔑 When to specify charge

  • Do specify: for metals that form more than one common positive ion (e.g., iron, copper, tin, lead, chromium, gold).
  • Don't specify: for metals that form only one common ion (e.g., sodium, calcium, aluminum, potassium, magnesium, zinc, silver).
  • Example: Na⁺ is simply "sodium ion," not "sodium(I) ion," because sodium forms only a 1+ ion.

🔑 Stock vs. common system

  • Stock system: more modern, uses roman numerals—clearer and unambiguous.
  • Common system: older, uses Latin stems and -ic/-ous suffixes—still prevalent in health sciences.
  • Both are acceptable; the excerpt shows both in examples.
  • Example: Cu⁺ is copper(I) ion (Stock) or cuprous ion (common); Cu²⁺ is copper(II) ion (Stock) or cupric ion (common).
19

Formula Mass

Formula Mass

🧭 Overview

🧠 One-sentence thesis

Formula mass enables chemists to calculate the total mass of an ionic compound by summing the atomic masses of all atoms in its chemical formula, a skill essential for quantitative chemistry work.

📌 Key points (3–5)

  • What formula mass is: the sum of the atomic masses of each individual atom in the formula of an ionic compound.
  • How to calculate it: add up atomic masses from the periodic table, multiplying by the number of each type of atom present.
  • Key challenge with polyatomic ions: subscripts outside parentheses multiply every atom inside the polyatomic ion.
  • Common confusion: forgetting to distribute subscripts through parentheses when multiple polyatomic ions are present.
  • Why ions can be treated as atoms: because proper formulas are electrically neutral (no net electrons gained or lost), ions can be considered atoms for mass calculation purposes.

🧮 Basic calculation method

🔢 Simple ionic compounds

Formula mass: the sum of the masses of the elements in the formula of an ionic compound.

  • Start with the chemical formula (e.g., NaCl).
  • Look up each element's atomic mass on the periodic table (typically rounded to two decimal places).
  • Add the atomic masses together.
  • Example: For NaCl, sodium is 22.99 u and chlorine is 35.45 u, giving a total of 58.44 u.

✖️ Compounds with multiple ions

When a formula contains more than one of the same ion, multiply the atomic mass by the number present:

  • For calcium fluoride (CaF₂), the subscript 2 means two fluorine atoms.
  • Calculation: Ca (1 × 40.08) + F (2 × 19.00) = 40.08 + 38.00 = 78.08 u.
  • The subscript tells you how many times to count that atom's mass.

🔷 Polyatomic ions

🧩 Single polyatomic ion

When the formula includes a polyatomic ion like nitrate (NO₃⁻):

  • Count every atom in the polyatomic ion.
  • Example: Potassium nitrate (KNO₃) contains 1 K, 1 N, and 3 O atoms.
  • Calculation: K (39.10) + N (14.00) + O (3 × 16.00) = 39.10 + 14.00 + 48.00 = 101.10 u.

⚠️ Multiple polyatomic ions in parentheses

Critical rule: A subscript outside parentheses multiplies every atom inside.

  • For calcium nitrate Ca(NO₃)₂, the subscript 2 refers to the entire nitrate ion.
  • This means 2 nitrogen atoms (1 × 2) and 6 oxygen atoms (3 × 2).
  • Calculation: Ca (1 × 40.08) + N (2 × 14.00) + O (6 × 16.00) = 40.08 + 28.00 + 96.00 = 164.08 u.
  • Don't confuse: The subscript doesn't just apply to the last element—it applies to the whole group in parentheses.

📝 Step-by-step for complex formulas

For ammonium phosphate (NH₄)₃PO₄:

  1. Distribute the subscript 3 through the ammonium ion: 3 nitrogen atoms, 12 hydrogen atoms.
  2. Count atoms in the phosphate part: 1 phosphorus, 4 oxygen atoms.
  3. Calculate: N (3 × 14.00) + H (12 × 1.00) + P (30.97) + O (4 × 16.00) = 42.00 + 12.00 + 30.97 + 64.00 = 148.97 u.

💧 Special case: Hydrates

💎 What hydrates are

Hydrates: ionic compounds with water (H₂O) incorporated within their formula unit; they are solids, not liquids or solutions, despite containing water.

  • Each formula unit has a characteristic number of water molecules.
  • Written with a centered dot separating the compound from the water: CuSO₄·5H₂O.
  • Named with Greek prefixes: copper(II) sulfate pentahydrate (penta- = five water units).

🏥 Common hydrates and uses

FormulaNameUse
CaSO₄·½H₂OCalcium sulfate hemihydrate (plaster of Paris)Casts for broken bones
MgSO₄·7H₂OMagnesium sulfate heptahydrate (Epsom salts)Laxative, bathing salt
AlCl₃·6H₂OAluminum chloride hexahydrateAntiperspirant

🧮 Calculating formula mass with hydrates

Include the water molecules in your calculation:

  • For CuSO₄·5H₂O, add the mass of CuSO₄ plus 5 times the mass of H₂O.
  • Each water molecule contributes (2 × 1.00) + 16.00 = 18.00 u.

🎯 Key takeaway

The essential skill is to correctly count each atom in the formula and multiply atomic masses accordingly—especially remembering that subscripts outside parentheses distribute to all atoms within the polyatomic ion.

20

Covalent Bonds

Covalent Bonds

🧭 Overview

🧠 One-sentence thesis

Covalent bonds form when atoms share electrons to achieve stable, filled valence shells, creating molecules that differ fundamentally from ionic compounds.

📌 Key points (3–5)

  • How covalent bonds form: atoms share electrons rather than transferring them, allowing both atoms to fill their valence shells.
  • What defines a molecule: a discrete group of atoms connected by covalent bonds, represented by Lewis diagrams or dashes for bonding pairs.
  • Bonding vs nonbonding electrons: bonding pairs join atoms together; lone pairs belong to a single atom and do not participate in bonds.
  • Common confusion: covalent bonding occurs between nonmetals, while ionic bonding involves metals and nonmetals—some compounds contain both types.
  • Predictable patterns: atoms typically form a characteristic number of covalent bonds based on their position in the periodic table.

🔗 How electron sharing works

🔗 The alternative to electron transfer

  • Chapter 3 covered ionic bonding through electron transfer; covalent bonding offers a different path to stability.
  • Instead of one atom losing and another gaining electrons, atoms can share electrons to fill their valence shells.
  • Both approaches satisfy the octet rule (eight electrons in the outer shell for most atoms).

🔗 Hydrogen molecule example

  • Each hydrogen atom starts with one valence electron.
  • When two hydrogen atoms get close enough, they share their electrons.
  • Result: both atoms now have two electrons in their valence shells (filled for hydrogen's first shell).
  • This shared arrangement is more stable than two separate atoms.

Covalent bond: the sharing of electrons between atoms.

Bonding pair of electrons: the two electrons that join atoms in a covalent bond.

Molecule: a discrete group of atoms connected by covalent bonds—the smallest part of a compound that retains its chemical identity.

📐 Representing covalent bonds

📐 Lewis diagrams

  • Chemists use Lewis diagrams to show valence electrons as dots around atomic symbols.
  • For a hydrogen molecule, two separate atoms each show one dot; when bonded, the shared electrons appear between them.
  • A dash can replace the bonding pair for simplicity: H—H represents the hydrogen molecule.

Single bond: a covalent bond formed by a single pair of electrons (represented by a dash).

📐 Bond length and forces

  • The bond in a hydrogen molecule is about 74 picometers (74 × 10⁻¹² meters).
  • This distance balances multiple forces:
    • Attraction between oppositely charged electrons and nuclei
    • Repulsion between two negatively charged electrons
    • Repulsion between two positively charged nuclei
  • Closer nuclei → stronger repulsion; farther nuclei → weaker attraction.

📐 Nonbonding electrons

  • Not all valence electrons participate in bonding.
  • Example: fluorine atoms form F—F, but each fluorine has six additional electrons (three pairs) that don't bond.

Nonbonding pairs (or lone pairs): electron pairs that do not participate in covalent bonds; they belong to a single atom.

🧪 Bonding between different elements

🧪 Hydrogen fluoride example

  • A hydrogen atom (one valence electron) combines with a fluorine atom (seven valence electrons).
  • Each contributes one electron to form a shared pair: H—F.
  • Hydrogen's valence shell is now filled (two electrons); fluorine's is filled (eight electrons).
  • Fluorine retains six nonbonding electrons; hydrogen has none.

🧪 Larger molecules

  • Water (H₂O): oxygen forms two covalent bonds with two hydrogen atoms.
  • Methane (CH₄): carbon forms four covalent bonds with four hydrogen atoms.
  • Some atoms participate in multiple covalent bonds within the same molecule.

🧪 Characteristic bonding patterns

  • The excerpt notes that atoms typically form a predictable number of covalent bonds in compounds.
  • Figure 4.2 in the source shows these patterns based on periodic table position.
  • Example from exercises: hydrogen forms only one bond (only one valence electron to share); oxygen typically forms two bonds.

⚖️ Covalent vs ionic bonding

⚖️ When covalent bonds form

  • Covalent bonds form when two or more nonmetals combine.
  • Example: water (H₂O) is made from hydrogen and oxygen, both nonmetals.
  • Don't confuse: ionic compounds form between metals and nonmetals.

⚖️ Compounds with both bond types

  • Some compounds contain both ionic and covalent bonds.
  • Example: ammonium chloride (NH₄Cl) has:
    • Ionic bonds between the ammonium ion (NH₄⁺) and chloride ion (Cl⁻)
    • Covalent bonds within the ammonium ion (between nitrogen and hydrogen atoms)
  • Polyatomic ions are held together by covalent bonds but participate in ionic bonding as a unit.
Compound typeBond participantsExample
Purely covalentNonmetal + nonmetalN₂O₄ (both nitrogen and oxygen are nonmetals)
Purely ionicMetal + nonmetalNa₂O (sodium is a metal, oxygen is a nonmetal)
Both typesMetal + polyatomic ion (which has internal covalent bonds)Na₃PO₄ (ionic between sodium and phosphate; covalent within phosphate)

⚖️ Molecular formulas

  • The excerpt introduces the term molecular formulas for covalent compounds.
  • These formulas describe molecules (discrete groups of covalently bonded atoms), not the ionic lattice structures of ionic compounds.
21

Covalent Compounds: Formulas and Names

Covalent Compounds: Formulas and Names

🧭 Overview

🧠 One-sentence thesis

Covalent compounds form when nonmetals combine, and their naming follows a systematic prefix-based system that differs from ionic compound naming by using numerical prefixes to indicate the number of atoms of each element.

📌 Key points (3–5)

  • What forms covalent bonds: two or more nonmetals combining (unlike ionic bonds between metals and nonmetals).
  • Molecular formulas: covalent compounds use molecular formulas because they exist as separate, discrete molecules.
  • Naming system: the first element keeps its name; the second element gets the stem + "-ide" suffix; numerical prefixes specify atom counts.
  • Common confusion: polyatomic ions contain covalent bonds internally but participate in ionic bonding as a whole unit—so some compounds contain both bond types.
  • Key exceptions: some simple covalent compounds (water, ammonia, methane) use common names instead of systematic names.

🔗 What forms covalent bonds

🔗 Nonmetal combinations

Covalent bonds form when two or more nonmetals combine.

  • This is the defining characteristic that distinguishes covalent from ionic bonding.
  • Ionic bonds form between metals and nonmetals; covalent bonds form between nonmetals only.
  • Example: hydrogen and oxygen are both nonmetals, so water (H₂O) forms through covalent bonding.

⚠️ Mixed bonding situations

  • Some compounds contain both ionic and covalent bonds.
  • Polyatomic ions have covalent bonds holding the atoms together internally, but the ion as a whole participates in ionic bonding.
  • Example: ammonium chloride has ionic bonds between the ammonium ion (NH₄⁺) and chloride ions (Cl⁻), but within the ammonium ion, nitrogen and hydrogen are connected by covalent bonds.
  • Don't confuse: the presence of a polyatomic ion means the compound has both bond types, not just one.

📝 Writing molecular formulas

📝 Formula structure rules

Molecular formulas: chemical formulas for covalent compounds, called this because these compounds exist as separate, discrete molecules.

  • The nonmetal closest to the lower left corner of the periodic table is typically written first.
  • Exception: hydrogen is almost never written first (H₂O is the prominent exception).
  • Other nonmetal symbols follow in order.
  • Numerical subscripts indicate more than one atom of a particular element.

🔍 Recognizing bond types from formulas

Compound typeHow to identifyExample
Ionic onlyMetal + nonmetalNa₂O
Covalent onlyNonmetal + nonmetalN₂O₄
Both ionic and covalentMetal + polyatomic ionNa₃PO₄

🏷️ Naming binary covalent compounds

🏷️ The systematic naming rules

The naming system follows these steps:

  1. First element: use the element name as-is (no prefix if only one atom).
  2. Second element: take the stem of the element name and add "-ide" suffix.
  3. Numerical prefixes: specify the number of atoms in the molecule.

🔢 Numerical prefix system

Number of atomsPrefix
1mono-*
2di-
3tri-
4tetra-
5penta-
6hexa-
7hepta-
8octa-
9nona-
10deca-

*The "mono-" prefix is not used for the first element's name.

🎯 Applying the naming system

  • No prefix on the first element's name means only one atom is present.
  • Always use numerical prefixes for the second element if more than one atom.
  • Special rule for oxygen: omit the trailing vowel from polysyllabic prefixes (say "monoxide" not "monooxide"; "trioxide" not "troxide") but keep it for monosyllabic prefixes.

Example: CCl₄ becomes "carbon tetrachloride"—carbon (first element, no prefix needed for one atom) + tetra (four) + chlor (stem) + ide.

📋 Working from name to formula

When converting names to formulas:

  • If no prefix appears on the first element, assume one atom.
  • The prefix on the second element always tells you the exact number of atoms.

Example: "dinitrogen pentoxide" → N₂O₅ (di- means two nitrogen atoms, penta- means five oxygen atoms).

🌟 Common name exceptions

🌟 Simple compounds with traditional names

Three simple covalent compounds use common names rather than systematic names:

  • H₂O: water (not "dihydrogen monoxide")
  • NH₃: ammonia (not "nitrogen trihydride")
  • CH₄: methane (not "carbon tetrahydride")

🧪 Organic compounds

Organic compound: a compound containing carbon atoms.

  • Methane is the simplest organic compound.
  • Organic compounds are named by a separate nomenclature system (not covered in this excerpt).
  • This is why methane uses a common name instead of following the binary covalent naming rules.
22

Multiple Covalent Bonds

Multiple Covalent Bonds

🧭 Overview

🧠 One-sentence thesis

Some molecules require multiple covalent bonds—double or triple bonds—between atoms to satisfy the octet rule when single bonds alone cannot provide each atom with eight valence electrons.

📌 Key points (3–5)

  • Double bonds: two pairs of electrons shared between two atoms, represented by a double dash.
  • Triple bonds: three pairs of electrons shared between two atoms (e.g., acetylene C₂H₂ and N₂).
  • When multiple bonds form: if single bonds between all atoms do not give all atoms (except hydrogen) an octet, multiple covalent bonds may be present.
  • Common confusion: hydrogen atoms never form double bonds—they can accept only one more electron, while multiple bonds require more than one electron pair to be shared.
  • Why it matters: multiple bonds are necessary to complete the valence electron shells of many molecules.

🔗 Types of multiple bonds

🔗 Double bonds

Double bond: two pairs of electrons shared between two atoms in a molecule.

  • Represented by a double dash (=) in Lewis diagrams.
  • Forms when single bonds alone cannot provide eight electrons around each atom.
  • Example: In formaldehyde (CH₂O), the carbon atom forms a double bond with the oxygen atom to satisfy the octet rule for both atoms.

🔗 Triple bonds

Triple bond: three pairs of electrons shared by two atoms in a molecule.

  • Represented by a triple dash (≡) in Lewis diagrams.
  • Example: Acetylene (C₂H₂) contains a triple bond between the two carbon atoms.
  • Example: Nitrogen gas (N₂) has a triple bond between the two nitrogen atoms.

🧮 Drawing Lewis diagrams with multiple bonds

🧮 The process

  • Start by attempting to draw single bonds between all atoms.
  • Count the electrons around each atom (except hydrogen, which needs only two).
  • If an atom does not have eight electrons (an octet), add additional bonds between atoms.
  • Each additional shared pair creates a double or triple bond.

🧮 Example: Formaldehyde (CH₂O)

  • The carbon atom is the central atom, surrounded by two hydrogen atoms and one oxygen atom.
  • Single bonds alone do not give carbon and oxygen complete octets.
  • A double bond between carbon and oxygen provides eight electrons around each atom.
  • Note: Formaldehyde is also called CH₂O; aqueous solutions are called formalin and are used to preserve biological specimens.

🧮 Example: Nitrogen gas (N₂)

  • Each nitrogen atom needs eight valence electrons.
  • A triple bond between the two nitrogen atoms satisfies the octet rule for both.

🚫 Limitations and special cases

🚫 Why hydrogen never forms double bonds

  • Hydrogen can accept only one more electron to complete its valence shell (which holds a maximum of two electrons).
  • Multiple bonds require more than one electron pair to be shared.
  • Therefore, hydrogen always forms single bonds only.

🚫 When not to draw multiple bonds

  • Don't confuse covalent multiple bonds with ionic bonding.
  • Example: It is incorrect to draw a double bond in the Lewis diagram for MgO because MgO is an ionic compound, not a covalent molecule.

🔍 Recognizing when multiple bonds are needed

🔍 The key clue

  • If single bonds between all atoms do not give all atoms (except hydrogen) an octet, multiple covalent bonds may be present.
  • This is the primary indicator that you need to add double or triple bonds to your Lewis diagram.
  • Always check: does each atom (other than hydrogen) have eight electrons around it?

🔍 Practice molecules

MoleculeType of multiple bondNotes
CS₂Double bondsCarbon is the central atom
C₂F₄Double bondBetween the two carbon atoms
O₂Double bondBetween the two oxygen atoms
C₂H₄Double bondBetween the two carbon atoms
HCNTriple bondCarbon is the central atom; triple bond between C and N
23

Characteristics of Covalent Bonds

Characteristics of Covalent Bonds

🧭 Overview

🧠 One-sentence thesis

Covalent bonds vary in length and polarity depending on the atoms involved, with bond length decreasing as bond multiplicity increases and polarity determined by the difference in electronegativity between bonded atoms.

📌 Key points (3–5)

  • Bond length depends on identity and bond type: different atom pairs have characteristic bond lengths, and multiple bonds are shorter than single bonds between the same atoms.
  • Electronegativity determines polarity: the difference in electronegativity between two atoms determines whether a bond is nonpolar, polar covalent, or ionic.
  • Common confusion—equal vs unequal sharing: nonpolar bonds share electrons equally (same element or very small electronegativity difference), while polar bonds share unequally (moderate difference), and ionic bonds transfer electrons (large difference).
  • Thresholds for bond types: electronegativity differences less than ~0.4 are nonpolar, greater than ~0.4 are polar, and greater than ~1.8 are ionic.
  • Molecular polarity vs bond polarity: even if individual bonds are polar, the molecule's overall polarity depends on how those bonds are oriented in space.

📏 Bond length patterns

📏 What determines bond length

Bond length: the distance between two atoms in a covalent bond.

  • Bond lengths are characteristic for specific atom pairs and depend on:
    • The identities of the atoms in the bond
    • Whether the bond is single, double, or triple
  • The excerpt provides tables of approximate bond lengths that are close to actual values but may vary slightly depending on the molecule.

🔗 Single bond lengths

The excerpt provides a table of approximate single bond lengths (in units of 10⁻¹² m):

BondLength
H–H74
H–C110
H–O97
C–C154
C–O143
N–N145
  • These are reference values for comparing different bonds.
  • Example: a C–C bond (154) is longer than a C–O bond (143).

⚡ Multiple bonds are shorter

Key pattern: as the number of covalent bonds between two atoms increases, the bond length decreases—without exception.

Bond typeC–CC=CC≡C
Length154134120
Bond typeC–OC=OC≡O
Length143120113
  • Why this happens: with more electrons between the two nuclei, the nuclei can get closer together before internuclear repulsion balances the attraction.
  • Example: a triple bond (C≡C at 120) is significantly shorter than a single bond (C–C at 154) between the same atoms.

⚖️ Electronegativity and bond polarity

⚖️ What electronegativity measures

Electronegativity: a relative measure of how strongly an atom attracts electrons when it forms a covalent bond.

  • It is not about how many electrons an atom has, but how strongly it pulls on shared electrons in a bond.
  • The excerpt references the Pauling scale, where fluorine has the highest value (4.0).
  • Different elements have different electronegativities; this difference determines bond polarity.

🔄 Equal vs unequal electron sharing

Covalent bonds fall into two categories based on electron distribution:

Nonpolar covalent bond: a covalent bond with a balanced (equal) electron distribution across the bond.

Polar covalent bond: a covalent bond with an unbalanced (unequal) electron distribution across the bond.

Key distinction:

  • Nonpolar: electrons are equally shared by both atoms (e.g., H–H, where both atoms are identical).
  • Polar: one atom attracts electrons more strongly, creating partial charges (δ− on one side, δ+ on the other).
  • Example: in H–F, fluorine attracts electrons more than hydrogen, leading to an imbalance—this is polar.

📊 Using electronegativity differences to predict bond type

Electronegativity differenceBond typeElectron behavior
ZeroNonpolar covalentEqual sharing
Less than ~0.4Nonpolar covalentNearly equal sharing
Greater than ~0.4Polar covalentUnequal sharing
Greater than ~1.8IonicTransfer (not sharing)
  • General rule: the greater the difference in electronegativities, the greater the imbalance of electron sharing.
  • Don't confuse: all bonds between different elements are technically polar, but only those with differences greater than ~0.4 are considered meaningfully polar.
  • Ionic bonds can be thought of as the extreme case of polarity—electrons are transferred rather than shared.

🧪 Examples of electronegativity differences

The excerpt provides worked examples:

C and H:

  • Carbon: 2.5, Hydrogen: 2.1
  • Difference: 0.4 (rather small)
  • Result: nonpolar C–H bond

Na and Cl:

  • Sodium: 0.9, Chlorine: 3.0
  • Difference: 2.1 (rather high)
  • Result: ionic compound (not covalent)

O and H:

  • Oxygen: 3.5, Hydrogen: 2.1
  • Difference: 1.4
  • Result: very polar bond, but not ionic

H and H:

  • Both: 2.1
  • Difference: 0
  • Result: nonpolar bond

🌐 Molecular polarity vs bond polarity

🌐 How bond orientation affects molecular polarity

Even when individual bonds are polar, the molecule's overall polarity depends on geometry:

Water (H₂O):

  • Two O–H bonds are polar (oxygen attracts electrons more strongly).
  • The bonds are oriented in a bent shape.
  • Result: one end of the molecule has partial positive charge, the other has partial negative charge—the molecule itself is polar.
  • Impact: water's polarity causes strong intermolecular attraction, leading to a high boiling point (100°C).

Carbon dioxide (CO₂):

  • Two C=O bonds are polar.
  • The bonds lie directly opposite each other (linear geometry).
  • Result: the polar effects cancel each other out—the molecule is nonpolar overall.
  • Impact: carbon dioxide becomes a gas at −77°C, almost 200° lower than water's boiling point.

🔍 Don't confuse bond polarity with molecular polarity

  • A molecule can have polar bonds but be nonpolar overall if the bond dipoles cancel due to symmetry.
  • Example: CO₂ has polar bonds but is a nonpolar molecule; H₂O has polar bonds and is a polar molecule.
24

Characteristics of Molecules

Characteristics of Molecules

🧭 Overview

🧠 One-sentence thesis

Covalent molecules are discrete units with a calculable mass and a three-dimensional shape determined by electron-pair repulsion, unlike ionic compounds that form extended crystal lattices.

📌 Key points (3–5)

  • Molecular mass: the sum of the masses of all atoms in a molecule, calculated by tracking each element's count in the molecular formula.
  • Discrete units vs lattices: covalent molecules exist as separate units with characteristic mass and shape, unlike ionic compounds arranged in crystal lattices.
  • VSEPR theory: molecular shape is determined by electron pairs (bonded and lone) repelling each other to maximize distance.
  • Common confusion: molecular shape is described by atom positions only, not by lone electron pairs—e.g., NH₃ is pyramidal (not tetrahedral) even though four electron pairs arrange tetrahedrally.
  • Multiple bonds: treated as one group when determining shape, simplifying the geometry prediction.

🧮 Molecular mass calculation

🧮 What molecular mass means

Molecular mass: the mass of a molecule, which is the sum of the masses of its atoms.

  • Also called molecular weight.
  • Unlike formula mass for ionic compounds, molecular mass applies to discrete covalent molecules.
  • Each molecule has a characteristic, fixed mass.

📝 How to calculate molecular mass

  • Step 1: Identify the molecular formula and count each type of atom.
  • Step 2: Look up atomic masses from the periodic table.
  • Step 3: Multiply each atom's mass by its count in the formula.
  • Step 4: Sum all the results.

Example: For H₂O, two hydrogen atoms (2 × 1.01 = 2.02 u) plus one oxygen atom (16.00 u) gives a total molecular mass of 18.02 u.

⚠️ Tracking atom counts

  • The most important step is keeping track of the number of atoms of each element.
  • Different compounds with the same elements can have very different molecular masses.
  • Example: NO₂ has a molecular mass of 46.01 u, while N₂O₅ has 108.02 u—both contain nitrogen and oxygen but in different proportions.

🔷 Molecular shape fundamentals

🔷 Why shape matters

  • Covalent molecules have specific three-dimensional shapes, unlike the extended lattices of ionic crystals.
  • Shape is determined by the arrangement of atoms in space.
  • The shape affects molecular properties and behavior.

🔋 VSEPR theory basics

Valence shell electron pair repulsion (VSEPR) theory: the general concept that estimates the shape of a simple molecule based on electron-pair repulsion.

  • Core principle: covalent bonds are composed of negatively charged electrons that repel one another.
  • Electron pairs (both bonded pairs and lone pairs) arrange themselves to be as far apart as possible.
  • This repulsion determines the three-dimensional geometry of the molecule.

📐 Common molecular geometries

📐 Linear shape

  • Occurs when two electron groups repel each other.
  • The groups end up 180° apart.
  • Example: BeCl₂ has two covalent bonds that stay as far from each other as possible, resulting in a linear molecule.
  • Example: CO₂ is linear because the two double bonds (treated as one group each) repel to 180° apart.

🔺 Trigonal planar shape

  • Occurs when three electron groups repel each other.
  • The groups form 120° angles in a plane.
  • Example: BF₃ has three covalent bonds that repel to form a flat, triangular arrangement.
  • Molecules with double bonds can also adopt this shape when they have three groups around the central atom.

🔶 Tetrahedral arrangement

  • Occurs when four electron groups repel each other.
  • The groups point toward the corners of a tetrahedron, making bond angles of 109.5°.
  • Example: CCl₄ has four covalent bonds arranged three-dimensionally in a tetrahedral shape.

🔻 Pyramidal shape

  • Based on a tetrahedral electron arrangement but with one lone pair.
  • Key distinction: the shape is described by atom positions only, not electron pairs.
  • Example: NH₃ has four electron pairs (three bonded, one lone) arranged tetrahedrally, but the molecular shape is pyramidal because only the three atoms are counted.
  • Don't confuse: the electron arrangement is tetrahedral, but the molecular shape is pyramidal.

🌊 Bent shape

  • Occurs when the central atom has lone pairs in addition to bonded pairs.
  • Example: H₂O has four electron pairs (two bonded, two lone) in a tetrahedral arrangement, but the molecular shape is bent because only the two hydrogen atoms define the shape.
  • The lone pairs influence the geometry but are not included in the shape description.

🔍 Determining molecular shape

🔍 Step-by-step process

  1. Draw the Lewis diagram for the molecule to identify all electron pairs.
  2. Count electron groups around the central atom (bonded pairs + lone pairs).
  3. Determine electron arrangement based on repulsion (linear, trigonal planar, tetrahedral, etc.).
  4. Describe the molecular shape using only the positions of atoms, ignoring lone pairs.

🔗 Multiple bonds simplification

  • Multiple bonds (double or triple) are treated as one group for shape determination.
  • This simplifies the geometry prediction.
  • Example: CH₂O has a double bond to oxygen, but this is treated as one group, giving the molecule a shape similar to BF₃ (trigonal planar around the carbon).

🎯 Shape vs electron arrangement

Electron pairsElectron arrangementExample moleculeMolecular shape
2 bonded, 0 loneLinearCO₂Linear
3 bonded, 0 loneTrigonal planarBF₃Trigonal planar
4 bonded, 0 loneTetrahedralCCl₄Tetrahedral
3 bonded, 1 loneTetrahedralNH₃Pyramidal
2 bonded, 2 loneTetrahedralH₂OBent
25

Introduction to Organic Chemistry

Introduction to Organic Chemistry

🧭 Overview

🧠 One-sentence thesis

Organic chemistry focuses on carbon compounds because carbon's unique ability to form strong bonds with itself and other elements creates an unmatched chemical diversity that underlies all living things.

📌 Key points (3–5)

  • Why carbon is special: Carbon bonds strongly with other carbon atoms, bonds strongly with other elements, and makes four covalent bonds—giving it unrivaled chemical diversity.
  • Hydrocarbons as building blocks: The simplest organic compounds contain only carbon and hydrogen, classified by bond types (single, double, or triple).
  • Functional groups define reactivity: Specific structural arrangements of atoms or bonds (functional groups) give molecules characteristic chemical behaviors.
  • Common confusion: Carbon-containing compounds like carbonates, bicarbonates, CO₂, and CO are excluded from organic chemistry by convention, even though they contain carbon.
  • Health connection: Simple structural differences (e.g., single vs. double bonds in fats) can significantly impact human health.

🔬 What makes carbon unique

🔬 Carbon's bonding characteristics

Organic chemistry: the study of the chemistry of carbon compounds.

Carbon is singled out for three key reasons:

  • Carbon atoms bond reasonably strongly with other carbon atoms.
  • Carbon atoms bond reasonably strongly with atoms of other elements.
  • Carbon atoms make a large number of covalent bonds (four).

These properties allow carbon to form chains, branches, and complex structures that no other element can match.

🌍 Carbon's role despite scarcity

  • Elemental carbon is not particularly abundant in Earth's crust.
  • Nevertheless, all living things consist of organic compounds.
  • Most organic chemicals are covalent compounds.

⚠️ Convention exceptions

Don't confuse: Compounds containing carbonate ions, bicarbonate ions, carbon dioxide, and carbon monoxide are not considered part of organic chemistry, even though they contain carbon.

🔗 Hydrocarbon families

⛓️ Alkanes (saturated hydrocarbons)

Hydrocarbons: the simplest organic compounds, composed of carbon and hydrogen atoms only.

Alkanes (saturated hydrocarbons): hydrocarbons with only single covalent bonds, existing as a chain of carbon atoms also bonded to hydrogen atoms.

  • Alkanes have only single bonds and appear as chains (straight or branched).
  • Named with a stem indicating carbon count plus the ending -ane.
  • Examples: meth- = one carbon (methane), eth- = two carbons (ethane), prop- = three carbons (propane).

🔀 Alkenes

Alkenes: hydrocarbons with one or more carbon–carbon double bonds.

  • Contain one or more carbon–carbon double bonds (C=C).
  • Named with the same stem as alkanes but with the ending -ene.
  • Examples: ethene (two carbons, one double bond), propene (three carbons, one double bond).
  • Common names: ethene is commonly called ethylene; propene is commonly called propylene.

≡ Alkynes

Alkynes: hydrocarbons with a carbon–carbon triple bond.

  • Contain a carbon–carbon triple bond (C≡C).
  • Named with the same stem as alkanes but with the ending -yne.
  • Examples: ethyne (commonly called acetylene), propyne.
Hydrocarbon typeBond typeEndingExample
AlkaneSingle bonds only-aneMethane (CH₄)
AlkeneOne or more double bonds-eneEthene (C₂H₄)
AlkyneTriple bond-yneEthyne (C₂H₂)

🧪 Functional groups

🧪 What functional groups are

Functional group: a specific structural arrangement of atoms or bonds that imparts a characteristic chemical reactivity to a molecule.

  • Alkanes have no functional group.
  • Carbon–carbon double and triple bonds are functional groups because they react in specific ways that differ from alkanes.
  • Example: Under certain circumstances, alkenes react with water; alkanes do not.

🍷 Alcohol functional group

Alcohol: an organic compound with an OH functional group.

  • An OH group (hydroxyl group) substituted for a hydrogen atom in a hydrocarbon.
  • Named using the parent hydrocarbon name with the final -e dropped and the suffix -ol attached.
  • Examples: methanol (one carbon), ethanol (two carbons).
  • Note: Ethanol is the alcohol in alcoholic beverages; methanol and isopropyl alcohol are toxic and should not be ingested.

🧂 Carboxyl functional group

Carboxyl group: a functional group that contains a carbon–oxygen double bond and an OH group also attached to the same carbon atom.

Carboxylic acids: organic compounds that have a carboxyl functional group.

  • A carbon atom is double-bonded to an oxygen atom and to an OH group.
  • Named with the ending -oic acid.
  • Sometimes written as COOH in molecular formulas.
  • Examples: formic acid (found in ant stingers), acetic acid (found in vinegar).

🏥 Health implications

🥑 Saturated vs. unsaturated fats

Fats are combinations of long-chain organic compounds (fatty acids) and glycerol. The carbon chains can have:

  • All single bonds → classified as saturated fats (typically solids at room temperature, e.g., beef fat).
  • One or more double bonds → classified as monounsaturated or polyunsaturated fats (typically liquids/oils at room temperature, e.g., olive oil, fish oils).

📊 Health correlations

Fat typePhysical stateHealth correlation
SaturatedSolid at room tempLinked to higher likelihood of heart disease, high cholesterol
Unsaturated (mono- or poly-)Liquid at room tempLinked to lower incidence of certain diseases
Trans fatsVariesImplicated in heart disease; now required on US food labels

Don't confuse: The difference is as simple as a single vs. double carbon–carbon bond, yet it can have significant health impacts.

🍽️ Dietary recommendations

  • Government bodies and health associations recommend decreasing saturated fat and increasing unsaturated fat proportions.
  • Most organizations also recommend decreasing total fat intake.
  • US law now requires food labels to list trans fat content per serving.

🔍 Complexity in organic molecules

🔍 Multiple functional groups

  • Many organic compounds contain more than one functional group.
  • Example: Cholesterol (mentioned in the chapter-opening essay) has an alcohol functional group.
  • Formal names can be quite complex for molecules with multiple functional groups.

🧬 Beyond simple examples

The excerpt notes that many organic compounds are considerably more complex than the simple examples described, and further chapters will examine additional important organic compounds and functional groups in detail.

26

The Law of Conservation of Matter

The Law of Conservation of Matter

🧭 Overview

🧠 One-sentence thesis

The law of conservation of matter establishes that the amount of matter in a closed system remains constant, meaning chemical reactions must have the same number and type of atoms before and after the change.

📌 Key points (3–5)

  • What the law states: in any closed system, the amount of matter stays constant and is conserved.
  • Status as scientific law: laws are the highest form of scientific knowledge, verified many times under many conditions and considered inviolable.
  • Application to chemistry: chemical changes must preserve the same number and type of atoms because matter is neither created nor destroyed.
  • Common confusion: you cannot change chemical formulas to balance equations—only coefficients (the number of molecules) can be adjusted.
  • Why it matters: this law is the foundation for understanding chemical reactions and requires that chemical equations be balanced.

🔬 What scientific laws are

🔬 Definition and status

A law: a general statement that explains a large number of observations.

  • Before acceptance, a law must be verified many times under many conditions.
  • Laws are considered the highest form of scientific knowledge.
  • They are generally thought to be inviolable (cannot be violated).
  • Scientific laws form the core of scientific knowledge.

⚖️ The conservation principle

⚖️ The law of conservation of matter

The law of conservation of matter: In any given system that is closed to the transfer of matter (in and out), the amount of matter in the system stays constant.

  • A concise way to express this: the amount of matter in a system is conserved.
  • "Closed to the transfer of matter" means no matter enters or leaves the system.
  • The law applies to any given system, not just chemical reactions.

🔄 What "conserved" means

  • Matter is neither created nor destroyed.
  • The total amount stays the same throughout any process.
  • Example: If a closed container starts with 100 grams of matter, it will still contain 100 grams after any changes inside.

🧪 How the law applies to chemistry

🧪 Chemical changes and atoms

  • In any chemical change, one or more initial substances change into different substances.
  • Both initial and final substances are composed of atoms (all matter is composed of atoms).
  • According to the law: we must have the same number and type of atoms after the chemical change as were present before.

⚛️ Counting atoms matters

  • The law requires tracking every atom through a reaction.
  • You cannot lose atoms or gain new ones during a chemical reaction.
  • Example: If you start with 2 hydrogen atoms and 2 oxygen atoms, you must end with exactly 2 hydrogen atoms and 2 oxygen atoms, even if they are rearranged into different molecules.

📝 Chemical equations must reflect conservation

  • Chemical equations are abbreviated ways of using symbols to represent chemical changes.
  • An equation that does not have the same number of atoms of each element on both sides does not satisfy the law of conservation of matter.
  • Such equations are called "not balanced."

⚠️ Common mistakes and clarifications

⚠️ What you cannot do

  • You cannot change chemical formulas to balance equations.
  • Every substance has a characteristic chemical formula that cannot be altered.
  • Example: You cannot change elemental oxygen from O₂ to O just to make the numbers work.

✅ What you can do

  • You can adjust coefficients—the numbers in front of formulas.
  • Coefficients indicate how many molecules of each substance are involved.
  • Example: Writing 2H₂O means two water molecules are formed, giving you 4 hydrogen atoms and 2 oxygen atoms total.

🔍 Don't confuse: formula vs. coefficient

AspectChemical formulaCoefficient
What it isThe symbols showing which atoms make up a substance (e.g., H₂O)The number in front of a formula (e.g., the "2" in 2H₂O)
Can you change it?No—it defines the substance's identityYes—to balance the equation
What it tells youWhich elements and how many of each in one moleculeHow many molecules participate in the reaction

📊 Practical implications

📊 Mass conservation in reactions

  • The law of conservation of matter says that in chemical reactions, the total mass of the products must equal the total mass of the reactants.
  • This is a practical consequence: if you weigh everything before and after a reaction in a closed system, the mass will be the same.

📊 Foundation for chemistry

  • The law provides the foundation for understanding in chemistry.
  • It is the reason chemists must balance chemical equations.
  • Without this law, we could not predict or understand chemical behavior reliably.
27

Chemical Equations

Chemical Equations

🧭 Overview

🧠 One-sentence thesis

Chemical equations use symbols and coefficients to represent reactions in a way that satisfies the law of conservation of matter by ensuring equal numbers of each element's atoms on both sides.

📌 Key points (3–5)

  • What a chemical equation is: an abbreviated symbolic representation of a chemical reaction, showing reactants (left of arrow) and products (right of arrow).
  • Why balancing matters: equations must be balanced to satisfy the law of conservation of matter—the same number of atoms of each element must appear on both sides.
  • How to balance: adjust coefficients (numbers in front of formulas) to get equal atom counts; you cannot change the chemical formulas themselves.
  • Common confusion: coefficients vs. formulas—you must use the proper chemical formula and only change the coefficients, not the subscripts in the formula.
  • What stoichiometry means: the study of numerical relationships between reactants and products based on the coefficients in a balanced equation.

🧪 What chemical equations represent

🧪 From words to symbols

  • A chemical reaction can be described in words: "hydrogen and oxygen react to make water."
  • Chemical equations replace names with formulas and use symbols:
    • Plus sign (+) connects multiple reactants or products.
    • Arrow (→) represents the chemical change.
  • Example: H₂ + O₂ → H₂O

🏷️ Parts of a chemical equation

Chemical equation: an abbreviated way of using symbols to represent a chemical change.

Reactants: substances on the left side of the arrow in a chemical equation.

Products: substances on the right side of the arrow in a chemical equation.

  • Phase labels are often included: (s) solid, (ℓ) liquid, (g) gas, (aq) aqueous solution.
  • Example with phases: H₂(g) + O₂(g) → H₂O(ℓ)

⚖️ Balancing chemical equations

⚖️ Why equations must be balanced

  • An equation must satisfy the law of conservation of matter.
  • This means: the same number of atoms of each element must appear on both sides.
  • Example problem: H₂(g) + O₂(g) → H₂O(ℓ) has two oxygen atoms on the left but only one on the right—not balanced.

🔢 What coefficients do

Coefficient: a number that gives the number of molecules of a substance in a balanced chemical equation.

  • Coefficients are placed in front of chemical formulas.
  • They multiply the entire formula.
  • Example: 2H₂O means two water molecules (four hydrogen atoms, two oxygen atoms total).

Critical rule: You cannot change the chemical formula itself to balance an equation; you must use coefficients only.

🔧 How to balance an equation

The excerpt describes a back-and-forth approach:

  1. Count atoms of one element on both sides.
  2. Adjust a coefficient if needed to make the counts equal.
  3. Move to another element and repeat.
  4. Continue until all elements have equal atom counts on both sides.

Example walkthrough (from the excerpt):

  • Start: H₂(g) + O₂(g) → H₂O(ℓ)
  • Add coefficient 2 to water: H₂(g) + O₂(g) → 2H₂O(ℓ) (now oxygen is balanced but hydrogen is not)
  • Add coefficient 2 to hydrogen: 2H₂(g) + O₂(g) → 2H₂O(ℓ) (now both are balanced)

Balanced: a property of a chemical equation when there are the same number of atoms of each element in the reactants and products.

✅ Checking if an equation is balanced

Count atoms of each element on each side:

EquationBalanced?Reason
2Na(s) + O₂(g) → 2Na₂O(s)NoTwo Na and two O on left; four Na and two O on right
CH₄(g) + 2O₂(g) → CO₂(g) + 2H₂O(ℓ)YesOne C, four H, four O on each side

Don't confuse: different numbers of molecules (coefficients) vs. different numbers of atoms—balancing requires equal atom counts, not equal molecule counts.

📐 Stoichiometry and quantitative relationships

📐 What stoichiometry studies

Stoichiometry: the study of the numerical relationships between the reactants and the products in a balanced chemical equation.

  • The coefficients in a balanced equation determine the molecular ratio in which substances react and form.
  • These ratios allow quantitative predictions.

🔗 Ratios from balanced equations

From the balanced equation 2C₂H₂ + 5O₂ → 4CO₂ + 2H₂O, we can construct ratios:

StatementRatioInverse ratio
Two C₂H₂ molecules react with five O₂ molecules2C₂H₂ / 5O₂5O₂ / 2C₂H₂
Two C₂H₂ molecules make four CO₂ molecules2C₂H₂ / 4CO₂4CO₂ / 2C₂H₂
Five O₂ molecules make two H₂O molecules5O₂ / 2H₂O2H₂O / 5O₂

These ratios work like conversion factors for predicting amounts.

🍪 Everyday analogy: cooking recipes

The excerpt uses a biscuit recipe analogy:

  • A recipe (like a chemical equation) shows ratios: 2 cups flour + 1 egg + other ingredients → 12 biscuits.
  • If you have 4 cups of flour, you can predict: (4 cups flour) × (12 biscuits / 2 cups flour) = 24 biscuits.
  • Doubling or halving a recipe is a type of stoichiometry.
  • Example: the ratio "12 biscuits / 2 cups flour" acts as a conversion factor, just like molecular ratios in chemistry.
28

Quantitative Relationships Based on Chemical Equations

Quantitative Relationships Based on Chemical Equations

🧭 Overview

🧠 One-sentence thesis

Stoichiometry uses the coefficients in a balanced chemical equation to predict how much of one substance will react with or be produced from a given amount of another substance.

📌 Key points (3–5)

  • What stoichiometry is: the study of numerical relationships between reactants and products in a balanced chemical equation.
  • Where the ratios come from: the coefficients in the balanced equation determine the molecular ratios in which substances react and form.
  • How to use stoichiometric ratios: construct conversion factors from the coefficients, then multiply the given amount by the appropriate ratio to find the unknown amount.
  • Common confusion: stoichiometry only works with a balanced equation—without balancing first, predictions will be incorrect.
  • Why it matters: stoichiometry allows powerful predictive calculations about how much product forms or how much reactant is needed.

🔢 What stoichiometry measures

🔢 Definition and origin

Stoichiometry: the study of the numerical relationships between the reactants and the products in a balanced chemical equation.

  • The word is pronounced "stow-eh-key-OM-et-tree."
  • It comes from mixed Greek and English origins, meaning roughly "measure of an element."
  • It is not about the chemical properties themselves, but about the quantities involved.

🧮 The role of coefficients

  • A balanced chemical equation shows what reacts with what to make what products.
  • The coefficients (the numbers in front of each formula) determine the molecular ratio in which reactants react and products are made.
  • These coefficients are the foundation of all stoichiometric calculations.
  • Example: In the equation 2 C₂H₂ + 5 O₂ → 4 CO₂ + 2 H₂O, the coefficient 2 in front of C₂H₂ means 2 molecules of C₂H₂ react with 5 molecules of O₂.

🍪 Building stoichiometric ratios

🍪 The cooking analogy

  • The excerpt uses a biscuit recipe to illustrate stoichiometry:
    • 2 cups flour + 1 egg + 4 tablespoons shortening + 1 teaspoon salt + 1 teaspoon baking soda + 1 cup milk → 12 biscuits.
  • This "equation" gives ratios: 2 cups of flour (with the right amounts of other ingredients) yields 12 biscuits.
  • You can construct conversion factors: 12 biscuits per 2 cups flour.
  • Example: If you have 4 cups of flour, you can make 4 cups flour × (12 biscuits / 2 cups flour) = 24 biscuits.
  • Key insight: Doubling or halving a recipe is a type of stoichiometry.

⚖️ Constructing ratios from chemical equations

  • From a balanced equation, you can make statements and ratios.
  • Example: For 2 C₂H₂ + 5 O₂ → 4 CO₂ + 2 H₂O, you can say:
    • "Two C₂H₂ molecules react with five O₂ molecules" → ratio: 2 C₂H₂ / 5 O₂ (or its inverse 5 O₂ / 2 C₂H₂).
    • "Two C₂H₂ molecules react to make four CO₂ molecules" → ratio: 2 C₂H₂ / 4 CO₂ (or its inverse).
    • "Five O₂ molecules react to make two H₂O molecules" → ratio: 5 O₂ / 2 H₂O (or its inverse).
    • "Four CO₂ molecules are made at the same time as two H₂O molecules" → ratio: 4 CO₂ / 2 H₂O (or its inverse).
  • The excerpt notes that 12 different conversion factors can be constructed from this one equation.
  • In each ratio, the unit is assumed to be molecules (because that is how we interpret the chemical equation).
Statement from the equationRatioInverse ratio
Two C₂H₂ react with five O₂2 C₂H₂ / 5 O₂5 O₂ / 2 C₂H₂
Two C₂H₂ make four CO₂2 C₂H₂ / 4 CO₂4 CO₂ / 2 C₂H₂
Five O₂ make two H₂O5 O₂ / 2 H₂O2 H₂O / 5 O₂
Four CO₂ made with two H₂O4 CO₂ / 2 H₂O2 H₂O / 4 CO₂

🧪 Using stoichiometric ratios in calculations

🧪 The conversion-factor method

  • Any stoichiometric ratio can be used as a conversion factor to relate an amount of one substance to an amount of another.
  • General approach:
    1. Start with the amount you are given.
    2. Multiply by a conversion factor that cancels out the original unit and introduces the unit you want.
    3. The conversion factor comes directly from the coefficients in the balanced equation.

🔬 Worked example from the excerpt

  • Question: How many CO₂ molecules are formed when 26 molecules of C₂H₂ are reacted?
  • Equation: 2 C₂H₂ + 5 O₂ → 4 CO₂ + 2 H₂O
  • From the equation, the ratio is 4 CO₂ / 2 C₂H₂.
  • Calculation:
    • 26 C₂H₂ × (4 CO₂ / 2 C₂H₂) = 52 CO₂
  • The C₂H₂ units cancel, leaving CO₂.
  • Result: 52 molecules of CO₂ are formed.

⚠️ Why balancing is essential

  • The excerpt emphasizes: "This application of stoichiometry is extremely powerful in its predictive ability, as long as we begin with a balanced chemical equation."
  • Without a balanced equation, the predictions made by stoichiometric calculations will be incorrect.
  • Don't confuse: you cannot use stoichiometry on an unbalanced equation—the coefficients must reflect the true molecular ratios.

📝 Verifying and applying stoichiometry

📝 Example with a complex equation

  • Equation: KMnO₄ + 8 HCl + 5 FeCl₂ → 5 FeCl₃ + MnCl₂ + 4 H₂O + KCl
  • The excerpt walks through verifying balance:
    • Each side has 1 K atom and 1 Mn atom.
    • H atoms: 8 from HCl on the left, 8 from 4 H₂O on the right → balanced.
    • Fe atoms: 5 from 5 FeCl₂ on the left, 5 from 5 FeCl₃ on the right → balanced.
    • Cl atoms: 8 from HCl + 10 from 5 FeCl₂ = 18 on the left; 15 from 5 FeCl₃ + 2 from MnCl₂ + 1 from KCl = 18 on the right → balanced.
  • Two ratios relating HCl and FeCl₃:
    • 8 HCl / 5 FeCl₃
    • 5 FeCl₃ / 8 HCl
  • The excerpt notes that a total of 42 possible ratios can be constructed from this equation.

📝 Another example

  • Equation: 2 KMnO₄ + 3 CH₂=CH₂ + 4 H₂O → 2 MnO₂ + 3 HOCH₂CH₂OH + 2 KOH
  • The excerpt asks the reader to verify balance and construct ratios between KMnO₄ and CH₂=CH₂.
  • A total of 30 relationships can be constructed from this equation.

🎯 Key takeaway and concept review

🎯 The main lesson

A balanced chemical equation gives the ratios in which molecules of substances react and are produced in a chemical reaction.

  • Stoichiometric ratios are made using the coefficients of the substances in the balanced chemical equation.
  • A balanced chemical equation is necessary so one can construct the proper stoichiometric ratios.
  • Without balancing, the ratios are meaningless and predictions will be wrong.

🎯 How to construct stoichiometric ratios

  1. Start with a balanced chemical equation.
  2. Identify the coefficients in front of each substance.
  3. Write ratios using those coefficients (e.g., coefficient of A / coefficient of B).
  4. Use these ratios as conversion factors in calculations.
29

Some Types of Chemical Reactions

Some Types of Chemical Reactions

🧭 Overview

🧠 One-sentence thesis

Most chemical reactions can be classified into a small number of general types—combination, decomposition, and combustion—which helps us recognize patterns and predict products.

📌 Key points (3–5)

  • Why classify reactions: to recognize similarities and to predict products of reactions.
  • Combination reactions: two or more reactants make a single substance.
  • Decomposition reactions: a single substance breaks down into two or more products (the reverse of combination).
  • Combustion reactions: a substance combines with molecular oxygen to make oxygen-containing compounds, usually with heat/light.
  • Common confusion: a reaction can fall into more than one category; for example, some reactions can be both combination and combustion.

🔗 Combination reactions

🔗 What combination means

Combination (composition) reaction: a chemical reaction that makes a single substance from two or more reactants.

  • There may be more than one molecule of product in the balanced equation, but only one substance is produced.
  • The key is "multiple reactants → one product substance."

🧪 Examples of combination

  • Elements combining: 4Fe + 3O₂ → 2Fe₂O₃ (iron and oxygen make iron oxide).
  • Compounds combining: Fe₂O₃ + 3SO₃ → Fe₂(SO₄)₃ (iron oxide combines with sulfur trioxide).
  • Combination reactions do not have to combine elements; compounds can also combine.

✅ How to identify

  • Look for multiple reactants on the left side.
  • Look for a single product substance on the right side.
  • Example: Co(s) + Cl₂(g) → CoCl₂(s) is a combination reaction (two reactants, one product).
  • Example: N₂H₄(ℓ) + O₂(g) → N₂(g) + 2H₂O(ℓ) is not a combination reaction (multiple products).

💥 Decomposition reactions

💥 What decomposition means

Decomposition reaction: a chemical reaction in which a single substance is converted into two or more products.

  • This is the reverse of a combination reaction.
  • There may be more than one molecule of the reactant, but there is only one substance initially.

🧪 Examples of decomposition

  • Baking soda decomposition: 2NaHCO₃(s) → Na₂CO₃(s) + CO₂(g) + H₂O(ℓ) (occurs when heated).
  • Potassium chlorate decomposition: 2KClO₃(s) → 2KCl(s) + 3O₂(g) (once commonly used to generate oxygen in labs).

✅ How to identify

  • Look for a single reactant substance on the left side.
  • Look for multiple products on the right side.
  • Example: (NH₄)₂Cr₂O₇(s) → N₂(g) + Cr₂O₃(s) + 4H₂O(ℓ) is a decomposition reaction (one reactant, several products).

🔥 Real-world application

  • The decomposition of NaHCO₃ (baking soda) is used when baking soda is poured on a small kitchen fire.
  • The H₂O and CO₂ produced by the decomposition smother the flames.

🔥 Combustion reactions

🔥 What combustion means

Combustion reaction: a chemical reaction that occurs when a substance combines with molecular oxygen to make oxygen-containing compounds of other elements in the reaction.

  • Oxygen (in its elemental form) is a crucial reactant.
  • Oxygen is also present in the products.
  • Typically a vigorous reaction accompanied by light and/or heat.

🧪 Examples of combustion

  • Acetylene burning: 2C₂H₂ + 5O₂ → 4CO₂ + 2H₂O (used in torches).
  • Methane burning: CH₄(g) + 2O₂(g) → CO₂(g) + 2H₂O(ℓ).

✅ How to identify

  • Look for molecular oxygen (O₂) as a reactant.
  • Look for oxygen-containing compounds (like CO₂ and H₂O) as products.
  • Energy in the form of heat is usually given off as a product.
  • Example: C₂H₅OH + 3O₂ → 2CO₂ + 3H₂O is a combustion reaction (oxygen reacts with a compound to make carbon dioxide and water).

⚠️ Don't confuse with combination

  • A combustion reaction is usually a vigorous reaction with oxygen, accompanied by light and/or heat.
  • A combination reaction simply produces a certain substance from multiple reactants.
  • Some reactions can be both: for example, 2Ca(s) + O₂(g) → 2CaO(s) is both a combination (two reactants → one product) and a combustion (reaction with oxygen).

🔄 Multiple classifications

🔄 Reactions can fit more than one type

  • The excerpt states: "A particular reaction may fall into more than one of the categories."
  • Example: Hg(ℓ) + ½O₂(g) → HgO(s) can be classified as both combustion (reaction with oxygen) and combination (two reactants → one product).

📋 Summary table

Reaction typeKey featureExample
CombinationMultiple reactants → one product substance2K(s) + S(s) + 2O₂(g) → K₂SO₄(s)
DecompositionOne reactant substance → multiple products2NaHCO₃(s) → Na₂CO₃(s) + CO₂(g) + H₂O(ℓ)
CombustionReaction with O₂ → oxygen-containing products, usually with heat/lightCH₄(g) + 2O₂(g) → CO₂(g) + 2H₂O(ℓ)

🎯 Why classification matters

  • Helps recognize similarities among millions of possible reactions.
  • Enables prediction of products for certain reactions.
  • Makes learning and understanding chemistry more systematic.
30

Oxidation-Reduction (Redox) Reactions

Oxidation-Reduction (Redox) Reactions

🧭 Overview

🧠 One-sentence thesis

Redox reactions involve the transfer of electrons between substances, and they are central to energy production in combustion, batteries, and biological metabolism.

📌 Key points (3–5)

  • What redox reactions are: chemical reactions in which electrons are transferred from one atom to another; oxidation and reduction always occur together.
  • Oxidation vs reduction: oxidation is the loss of electrons (or gain of oxygen/loss of hydrogen); reduction is the gain of electrons (or loss of oxygen/gain of hydrogen).
  • How to track electron transfer: half reactions separate the oxidation and reduction parts, showing electrons as products (oxidation) or reactants (reduction); electrons must cancel when half reactions are combined.
  • Common confusion: oxidation can be defined three ways—loss of electrons, addition of oxygen, or removal of hydrogen—but all describe the same process from different perspectives.
  • Why redox matters: all batteries, combustion reactions, respiration, and many organic chemistry transformations depend on redox reactions.

⚡ What happens in a redox reaction

⚡ Electron transfer between atoms

Oxidation-reduction reactions (redox reactions): chemical reactions in which electrons are transferred from one atom to another.

  • The excerpt illustrates this with zinc metal reacting with hydrochloric acid: electrons are transferred from zinc atoms to hydrogen ions.
  • The zinc atoms lose electrons (changing from Zn to Zn²⁺), and the hydrogen ions gain electrons (changing from H⁺ to H₂ gas).
  • Because one substance must lose electrons for another to gain them, oxidation and reduction always occur together—they are two sides of the same reaction.

🔄 Oxidation and reduction defined

Oxidation: the loss of electrons by an atom.

Reduction: the gain of electrons by an atom.

  • The atom that loses electrons is oxidized; the atom that gains electrons is reduced.
  • Oxidizing agent: the species being reduced (it causes oxidation in the other substance).
  • Reducing agent: the species being oxidized (it causes reduction in the other substance).
  • Example: In the zinc–hydrogen reaction, zinc is the reducing agent (it is oxidized), and hydrogen ions are the oxidizing agent (they are reduced).

🧮 Balancing redox reactions with half reactions

🧮 What half reactions show

Half reactions: chemical reactions that show only oxidation or reduction.

  • Each half reaction includes:
    • The reactant being oxidized or reduced
    • The corresponding product
    • Any other species needed to balance the equation
    • The electrons being transferred
  • Electrons lost are written as products; electrons gained are written as reactants.
  • Example: For zinc oxidation, the half reaction is Zn → Zn²⁺ + 2e⁻ (two electrons appear as products).

⚖️ Balancing charge and electrons

  • Each half reaction must be balanced for both atoms and overall charge.
  • Example: The reduction half reaction for hydrogen is 2H⁺ + 2e⁻ → H₂. The two electrons (reactants) neutralize the 2+ charge on the hydrogen ions, so both sides have zero net charge.
  • When combining half reactions, the electrons must cancel exactly—this is the key criterion for a balanced redox reaction.
  • Sometimes you must multiply one half reaction by an integer so that the number of electrons matches.

🔢 Example: silver and aluminum

The excerpt walks through balancing the reaction of silver ions with aluminum metal:

  • Silver is reduced: Ag⁺ + e⁻ → Ag
  • Aluminum is oxidized: Al → Al³⁺ + 3e⁻
  • To cancel all electrons, multiply the silver half reaction by 3:
    • 3Ag⁺ + 3e⁻ → 3Ag
    • Al → Al³⁺ + 3e⁻
  • Combined: 3Ag⁺ + Al → 3Ag + Al³⁺ (the three electrons on each side cancel).
  • The overall charge is balanced: +3 on the left (from 3Ag⁺) and +3 on the right (from Al³⁺).

🧪 Alternative definitions: oxygen and hydrogen

🧪 Oxidation and reduction in terms of composition

The excerpt notes that oxidation and reduction can also be defined by changes in oxygen or hydrogen content:

DefinitionOxidationReduction
Electron transferLoss of electronsGain of electrons
OxygenAddition of oxygenLoss of oxygen
HydrogenLoss of hydrogenAddition of hydrogen
  • These definitions describe the same underlying process from different perspectives.
  • Example (oxygen): Acetaldehyde (CH₃CHO) takes on an oxygen atom to become acetic acid (CH₃COOH), so acetaldehyde is being oxidized.
  • Example (hydrogen): Acetaldehyde (CH₃CHO) adds hydrogen atoms to become ethanol (CH₃CH₂OH), so acetaldehyde is being reduced.

🔍 Recognizing oxidation or reduction

  • If a molecule adds oxygen atoms, it is being oxidized.
  • If a molecule loses oxygen atoms, it is being reduced.
  • If a molecule adds hydrogen atoms, it is being reduced.
  • If a molecule loses hydrogen atoms, it is being oxidized.
  • Don't confuse: the same molecule can be oxidized in one reaction and reduced in another, depending on what is added or removed.

🔋 Applications of redox reactions

🔋 Batteries and pacemakers

  • All batteries are based on redox reactions because batteries supply electricity (a stream of electrons).
  • Example: Pacemakers used to use NiCad batteries, in which cadmium is oxidized and nickel is reduced: Cd(s) + 2NiOOH(s) + 2H₂O(ℓ) → Cd(OH)₂(s) + 2Ni(OH)₂(s).
  • Modern pacemakers use lithium/iodine batteries: 2Li(s) + I₂(s) → 2LiI(s). Lithium is oxidized, and iodine is reduced.
  • Although lithium/iodine batteries cannot be recharged, they last up to 10 years.

🔥 Combustion reactions

  • All combustion reactions are redox reactions.
  • Example: Burning methane (natural gas): CH₄ + 2O₂ → CO₂ + 2H₂O. Methane is oxidized (gains oxygen), and oxygen is reduced.
  • Similar redox reactions occur when burning gasoline and coal.

🫁 Respiration and metabolism

Respiration: the biochemical process by which the oxygen we inhale oxidizes foodstuffs to carbon dioxide and water.

  • Redox reactions in respiration provide energy to living cells.
  • Example: Oxidation of glucose (C₆H₁₂O₆): C₆H₁₂O₆ + 6O₂ → 6CO₂ + 6H₂O. Glucose is oxidized, and oxygen is reduced.
  • The metabolism of foods that keeps us alive involves redox reactions.

🧬 Organic chemistry transformations

  • Organic chemists use redox reactions to transform molecules.
  • Example: Potassium dichromate (K₂Cr₂O₇) oxidizes alcohols (ROH).
    • If the OH group is on a terminal carbon and the product is distilled off, the product is an aldehyde (RCHO).
    • Example: Ethyl alcohol (C₂H₅OH) is oxidized to acetaldehyde (CH₃CHO) in the Breathalyzer test: 3C₂H₅OH + Cr₂O₇²⁻ + 8H⁺ → 3CH₃CHO + 2Cr³⁺ + 7H₂O.
    • If acetaldehyde is not removed, it is further oxidized to acetic acid (CH₃COOH).
    • If the OH group is on an interior carbon, oxidation produces a ketone (RCOR). Example: 2-propanol (CH₃CHOHCH₃) is oxidized to acetone [(CH₃)₂CO].
  • In these reactions, the chromium atom is reduced (from Cr₂O₇²⁻ to Cr³⁺), and the alcohol is oxidized.
31

Redox Reactions in Organic Chemistry and Biochemistry

Redox Reactions in Organic Chemistry and Biochemistry

🧭 Overview

🧠 One-sentence thesis

Redox reactions are central to both organic chemistry and biochemistry, powering combustion, respiration, metabolism, and photosynthesis—the fundamental processes that sustain civilization and life on Earth.

📌 Key points

  • Combustion and respiration are redox reactions: burning fuels and metabolizing food both involve oxidation-reduction processes that release energy.
  • Organic redox reactions transform functional groups: alcohols can be oxidized to aldehydes, ketones, or carboxylic acids; aldehydes and ketones can be reduced back to alcohols.
  • Antioxidants are reducing agents: substances like vitamin C and vitamin E protect living cells by undergoing reduction reactions that prevent harmful oxidation.
  • Photosynthesis is the ultimate redox reaction: plants reduce carbon dioxide to glucose and oxidize water to oxygen, making almost all life on Earth possible.
  • Common confusion—direction of electron transfer: oxidation means losing electrons (or gaining oxygen, or losing hydrogen); reduction means gaining electrons (or losing oxygen, or gaining hydrogen).

🔥 Combustion and respiration as redox reactions

🔥 Combustion of fuels

Combustion reactions: reactions that combine molecular oxygen with the atoms of another reactant; all combustion reactions are also redox reactions.

  • Burning fuels provides the energy that maintains civilization.
  • Example: methane (natural gas) combustion:
    • CH₄ + 2O₂ → CO₂ + 2H₂O
    • Methane is oxidized; oxygen is reduced.
  • Similar reactions occur with gasoline and coal.

🫁 Respiration in living cells

Respiration: the biochemical process by which the oxygen we inhale in air oxidizes foodstuffs to carbon dioxide and water.

  • Respiration provides energy to living cells through redox reactions.
  • Example: oxidation of glucose (C₆H₁₂O₆):
    • C₆H₁₂O₆ + 6O₂ → 6CO₂ + 6H₂O
    • Glucose is oxidized; oxygen is reduced.
    • This is the same simple sugar that makes up the diet of yeast.
  • Don't confuse: combustion and respiration both oxidize organic molecules with oxygen, but respiration occurs in controlled biochemical steps inside cells, while combustion is rapid burning.

🧪 Redox reactions in organic chemistry

🍷 Oxidation of alcohols

  • Organic chemists use redox reactions to transform functional groups.
  • Potassium dichromate (K₂Cr₂O₇) is a common oxidizing agent for alcohols (ROH).
  • The product depends on:
    • Location of the OH group in the molecule.
    • Relative proportions of alcohol and dichromate.
    • Reaction conditions (e.g., temperature).

🧴 Terminal alcohols → aldehydes or carboxylic acids

  • When the OH group is attached to a terminal carbon atom:
    • If the product is distilled off as it forms → aldehyde (RCHO) with a terminal carbonyl group (C=O).
    • Example: ethyl alcohol (C₂H₅OH) oxidized to acetaldehyde (CH₃CHO):
      • 3C₂H₅OH + Cr₂O₇²⁻ + 8H⁺ → 3CH₃CHO + 2Cr³⁺ + 7H₂O
      • This reaction is used by the Breathalyzer to detect alcohol in breath.
    • If acetaldehyde is not removed, it is further oxidized to acetic acid (CH₃COOH):
      • 3C₂H₅OH + 2Cr₂O₇²⁻ + 16H⁺ → 3CH₃COOH + 4Cr³⁺ + 11H₂O
  • In both reactions, chromium is reduced from Cr₂O₇²⁻ to Cr³⁺.

🧪 Interior alcohols → ketones

  • When the OH group is bonded to an interior carbon atomketone (RCOR, with C=O double bond).
  • Example: 2-propanol (CH₃CHOHCH₃) oxidized to acetone [(CH₃)₂CO]:
    • 3CH₃CHOHCH₃ + Cr₂O₇²⁻ + 8H⁺ → 3(CH₃)₂CO + 2Cr³⁺ + 7H₂O
    • Acetone is a common solvent used in varnishes, lacquers, rubber cement, and nail polish remover.

🔄 Reduction of aldehydes and ketones

  • Aldehydes and ketones can be reduced back to alcohols.
  • Reduction of the carbonyl group is important in living organisms.

🧬 Redox reactions in biochemistry

🏃 Anaerobic metabolism

Anaerobic metabolism: a biochemical process that takes place in the absence of oxygen.

  • Example: pyruvic acid (CH₃COCOOH) is reduced to lactic acid (CH₃CHOHCOOH) in muscles:
    • CH₃COCOOH → CH₃CHOHCOOH
    • Pyruvic acid is both a carboxylic acid and a ketone; only the ketone group is reduced.
  • The buildup of lactic acid during vigorous exercise is responsible in large part for the fatigue we experience.

🛡️ Antioxidants as reducing agents

Antioxidants: substances in foods that act as reducing agents.

  • Antioxidants are reducing agents that protect living cells by undergoing reduction reactions.
  • Ascorbic acid (vitamin C, C₆H₈O₆):
    • Thought to retard potentially damaging oxidation of living cells.
    • In the process, it is oxidized to dehydroascorbic acid (C₆H₆O₆).
    • In the stomach, ascorbic acid reduces nitrite ion (NO₂⁻) to nitric oxide (NO):
      • C₆H₈O₆ + 2H⁺ + 2NO₂⁻ → C₆H₆O₆ + 2H₂O + 2NO
    • Why this matters: if this reaction did not occur, nitrite ions from foods would oxidize the iron in hemoglobin, destroying its ability to carry oxygen.
  • Tocopherol (vitamin E):
    • Also an antioxidant.
    • In the body, thought to act by scavenging harmful by-products of metabolism, such as highly reactive molecular fragments called free radicals.
    • In foods, vitamin E prevents fats from being oxidized and becoming rancid.
  • Citrus fruits (oranges, lemons, limes) are good sources of vitamin C.

🌱 Photosynthesis: the ultimate redox reaction

🌿 How photosynthesis works

Photosynthesis: the process by which plants use solar energy to convert carbon dioxide and water to glucose and oxygen.

  • Green plants carry out the redox reaction that makes possible almost all life on Earth.
  • The overall change:
    • 6CO₂ + 6H₂O → C₆H₁₂O₆ + 6O₂
    • Carbon dioxide is reduced to glucose.
    • Water is oxidized to oxygen gas.
  • The synthesis of glucose requires:
    • A variety of proteins called enzymes.
    • A green pigment called chlorophyll that converts sunlight into chemical energy.

🌍 Why photosynthesis matters

  • Other reactions convert the glucose to more complex carbohydrates, plant proteins, and oils.
  • Photosynthesis is the fundamental process that sustains almost all life on Earth.
  • It is the ultimate source of all food on Earth.
  • Don't confuse: photosynthesis is the reverse of respiration in terms of overall reactants and products, but the mechanisms and purposes are completely different—photosynthesis stores energy, respiration releases it.

🔍 Summary of key redox concepts

ProcessWhat is oxidizedWhat is reducedRole in life
CombustionFuel (e.g., methane)OxygenProvides energy for civilization
RespirationGlucoseOxygenProvides energy to living cells
Anaerobic metabolism(varies)Pyruvic acid → lactic acidEnergy production without oxygen
AntioxidantsVitamin C, vitamin EHarmful oxidizing agentsProtects cells from damage
PhotosynthesisWaterCarbon dioxideProduces glucose and oxygen; basis of food chain

🧠 How to identify oxidation vs. reduction

  • Oxidation: loses electrons, gains oxygen atoms, or loses hydrogen atoms.
  • Reduction: gains electrons, loses oxygen atoms, or gains hydrogen atoms.
  • Oxidizing agent: the species being reduced (it causes oxidation in another species).
  • Reducing agent: the species being oxidized (it causes reduction in another species).
32

The Mole

The Mole

🧭 Overview

🧠 One-sentence thesis

The mole is a unit that represents 6.022 × 10²³ items (Avogadro's number) and allows chemists to relate macroscopic masses of substances to the number of atoms or molecules they contain.

📌 Key points (3–5)

  • What a mole is: A counting unit equal to 6.022 × 10²³ things (atoms, molecules, or formula units).
  • Why we need it: Individual atoms are too small to count one-by-one, so the mole lets us work with billions of billions of particles using measurable masses.
  • Key relationship: 1 mole of any substance has a mass in grams numerically equal to one atom/molecule's mass in atomic mass units (u).
  • Common confusion: The mole is a number (like "dozen"), not a type of particle—you must specify moles of what (atoms, molecules, or formula units).
  • Practical use: Molar mass allows conversion between the number of moles and the mass in grams of a substance.

🔢 What the mole unit means

🔢 Definition and scale

Mole (mol): A number of things equal to 6.022 × 10²³ items.

Avogadro's number: The value 6.022 × 10²³.

  • Just as "dozen" means 12, "mole" means 6.022 × 10²³.
  • This is an enormous number: if 1 mol of quarters were stacked, the column could stretch between Earth and the sun 6.8 billion times.
  • Example: 1 mol of O atoms = 6.022 × 10²³ O atoms; 2 mol of Na atoms = 2 × (6.022 × 10²³) = 1.2044 × 10²⁴ Na atoms.

🧪 What you can count in moles

  • The mole can apply to different chemical entities:
    • Atoms (e.g., 1 mol of H atoms)
    • Molecules (e.g., 0.5 mol of C₆H₆ molecules)
    • Formula units of ionic compounds (e.g., 2.34 mol of NaCl)
  • Don't confuse: "Mole" by itself doesn't specify what is being counted—you must state moles of atoms, molecules, or formula units.

🔗 Relating moles to atoms in compounds

🔗 Molecular relationships

  • Chemical formulas show how many atoms of each element are in one molecule or formula unit.
  • This ratio scales up to moles.

Example with ethanol (C₂H₆O):

1 molecule of C₂H₆O contains1 mol of C₂H₆O contains
2 C atoms2 mol of C atoms
6 H atoms6 mol of H atoms
1 O atom1 mol of O atoms
  • If you have 2.5 mol of C₂H₆O molecules, you have:
    • 2.5 mol × (2 mol C / 1 mol C₂H₆O) = 5.0 mol of C atoms
    • 2.5 mol × (6 mol H / 1 mol C₂H₆O) = 15 mol of H atoms
    • 2.5 mol × (1 mol O / 1 mol C₂H₆O) = 2.5 mol of O atoms

🔄 Converting moles to number of particles

  • Use Avogadro's number as a conversion factor.
  • Example: How many formula units in 2.34 mol of NaCl?
    • 2.34 mol NaCl × (6.022 × 10²³ units / 1 mol) = 1.41 × 10²⁴ NaCl units
    • Since each NaCl has 2 ions, total ions = 1.41 × 10²⁴ × 2 = 2.82 × 10²⁴ ions

⚖️ Molar mass: connecting moles to grams

⚖️ The key principle

One mole of a substance has the same mass in grams that one atom or molecule has in atomic mass units.

  • 1 hydrogen atom ≈ 1 u → 1 mol of H atoms ≈ 1 g
  • 1 sodium atom ≈ 23 u → 1 mol of Na atoms ≈ 23 g
  • The periodic table atomic masses tell you both the mass of one atom (in u) and the mass of 1 mol of atoms (in g).

⚖️ Calculating molar mass for compounds

Molar mass: The mass of 1 mol of a substance (element, ionic compound, or covalent compound).

How to calculate:

  • Sum the molar masses of all atoms in the chemical formula.
  • Multiply each element's molar mass by the number of atoms of that element in the formula.

Example: NaCl

  • 1 Na: 23.00 g
  • 1 Cl: 35.45 g
  • Total molar mass = 58.45 g/mol

Example: C₃₃H₃₆N₄O₆ (bilirubin)

  • 33 C: 33 × 12.01 = 396.33 g
  • 36 H: 36 × 1.01 = 36.36 g
  • 4 N: 4 × 14.00 = 56.00 g
  • 6 O: 6 × 16.00 = 96.00 g
  • Total molar mass = 584.69 g/mol

⚖️ Why mass ratios stay constant

  • The ratio of masses of equal numbers of different atoms is always the same.
  • Example: oxygen atom to hydrogen atom mass ratio ≈ 16:1
    • 2 O atoms : 2 H atoms ≈ 32:2 = 16:1
    • 100 O atoms : 100 H atoms ≈ 1600:100 = 16:1
  • This consistency allows us to use mass measurements instead of counting individual atoms.

🎯 Why the mole matters

🎯 Practical necessity

  • Atoms and molecules are far too small and numerous to count individually.
  • Even tiny samples contain billions of billions of particles.
  • The mole bridges the gap between the atomic scale (measured in u) and the laboratory scale (measured in grams).

🎯 Real-world context

  • The excerpt opens with a historical example: Lavoisier used mass measurements to demonstrate the law of conservation of matter (total mass before = total mass after).
  • Modern applications mentioned:
    • Medical dosing (the chapter-opening essay references a dosing error)
    • Food science (test kitchens tracking ingredient amounts)
    • Quality control (measuring substances in products)
    • Commerce (weighing meat and produce)
  • Stoichiometry (the study of numerical relationships between reactants and products in chemical reactions) depends on the mole concept.
33

Atomic and Molar Masses

Atomic and Molar Masses

🧭 Overview

🧠 One-sentence thesis

The mole connects atomic-scale masses (in atomic mass units) to laboratory-scale masses (in grams) because one mole of any substance has the same numerical mass in grams that one atom or molecule has in atomic mass units.

📌 Key points (3–5)

  • The core relationship: 1 mole of a substance has the same mass in grams that one atom or molecule has in atomic mass units (u).
  • Why Avogadro's number matters: the number 6.022 × 10²³ is chosen specifically to make this gram-to-u correspondence work.
  • Molar mass definition: the mass of 1 mol of atoms or molecules, expressed in grams per mole (g/mol).
  • How to calculate molar mass for compounds: sum the molar masses of all individual atoms in the formula, counting carefully when polyatomic ions have subscripts.
  • Common confusion: the periodic table atomic mass tells you both the mass of one atom in u and the mass of 1 mol of atoms in grams—same number, different units.

🔗 The mole-to-mass connection

🔗 Why the mole uses that specific number

  • The excerpt asks: why is a mole 6.022 × 10²³ and not some other number?
  • Answer: Avogadro's number is related to the relative sizes of the atomic mass unit and the gram.
  • This relationship creates a direct numerical correspondence between atomic-scale and lab-scale masses.

⚖️ The fundamental correspondence rule

One mole of a substance has the same mass in grams that one atom or molecule has in atomic mass units.

  • Example: one hydrogen atom has a mass of approximately 1 u → 1 mol of H atoms has a mass of approximately 1 gram.
  • Example: one sodium atom has an approximate mass of 23 u → 1 mol of Na atoms has an approximate mass of 23 grams.
  • This is not a coincidence; it is the defining feature of the mole.

📖 Reading the periodic table for molar mass

  • The atomic masses listed in the periodic table serve a dual purpose:
    • They tell the mass of one atom in atomic mass units (u).
    • They tell the mass of 1 mol of atoms in grams (g).
  • Example: aluminum's atomic mass is 26.98, so 1 mol of Al atoms has a mass of 26.98 g.
  • Example: uranium's atomic mass is 238.03, so 1 mol of U atoms has a mass of 238.03 g, and 2 mol has a mass of 476.06 g.

🧮 Calculating molar mass for compounds

🧮 Extending the concept to molecules and formula units

  • The same principle applies to molecules and ionic compounds.
  • A single molecule of O₂ has a mass of 32.00 u → 1 mol of O₂ molecules has a mass of 32.00 g.
  • To find the molar mass of any substance, sum the masses of all individual atoms in its formula.

🧪 Step-by-step calculation for simple compounds

Example: NaCl

  • 1 Na atom: molar mass 23.00 g
  • 1 Cl atom: molar mass 35.45 g
  • Total molar mass of NaCl: 58.45 g/mol

Example: bilirubin (C₃₃H₃₆N₄O₆)

  • 33 C atoms: 33 × 12.01 g = 396.33 g
  • 36 H atoms: 36 × 1.01 g = 36.36 g
  • 4 N atoms: 4 × 14.00 g = 56.00 g
  • 6 O atoms: 6 × 16.00 g = 96.00 g
  • Total molar mass: 584.69 g/mol

⚠️ Counting atoms in formulas with parentheses

  • Be careful with polyatomic ions in parentheses: the subscript outside applies to every atom inside.
  • Example: Ba(OH)₂
    • 1 Ba atom: 1 × 137.33 g = 137.33 g
    • 2 O atoms (from the subscript 2 outside parentheses): 2 × 16.00 g = 32.00 g
    • 2 H atoms (from the subscript 2 outside parentheses): 2 × 1.01 g = 2.02 g
    • Total: 171.35 g/mol
  • Don't confuse: the subscript outside parentheses multiplies all atoms inside, not just the last one.

📏 Expressing and using molar mass

📏 Units: grams per mole

  • Molar mass is defined as the mass for 1 mol of a substance.
  • It is expressed in grams per mole (g/mol).
  • The division sign "/" means "per," and "1" is implied in the denominator.
  • Example: bilirubin's molar mass is 584.05 g/mol, read as "five hundred eighty-four point zero five grams per mole."

🔄 Molar mass as a conversion factor

  • Molar mass connects mole units and mass units.
  • For aluminum: 1 mol Al = 26.98 g Al
  • This equality gives two conversion factors:
    • (1 mol Al) / (26.98 g Al) — to convert from mass to moles
    • (26.98 g Al) / (1 mol Al) — to convert from moles to mass

Example: What is the mass of 3.987 mol of Al?

  • Use the conversion factor (26.98 g Al) / (1 mol Al) to cancel mole units.
  • Calculation: 3.987 mol Al × (26.98 g Al / 1 mol Al) = 107.6 g Al
  • The mol units cancel algebraically, leaving grams.

🧩 Summary table

ConceptWhat it meansHow to use it
Atomic mass (from periodic table)Mass of one atom in uAlso the molar mass in g/mol
Molar massMass of 1 mol in gramsSum atomic masses for all atoms in formula
Conversion factorRelates moles and gramsMultiply by (g/mol) or (mol/g) to switch units
34

Mole-Mass Conversions

Mole-Mass Conversions

🧭 Overview

🧠 One-sentence thesis

Mole-mass conversions use molar mass as a conversion factor to translate between the number of moles of a substance and its mass in grams, enabling quantitative predictions in chemical reactions.

📌 Key points (3–5)

  • What molar mass enables: it acts as a bridge between the mole unit (counting particles) and mass in grams.
  • The conversion factor relationship: 1 mol of any substance equals its molar mass in grams, which can be flipped depending on the direction of conversion.
  • Two-step mole-mass problems: convert moles of substance A to moles of substance B using the balanced equation, then convert moles of B to grams using molar mass.
  • Three-step mass-mass problems: convert grams of A to moles of A, then moles of A to moles of B, then moles of B to grams of B.
  • Common confusion: remembering which conversion factor to use—check whether you need to cancel moles or grams in the starting quantity.

🔄 The basic mole-mass conversion

🔄 How molar mass works as a conversion factor

Molar mass: the mass in grams of one mole of a substance, numerically equal to the atomic or formula mass in amu.

  • The excerpt establishes that 1 mol Al = 26.98 g Al.
  • This equality can be written as two conversion factors:
    • 1 mol Al / 26.98 g Al (converts mass to moles)
    • 26.98 g Al / 1 mol Al (converts moles to mass)
  • Which factor you use depends on what unit you want to cancel.

🧮 Choosing the correct conversion factor

  • Start with the given quantity and identify its unit.
  • If you start with moles and want grams, use the factor with grams in the numerator.
  • If you start with grams and want moles, use the factor with moles in the numerator.
  • Example: To find the mass of 3.987 mol of Al, multiply by (26.98 g Al / 1 mol Al) so the mol unit cancels, yielding 107.6 g Al.

⚠️ Don't confuse the direction

  • The excerpt emphasizes that the algebra is the same as unit conversions from earlier chapters.
  • Always write out units and cancel them explicitly to avoid errors.

🧪 Mole-mass calculations in reactions

🧪 Combining stoichiometry with molar mass

  • A mole-mass calculation links moles of one substance in a reaction to the mass of another substance.
  • The sequence is:
    1. Start with moles of substance A.
    2. Use the balanced equation coefficients to find moles of substance B.
    3. Use the molar mass of B to convert moles of B to grams of B.

📐 Example walkthrough

  • The excerpt gives the reaction: Fe₂O₃ + 3 SO₃ → Fe₂(SO₄)₃
  • Question: If you have 3.59 mol of Fe₂O₃, how many grams of SO₃ react?
  • Step 1: Use the molar ratio (3 mol SO₃ / 1 mol Fe₂O₃) to find moles of SO₃: 3.59 mol Fe₂O₃ × (3 mol SO₃ / 1 mol Fe₂O₃) = 10.77 mol SO₃.
  • Step 2: Convert moles of SO₃ to grams using molar mass (80.06 g/mol): 10.77 mol SO₃ × (80.06 g SO₃ / 1 mol SO₃) = 862 g SO₃.
  • The excerpt notes you can do both steps in one line or separately; the answer is the same.

🔗 Why this matters

  • Real lab work measures masses, not moles directly.
  • Mole-mass conversions let you predict how much of a reactant you need or how much product you will get.

⚖️ Mass-mass calculations

⚖️ The three-step sequence

Mass-mass calculation: a stoichiometry problem that starts with the mass of one substance and finds the mass of another substance in the same reaction.

  • The full sequence is:
    1. Convert grams of substance A to moles of A (using molar mass of A).
    2. Convert moles of A to moles of B (using the balanced equation).
    3. Convert moles of B to grams of B (using molar mass of B).

📝 Example walkthrough

  • Reaction: CH₄ + 4 Cl₂ → CCl₄ + 4 HCl
  • Question: How many grams of HCl are produced from 100.0 g of CH₄?
  • Step 1: 100.0 g CH₄ × (1 mol CH₄ / 16.05 g CH₄) = 6.231 mol CH₄.
  • Step 2: 6.231 mol CH₄ × (4 mol HCl / 1 mol CH₄) = 24.92 mol HCl.
  • Step 3: 24.92 mol HCl × (36.46 g HCl / 1 mol HCl) = 908.5 g HCl.
  • The excerpt shows you can also write all three conversions in one line.

🎯 Stepwise vs. single-line calculation

  • Doing the calculation in separate steps lets you round at each stage (may introduce small rounding differences).
  • Doing it in one line keeps all intermediate precision until the final answer.
  • The excerpt notes both methods give essentially the same result.

🧬 Real-world application: complex molecules

🧬 Calculating with large formulas

  • The excerpt includes an example with bilirubin (C₃₃H₃₆N₄O₆), molar mass 584.69 g.
  • To find the mass of 0.00655 mol of bilirubin: 0.00655 mol × (584.69 g / 1 mol) = 3.83 g.
  • The same logic applies no matter how complicated the molecule.

💊 Health context: Taxol synthesis

  • The excerpt describes Taxol (C₄₇H₅₁NO₁₄), a cancer drug originally from Pacific yew trees.
  • Laboratory synthesis requires over 30 reactions with less than 0.05% efficiency.
  • To get a single 300 mg dose, you must start with 600 g of material—illustrating why improving synthesis efficiency matters.
  • This shows how mole-mass conversions underpin practical pharmaceutical production.

🌱 Dietary minerals

  • The excerpt includes a table of recommended daily intakes (RDIs) for minerals, given in both mass (mg or μg) and moles.
  • Example: an adult male needs 1,000 mg (0.025 mol) of calcium per day.
  • Iron needs differ by sex: women need 18 mg (3.2 × 10⁻⁴ mol) vs. 8 mg (1.4 × 10⁻⁴ mol) for men.
  • This illustrates that mole amounts vary widely across different minerals, and molar thinking helps compare nutritional needs on a particle basis.

📊 Summary of conversion pathways

Starting quantityTarget quantityConversion pathway
Moles of AGrams of AMultiply by molar mass of A
Grams of AMoles of ADivide by molar mass of A (or multiply by 1/molar mass)
Moles of AMoles of B (in reaction)Use coefficient ratio from balanced equation
Moles of AGrams of B (in reaction)Moles A → moles B → grams B (two steps)
Grams of AGrams of B (in reaction)Grams A → moles A → moles B → grams B (three steps)
35

Mole-Mole Relationships in Chemical Reactions

Mole-Mole Relationships in Chemical Reactions

🧭 Overview

🧠 One-sentence thesis

Balanced chemical equations can be interpreted in terms of moles, allowing us to use molar ratios to predict how much of one substance will react with or produce a given amount of another substance.

📌 Key points (3–5)

  • Coefficients represent moles: The numbers in front of chemical formulas represent not just molecules but also molar amounts.
  • Molar ratios from balanced equations: Any ratio of coefficients (e.g., 2:1:2) can be used to construct conversion factors between substances.
  • Stoichiometry definition: The study of numerical relationships between reactants and products in balanced chemical reactions.
  • Common confusion: Coefficients can be written in different multiples (4:2:4 or 22:11:22) as long as they reduce to the same ratio—the equation remains balanced.
  • Practical use: These molar ratios allow us to calculate how many moles of one substance are needed or produced when given moles of another substance.

🔢 Understanding coefficients as moles

🔢 From molecules to moles

  • Chemical equations are traditionally written with the lowest whole-number coefficients (e.g., 2H₂ + O₂ → 2H₂O).
  • The equation remains balanced as long as the coefficient ratio stays the same.
  • Example: 4H₂ + 2O₂ → 4H₂O has a 4:2:4 ratio, which reduces to 2:1:2—still balanced.

🧪 The mole interpretation

Balanced chemical equations are balanced not only at the molecular level but also in terms of molar amounts of reactants and products.

  • Since 6.022 × 10²³ molecules = 1 mol, we can scale up coefficients to molar quantities.
  • The equation 2H₂ + O₂ → 2H₂O means "two moles of hydrogen react with one mole of oxygen to produce two moles of water."
  • This interpretation is just as valid as counting individual molecules.

⚖️ Multiple valid forms

  • An equation like 12.044 × 10²³ H₂ + 6.022 × 10²³ O₂ → 12.044 × 10²³ H₂O is balanced because the ratio is still 2:1:2.
  • This simplifies to 2 mol H₂ + 1 mol O₂ → 2 mol H₂O.
  • Don't confuse: different coefficient sets are valid as long as they maintain the same ratio.

🧮 Constructing and using molar ratios

🧮 Building conversion factors

For the reaction 2H₂ + O₂ → 2H₂O, we can construct several molar ratios:

  • 2 mol H₂ : 1 mol O₂
  • 2 mol H₂O : 1 mol O₂
  • 2 mol H₂ : 2 mol H₂O

Each ratio can be written as a fraction in two ways (numerator/denominator can be flipped depending on what you need to cancel).

🔄 Applying ratios in calculations

  • These ratios work as conversion factors to determine amounts of substances.
  • Example from the excerpt: To find how many moles of O₂ react to produce 27.6 mol of H₂O:
    • Use the ratio with H₂O in the denominator (to cancel) and O₂ in the numerator (to introduce).
    • Calculation: 27.6 mol H₂O × (1 mol O₂ / 2 mol H₂O) = 13.8 mol O₂
  • The key is choosing the correct ratio orientation so units cancel properly.

📚 Stoichiometry fundamentals

📚 What stoichiometry means

Stoichiometry: The study of the numerical relationships between the reactants and the products in balanced chemical reactions.

  • It is the quantitative aspect of chemistry—how much reacts and how much is produced.
  • All stoichiometric calculations rely on the balanced equation as the foundation.

🎯 Key takeaway from the excerpt

  • The balanced chemical reaction can be used to determine molar relationships between substances.
  • This extends the usefulness of balanced equations beyond just showing what reacts to showing how much reacts.

🔍 How to relate molar amounts

  • Amounts of substances in chemical reactions are related by their coefficients in the balanced chemical equation.
  • The coefficients provide the fixed ratios that govern all quantitative predictions about the reaction.
  • Don't confuse: the coefficients tell you the ratio, not the absolute amounts—you can scale up or down as needed for a particular problem.
36

Mole-Mass and Mass-Mass Problems

Mole-Mass and Mass-Mass Problems

🧭 Overview

🧠 One-sentence thesis

Balanced chemical equations allow us to convert between masses and moles of different substances in a reaction by using molar ratios and molar masses as conversion factors in a systematic sequence.

📌 Key points (3–5)

  • Mole-mass calculations: convert from moles of one substance to mass of another using a two-step sequence (moles → moles → mass).
  • Mass-mass calculations: convert from mass of one substance to mass of another using a three-step sequence (mass → moles → moles → mass).
  • The conversion sequence: always use the balanced equation to find molar ratios between substances, then apply molar mass as the final conversion factor.
  • Common confusion: you must convert mass to moles first before using the molar ratio from the balanced equation; you cannot directly convert mass to mass without going through moles.
  • Why it matters: these calculations let you determine how much of a reactant is needed or how much product will form in real-world chemical reactions.

🔄 The mole-mass calculation sequence

🔄 What mole-mass calculations do

Mole-mass calculations: a stoichiometry calculation converting between masses and moles of different substances in a chemical reaction.

  • You start with a known number of moles of one substance.
  • You end with the mass of a different substance.
  • The process uses two conversion steps.

📐 The two-step sequence

The excerpt describes the following order:

  1. Moles of first substance → moles of second substance: use the molar ratio from the balanced equation.
  2. Moles of second substance → mass of second substance: use the molar mass of the second substance.

Example: Given the equation Fe₂O₃ + 3SO₃ → Fe₂(SO₄)₃, if you have 3.59 mol of Fe₂O₃, how many grams of SO₃ can react?

  • Step 1: Convert 3.59 mol Fe₂O₃ to moles of SO₃ using the ratio 3 mol SO₃ / 1 mol Fe₂O₃ = 10.77 mol SO₃.
  • Step 2: Convert 10.77 mol SO₃ to grams using molar mass 80.06 g/mol = 862 g SO₃.

✏️ Single-line vs stepwise

  • You can perform both steps separately and round at each stage.
  • Or you can combine all conversion factors into one continuous calculation.
  • The excerpt notes that both methods give essentially the same answer, though slight differences may appear due to rounding at intermediate steps.

🔁 The mass-mass calculation sequence

🔁 What mass-mass calculations do

Mass-mass calculations: a stoichiometry calculation converting between the mass of one substance and the mass of a different substance in a chemical reaction.

  • You start with a known mass of one substance.
  • You end with the mass of a different substance.
  • This requires three conversion steps.

📏 The three-step sequence

The excerpt describes this order:

  1. Mass of first substance → moles of first substance: use the molar mass of the first substance.
  2. Moles of first substance → moles of second substance: use the molar ratio from the balanced equation.
  3. Moles of second substance → mass of second substance: use the molar mass of the second substance.

Example: For the reaction CH₄ + 4Cl₂ → CCl₄ + 4HCl, how many grams of HCl are produced from 100.0 g of CH₄?

  • Step 1: Convert 100.0 g CH₄ to moles using molar mass 16.05 g/mol = 6.231 mol CH₄.
  • Step 2: Convert to moles HCl using ratio 4 mol HCl / 1 mol CH₄ = 24.92 mol HCl.
  • Step 3: Convert to grams HCl using molar mass 36.46 g/mol = 908.5 g HCl.

⚠️ Critical rule: always go through moles

  • You cannot skip the mole-to-mole conversion step.
  • The balanced equation gives ratios in moles, not in grams.
  • Don't confuse: you must convert mass to moles before applying the molar ratio from the equation.

🔑 Key tools and concepts

🔑 Molar mass as a conversion factor

  • Molar mass connects mass (grams) and amount (moles) for a single substance.
  • When converting mass → moles, invert the molar mass so gram units cancel.
  • When converting moles → mass, use molar mass directly.

🔑 Molar ratio from balanced equations

  • The coefficients in a balanced equation give the ratio of moles between substances.
  • This ratio is the only way to convert from moles of one substance to moles of another.
  • The excerpt emphasizes: "We have established that a balanced chemical equation is balanced in terms of moles as well as atoms or molecules."

🔑 Significant figures

  • Limit intermediate answers to the proper number of significant figures if calculating stepwise.
  • If combining all steps in one line, only the final answer needs to be rounded.
  • The excerpt shows that both approaches give "essentially the same" result, with only minor differences.

📊 Summary comparison

Calculation typeStarting pointEnding pointNumber of steps
Mole-massMoles of substance AMass of substance B2
Mass-massMass of substance AMass of substance B3

Common pattern: Both types require using the molar ratio from the balanced equation; the difference is whether you start with moles (2 steps) or mass (3 steps).

37

Energy and Its Units

Energy and Its Units

🧭 Overview

🧠 One-sentence thesis

Energy, defined as the ability to do work, is measured in joules or calories and is transferred between objects as heat when temperature differences exist.

📌 Key points (3–5)

  • What energy is: the ability to do work; when you feel energetic, you can perform more work.
  • Heat as energy transfer: heat is energy moving from one object to another due to temperature differences.
  • Units and conversions: energy, work, and heat share the same units—joules (J) and calories (cal), with 1 cal = 4.184 J.
  • Common confusion: nutritional Calories (capital C) vs. calories—1 Cal = 1,000 cal = 1 kcal.
  • Why it matters: understanding energy units is essential for interpreting food energy content, exercise expenditure, and chemical processes.

🔋 What energy and heat are

🔋 Energy as the ability to do work

Energy: the ability to do work.

  • Think of feeling "energetic"—you feel ready to jump up and get something done.
  • When you have a lot of energy, you can perform a lot of work; when you lack energy, you have little desire to do anything.
  • This applies not only to people but to all physical and chemical processes.
  • The quantity of work that can be done is directly related to the quantity of energy available.

🔥 Heat as energy transfer

Heat: the transfer of energy from one part of the universe to another due to temperature differences.

  • Energy can be transferred between objects if they have different temperatures.
  • Example: holding an ice cube—energy (as heat) flows from your warm hand to the cold ice, melting the ice and making your hand feel cold.
  • Heat is not "hotness" itself; it is the movement of energy caused by temperature differences.
  • Because of their interrelationships, energy, work, and heat all have the same units.

📏 Units of energy and heat

📏 The joule (SI unit)

Joule (J): the SI unit of energy, work, and heat.

  • A joule is a tiny amount of energy.
  • Example: it takes about 4 J to warm 1 mL of water by 1°C.
  • Many processes involve thousands of joules, so the kilojoule (kJ) is also common.

🍎 The calorie (everyday and health professions)

Calorie (cal): a unit of energy widely used in the health professions and everyday life.

  • Originally defined as the amount of energy needed to warm 1 g of water by 1°C.
  • In modern times, the calorie is directly related to the joule: 1 cal = 4.184 J.
  • Because a calorie is small, nutritional energies are usually expressed in kilocalories (kcal), also called Calories (capital C).
  • Don't confuse: 1 Cal (capital C, nutritional Calorie) = 1,000 cal = 1 kcal.

🔄 Converting between units

FromToConversion
Calories (Cal)calories (cal)1 Cal = 1,000 cal
calories (cal)joules (J)1 cal = 4.184 J
joules (J)kilojoules (kJ)1,000 J = 1 kJ
kilocalories (kcal)kilojoules (kJ)1 kcal = 4.184 kJ
  • Example: A candy bar provides 120 Cal of energy, which equals 120,000 cal.
  • Example: 70.0 Cal of bread = 70,000 cal = 293,000 J = 293 kJ.

🍽️ Nutritional energy

🍽️ Food energy content

  • The energy values of foods are reported in kilocalories (kcal) or Calories (Cal).
  • Proteins and carbohydrates supply 4 kcal/g.
  • Fat supplies 9 kcal/g (more than twice the energy per gram).
  • Example: one cup of honey contains 1,030 Cal = 1,030,000 cal = about 4.3 million joules.

🏃 Energy expenditure during exercise

  • Exercise expends energy, also reported in kilocalories per hour.
  • Energy expenditures vary widely depending on the activity:
    • Walking at 4 mph: about 440 kcal/h
    • Mountain biking at 20 mph: about 1,870 kcal/h
    • Basketball: 940 kcal/h
    • Yoga: 280 kcal/h
  • After obtaining energy from food, we need to expend it through activity, or our bodies will store it in unhealthy ways.
  • Most health professionals agree that exercise is a valuable component of a healthy lifestyle—it strengthens the body, develops muscle tone, and expends energy.
38

Heat

Heat

🧭 Overview

🧠 One-sentence thesis

Heat transfer is proportional to mass and temperature change through a substance-specific constant called specific heat, which determines how much energy is needed to change a substance's temperature.

📌 Key points (3–5)

  • What heat is: energy that flows due to temperature differences between objects or systems.
  • The heat equation: heat equals mass times temperature change times specific heat (heat = mcΔT).
  • Specific heat definition: the amount of energy needed to change 1 gram of a substance by 1 degree.
  • Direction matters: positive ΔT and heat mean energy flows in; negative values mean energy flows out.
  • Common confusion: don't confuse specific heat (energy per gram per degree) with total heat transferred (which also depends on mass and temperature change).

🌡️ Temperature differences and heat flow

🌡️ What drives heat transfer

  • Heat flows because of temperature differences between objects.
  • Energy moves from hotter objects to cooler ones.
  • Example: touching a hot object → energy flows into your fingers; holding ice → energy flows out of your hand.

🔄 What happens to the receiving system

  • Generally, the system's temperature changes when it gains or loses heat.
  • Greater original temperature difference → greater heat transfer → greater temperature change.
  • The relationship is proportional: heat ∝ ΔT (where ΔT = T_final − T_initial).

🧮 The heat transfer equation

🧮 Building the equation

The excerpt develops the equation in steps:

  1. Temperature proportionality: heat ∝ ΔT
  2. Mass matters: more mass requires more heat for the same temperature change → heat ∝ mΔT
  3. The proportionality constant: to make it an equality, add specific heat (c) → heat = mcΔT

📏 What each variable means

VariableMeaningNotes
heatEnergy transferredPositive = energy in; negative = energy out
mMass of substanceIn grams
cSpecific heatCharacteristic of each substance
ΔTTemperature changeT_final − T_initial

🔢 Specific heat definition

Specific heat: the amount of energy that must be transferred to or from 1 g of a substance to change its temperature by 1°.

  • Symbol: c
  • Units: cal/g·°C or cal/g·K
  • Every substance has its own characteristic value.
  • Also called "specific heat capacity" (the term "heat capacity" alone is incorrect).

📊 Specific heat values and patterns

📊 Substance comparison

The excerpt provides a table showing specific heats vary widely:

  • Highest: hydrogen (3.419 cal/g·°C)
  • Water: 1.00 cal/g·°C (reference value)
  • Lowest in table: mercury (0.033 cal/g·°C)

🔍 What the values tell you

  • Lower specific heat → less energy needed for the same temperature change → larger temperature change for the same heat input.
  • Higher specific heat → more energy needed → smaller temperature change for the same heat input.
  • Example: if 1.00 g of each substance absorbed 100 cal, mercury would experience the largest temperature change (lowest c), and hydrogen would experience the smallest (highest c).

🧪 Applying the equation

🧪 Calculating heat transferred

When you know mass, temperature change, and specific heat:

  • Determine ΔT = T_final − T_initial
  • Look up specific heat for the substance
  • Substitute into heat = mcΔT
  • Check units cancel properly (grams and °C should cancel, leaving calories)

Example from excerpt: 150.0 g iron heated from 25.0°C to 73.3°C

  • ΔT = 73.3°C − 25.0°C = 48.3°C
  • c for iron = 0.108 cal/g·°C
  • heat = (150.0 g)(0.108 cal/g·°C)(48.3°C) = 782 cal
  • Direction: temperature increased, so energy flowed into the metal

🔬 Finding specific heat from data

When you know heat, mass, and temperature change:

  • Calculate ΔT
  • Rearrange equation: c = heat / (m × ΔT)
  • Pay attention to signs (heat lost = negative value)

Example from excerpt: 10.3 g metal gave off 71.7 cal, temperature dropped from 97.5°C to 22.0°C

  • ΔT = 22.0°C − 97.5°C = −75.5°C
  • Heat lost, so heat = −71.7 cal
  • c = −71.7 cal / [(10.3 g)(−75.5°C)] = 0.0923 cal/g·°C
  • This matches copper's specific heat, identifying the metal

⚠️ Sign conventions

Don't confuse the direction of heat flow:

  • Energy into object: total energy increases → heat and ΔT are positive
  • Energy out of object: total energy decreases → heat and ΔT are negative
  • The equation itself doesn't show direction; you determine it from the sign of the values
39

Phase Changes

Phase Changes

🧭 Overview

🧠 One-sentence thesis

Phase changes occur at characteristic temperatures (melting and boiling points) where substances transition between solid, liquid, and gas phases without changing temperature, requiring specific amounts of heat energy per gram or mole of material.

📌 Key points (3–5)

  • What phase changes are: physical processes where substances transition between solid, liquid, and gas phases at specific temperatures (melting point or boiling point).
  • Isothermal nature: temperature remains constant during a phase change; added heat changes the phase, not the temperature.
  • Two phases coexist: at the melting or boiling point, both phases can exist simultaneously (e.g., ice and liquid water both at 0°C).
  • Heat requirements: each substance has characteristic heats of fusion (for melting/freezing) and vaporization (for boiling/condensing) that determine how much energy is needed per gram or mole.
  • Common confusion: heat going in vs. out—adding heat causes solid→liquid→gas transitions; removing heat causes gas→liquid→solid transitions.

🌡️ Phase change temperatures and definitions

🌡️ Melting point

The melting point is the temperature at which a substance goes from a solid to a liquid (or from a liquid to a solid).

  • This is a fixed temperature for each pure substance.
  • Example: water has a melting point of 0°C on the Celsius scale.
  • At this temperature, solid and liquid phases can coexist.

🌡️ Boiling point

The boiling point is the temperature at which a substance goes from a liquid to a gas (or from a gas to a liquid).

  • Also a characteristic fixed temperature for each substance.
  • Example: water has a boiling point of 100°C.
  • Both liquid and gas phases can exist together at this temperature.

🔄 Direction matters

  • Heat going in: solid → liquid (melting) or liquid → gas (vaporization).
  • Heat going out: gas → liquid (condensation) or liquid → solid (solidification/freezing).
  • The direction of heat transfer determines which phase change occurs.

🧊 Key principle: isothermal phase changes

🧊 Temperature stays constant

Phase changes are isothermal (isothermal means "constant temperature").

  • When a substance is at its melting or boiling point, adding or removing heat does not change the temperature.
  • Instead, the heat energy goes into changing the phase.
  • Example: ice at 0°C that receives heat will melt into liquid water also at 0°C; the temperature does not rise until all the ice has melted.

🔀 Two phases coexist

  • At the melting point, solid and liquid can both be present at the same temperature.
  • At the boiling point, liquid and gas can both be present at the same temperature.
  • Example: at 100°C, liquid water and steam (gaseous water) coexist.
  • Only after the phase change is complete does further heat addition change the temperature.

🔥 Heat of fusion and heat of vaporization

🔥 Heat of fusion (ΔHfus)

The heat of fusion is the amount of heat per gram (or per mole) required for a phase change that occurs at the melting point.

  • This is the energy needed to melt a solid into a liquid (or released when a liquid freezes into a solid).
  • Each substance has its own characteristic heat of fusion.
  • Example: water has a heat of fusion of 79.9 cal/g.

Calculation formulas:

  • heat = n × ΔHfus (where n is the number of moles)
  • heat = m × ΔHfus (where m is the mass in grams)

💨 Heat of vaporization (ΔHvap)

The heat of vaporization is the amount of heat per gram (or per mole) required for a phase change that occurs at the boiling point.

  • This is the energy needed to vaporize a liquid into a gas (or released when a gas condenses into a liquid).
  • Example: water has a heat of vaporization of 540 cal/g.

Calculation formulas:

  • heat = n × ΔHvap (where n is the number of moles)
  • heat = m × ΔHvap (where m is the mass in grams)

📊 Comparison table

SubstanceΔHfus (cal/g)ΔHvap (cal/g)
Water (H₂O)79.9540
Aluminum (Al)94.02,602
Gold (Au)15.3409
Iron (Fe)63.21,504
Sodium chloride (NaCl)123.5691
Ethanol (C₂H₅OH)45.2200.3
Benzene (C₆H₆)30.494.1

Note: Vaporization typically requires much more energy than fusion for the same substance.

❄️ Special case: sublimation

❄️ Direct solid-to-gas transition

Sublimation is a phase change where a solid goes directly to a gas: solid → gas.

  • This skips the liquid phase entirely.
  • Each substance has a characteristic heat of sublimation (ΔHsub).
  • Example: water has a heat of sublimation of 620 cal/g.

🧊 Practical examples

  • Dry ice: solid carbon dioxide (CO₂) sublimes at −78.5°C, going directly from solid to gas without becoming liquid.
  • Frozen water: even below 0°C, ice and snow slowly sublime over time.
  • Ice cubes in freezers: get smaller over time as solid water sublimes and redeposits on cooling elements.
  • Freezer burn: water sublimes from frozen foods, creating an unattractive appearance (not actual burning; the food is still safe but looks unappetizing).

Don't confuse: Dry ice is called "dry" because it does not pass through a liquid phase; it goes directly from solid to gas. Carbon dioxide can exist as a liquid, but only under high pressure.

40

Bond Energies and Chemical Reactions

Bond Energies and Chemical Reactions

🧭 Overview

🧠 One-sentence thesis

Atoms bond together because doing so releases energy and moves them to a lower, more stable energy state, and chemical reactions always involve energy changes because bonds break and form with different characteristic energies.

📌 Key points (3–5)

  • Why atoms bond: atoms combine to form compounds because bonded atoms have lower energy than separated atoms, and energy is released (usually as heat) when bonds form.
  • Bond energy definition: the characteristic amount of energy needed to break a bond between specific atoms, which is the same amount released when that bond forms.
  • Energy always changes in reactions: when reactants rearrange into products, the total bond energy changes, so every chemical reaction absorbs or releases energy.
  • Exothermic vs endothermic: exothermic reactions release energy (products have lower energy than reactants); endothermic reactions absorb energy (products have higher energy than reactants).
  • Common confusion: bond breaking requires energy (endothermic), but bond making releases energy (exothermic)—the net effect determines whether the overall reaction absorbs or releases energy.

⚛️ Why atoms form bonds

⚛️ Atoms move toward lower energy

  • The excerpt uses an analogy: a basketball on a slide always rolls down (to lower gravitational potential energy) unless someone does work to push it up.
  • Atoms behave similarly: they spontaneously move to positions of minimum energy.
  • General principle: all objects tend to move spontaneously to minimum energy unless acted on by another force.

🔗 Bonding releases energy

When atoms combine to make a compound, energy is always given off, and the compound has a lower overall energy.

  • Bonded atoms have lower energy than the same atoms separated.
  • The energy difference between bonded and separated states is released (usually as heat) when the bond forms.
  • Example: when two atoms bond, they "roll downhill" energetically, just like the basketball.

🔄 Breaking bonds requires energy input

  • Reversing the process (breaking bonds) requires putting energy back in, just as lifting the basketball back up the slide requires work.
  • The amount of energy needed to break a bond equals the amount released when that bond formed.

🔢 Bond energy values

🔢 What bond energy means

Bond energy: the strength of interactions between atoms that make covalent bonds.

  • Bond energy describes how much energy is needed to break a specific type of covalent bond.
  • For ionic compounds, the term lattice energy is used instead (for attractions between opposite charges).

📊 Characteristic energies for different bonds

  • Each molecule has its own exact bond energy, but bonds between the same pair of elements have roughly the same value across different molecules.
  • Example: all C–H bonds have bond energy around 100 kcal/mol, regardless of which molecule they are in.
  • The excerpt provides a table of approximate values:
Bond typeApproximate energy (kcal/mol)Notes
C–H100Single bond
C–C85Single bond
C=C145Double bond (stronger)
C≡C200Triple bond (strongest)
C–O86Single bond
C=O190Double bond
C–N70Single bond
N–H93Single bond
H–H105Single bond
  • Pattern: multiple bonds (double, triple) are stronger and require more energy to break than single bonds between the same atoms.

🔥 Energy changes in chemical reactions

🔥 Why reactions always involve energy change

When chemical reactions occur, the atoms in the reactants rearrange their chemical bonds to make products. The new arrangement of bonds does not have the same total energy as the bonds in the reactants. Therefore, when chemical reactions occur, there will always be an accompanying energy change.

  • Reactants have one set of bonds with a certain total energy.
  • Products have a different arrangement of bonds with a different total energy.
  • The difference must be absorbed from or released to the surroundings.

⬇️ Exothermic reactions

Exothermic: a process that gives off energy.

  • What happens: the energy of products is lower than the energy of reactants.
  • Result: substances lose energy to the surrounding environment during the reaction.
  • Most common form: energy is given off as heat (though a few reactions give off light).
  • How to recognize: energy appears as a product in the equation.
  • Example from the excerpt: 2H₂(g) + O₂(g) → 2H₂O(ℓ) + 135 kcal — energy is a product, so this is exothermic.

⬆️ Endothermic reactions

Endothermic: a process that absorbs energy.

  • What happens: products have higher energy than reactants.
  • Result: reactants must absorb energy from their environment to react.
  • How to recognize: energy appears as a reactant in the equation.
  • Example from the excerpt: N₂(g) + O₂(g) + 45 kcal → 2NO(g) — energy is a reactant, so this is endothermic.

🧩 Energy as reactant or product

  • Exothermic reactions: think of energy as a product (the reaction "produces" energy).
  • Endothermic reactions: think of energy as a reactant (the reaction "consumes" energy).
  • This mental model helps identify the type of reaction from a chemical equation.

🧬 Energy in biochemical reactions

🧬 Glucose oxidation as an energy source

  • The human body (and all living organisms) follows the same energy principles as other chemical reactions.
  • Key reaction: oxidation of glucose provides energy for the body.
    • C₆H₁₂O₆(s) + 6O₂(g) → 6CO₂(g) + 6H₂O(ℓ) + 670 kcal
  • One mole of glucose (about 115 mL volume) releases 670 kcal, making it a compact energy source.

🍽️ Dietary energy sources

Carbohydrates: one of the three main dietary components; all carbohydrates supply approximately 4 kcal/g.

  • Carbohydrates (like glucose and other sugars): supply about 4 kcal per gram.
    • You can verify this by dividing the heat of reaction (670 kcal/mol) by glucose's molar mass.
  • Proteins (building blocks of muscle and skin): also supply about 4 kcal per gram.
  • Fats (largely hydrocarbon chains): mentioned as other important energy sources (the excerpt cuts off before giving their energy value).

🔑 Don't confuse: bond breaking vs bond making

  • Bond breaking is endothermic (requires energy input).
  • Bond making is exothermic (releases energy).
  • The overall reaction can be either exothermic or endothermic depending on whether more energy is released by new bonds forming or consumed by old bonds breaking.
  • Example: even though breaking bonds in reactants costs energy, if forming new bonds in products releases more energy, the net reaction is exothermic.
41

The Energy of Biochemical Reactions

The Energy of Biochemical Reactions

🧭 Overview

🧠 One-sentence thesis

Biochemical reactions in the human body follow the same energy principles as other chemical reactions, with energy coming primarily from the oxidation of glucose and the conversion of ATP to ADP, while dietary carbohydrates and proteins supply about 4 kcal/g and fats supply about 9 kcal/g.

📌 Key points (3–5)

  • Energy source for the body: The oxidation of glucose (C₆H₁₂O₆) is an important reaction that provides energy, releasing 670 kcal per mole.
  • ATP to ADP conversion: Breaking an O–P bond in ATP and forming new bonds releases about 7.5 kcal/mol, which fuels other cellular reactions.
  • Dietary energy content: Carbohydrates and proteins each supply approximately 4 kcal/g, while fats provide about 9 kcal/g.
  • Common confusion: Even though 7.5 kcal/mol from ATP seems small compared to glucose oxidation (670 kcal/mol), it is sufficient to power many biochemical reactions in cells.
  • Core principle: Complex biological reactions must obey the basic rules of chemistry, including energy change principles.

🍬 Energy from dietary components

🍬 Carbohydrates as energy sources

Carbohydrates: One of the three main dietary components of a human diet, like glucose and other sugars, that supplies energy for the body.

  • All carbohydrates supply approximately 4 kcal/g.
  • Glucose is a compact source of energy: 1 mol of glucose (about 115 mL volume) releases 670 kcal when oxidized.
  • You can verify the 4 kcal/g value by dividing the heat of reaction for glucose oxidation by its molar mass.

🥩 Proteins as energy sources

Proteins: Building blocks of structural tissues, like muscle and skin.

  • Proteins also supply about 4 kcal/g, the same as carbohydrates.
  • They serve dual roles: structural function and energy provision.

🥑 Fats as energy sources

Fats: A compound, composed largely of hydrocarbon chains, that supplies energy for the body.

  • Fats are largely hydrocarbon chains.
  • They provide even more energy per gram: about 9 kcal/g.
  • This is more than twice the energy density of carbohydrates or proteins.

Comparison table:

Dietary componentEnergy contentChemical nature
Carbohydrates~4 kcal/gSugars like glucose
Proteins~4 kcal/gStructural tissue building blocks
Fats~9 kcal/gHydrocarbon chains

⚡ Key biochemical energy reactions

⚡ Glucose oxidation reaction

The oxidation of glucose is an important reaction that provides energy for our bodies:

  • Reaction: C₆H₁₂O₆ (solid) + 6O₂ (gas) → 6CO₂ (gas) + 6H₂O (liquid) + 670 kcal
  • Energy released: 670 kcal per mole of glucose.
  • Why it matters: This is one of the primary ways the body extracts energy from food.
  • Efficiency: Considering that 1 mol of glucose has a volume of about 115 mL, glucose is a compact source of energy.

Example: When you eat foods containing glucose or other sugars, your body oxidizes them through this reaction to power cellular activities.

🔋 ATP to ADP conversion

Another important reaction is the conversion of adenosine triphosphate (ATP) to adenosine diphosphate (ADP):

  • Energy released: About 7.5 kcal/mol of ATP under physiological conditions.
  • What happens chemically: Breaking an O–P bond and forming an O–P bond and two O–H bonds.
  • Why it matters: This energy fuels other biochemically important chemical reactions in our cells.

Don't confuse: The 7.5 kcal/mol from ATP may not seem like much compared to the 670 kcal from glucose oxidation, but it is enough energy to power many cellular processes. The body uses glucose oxidation to generate ATP, which then powers individual cellular reactions.

🔄 Reversibility of ATP/ADP

  • If ATP → ADP gives off 7.5 kcal/mol, then the reverse process ADP → ATP requires 7.5 kcal/mol to proceed.
  • This means the body must invest energy (from glucose or other sources) to regenerate ATP from ADP.
  • The cycle allows energy to be stored (in ATP) and released (to ADP) as needed.

🧬 Fundamental principle

🧬 Biochemical reactions follow chemistry rules

The excerpt emphasizes a key principle:

Note: Even complex biological reactions must obey the basic rules of chemistry.

  • The chemistry of the human body, or any living organism, is very complex.
  • However: The chemical reactions found in the human body follow the same principles of energy that other chemical reactions follow.
  • This means concepts like exothermic/endothermic reactions, bond energies, and energy conservation apply to biological systems just as they do to simpler chemical reactions.

Why this matters: Understanding basic chemistry principles allows us to understand how energy flows through living systems, even when the specific reactions are complicated.

42

Intermolecular Interactions

Intermolecular Interactions

🧭 Overview

🧠 One-sentence thesis

The strength of intermolecular interactions between particles determines the temperatures at which substances transition between solid, liquid, and gas phases, with stronger interactions requiring higher temperatures to overcome.

📌 Key points (3–5)

  • What phases are: A phase is a form of matter with consistent physical properties throughout (solid, liquid, or gas).
  • What determines phase transitions: The strength of intermolecular interactions dictates melting and boiling points—stronger interactions require more thermal energy (higher temperature) to change phases.
  • Types of intermolecular forces: From strongest to weakest: covalent network bonding, ionic interactions, hydrogen bonding, dipole-dipole interactions, and dispersion forces.
  • Common confusion—polar vs. nonpolar molecules: A molecule can have polar covalent bonds but still be nonpolar overall if the bond dipoles cancel due to molecular geometry (e.g., CO₂).
  • Why it matters: Understanding intermolecular interactions explains the wide variability in melting and boiling points across different substances.

🔬 What are phases and what controls them

🔬 Definition of a phase

Phase: A certain form of matter that includes a specific set of physical properties; the atoms, molecules, or ions make up the phase in a consistent manner throughout.

  • The excerpt recognizes three stable phases: solid, liquid, and gas.
  • Solid phase: Individual particles are in contact and held in place.
  • Liquid phase: Individual particles are in contact but moving with respect to each other.
  • Gas phase: Individual particles are separated by relatively large distances.

🌡️ Temperature and pressure effects

  • Temperature is the primary factor determining which phase a substance adopts.
  • Example: H₂O exists as ice when very cold, liquid water when warmer, and steam at even higher temperatures.
  • Pressure can also affect phase presence (e.g., carbon dioxide does not exhibit a liquid phase unless pressure exceeds about six times normal atmospheric pressure), but its effects are less obvious in everyday conditions.

📏 Melting and boiling points

Melting point: The temperature that separates a solid and a liquid.

Boiling point: The temperature that separates a liquid and a gas.

  • Different substances have vastly different temperature ranges for their phases.
  • Example comparison from the excerpt:
SubstanceSolid Phase BelowLiquid Phase AboveGas Phase Above
Hydrogen (H₂)−259°C−259°C−253°C
Water (H₂O)0°C0°C100°C
Sodium chloride (NaCl)801°C801°C1413°C
  • This extreme variability depends entirely on the strength of intermolecular interactions.

💪 Types of intermolecular interactions

💪 What intermolecular interactions are

Intermolecular interactions: A force of attraction between different molecules (the term is also used to include interactions between ions in ionic compounds).

  • Substances with strong intermolecular interactions require higher temperatures to become liquids and gases.
  • Substances with weak intermolecular interactions need less energy (lower temperature) to become liquids and gases.

🔗 Covalent network bonding (strongest)

Covalent network bonding: A type of interaction in which all the atoms in a sample are covalently bonded to other atoms.

  • This is actually a covalent bond, not just an intermolecular force.
  • The entire sample is essentially one large molecule.
  • These substances are solid over a large temperature range because disrupting all covalent bonds at once requires enormous energy.
  • Example: Diamond (pure carbon) finally vaporizes only at temperatures over 3,500°C.
  • Don't confuse: This is different from discrete molecules held together by weaker forces; here, every atom is covalently bonded to neighbors throughout the sample.

⚡ Ionic interactions (very strong)

Ionic interactions: An attraction due to ions of opposite charges.

  • The strongest force between any two particles is the ionic bond (two ions of opposing charge attracted to each other).
  • Substances with ionic interactions are relatively strongly held together, so they typically have high melting and boiling points.
  • Example: Sodium chloride (NaCl) has a melting point of 801°C and boiling point of 1413°C.

🧲 Hydrogen bonding (strong dipole-dipole)

Hydrogen bonding: A particularly strong type of dipole-dipole interaction caused by a hydrogen atom being bonded to a very electronegative element.

  • Occurs in molecules with H–F, O–H, or N–H bonds.
  • These bonds are strongly polar, creating particularly strong dipole-dipole interactions (as strong as 10% of a true covalent bond).
  • Example: Water molecules experience hydrogen bonding between the O–H bonds, which strongly affects water's physical properties.
  • The excerpt shows hydrogen bonding allows molecules to interact through their oppositely charged ends.

🔄 Dipole-dipole interactions (moderate)

Dipole-dipole interaction: An attraction between polar molecules.

  • Occurs when molecules have polar covalent bonds with unequal electron sharing.
  • Polar covalent bond: A covalent bond with unequal sharing of electrons (one atom attracts electrons more strongly).
  • Polar molecule: A molecule with a net unequal distribution of electrons in its covalent bonds.
  • Example: In HF, fluorine attracts electrons more strongly than hydrogen, creating a partial negative charge (δ−) on the fluorine side and partial positive charge (δ+) on the hydrogen side.
  • Oppositely charged ends of different polar molecules attract each other.

🌫️ Dispersion forces (weakest)

Dispersion forces (or London forces): A force caused by the instantaneous imbalance of electrons about a molecule.

  • These forces exist between all molecules, caused by electrons being in different places at any moment, creating a temporary charge separation that disappears almost instantly.
  • Very weak intermolecular interactions.
  • Substances experiencing only dispersion forces are typically soft in the solid phase and have relatively low melting points.
  • However, larger molecules with many electrons can experience substantial dispersion forces.
  • Example: Waxes are long hydrocarbon chains that are solid at room temperature because the molecules have so many electrons that the resulting dispersion forces are strong enough to hold them in the solid phase.

🔀 Polar vs. nonpolar molecules

🔀 When polar bonds don't make a polar molecule

Nonpolar covalent bond: A covalent bond that has an equal sharing of electrons (same atom on each side).

Nonpolar molecule: A molecule where the individual polar bonds cancel each other out due to spatial orientation.

  • Some molecules have polar covalent bonds, but the bonds are oriented in space such that they cancel each other out.
  • The individual bonds are polar, but the overall molecule is not polar.
  • Such molecules experience little or no dipole-dipole interactions.

📐 Examples of nonpolar molecules with polar bonds

  • Carbon dioxide (CO₂): Has polar C=O bonds, but they point in opposite directions and cancel out.
  • Carbon tetrachloride (CCl₄): Has polar C–Cl bonds, but their spatial arrangement causes the dipoles to cancel.
  • Don't confuse: Having polar bonds does not automatically mean the molecule is polar—geometry matters.

📊 Summary comparison of intermolecular forces

Type of InteractionRelative StrengthExample SubstanceKey Characteristic
Covalent network bondingStrongestDiamond (C)All atoms covalently bonded throughout sample
Ionic interactionsVery strongSodium chloride (NaCl)Oppositely charged ions attract
Hydrogen bondingStrong (10% of covalent bond)Water (H₂O)H bonded to F, O, or N
Dipole-dipole interactionsModerateHydrogen fluoride (HF)Polar molecules attract via opposite partial charges
Dispersion forcesWeakestWaxes, Br₂Temporary electron imbalances; present in all molecules

🎯 How to predict phase behavior

  • Identify the strongest intermolecular interaction present in a substance.
  • Stronger interactions → higher melting and boiling points → substance remains solid or liquid at higher temperatures.
  • Weaker interactions → lower melting and boiling points → substance becomes liquid or gas at lower temperatures.
  • Example: Hydrogen (H₂) has only weak dispersion forces, so it becomes a gas at −253°C; sodium chloride has strong ionic interactions, so it doesn't become a gas until 1413°C.
43

Solids and Liquids

Solids and Liquids

🧭 Overview

🧠 One-sentence thesis

Solids and liquids are condensed phases whose particles remain in virtual contact, but solids hold particles in fixed positions with definite shape while liquids allow particles to move about each other and take the shape of their container.

📌 Key points (3–5)

  • Condensed phases: solids and liquids are collectively called condensed phases because their particles are in virtual contact, unlike gases.
  • Key difference in particle motion: solids have particles in fixed positions (not enough thermal energy to overcome intermolecular interactions), while liquids have particles that can move about each other (enough energy to partially overcome interactions).
  • Shape and volume: solids have definite shape and volume; liquids have definite volume but indefinite shape; gases have neither.
  • Common confusion: both solids and liquids have definite volume, but only solids have definite shape—don't confuse "in contact" with "fixed in place."
  • Intermolecular interaction strength: solids have the strongest intermolecular interactions, liquids moderate, and gases weak.

🧊 The solid state

🔒 Fixed particle positions

Solid: the individual particles of a substance are in fixed positions with respect to each other because there is not enough thermal energy to overcome the intermolecular interactions between the particles.

  • Particles cannot move around each other; they are locked in place.
  • This fixed arrangement gives solids a definite shape and volume.
  • Most solids are hard, but some (like waxes) are relatively soft.
  • Many solids composed of ions can be quite brittle.

💎 Crystalline vs amorphous solids

Crystal: a regular, three-dimensional array of alternating positive and negative ions.

  • Crystalline solids: particles arranged in a regular, repeating three-dimensional pattern.
    • Many solids composed of ions form crystals.
    • The regular arrangement is sometimes visible macroscopically (you can see the crystal structure with your eyes).
    • Example: Some large crystals show their structure because of the regular arrangement of atoms or ions.

Amorphous solid: a solid with no regular structure (literally, "without form").

  • Amorphous solids: no regular crystal structure.
    • Especially common in solids composed of large molecules that cannot easily organize into regular patterns.
    • Example: Glass is an amorphous solid.

💧 The liquid state

🌊 Particles in contact but mobile

  • In liquids, particles have enough energy to partially overcome intermolecular interactions.
  • Particles can move about each other while remaining in contact.
  • This explains why liquids have:
    • Definite volume (particles still touch, so the substance doesn't expand freely).
    • No definite shape (particles can slide past each other, so the liquid takes the shape of its container).

🔄 How liquids differ from solids and gases

  • vs. Solids: Liquids have weaker intermolecular interactions than solids, allowing particle movement.
  • vs. Gases: Liquids have stronger intermolecular interactions than gases, keeping particles in contact.
  • Don't confuse: "in contact" (liquids and solids) vs. "fixed in place" (solids only).

📊 Comparing the three states

📋 Summary table

CharacteristicSolidLiquidGas
ShapeDefiniteIndefiniteIndefinite
VolumeDefiniteDefiniteIndefinite
Intermolecular interaction strengthStrongModerateWeak
Particle positionsIn contact and fixed in placeIn contact but not fixedNot in contact, random positions

🔥 Energy and phase transitions

  • Solid → Liquid: Particles gain enough thermal energy to partially overcome intermolecular interactions and move about each other.
  • Liquid → Gas: Particles gain enough energy to completely overcome intermolecular interactions and separate from each other.
  • The change from solid to liquid usually does not significantly change volume.
  • The change from liquid to gas significantly increases volume, by a factor of 1,000 or more.

⚖️ Why intermolecular strength matters

  • Stronger interactions → particles held more tightly → solid state likely at higher temperatures.
  • Weaker interactions → particles can separate more easily → liquid or gas state likely at lower temperatures.
  • Example: Substances with strong intermolecular interactions are likely to be solids at higher temperatures because their interactions are strong enough to hold particles in place.

🌍 Special case: water

💦 Unique properties of water

The excerpt includes a "Looking Closer" section on water as the most important liquid:

  • Universal solvent: Water is an excellent solvent; it dissolves many substances and allows them to react in solution.
  • Unusually high melting and boiling points: 0°C and 100°C, respectively, for such a small molecule.
    • Similar-sized molecules like methane (BP = −162°C) and ammonia (BP = −33°C) have boiling points more than 100° lower.
    • Water molecules experience relatively strong intermolecular interactions that maintain the liquid phase at higher temperatures than expected.
  • Ice floats: The solid form of water is less dense than its liquid form, allowing ice to float.
    • In colder weather, lakes and rivers freeze from the top, allowing animals and plants to live underneath.
  • High energy requirement for temperature change: Water requires an unusually large amount of energy to change temperature.
    • 100 J of energy changes 1 g of Fe by 230°C, but only changes 1 g of H₂O by 100°C.
    • Water changes temperature slowly as heat is added or removed, impacting weather and storm systems like hurricanes.

🌊 Why water matters

  • Earth is the only known body in our solar system with liquid water freely on its surface.
  • Life on Earth would not be possible without liquid water.
  • Water's properties have a major impact on the world around us.
44

Gases and Pressure

Gases and Pressure

🧭 Overview

🧠 One-sentence thesis

The kinetic theory of gases allows us to model all gases similarly regardless of their chemical identity, and the pressure they exert arises from constant collisions of gas particles with container walls.

📌 Key points (3–5)

  • Why gases are unique: simple models can predict the physical behavior of all gases independent of their identities, unlike solids and liquids.
  • Kinetic theory foundation: gases consist of tiny, widely separated particles in constant motion with no intermolecular attractions, making their identity irrelevant to certain physical properties.
  • What pressure is: the force generated by gas particles colliding with container walls, divided by the area of those walls.
  • Common confusion: ideal vs. real gases—ideal gases follow kinetic theory perfectly; real gases show slight deviations but the theory remains important.
  • Multiple pressure units: pressure can be expressed in pascals, bars, atmospheres, torr, or millimeters of mercury, and converting between them is a useful skill.

🔬 The kinetic theory of gases

🔬 Core statements of the theory

Kinetic theory of gases: the fundamental theory of the behavior of gases.

The theory consists of four key statements:

  • Gases are composed of tiny particles separated by large distances.
  • Gas particles are constantly moving, experiencing collisions with other gas particles and the walls of their container.
  • The velocity of gas particles is related to the temperature of a gas.
  • Gas particles do not experience any force of attraction or repulsion with each other.

Why this matters: None of these statements relates to the identity of the gas, meaning all gases should behave similarly.

🎯 Ideal vs. real gases

Ideal gas: a gas that follows the kinetic theory statements perfectly.

Real gases: gases that show slight deviations from the kinetic theory statements.

  • Most gases are real gases, but the deviations are small enough that the kinetic theory remains useful.
  • The theory assumes gas particles are so far apart that individual particles don't "feel" each other, allowing us to treat them as tiny bits of matter whose identity isn't important to certain physical properties.
  • Don't confuse: the existence of real gases does not diminish the importance of the kinetic theory.

📜 Historical significance

  • The development of understanding gas behavior represents the historical dividing point between alchemy and modern chemistry.
  • Initial advances were made in the mid-1600s by Robert Boyle, who founded the Royal Society.
  • Example: This was one of the world's oldest scientific organizations.

💥 Gas pressure and collisions

💥 How pressure arises

Pressure: force divided by area.

  • Gas particles are constantly moving and constantly colliding with each other and with the walls of their container.
  • Forces are generated as gas particles bounce off the container walls.
  • The force generated by gas particles divided by the area of the container walls yields pressure.
  • Pressure is a property we can measure for a gas, but we typically do not consider pressure for solids or liquids.

📏 Units of pressure

The basic unit of pressure is the newton per square meter (N/m²), but several other units are commonly used:

UnitDefinitionRelationship
Pascal (Pa)Redefined N/m²Basic unit; 1 Pa is not very large
Bar100,000 PaMore useful than pascal
Atmosphere (atm)Originally average pressure of Earth's atmosphere at sea levelExactly 760 torr = 1 atm
Millimeters of mercury (mmHg)Pressure generated by a column of mercury 1 mm high1 mmHg = 1 torr
TorrNamed after Evangelista TorricelliSame as 1 mmHg

Key relationships:

  • 1 bar = 100,000 Pa
  • 1 atm = 760 torr (exactly)
  • 1 bar = 1.01325 atm
  • 1 mmHg = 1 torr

🔄 Converting pressure units

The ability to convert from one pressure unit to another is a useful skill.

Example: To convert 1,547 mmHg to atmospheres:

  • First recognize that 1 mmHg equals 1 torr, so 1,547 mmHg = 1,547 torr.
  • Use the conversion factor: 1 atm = 760 torr.
  • Calculate: 1,547 torr × (1 atm / 760 torr) = 2.04 atm.
  • Note how the torr units cancel algebraically.

Don't confuse: When converting, ensure the units you're converting from cancel out algebraically, leaving only the desired unit.

45

Gas Laws

Gas Laws

🧭 Overview

🧠 One-sentence thesis

Gas laws are mathematical relationships that allow us to predict how the physical properties of gases—pressure, volume, temperature, and amount—change under different conditions or relate to one another at any given moment.

📌 Key points (3–5)

  • Boyle's law: pressure and volume are inversely related when temperature and amount stay constant (increase pressure → decrease volume).
  • Charles's law: volume and absolute temperature are directly proportional when pressure and amount stay constant (increase temperature → increase volume).
  • Combined gas law: brings together pressure, volume, and temperature relationships for changing conditions.
  • Ideal gas law: relates all four properties (P, V, n, T) under any conditions using the constant R, not just changes.
  • Common confusion: temperature must always be in Kelvin for gas law calculations, not Celsius; units must match across similar quantities.

🔄 Boyle's Law: Pressure and Volume

🔄 The inverse relationship

Boyle's law: the relationship between the pressure and volume of a gas when temperature and amount remain constant, expressed as P₁V₁ = P₂V₂.

  • When pressure increases, volume decreases; when pressure decreases, volume increases.
  • The product of pressure and volume stays constant for a fixed amount of gas at constant temperature.
  • Example: If initial pressure is 1.56 atm and initial volume is 7.02 L, and pressure drops to 0.987 atm, the final volume becomes 11.1 L—the volume increases because pressure decreased.

⚠️ Unit consistency requirement

  • Both pressure values must use the same unit (both in atm, or both in torr, etc.).
  • Both volume values must use the same unit.
  • If units don't match, convert one quantity to the other's unit before calculating.
  • Example: 1.56 atm can be converted to 1,190 torr by multiplying by 760 torr/1 atm.

🫁 Real-world application: Breathing

  • Breathing is an application of Boyle's law in the human body.
  • When the diaphragm moves down, lung volume expands → pressure inside lungs decreases slightly (by ~3 torr) → air rushes in (inhalation).
  • When the diaphragm relaxes, lung volume decreases → pressure increases slightly (by 1–2 torr) → air is forced out (exhalation).
  • Each breath involves only 0.5–1.0 L of air and very small pressure changes (~0.4% of atmospheric pressure).

🌡️ Charles's Law: Volume and Temperature

🌡️ The direct relationship

Charles's law: the relationship between volume and absolute temperature of a gas when pressure and amount remain constant, expressed as V₁/T₁ = V₂/T₂.

  • As temperature increases, volume increases proportionally.
  • As temperature decreases, volume decreases proportionally.
  • The ratio of volume to temperature stays constant.

🔢 The Kelvin requirement

  • Gas volumes relate directly to Kelvin temperature, not Celsius.
  • Conversion formula: Kelvin = Celsius + 273.
  • The Kelvin scale is the absolute scale with zero at absolute zero (the coldest possible temperature).
  • Example: 20°C converts to 293 K; 60°C converts to 333 K.
  • Don't confuse: Always convert Celsius to Kelvin before using Charles's law, even if the problem gives temperatures in Celsius.

📐 Calculation example

  • A gas at 20°C (293 K) with volume 20.0 L is heated to 60°C (333 K).
  • Using Charles's law: (20.0 L)/(293 K) = V₂/(333 K).
  • Solving: V₂ = 22.7 L.
  • The volume increased because temperature increased, which makes sense for a direct relationship.

🔗 Combined and Ideal Gas Laws

🔗 Combined gas law

Combined gas law: relates pressure, volume, and temperature changes together, expressed as (P₁V₁)/T₁ = (P₂V₂)/T₂.

  • Brings Boyle's and Charles's laws together.
  • The amount of gas must remain constant.
  • Temperature must be in Kelvin; similar quantities must have matching units.
  • Example: A balloon in Cleveland (22°C, 1.09 atm, 1,070 mL) is transported to Denver (11°C, 655 torr). After converting units and applying the law, the new volume is 1,300 mL.

⚗️ Ideal gas law

Ideal gas law: PV = nRT, where P is pressure, V is volume, n is amount in moles, T is absolute temperature, and R is the ideal gas law constant.

  • Unlike other gas laws, this relates properties under any conditions, not just changes.
  • R = 0.08205 (L·atm)/(mol·K) when volume is in liters and pressure in atmospheres.
  • Example: To find volume of 1.45 mol N₂ at 298 K and 3.995 atm, substitute into PV = nRT and solve for V = 8.87 L.

📏 Standard Temperature and Pressure (STP)

STP: standard conditions defined as 273 K (0°C) and 1.00 atm pressure.

  • At STP, 1 mol of any gas occupies about 22.4 L.
  • This provides a convenient conversion: 1 mol gas = 22.4 L at STP.
  • Example: A 100.0 L sample at STP contains (100.0 L) × (1 mol/22.4 L) = 4.46 mol of gas.

🧮 Problem-Solving Strategy

🧮 Identifying the right law

SituationWhich law to useWhat stays constant
Pressure and volume changeBoyle's lawTemperature, amount
Volume and temperature changeCharles's lawPressure, amount
Pressure, volume, and temperature all changeCombined gas lawAmount
Need to find one property given the othersIdeal gas lawNothing (any conditions)

✅ Key steps for calculations

  1. Convert temperature to Kelvin if given in Celsius.
  2. Check units for matching quantities (both pressures in same unit, both volumes in same unit).
  3. Convert if needed before substituting into equations.
  4. Substitute values into the appropriate gas law equation.
  5. Cancel units algebraically to verify the answer will have correct units.
  6. Solve for the unknown variable.
  7. Check if the answer makes sense based on the relationships (inverse for Boyle's, direct for Charles's).

🎯 Common pitfalls

  • Forgetting to convert Celsius to Kelvin (always add 273).
  • Mixing units (e.g., one pressure in atm, another in torr) without converting.
  • Using the wrong gas law for the situation.
  • Not recognizing that the ideal gas law applies to static conditions, not changes.

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46

Solutions

Solutions

🧭 Overview

🧠 One-sentence thesis

Solutions are homogeneous mixtures whose concentrations can be expressed in multiple units (percent, molarity, ppm/ppb), and these concentration measures enable precise stoichiometric calculations and dilution adjustments in chemistry.

📌 Key points (3–5)

  • What a solution is: a homogeneous mixture of solute (minority component) dissolved in solvent (majority component); solutions can be solid, liquid, or gas.
  • Concentration vs. solubility: solubility is the maximum amount that can dissolve; concentration is the actual amount dissolved (which may be less).
  • Multiple concentration units: mass/mass %, volume/volume %, mass/volume %, ppm, ppb, molarity (mol/L), and equivalents—each suited to different contexts.
  • Common confusion: dilute/concentrated are relative terms; precise concentration units are needed for calculations.
  • Why it matters: molarity links concentration directly to moles, enabling stoichiometry in solution reactions and accurate dilution calculations.

🧪 What solutions are

🧪 Definition and components

Solution: a homogeneous mixture.

  • A solvent is the majority component; a solute is the minority component.
  • Solutions are not limited to liquids—air is a gaseous solution, and some alloys are solid solutions.
  • A solution can contain more than one solute (e.g., multiple substances dissolved in water).

💉 Examples in the body

  • Blood plasma, stomach acid, and urine are all solutions containing various solutes.
  • Blood plasma contains ions like Na⁺ (0.138 M), K⁺ (0.005 M), Cl⁻ (0.110 M), and others.
  • Stomach acid is approximately 0.10 M HCl.

🔬 Solubility vs. concentration

🔬 Solubility limit

Solubility: the limit of how much solute can be dissolved in a given amount of solvent.

  • Solubility varies with temperature and is often reported per 100 mL of water at a specific temperature.
  • Example: NaCl solubility is 36.0 g per 100 mL H₂O at 25°C.

📊 Saturation states

StateDefinitionStability
SaturatedSolute concentration at the solubility limitStable
UnsaturatedSolute concentration below the limitStable
SupersaturatedSolute concentration exceeds the limitUnstable; excess can recrystallize
  • Most everyday solutions are unsaturated, so solubility alone doesn't tell you the actual concentration.
  • Don't confuse: "dilute" and "concentrated" are relative terms; they don't specify exact amounts.

📏 Concentration units: percent and trace

📏 Mass/mass percent (% m/m)

  • Formula: (mass of solute / mass of solution) × 100
  • Both masses must use the same units.
  • Example: 36.5 g NaCl in 355 g solution = 10.3% m/m.

📏 Volume/volume percent (% v/v)

  • Formula: (volume of solute / volume of solution) × 100
  • Used for liquid or gas solutions.
  • Example: 45.0% v/v ethanol means 45 mL ethanol per 100 mL solution.

📏 Mass/volume percent (% m/v)

  • Formula: (mass of solute in g / volume of solution in mL) × 100
  • Commonly used for IV fluids.
  • Example: "normal saline" is 0.9% m/v NaCl (9.0 g NaCl per 1,000 mL).

🔍 Parts per million (ppm) and parts per billion (ppb)

  • ppm = (mass of solute / mass of solution) × 1,000,000
  • ppb = (mass of solute / mass of solution) × 1,000,000,000
  • Used for trace elements and pollutants.
  • In aqueous solutions: 1 ppm ≈ 1 mg/L; 1 ppb ≈ 1 μg/L.
  • Example: cobalt in the human body is about 21 ppb; arsenic toxicity starts around 7,000 ppb.

⚠️ "The dose makes the poison"

  • Even essential trace elements (like arsenic at ~50 ppb) become toxic at higher concentrations (7,000+ ppb).
  • Water itself can be dangerous if consumed too quickly (water intoxication dilutes essential salts).

🧮 Molarity and stoichiometry

🧮 Molarity definition

Molarity (M): number of moles of solute per liter of solution.

  • Formula: M = (moles of solute) / (liters of solution)
  • Units: mol/L (often abbreviated M).
  • Example: 1.5 mol NaCl in 0.500 L = 3.0 M NaCl.

🔄 Using molarity in calculations

  • Molarity connects concentration to moles, enabling stoichiometry.
  • Typical workflow for solution stoichiometry:
    1. Convert mass of substance A to moles of A.
    2. Use balanced equation to find moles of substance B.
    3. Use molarity to find volume of solution B (or vice versa).
  • Example: To react 185 g NaOH with HCl (2.75 M), first convert NaOH to moles (4.63 mol), then use 1:1 ratio to find moles HCl needed (4.63 mol), then solve for volume: 4.63 mol ÷ 2.75 M = 1.68 L.

⚡ Equivalents (Eq)

Equivalent: one mole of positive or negative charge.

  • 1 mol/L of Na⁺ = 1 Eq/L (charge is 1+).
  • 1 mol/L of Ca²⁺ = 2 Eq/L (charge is 2+).
  • Blood plasma has about 150 mEq/L total ion concentration.

💧 Dilution

💧 Dilution principle

  • Adding solvent changes volume but not the amount (moles) of solute.
  • Formula: (concentration × volume)initial = (concentration × volume)final
  • Any concentration and volume units work, as long as they match on both sides.

💧 Dilution example

  • A 125 mL sample of 0.900 M NaCl diluted to 1,125 mL:
    • (0.900 M × 125 mL) = (concentration × 1,125 mL)
    • Final concentration = (0.900 × 125) ÷ 1,125 = 0.100 M
  • Don't confuse: dilution reduces concentration but does not change the total moles of solute.
47

The Dissolution Process

Concentration

🧭 Overview

🧠 One-sentence thesis

When a solute dissolves in a solvent, individual solute particles become surrounded by solvent molecules and separate from each other, with ionic solutes dissociating into ions that can conduct electricity while molecular solutes remain as neutral molecules.

📌 Key points (3–5)

  • Solvation mechanism: solute particles interact with solvent particles so strongly that they separate and become surrounded by solvent molecules.
  • Ionic vs molecular behavior: ionic solutes dissociate into separate cations and anions, while molecular solutes dissolve as intact neutral molecules.
  • Electrical conductivity: ionic compounds that dissociate are electrolytes (conduct electricity), while molecular compounds that don't dissociate are nonelectrolytes.
  • Common confusion: not all dissolved substances behave the same—ionic solutes split into ions, molecular solutes stay as whole molecules.
  • Strength variation: some ionic compounds dissociate completely (strong electrolytes) while others dissociate only partially (weak electrolytes).

🔬 How dissolution works at the molecular level

🧲 The solvation process

Solvation: the process by which solute particles are surrounded by solvent particles.

  • When a soluble solute enters a solvent, solvent particles interact with solute particles.
  • These interactions are strong enough to pull individual solute particles away from each other.
  • Each separated solute particle becomes surrounded by solvent molecules.
  • The "like dissolves like" rule applies—substances need similar intermolecular forces to form solutions.

💧 Hydration (special case)

Hydration: solvation by water molecules.

  • When the solvent is specifically water, the process is called hydration rather than solvation.
  • The mechanism is the same, but the term distinguishes water as the solvent.

⚡ Ionic solutes and dissociation

🔌 What happens to ionic compounds

Dissociation: the process of cations and anions of an ionic solute separating when the solute dissolves.

  • Ionic solutes don't just separate as whole formula units—they split into individual ions.
  • Cations and anions separate from each other completely.
  • Each ion becomes surrounded by solvent particles independently.
  • Example: When sodium chloride dissolves, Na⁺ ions and Cl⁻ ions separate and are each surrounded by water molecules.

Don't confuse with: molecular dissolution, where molecules stay intact and don't split into charged particles.

⚡ Electrolytes and electrical conductivity

Electrolyte: an ionic compound that dissolves in water.

  • Dissolved ionic compounds conduct electricity because their separated ions can move freely.
  • The ions carry electrical charge through the solution.
  • This property distinguishes ionic solutions from molecular solutions.
TypeDefinitionConductivityExample
Strong electrolyteIonizes completely when dissolvedHighSodium chloride (NaCl)
Weak electrolyteIonizes only partially when dissolvedLowAcetic acid (CH₃COOH)
NonelectrolyteDoes not ionize at all when dissolvedNoneTable sugar (C₁₂H₂₂O₁₁)

🧪 Molecular solutes

🔬 How molecular compounds dissolve

  • Molecular solutes like glucose dissolve as individual intact molecules.
  • No dissociation into ions occurs.
  • Each molecule separates from other molecules but remains a complete neutral particle.
  • Example: When fructose dissolves, each C₆H₁₂O₆ molecule stays as one unit surrounded by water molecules.

🚫 Nonelectrolytes

Nonelectrolyte: a compound that does not ionize at all when it dissolves.

  • Molecular compounds are typically nonelectrolytes.
  • They don't conduct electricity because they produce no charged particles.
  • The solution contains only neutral molecules, not ions.
  • Example: Isopropyl alcohol dissolves into individual molecules but creates no ions, so it doesn't conduct electricity.

🏥 Practical distinction

🔍 How to classify a dissolved substance

Step 1: Determine if the compound is ionic or molecular

  • Ionic compounds (metal + nonmetal, or polyatomic ions) → likely electrolyte
  • Molecular compounds (covalent bonding throughout) → likely nonelectrolyte

Step 2: Check the bonding type

  • If ionic: it will dissociate into ions (electrolyte)
  • If molecular: it will dissolve as whole molecules (nonelectrolyte)

Example classification:

  • Potassium chloride (KCl): ionic compound → dissociates into K⁺ and Cl⁻ → electrolyte
  • Fructose (C₆H₁₂O₆): molecular compound → stays as whole molecules → nonelectrolyte
  • Magnesium hydroxide [Mg(OH)₂]: ionic compound → dissociates into Mg²⁺ and OH⁻ → electrolyte

Medical note: In medicine, "electrolyte" refers to important ions dissolved in body fluids, including Na⁺, K⁺, Ca²⁺, Mg²⁺, and Cl⁻.

48

Properties of Solutions

The Dissolution Process

🧭 Overview

🧠 One-sentence thesis

Solutions exhibit colligative properties—vapor pressure depression, boiling point elevation, freezing point depression, and osmotic pressure—that depend only on the number of dissolved particles, not their chemical identity, and these properties have critical applications in everyday life and biological systems.

📌 Key points (3–5)

  • What colligative properties are: characteristics of solutions that depend only on the number of dissolved particles, not what those particles are.
  • Four main colligative properties: vapor pressure depression, boiling point elevation, freezing point depression, and osmotic pressure.
  • Ionic vs molecular solutes: ionic compounds produce more particles per mole when they dissolve (e.g., NaCl → 2 particles) than molecular compounds (e.g., glucose → 1 particle), so ionic solutes have a larger effect on colligative properties.
  • Common confusion: 1 M NaCl and 1 M glucose do not have the same effect on colligative properties because NaCl produces two particles per formula unit while glucose produces only one.
  • Why it matters: these properties explain practical phenomena like antifreeze in car engines, salting roads in winter, and osmotic balance in living cells.

🔬 What makes colligative properties special

🔬 Dependence on particle count, not identity

Colligative properties: characteristics of solutions that depend only on the number of dissolved particles.

  • The key word is number—not the type, size, or charge of the particles.
  • Whether you dissolve salt, sugar, or any other solute, the effect on vapor pressure, boiling point, freezing point, and osmotic pressure is determined by how many particles end up in solution.
  • Example: dissolving 1 mole of glucose (which stays as individual molecules) produces 1 mole of particles; dissolving 1 mole of NaCl (which separates into Na⁺ and Cl⁻) produces 2 moles of particles, so NaCl has twice the effect.

🧪 Ionic vs molecular solutes

Solute typeWhat happens when it dissolvesParticles per moleEffect on colligative properties
Molecular (e.g., glucose C₆H₁₂O₆)Separates into individual molecules1 mole of particlesBaseline effect
Ionic (e.g., NaCl)Separates into constituent ions (Na⁺ + Cl⁻)2 moles of particlesTwice the effect of molecular solute
Ionic (e.g., CaCl₂)Separates into three ions (Ca²⁺ + 2 Cl⁻)3 moles of particlesThree times the effect of molecular solute
  • Don't confuse: equal molarities of NaCl and glucose do not produce equal effects—NaCl produces more particles.

💨 Vapor pressure depression

💨 How solute lowers vapor pressure

Vapor pressure: the pressure of a vapor that is in equilibrium with its liquid phase.

Vapor pressure depression: the lowering of the vapor pressure of a solution versus the pure solvent.

  • Pure liquids evaporate until the rate of evaporation equals the rate of condensation; the pressure at that point is the vapor pressure.
  • When a solid solute is dissolved, solute particles block some liquid particles from evaporating.
  • Result: the solution evaporates more slowly and has a lower vapor pressure than the pure solvent.
  • Exception: if the solute itself is a liquid or gas, it can also evaporate and contribute to vapor pressure (not covered in this excerpt).

🌡️ Boiling point elevation and freezing point depression

🌡️ Boiling point elevation

Boiling point elevation: the raising of the boiling point of a solution versus the pure solvent.

  • Because solute particles lower vapor pressure, more heat (higher temperature) is needed to make the solution boil.
  • Quantitative rule from the excerpt: for every mole of particles dissolved in a liter of water, the boiling point increases by about 0.5°C.
  • Example: a 1 M NaCl solution (which produces 2 moles of particles per liter) raises the boiling point by about 1.0°C.
  • Practical application: water-ethylene glycol mixtures in car radiators have boiling points above 100°C, preventing overheating.

❄️ Freezing point depression

Freezing point depression: the lowering of the freezing point of a solution versus the pure solvent.

  • When a solution freezes, only solvent particles form the solid; solute particles interfere with this process.
  • More energy must be removed (lower temperature) for the solvent to freeze.
  • Quantitative rule from the excerpt: for every mole of particles in a liter of water, the freezing point decreases by about 1.9°C.
  • Example: a 1 M CaCl₂ solution (which produces 3 moles of particles per liter) lowers the freezing point by about 5.7°C.
  • Practical applications:
    • Salts like NaCl and CaCl₂ are spread on roads and sidewalks in winter to prevent ice formation.
    • CaCl₂ is more effective than NaCl mole-for-mole because it produces three particles instead of two.

🧂 Comparing ionic salts

  • The excerpt gives an example: which has a greater effect on freezing point, 1 M NaCl or 1 M CaCl₂?
  • Answer: CaCl₂, because it separates into three ions (one Ca²⁺ and two Cl⁻) while NaCl separates into only two (Na⁺ and Cl⁻).
  • Mole for mole, CaCl₂ has 50% more impact on freezing point depression than NaCl.

🍝 Common misconception: salting pasta water

  • Some people claim that adding salt to pasta water makes it boil faster because the boiling point is higher.
  • The excerpt clarifies: the amount of salt typically used is so small that the boiling point is practically unchanged.

🧬 Osmotic pressure and biological systems

🧬 What osmosis is

Osmosis: the process by which solvent molecules can pass through certain membranes but solute particles cannot.

Semipermeable membranes: membranes that allow solvent molecules to pass but block solute particles.

Osmotic pressure: the tendency for solvent molecules to move from the more dilute solution to the more concentrated solution until the concentrations of the two solutions are equal.

  • When two solutions of different concentration are separated by a semipermeable membrane, solvent flows from the dilute side to the concentrated side.
  • External pressure can be applied to stop this flow; the pressure needed to halt osmosis equals the osmotic pressure of the solution.

🧮 Osmolarity: measuring osmotic pressure

Osmolarity (osmol): a way of reporting the total number of particles in a solution to determine osmotic pressure; defined as the molarity of a solute times the number of particles a formula unit makes when it dissolves (represented by i).

Formula: osmol = M × i

  • M = molarity of the solution
  • i = number of particles produced per formula unit
  • Example: 0.50 M NaCl → osmol = 0.50 × 2 = 1.0 osmol
  • Example: 0.30 M Ca(NO₃)₂ → osmol = 0.30 × 3 = 0.90 osmol (one Ca²⁺ and two NO₃⁻)
  • If multiple solutes are present, add their individual osmolarities to get the total.

🔄 Predicting solvent flow

  • Solutions with the same osmolarity have the same osmotic pressure.
  • If solutions of different osmolarity are on opposite sides of a semipermeable membrane, solvent transfers from the lower-osmolarity side to the higher-osmolarity side.
  • Example from the excerpt: 0.50 M NaCl (osmol = 1.0) and 0.30 M Ca(NO₃)₂ (osmol = 0.90) → water flows from the Ca(NO₃)₂ side to the NaCl side.

🌊 Reverse osmosis

Reverse osmosis: applying pressure higher than the osmotic pressure to force solvent from the high-osmolarity solution to the low-osmolarity solution.

  • Used to make fresh water from saltwater in areas where fresh water is scarce.

🩸 Osmosis in biological systems

🩸 Dialysis and kidney function

  • The kidneys filter blood to remove wastes and excess water, which are expelled as urine.
  • When kidneys fail, dialysis can remove waste materials and excess water from the blood.
  • Hemodialysis: blood is passed through tubing with a semipermeable membrane immersed in a sterile solution (water, glucose, amino acids, electrolytes).
  • Osmotic pressure forces waste molecules and excess water through the membrane into the sterile solution; red and white blood cells are too large to pass through.
  • Typically, 5–10 pounds of waste-containing fluid is removed per session; sessions last 2–8 hours and must be performed several times a week.
  • Dialysis is a temporary solution; a kidney transplant is more permanent.

🔴 Red blood cells and osmotic balance

  • Cell walls are semipermeable membranes, so osmotic pressure affects cells.
  • Three scenarios:
Solution typeOsmolarity relative to cell interiorWhat happensProcess name
HypotonicLower than inside the cellWater enters cells; cells swell and burstHemolysis
HypertonicHigher than inside the cellWater leaves cells; cells shrivel and dieCrenation
IsotonicSame as inside the cellNo net water movement; cells unaffected(Normal)
  • Isotonic solutions for blood plasma: approximately 0.31 M glucose or 0.16 M NaCl.
  • Note: NaCl concentration is half that of glucose because NaCl produces two particles per formula unit, while glucose produces one, so their osmolarities are equal.

🌊 Why not drink seawater?

  • Seawater has an osmolarity about three times higher than bodily fluids (hypertonic).
  • Drinking seawater would draw water out of your cells to dilute the salty water you ingested, making you thirstier and ultimately killing cells.
  • The body handles hypotonic solutions better: excess water is collected by the kidneys and excreted.

🥒 Food industry applications

  • Osmotic pressure is used to make pickles from cucumbers and to brine meat for corned beef.
  • It also plays a role in transporting water from tree roots to the tops of trees.
49

Properties of Solutions

Properties of Solutions

🧭 Overview

🧠 One-sentence thesis

Acids and bases are fundamental chemical classes defined by their ability to increase hydrogen or hydroxide ion concentrations in aqueous solutions, and they react together in neutralization reactions to form salts and water.

📌 Key points (3–5)

  • Arrhenius definitions: acids increase H⁺ concentration; bases increase OH⁻ concentration in aqueous solution.
  • Naming conventions: binary acids use "hydro-" prefix and "-ic acid" suffix; bases are typically named as hydroxide compounds.
  • Neutralization reactions: acids and bases react to produce water and a salt, and these reactions must be balanced for stoichiometry calculations.
  • Common confusion: not all bases contain hydroxide in their formula—ammonia (NH₃) is a base because it reacts with water to produce hydroxide ions.
  • Everyday prevalence: acids and bases are common in daily life, from stomach acid (hydrochloric acid) to cleaning products.

🔬 Arrhenius acid-base definitions

🧪 What makes a compound an acid

Arrhenius acid: a compound that increases the concentration of hydrogen ion (H⁺) in aqueous solution.

  • Many acids release a hydrogen cation when they dissolve in water.
  • Acids share common characteristics: sour taste, turn litmus red, dissolve certain metals while producing hydrogen gas.
  • Example: hydrochloric acid (HCl) dissolves in water and releases H⁺ ions.

🧴 What makes a compound a base

Arrhenius base: a compound that increases the concentration of hydroxide ion (OH⁻) in aqueous solution.

  • Many bases are ionic compounds containing hydroxide ions that are released when dissolved.
  • Bases share common characteristics: slippery texture, bitter taste, turn litmus blue.
  • Example: sodium hydroxide (NaOH) is both an ionic compound and releases OH⁻ when dissolved.

💧 The ammonia exception

  • Ammonia (NH₃) does not contain hydroxide in its formula but still qualifies as a base.
  • It reacts with water molecules: ammonia takes a hydrogen ion from water, producing an ammonium ion (NH₄⁺) and a hydroxide ion (OH⁻).
  • This reaction increases hydroxide concentration, satisfying the Arrhenius base definition.
  • Don't confuse: a base doesn't need to contain hydroxide in its formula; it only needs to increase hydroxide concentration in solution.

📝 Naming acids and bases

🏷️ Binary acid names

  • Binary acids contain hydrogen and one other element.
  • Naming pattern: "hydro-" + element root + "-ic acid"
  • Examples from the excerpt:
    • HCl(aq) → hydrochloric acid
    • H₂S(aq) → hydrosulfuric acid
    • HBr(aq) → hydrobromic acid

🏷️ Polyatomic acid names

  • These acids contain hydrogen, oxygen, and another element.
  • Suffixes depend on oxygen atom count: "-ic acid" or "-ous acid"
  • Additional prefixes like "per-" and "hypo-" appear in some names.
  • The excerpt notes there is no strict rule for oxygen numbers; names are best memorized.
  • Examples: HNO₃ (nitric acid), H₂SO₄ (sulfuric acid), HClO₃ (chloric acid)

🏷️ Base names

  • Most bases follow normal ionic compound naming rules.
  • Named as hydroxide compounds when hydroxide appears in the formula.
  • Examples: NaOH (sodium hydroxide), Ca(OH)₂ (calcium hydroxide), Mg(OH)₂ (magnesium hydroxide)

⚗️ Neutralization reactions

🔄 The general neutralization pattern

Neutralization: the reaction of acid and base to make water and a salt.

  • General equation: acid + base → water + salt
  • A salt is any ionic compound formed from an acid and a base.
  • These reactions must be properly balanced like any chemical equation.

⚖️ Balancing neutralization equations

  • Coefficients must balance the number of hydrogen ions from the acid with hydroxide ions from the base.
  • Example with 1:1 ratio: NaOH(aq) + HCl(aq) → NaCl(aq) + H₂O(ℓ)
  • Example with 2:1 ratio: 2NaOH(aq) + H₂SO₄(aq) → Na₂SO₄(aq) + 2H₂O(ℓ)
  • The excerpt shows that sulfuric acid requires two sodium hydroxide molecules because it can release two hydrogen ions.

🧮 Stoichiometry applications

  • Once balanced, neutralization equations can be used for stoichiometry calculations.
  • The excerpt mentions calculating masses and volumes needed for complete neutralization.
  • Example setup: given grams of acid, calculate grams of base needed to neutralize it.

🏥 Real-world context: stomach acid

🩺 Stomach acid composition

  • Stomach acid can be approximated as 0.05 M hydrochloric acid solution.
  • This concentration is strong enough to dissolve some metals in a laboratory setting.
  • Special cells in the stomach wall secrete this acid along with enzymes for digestion.

🛡️ Protection mechanisms

  • The stomach lining is coated with mucus containing bicarbonate ions (HCO₃⁻).
  • Bicarbonate reacts with hydrochloric acid to produce water, carbon dioxide, and harmless chloride ions.
  • The gastric epithelium (surface layer of stomach cells) is constantly shed and replaced if damaged by acid.

🩹 Ulcer formation and treatment

  • Ulcers occur when the gastric epithelium is destroyed faster than it can be replaced.
  • Severe ulcers can expose blood vessels and cause bleeding.
  • Ulcers can also result from Helicobacter pylori bacteria (mechanism not fully understood).
  • Two main treatments: (1) antacids to react with excess acid, (2) antibiotics to destroy H. pylori bacteria.
50

Brønsted-Lowry Definition of Acids and Bases

Arrhenius Definition of Acids and Bases

🧭 Overview

🧠 One-sentence thesis

The Brønsted-Lowry definition expands acid-base chemistry beyond the Arrhenius framework by focusing on proton transfer, allowing water and other substances to act as either acids or bases depending on the reaction context.

📌 Key points (3–5)

  • Core definitions: A Brønsted-Lowry acid is a proton (H⁺) donor; a Brønsted-Lowry base is a proton (H⁺) acceptor.
  • Broader scope: All Arrhenius acids and bases are also Brønsted-Lowry acids and bases, but not all Brønsted-Lowry acids and bases qualify under the Arrhenius definition.
  • Hydronium ion reality: In aqueous solution, H⁺ ions do not exist as bare protons—they attach to water molecules to form H₃O⁺ (hydronium ions).
  • Common confusion: Water can act as either a Brønsted-Lowry acid or base depending on what it reacts with; this dual behavior is called being amphiprotic.
  • Practical applications: Pharmaceutical drugs containing nitrogen atoms can be converted to more water-soluble hydrochloride or hydrobromide salts through Brønsted-Lowry acid-base reactions.

🔄 Proton transfer mechanism

🔄 What proton transfer means

Brønsted-Lowry acid: a compound that supplies a hydrogen ion (H⁺) in a reaction; a proton donor.

Brønsted-Lowry base: a compound that accepts a hydrogen ion (H⁺) in a reaction; a proton acceptor.

  • The key idea is movement of H⁺ from one molecule to another.
  • Unlike Arrhenius definitions (which focus on producing H⁺ or OH⁻ in water), Brønsted-Lowry definitions focus on the transfer process itself.
  • Example: When ammonia (NH₃) dissolves in water, the water molecule donates a hydrogen ion to ammonia. Water is the Brønsted-Lowry acid; ammonia is the Brønsted-Lowry base.

💧 The hydronium ion (H₃O⁺)

  • A hydrogen ion is a single proton (the hydrogen atom minus its electron).
  • Bare protons do not float freely in aqueous solution—they attach to water molecules.
  • The H⁺ ion attaches to H₂O to form H₃O⁺, the hydronium ion.
  • For most purposes, H⁺ and H₃O⁺ represent the same species, but writing H₃O⁺ shows understanding that protons are attached to solvent molecules.
  • Don't confuse: A proton in solution may be surrounded by multiple water molecules (e.g., H₅O₂⁺ or H₉O₄⁺), but H₃O⁺ is the simplest representation.

🔬 Brønsted-Lowry vs. Arrhenius

🔬 How HCl behaves in both frameworks

When HCl dissolves in water:

HCl + H₂O(ℓ) → H₃O⁺(aq) + Cl⁻(aq)
  • Arrhenius view: HCl is an acid because it produces H⁺ in water.
  • Brønsted-Lowry view: HCl donates a hydrogen ion to H₂O, making HCl the acid and H₂O the base.
  • The Brønsted-Lowry definition classifies this as a reaction between an acid and a base, whereas the Arrhenius definition would not label H₂O a base here.

📊 Relationship between the two definitions

AspectArrheniusBrønsted-Lowry
Acid definitionProduces H⁺ in waterDonates H⁺ (proton donor)
Base definitionProduces OH⁻ in waterAccepts H⁺ (proton acceptor)
ScopeOnly aqueous solutionsAny solvent; broader applicability
OverlapAll Arrhenius acids/bases are Brønsted-Lowry acids/basesNot all Brønsted-Lowry acids/bases are Arrhenius acids/bases

🌍 Beyond water: reactions in other solvents

Example: Sodium amide (NaNH₂) in methanol (CH₃OH):

NH₂⁻(solv) + CH₃OH(ℓ) → NH₃(solv) + CH₃O⁻(solv)
  • The label (solv) indicates the species are dissolved in some solvent (not necessarily water).
  • NH₂⁻ accepts a proton from CH₃OH, so NH₂⁻ is the Brønsted-Lowry base and CH₃OH is the Brønsted-Lowry acid.
  • The Brønsted-Lowry framework works for non-aqueous reactions, unlike the Arrhenius definition.

🔀 Amphiprotic substances: water's dual role

🔀 Water as both acid and base

Amphiprotic compound: a substance that can either donate or accept a proton, depending on the circumstances.

  • Water (H₂O) can act as a Brønsted-Lowry acid or a Brønsted-Lowry base.
  • As a base: When HCl dissolves, water accepts a proton from HCl to form H₃O⁺.
  • As an acid: When ammonia dissolves, water donates a proton to NH₃ to form OH⁻ and NH₄⁺.

💦 Autoionization of water

Water can react with itself:

H₂O(ℓ) + H₂O(ℓ) → H₃O⁺(aq) + OH⁻(aq)
  • About 6 in every 100 million water molecules undergo this reaction.
  • This process is called autoionization of water and occurs in every sample of water, pure or in solution.
  • One water molecule acts as the acid (proton donor), the other as the base (proton acceptor).
  • Autoionization occurs to some extent in any amphiprotic liquid (e.g., liquid ammonia, though much less frequently—about 1 in a million billion molecules).

🧪 Identifying water's role in reactions

Example 1: Water as acid

H₂O(ℓ) + NO₂⁻(aq) → HNO₂(aq) + OH⁻(aq)
  • Water donates a proton to NO₂⁻, so water is the Brønsted-Lowry acid.

Example 2: Water as base

HC₂H₃O₂(aq) + H₂O(ℓ) → H₃O⁺(aq) + C₂H₃O₂⁻(aq)
  • Water accepts a proton from HC₂H₃O₂, so water is the Brønsted-Lowry base.

Don't confuse: The same substance (water) can be an acid in one reaction and a base in another—it depends on what it reacts with.

💊 Pharmaceutical applications

💊 Making drugs water-soluble

  • Many complex organic drugs are not soluble or only slightly soluble in water.
  • Drugs containing proton-accepting nitrogen atoms can be reacted with dilute hydrochloric acid.
  • The nitrogen atoms (acting as Brønsted-Lowry bases) accept hydrogen ions from the acid to form ions, which are much more soluble in water.

🧂 Hydrochloride and hydrobromide salts

General reaction:

RN(sl aq) + H⁺(aq) → RNH⁺(aq) → RNHCl(s)

(where RN represents an organic compound containing nitrogen; "sl aq" means "slightly aqueous" or slightly soluble)

  • The modified drug molecules are isolated as hydrochloride salts (when HCl is used) or hydrobromide salts (when HBr is used).
  • Example: Codeine is commonly administered as codeine hydrochloride; dextromethorphan (a cough medicine ingredient) is dispensed as dextromethorphan hydrobromide.
  • This Brønsted-Lowry acid-base reaction increases drug effectiveness by improving water solubility.

🔄 The dissolution process

When a hydrochloride salt dissolves in water:

  • It separates into chloride ions (Cl⁻) and the appropriate cation.
  • Example: Cocaine hydrochloride (C₁₇H₂₂ClNO₄) dissolves and can donate a proton to a water molecule.
  • This is the reverse of the salt-formation reaction—the drug cation can act as a Brønsted-Lowry acid in solution.
51

Brønsted-Lowry Definition of Acids and Bases

Brønsted-Lowry Definition of Acids and Bases

🧭 Overview

🧠 One-sentence thesis

The Brønsted-Lowry definition expands acid-base chemistry beyond the Arrhenius framework by classifying acids as proton donors and bases as proton acceptors, allowing reactions to be understood as proton transfers even in non-aqueous solvents.

📌 Key points (3–5)

  • Core definitions: A Brønsted-Lowry acid donates a hydrogen ion (proton); a Brønsted-Lowry base accepts a hydrogen ion (proton).
  • Proton transfer mechanism: Brønsted-Lowry acid-base reactions are essentially proton transfer reactions between donor and acceptor.
  • Broader scope than Arrhenius: All Arrhenius acids and bases are also Brønsted-Lowry acids and bases, but not all Brønsted-Lowry acids and bases qualify under the Arrhenius definition.
  • Common confusion: Water can act as either an acid or a base depending on the reaction—it's a base when accepting a proton from HCl, but an acid when donating a proton to ammonia.
  • Works in non-aqueous solvents: The Brønsted-Lowry framework applies to reactions in solvents other than water, unlike the Arrhenius definition.

🔄 Core definitions and proton transfer

🔬 What defines a Brønsted-Lowry acid

A Brønsted-Lowry acid: a compound that supplies a hydrogen ion (H⁺) in a reaction; a proton donor.

  • The key action is donating a hydrogen ion to another species.
  • The hydrogen ion (H⁺) is essentially a proton—a hydrogen atom with its electron removed.
  • Example: HCl donates a proton to water, making HCl the acid in that reaction.

🔬 What defines a Brønsted-Lowry base

A Brønsted-Lowry base: a compound that accepts a hydrogen ion (H⁺) in a reaction; a proton acceptor.

  • The key action is accepting a hydrogen ion from another species.
  • Example: Ammonia (NH₃) accepts a proton from water, making ammonia the base.

⚡ Proton transfer as the central mechanism

  • Every Brønsted-Lowry acid-base reaction involves one species giving up a proton and another species receiving it.
  • The excerpt emphasizes: "Brønsted-Lowry acid-base reactions are essentially proton transfer reactions."
  • This framing shifts focus from "what dissolves in water" to "what transfers protons."

💧 Water's dual role and the hydronium ion

💧 Water as a base

  • When HCl dissolves in water, the reaction is: HCl + H₂O → H₃O⁺ + Cl⁻
  • Water accepts a proton from HCl, so water acts as a Brønsted-Lowry base.
  • The Arrhenius definition would not label water a base in this case, but the Brønsted-Lowry definition does.

💧 Water as an acid

  • When ammonia dissolves in water, the reaction is: NH₃ + H₂O → NH₄⁺ + OH⁻
  • Water donates a proton to ammonia, so water acts as a Brønsted-Lowry acid.
  • Ammonia is the base because it accepts the proton.

🧪 The hydronium ion (H₃O⁺)

  • Bare protons (H⁺) do not actually float freely in aqueous solution.
  • Instead, the proton attaches to a water molecule to form the hydronium ion (H₃O⁺).
  • For most purposes, H⁺ and H₃O⁺ represent the same species, but writing H₃O⁺ shows understanding that protons are attached to solvent molecules.
  • Don't confuse: The excerpt notes that protons may be surrounded by multiple water molecules (e.g., H₅O₂⁺ or H₉O₄⁺), but H₃O⁺ is the simpler representation.

🔀 Relationship to Arrhenius definitions

🔀 Overlap and extension

AspectArrheniusBrønsted-Lowry
ScopeOnly aqueous solutionsAny solvent
Acid definitionProduces H⁺ in waterDonates H⁺ (proton donor)
Base definitionProduces OH⁻ in waterAccepts H⁺ (proton acceptor)
RelationshipAll Arrhenius acids/bases are also Brønsted-Lowry acids/basesNot all Brønsted-Lowry acids/bases are Arrhenius acids/bases

🔀 Why the expansion matters

  • The excerpt shows that ammonia acts as a base in both the Arrhenius sense (produces OH⁻) and the Brønsted-Lowry sense (accepts H⁺).
  • HCl is an acid in both frameworks, but the Brønsted-Lowry view reveals the proton transfer to water.
  • The Brønsted-Lowry framework captures reactions the Arrhenius definition misses, such as water acting as a base when dissolving HCl.

🧪 Applications beyond water

🧪 Non-aqueous solvent reactions

  • The Brønsted-Lowry definitions work in solvents other than water.
  • Example from the excerpt: Sodium amide (NaNH₂) in methanol (CH₃OH):
    • Reaction: NH₂⁻ + CH₃OH → NH₃ + CH₃O⁻
    • NH₂⁻ accepts a proton from methanol, so NH₂⁻ is the base.
    • Methanol donates a proton, so CH₃OH is the acid.
  • The label "(solv)" indicates dissolved in some solvent, contrasting with "(aq)" for aqueous solutions.

💊 Pharmaceutical applications

  • Many drugs contain nitrogen atoms that can accept protons (act as Brønsted-Lowry bases).
  • These drugs can be reacted with dilute hydrochloric acid to form hydrochloride salts, which are much more water-soluble.
  • The nitrogen atom accepts a hydrogen ion from HCl, forming an ion that dissolves better.
  • Example: Codeine is commonly administered as codeine hydrochloride; dextromethorphan is dispensed as dextromethorphan hydrobromide.
  • This proton-transfer reaction improves drug effectiveness by increasing solubility.
52

Water: Both an Acid and a Base

Water: Both an Acid and a Base

🧭 Overview

🧠 One-sentence thesis

Water can act as either a Brønsted-Lowry acid or a Brønsted-Lowry base depending on the chemical circumstances, making it an amphiprotic compound.

📌 Key points (3–5)

  • Water as a base: H₂O can accept a proton from an acid (e.g., when HCl dissolves in water).
  • Water as an acid: H₂O can donate a proton to a base (e.g., when reacting with amide ion).
  • Amphiprotic definition: a substance that can either donate or accept a proton depending on circumstances.
  • Autoionization: even in pure water, about 6 in 100 million water molecules spontaneously react with each other to form hydronium and hydroxide ions.
  • Common confusion: water's role is not fixed—it depends on what other substance is present in the reaction.

💧 Water's dual behavior

💧 Acting as a Brønsted-Lowry base

  • When water accepts a proton, it becomes a base.
  • Example: HCl + H₂O → H₃O⁺ + Cl⁻
    • The water molecule accepts a proton from HCl
    • Water becomes hydronium ion (H₃O⁺)
    • HCl is the acid (proton donor), water is the base (proton acceptor)

💧 Acting as a Brønsted-Lowry acid

  • When water donates a proton, it becomes an acid.
  • Example: H₂O + NH₂⁻ → OH⁻ + NH₃
    • The water molecule donates a proton to the amide ion
    • Water becomes hydroxide ion (OH⁻)
    • NH₂⁻ is the base (proton acceptor), water is the acid (proton donor)

🔄 What determines water's role

  • The role depends on the other substance present in the reaction.
  • If the other substance is a stronger acid, water acts as a base.
  • If the other substance is a stronger base, water acts as an acid.
  • Don't confuse: water itself doesn't change—its behavior changes based on its reaction partner.

🔬 Amphiprotic compounds

🔬 Definition and significance

Amphiprotic compound: a substance that can either donate or accept a proton, depending on the circumstances.

  • Water is the most common and most important example.
  • Other substances can also be amphiprotic, but water is encountered most frequently.
  • This dual capability makes water unique and central to acid-base chemistry.

🔬 Other amphiprotic substances

  • Water is not the only amphiprotic substance.
  • Any amphiprotic liquid can undergo similar behavior.
  • Example mentioned: liquid ammonia also shows amphiprotic behavior (though to a much lesser extent).

⚡ Autoionization of water

⚡ What autoionization means

Autoionization of water: the process by which water ionizes into hydronium ions and hydroxide ions as it acts as an acid and a base.

  • Water molecules can react with each other even in pure water.
  • One water molecule acts as an acid, the other as a base.
  • Chemical equation: H₂O + H₂O → H₃O⁺ + OH⁻

⚡ How often it happens

  • Approximately 6 in every 100 million (6 in 10⁸) water molecules undergo this reaction.
  • This is a very small fraction but occurs in every water sample.
  • It happens whether the water is pure or part of a solution.

⚡ Comparison to other liquids

  • Autoionization occurs to some extent in any amphiprotic liquid.
  • Liquid ammonia also autoionizes, but much less frequently.
  • Only about 1 molecule in a million billion (1 in 10¹⁵) ammonia molecules react with another ammonia molecule.
  • Water autoionizes much more readily than ammonia (about 10 million times more).

🎯 Identifying water's role in reactions

🎯 Step-by-step approach

To determine whether water is acting as an acid or base:

  1. Look at what water becomes in the products
  2. If water becomes H₃O⁺ (gains a proton) → water is a base
  3. If water becomes OH⁻ (loses a proton) → water is an acid

🎯 Practice scenarios

ReactionWater becomesWater's roleWhy
H₂O + NO₂⁻ → HNO₂ + OH⁻OH⁻AcidWater donated a proton
HC₂H₃O₂ + H₂O → H₃O⁺ + C₂H₃O₂⁻H₃O⁺BaseWater accepted a proton
H₂O + NH₄⁺ → H₃O⁺ + NH₃H₃O⁺BaseWater accepted a proton
CH₃⁻ + H₂O → CH₄ + OH⁻OH⁻AcidWater donated a proton

🎯 Key reminder

  • Don't confuse the product with the role: if water becomes H₃O⁺, it accepted a proton (base behavior), not donated one.
  • The direction of proton transfer determines the role, not the final charge.
53

The Strengths of Acids and Bases

The Strengths of Acids and Bases

🧭 Overview

🧠 One-sentence thesis

Acids and bases vary in strength based on their degree of ionization in solution, with strong acids and bases ionizing essentially 100% while weak acids and bases ionize only partially and reach a dynamic equilibrium between forward and reverse reactions.

📌 Key points (3–5)

  • Strong vs weak distinction: strong acids/bases ionize ~100% in solution; weak acids/bases ionize much less (sometimes only 1–5%).
  • Very few strong acids and bases exist: only a handful of compounds (like HCl, HNO₃, NaOH, KOH) are strong; most others are weak.
  • Chemical equilibrium: weak acid/base ionization is reversible—forward and reverse reactions occur simultaneously at equal rates, creating a dynamic balance.
  • Common confusion: equilibrium does not mean reactions stop; both directions continue but cancel each other out (dynamic equilibrium).
  • pH scale application: pH quantifies acidity/basicity—below 7 is acidic, 7 is neutral, above 7 is basic—and helps compare solution strengths.

💪 Strong acids and bases

💪 What makes an acid or base "strong"

Strong acid: a compound that is essentially 100% ionized in aqueous solution.

Strong base: a compound that is essentially 100% ionized in aqueous solution.

  • "Essentially 100%" means nearly every molecule separates into ions when dissolved.
  • Example: when HCl dissolves in water, every HCl molecule separates into hydronium ion (H₃O⁺) and chloride ion (Cl⁻).
  • The reaction goes essentially to completion in one direction.

📋 The short list of strong acids and bases

Strong AcidsStrong Bases
HClLiOH
HBrNaOH
HIKOH
HNO₃Mg(OH)₂
H₂SO₄Ca(OH)₂
HClO₄
  • There are very few strong acids and bases.
  • If an acid is not on this list, it is likely weak.
  • Similarly, if a base is not on this list, it is likely weak.

🔄 Weak acids and bases

🔄 What makes an acid or base "weak"

Weak acid: a compound that is not 100% ionized in aqueous solution.

Weak base: a compound that is not 100% ionized in aqueous solution.

  • Only a small fraction of molecules ionize.
  • Example: acetic acid (HC₂H₃O₂) ionizes only 1–5% depending on concentration.
  • The ionization reaction: HC₂H₃O₂(aq) + H₂O(ℓ) → H₃O⁺(aq) + C₂H₃O₂⁻(aq)
  • Most of the acid remains in molecular form.

🏠 Common household examples

Weak acids:

  • Vinegar (acetic acid, HC₂H₃O₂)
  • Vitamin C (ascorbic acid, HC₆H₇O₆)
  • Many food products are slightly acidic due to weak acids

Weak bases:

  • Ammonia (NH₃) in cleaning products
  • Soaps (contain compounds that accept protons from water, forming excess hydroxide ions—this is why soap solutions feel slippery)

Strong acids/bases in the home:

  • Muriatic acid (HCl) for pool cleaning
  • Lye (sodium hydroxide, NaOH) in drain cleaners—extremely caustic and dangerous

Don't confuse: If food products contained strong acids instead of weak acids, they would be inedible due to extreme acidity.

⚖️ Chemical equilibrium

⚖️ What happens with weak acids and bases

Chemical equilibrium (or equilibrium): the condition in which the extent of a chemical reaction does not change any further.

  • Weak acid/base ionization does not simply stop when some molecules ionize.
  • The reverse process (reformation of molecular form) also occurs.
  • Eventually, the forward and reverse reactions occur at the same rate.

🔁 Dynamic equilibrium in action

For acetic acid:

  • Forward reaction: HC₂H₃O₂(aq) + H₂O(ℓ) → H₃O⁺(aq) + C₂H₃O₂⁻(aq)
  • Reverse reaction: H₃O⁺(aq) + C₂H₃O₂⁻(aq) → HC₂H₃O₂(aq) + H₂O(ℓ)
  • At equilibrium: HC₂H₃O₂(aq) + H₂O(ℓ) ⇌ H₃O⁺(aq) + C₂H₃O₂⁻(aq)

The double arrow (⇌) shows both reactions occurring simultaneously.

⚠️ Common misconception about equilibrium

  • Wrong idea: reactions stop at equilibrium.
  • Correct understanding: reactions continue in both directions but balance each other out—this is called dynamic equilibrium.
  • There is no net change because forward and reverse effects cancel out.
  • Example: water autoionization is also an equilibrium: H₂O(ℓ) + H₂O(ℓ) ⇌ H₃O⁺(aq) + OH⁻(aq)

📏 The pH scale

📏 What pH measures

pH scale: a logarithmic scale that relates the concentration of the hydrogen ion in solution.

  • pH is a quantitative measure of acidity or basicity.
  • Based on the concentration of hydronium (or hydrogen) ion in aqueous solution.
  • Provides a succinct way to communicate how acidic or basic a solution is.

🎯 Interpreting pH values

pH ValueMeaning
pH = 7Neutral (equal H⁺ and OH⁻ concentrations)
pH < 7Acidic (lower pH = more acidic)
pH > 7Basic (higher pH = more basic)
  • A neutral solution has the same concentration of hydrogen and hydroxide ions.
  • Lower pH values correspond to increasingly acidic solutions.
  • Higher pH values correspond to increasingly basic solutions.

🧪 pH of common substances

SubstancepHCategory
Battery acid0.3Extremely acidic
Stomach acid1–2Very acidic
Lemon/lime juice2.1Acidic
Vinegar2.8–3.0Acidic
Coffee5Slightly acidic
Milk6Slightly acidic
Pure water7Neutral
Blood7.3–7.5Slightly basic
Sea water8Basic
Ammonia (1 M)11.6Very basic
Bleach12.6Very basic
NaOH (1 M)14.0Extremely basic

Key observations:

  • Many food products are slightly acidic (contain weak acids).
  • Some biological fluids (like stomach acid and blood) are nowhere near neutral.
  • If food acids were strong instead of weak, the food would likely be inedible.
54

Buffers

Buffers

🧭 Overview

🧠 One-sentence thesis

Buffers resist dramatic pH changes by containing paired solutes (a weak acid plus its salt or a weak base plus its salt) that react with added strong acids or bases to minimize pH shifts, a mechanism critical for biological systems like blood.

📌 Key points (3–5)

  • What a buffer is: a solution that resists dramatic changes in pH when strong acids or bases are added.
  • What makes a buffer: either a weak acid plus a salt derived from that weak acid, or a weak base plus a salt derived from that weak base.
  • How buffers work: the weak acid component reacts with added strong base, and the salt's anion reacts with added strong acid, preventing large pH swings.
  • Common confusion: buffers cannot be made from strong acids/bases; only weak acids/bases paired with their salts can buffer.
  • Buffer capacity: buffers work only for limited amounts of added strong acid or base; once one component is consumed, the buffer is exhausted and pH changes rapidly.

🧪 What buffers are and why they matter

🧪 The problem buffers solve

  • Strong acids and bases can change pH very quickly, even in tiny amounts.
  • Example: 1 mL of stomach acid (approximated as 0.05 M HCl) added to bloodstream would shift pH from about 7.4 to about 4.9—a pH incompatible with life—if no correcting mechanism existed.
  • The body needs a mechanism to minimize such dramatic pH changes.

🛡️ Definition and composition

Buffer: a solution that resists dramatic changes in pH.

A buffer is composed of certain pairs of solutes:

  • Either a weak acid plus a salt derived from that weak acid
  • Or a weak base plus a salt derived from that weak base

Examples:

  • Acetic acid (HC₂H₃O₂, a weak acid) + sodium acetate (NaC₂H₃O₂, a salt from that acid)
  • Ammonia (NH₃, a weak base) + ammonium chloride (NH₄Cl, a salt from that base)

⚙️ How buffers work with acids and bases

⚙️ Reacting with strong bases

When a strong base (source of OH⁻ ions) is added to a buffer:

  • The hydroxide ions react with the weak acid component.
  • Example (acetic acid–sodium acetate buffer):
    • HC₂H₃O₂(aq) + OH⁻(aq) → H₂O(ℓ) + C₂H₃O₂⁻(aq)
  • Rather than making the solution basic and changing pH dramatically, the added hydroxide ions react to make water.
  • The pH does not change much.

⚙️ Reacting with strong acids

When a strong acid (source of H⁺ ions) is added to a buffer:

  • The hydrogen ions react with the anion from the salt.
  • Because the weak acid is not ionized much, lots of hydrogen ions and acetate ions (from sodium acetate) come together to make acetic acid:
    • H⁺(aq) + C₂H₃O₂⁻(aq) → HC₂H₃O₂(aq)
  • Rather than making the solution acidic and changing pH dramatically, the added hydrogen ions react to make molecules of a weak acid.

⚙️ Weak base buffers work similarly

For a buffer containing NH₃ and NH₄Cl:

  • With strong acid: ammonia molecules react with excess hydrogen ions:
    • NH₃(aq) + H⁺(aq) → NH₄⁺(aq)
  • With strong base: the ammonium ion reacts with hydroxide ions:
    • NH₄⁺(aq) + OH⁻(aq) → NH₃(aq) + H₂O(ℓ)

🔍 Identifying valid buffer combinations

🔍 What makes a valid buffer

A buffer requires:

  • A weak acid or base (not strong)
  • Plus a salt derived from that weak acid or base

Don't confuse: Strong acids/bases cannot form buffers. HCl + NaCl is not a buffer because HCl is a strong acid. NH₃ + NaOH is not a buffer because NaOH is a strong base.

🔍 Examples from the excerpt

CombinationValid buffer?Reason
HCHO₂ + NaCHO₂✅ YesFormic acid (weak acid) + formate salt
HCl + NaCl❌ NoHCl is a strong acid
CH₃NH₂ + CH₃NH₃Cl✅ YesMethylamine (weak base) + its salt
NH₃ + NaOH❌ NoNaOH is a strong base
H₃PO₄ + NaH₂PO₄✅ YesPhosphoric acid (weak) + phosphate salt

📏 Buffer capacity and limits

📏 What capacity means

Buffer capacity: the amount of strong acid or base a buffer can counteract.

  • Buffers work well only for limited amounts of added strong acid or base.
  • Once either solute is all reacted, the solution is no longer a buffer.
  • Rapid changes in pH may occur after the buffer is exhausted.

📏 What affects capacity

  • Buffers that have more solute dissolved in them to start with have larger capacities.
  • Example: The excerpt compares two buffer solutions with the same concentrations—the one made from phosphoric acid and sodium phosphate should have larger capacity than one made from hydrocyanic acid and sodium cyanide (because phosphoric acid is a stronger weak acid).

🩸 Biological buffer systems

🩸 Blood buffering

  • Human blood has a buffering system to minimize extreme changes in pH.
  • One buffer in blood is based on the presence of HCO₃⁻ and H₂CO₃ (another way to write CO₂(aq)).
  • With this buffer present, even if some stomach acid were to find its way directly into the bloodstream, the change in blood pH would be minimal.

🩸 Cellular buffering

  • Inside many of the body's cells, there is a buffering system based on phosphate ions.
  • The complete phosphate buffer system is based on four substances: H₃PO₄, H₂PO₄⁻, HPO₄²⁻, and PO₄³⁻.
  • Different buffer solutions can be made by combining: H₃PO₄ + H₂PO₄⁻, H₂PO₄⁻ + HPO₄²⁻, and HPO₄²⁻ + PO₄³⁻.

🩸 Buffered aspirin

  • Many people are aware of buffers from buffered aspirin.
  • Buffered aspirin contains aspirin (itself a weak acid) plus magnesium carbonate, calcium carbonate, magnesium oxide, or some other salt.
  • The salt acts like a base, forming a buffer system.
55

Radioactivity

Radioactivity

🧭 Overview

🧠 One-sentence thesis

Radioactive decay occurs when unstable atomic nuclei spontaneously emit particles or radiation, transforming into different isotopes through processes that follow predictable patterns such as half-life.

📌 Key points (3–5)

  • Three major types of radioactive emissions: alpha particles (helium nuclei), beta particles (electrons from the nucleus), and gamma rays (high-energy electromagnetic radiation).
  • Conservation of matter in decay: atomic numbers and mass numbers must balance on both sides of nuclear equations; the parent isotope transforms into a daughter isotope.
  • Penetration differences: alpha particles are easily stopped by matter, beta particles penetrate a few centimeters, and gamma rays penetrate deeply into tissues.
  • Common confusion: beta particles are electrons ejected from the nucleus (not from electron shells), and their emission converts a neutron into a proton.
  • Half-life constancy: the time for half of a radioactive isotope to decay is fixed and unaffected by conditions or initial amount.

☢️ The three types of radioactive emissions

⚛️ Alpha particles

Alpha particle: a type of radioactive emission composed of two protons and two neutrons, equivalent to a helium nucleus.

  • Symbolized by α or He-4 (sometimes written as ₂⁴He).
  • Carries a 2+ charge.
  • Effect on the nucleus: when emitted, the parent atom loses 2 protons (atomic number decreases by 2) and 4 nuclear particles total (mass number decreases by 4).
  • Example: Uranium-235 decays to thorium-231 by emitting an alpha particle: ₉₂²³⁵U → ₂⁴He + ₉₀²³¹Th.
  • Penetration: minimal; easily stopped by matter and will not penetrate skin.

🔵 Beta particles

Beta particle: an electron ejected from the nucleus (not from electron shells) with a 1− charge.

  • Symbolized by β or ₋₁⁰e or β−.
  • Effect on the nucleus: a neutron is converted to a proton; mass number stays the same, but atomic number increases by one.
  • Example: Carbon-14 decays to nitrogen-14 by emitting a beta particle: ₆¹⁴C → ₇¹⁴N + ₋₁⁰e.
  • Don't confuse: beta particles come from the nucleus (nuclear transformation), not from the atom's electron shells.
  • Penetration: short; will penetrate skin and some tissues slightly, perhaps a few centimeters at most.

🌊 Gamma rays

Gamma rays: a very energetic form of electromagnetic radiation emitted from the nucleus.

  • Symbolized by γ.
  • No charge or mass number: gamma rays are not particles; they are electromagnetic radiation.
  • Often emitted simultaneously with alpha or beta particles.
  • Example: Radon-222 emits both an alpha particle and a gamma ray: ₈₆²²²Rn → ₈₄²¹⁸Po + ₂⁴He + γ.
  • Energy: the gamma ray from radon-222 decay has 8.2 × 10⁻¹⁴ J per nucleus; if 1 mole decayed, total gamma energy would be 49 million kJ.
  • Ionizing radiation: gamma rays can knock electrons out of atoms, making matter electrically charged.
  • Penetration: deep; will penetrate tissues deeply and impart large amounts of energy to surrounding matter.

🧮 Writing nuclear equations

🧮 Conservation rules

  • Law of conservation of matter: matter cannot be created or destroyed, so the sum of atomic numbers and the sum of mass numbers must be the same on both sides of the equation.
  • Identifying the daughter isotope: use subtraction to find the remaining protons and nuclear particles.
  • Example: Radon-222 (atomic number 86, mass number 222) emits an alpha particle → daughter has 86 − 2 = 84 protons (polonium) and 222 − 4 = 218 mass number → ₈₆²²²Rn → ₂⁴He + ₈₄²¹⁸Po.

🏷️ Parent and daughter isotopes

  • Parent isotope: the original radioactive atom before decay.
  • Daughter isotope: the product atom (other than the emitted particle) after decay.
  • Example: In uranium-235 decay, ₉₂²³⁵U is the parent and ₉₀²³¹Th is the daughter.

Radioactive decay: when one element changes into another through emission of particles or radiation.

📝 Beta decay details

  • The electron is assigned an "atomic number" of −1 (equal to its charge) to balance equations.
  • Example: Boron-12 decays by beta emission with simultaneous gamma emission: ₅¹²B → ₆¹²C + ₋₁⁰e + γ.
  • The daughter (carbon-12) has one more proton than the parent (boron-12) because a neutron converted to a proton.

💥 Spontaneous fission

💥 What fission is

Spontaneous fission (or fission): the breaking apart of an atomic nucleus into smaller nuclei.

  • Found only in large nuclei; the smallest nucleus that exhibits spontaneous fission is lead-208.
  • Varied products: daughter isotopes are a mixed set of products, not a specific isotope as with alpha/beta emission.
  • Often produces excess neutrons that may be captured by other nuclei, possibly inducing additional radioactive events.

🔬 Uranium-235 fission example

  • Uranium-235 undergoes spontaneous fission to a small extent.
  • One typical reaction: ₉₂²³⁵U → ₅₆¹³⁹Ba + ₃₆⁹⁴Kr + 2 ₀¹n (where ₀¹n is a neutron).
  • As with any nuclear process, sums of atomic numbers and mass numbers must be the same on both sides.
  • Application: fission is the radioactive process used in nuclear power plants and one type of nuclear bomb.

⏱️ Half-life

⏱️ Definition and constancy

Half-life: the amount of time it takes for one-half of a radioactive isotope to decay.

  • Constant property: the half-life of a specific radioactive isotope is constant; it is unaffected by conditions and independent of the initial amount of that isotope.
  • Whether an isotope is radioactive is a characteristic of that particular isotope; some are stable indefinitely, others decay through characteristic emissions.

📉 Decay over time

  • As time passes, less and less of the radioactive isotope remains, and the level of radioactivity decreases.
  • Example: Start with 100.0 g of tritium (³H, half-life 12.3 years).
    • After 12.3 y: half decays to ³He → 50.0 g of ³H remains.
    • After another 12.3 y (total 24.6 y): half of the remaining decays → 25.0 g of ³H remains.
    • After another 12.3 y (total 36.9 y): half of the remaining decays → 12.5 g of ³H remains.
  • Pattern: each half-life period reduces the remaining amount by half, regardless of how much was present at the start of that period.

🛡️ Penetration and protection

🛡️ Comparison table

Emission typePenetration depthShielding / protection
Alpha particlesMinimal (will not penetrate skin)Easily stopped by matter; appropriate thickness shielding
Beta particlesShort (will penetrate skin and some tissues slightly, a few cm at most)Shielding of appropriate thickness can protect
Gamma raysDeep (will penetrate tissues deeply)Requires dense/thick shielding; imparts large energy to surrounding matter

⚠️ Practical implications

  • Alpha: large particles, easily stopped, but can impart significant energy to matter they contact.
  • Beta: smaller, penetrate slightly into matter.
  • Gamma: no mass or charge, so they penetrate deeply and can cause ionization deep in tissues.
  • Don't confuse: gamma rays are not "particles"—they are electromagnetic radiation, so the term "gamma particles" is inappropriate.

🌍 Real-world applications

🔥 Smoke detectors

  • Contain americium (a radioactive element with atomic number 95).
  • Americium emits alpha particles that ionize air between metal plates, creating a tiny current.
  • When smoke particles enter, they interfere with the ions, interrupting the current.
  • When current drops below a set value, a circuit triggers a loud alarm.
  • Safety: the americium is embedded in plastic and is not harmful unless the package is taken apart (unlikely).
  • Impact: although many people have unfounded fear of radioactivity, smoke detectors save thousands of lives every year.

🏥 Broader applications

  • Nuclear chemistry applications are more widespread than many realize.
  • Beyond nuclear power plants and atomic bombs: medicine, sterilization of food, analysis of ancient artifacts.
  • Most chemists focus on the number of protons (which determines element identity), but in nuclear chemistry the composition of the nucleus and changes within it are central.
56

Half-Life

Half-Life

🧭 Overview

🧠 One-sentence thesis

Half-life is a constant time interval in which exactly half of any radioactive isotope decays, allowing us to predict how much radioactive material remains after any number of half-lives.

📌 Key points (3–5)

  • What half-life measures: the time required for one-half of a radioactive isotope to decay—a constant property unaffected by conditions or initial amount.
  • How decay progresses: after each half-life period, exactly half of the remaining material decays (not half of the original).
  • Calculation method: amount remaining equals initial amount multiplied by one-half raised to the power of the number of half-lives.
  • Common confusion: half-life is not "how long the material is radioactive"—it's the time for half to decay; the remainder continues to be radioactive.
  • Range of half-lives: isotopes vary enormously, from microseconds to billions of years.

⏱️ The half-life concept

⏱️ Definition and constancy

Half-life: the amount of time it takes for one-half of a radioactive isotope to decay.

  • Half-life is a characteristic property of each specific radioactive isotope.
  • It remains constant regardless of:
    • External conditions (temperature, pressure, etc.)
    • The initial amount of material present
  • Some isotopes are stable indefinitely; others decay with characteristic half-lives.

🔄 How sequential decay works

The excerpt illustrates decay with tritium (hydrogen-3):

  • Start: 100.0 g of tritium (half-life = 12.3 years)
  • After 12.3 y: 50.0 g remains (half decayed to helium-3)
  • After 24.6 y total: 25.0 g remains (half of the 50.0 g decayed)
  • After 36.9 y total: 12.5 g remains (half of the 25.0 g decayed)

Key insight: Each half-life period removes half of what is currently present, not half of the original amount.

Example: If you start with any amount, after three half-lives you have one-eighth remaining (½ × ½ × ½ = ⅛), not zero.

⚠️ Common misunderstanding

Don't confuse: "Half-life is how long the element is radioactive."

  • Wrong interpretation: After one half-life, the material stops being radioactive.
  • Correct interpretation: After one half-life, half the material has decayed; the other half remains radioactive and continues decaying.
  • The excerpt emphasizes: "Many people think that the half-life of a radioactive element represents the amount of time an element is radioactive. In fact, it is the time required for half—not all—of the element to decay."

🧮 Calculating remaining amounts

🧮 The half-life formula

The excerpt provides this expression:

amount remaining = initial amount × (1/2) raised to the power n

where n = the number of half-lives that have elapsed.

  • This formula works even when n is not a whole number.
  • To find n: divide the elapsed time by the half-life duration.

📝 Worked example from the excerpt

Problem: Fluorine-20 has a half-life of 11.0 s. Starting with 5.00 g, how much remains after 44.0 s?

Steps:

  1. Calculate number of half-lives: 44.0 s ÷ 11.0 s = 4 half-lives
  2. Apply formula: 5.00 g × (1/2)^4
  3. Simplify: 5.00 g × 1/16 = 0.313 g

Result: Less than one-third of a gram remains.

📊 Half-life ranges in nature

The excerpt provides a table showing enormous variation:

IsotopeHalf-LifeScale
Seaborgium-2604 millisecondsExtremely short
Berkelium-24823.7 hoursHours
Iodine-1318.04 daysDays
Tritium (H-3)12.3 yearsYears
Americium-241432.7 yearsCenturies
Carbon-145,730 yearsThousands of years
Uranium-2357.04 × 10⁸ yearsHundreds of millions
Uranium-2384.47 × 10⁹ yearsBillions of years

Practical implications:

  • Very short half-lives (e.g., lawrencium-252 at 0.36 s) challenge scientists to conduct experiments quickly.
  • Very long half-lives (e.g., americium-241 in smoke detectors) mean minimal decay over human timescales—less than 4% loss in 10 years.

📏 Units of radioactivity

📏 Activity-based units

The excerpt introduces two units that measure decays per time:

Becquerel (Bq): one radioactive decay per second.

Curie (Ci): 3.7 × 10¹⁰ decays per second (originally based on 1 g of radium).

  • These units describe the rate of decay, not mass.
  • Common to use smaller units: microcuries (μCi), millicuries (mCi).
  • Example from excerpt: americium in a smoke detector has activity of 0.9 μCi.

🔁 Activity decreases over half-lives

The excerpt shows that activity (measured in Ci or Bq) also halves with each half-life:

Example: Radium sample with 16.0 mCi activity and 1,600-year half-life:

  • After 1,600 y: 8.0 mCi
  • After 3,200 y: 4.0 mCi
  • After 4,800 y: 2.0 mCi
  • After 6,400 y: 1.0 mCi

The same halving pattern applies whether you measure in grams or in activity units.

👤 Named after pioneers

  • Becquerel: named after Henri Becquerel, who discovered radioactivity in 1896.
  • Curie: named after Marie Curie, who performed early investigations into radioactive phenomena in the 1900s.
57

Units of Radioactivity

Units of Radioactivity

🧭 Overview

🧠 One-sentence thesis

Radioactivity can be quantified using multiple units that measure either the rate of decay (becquerel and curie) or the biological effects of radiation exposure (rad, gray, rem, and sievert), with most human exposure coming from unavoidable natural sources.

📌 Key points (3–5)

  • Two categories of units: decay-rate units (becquerel, curie) measure disintegrations per second; absorption units (rad, gray, rem, sievert) measure energy absorbed by tissue and biological damage.
  • Activity decreases over half-lives: a sample's activity halves with each half-life period, so multiple half-lives compound the reduction.
  • Rem accounts for radiation type: the rem unit multiplies rad by a factor that reflects the type of emission and tissue, because alpha particles and beta particles damage tissue differently.
  • Common confusion: rad vs rem—rad measures absorbed energy only; rem adjusts for the biological effectiveness of different radiation types.
  • Most exposure is natural: approximately 82% of annual radiation exposure comes from unavoidable natural sources like radon gas, cosmic rays, and radioactive atoms in our own bodies.

⚛️ Units that measure decay rate

⚛️ Becquerel (Bq)

Becquerel: a unit of radioactivity equal to one decay per second.

  • Named after Henri Becquerel, who discovered radioactivity in 1896.
  • It is the SI unit for activity.
  • Example: if a sample has an activity of 60,000 Bq, it undergoes 60,000 disintegrations every second.

⚛️ Curie (Ci)

Curie: a unit of radioactivity equal to 3.7 × 10¹⁰ decays per second.

  • Named after Marie Curie, who performed early investigations into radioactive phenomena in the 1900s.
  • Originally defined as the number of decays per second in 1 gram of radium.
  • Much larger than the becquerel: 1 Ci = 3.7 × 10¹⁰ Bq.
  • Commonly used in millicuries (mCi) or microcuries (μCi) for practical samples.
  • Example: the americium in an average smoke detector has an activity of 0.9 μCi.

🔄 Activity over time

  • Both becquerel and curie can replace grams to describe quantities of radioactive material.
  • Activity decreases by half with each half-life.
  • Example: a radium sample with 16.0 mCi activity and a half-life of 1,600 years will drop to 8.0 mCi after 1,600 years, 4.0 mCi after 3,200 years, 2.0 mCi after 4,800 years, and 1.0 mCi after 6,400 years (four half-lives).

🧬 Units that measure tissue absorption

🧬 Rad (radiation absorbed dose)

Rad: a unit of radioactive exposure equal to 0.01 joules per gram of tissue.

  • Formula: 1 rad = 0.01 J/g.
  • Measures the energy transferred to tissue, either through kinetic energy of particles or electromagnetic energy of gamma rays.
  • The transferred energy can damage tissue, similar to thermal energy from boiling water.
  • Example: absorption of 1 rad by 70,000 g of water (roughly a 150 lb person) raises temperature by only 0.002°C, but breaks about 1 × 10²¹ molecular carbon-carbon bonds in the body—enough to cause harm.

🧬 Gray (Gy)

Gray: a unit of radiation absorption where 1 Gy = 100 rad.

  • An alternative to the rad; the rad is more commonly used.

🩺 Units that account for biological effects

🩺 Rem (roentgen equivalent, man)

Rem: a unit of radioactive exposure that includes a factor to account for the type of radioactivity.

  • Formula: rem = rad × factor.
  • The factor is greater than or equal to 1 and depends on the type of emission and sometimes the tissue exposed.
  • Why the factor matters: different emissions and tissues respond differently to radiation.
Emission typeTissueFactor
Beta particlesMost tissues1
Alpha particlesMost tissues10
Alpha particlesEye tissue30
  • Most exposures people receive are on the order of a few dozen millirems (mrem) or less.
  • Example: a medical X-ray is about 20 mrem.
  • Don't confuse: rad measures absorbed energy; rem adjusts that energy for biological damage based on radiation type.

🩺 Sievert (Sv)

Sievert: a unit defined as 100 rem.

  • A related unit to the rem, used in some contexts.

🌍 Sources and levels of exposure

🌍 Natural vs avoidable sources

The excerpt provides a table of average annual radiation exposure:

SourceAmount (mrem)Percentage of total
Radon gas200~56%
Medical sources53~15%
Radioactive atoms in the body naturally39~11%
Terrestrial sources28~8%
Cosmic sources28~8%
Consumer products10~3%
Nuclear energy0.05<1%
Total358100%
  • 82% of exposure is from natural sources that cannot be avoided.
  • 10% comes from our own bodies, largely from carbon-14 and potassium-40.
  • Example: flying from New York City to San Francisco adds 5 mrem because the plane flies above much of the atmosphere, which normally protects us from cosmic radiation.

⚠️ Health effects of short-term exposure

The excerpt lists effects at various exposure levels over hours or days:

Exposure (rem)Effect
1 (over a full year)No detectable effect
~20Increased risk of some cancers
~100Damage to bone marrow and other tissues; possible internal bleeding; decrease in white blood cell count
200–300Visible "burns" on skin, nausea, vomiting, and fatigue
>300Loss of white blood cells; hair loss
~600Death
  • Actual effects depend on the type of radioactivity, length of exposure, and tissues exposed.

🔬 Detection methods

🔬 Film badge

  • Uses a piece of photographic film embedded in a badge or pen.
  • The film is developed regularly and checked for exposure.
  • Comparing the film's exposure level with standard exposures indicates the amount of radiation a person was exposed to.

🔬 Geiger counter

  • An electrical device that detects radioactivity.
  • Contains a gas-filled chamber (usually argon) with a thin membrane on one end.
  • Radiation enters the chamber and knocks electrons off gas atoms.
  • The presence of electrons and positively charged ions causes a small current.
  • The current is detected and converted to a signal on a meter or an audio circuit to produce an audible "click."
58

Uses of Radioactive Isotopes

Uses of Radioactive Isotopes

🧭 Overview

🧠 One-sentence thesis

Radioactive isotopes serve society through their detectable emissions and energy release, enabling applications in tracing pathways, determining ages, preserving food, and diagnosing or treating medical conditions.

📌 Key points (3–5)

  • Two main reasons isotopes are useful: their radioactivity is easy to detect, and they release usable energy.
  • Tracers exploit detectability: radioactive atoms can be followed through structures or chemical reactions because their emissions are measurable.
  • Dating relies on constant half-lives: environmental factors don't change decay rates, so isotopes act as internal clocks for determining ages of rocks, artifacts, and once-living objects.
  • Medical applications split into two types: diagnostic (small doses to image organs) versus therapeutic (large doses to destroy diseased tissue).
  • Common confusion: irradiating food with radioactive emissions does NOT make the food itself radioactive.

🔬 Tracers and pathway detection

🔍 What a tracer is

Tracer: a substance that can be used to follow the pathway of that substance through some structure.

  • The key is that radioactivity is easy to detect, so scientists can track where the radioactive atoms go.
  • The excerpt emphasizes that tracers work because their emissions can be measured externally.

💧 Detecting leaks and following reactions

  • Leak detection example: tritium (hydrogen-3) in water pipes can be tracked with a Geiger counter to find underground leaks.
  • Chemical reaction tracking: researchers incorporate radioactive atoms into reactant molecules, then follow the atoms through each step by detecting radioactivity.
  • Photosynthesis research: carbon-14 was used to determine the steps of photosynthesis in plants by tracking the radioactive carbon throughout the process.

⏳ Radioactive dating

⏱️ How dating works

  • Core principle: half-life is unaffected by environmental factors, so the isotope acts like an internal clock.
  • Method: analyze how much of the original isotope remains versus how much has decayed into daughter isotopes.
  • Example: if half the uranium-235 in a rock has decayed, the rock's age equals one half-life of uranium-235 (about 4.5 billion years).

🌍 Dating Earth and rocks

  • Many analyses using various isotopes indicate Earth itself is over 4 billion years old.
  • Uranium-235 is one isotope used for dating very old geological samples.

🕰️ Carbon-14 for once-living objects

  • Why carbon-14 works: it has a half-life of 5,370 years and is particularly useful for once-living artifacts (animal or plant matter).
  • How it accumulates: a tiny amount is produced naturally in the atmosphere; living things incorporate it into tissues at a constant low level.
  • After death: the organism stops acquiring carbon-14, and existing carbon-14 decays over time.
  • Age determination: compare remaining carbon-14 to the known constant level in living tissue.

📜 Historical examples

  • Shroud of Turin: carbon-14 dating showed the linen was only 600–700 years old, not 2,000 years as some claimed.
  • Alpine mummy: radiocarbon dating revealed the body was 5,300 years old.
  • Wine verification: tritium dating has been used to verify stated vintages of old fine wines.

🍅 Food preservation

☢️ How irradiation extends shelf life

  • Emissions from cobalt-60 or cesium-137 kill microorganisms that cause spoilage.
  • Foods that can be irradiated: tomatoes, mushrooms, sprouts, berries, eggs, beef, pork, and poultry.
  • Important clarification: irradiation does NOT make the food itself radioactive (a common misconception).

🏥 Medical applications

🩺 Diagnostic uses (small doses)

PurposeHow it worksKey point
Imaging organsAdminister radioactive isotope; detect emissions externallyVery little material needed because radiation is easy to detect
Thyroid testingIodine-131 collects in thyroid; scanner measures radioactivity the next dayAmount collected relates directly to thyroid activity
  • Iodine-131 for thyroid: the thyroid gland is one of the few body sites with significant iodine concentration; a measured dose is given, and activity is measured the next day to diagnose hyperthyroidism or hypothyroidism.
  • Short half-life advantage: iodine-131's 8-day half-life minimizes damage potential.
  • Other organs: bones, heart, brain, liver, lungs can be imaged using appropriate radioactive isotopes (e.g., technetium-99 for thyroid function).

💊 Therapeutic uses (large doses)

  • Purpose: preferentially kill diseased tissues.
  • Dose difference: therapeutic applications require thousands of rem versus diagnostic doses under 40 rem.
  • Thyroid tumor example: a much larger infusion of iodine-131 can destroy tumor cells.
  • Bone cancer: radioactive strontium both detects and eases pain of bone cancers.

🎯 External radiation therapy

  • Gamma ray emissions from isotopes like cobalt-60 can be directed toward tissue to be destroyed, rather than administering the isotope internally.

🔬 Positron emission tomography (PET)

  • What positron emission is: a rare form of radioactivity where a nucleus emits a positively charged electron (positron), which is antimatter.
  • Annihilation process: when a positron meets an electron, both convert into high-energy gamma radiation.
  • PET procedure: patient receives a positron-emitting isotope (intravenously or by ingestion); sensors detect gamma radiation from positron-electron annihilation; computer constructs 3D images.
  • Common isotopes: carbon-11 (half-life 20.4 minutes) and fluorine-18 (half-life 110 minutes), both incorporated into sugar molecules.
  • Cancer detection: fast-metabolizing tissue (a sign of malignancy) shows higher gamma ray emission intensity.
  • Brain research: similar techniques map brain areas most active during specific tasks like reading or speaking.

📋 Medical isotopes summary table

IsotopeMedical use
Phosphorus-32Cancer detection/treatment (eyes and skin)
Iron-59Anemia diagnosis
Cobalt-60Gamma ray irradiation of tumors
Technetium-99mBrain, thyroid, liver, bone marrow, lung, heart, intestinal scanning; blood volume determination
Iodine-131Thyroid function diagnosis and treatment
Xenon-133Lung imaging
Gold-198Liver disease diagnosis
59

Nuclear Energy

Nuclear Energy

🧭 Overview

🧠 One-sentence thesis

Nuclear reactions release enormous amounts of energy—billions of kilojoules per mole—by converting tiny amounts of mass into energy, and this energy can be harvested through controlled fission in nuclear reactors or released explosively in atomic bombs.

📌 Key points (3–5)

  • Mass-energy conversion: Nuclear reactions convert a small mass difference between reactants and products into huge amounts of energy via Einstein's equation E = mc².
  • Fission vs fusion: Fission splits large nuclei (like uranium-235) into smaller ones; fusion combines small nuclei (like hydrogen) into larger ones; both release energy.
  • Controlled vs uncontrolled reactions: Nuclear reactors carefully control fission by managing neutron injection; atomic bombs allow uncontrolled chain reactions that grow exponentially.
  • Common confusion: Natural uranium cannot fuel reactors or bombs—it must be enriched to increase uranium-235 concentration (3% for reactors, 70%+ for bombs).
  • Why it matters: Nuclear energy provides a significant power source for electricity generation, but requires careful control and enrichment processes.

⚛️ Where nuclear energy comes from

⚛️ Mass-energy conversion

Nuclear energy: the controlled harvesting of energy from fission reactions.

  • In nuclear reactions, the total mass of products is slightly less than the mass of reactants.
  • This "missing" mass is converted into energy according to Einstein's equation: E = mc², where c is the speed of light (3.00 × 10⁸ m/s).
  • Example: When 1 mole of uranium-235 undergoes fission, the mass drops by 0.0001834 kg, releasing 16.5 billion kJ of energy.

🔥 Energy scale comparison

Reaction typeEnergy per moleScale
Hydrocarbon combustion~650 kJ/mol per CH₂ unitHundreds of kilojoules
Nuclear fission~16.5 billion kJ/molBillions of kilojoules
  • Nuclear reactions release energy on a completely different scale—millions of times more than chemical reactions.
  • Don't confuse: This is not just "more energy"; it's energy from a fundamentally different source (mass conversion, not bond breaking).

🔬 Two types of nuclear reactions

💥 Fission (splitting large nuclei)

  • Large nuclei like uranium-235 split into smaller nuclei when struck by a neutron.
  • The excerpt gives this example: ²³⁵U + ¹n → ¹³⁹Ba + ⁹⁴Kr + 3¹n + energy
  • Each fission produces more neutrons than it consumes (1 neutron in, 3 neutrons out in this example).
  • These extra neutrons can trigger more fission events.

🌟 Fusion (combining small nuclei)

  • Small nuclei combine to form larger nuclei, releasing energy.
  • Example: 4 hydrogen atoms fuse to make 1 helium atom, releasing 2.58 × 10¹² J per mole.
  • On a per-gram basis, fusion releases many times more energy than fission.
  • The product (helium gas) is simpler and safer than fission products (which include many radioactive isotopes).

⚠️ The fusion challenge

  • Fusion requires extremely high pressures and temperatures.
  • Currently, stable fusion only occurs inside stars.
  • Scientists have not yet achieved safe, controlled fusion for energy production.
  • Don't confuse: Fusion releases more energy per gram, but is much harder to control than fission.

⚙️ How nuclear reactors work

⚙️ Controlled fission process

Nuclear reactor: an apparatus designed to carefully control the progress of a nuclear reaction and extract the resulting energy for useful purposes.

  • Uranium-235 fission can be artificially initiated by injecting a neutron into the nucleus.
  • The reactor carefully adds extra neutrons to control the fission rate.
  • Energy from the controlled reaction converts liquid water into high-pressure steam.
  • The steam runs turbines that generate electricity.

🔗 Chain reactions

Chain reaction: an exponential growth in a process.

  • Each fission event produces 2+ neutrons.
  • These neutrons can trigger more fission events: 1 → 2 → 4 → 8 → 16 → 32 → 64...
  • Energy production grows exponentially along with the neutron count.
  • In a reactor, this chain reaction is carefully controlled to maintain steady energy output.
  • In an atomic bomb, the chain reaction is uncontrolled, producing a rapid explosion.

🎯 The enrichment requirement

  • Natural uranium is only 0.7% uranium-235; the rest is mostly uranium-238.
  • Uranium-238 does not undergo fission, so natural uranium cannot sustain a chain reaction.
  • For nuclear reactors: uranium must be enriched to about 3% uranium-235.
  • For atomic bombs: uranium must be enriched to 70% or more uranium-235.
  • Below these concentrations, the chain reaction cannot sustain itself.
  • Don't confuse: The radioactive process is characteristic of the specific isotope—you cannot make uranium-238 behave like uranium-235.

💣 Controlled vs uncontrolled reactions

💣 Atomic bombs

Atomic bomb: a weapon that depends on a nuclear chain reaction to generate immense forces.

  • An atomic bomb allows the chain reaction to proceed without control.
  • The exponential growth of fission events produces energy explosively.
  • Requires highly enriched uranium (70%+ uranium-235).
  • The first controlled chain reaction was achieved December 2, 1942, in a laboratory under a football stadium at the University of Chicago, supervised by Enrico Fermi.

🛡️ Safety through control

  • Nuclear reactors prevent exponential growth by carefully managing neutron availability.
  • Lower enrichment levels (3% vs 70%+) make runaway reactions impossible.
  • The reactor design allows energy extraction at a steady, controlled rate.
  • Example: A reactor maintains a stable chain reaction where each fission event triggers exactly one more fission event on average, not an exponentially growing number.

👨‍⚕️ Nuclear medicine applications

👨‍⚕️ Nuclear medicine technologist role

  • Administers substances containing radioactive isotopes to diagnose and treat disease.
  • Operates apparatus that detects radiation from radioactive decay (from simple film to complex computer-controlled detectors).
  • Images are interpreted by specially trained physicians.

🛡️ Safety responsibilities

  • Improper exposure to radioactivity harms both patient and technologist.
  • Must adhere to strict safety standards to minimize unnecessary exposure.
  • Must know how to dispose of waste materials safely and appropriately.
  • Don't confuse: Nuclear medicine uses radioactive isotopes for diagnosis/treatment, not the high-energy nuclear reactions used in power generation.
60

Organic Chemistry

Organic Chemistry

🧭 Overview

🧠 One-sentence thesis

Organic chemistry is the study of carbon compounds—which form the overwhelming majority of known chemical substances—and is distinguished from inorganic chemistry by the unique ability of carbon atoms to form stable covalent bonds with each other and other elements in countless variations.

📌 Key points (3–5)

  • Historical shift: organic compounds were once thought to require a "vital force" from living organisms, but the 1828 synthesis of urea from inorganic materials disproved this theory.
  • Modern definition: organic chemistry studies carbon compounds; inorganic chemistry studies all other elements.
  • Why carbon is special: carbon atoms can form stable covalent bonds with each other and other elements in a multitude of variations, creating molecules from one to millions of carbon atoms.
  • Common confusion: "organic" has multiple meanings—originally "from living organisms," also "grown without synthetic chemicals" (foods), and in chemistry simply "carbon compounds."
  • Typical property differences: organic compounds generally have lower melting/boiling points, are flammable, insoluble in water, and exhibit covalent bonding, while inorganic compounds tend to have opposite properties.

🧪 The vital force theory and its decline

🕰️ Early beliefs about organic compounds

  • 18th and early 19th century scientists labeled compounds from plants and animals as "organic" because they came from "organized" (living) systems.
  • Compounds from rocks, ores, atmosphere, and oceans were labeled "inorganic."
  • Scientists believed organic compounds could only be made by living organisms possessing a special "vital force."

🔬 Wöhler's breakthrough experiment (1828)

  • German chemist Friedrich Wöhler reacted silver cyanate (AgOCN) with ammonium chloride (NH₄Cl).
  • He expected to produce ammonium cyanate (NH₄OCN).
  • Instead, he obtained urea (NH₂CONH₂), a well-known organic material normally isolated from urine.
  • This result led to a series of experiments producing many organic compounds from inorganic starting materials.
  • The vital force theory gradually disappeared as chemists demonstrated they could synthesize organic compounds in the laboratory.

🔍 Modern definitions and scope

📚 Current definitions

Organic chemistry: the study of the chemistry of carbon compounds.

Inorganic chemistry: the study of the chemistry of all other elements.

🤔 Why divide chemistry this way?

  • It may seem strange to dedicate one branch to compounds of a single element while grouping 100+ remaining elements together.
  • The division is reasonable because of tens of millions of characterized compounds, the overwhelming majority are carbon compounds.
  • Carbon's unique bonding ability justifies this special treatment.

🌱 Multiple meanings of "organic"

Don't confuse these three uses:

  • Original biological sense: derived from living organisms (e.g., organic fertilizer like cow manure).
  • Agricultural/food sense: foods grown without synthetic pesticides or fertilizers.
  • Chemical sense: compounds containing carbon.

🧬 Why carbon is unique

🔗 Carbon's bonding versatility

  • Carbon atoms can form stable covalent bonds with:
    • Each other
    • Atoms of other elements
  • These bonds can be arranged in a multitude of variations.
  • The resulting molecules can contain anywhere from one to millions of carbon atoms.

🗂️ Organization by functional groups

  • The excerpt indicates organic chemistry is surveyed by dividing compounds into families based on functional groups.
  • The study begins with the simplest family members (alkanes—compounds with only carbon, hydrogen, and single bonds).
  • It then progresses to molecules that are "organic in the original sense"—made by and found in living organisms.
  • Complex carbon-containing molecules determine the forms and functions of living systems and are the subject of biochemistry.

📊 Comparing organic and inorganic compounds

⚖️ General property contrasts

The excerpt emphasizes that organic compounds obey all natural laws like inorganic compounds, and there is often no clear distinction in chemical or physical properties. Nevertheless, typical members show these contrasts:

PropertyTypical OrganicExample: Hexane (C₆H₁₄)Typical InorganicExample: NaCl
Melting pointLow−95°CHigh801°C
Boiling pointLow69°CHigh1,413°C
Water solubilityLow; high in nonpolar solventsInsoluble in water; soluble in gasolineHigh; low in nonpolar solventsSoluble in water; insoluble in gasoline
FlammabilityFlammableHighly flammableNonflammableNonflammable
Electrical conductivity (aqueous)Do not conductNonconductiveConduct electricityConductive
Bonding typeCovalentCovalent bondsIonicIonic bonds

🧪 Illustrative examples

  • Hexane (C₆H₁₄): an organic solvent used to extract soybean oil from soybeans.
  • Sodium chloride (NaCl): common table salt, an inorganic compound.

⚠️ Important caveat

The excerpt warns that there are exceptions to every category in the comparison table. These are typical properties, not absolute rules.

🧱 Introduction to alkanes

🔗 What are hydrocarbons?

Hydrocarbons: the simplest organic compounds, composed of carbon and hydrogen atoms only.

  • Different kinds of hydrocarbons are distinguished by the types of bonding between carbon atoms and the resulting properties.

⛓️ Alkanes (saturated hydrocarbons)

Alkanes (or saturated hydrocarbons): hydrocarbons with only carbon-to-carbon single bonds (C–C) and existing as a continuous chain of carbon atoms also bonded to hydrogen atoms.

  • "Saturated" means each carbon atom is bonded to four other atoms (hydrogen or carbon).
  • Alkanes are the starting point for studying organic chemistry because they contain only two elements (carbon and hydrogen) and have only single bonds.

🛣️ The study path ahead

The excerpt outlines the progression of topics:

  1. Alkanes (only single bonds)
  2. Hydrocarbons with double bonds, triple bonds, and special "aromaticity" bonding
  3. Compounds derived from hydrocarbons by replacing hydrogen atoms with oxygen-containing groups
  4. Organic acids and bases
  5. Biochemistry (chemistry of life) in the remaining chapters

🧴 Practical application mentioned

  • Alkane mixtures (higher carbon atoms per molecule) act as emollients (skin softeners).
  • Mineral oil and petroleum jelly can be applied as protective films.
  • Water and aqueous solutions (like urine) will not dissolve such films.
  • Example: petroleum jelly protects a baby's tender skin from diaper rash because it forms a water-resistant barrier.
61

Structures and Names of Alkanes

Structures and Names of Alkanes

🧭 Overview

🧠 One-sentence thesis

Alkanes form a homologous series in which each member differs from the next by a CH₂ unit, allowing us to predict molecular formulas and properties systematically rather than treating each compound as an isolated case.

📌 Key points (3–5)

  • What alkanes are: hydrocarbons with only carbon-to-carbon single bonds (C–C) in a continuous chain, also bonded to hydrogen atoms; also called saturated hydrocarbons because each carbon is bonded to four other atoms with no double or triple bonds.
  • The homologous series pattern: adjacent alkanes differ by exactly one CH₂ unit, enabling a general formula CₙH₂ₙ₊₂ that works for any straight-chain alkane.
  • Why "saturated" matters: the term means the molecule has no carbon-to-carbon double bonds (C=C), the same meaning as in dietary fats and oils.
  • Common confusion: flat structural drawings do not show true 3D geometry—methane is actually tetrahedral, not flat.
  • Predictable properties: because homologs differ by a constant factor, their properties vary in a regular and predictable manner, organizing organic chemistry much like the periodic table organizes inorganic chemistry.

🔗 What defines alkanes

🔗 Core definition and bonding

Alkanes (or saturated hydrocarbons): hydrocarbons with only carbon-to-carbon single bonds (C–C) and existing as a continuous chain of carbon atoms also bonded to hydrogen atoms.

  • Alkanes are a subset of hydrocarbons—the simplest organic compounds composed only of carbon and hydrogen.
  • "Saturated" means each carbon atom is bonded to four other atoms (hydrogen or carbon)—the maximum possible.
  • There are no double or triple bonds in alkane molecules.
  • Example: methane (CH₄), ethane (C₂H₆), and propane (C₃H₈) are the three simplest alkanes.

🧊 What "saturated" means

  • The term has the same meaning for hydrocarbons as for dietary fats and oils: the molecule has no carbon-to-carbon double bonds (C=C).
  • This is a structural feature, not a statement about how much of the compound is present.
  • Don't confuse: "saturated" refers to bond type (single vs. double), not concentration or solubility.

🧬 The homologous series

🧬 The CH₂ pattern

Homologous series: any family of compounds in which adjacent members differ from each other by a definite factor (here a CH₂ group).

  • Starting from propane (C₃H₈), each step up the series adds one CH₂ unit.
  • Members of such a series are called homologs.
  • Example: methane (CH₄) → ethane (C₂H₆) → propane (C₃H₈) → butane (C₄H₁₀); each step adds one carbon and two hydrogens.

📐 The general formula CₙH₂ₙ₊₂

  • This formula allows us to write the molecular formula for any straight-chain alkane with a given number of carbon atoms.
  • Example: an alkane with 8 carbon atoms has the formula C₈H₍₂ ₓ ₈₎ ₊ ₂ = C₈H₁₈.
  • Example: an alkane with 12 carbon atoms has the formula C₁₂H₂₆.
  • The formula works because the pattern is consistent across the entire series.

🔄 Why homology matters

  • Homologs have properties that vary in a regular and predictable manner.
  • Instead of memorizing each individual carbon compound, we can study a few members of the series and deduce properties of others.
  • The principle of homology organizes organic chemistry in much the same way the periodic table organizes inorganic chemistry.
  • This transforms a "bewildering array of individual carbon compounds" into a manageable, systematic framework.

📊 The first ten straight-chain alkanes

📊 Table of alkanes

NameMolecular FormulaCondensed Structural FormulaNumber of Possible Isomers
methaneCH₄CH₄
ethaneC₂H₆CH₃CH₃
propaneC₃H₈CH₃CH₂CH₃
butaneC₄H₁₀CH₃CH₂CH₂CH₃2
pentaneC₅H₁₂CH₃CH₂CH₂CH₂CH₃3
hexaneC₆H₁₄CH₃CH₂CH₂CH₂CH₂CH₃5
heptaneC₇H₁₆CH₃CH₂CH₂CH₂CH₂CH₂CH₃9
octaneC₈H₁₈CH₃CH₂CH₂CH₂CH₂CH₂CH₂CH₃18
nonaneC₉H₂₀CH₃CH₂CH₂CH₂CH₂CH₂CH₂CH₂CH₃35
decaneC₁₀H₂₂CH₃CH₂CH₂CH₂CH₂CH₂CH₂CH₂CH₂CH₃75
  • The table shows that as the chain lengthens, the number of possible isomers increases rapidly.
  • Starting with butane (4 carbons), multiple structural arrangements become possible.

🎨 Molecular geometry and representation

🎨 Flat vs. 3D structure

  • Flat structural representations do not accurately portray bond angles or molecular geometry.
  • Methane has a tetrahedral shape, not a flat shape.
  • Chemists use wedges to indicate bonds coming out toward you and dashed lines for bonds going back away from you.
  • An ordinary solid line indicates a bond in the plane of the page.
  • Don't confuse: the 2D drawing is a convenience; the actual molecule is three-dimensional.

🔺 Tetrahedral methane

  • VSEPR theory correctly predicts a tetrahedral shape for the methane molecule (CH₄).
  • This geometry arises because each carbon atom forms four bonds, which arrange themselves to minimize repulsion.
  • Example: in methane, the four hydrogen atoms are positioned at the corners of a tetrahedron with the carbon at the center.
62

Branched-Chain Alkanes

Branched-Chain Alkanes

🧭 Overview

🧠 One-sentence thesis

Alkanes with four or more carbon atoms can arrange their atoms in different branched structures, creating isomers—distinct compounds with the same molecular formula but different properties.

📌 Key points (3–5)

  • What isomers are: different compounds that share the same molecular formula but have different structural arrangements and properties.
  • When branching appears: alkanes with four or more carbon atoms (C₄H₁₀ and larger) can exist in both straight-chain and branched-chain forms.
  • Common confusion: bending or rotating a chain does not create a different compound—only changing which carbon atoms are bonded to which creates a true isomer.
  • Property differences: isomers have measurably different physical properties, such as boiling points.
  • Naming convention: branched isomers receive distinct names (e.g., butane vs. isobutane) to distinguish them from their straight-chain counterparts.

🔗 What makes branched-chain alkanes possible

🧱 The butane example

  • Butane has the molecular formula C₄H₁₀.
  • One way to arrange it: four carbon atoms in a continuous row (–C–C–C–C–), then add hydrogen atoms to give each carbon four bonds.
  • Another way: place three carbon atoms in a row and branch the fourth carbon off the middle carbon atom.
  • Both arrangements satisfy C₄H₁₀, but they are different compounds with different properties.

Isomers: different compounds having the same molecular formula but different structural formulas and properties.

📊 Butane vs. isobutane

CompoundStructureBoiling point
ButaneFour-carbon continuous chain−0.5°C
IsobutaneThree-carbon chain with one branch off the middle−11.7°C
  • The branched compound is called isobutane.
  • Example: both have C₄H₁₀, but isobutane boils at a lower temperature.

🔄 What does not create a new isomer

🔄 Rotation and bending

  • The groups around C–C bonds can rotate freely.
  • Bending a chain in various ways does not change the identity of the compound.
  • All of the following represent the same compound (the excerpt shows multiple bent representations of the same structure):
    • A four-carbon chain can be drawn bent or straight; it remains the same molecule.
  • Don't confuse: drawing a chain at different angles ≠ creating a different isomer. Only changing which atoms are bonded to which creates a true isomer.

🚫 Why smaller alkanes have no isomers

  • Methane (CH₄), ethane (C₂H₆), and propane (C₃H₈) do not exist in isomeric forms.
  • Reason: there is only one way to arrange the atoms in each formula so that each carbon atom has four bonds.
  • Isomers only appear starting at C₄H₁₀.

🌿 Pentane and its isomers

🌿 Three forms of C₅H₁₂

  • Pentane has the molecular formula C₅H₁₂.
  • Three distinct isomers exist:
NameStructure descriptionBoiling point
PentaneAll five carbon atoms in a continuous chain36.1°C
IsopentaneFour-carbon chain with one CH₃ branch off the second carbon27.7°C
NeopentaneNamed from Greek neos ("new"); discovered after the other two9.5°C
  • All three have the same molecular formula but different properties.
  • Example: the boiling points differ by more than 25°C across the three isomers.

📏 Straight-chain terminology

  • A continuous (unbranched) chain of carbon atoms is often called a straight chain, even though the tetrahedral arrangement around each carbon gives it a zigzag shape.
  • Straight-chain alkanes are sometimes called normal alkanes and given the prefix n- (e.g., n-butane).
  • The excerpt notes this prefix is not part of the International Union of Pure and Applied Chemistry system and will not be used.

🧪 Recognizing valid branching

🧪 What counts as a branch

  • A branch must create a structure that cannot be redrawn as a longer continuous chain.
  • Example from concept review: a two-carbon branch off the second carbon of a four-carbon chain is not a valid branch—it would make the longest continuous chain five carbon atoms, not four.
  • Don't confuse: if you can redraw the structure with a longer continuous chain, it is not a true branch; it is simply a bent representation of a longer straight chain.

✅ Identifying true isomers

  • Two structural formulas represent different isomers only if they cannot be redrawn to show the same connectivity.
  • Example from exercises: a five-carbon horizontal line vs. a four-carbon line with a CH₃ group extending from the third carbon—both are actually five-carbon continuous chains, so they represent the same compound, not isomers.
  • The key test: count the longest continuous chain and check if branches truly shorten that chain.
63

Condensed Structural and Line-Angle Formulas

Condensed Structural and Line-Angle Formulas

🧭 Overview

🧠 One-sentence thesis

Condensed structural formulas and line-angle formulas simplify the representation of organic molecules by reducing the space and complexity needed to show molecular structure while still identifying specific isomers.

📌 Key points (3–5)

  • Why condensed formulas exist: structural formulas are difficult to type/write and take up too much space, so chemists use condensed versions.
  • How condensed formulas work: hydrogen atoms are shown right next to the carbon atoms to which they are attached.
  • What line-angle formulas do: carbon atoms are implied at corners and ends of lines; each carbon is understood to have enough hydrogens to make four bonds total.
  • Common confusion: molecular formulas vs structural formulas—molecular formulas (e.g., C₄H₁₀) show only atom counts and cannot distinguish isomers like butane and isobutane, while structural formulas show the order of attachment.
  • Parentheses notation: in condensed formulas, parentheses indicate that the enclosed group is attached to the adjacent carbon atom.

📝 Types of chemical formulas

🔢 Molecular formula

A molecular formula shows only the kinds and numbers of atoms in a molecule.

  • It tells you what atoms are present and how many of each.
  • It does not tell you how the atoms are connected.
  • Example: C₄H₁₀ tells us there are 4 carbon atoms and 10 hydrogen atoms, but it doesn't distinguish between butane and isobutane.
  • Don't confuse: molecular formula vs structural formula—the molecular formula cannot identify which isomer you have.

🏗️ Structural formula

A structural formula shows all the carbon and hydrogen atoms and the bonds attaching them.

  • It shows the order of attachment of the various atoms.
  • This allows you to identify the specific isomer.
  • Problem: structural formulas are difficult to type/write and take up a lot of space.
  • Example: for butane, you would draw out every C, every H, and every bond between them.

✂️ Condensed structural formulas

✂️ What condensed formulas are

Condensed structural formulas show hydrogen atoms (or other atoms or groups) right next to the carbon atoms to which they are attached.

  • Purpose: to alleviate the problems of typing/writing and space that full structural formulas create.
  • The excerpt illustrates this for butane (though the actual condensed formula is not reproduced in the text).
  • Key advantage: easier to type and more compact than full structural formulas, while still showing connectivity.

📎 Parentheses notation

  • In condensed structural formulas, parentheses indicate that the enclosed grouping of atoms is attached to the adjacent carbon atom.
  • Example: (CH₃)₂CHCH₂CH₂CH₃ for isohexane means two CH₃ groups are attached to the same carbon (the one shown as CH).
  • Don't confuse: the parentheses are not just for grouping visually—they specify which carbon the group is bonded to.

📐 Line-angle formulas

📐 What line-angle formulas are

A line-angle formula is an organic chemical formula in which carbon atoms are implied at the corners and ends of lines. Each carbon atom is understood to be attached to enough hydrogen atoms to give each carbon atom four bonds.

  • This is the ultimate condensed formula according to the excerpt.
  • Carbon atoms are not drawn explicitly; they are implied wherever a line changes direction (corner) or stops (end).
  • Hydrogen atoms on carbon are not drawn; you assume each carbon has enough H atoms to make a total of four bonds.

🔍 How to read line-angle formulas

  • Each line represents a bond.
  • Each corner or end of a line represents a carbon atom.
  • Count the bonds already shown for that carbon; the remaining bonds (up to four total) are C–H bonds.
  • Example: pentane (CH₃CH₂CH₂CH₂CH₃) and isopentane [(CH₃)₂CHCH₂CH₃] can both be drawn as line-angle formulas (the excerpt mentions this but does not reproduce the drawings).

🎯 Why line-angle formulas matter

  • They are the most compact way to represent organic structures.
  • They reduce clutter and make it easier to see the carbon skeleton and branching patterns.
  • Trade-off: you must remember the implicit hydrogens—they are not shown, but they are there.

📊 Comparison of formula types

Formula typeWhat it showsWhat it hidesUse case
MolecularAtom counts onlyConnectivity and isomer identityQuick composition summary
StructuralAll atoms and bonds(nothing hidden)Full detail, but space-intensive
Condensed structuralAtoms grouped by attachmentSome bond linesEasier typing, moderate space
Line-angleCarbon skeletonC and H atoms (implied)Maximum compactness, quick sketching
64

IUPAC Nomenclature

IUPAC Nomenclature

🧭 Overview

🧠 One-sentence thesis

The IUPAC system provides a systematic, worldwide set of rules for naming alkanes that assigns each unique compound its own exclusive name by identifying the longest continuous carbon chain and numbering substituent positions.

📌 Key points (3–5)

  • Why systematic naming is needed: as carbon atoms increase, isomers multiply rapidly (3 pentanes, 5 hexanes, 9 heptanes, 18 octanes), making individual memorable names impractical.
  • Core IUPAC approach: identify the longest continuous carbon chain (LCC) for the base name, then name and number substituents attached to that chain.
  • Alkyl groups vs alkanes: an alkyl group is derived from an alkane by removing one hydrogen atom and is named by replacing -ane with -yl (e.g., methane → methyl); alkyl groups are not independent molecules but parts of molecules.
  • Common confusion: the LCC need not be written in a straight line—you must identify the longest chain regardless of how the structure is drawn.
  • Bidirectional numbering rule: number the LCC in the direction that gives the lowest numbers to carbon atoms with attached substituents.

🏗️ Foundation concepts

🏗️ IUPAC System of Nomenclature

IUPAC System of Nomenclature: a systematic way of naming chemical substances so that each has a unique name.

  • Developed by the International Union of Pure and Applied Chemistry.
  • Used worldwide.
  • Contrasts with common names (e.g., isobutane, isopentane, neopentane) that do not follow these rules.
  • The excerpt emphasizes that the rules enable you to both name a compound from a structure and draw a structure from a name.

🔗 Longest continuous chain (LCC)

  • The LCC determines the parent chain and the base name.
  • The base name uses a stem indicating the number of carbon atoms (Table 12.3):
StemNumber of carbons
meth-1
eth-2
prop-3
but-4
pent-5
hex-6
hept-7
oct-8
non-9
dec-10
  • Add the suffix -ane to indicate the molecule is an alkane.
  • Don't confuse: the LCC is based on the longest continuous chain of carbon atoms, not the total number of carbon atoms in the molecule.

🧩 Alkyl groups

Alkyl group: a group of atoms that results when one hydrogen atom is removed from an alkane.

  • Named by replacing the -ane suffix with -yl.
  • Example: methane (CH₄) minus one hydrogen → methyl group (CH₃–).
  • Common alkyl groups (Table 12.4):
Parent alkaneAlkyl groupFormula
methanemethylCH₃–
ethaneethylCH₃CH₂–
propanepropylCH₃CH₂CH₂–
propaneisopropyl(CH₃)₂CH–
butanebutylCH₃CH₂CH₂CH₂–
  • Key distinction: an alkane is a molecule; an alkyl group is not an independent molecule but a part of a molecule considered as a unit.
  • Alkyl groups are called substituents when attached to the parent carbon chain.

🔢 Substituents

Substituents: atoms or groups attached to the parent carbon chain.

  • For now, the excerpt considers only alkyl groups as substituents.
  • Substituents are named and their positions indicated by numbers.

📋 Simplified IUPAC naming rules

📋 Rule 1: Name by the LCC

  • Name alkanes according to the LCC of carbon atoms, not the total number.
  • The LCC determines the parent chain and base name.
  • Add suffix -ane.
  • Example: if the LCC has five carbon atoms, the parent compound is pentane.

🔢 Rule 2: Number the LCC if branched

  • Number the carbon atoms of the LCC.
  • Direction rule: assign numbers in the direction that gives the lowest numbers to carbon atoms with attached substituents.
  • Formatting:
    • Hyphens separate numbers from substituent names.
    • Commas separate numbers from each other.
  • Important note: the LCC need not be written in a straight line; you must identify it regardless of how the structure is drawn.

🔤 Rule 3: Alphabetize substituent names

  • Place substituent group names in alphabetical order before the parent compound name.
  • If the same alkyl group appears more than once:
    • Express the numbers of all carbon atoms to which it is attached.
    • If the same group appears multiple times on the same carbon, repeat that carbon's number.
    • Use Greek prefixes: di-, tri-, tetra-, etc.
    • Alphabetization rule: these prefixes are not considered when determining alphabetical order (e.g., ethyl comes before dimethyl; the "di-" is ignored).
  • The last alkyl group named is prefixed to the parent alkane name to form one word.

🛠️ Applying the rules

🛠️ Naming from structure (Example 1)

The excerpt provides three worked examples:

Example 1a: A five-carbon LCC with a methyl group on the second carbon.

  • LCC = 5 carbons → pentane.
  • Methyl on carbon 2.
  • Name: 2-methylpentane.

Example 1b: A six-carbon LCC with methyl groups on carbons 2 and 5.

  • LCC = 6 carbons → hexane.
  • Methyl groups on carbons 2 and 5.
  • Name: 2,5-dimethylhexane.

Example 1c: An eight-carbon LCC with methyl and ethyl groups both on carbon 4.

  • LCC = 8 carbons → octane.
  • Counting from the right gives carbon 4 a lower number.
  • Ethyl and methyl both on carbon 4.
  • Alphabetize: ethyl before methyl.
  • Name: 4-ethyl-4-methyloctane.

🖊️ Drawing from name (Example 2)

The excerpt emphasizes: always start with the parent chain.

Example 2a: 2,3-dimethylbutane

  • Parent chain: butane (4 carbons).
  • Add methyl groups on carbons 2 and 3.
  • Fill in hydrogen atoms so each carbon has four bonds.

Example 2b: 4-ethyl-2-methylheptane

  • Parent chain: heptane (7 carbons).
  • Add ethyl group on carbon 4.
  • Add methyl group on carbon 2.
  • Fill in hydrogen atoms.
  • Note: bonds (dashes) can be shown or not; sometimes needed for spacing.

🔄 Consistency in numbering

  • You can number the parent chain from either direction.
  • Be consistent: don't change directions before the structure is done.
  • The direction that gives the lowest numbers to substituents is correct.

🎯 Key takeaways from the excerpt

🎯 Unique names

  • When the IUPAC rules are followed, every unique compound receives its own exclusive name.
  • The rules enable bidirectional work: name → structure and structure → name.

🎯 Learning approach

  • The excerpt advises: "The best way to learn how to use the IUPAC system is to put it to work, not just memorize the rules. It's easier than it looks."

🎯 Common vs IUPAC names

TypeCharacteristics
Common namesWidely used but not very systematic (e.g., isobutane, neopentane)
IUPAC namesIdentify a parent compound and name other groups as substituents; use numbers to locate substituents

🎯 Substituent vs functional group

  • The excerpt's concept review asks: "What is a CH₃ group called when it is attached to a chain of carbon atoms?"
  • Answer: substituent (not a functional group in this context).
65

Physical Properties of Alkanes

Physical Properties of Alkanes

🧭 Overview

🧠 One-sentence thesis

Alkanes serve as a baseline for comparing other organic compounds because their physical properties—nonpolarity, low density, water insolubility, and predictable boiling points—follow systematic trends based on molecular size and structure.

📌 Key points (3–5)

  • Polarity and solubility: Alkanes are nonpolar, so they dissolve in nonpolar solvents but not in water (a polar solvent).
  • Density pattern: Nearly all alkanes have densities less than 1.0 g/mL, making them less dense than water and causing them to float.
  • Boiling point trend: Straight-chain alkanes show increasing boiling points as molar mass increases due to greater surface area and stronger intermolecular forces.
  • Common confusion: Gas vs liquid alkanes—the first four straight-chain alkanes are gases at room temperature; larger ones are liquids; density units change from g/L (gases) to g/mL (liquids).
  • Why it matters: Understanding alkane properties is essential because petroleum products are primarily alkanes, and alkane-like regions appear in biological molecules like lipids.

🔬 Solubility and polarity behavior

🔬 Why alkanes don't mix with water

Alkane molecules are nonpolar, making them insoluble in water (a polar solvent) but soluble in nonpolar and slightly polar solvents.

  • The nonpolar nature means alkanes lack charged regions that could interact with water's polar molecules.
  • This explains everyday observations: oil and grease float on water rather than dissolving.
  • Example: If you add 25 mL of hexane to 100 mL of water, the hexane will not dissolve and will float on top.

🧪 Alkanes as solvents

  • Because alkanes are nonpolar, they work well as solvents for other low-polarity substances.
  • Common uses: dissolving fats, oils, and waxes.
  • The principle: "like dissolves like"—nonpolar substances dissolve in nonpolar solvents.

⚖️ Density characteristics

⚖️ Less dense than water

  • Nearly all alkanes have densities below 1.0 g/mL (water's density at 20°C is 1.00 g/mL).
  • This property explains why oil floats on water surfaces.
  • Real-world implication: Oil spills spread across water surfaces rather than sinking, making cleanup challenging.

📏 Unit changes for gases vs liquids

Physical StateDensity UnitsExamples from excerpt
Gas (first 4 alkanes)grams per liter (g/L)Methane: 0.668 g/L; Butane: 2.493 g/L
Liquid (5+ carbons)grams per milliliter (g/mL)Pentane: 0.626 g/mL; Hexane: 0.659 g/mL
  • Don't confuse: The unit change reflects the phase difference, not a density increase—gases are measured at 1 atm pressure.

🔥 Gas density and fire hazards

  • Natural gas (mostly methane) has density ~0.67 g/L, less than air (~1.29 g/L), so it rises when leaked.
  • Bottled gas (propane ~1.88 g/L or butane ~2.5 g/L) is heavier than air and sinks.
  • Safety implication: Bottled gas leaks collect near the floor, creating a more serious fire hazard that's harder to clear.

🌡️ Boiling point trends

🌡️ How molar mass affects boiling points

  • The excerpt states: "the boiling points of the straight-chain alkanes increase with increasing molar mass."
  • This is a general rule for all straight-chain homologs in organic compound families.
  • Example from the data: Pentane (C₅H₁₂) boils at 36°C, while decane (C₁₀H₂₂) boils at 174°C.

🔗 Why larger molecules boil at higher temperatures

  • Larger molecules have greater surface areas.
  • Greater surface area means stronger interactions between molecules.
  • More energy is required to separate them, raising the boiling point.

💨 Why alkane boiling points are relatively low

  • For a given molar mass, alkanes have lower boiling points than many other compound types.
  • Reason: Nonpolar molecules have only weak dispersion forces holding them together in the liquid state.
  • These weak forces are easier to overcome compared to polar molecules with stronger intermolecular attractions.

🧬 Broader significance

🧬 Alkanes as a comparison baseline

  • The excerpt emphasizes that alkanes "serve as a basis of comparison for the properties of many other organic compound families."
  • Because alkanes have predictable properties and undergo few reactions besides combustion, they provide a reference point.

🧫 Connection to biological molecules

  • Large portions of lipid structures consist of nonpolar alkyl groups (alkane-like chains).
  • Lipids include dietary fats and structural compounds like phospholipids and sphingolipids.
  • These molecules have both polar and nonpolar regions, allowing them to bridge water-soluble and water-insoluble phases.
  • This dual nature is essential for cell membrane permeability.
  • Example comparison: Tripalmitin (a fat molecule) has long hydrocarbon chains similar to hexadecane (a 16-carbon alkane).

🛢️ Practical applications

  • Petroleum, natural gas, and derived products (gasoline, bottled gas, solvents, plastics) are composed primarily of alkanes.
  • Understanding alkane properties is fundamental to working with these materials.
66

Chemical Properties of Alkanes

Chemical Properties of Alkanes

🧭 Overview

🧠 One-sentence thesis

Alkanes are remarkably unreactive with most chemicals but do undergo two important reactions—combustion with oxygen and halogenation with halogens—under specific conditions.

📌 Key points (3–5)

  • Why alkanes are called "paraffins": they have "little affinity" for most reagents because they are nonpolar and do not attract ions.
  • Two key reactions: combustion (with oxygen) and halogenation (with chlorine and bromine).
  • Combustion products vary by oxygen supply: complete combustion yields carbon dioxide and water; limited oxygen produces toxic carbon monoxide.
  • Common confusion: not all halogens react equally—fluorine reacts explosively, chlorine and bromine react readily with UV light or heat, and iodine is relatively unreactive.
  • Why it matters: combustion provides heat for cooking and heating; incomplete combustion can cause fatal carbon monoxide poisoning.

🛡️ Low reactivity of alkanes

🛡️ Why alkanes are unreactive

Paraffins: alkanes are sometimes called paraffins, from the Latin parum affinis, meaning "little affinity."

  • Alkanes are nonpolar molecules.
  • Neither positive ions nor negative ions are attracted to nonpolar molecules.
  • This means alkanes do not react with ionic compounds such as most laboratory acids, bases, oxidizing agents, or reducing agents.
  • Example: mixing an alkane with a typical acid at room temperature produces no reaction.

🔍 What "little affinity" means

  • The excerpt emphasizes that alkanes undergo so few reactions that the term "paraffins" captures their chemical inertness.
  • Don't confuse: "unreactive" does not mean "no reactions at all"—alkanes do undergo combustion and halogenation under the right conditions.

🔥 Combustion reactions

🔥 Complete combustion

  • Activation requirement: alkanes do not react with oxygen at room temperature; a flame or spark is needed to provide activation energy.
  • Once started, combustion is highly exothermic (releases heat) and proceeds vigorously.
  • For methane (CH₄): methane plus oxygen yields carbon dioxide, water, and heat.
    • Written in words: CH₄ + 2O₂ → CO₂ + 2H₂O + heat
  • Uses: the heat is used for cooking foods, heating homes, and drying clothes.

⚠️ Incomplete combustion and carbon monoxide

  • When oxygen is limited, the products change: carbon monoxide (CO) is formed instead of carbon dioxide.
    • For methane: 2CH₄ + 3O₂ → 2CO + 4H₂O
  • Danger: carbon monoxide is toxic and responsible for dozens of deaths each year from unventilated or improperly adjusted gas heaters (and kerosene heaters).
  • Don't confuse: "ideal" combustion (adequate mixing, sufficient oxygen) produces only CO₂ and H₂O; real-world conditions are rarely ideal, so other products like CO frequently form.

🧪 Halogenation reactions

🧪 How halogens react with alkanes

  • Alkanes react with chlorine (Cl₂) and bromine (Br₂) in the presence of ultraviolet light or high temperatures.
  • The reaction produces chlorinated and brominated alkanes (halogenated hydrocarbons).
  • Example: chlorine reacts with excess methane to give methyl chloride (CH₃Cl).
    • Written in words: CH₄ + Cl₂ → CH₃Cl + HCl
  • With more chlorine, a mixture of products is obtained: CH₃Cl, CH₂Cl₂, CHCl₃, and CCl₄.

🌈 Reactivity differences among halogens

HalogenReactivity with alkanes
Fluorine (F₂)Combines explosively with most hydrocarbons
Chlorine (Cl₂)Reacts readily with UV light or heat
Bromine (Br₂)Reacts readily with UV light or heat
Iodine (I₂)Relatively unreactive
  • Fluorinated and iodinated alkanes are produced by indirect methods (not direct reaction).
  • Don't confuse: the lightest halogen (fluorine) is the most reactive, not the least; iodine is the least reactive.

🔬 What halogenation produces

Halogenated hydrocarbons: compounds in which one or more hydrogen atoms of a hydrocarbon have been replaced by halogen atoms.

  • The simplest halogenated hydrocarbons have a single halogen atom substituted for a hydrogen atom of the alkane.
  • The excerpt mentions that names and uses of halogenated hydrocarbons are discussed in a later section (not included in this excerpt).
67

Halogenated Hydrocarbons

Halogenated Hydrocarbons

🧭 Overview

🧠 One-sentence thesis

Halogenated hydrocarbons are formed when hydrogen atoms in alkanes are replaced by halogen atoms, and they have diverse uses but also raise environmental and health concerns.

📌 Key points (3–5)

  • What they are: compounds formed when one or more hydrogen atoms of a hydrocarbon are replaced by halogen atoms (F, Cl, Br, or I).
  • Naming systems: common names use the alkyl group name plus the halogen stem with "-ide"; IUPAC names use the parent alkane with halogen prefixes (fluoro-, chloro-, bromo-, iodo-) and position numbers.
  • Practical applications: halogenated hydrocarbons serve as refrigerants, solvents, anesthetics, fire extinguishers, and foaming agents.
  • Health and environmental risks: many chlorinated hydrocarbons are suspected carcinogens and cause liver damage; CFCs destroy the ozone layer.
  • Common confusion: CFCs vs. safer alternatives—HFCs contain no Cl or Br, while HCFCs break down more readily in the lower atmosphere before reaching the stratosphere.

🔬 Formation and basic structure

🔬 How halogenated hydrocarbons form

Halogenated hydrocarbons: compounds in which one or more hydrogen atoms of a hydrocarbon have been replaced by halogen atoms.

  • Alkanes react with halogens (F₂, Cl₂, Br₂, I₂) to produce these compounds.
  • The simplest type has a single halogen atom substituted for one hydrogen atom.
  • Example: methane (CH₄) can react with chlorine, replacing one, two, three, or all four hydrogen atoms with Cl atoms.

🧪 Alkyl halides (haloalkanes)

Alkyl halide (or haloalkane): the compound resulting from the replacement of a hydrogen atom of an alkane with a halogen atom.

  • This is the simplest category, where only one hydrogen is replaced.
  • The halogen can be fluorine, chlorine, bromine, or iodine.

📝 Naming conventions

📝 Common naming system

  • Structure: alkyl group name + halogen stem + "-ide"
  • The halogen stems: fluor-, chlor-, brom-, iod-
  • Example: CH₃CH₂Cl is called "ethyl chloride" (ethyl group + chlor + ide)
  • Example: CH₃CH₂CH₂Br is called "propyl bromide" (propyl group + brom + ide)
  • Typically used for simple alkyl groups with one to four carbon atoms.

📝 IUPAC naming system

  • Structure: halogen prefix + position number + parent alkane name
  • The prefixes: fluoro-, chloro-, bromo-, iodo-
  • Position numbers indicate which carbon atom the halogen is attached to.
  • Example: CH₃CH₂Cl is "chloroethane" (chloro + ethane)
  • Example: CH₃CH₂CH₂Br is "1-bromopropane" (bromo at position 1 + propane)
  • When multiple substituents exist, list them alphabetically with their position numbers.
  • Example: a hexane chain with Br at position 4 and CH₃ at position 2 becomes "4-bromo-2-methylhexane"
  • Usually used for compounds with larger numbers of carbon atoms (more than four).

🧰 Applications and examples

🧰 Methane-derived compounds

The excerpt provides a table showing various halogenated compounds derived from methane:

FormulaCommon NameIUPAC NameUses
CH₃Clmethyl chloridechloromethanerefrigerant; manufacturing silicones, methyl cellulose, synthetic rubber
CH₂Cl₂methylene chloridedichloromethanelaboratory and industrial solvent
CHCl₃chloroformtrichloromethaneindustrial solvent
CCl₄carbon tetrachloridetetrachloromethanedry-cleaning solvent and fire extinguishers (no longer recommended)
CBrF₃halon-1301bromotrifluoromethanefire extinguisher systems
CCl₃FCFC-11trichlorofluoromethanefoaming plastics
CCl₂F₂CFC-12dichlorodifluoromethanerefrigerant

🧰 Ethane-derived compounds

FormulaCommon NameIUPAC NameUses
CH₃CH₂Clethyl chloridechloroethanelocal anesthetic
ClCH₂CH₂Clethylene dichloride1,2-dichloroethanesolvent for rubber
CCl₃CH₃methylchloroform1,1,1-trichloroethanesolvent for cleaning computer chips and plastic molds

⚠️ Health and safety concerns

⚠️ Toxicity and carcinogenic risks

  • Many chlorinated hydrocarbons are suspected carcinogens (cancer-causing substances).
  • They are known to cause severe liver damage.
  • Even small amounts of vapor can cause serious illness if exposure is prolonged.

⚠️ Carbon tetrachloride hazards

  • Once widely used as a dry-cleaning solvent and in fire extinguishers.
  • No longer recommended for either use due to health risks.
  • Reacts with water at high temperatures to form deadly phosgene (COCl₂) gas.
  • This reaction makes its use in fire extinguishers particularly dangerous.

⚠️ Safer halogenated compounds

  • Ethyl chloride is used as an external local anesthetic.
  • When sprayed on skin, it evaporates quickly and cools the area enough to make it insensitive to pain.
  • Can also be used as an emergency general anesthetic.
  • Bromine-containing compounds are used in fire extinguishers and as fire retardants on clothing and materials, though they are also toxic and have adverse environmental effects.

🌍 Environmental impact: CFCs and ozone depletion

🌍 What CFCs are and how they're used

Chlorofluorocarbons (CFCs): alkanes substituted with both fluorine and chlorine atoms.

  • Used as dispersing gases in aerosol cans.
  • Used as foaming agents for plastics.
  • Used as refrigerants.
  • Examples from the table: CFC-11 (CCl₃F) and CFC-12 (CCl₂F₂).

🌍 How CFCs destroy the ozone layer

The excerpt describes a two-step process:

  1. Lower atmosphere: CFCs contribute to the greenhouse effect.
  2. Stratosphere destruction:
    • CFCs diffuse upward into the stratosphere.
    • Ultraviolet (UV) radiation breaks down CFC molecules.
    • This releases Cl atoms.
    • These Cl atoms break down ozone (O₃) molecules.
    • Ozone normally protects Earth from harmful UV radiation.
  • UV radiation can cause skin cancer in humans and harm other animals and plants.
  • Ozone "holes" are large areas of substantial ozone depletion, occurring mainly over Antarctica from late August through early October.
  • The largest ozone hole ever observed occurred on 24 September 2006.

🌍 Safer alternatives to CFCs

Worldwide action has reduced CFC use. Two types of replacements are mentioned:

AlternativeStructureHow it's safer
Hydrofluorocarbons (HFCs)Example: CH₂FCF₃Have no Cl or Br to form radicals that destroy ozone
Hydrochlorofluorocarbons (HCFCs)Example: CHCl₂CF₃Break down more readily in the troposphere, so fewer ozone-destroying molecules reach the stratosphere

Don't confuse: All three types (CFCs, HFCs, HCFCs) are halogenated compounds, but HFCs and HCFCs are designed to be less harmful to the ozone layer than CFCs.

68

Cycloalkanes

Cycloalkanes

🧭 Overview

🧠 One-sentence thesis

Cycloalkanes are ring-structured hydrocarbons with only single bonds that behave similarly to open-chain alkanes, with five- and six-membered rings being particularly stable due to minimal angle strain.

📌 Key points (3–5)

  • What cycloalkanes are: cyclic hydrocarbons formed when carbon atoms join to form rings instead of open chains, with only single bonds present.
  • How they are named: by adding the prefix "cyclo-" to the name of the open-chain alkane with the same number of carbon atoms.
  • Ring stability varies: cyclopropane has high strain (60° angles vs. preferred 109.5°), while cyclopentane and cyclohexane are particularly stable with angles near the preferred values.
  • Common confusion: cycloalkanes act very much like noncyclic alkanes in their properties, except cyclopropane which behaves differently due to ring strain.
  • Representation shortcut: line-angle formulas show rings as geometric figures where each corner represents a carbon atom plus enough hydrogen atoms to give four bonds.

🔗 Formation and structure

🔗 How rings form

  • When a chain contains three or more carbon atoms, the atoms can join to form ring or cyclic structures.
  • The simplest cyclic hydrocarbon has the formula C₃H₆ (cyclopropane).
  • Each carbon atom in cyclopropane has two hydrogen atoms attached.

📐 Line-angle representation

Line-angle formulas: representations that result in regular geometric figures for cyclic compounds.

  • Each corner of the geometric figure represents a carbon atom.
  • Each carbon is understood to be attached to as many hydrogen atoms as needed to give it four bonds total.
  • Example: cyclopentane can be represented as a pentagon, cyclohexane as a hexagon.

🏷️ Naming cycloalkanes

🏷️ Basic naming rules

Cycloalkanes: cyclic hydrocarbons with only single bonds, named by adding the prefix "cyclo-" to the name of the open-chain compound having the same number of carbon atoms as in the ring.

  • Cyclobutane = cyclic compound with four carbon atoms (C₄H₈).
  • Cyclopentane = cyclic compound with five carbon atoms.
  • Cyclohexane = cyclic compound with six carbon atoms.

🔖 Naming with substituents

  • Cyclic compounds can have substituent groups attached.
  • Methylcyclobutane = a cyclic alkane with four carbon atoms in the ring plus a CH₃ group attached.
  • Ethylcyclohexane = a six-membered ring with an ethyl group attached.
  • Monosubstituted derivatives need no number to indicate position.
  • For disubstituted derivatives, numbering starts at one substituent (C1) and proceeds to the second by the shortest route.

⚗️ Properties and stability

⚗️ General properties

  • Cycloalkanes act very much like noncyclic alkanes in their properties.
  • Exception: cyclopropane behaves differently due to high ring strain.
  • The properties of cyclic hydrocarbons are generally quite similar to those of the corresponding open-chain compounds.

🔺 Ring strain and stability

Ring sizeStabilityReason
Cyclopropane (3 carbons)Highly strainedC–C–C angles are 60°, far from preferred 109.5° tetrahedral angle
Cyclopentane (5 carbons)Particularly stableC–C–C angles are near the preferred angles
Cyclohexane (6 carbons)Particularly stableC–C–C angles are near the preferred angles
  • Cyclopentane and cyclohexane rings have little strain.
  • Five- or six-membered rings are particularly stable structures.
  • Don't confuse: not all cycloalkanes have the same stability—smaller rings (especially three-membered) are strained, while five- and six-membered rings are stable.

🧬 Biological relevance

  • Some carbohydrates (sugars) form five- or six-membered rings in solution.
  • The stability of these ring sizes makes them common in biological molecules.

💊 Historical application

💊 Cyclopropane as anesthetic

  • Cyclopropane has a boiling point of −33°C, making it a gas at room temperature.
  • It was a potent, quick-acting anesthetic with few undesirable side effects in the body.
  • It is no longer used in surgery because it forms explosive mixtures with air at nearly all concentrations.
  • Example: Despite its medical effectiveness, safety concerns (explosive nature) led to its discontinuation in surgical use.
69

Alkenes: Structures and Names

Alkenes: Structures and Names

🧭 Overview

🧠 One-sentence thesis

Alkenes are unsaturated hydrocarbons containing carbon-carbon double bonds that follow specific IUPAC naming rules prioritizing the double bond position, and they serve as building blocks for many important industrial materials.

📌 Key points (3–5)

  • What alkenes are: hydrocarbons with carbon-to-carbon double bonds (R₂C=CR₂), making them unsaturated because they have fewer hydrogen atoms than alkanes with the same number of carbons.
  • Why they matter industrially: alkenes are highly reactive and serve as building blocks for plastics (polyethylene, vinyl, acrylics), alcohols, antifreeze, and detergents.
  • Naming priority rule: the double bond always gets the lowest number when numbering the parent chain, even if that means substituents get higher numbers.
  • Common confusion: the longest chain overall vs. the longest chain containing the double bond—always choose the longest chain that includes the double bond as the parent.
  • Cycloalkenes exist: ring compounds with double bonds, named with the prefix "cyclo-" attached to the alkene name.

🔬 What makes alkenes different

🔬 Definition and structure

Alkenes: hydrocarbons with one or more carbon-carbon double bonds.

Unsaturated hydrocarbons: alkenes or alkynes having one or more multiple (double or triple) bonds between carbon atoms.

  • Alkenes have the general formula showing they contain fewer hydrogens than alkanes with the same number of carbons.
  • The double bond is shared by two carbon atoms and does not involve hydrogen atoms.
  • Example: ethene has the formula C₂H₄, whereas ethane (the corresponding alkane) has C₂H₆.

⚗️ Reactivity and industrial importance

  • Saturated hydrocarbons (alkanes) have relatively few important chemical properties other than combustion and halogen reactions.
  • Unsaturated hydrocarbons (alkenes) are quite reactive, making them useful building blocks.
  • Ethylene (ethene) is a major commercial chemical—the US chemical industry produces about 25 billion kilograms annually, more than any other synthetic organic chemical.
  • More than half of ethylene production goes into manufacturing polyethylene plastic.
  • Propylene (propene) is converted to plastics, isopropyl alcohol, and other products.

📝 IUPAC naming rules for alkenes

📝 Rule 1: Identify the parent chain

  • The longest chain of carbon atoms containing the double bond is the parent chain.
  • Named using the same stem as the corresponding alkane but ending in -ene to identify it as an alkene.
  • Example: CH₂=CHCH₃ is propene (three carbons with a double bond).
  • Don't confuse: the longest chain overall might be different from the longest chain containing the double bond—always choose the chain with the double bond.

🔢 Rule 2: Number to give the double bond priority

  • If there are four or more carbon atoms, indicate the position of the double bond.
  • Number the carbon atoms so that the first of the two doubly bonded carbons gets the lower number.
  • Example: CH₃CH=CHCH₂CH₃ is 2-pentene (not 3-pentene), because numbering from the left gives the double bond the lower starting position.

🏷️ Rule 3: Name and number substituents

  • Substituent groups are named as with alkanes, with their position indicated by a number.
  • The double bond always has priority in numbering, even if that causes a substituent to have a higher number.
  • Example: A five-carbon chain with a double bond starting at carbon 2 and a methyl group on carbon 4 is named 4-methyl-2-pentene.

⭕ Cycloalkenes

  • Ring compounds with double bonds exist and are named like alkenes.
  • Add the prefix cyclo- to the beginning of the parent alkene name.
  • Example: A six-carbon ring with one double bond is cyclohexene.
  • The parts of the name: "cyclo" = ring compound, "hex" = 6 carbon atoms, "-ene" = double bond.

📊 Common alkenes and their properties

📊 Simple alkenes

IUPAC NameCommon NameMolecular FormulaCondensed FormulaKey Uses
EtheneEthyleneC₂H₄CH₂=CH₂Major industrial chemical; polyethylene production
PropenePropyleneC₃H₆CH₂=CHCH₃Plastics, isopropyl alcohol
  • The first two alkenes—ethene and propene—are most often called by their common names: ethylene and propylene.
  • Both have important industrial applications as building blocks for larger molecules.

🌡️ Physical properties pattern

  • As the number of carbons increases, melting and boiling points generally increase.
  • Example from the excerpt: 1-butene (4 carbons) boils at -6°C, while 1-octene (8 carbons) boils at 121°C.
  • All the simple alkenes listed have relatively low boiling points, with the smallest ones being gases at room temperature.

🎯 Worked examples and problem-solving

🎯 Naming from structure

When given a structure:

  1. Find the longest chain containing the double bond (parent chain).
  2. Number from the end that gives the double bond the lowest number.
  3. Identify and number any substituents.
  4. Assemble the name: [substituent number]-[substituent name]-[double bond position]-[parent name with -ene ending].

Example from excerpt: A five-carbon chain with a double bond between carbons 2-3 and a methyl group on carbon 4 → 4-methyl-2-pentene.

🎯 Drawing from name

When given a name like "3-methyl-2-pentene":

  1. Draw the parent chain (pentene = 5 carbons).
  2. Add the double bond at the specified position (between carbons 2 and 3).
  3. Add substituents at their specified positions (methyl on carbon 3).
  4. Add enough hydrogen atoms to give each carbon four total bonds.

Don't confuse: Make sure the double bond is in the correct position before adding substituents—the double bond position determines the numbering system for everything else.

70

Cis-Trans Isomers (Geometric Isomers)

Cis-Trans Isomers (Geometric Isomers)

🧭 Overview

🧠 One-sentence thesis

Restricted rotation around double bonds creates cis-trans isomers when each doubly bonded carbon atom has two different groups attached, resulting in compounds with permanently different spatial arrangements.

📌 Key points (3–5)

  • Why cis-trans isomerism exists: double bonds prevent rotation, making the positions of groups above or below the bond significant and permanent.
  • Two requirements for cis-trans isomers: (1) restricted rotation in the molecule, and (2) two nonidentical groups on each doubly bonded carbon atom.
  • Cis vs trans: cis means substituent groups are on the same side of the double bond or ring; trans means groups are on opposite sides.
  • Common confusion: not all double bonds create isomers—if either carbon has two identical groups (like C=CH₂ or C=CR₂ where both R are the same), cis-trans isomerism does not occur.
  • Where it occurs: both alkenes (due to double bonds) and cyclic compounds (due to restricted ring rotation) can exhibit cis-trans isomerism.

🔒 Restricted rotation and rigid structure

🔒 Free rotation in alkanes vs restricted rotation in alkenes

  • Alkanes: free rotation about carbon-to-carbon single bonds (C–C) allows different-looking structures to represent the same molecule.
  • Alkenes: the double bond structure requires that the carbon atoms of the double bond and the two atoms bonded to each carbon all lie in a single plane, with each doubly bonded carbon at the center of a triangle.
  • This planar structure is rigid; rotation about doubly bonded carbon atoms is not possible without breaking the bond.

Example: In 1,2-dichloroethane (single bond), the two structures shown can interconvert by twisting one end relative to the other—they are the same molecule, not isomers. In 1,2-dichloroethene (double bond), restricted rotation means the relative positions of chlorine atoms above or below the double bond are significant and permanent.

🔄 Why restricted rotation matters

  • Because rotation is blocked, the positions of substituent groups become fixed in space.
  • Groups permanently in different places create different configurations, leading to isomerism.
  • Don't confuse: "different-looking" structures around single bonds are the same molecule (free rotation); "different-looking" structures around double bonds can be true isomers (no rotation).

🧩 Defining cis and trans isomers

🧩 What cis-trans isomers are

Cis-trans isomers (or geometric isomers): compounds that have different configurations (groups permanently in different places in space) because of the presence of a rigid structure in their molecule.

  • The rigid structure can be a double bond or a ring.
  • These isomers have different physical, chemical, and physiological properties.

🔀 Cis vs trans configurations

TermMeaningPosition of groups
CisLatin "on this side"Two substituent groups on the same side of the double bond or ring
TransLatin "across"Two substituent groups on opposite sides of the double bond or ring

Example: In 1,2-dichloroethene, the cis isomer has both chlorine atoms on the same side of the molecule (cis-1,2-dichloroethene); the trans isomer has the two chlorine atoms on opposite sides (trans-1,2-dichloroethene).

Example: In 2-butene (CH₃CH=CHCH₃), cis-2-butene has both methyl groups on the same side of the double bond; trans-2-butene has the methyl groups on opposite sides.

✅ Two requirements for cis-trans isomerism

✅ Requirement 1: Restricted rotation

  • The molecule must have a rigid structure that prevents rotation.
  • This can be:
    • A carbon-to-carbon double bond (in alkenes)
    • A ring structure (in cycloalkanes)
  • Without restricted rotation, groups can move freely and no permanent different configurations exist.

✅ Requirement 2: Two nonidentical groups on each doubly bonded carbon

  • Both carbon atoms involved in the double bond must have two different groups attached.
  • If either carbon has two identical groups, cis-trans isomerism does not occur.

General rules for alkenes:

  • Alkenes with a C=CH₂ unit do not exist as cis-trans isomers (one carbon has two H atoms).
  • Alkenes with a C=CR₂ unit, where the two R groups are the same, do not exist as cis-trans isomers (one carbon has two identical R groups).
  • Alkenes of the type R–CH=CH–R can exist as cis and trans isomers: cis if the two R groups are on the same side of the double bond, and trans if the two R groups are on opposite sides.

🚫 When cis-trans isomerism does NOT occur

Example: Propene structures may look different on paper, but if you flip one structure top to bottom, you see they are identical. One of the doubly bonded carbon atoms has two different groups attached, but the other carbon has two hydrogen atoms—the second requirement is not fulfilled.

Example: CH₂=CBrCH₃ has two hydrogen atoms on one doubly bonded carbon; it fails the second rule and does not exist as cis-trans isomers.

Example: (CH₃)₂C=CHCH₂CH₃ has two methyl groups on one doubly bonded carbon; it fails the second rule and does not exist as cis-trans isomers.

🔁 Cis-trans isomerism in cyclic compounds

🔁 How rings create restricted rotation

  • In ring structures, groups are unable to rotate about any of the ring carbon–carbon bonds.
  • Therefore, groups can be either on the same side of the ring (cis) or on opposite sides of the ring (trans).
  • For representation, cycloalkanes are shown as planar structures, with group positions indicated as either above or below the plane of the ring.

🔁 Cis and trans in rings

  • Cis: substituent groups are on the same side of the ring plane.
  • Trans: substituent groups are on opposite sides of the ring plane.

Example: A cyclic compound can have two substituents both above the ring (cis) or one above and one below (trans).

71

Physical Properties of Alkenes

Physical Properties of Alkenes

🧭 Overview

🧠 One-sentence thesis

Alkenes have physical properties very similar to alkanes—boiling points increase with molar mass, and they are insoluble in water but soluble in organic solvents.

📌 Key points (3–5)

  • Boiling point trend: straight-chain alkenes show increasing boiling points as molar mass increases, just like alkanes.
  • Similarity to alkanes: molecules with the same number of carbon atoms and shape differ only slightly in boiling point (about 2 u difference, equivalent to two hydrogen atoms).
  • Solubility pattern: alkenes are insoluble in water but soluble in organic solvents, like other hydrocarbons.
  • Common confusion: don't assume alkenes behave differently from alkanes in physical properties—they are very similar; the double bond does not drastically change boiling points or solubility.

🌡️ Boiling point behavior

🌡️ How molar mass affects boiling points

The boiling points of straight-chain alkenes increase with increasing molar mass.

  • This trend mirrors the pattern seen in alkanes.
  • The excerpt emphasizes that this is a predictable, systematic relationship.
  • Example: ethene has a lower boiling point than propene, which is lower than 1-butene, which is lower than 1-hexene.

🔬 Comparing alkenes and alkanes with the same carbon count

  • For molecules with the same number of carbon atoms and the same general shape, boiling points differ only slightly.
  • The difference corresponds to a molar mass difference of only 2 u (two hydrogen atoms).
  • This small difference means alkenes and their corresponding alkanes have very similar boiling points.
  • Don't confuse: the presence of a double bond does not create a large boiling point difference when comparing molecules of similar size and shape.

💧 Solubility characteristics

💧 Water vs organic solvents

Like other hydrocarbons, the alkenes are insoluble in water but soluble in organic solvents.

  • Alkenes behave as typical hydrocarbons in terms of solubility.
  • They do not dissolve in water.
  • They do dissolve in organic solvents.
  • Example: cyclohexene would be soluble in pentane (an organic solvent) but not in water.

📋 Summary comparison

PropertyAlkenesComparison to alkanes
Boiling point trendIncreases with molar massSame trend as alkanes
Boiling point magnitudeSlightly different for same carbon countDiffer by only ~2 u (two H atoms)
Water solubilityInsolubleSame as alkanes
Organic solvent solubilitySolubleSame as alkanes

🔑 Key takeaway

The excerpt concludes that alkenes have physical properties (low boiling points, insoluble in water) quite similar to those of their corresponding alkanes. The double bond does not significantly alter these fundamental physical characteristics.

72

Chemical Properties of Alkenes

Chemical Properties of Alkenes

🧭 Overview

🧠 One-sentence thesis

Alkenes undergo addition reactions in which substances such as hydrogen, halogens, and water add across the carbon-to-carbon double bond, forming saturated products with single bonds.

📌 Key points (3–5)

  • What addition reactions are: reactions where substituent groups join to hydrocarbon molecules at points of unsaturation (the double or triple bonds), with the double bond breaking and the carbon atoms remaining joined by a single bond.
  • Three main addition reactions: hydrogenation (adding H₂), halogenation (adding halogens like Br₂), and hydration (adding H₂O).
  • Practical test for alkenes: bromine solutions (brownish red) lose their color when added to an alkene because the alkene reacts with the bromine.
  • Common confusion: addition reactions are the principal difference between alkenes and alkanes—alkenes undergo addition reactions, alkanes do not (though both burn).
  • Product structure: the reagent adds across the double bond, producing an alkane with the same carbon skeleton (for hydrogenation) or adding the reagent atoms to the carbon atoms that were double-bonded.

🔬 What addition reactions are

🔬 Definition and mechanism

Addition reaction: a reaction in which substituent groups join to hydrocarbon molecules at points of unsaturation—the double or triple bonds.

  • The double bond breaks during the reaction.
  • The two carbon atoms that were double-bonded remain joined to each other by a single bond.
  • New atoms or groups attach to these carbon atoms.
  • Example: an alkene with a C=C double bond becomes an alkane-like structure with a C–C single bond plus added groups.

🔍 How alkenes differ from alkanes

PropertyAlkenesAlkanes
Addition reactionsYes—undergo addition reactionsNo—do not undergo addition reactions
CombustionYes—both burnYes—both burn
  • The principal difference is that alkenes undergo addition reactions; alkanes do not.
  • Don't confuse: both types of hydrocarbons can burn, but only alkenes have the reactive double bond that allows addition reactions.

⚗️ Three main addition reactions

⚗️ Hydrogenation (adding H₂)

Hydrogenation: a reaction in which hydrogen gas reacts at a carbon-to-carbon double or triple bond or a carbon-to-oxygen double bond to add hydrogen atoms to carbon atoms.

  • Requires a catalyst such as nickel (Ni) or platinum (Pt).
  • The product is an alkane having the same carbon skeleton as the alkene.
  • The hydrogen atoms add to the carbon atoms that were double-bonded.
  • Example: the excerpt mentions this reaction is used to convert unsaturated vegetable oils to saturated fats.

🟤 Halogenation (adding halogens)

Halogenation: a reaction in which a halogen reacts at a carbon-to-carbon double or triple bond to add halogen atoms to carbon atoms.

  • Alkenes readily undergo halogenation—the addition of halogens.
  • The reaction with bromine (Br₂) can be used to test for alkenes.
  • Visual test: Bromine solutions are brownish red; when added to an alkene, the color disappears because the alkene reacts with the bromine.
  • The halogen atoms add across the double bond.
  • Example: when Br₂ adds to an alkene, two bromine atoms attach to the two carbon atoms that were double-bonded.

💧 Hydration (adding H₂O)

Hydration: the addition of water to a substance; in organic chemistry, the addition of water across the carbon-to-carbon double bond of an alkene or the carbon-to-oxygen double bond of an aldehyde or ketone.

  • The reaction between an alkene and water forms an alcohol.
  • Requires a catalyst—usually a strong acid, such as sulfuric acid (H₂SO₄).
  • Water adds across the double bond: the H and OH from water attach to the two carbon atoms.
  • Example: this reaction is used in the synthesis of alcohols.

📋 How to write addition reaction equations

📋 General pattern

  • In each reaction, the reagent adds across the double bond.
  • The double bond in the alkene becomes a single bond in the product.
  • The atoms from the reagent attach to the two carbon atoms that were double-bonded.

📋 Examples from the excerpt

The excerpt provides three worked examples with the same starting alkene (CH₃CH=CHCH₃):

ReagentCatalyst/ConditionWhat adds across the double bondProduct type
H₂Ni catalystTwo hydrogen atomsAlkane (same carbon skeleton)
Br₂None neededTwo bromine atomsDibromoalkane
H₂OH₂SO₄ catalystH and OH from waterAlcohol
  • Don't confuse: each reaction adds a different substance, but the mechanism is the same—addition across the double bond.
73

Polymers

Polymers

🧭 Overview

🧠 One-sentence thesis

Polymers are giant molecules assembled from small monomer units through polymerization reactions, with addition polymerization joining monomers containing carbon-to-carbon double bonds into chains that retain all atoms from the starting materials.

📌 Key points (3–5)

  • What polymers are: giant molecules built from small repeating units called monomers, as different from their monomers as spaghetti is from flour.
  • Addition polymerization mechanism: monomers add together so the polymer contains all atoms of the starting monomers; requires carbon-to-carbon double bonds.
  • Key structural feature: monomers used in addition polymerization characteristically have carbon-to-carbon double bonds.
  • Common confusion: don't confuse the two polymerization types—addition polymerization retains all monomer atoms, while condensation polymerization (mentioned but not detailed) works differently.
  • Real-world importance: over half of chemical industry compounds are synthetic polymers, used in everything from plastic bags to medical implants.

🔬 Core concepts

🧱 Monomers and polymers defined

Monomer: a small molecule that can be combined with other small molecules to make polymers (from Greek monos = "one" and meros = "parts").

Polymer: a giant molecule formed by the combination of monomers in a repeating manner (from Greek poly = "many" and meros = "parts").

  • The difference in scale is dramatic: polyethylene (waxy plastic bag material) is made from ethylene gas.
  • Polymer molecules are much larger than typical small organic molecules discussed in earlier chemistry contexts.
  • Example: A polymer formed from 175 vinyl chloride molecules (CH₂=CHCl) has the molecular formula C₃₅₀H₅₂₅Cl₁₇₅.

⚗️ Addition polymerization mechanism

Addition polymerization: a reaction in which monomers add to one another to produce a polymeric product that contains all the atoms of the starting monomers.

  • Monomers join together in long chains.
  • All atoms (every carbon and hydrogen) from each monomer are incorporated into the polymer structure.
  • The general representation: n CH₂=CH₂ → [CH₂CH₂]ₙ, where n represents many repeating units.
  • Bond lines extending at the ends of structural formulas indicate the structure continues for many units in each direction.

🔗 Structural requirements

🎯 The double bond requirement

  • All monomers suitable for addition polymerization have carbon-to-carbon double bonds.
  • This is the characteristic structural feature that enables addition polymerization.
  • The double bond opens up during polymerization, allowing monomers to link together.

📋 Common addition polymers

The excerpt provides a table of examples:

MonomerPolymer NameCommon Uses
CH₂=CH₂ (ethylene)PolyethylenePlastic bags, bottles, toys, electrical insulation
CH₂=CHCH₃ (propylene)PolypropyleneCarpeting, bottles, luggage, exercise clothing
CH₂=CHCl (vinyl chloride)Polyvinyl chlorideIV solution bags, pipes, tubing, floor coverings
CF₂=CF₂PolytetrafluoroethyleneNonstick coatings, electrical insulation

🌍 Scope and applications

🏭 Industrial significance

  • More than half the compounds produced by the chemical industry are synthetic polymers.
  • Polymers range from mundane items (plastic bags, food wrap, toys, tableware) to advanced materials.
  • Some polymers conduct electricity, have exceptional adhesive properties, or are stronger than steel but much lighter.

🏥 Medical applications

  • Replacement of diseased, worn out, or missing body parts.
  • Approximately 250,000 hip joints and 500,000 knees replaced annually in US hospitals.
  • Artificial hip joints use special steel (ball) and plastic (socket) components.
  • Heart valve replacements based on synthetic polymers help patients with circulatory problems.
  • These applications provide freedom of movement and pain relief for patients crippled by arthritis or injuries.

🌿 Natural vs synthetic

  • Many natural materials are polymers: proteins, cellulose, starch, and complex silicate minerals.
  • Artificial polymers include fibers, films, plastics, semisolid resins, and rubbers.
  • Both natural and synthetic polymers share the fundamental structure of repeating monomer units.
74

Alkynes

Alkynes

🧭 Overview

🧠 One-sentence thesis

Alkynes are unsaturated hydrocarbons with a carbon-to-carbon triple bond, and their properties and naming conventions closely resemble those of alkenes.

📌 Key points (3–5)

  • What alkynes are: hydrocarbons containing a carbon-to-carbon triple bond.
  • General formula: C_n H_(2n − 2), which distinguishes them from alkenes (C_n H_2n).
  • Properties: quite similar to alkenes in behavior and reactivity.
  • Naming convention: named much like alkenes but with the ending -yne instead of -ene.
  • Common confusion: alkynes vs alkenes—both are unsaturated, but alkynes have a triple bond (and two fewer hydrogens per carbon count) while alkenes have a double bond.

🔬 Definition and structure

🔬 What alkynes are

Alkynes: hydrocarbons that have a carbon-to-carbon triple bond.

  • They belong to the broader category of unsaturated hydrocarbons (any hydrocarbon containing either a double or triple bond).
  • The triple bond is the defining structural feature.
  • Example: a molecule with two carbon atoms connected by three shared electron pairs is an alkyne.

🧮 General formula

  • The general formula for alkynes is C_n H_(2n − 2).
  • This means for n carbon atoms, there are 2n − 2 hydrogen atoms.
  • Comparison with alkenes:
Hydrocarbon typeBond typeGeneral formula
AlkenesCarbon-to-carbon double bondC_n H_2n
AlkynesCarbon-to-carbon triple bondC_n H_(2n − 2)
  • The alkyne formula has two fewer hydrogens than the alkene formula for the same number of carbons, reflecting the additional bond.

🧪 Properties and behavior

🧪 Similarity to alkenes

  • The excerpt states that "the properties of alkynes are quite similar to those of alkenes."
  • This means alkynes likely share:
    • Similar physical properties (e.g., solubility patterns).
    • Similar reactivity patterns (though the excerpt does not detail specific reactions for alkynes).
  • Don't confuse: similar properties do not mean identical structure—the triple bond vs. double bond distinction remains fundamental.

🏷️ Nomenclature

🏷️ Naming system

  • Alkynes are "named much like alkenes but with the ending -yne."
  • The naming follows the International Union of Pure and Applied Chemistry (IUPAC) system.
  • The suffix change signals the bond type:
    • Alkenes end in -ene (double bond).
    • Alkynes end in -yne (triple bond).
  • Example: if an alkene is named "ethene," the corresponding alkyne (with a triple bond) would be "ethyne."

🔍 How to distinguish in naming

  • When you see a hydrocarbon name:
    • Ending in -yne → triple bond → alkyne.
    • Ending in -ene → double bond → alkene.
    • Ending in -ane → no double or triple bonds → alkane (saturated).
75

Aromatic Compounds: Benzene

Aromatic Compounds: Benzene

🧭 Overview

🧠 One-sentence thesis

Benzene and aromatic hydrocarbons, despite appearing highly unsaturated, are unusually stable and do not readily undergo the addition reactions typical of alkenes because their electrons are delocalized equally across all six carbon atoms.

📌 Key points (3–5)

  • What makes benzene special: molecular formula C₆H₆ suggests high unsaturation, but benzene is remarkably unreactive compared to alkenes.
  • Bonding structure: benzene has a cyclic, hexagonal, planar structure where valence electrons are delocalized (spread equally) over all six carbon atoms.
  • Common confusion: benzene looks unsaturated (like alkenes) but does not readily undergo addition reactions—it behaves very differently from alkenes.
  • Representation: chemists draw benzene as a hexagon with an inscribed circle to show electron delocalization, not as alternating single and double bonds.
  • Health and uses: benzene is commercially important for plastics, drugs, and detergents, but is a known carcinogen causing aplastic anemia with repeated exposure.

🔬 Benzene's unusual behavior

🔬 Expected vs actual reactivity

  • The formula C₆H₆ suggests benzene should be highly unsaturated (compare to hexane, C₆H₁₄, which has eight more hydrogen atoms).
  • Despite this apparent unsaturation, benzene is rather unreactive.
  • Key difference from alkenes: benzene does not readily react with bromine, which is a standard test for unsaturation in alkenes.
  • Example: an alkene would quickly undergo addition with bromine, but benzene does not.

🧪 Why benzene is stable

  • Experimental evidence shows all carbon-to-carbon bonds in benzene are equivalent (the same length and strength).
  • The molecule is unusually stable compared to what would be expected from a structure with alternating single and double bonds.
  • This stability comes from the special bonding arrangement described below.

🔗 Bonding structure in benzene

🔗 Physical structure

Benzene has a cyclic, hexagonal, planar structure of six carbon atoms with one hydrogen atom bonded to each.

  • Each corner of the hexagon is occupied by one carbon atom.
  • Each carbon atom has one hydrogen atom attached to it.
  • The molecule is flat (planar).

⚡ Electron delocalization

Delocalized electrons: valence electrons that are shared equally by all six carbon atoms, spread out over all the carbon atoms rather than localized between pairs of atoms.

  • The six valence electrons are not confined to alternating double bonds.
  • Instead, they are distributed equally across all six carbon atoms.
  • This equal sharing makes all carbon-to-carbon bonds equivalent.
  • Don't confuse: although we can draw benzene with alternating single and double bonds, this does not accurately represent the true electron distribution.

🖼️ How chemists represent benzene

Chemists use two representations:

RepresentationDescriptionAccuracy
Alternating bondsHexagon with alternating single and double bondsOlder; still used but less accurate
Circle inside hexagonHexagon with inscribed circleModern; the circle shows electron delocalization
  • The inscribed circle indicates that valence electrons are shared equally by all six carbon atoms.
  • It is understood that each corner has one carbon and one hydrogen (unless another atom or group is explicitly shown).
  • Any substituent (atom or group replacing hydrogen) must be shown bonded to a particular corner.

🏭 Properties and significance

🏭 Physical properties

  • Benzene is a liquid that smells like gasoline.
  • Boils at 80°C.
  • Freezes at 5.5°C.
  • It is the aromatic hydrocarbon produced in the largest volume.

🏭 Commercial uses

Benzene is a precursor for producing:

  • Plastics (Styrofoam, nylon)
  • Drugs
  • Detergents
  • Synthetic rubber
  • Pesticides
  • Dyes

Also used as:

  • A solvent for cleaning and maintaining printing equipment
  • A solvent for adhesives (e.g., attaching soles to shoes)
  • A natural constituent of petroleum products

⚠️ Health hazards

Aplastic anemia: a condition in which the bone marrow's ability to make new blood cells is destroyed, resulting in decreased numbers of both red and white blood cells.

Short-term exposure:

  • Inhalation of large concentrations can cause nausea.
  • Can cause death due to respiratory or heart failure.

Long-term exposure:

  • Repeated exposure leads to a progressive disease.
  • Eventually destroys the bone marrow's ability to make new blood cells.
  • Results in aplastic anemia.

Historical context:

  • Formerly used to decaffeinate coffee.
  • Was in many consumer products: paint strippers, rubber cements, home dry-cleaning spot removers.
  • Removed from many products in the 1950s, others in the 1970s when associated with leukemia deaths.
  • Now recognized as a known carcinogen.
  • Its use as a gasoline additive is now limited.

🔑 Defining aromatic compounds

🔑 What "aromatic" means

Aromatic compound: any compound that contains a benzene ring or has certain benzene-like properties (but not necessarily a strong aroma).

  • Historical origin: benzene-like substances were originally called "aromatic" because they had distinctive aromas.
  • Modern definition: the term now refers to structural and chemical properties, not smell.
  • You can recognize aromatic compounds by the presence of one or more benzene rings in their structure.

🔑 How aromatic compounds differ from other unsaturated hydrocarbons

  • Aromatic hydrocarbons have molecular formulas like those of unsaturated hydrocarbons.
  • Unlike alkenes, they do not readily undergo addition reactions.
  • They comprise a distinct class with unique structures and properties.
  • The key feature is the special type of bonding (electron delocalization) rather than simple double bonds.
76

Structure and Nomenclature of Aromatic Compounds

Structure and Nomenclature of Aromatic Compounds

🧭 Overview

🧠 One-sentence thesis

Aromatic compounds are identified by the presence of a benzene ring and are named systematically using IUPAC rules that account for substituent positions, though many also retain historical common names.

📌 Key points (3–5)

  • What makes a compound aromatic: contains a benzene ring or has benzene-like properties (not necessarily a strong aroma despite the historical name).
  • How to recognize aromatic compounds: look for one or more benzene rings in the structure, represented as C₆H₅ when a substituent is attached.
  • Naming system: aromatic hydrocarbons are named as derivatives of benzene, with substituents named and numbered; positions can be indicated by numbers (1,2- etc.) or prefixes (ortho-, meta-, para-).
  • Common confusion: not all cyclic compounds are aromatic—only those with a benzene ring qualify; a compound can be cyclic without being aromatic.
  • Special groups: when a benzene ring acts as a substituent, it forms an aryl group (most commonly the phenyl group, C₆H₅).

🔍 Recognizing aromatic compounds

🔍 Definition and identification

Aromatic compound: any compound that contains a benzene ring or has certain benzene-like properties.

  • Historically called "aromatic" because benzene-like substances had distinctive aromas.
  • Today the term does not require a strong smell—it is a structural classification.
  • Key recognition rule: look for the benzene ring structure in the compound.

⚠️ Aromatic vs cyclic

The excerpt emphasizes that not all rings are aromatic:

  • A compound can be cyclic (ring-shaped) but not aromatic if it lacks a benzene ring.
  • Example from the excerpt: several cyclic structures were shown, but only those containing the benzene ring pattern were classified as aromatic.
  • Don't confuse: cyclic structure ≠ aromatic structure; aromatic specifically requires the benzene ring.

📛 Naming aromatic compounds

📛 IUPAC system basics

In the IUPAC system, aromatic hydrocarbons are named as derivatives of benzene:

  • The benzene ring is the parent structure.
  • Substituents replace hydrogen atoms and are named accordingly:
    • Cl → chloro
    • Br → bromo
    • I → iodo
    • NO₂ → nitro
    • CH₃CH₂ → ethyl
  • For a single substituent, position doesn't matter because the hexagon is symmetrical (all positions are equivalent).

🔢 Numbering for multiple substituents

When there is more than one substituent, position matters:

  • Numbering rule: start at the carbon bearing one substituent and count toward the other by the shortest path.
  • Three disubstitution patterns:
    • 1,2-disubstitution = ortho (o-)
    • 1,3-disubstitution = meta (m-)
    • 1,4-disubstitution = para (p-)
  • Substituent names are listed in alphabetical order.
  • The first substituent gets the lowest number.

🏷️ Common names

Some compounds use common names more frequently than IUPAC names:

  • When a common name is used, the carbon bearing the group responsible for that name is numbered as position 1.
  • Example from the excerpt: toluene (benzene with a methyl group) is a common name; other substituents are then numbered relative to the methyl group.
Position prefixNumber notationMeaning
ortho (o-)1,2-Adjacent positions
meta (m-)1,3-One carbon between
para (p-)1,4-Opposite positions

🧬 Special aromatic groups and structures

🧬 Aryl and phenyl groups

Aryl group: the group of atoms remaining when a hydrogen atom is removed from an aromatic compound.

  • The most common aryl group is the phenyl group (C₆H₅).
  • Derived from benzene (C₆H₆) by removing one hydrogen atom.
  • The name comes from "pheno," an old name for benzene.
  • When it appears: when an aromatic group is bonded to a nonaromatic entity or to another aromatic ring.

🔗 Polycyclic aromatic hydrocarbons (PAHs)

Polycyclic aromatic hydrocarbons (PAHs): aromatic hydrocarbons consisting of fused benzene rings that share a common side.

  • Examples mentioned: naphthalene, anthracene, phenanthrene.
  • These are colorless, crystalline solids generally obtained from coal tar.
  • Naphthalene has a pungent odor and is used in mothballs.
  • Health note: many PAHs are carcinogens; benzopyrene (found in coal tar, cigarette smoke, automobile exhaust) is a particularly active carcinogenic compound.

🌿 Biological and practical significance

🌿 Natural occurrence

Aromatic compounds are common in both plants and animals:

  • Plants can synthesize the benzene ring from carbon dioxide, water, and inorganic materials.
  • Animals cannot synthesize it but depend on certain aromatic compounds for survival (must obtain from food).
  • Essential amino acids containing benzene rings: phenylalanine, tyrosine, tryptophan.
  • Vitamins with benzene rings: K, B₂ (riboflavin), B₉ (folic acid).

💊 Pharmaceutical applications

Many important drugs contain a benzene ring:

  • Examples listed in the excerpt: aspirin, acetaminophen, ibuprofen, amphetamine, sulfanilamide.
  • The benzene ring is a common structural feature in medicinal chemistry.

⚠️ Health concerns

The excerpt notes specific health risks:

  • Workers in coal-tar refineries are susceptible to tar cancer (a type of skin cancer).
  • Benzopyrene requires only a few milligrams per kilogram of body weight to induce cancer in experimental animals.
  • More than 1,000 tons of benzopyrene are estimated to be emitted into the air over the United States each year.
77

Organic Compounds with Functional Groups

Organic Compounds with Functional Groups

🧭 Overview

🧠 One-sentence thesis

Functional groups—specific structural arrangements of atoms or bonds—determine the characteristic chemical reactivity and properties of entire families of organic compounds, making it possible to predict behavior across many molecules by understanding just a few key structural patterns.

📌 Key points (3–5)

  • What a functional group is: a specific structural arrangement of atoms or bonds that imparts characteristic chemical reactivity to a molecule.
  • Why functional groups matter: understanding one functional group means knowing the general properties of an entire class of compounds.
  • Families covered: oxygen-containing families (alcohols, ethers, aldehydes, ketones, carboxylic acids) and some nitrogen-containing families.
  • Common confusion: not all organic compounds have functional groups—simple hydrocarbons with only carbon, hydrogen, and single bonds (like long-chain alkanes) have no functional group.
  • How to identify: look for the characteristic structural feature (e.g., –OH for alcohols, C=C for alkenes, –O– for ethers).

🔬 What functional groups are

🔬 Definition and role

Functional group: a specific structural arrangement of atoms or bonds that imparts a characteristic chemical reactivity to the molecule.

  • It is not just "any group of atoms"—it must be a recognizable pattern that controls how the molecule behaves chemically.
  • The functional group is largely responsible for the properties of organic compound families.
  • Example: if you understand the –OH group's behavior, you understand alcohols in general, regardless of the rest of the molecule's structure.

🧩 General formula notation

  • Organic chemists use R to represent an alkyl group (the hydrocarbon part).
  • General formula ROH means "any alkyl group attached to a hydroxyl group."
  • This notation emphasizes that the functional group (–OH) is what matters; the R part can vary.

🗂️ Major functional group families

🗂️ Overview of families

The excerpt introduces families based on oxygen or nitrogen atoms. Key oxygen-containing families include:

FamilyGeneral FormulaFunctional GroupName Suffix
AlkaneRHnone-ane
AlkeneR₂C=CR₂C=C-ene
AlkyneRC≡CR–C≡C–-yne
AlcoholROH–OH-ol
ThiolRSH–SH-thiol
EtherROR–O–ether*
Aldehyde(structure not fully shown)(carbonyl-related)-al
Ketone(structure not fully shown)(carbonyl-related)-one
Carboxylic acid(structure not fully shown)(carboxyl-related)-oic acid

*Note: Ethers do not have a suffix in their common name; all ethers end with the word "ether."

🍷 Context: oxygen-containing compounds

  • The excerpt mentions ethanol (in wine) and resveratrol (a phenol, in grapes) as real-world examples.
  • Aldehydes and ketones are formed by oxidation of alcohols.
  • Ethers are made by dehydration of alcohols.
  • These relationships show that functional groups can be transformed into one another through chemical reactions.

🔍 Recognizing functional groups

🔍 Hydrocarbons vs. functional-group compounds

  • Hydrocarbons with only single bonds (e.g., CH₃CH₂CH₂CH₂CH₂CH₂CH₂CH₂CH₂CH₂CH₃) have no functional group.
  • They contain nothing but carbon and hydrogen atoms and all single bonds.
  • Don't confuse: alkenes (C=C) and alkynes (C≡C) do have functional groups, even though they are still hydrocarbons.

🧪 How to identify

  • Look for the characteristic structural feature listed in the table.
  • Example: 1-butanol (CH₃CH₂CH₂CH₂OH) has the –OH group → it is an alcohol.
  • Example: butyl bromide (CH₃CH₂CH₂CH₂Br) has a halogen (Br) attached → it is a halogenated hydrocarbon (not covered in this oxygen-focused chapter).

🎯 Why functional groups are useful

🎯 Predictive power

  • If you understand the behavior of a particular functional group, you know a great deal about the general properties of that class of compounds.
  • This makes studying organic chemistry systematic: instead of memorizing thousands of individual molecules, you learn a few functional groups and apply that knowledge broadly.

🧭 Organization of study

  • The excerpt organizes families by functional group: each family shares a common, simple functional group containing an oxygen or nitrogen atom.
  • This chapter and the next make a "brief yet systematic study" of these families.
  • The approach: learn the functional group → understand the family → predict reactivity and properties.
78

Alcohols: Nomenclature and Classification

Alcohols: Nomenclature and Classification

🧭 Overview

🧠 One-sentence thesis

Alcohols are named systematically by changing the parent alkane ending to "-ol" and are classified as primary, secondary, or tertiary based on how many carbon atoms are attached to the carbon bearing the OH group.

📌 Key points (3–5)

  • What alcohols are: organic compounds with a hydroxyl (OH) functional group on an aliphatic carbon atom, represented by the general formula ROH.
  • IUPAC naming rules: identify the longest continuous chain containing the OH group, number from the end nearest the OH, replace the "-e" ending of the parent alkane with "-ol," and prefix the position number.
  • Classification system: primary (1°) alcohols have the OH carbon attached to one other carbon; secondary (2°) to two; tertiary (3°) to three.
  • Common confusion: the classification depends on the carbon atom bearing the OH group, not on the total number of carbons in the molecule.
  • Common vs IUPAC names: simple alcohols (one to four carbons) are often called by common names (alkyl group + "alcohol"), but IUPAC names follow systematic rules.

🏗️ Structure and general formula

🏗️ What defines an alcohol

Alcohol: an organic compound with a hydroxyl (OH) functional group on an aliphatic carbon atom.

  • The OH group is the functional group of all alcohols.
  • General formula: ROH, where R is an alkyl group.
  • Example: ethanol (CH₃CH₂OH) is the active ingredient in alcoholic beverages; methanol (CH₃OH) and ethanol are the first two members of the homologous series of alcohols.

🔗 Relationship to other compounds

  • Alcohols are common in nature and include familiar substances like cholesterol and carbohydrates.
  • The excerpt notes that alcohols can be considered derivatives of water (H₂O).

📝 Naming alcohols

📝 Common names

  • Used for alcohols with one to four carbon atoms.
  • Format: name of the alkyl group + the word "alcohol."
  • Example: CH₃OH is methyl alcohol; CH₃CH₂OH is ethyl alcohol.
  • The excerpt notes that ethers do not have a suffix in their common name; all ethers end with the word "ether."

📝 IUPAC naming rules

The International Union of Pure and Applied Chemistry (IUPAC) provides systematic rules:

  1. Identify the longest continuous chain (LCC) containing the OH group as the parent alkane.
  2. Number the chain from the end nearest the OH group.
  3. Replace the "-e" ending of the parent alkane with "-ol".
  4. Prefix the position number of the OH group to the name.
  5. Name and number substituents as in alkanes.

📝 Special cases

  • Cyclic alcohols: the carbon atom bearing the OH group is designated C1, but the "1" is not used in the name.
  • Polyhydroxy alcohols (more than one OH group): use suffixes like "-diol" and "-triol"; retain the "-e" ending of the parent alkane.

📝 Naming examples from the excerpt

StructureIUPAC NameExplanation
10-carbon chain, OH on C3, methyl groups on C6 and C86,8-dimethyl-3-decanolLCC is decane; OH on position 3; substituents numbered from OH end
HOCH₂CH₂CH₂CH₂CH₂OH1,5-pentanediol5-carbon LCC (pentane); two OH groups on positions 1 and 5
6-carbon chain, OH on C22-hexanolLCC is hexane; OH on position 2
5-carbon chain, OH on C2, methyl on C33-methyl-2-pentanolLCC is pentane; OH on position 2; methyl substituent on position 3

Don't confuse: When numbering, always start from the end nearest the OH group, not from the end that would give substituents lower numbers.

Example: In 6,8-dimethyl-3-decanol, the correct name is NOT 3,5-dimethyl-8-decanol, because numbering must prioritize the OH group position.

🔢 Classification of alcohols

🔢 The three classes

Alcohols are grouped into three classes based on the number of carbon atoms attached to the specific carbon atom that bears the OH group:

ClassDefinitionGeneral FormulaKey Feature
Primary (1°)The carbon with OH is attached to one other carbonRCH₂OHOH carbon has 1 carbon neighbor
Secondary (2°)The carbon with OH is attached to two other carbonsR₂CHOHOH carbon has 2 carbon neighbors
Tertiary (3°)The carbon with OH is attached to three other carbonsR₃COHOH carbon has 3 carbon neighbors

🔢 How to classify

  • Look at the carbon atom bearing the OH group (not the total molecule).
  • Count how many other carbon atoms are directly bonded to that carbon.
  • Example: isobutyl alcohol [(CH₃)₂CHCH₂OH] is primary because the carbon bearing the OH is attached to only one other carbon atom.

🔢 Common name designations

  • Some common names reflect classification: sec- (secondary) or tert- (tertiary).
  • Example: sec-butyl alcohol, tert-butyl alcohol.
  • Don't confuse: These designations (sec-, tert-) are not used in the IUPAC nomenclature system for alcohols.

🔢 Examples of classification

CompoundCommon NameIUPAC NameClass
CH₃OHmethyl alcoholmethanol
CH₃CH₂OHethyl alcoholethanolprimary
CH₃CH₂CH₂OHpropyl alcohol1-propanolprimary
(CH₃)₂CHOHisopropyl alcohol2-propanolsecondary
CH₃CH₂CH₂CH₂OHbutyl alcohol1-butanolprimary
CH₃CH₂CHOHCH₃sec-butyl alcohol2-butanolsecondary
(CH₃)₂CHCH₂OHisobutyl alcohol2-methyl-1-propanolprimary
(CH₃)₃COHtert-butyl alcohol2-methyl-2-propanoltertiary
cyclohexyl alcohol (cyclic)cyclohexyl alcoholcyclohexanolsecondary

🔢 The four butyl alcohols

The excerpt notes there are four butyl alcohols, corresponding to four different butyl groups:

  • butyl group: CH₃CH₂CH₂CH₂–
  • Three other variations (isobutyl, sec-butyl, tert-butyl) based on branching and OH position.

🔍 Key distinctions and common confusions

🔍 LCC selection

  • The longest continuous chain (LCC) must contain the OH group.
  • Example: In 2-ethyl-1-hexanol, the actual longest chain has 7 carbon atoms, but the 6-atom chain is taken as the LCC because it includes the carbon atom bearing the OH group.
  • Don't confuse: The LCC is not always the absolute longest chain in the molecule; it is the longest chain that includes the OH group.

🔍 Classification vs. total carbons

  • Classification (primary, secondary, tertiary) depends on the carbon bearing the OH group, not the total number of carbons in the molecule.
  • Example: isobutyl alcohol has four carbons total but is classified as primary because the OH-bearing carbon is attached to only one other carbon.

🔍 Common names vs. IUPAC names

  • Common names are simpler for small alcohols (1–4 carbons) but do not scale well.
  • IUPAC names are systematic and work for any size molecule.
  • The excerpt shows both naming systems side by side in tables for comparison.
79

Physical Properties of Alcohols

Physical Properties of Alcohols

🧭 Overview

🧠 One-sentence thesis

Alcohols have significantly higher boiling points than hydrocarbons of similar size and show decreasing water solubility as their carbon chain lengthens, both due to the hydrogen-bonding capability of the OH group.

📌 Key points (3–5)

  • Why alcohols have high boiling points: the OH group enables hydrogen bonding between alcohol molecules, raising boiling points compared to ethers and alkanes of similar molar mass.
  • Water solubility pattern: alcohols with 1–3 carbons are completely soluble in water; solubility decreases as the chain lengthens; alcohols with 4–5+ carbons become essentially insoluble.
  • The role of hydrogen bonding: alcohols can hydrogen-bond both with each other (raising boiling points) and with water molecules (enabling solubility).
  • Common confusion: longer carbon chains make alcohols more hydrocarbon-like and less water-like, so don't assume all alcohols dissolve in water equally.
  • The borderline: solubility in water typically drops sharply at four or five carbon atoms in a family of organic compounds.

🔥 Boiling Points of Alcohols

🔥 Why alcohols boil at higher temperatures

The OH group allows alcohol molecules to engage in hydrogen bonding.

  • Hydrogen bonding is an intermolecular force stronger than the forces in ethers or alkanes.
  • This stronger attraction between molecules requires more energy (higher temperature) to break, so alcohols boil at higher temperatures.
  • Example: methanol (molar mass 32) boils at 65 °C, while ethane (molar mass 30) boils at –89 °C—despite similar molar masses, the alcohol boils much higher.

📊 Comparison with hydrocarbons and water

The excerpt provides a table comparing molar masses and boiling points:

FormulaNameMolar MassBoiling Point (°C)
CH₄methane16–164
HOHwater18100
C₂H₆ethane30–89
CH₃OHmethanol3265
C₃H₈propane44–42
CH₃CH₂OHethanol4678
C₄H₁₀butane58–1
CH₃CH₂CH₂OH1-propanol6097
  • Notice: alcohols consistently boil at much higher temperatures than alkanes of similar or even slightly higher molar mass.
  • The pattern holds across the series: as molar mass increases, boiling point increases, but the alcohol always outpaces the hydrocarbon.

🔗 Intermolecular hydrogen bonding mechanism

  • The excerpt shows that methanol molecules form hydrogen bonds with each other through their OH groups.
  • This intermolecular attraction is the key structural reason for elevated boiling points.
  • Don't confuse: this is hydrogen bonding between alcohol molecules, not with water (that comes into play for solubility).

💧 Water Solubility of Alcohols

💧 Why small alcohols dissolve in water

Alcohols can engage in hydrogen bonding with water molecules.

  • Water is a polar molecule with OH groups; alcohols also have OH groups.
  • Hydrogen bonding between alcohol OH and water OH allows the alcohol to mix with water.
  • Hydrocarbons cannot form hydrogen bonds, so they are insoluble in water.

📏 The effect of carbon chain length

  • Short chains (1–3 carbons): completely soluble in water.
    • Example: ethanol (2 carbons) is fully soluble because the OH group dominates the molecule's character.
  • Longer chains (4–5+ carbons): solubility decreases sharply.
    • The molecules become "more like hydrocarbons and less like water."
    • Example: 1-decanol (10 carbons, formula CH₃CH₂CH₂CH₂CH₂CH₂CH₂CH₂CH₂CH₂OH) is essentially insoluble in water.
  • The borderline: the excerpt states that solubility typically drops at four or five carbon atoms in a family of organic compounds.

🔄 Comparing ethanol and 1-hexanol

The excerpt provides a concept review question:

  • Why is ethanol more soluble than 1-hexanol?
    • Ethanol has one OH group and only 2 carbon atoms.
    • 1-hexanol has one OH group for 6 carbon atoms, so it is more like a nonpolar hydrocarbon.
    • The longer hydrocarbon chain in 1-hexanol overwhelms the polar OH group, reducing water solubility.

🧪 Hydrogen bonding with water molecules

  • The excerpt shows a figure illustrating hydrogen bonding between methanol molecules and water molecules.
  • This interaction accounts for methanol's solubility in water.
  • Don't confuse: the same OH group that causes high boiling points (by bonding alcohol to alcohol) also causes water solubility (by bonding alcohol to water).

🔬 Comparing Related Compounds

🔬 Molar mass and boiling point relationship

The excerpt provides another concept review question:

  • Why does 1-butanol have a lower boiling point than 1-hexanol?
    • The molar mass of 1-hexanol is greater than that of 1-butanol.
    • Larger molecules have more surface area and stronger van der Waals forces, in addition to hydrogen bonding.
    • So even within the alcohol family, boiling point increases with chain length.

🧩 Ordering alcohols by properties

The excerpt includes exercises (with answers) that reinforce the patterns:

  • Boiling point order: methanol < ethanol < 1-propanol
    • Increasing molar mass → increasing boiling point.
  • Solubility order: 1-octanol < 1-butanol < methanol
    • Increasing carbon chain → decreasing solubility in water.
  • Comparing alcohol to hydrocarbon: 1-propanol has a higher boiling point than butane (despite similar molar mass), because the alcohol can hydrogen-bond.
  • Comparing alcohol to alkane: 1-butanol and ethanol are both more soluble in water than pentane, because alcohols hydrogen-bond with water while alkanes do not.

🔑 Key Takeaways from the Excerpt

🔑 Summary of alcohol properties

The excerpt provides two key takeaways:

  1. Boiling points: Alcohols have higher boiling points than ethers and alkanes of similar molar masses because the OH group allows alcohol molecules to engage in hydrogen bonding.
  2. Solubility: Alcohols of four or fewer carbon atoms are soluble in water because the alcohol molecules engage in hydrogen bonding with water molecules; comparable alkane molecules cannot engage in hydrogen bonding.

⚠️ What to remember

  • The OH group is the defining feature: it enables both intermolecular hydrogen bonding (raising boiling points) and hydrogen bonding with water (enabling solubility).
  • As the hydrocarbon portion of the molecule grows, the nonpolar character dominates and solubility in water drops.
  • The borderline for water solubility is typically around four or five carbons.
80

Reactions That Form Alcohols

Reactions That Form Alcohols

🧭 Overview

🧠 One-sentence thesis

Alcohols can be synthesized industrially through hydration of alkenes or fermentation of sugars, and these preparation methods are fundamental to producing both simple alcohols like methanol and ethanol as well as more complex biological alcohols.

📌 Key points (3–5)

  • Methanol synthesis: produced by combining hydrogen gas and carbon monoxide at high temperatures and pressures with a metal oxide catalyst.
  • Alkene hydration: many simple alcohols are made by adding water to alkenes in the presence of an acid catalyst (e.g., sulfuric acid or phosphoric acid).
  • Fermentation route: ethanol is uniquely made by enzyme-catalyzed fermentation of sugars or starch from plant sources.
  • Common confusion: ethanol can be prepared two ways—from ethylene (industrial hydration) or from sugars (fermentation)—but methanol cannot be made from an alkene.
  • Biological relevance: alkene hydration reactions occur continuously in cellular metabolism (e.g., Krebs cycle), catalyzed by enzymes at body temperature.

🏭 Industrial synthesis methods

⚗️ Methanol from synthesis gas

Methanol is prepared by combining hydrogen gas and carbon monoxide at high temperatures and pressures in the presence of a zinc oxide (ZnO) and chromium oxide (Cr₂O₃) catalyst.

  • The reaction: 2H₂ + CO → CH₃OH (at 200 atm, 350°C, with ZnO/Cr₂O₃ catalyst).
  • Nearly 2 billion gallons of methanol are produced each year in the United States by this catalytic reduction.
  • Uses: methanol is an important solvent and automotive fuel (pure liquid in racing cars or as a gasoline additive).
  • Key point: this is the only preparation method mentioned for methanol; it cannot be made from an alkene because it has only one carbon atom.

💧 Hydration of alkenes

Many simple alcohols are made by the hydration of alkenes—adding water to the carbon-carbon double bond.

  • General process: an alkene reacts with water in the presence of an acid catalyst (sulfuric acid H₂SO₄ or phosphoric acid H₃PO₄).
  • The OH group and a hydrogen atom are added across the double bond.
  • Example: ethanol is made by hydrating ethylene (CH₂=CH₂) with H₂SO₄ as catalyst.
  • Example: isopropyl alcohol is produced by adding water to propene (propylene).
  • Example: 2-butene + water → 2-butanol (with H₂SO₄ catalyst).

🔄 Writing hydration equations

Step-by-step approach (from Example 3):

  1. Write the condensed structural formula of the alkene.
  2. Indicate that it reacts with water.
  3. Write the condensed structural formula of the alcohol product after the reaction arrow.
  4. Write the catalyst formula above the arrow.

Don't confuse: the catalyst (e.g., H₂SO₄) is written above the arrow, not as a reactant; it speeds up the reaction but is not consumed.

🌾 Fermentation of ethanol

🍞 Biological production

Ethanol is made by the fermentation of sugars or starch from various sources (potatoes, corn, wheat, rice, etc.).

  • Fermentation is catalyzed by enzymes found in yeast.
  • The process proceeds by an elaborate multistep mechanism (details not provided in the excerpt).
  • The overall process can be represented as converting sugars/starch to ethanol (simplified equation not shown in full).
  • Key distinction: ethanol has two preparation routes (hydration of ethylene or fermentation), but methanol cannot be made by fermentation.

🧬 Biological alcohol formation

🔁 Metabolic hydration reactions

  • Many OH compounds in living systems are formed by alkene hydration.
  • Example from the Krebs cycle: fumarate is hydrated to form malate.
  • These reactions occur continuously in cellular metabolism.
  • Enzymes serve as catalysts at body temperature (about 37°C), not the high temperatures used industrially.
  • Principle: dehydration and hydration reactions are reversible and occur constantly in metabolism.

☠️ Toxicity and physiological effects

🧪 Methanol toxicity

  • Methanol is quite poisonous to humans.
  • As little as 15 mL can cause blindness; 30 mL (1 oz) can cause death; usual fatal dose is 100–150 mL.
  • Mechanism: liver enzymes catalyze oxidation of methanol to formaldehyde (CH₂O).
  • Formaldehyde reacts rapidly with cell components, coagulating proteins (similar to cooking an egg).
  • This property of formaldehyde accounts for much of methanol's toxicity.

🍺 Ethanol metabolism

  • Ethanol is oxidized in the liver to acetaldehyde.
  • Acetaldehyde is further oxidized to acetic acid (HC₂H₃O₂), a normal cell constituent.
  • Acetic acid is then oxidized to carbon dioxide and water.
  • Toxicity: even so, ethanol is potentially toxic; rapid ingestion of 1 pint (~500 mL) of pure ethanol would kill most people.
  • Acute ethanol poisoning kills several hundred people each year (often in drinking contests).
  • Mechanism of harm: ethanol crosses into the brain, depresses the respiratory control center, causing respiratory muscle failure and suffocation.
  • It also acts on nerve cell membranes, diminishing speech, thought, cognition, and judgment.

🧴 Isopropyl (rubbing) alcohol

  • Rubbing alcohol is usually a 70% aqueous solution of isopropyl alcohol.
  • High vapor pressure causes rapid evaporation from skin, producing a cooling effect.
  • Toxic when ingested but less readily absorbed through the skin compared to methanol.
  • Why it cools: evaporation removes heat from the skin.

🔬 Key comparison table

AlcoholPreparation method(s)Oxidation productToxicity mechanism
MethanolH₂ + CO (catalytic)FormaldehydeFormaldehyde coagulates proteins
EthanolEthylene hydration OR fermentationAcetaldehyde → acetic acidRespiratory depression in brain
IsopropylPropene hydrationAcetoneLess readily absorbed through skin

Common confusion: Why is methanol more toxic than ethanol? Methanol is oxidized to formaldehyde (which destroys tissue), whereas ethanol is oxidized to acetaldehyde and then acetic acid (a normal metabolite).

81

Reactions of Alcohols

Reactions of Alcohols

🧭 Overview

🧠 One-sentence thesis

Alcohols undergo two major reaction types—dehydration (forming alkenes or ethers) and oxidation (forming aldehydes, ketones, or carboxylic acids depending on the alcohol class)—and the outcome depends on the structure of the alcohol and the reaction conditions.

📌 Key points (3–5)

  • Two major reaction types: dehydration (removes water to form alkenes or ethers) and oxidation (adds oxygen or removes hydrogen to form carbonyl compounds).
  • Dehydration conditions matter: higher temperature and excess acid yield alkenes; lower temperature and excess alcohol yield ethers.
  • Oxidation depends on alcohol class: primary alcohols → aldehydes (then carboxylic acids); secondary alcohols → ketones; tertiary alcohols resist oxidation.
  • Common confusion: primary vs secondary vs tertiary—count how many carbon atoms are attached to the carbon bearing the OH group (1, 2, or 3 respectively).
  • Why tertiary alcohols don't oxidize: the carbon with the OH has no hydrogen atom attached to it, so the required carbon-to-oxygen double bond cannot form.

🔥 Dehydration reactions

🔥 What dehydration does

Dehydration: an alcohol loses water (H₂O) in the presence of a catalyst to form an alkene or an ether.

  • The reaction removes the OH group from the alcohol carbon and a hydrogen atom from an adjacent carbon in the same molecule.
  • The result is a carbon-to-carbon double bond (alkene) or an ether linkage, depending on conditions.

🌡️ Conditions control the product

ConditionsProductWhat happens
Higher temperature, excess acidAlkeneIntramolecular dehydration: one alcohol molecule loses H₂O
Lower temperature, excess alcoholEtherIntermolecular dehydration: two alcohol molecules combine, losing H₂O
  • Intramolecular: within one molecule—the OH and an adjacent H are removed, forming a double bond.
  • Intermolecular: between two molecules—the entire OH from one molecule and only the H from the OH of the second molecule are removed, forming an ether.
  • Example: 2-propanol can dehydrate to form propene (alkene) or diisopropyl ether, depending on temperature and reagent amounts.

🧬 Dehydration in living systems

  • Dehydration and hydration reactions occur continuously in cellular metabolism.
  • Enzymes act as catalysts at body temperature (about 37°C).
  • The excerpt mentions the Embden–Meyerhof pathway as an example.
  • Don't confuse: the compounds in metabolism are complex, but the reaction type is the same—elimination of water.

🔬 Oxidation reactions

🔬 What oxidation does

  • Oxidation removes two hydrogen atoms from the alcohol: one from the OH group and one from the carbon bearing the OH.
  • The result is a carbon-to-oxygen double bond (a carbonyl group).
  • The excerpt uses [O] above the arrow to represent any oxidizing agent (e.g., potassium dichromate, liver enzymes).

🥇 Primary alcohols → aldehydes → carboxylic acids

  • Primary alcohol: the carbon with the OH is attached to only one other carbon atom.
  • Oxidation first forms an aldehyde.
  • Aldehydes are easily oxidized further to carboxylic acids.
  • Example: ethanol (primary) oxidizes to acetaldehyde (aldehyde), which can oxidize further to acetic acid (carboxylic acid).

🥈 Secondary alcohols → ketones

  • Secondary alcohol: the carbon with the OH is attached to two other carbon atoms.
  • Oxidation forms a ketone.
  • Ketones are relatively resistant to further oxidation, so no special precautions are needed to isolate them.
  • Example: isopropyl alcohol oxidizes to acetone (a ketone).
  • The excerpt notes that isocitric acid (a secondary alcohol in carbohydrate metabolism) oxidizes to a ketone in the same way.

🥉 Tertiary alcohols resist oxidation

  • Tertiary alcohol: the carbon with the OH is attached to three other carbon atoms.
  • No reaction occurs under normal oxidizing conditions.
  • Why: the carbon bearing the OH has no hydrogen atom attached—only other carbon atoms.
  • Oxidation requires breaking a carbon-to-hydrogen bond to form the double bond; carbon-to-carbon bonds do not break easily under oxidative conditions.
  • Example: if you try to oxidize a tertiary alcohol, write "no reaction" after the arrow.

🧪 How to classify alcohols

Alcohol classCarbon with OH attached toOxidation product
Primary1 other carbonAldehyde (then carboxylic acid)
Secondary2 other carbonsKetone
Tertiary3 other carbonsNo reaction
  • Don't confuse: count the carbons attached to the carbon bearing the OH, not the total number of carbons in the molecule.

🧫 Oxidation in living organisms

🧫 Enzyme-controlled oxidation

  • Oxidation reactions in cells provide the energy needed for useful work.
  • Enzymes control these reactions at body temperature.
  • Example: one step in carbohydrate metabolism oxidizes the secondary alcohol group in isocitric acid to a ketone group.
  • The overall reaction type is the same as in the laboratory (e.g., isopropyl alcohol to acetone).

🔑 The functional group principle

  • The excerpt emphasizes: if you know the chemistry of a particular functional group, you know the chemistry of hundreds of different compounds.
  • Even though metabolic compounds are complex, the reaction at the alcohol functional group follows the same pattern as simple alcohols.
82

Glycols and Glycerol

Glycols and Glycerol

🧭 Overview

🧠 One-sentence thesis

Glycols and glycerol are multi-hydroxyl alcohols whose toxicity or safety depends on what metabolites liver enzymes produce when they oxidize them.

📌 Key points (3–5)

  • What glycols are: alcohols with two OH groups on adjacent carbon atoms; glycerol is the most important trihydroxy alcohol.
  • Ethylene glycol toxicity: liver enzymes oxidize it to oxalate ion, which precipitates with calcium in kidneys, causing renal damage and potentially death.
  • Propylene glycol safety: though physically similar to ethylene glycol, it oxidizes to pyruvate ion (a normal metabolic intermediate), making it essentially nontoxic and safe for drugs and foods.
  • Common confusion: physical properties vs physiological properties—ethylene glycol and propylene glycol have similar physical properties but very different toxicity profiles.
  • Glycerol: a product of fat metabolism that is essentially nontoxic.

🧪 Structure and definitions

🧪 What glycols are

Glycols: alcohols with two OH groups on adjacent carbon atoms.

  • The defining feature is two hydroxyl groups on neighboring carbons.
  • Example compounds mentioned: 1,5-pentanediol (HOCH₂CH₂CH₂CH₂CH₂OH), propylene glycol.

🧪 What glycerol is

Glycerol: the most important trihydroxy alcohol.

  • "Trihydroxy" means three OH groups.
  • It is a product of fat metabolism.
  • It is essentially nontoxic.

☠️ Ethylene glycol toxicity

☠️ How poisoning happens

  • Ethylene glycol is found in antifreeze; people (especially children) sometimes drink it from garage floors or driveways.
  • Its toxicity is not from the glycol itself but from a metabolite.

☠️ The toxic metabolic pathway

  1. Liver enzymes oxidize ethylene glycol to oxalate ion (C₂O₄²⁻).
  2. In the kidneys, oxalate ion combines with calcium ion (Ca²⁺).
  3. This precipitates as calcium oxalate (CaC₂O₄), a solid.
  4. These crystals cause renal damage and can lead to kidney failure and death.
  • The reaction: Ca²⁺ (aqueous) + C₂O₄²⁻ (aqueous) → CaC₂O₄ (solid).
  • This is a precipitation reaction.

✅ Propylene glycol safety

✅ Physical vs physiological properties

  • Propylene glycol has physical properties much like those of ethylene glycol.
  • But its physiological properties are quite different.
  • Don't confuse: similar physical behavior does not mean similar biological effects.

✅ The safe metabolic pathway

  • Like other alcohols, propylene glycol is oxidized by liver enzymes.
  • However, the product is pyruvate ion, a normal intermediate in carbohydrate metabolism.
  • Because the metabolite is a normal part of metabolism, propylene glycol is essentially nontoxic.

✅ Safe uses

  • It can be used as a solvent for drugs.
  • It can be used as a moisturizing agent for foods.

🔄 Functional group changes in oxidation

🔄 Propylene glycol to pyruvic acid

  • Reactant functional groups involved: two OH groups.
  • New functional groups in the product: a ketone group and a carboxylic acid group.
  • This illustrates how oxidation transforms alcohol groups into carbonyl-containing groups.

🔄 Ethylene glycol to oxalate

  • The oxidation produces oxalate ion.
  • The oxalate ion then participates in a precipitation reaction (not further oxidation).

📋 Summary comparison

CompoundStructure typeMetaboliteToxicityUses
Ethylene glycolGlycol (two OH groups)Oxalate ion → calcium oxalate crystalsToxic; causes kidney damage/deathAntifreeze (hazardous)
Propylene glycolGlycol (two OH groups)Pyruvate ion (normal metabolite)Essentially nontoxicDrug solvent, food moisturizer
GlycerolTrihydroxy alcohol (three OH groups)(Fat metabolism product)Essentially nontoxic(Not specified in excerpt)
83

Phenols

Phenols

🧭 Overview

🧠 One-sentence thesis

Phenols are aromatic compounds with an OH group attached directly to a benzene ring, distinguished by their slight acidity and widespread use as antiseptics and disinfectants.

📌 Key points (3–5)

  • Structure: OH group attached directly to an aromatic ring (ArOH), not to an aliphatic carbon chain.
  • Chemical property: Phenols are slightly acidic in water and react with sodium hydroxide to form salts, unlike alcohols.
  • Common confusion: Phenols differ from alcohols (OH on aromatic vs aliphatic carbon) and from aromatic hydrocarbons (presence of OH group).
  • Medical uses: Widely used as antiseptics (kill microorganisms on living tissue) and disinfectants (kill microorganisms on objects).
  • Safety evolution: Phenol itself is toxic to humans; safer alternatives like 4-hexylresorcinol have been developed.

🔬 Structure and chemical behavior

🔬 What defines a phenol

Phenol: An aromatic compound with an OH group attached directly to a benzene ring.

  • The designation is ArOH (Ar = aromatic ring).
  • The parent compound C₆H₅OH is itself called phenol.
  • Old name: carbolic acid (emphasizing its slight acidity).
  • Physical form: white crystalline compound with a distinctive "hospital smell" odor.

⚗️ Acidic character

  • Phenols are slightly acidic in water, which distinguishes them from alcohols.
  • They react with aqueous sodium hydroxide: ArOH(aq) + NaOH(aq) → ArONa(aq) + H₂O
  • This salt formation is a key chemical difference from alcohols.
  • Example: When phenol encounters sodium hydroxide solution, it forms a sodium phenoxide salt plus water.

🏥 Medical and antiseptic applications

🏥 Historical use of phenol

  • Joseph Lister used phenol for antiseptic surgery in 1867—the first widely used antiseptic.
  • Problem: Phenol is toxic to humans and causes severe burns when applied to skin.
  • In the bloodstream, it acts as a systemic poison (carried to and affects all parts of the body).
  • These severe side effects led to searches for safer alternatives.

💊 Safer phenolic antiseptics

  • 4-hexylresorcinol (4-hexyl-1,3-dihydroxybenzene) is a safer alternative.
  • Much more powerful than phenol as a germicide.
  • Has fewer undesirable side effects.
  • Safe enough to be used as the active ingredient in mouthwashes and throat lozenges.
  • Example: Modern antiseptic preparations for use on skin often contain 4-hexylresorcinol instead of phenol.

🧼 Antiseptics vs disinfectants

TypeDefinitionUse
AntisepticSubstance that kills microorganisms on living tissueApplied to skin, wounds, or mucous membranes
DisinfectantSubstance that kills microorganisms on inanimate objectsUsed on furniture, floors, or equipment

🆚 How phenols differ from related compounds

🆚 Phenols vs alcohols

  • Structure difference: Phenols have OH attached directly to an aromatic ring; alcohols have OH on an aliphatic carbon chain.
  • Property difference: Phenols are weakly acidic; alcohols are not acidic.
  • Don't confuse: Both have OH groups, but the attachment point (aromatic vs aliphatic) changes the chemical behavior significantly.

🆚 Phenols vs aromatic hydrocarbons

  • Phenols have an OH group; aromatic hydrocarbons do not.
  • Phenols are somewhat soluble in water due to the OH group; pure aromatic hydrocarbons are not.
  • The OH group makes phenols polar enough to interact with water molecules.
84

Ethers

Ethers

🧭 Overview

🧠 One-sentence thesis

Ethers have lower boiling points than alcohols of similar molar mass because they lack intermolecular hydrogen bonding, yet they remain soluble in water by forming hydrogen bonds with water molecules.

📌 Key points (3–5)

  • What ethers are: organic compounds with an oxygen atom between two hydrocarbon groups (ROR′), derived from water or alcohols by replacing hydrogen atoms.
  • How to name them: use common names by naming the two groups attached to oxygen + "ether"; if both groups are the same, add the prefix "di-".
  • Why boiling points are low: ether molecules have no OH group, so no intermolecular hydrogen bonding occurs between ether molecules—boiling points are similar to alkanes of comparable molar mass.
  • Common confusion: ethers vs alcohols—ethers lack the OH group (no intermolecular H-bonding), but they do have an oxygen atom that can H-bond with water, giving them similar water solubility to isomeric alcohols.
  • Historical use: diethyl ether was the first general anesthetic; modern replacements include halothane, enflurane, and isoflurane.

🧪 Structure and derivation

🧪 What ethers are

Ether: an organic compound that has an oxygen atom between two hydrocarbon groups.

  • General formula: ROR′ (R and R′ are alkyl or aryl groups).
  • Can be thought of in two ways:
    • From water (H–O–H): replace both hydrogen atoms with alkyl/aryl groups.
    • From an alcohol (R–O–H): replace the hydrogen of the OH group with a second alkyl/aryl group.
  • Example: CH₃–O–CH₂CH₂CH₃ is an ether (methyl propyl ether).

🔍 Key structural feature

  • Ethers have an oxygen atom but no OH group.
  • This absence of OH is critical: it means no hydrogen atom is bonded to oxygen in the ether molecule itself.
  • Don't confuse: alcohols have R–O–H; ethers have R–O–R′.

🏷️ Naming ethers

🏷️ Common naming rules

  • Step 1: Identify the two groups attached to the oxygen atom.
  • Step 2: Name each group (e.g., methyl, ethyl, propyl, isopropyl).
  • Step 3: List the group names + "ether".
  • If both groups are identical: use the prefix "di-" before the group name.
Example formulaGroups attached to OCommon name
CH₃–O–CH₃methyl, methyldimethyl ether
CH₃CH₂–O–CH₂CH₃ethyl, ethyldiethyl ether
CH₃–O–CH₂CH₂CH₃methyl, propylmethyl propyl ether
CH₃CH₂CH₂–O–CH₂CH₂CH₃propyl, propyldipropyl ether

🧩 Example from the excerpt

  • CH₃CH₂CH₂OCH₂CH₂CH₃: both groups are propyl → dipropyl ether.
  • Isopropyl group (three carbons attached by the middle carbon) + methyl group → isopropyl methyl ether.

🌡️ Physical properties

🌡️ Boiling points: why ethers are low

  • Key reason: ether molecules have no OH group, so there is no intermolecular hydrogen bonding between ether molecules.
  • Result: ethers have boiling points similar to alkanes of comparable molar mass, and much lower than the corresponding alcohols.
CompoundFormulaMolar MassBoiling Point (°C)Intermolecular H-bonding?
PropaneCH₃CH₂CH₃44–42no
Dimethyl etherCH₃OCH₃46–25no
Ethyl alcoholCH₃CH₂OH4678yes
PentaneCH₃CH₂CH₂CH₂CH₃7236no
Diethyl etherCH₃CH₂OCH₂CH₃7435no
Butyl alcoholCH₃CH₂CH₂CH₂OH74117yes
  • Example: dimethyl ether (molar mass 46) boils at –25 °C, while ethyl alcohol (also molar mass 46) boils at 78 °C—a difference of over 100 °C due to intermolecular hydrogen bonding in the alcohol.

💧 Water solubility: ethers can H-bond with water

  • Although ether molecules cannot H-bond with each other, they do have an oxygen atom.
  • This oxygen can form hydrogen bonds with water molecules.
  • Result: an ether has about the same solubility in water as the alcohol that is isomeric with it (same molecular formula).
CompoundMolecular formulaWater solubility
Dimethyl etherC₂H₆Ocompletely soluble
EthanolC₂H₆Ocompletely soluble
Diethyl etherC₄H₁₀Obarely soluble (8 g/100 mL)
1-ButanolC₄H₁₀Obarely soluble (8 g/100 mL)
  • Don't confuse: ethers have low boiling points (no intermolecular H-bonding) but can still dissolve in water (H-bonding with water).

💊 Medical and practical uses

💊 Ethers as general anesthetics

General anesthetic: a substance that acts on the brain to produce unconsciousness and a general insensitivity to feeling or pain.

  • Diethyl ether (CH₃CH₂OCH₂CH₃) was the first general anesthetic used in surgery.
  • Introduced by William Morton (a Boston dentist) in 1846.
  • Mechanism: inhalation of ether vapor depresses the activity of the central nervous system, producing unconsciousness.

⚠️ Safety and replacements

  • Diethyl ether is relatively safe: wide gap between effective anesthesia dose and lethal dose.
  • Disadvantages: highly flammable and causes nausea.
  • Modern replacements: fluorine-containing compounds—halothane, enflurane, and isoflurane—are less flammable.
  • Safety concern: operating room personnel (especially women) exposed to halothane have higher miscarriage rates than the general population.

🧴 Antiseptic phenolic compounds (context from excerpt)

  • The excerpt mentions phenolic compounds (not ethers) used as antiseptics, e.g., 4-hexylresorcinol for skin preparations.
  • Phenols have an OH group attached directly to an aromatic ring; they are weakly acidic and somewhat soluble in water.
  • Don't confuse phenols with ethers: phenols have OH on an aromatic ring; ethers have R–O–R′ with no OH.

🔑 Key distinctions

🔑 Ethers vs alcohols

FeatureAlcohols (R–O–H)Ethers (R–O–R′)
Functional groupOH groupOxygen between two groups, no OH
Intermolecular H-bondingYes (between alcohol molecules)No (between ether molecules)
Boiling pointHigh for given molar massLow, similar to alkanes
H-bonding with waterYesYes (via oxygen atom)
Water solubilitySimilar to isomeric etherSimilar to isomeric alcohol
  • Example: ethanol (C₂H₆O, alcohol) and dimethyl ether (C₂H₆O, ether) are isomers—both dissolve completely in water, but ethanol boils at 78 °C while dimethyl ether boils at –25 °C.

🔑 Ethers vs alkanes

  • Ethers and alkanes of similar molar mass have similar boiling points (both lack intermolecular H-bonding).
  • Difference: ethers have an oxygen atom, so they can H-bond with water; alkanes cannot.
  • Example: pentane (C₅, molar mass 72) boils at 36 °C; diethyl ether (C₄H₁₀O, molar mass 74) boils at 35 °C—nearly identical.
85

Aldehydes and Ketones: Structure and Names

Aldehydes and Ketones: Structure and Names

🧭 Overview

🧠 One-sentence thesis

Aldehydes and ketones are two related families of organic compounds defined by the carbonyl group (a carbon-to-oxygen double bond), distinguished by whether the carbonyl carbon is bonded to at least one hydrogen atom (aldehyde) or to two carbon groups (ketone).

📌 Key points (3–5)

  • The carbonyl group: a carbon-to-oxygen double bond that defines both aldehydes and ketones and is ubiquitous in biological compounds.
  • Structural difference: aldehydes have at least one hydrogen attached to the carbonyl carbon; ketones have two carbon groups attached.
  • Common confusion: aldehydes are written CHO (not COH) in condensed formulas to avoid confusion with alcohols; the carbonyl double bond is understood but not shown.
  • Naming systems: both common names (based on carboxylic acid names for aldehydes; group names plus "ketone" for ketones) and IUPAC names (using -al for aldehydes, -one for ketones) are frequently used.
  • Why it matters: the carbonyl group appears in carbohydrates, fats, proteins, nucleic acids, hormones, and vitamins—compounds critical to living systems.

🧪 The carbonyl group and functional families

🔬 What the carbonyl group is

Carbonyl group: a carbon-to-oxygen double bond.

  • This functional group defines two related families: aldehydes and ketones.
  • The carbonyl group is found throughout biological compounds, including carbohydrates, fats, proteins, nucleic acids, hormones, and vitamins.
  • Because both families share the same functional group, aldehydes and ketones have many common properties, but they differ enough to be classified separately.

🏷️ Ketones: two carbon groups

Ketone: an organic compound whose molecules have a carbonyl functional group between two hydrocarbon groups.

  • General formula: R and R′ (alkyl groups) or Ar (aryl groups) are attached to the carbonyl carbon.
  • The carbonyl carbon must be attached to two carbon groups.
  • The simplest ketone has three carbon atoms (acetone).
  • Example: In a ketone, the carbonyl group is on an interior carbon atom, not at the end of the chain.

🏷️ Aldehydes: at least one hydrogen

Aldehyde: an organic compound with a carbonyl functional group that has a hydrogen atom attached and either a hydrocarbon group or a second hydrogen atom.

  • At least one of the groups attached to the carbonyl carbon must be hydrogen.
  • In condensed formulas, aldehydes are written as CHO (not COH) to avoid confusion with alcohols; this follows the rule that H comes after the atom it is attached to.
  • The carbon-to-oxygen double bond is understood to be present even when not shown.
  • Example: If the carbonyl group is on an end carbon atom, the compound is an aldehyde.

📛 Common naming conventions

📛 Aldehyde common names

  • Common names are taken from the names of the carboxylic acids into which aldehydes can be converted by oxidation.
  • Stems for the first four aldehydes:
    • 1 carbon: form- (formaldehyde)
    • 2 carbons: acet- (acetaldehyde)
    • 3 carbons: propion- (propionaldehyde)
    • 4 carbons: butyr- (butyraldehyde)

📛 Ketone common names

  • The simplest ketone (three carbons) is widely known as acetone, a unique name unrelated to other ketone names.
  • Generally, common names consist of the names of the groups attached to the carbonyl group, followed by the word ketone.
  • This is similar to the naming of ethers.
  • Example: Acetone can also be called dimethyl ketone; a four-carbon ketone is ethyl methyl ketone.
  • Example: If both alkyl groups are propyl groups, the name is dipropyl ketone; if one is isopropyl and one is methyl, the name is isopropyl methyl ketone.

🔢 IUPAC naming system

🔢 General IUPAC rules

  • Stem names are derived from the parent alkanes, defined by the longest continuous chain (LCC) of carbon atoms containing the functional group.
  • For aldehydes: drop the -e from the alkane name and add the ending -al.
    • Methanal is the IUPAC name for formaldehyde.
    • Ethanal is the name for acetaldehyde.
  • For ketones: drop the -e from the alkane name and add the ending -one.
    • Propanone is the IUPAC name for acetone.
    • Butanone is the name for ethyl methyl ketone.

🔢 Numbering for aldehydes

  • The carbonyl carbon atom is always considered to be C1.
  • It is unnecessary to designate this group by number.
  • Substituents are numbered from the carbonyl carbon.
  • Example: A five-carbon chain with a methyl group on the second carbon is 2-methylpentanal.

🔢 Numbering for ketones

  • Number the chain to give the carbonyl carbon atom the lowest possible number.
  • In cyclic ketones, it is understood that the carbonyl carbon is C1.
  • Example: A five-carbon chain with the carbonyl at C3 and methyl groups at C2 and C4 is 2,4-dimethyl-3-pentanone.
  • Example: A six-carbon ring ketone is cyclohexanone (no number needed because all positions are equivalent).

🔢 Drawing structures from IUPAC names

  • The stem (e.g., "octan-", "hexan-") tells you the number of carbons in the LCC.
  • For aldehydes, the carbonyl is always at C1.
  • For ketones, the number before "-one" tells you which carbon is the carbonyl carbon.
  • Other numbers indicate substituent positions.
  • Example: "7-chlorooctanal" means an eight-carbon chain with the aldehyde group at C1 and a chlorine atom at C7.
  • Example: "4-methyl-3-hexanone" means a six-carbon chain with the carbonyl at C3 and a methyl group at C4.

📋 Summary comparison

FeatureAldehydeKetone
Carbonyl positionAt least one H attachedTwo carbon groups attached
Simplest exampleFormaldehyde (1 carbon)Acetone (3 carbons)
Common name basisFrom carboxylic acid namesGroup names + "ketone"
IUPAC ending-al-one
Carbonyl carbon numberAlways C1Lowest possible number
Condensed formula notationCHOBetween two carbon groups
86

Properties of Aldehydes and Ketones

Properties of Aldehydes and Ketones

🧭 Overview

🧠 One-sentence thesis

Aldehydes and ketones have higher boiling points than ethers but lower than alcohols due to their polar carbonyl groups, and they differ critically in that aldehydes oxidize readily to carboxylic acids while ketones resist oxidation.

📌 Key points (3–5)

  • Polarity and boiling points: The carbon-to-oxygen double bond is quite polar, creating dipole-dipole interactions that raise boiling points above ethers and alkanes but keep them below alcohols (which have hydrogen bonding).
  • Solubility pattern: Aldehydes and ketones with four or fewer carbons are soluble in water due to hydrogen bonding with the carbonyl oxygen; solubility decreases as the carbon chain lengthens.
  • Key chemical difference: Aldehydes oxidize easily to carboxylic acids (even by air), whereas ketones resist oxidation under ordinary conditions.
  • Common confusion: Don't confuse the polar C=O double bond in carbonyls with the nonpolar C=C double bond in alkenes—the carbonyl bond has charge separation.
  • Practical uses: Formaldehyde (formalin) preserves biological specimens, acetaldehyde is a metabolic intermediate, and acetone is a widely used industrial solvent.

🔬 Molecular structure and polarity

⚡ The polar carbonyl bond

Carbon-to-oxygen double bond: quite polar, more polar than a carbon-to-oxygen single bond.

  • The electronegative oxygen atom attracts bonding electrons much more strongly than the carbon atom.
  • This creates charge separation: the carbon atom has a partial positive charge, and the oxygen atom has a partial negative charge.
  • Don't confuse: The C=O double bond is polar; the C=C double bond in alkenes is nonpolar because both atoms are carbon.

🌡️ Effect on boiling points

The charge separation in aldehydes and ketones leads to dipole-dipole interactions that significantly affect boiling points.

CompoundFamilyMolar MassType of Intermolecular ForcesBoiling Point (°C)
CH₃CH₂CH₂CH₃alkane58dispersion only–1
CH₃OCH₂CH₃ether60weak dipole6
CH₃CH₂CHOaldehyde58strong dipole49
CH₃CH₂CH₂OHalcohol60hydrogen bonding97
  • Polar single bonds in ethers have little effect on boiling points.
  • Aldehydes and ketones have strong dipole interactions, raising boiling points substantially above alkanes and ethers.
  • Hydrogen bonding between alcohol molecules is even stronger, giving alcohols the highest boiling points.

🌊 Solubility in water

The oxygen atom of the carbonyl group engages in hydrogen bonding with water molecules.

  • The solubility of aldehydes and ketones is about the same as that of alcohols and ethers.
  • Formaldehyde, acetaldehyde, and acetone are soluble in water.
  • As the carbon chain increases in length, solubility in water decreases.
  • Borderline rule: Solubility occurs at about four carbon atoms per oxygen atom.
  • All aldehydes and ketones are soluble in organic solvents and generally less dense than water.

🧪 Chemical reactivity

🔥 Oxidation: the critical difference

Aldehydes and ketones are much alike in many reactions due to the carbonyl functional group, but they differ greatly in oxidation behavior.

Aldehydes:

  • Readily oxidized to carboxylic acids.
  • Among the most easily oxidized organic compounds.
  • Oxidized by oxygen in air: 2RCHO + O₂ → 2RCOOH
  • The presence of the H atom on the carbonyl carbon makes aldehydes easier to oxidize.

Ketones:

  • Resist oxidation by ordinary laboratory oxidizing agents.
  • Do undergo combustion, like aldehydes.

Example: Acetaldehyde treated with potassium dichromate in acid solution forms acetic acid (CH₃COOH); acetone treated the same way forms no organic product.

🪞 Tollens' reagent test

A sufficiently mild oxidizing agent can distinguish aldehydes not only from ketones but also from alcohols.

Tollens' reagent: an alkaline solution of silver ion (Ag⁺) complexed with ammonia (NH₃), which keeps the Ag⁺ ion in solution.

  • When Tollens' reagent oxidizes an aldehyde, the Ag⁺ ion is reduced to free silver (Ag).
  • Deposited on a clean glass surface, the silver produces a mirror.
  • Ordinary ketones do not react with Tollens' reagent.
  • Example: Acetaldehyde treated with Ag⁺(aq) produces silver metal (Ag).

🏭 Common compounds and applications

🧴 Formaldehyde and formalin

  • Formaldehyde is a gas at room temperature with an irritating odor.
  • Because of its reactivity, it is difficult to handle in gaseous state.
  • Formalin: a 37% to 40% aqueous solution of formaldehyde.
  • Formaldehyde denatures proteins, rendering them insoluble in water and resistant to bacterial decay.
  • Uses: embalming solutions, preserving biological specimens, making phenol-formaldehyde resins for plywood gluing and building adhesives.
  • Health concern: Sometimes formaldehyde escapes from materials and causes coughing, wheezing, eye irritation, and other symptoms in some people.

💧 Acetaldehyde

  • An extremely volatile, colorless liquid.
  • A starting material for the preparation of many other organic compounds.
  • Formed as a metabolite in the fermentation of sugars and in the detoxification of alcohol in the liver.
  • Boils at 20°C; in an open vessel, it boils away in a warm room.

🧪 Acetone

Acetone: the simplest and most important ketone.

  • Miscible with water as well as with most organic solvents.
  • Chief use: industrial solvent (for paints and lacquers).
  • Chief ingredient in some brands of nail polish remover.
  • Has a pleasant odor (most higher ketone homologs have rather bland odors).

🩺 Acetone in the body

  • Formed in the human body as a by-product of lipid metabolism.
  • Normally does not accumulate because it is oxidized to carbon dioxide and water.
  • Normal concentration: less than 1 mg/100 mL of blood.
  • In certain disease states (e.g., uncontrolled diabetes mellitus), acetone concentration rises to higher levels.
  • Then excreted in the urine, where it is easily detected.
  • In severe cases, its odor can be noted on the breath.

🌿 Other aldehydes and ketones

Aldehydes:

  • Lower members of the homologous series have pungent odors.
  • Many higher aldehydes have pleasant odors and are used in perfumes and artificial flavorings.
  • Benzaldehyde: an oil found in almonds.
  • Cinnamaldehyde: oil of cinnamon.
  • Vanillin: gives vanilla its flavor.
  • cis-3-hexenal: provides an herbal "green" odor (odor of green leaves), used in shampoos.

Ketones:

  • 2,3-butanedione: butter flavoring.
  • β-ionone: responsible for the odor of violets.
  • Muscone: musk oil, an ingredient in perfumes.
  • Camphor: used in some insect repellents.
  • Certain steroid hormones (progesterone, testosterone) have the ketone functional group as part of their structure.
87

Organic Sulfur Compounds

Organic Sulfur Compounds

🧭 Overview

🧠 One-sentence thesis

Sulfur forms organic compounds analogous to oxygen compounds—thiols (like alcohols), disulfides (from mild oxidation of thiols), and thioethers (like ethers)—and these sulfur-containing functional groups play critical roles in protein structure and biological molecules.

📌 Key points (3–5)

  • Sulfur and oxygen similarity: Sulfur is in the same periodic table group (6A) as oxygen, so it forms similar organic compounds.
  • Three main sulfur compound types: thiols (RSH, sulfur analogs of alcohols), disulfides (RSSR, from mild oxidation of thiols), and thioethers (RSR′, sulfur analogs of ethers).
  • Biological importance: The amino acids cysteine and methionine contain sulfur; disulfide linkages (–S–S–) are extremely important in protein structure.
  • Common confusion: Don't confuse thiols (–SH group) with thioethers (sulfur between two carbon groups); thiols can be oxidized to disulfides, but thioethers are already a different functional group.

🔗 Thiols and their oxidation

🧪 What thiols are

Thiols (also called mercaptans): sulfur analogs of alcohols with the general formula RSH.

  • The functional group is –SH (sulfhydryl group).
  • They are structurally similar to alcohols (ROH), but with sulfur replacing oxygen.
  • Example: Methanethiol has the formula CH₃SH; ethanethiol (ethyl mercaptan) is CH₃CH₂SH.
  • Ethanethiol is commonly used as an odorant for liquid propane (LP) gas, making leaks detectable.

⚗️ Mild oxidation produces disulfides

The excerpt gives the reaction:

2 RSH → [O] → RSSR

  • When thiols undergo mild oxidation, two thiol molecules combine to form a disulfide.
  • The disulfide functional group is –S–S– (a sulfur-sulfur bond).
  • Example: Two molecules of ethanethiol (CH₃CH₂SH) oxidize to form diethyl disulfide (CH₃CH₂SSCH₂CH₃).
  • Don't confuse: This is a mild oxidation; the excerpt does not describe what happens under harsher conditions.

🧬 Biological sulfur compounds

🧬 Sulfur-containing amino acids

The excerpt mentions two amino acids:

Amino acidFormulaSulfur functional group
CysteineHSCH₂CH(NH₂)COOHThiol (–SH)
MethionineCH₃SCH₂CH₂CH(NH₂)COOHThioether (–S–)
  • All proteins that contain these amino acids will have sulfur atoms.
  • Cysteine has a thiol group; methionine has a thioether group.

🔗 Disulfide linkages in proteins

Disulfide linkages (–S–S–) between protein chains are extremely important in protein structure.

  • These linkages form when cysteine residues in proteins are oxidized.
  • They create cross-links between different parts of a protein chain or between different protein chains.
  • This is critical for stabilizing three-dimensional protein structure.
  • Example: Two cysteine side chains in a protein can oxidize to form a disulfide bridge, holding parts of the protein together.

🌫️ Thioethers

🌫️ Structure and examples

Thioethers: sulfur analogs of ethers with the general formula RSR′.

  • In ethers, oxygen sits between two carbon groups (ROR′); in thioethers, sulfur replaces that oxygen.
  • Example: Dimethylsulfide (CH₃SCH₃) is responsible for the sometimes unpleasant odor of cooking cabbage and related vegetables.
  • The excerpt notes that methionine (one of the amino acids above) contains a thioether functional group.
  • Don't confuse: Thioethers (RSR′) have sulfur between two carbon groups; thiols (RSH) have sulfur bonded to hydrogen at the end of the molecule.
88

Functional Groups of the Carboxylic Acids and Their Derivatives

Functional Groups of the Carboxylic Acids and Their Derivatives

🧭 Overview

🧠 One-sentence thesis

Understanding the functional groups of carboxylic acids and their derivatives (esters, amines, and amides) provides the foundation for comprehending biologically important molecules like fats, proteins, and other essential compounds.

📌 Key points (3–5)

  • Four main compound families: carboxylic acids, esters, amines, and amides—each with a distinct functional group structure.
  • Derivatives relationship: esters and amides are derivatives of carboxylic acids because the OH in the carboxyl group is replaced with another group (OR for esters, nitrogen-containing group for amides).
  • Carbonyl group presence: carboxylic acids, esters, and amides all contain the carbonyl group (C=O), but it is only part of their functional group, giving them different properties than aldehydes and ketones.
  • Common confusion: esters look somewhat like ethers and carboxylic acids, but they react like neither—they form a distinctive family with no acidic hydrogen (unlike acids) but with a carbonyl group (unlike ethers).
  • Biological significance: these compounds underlie important biomolecules—soaps (carboxylic acid salts), fats and oils (esters), and proteins (polyamides).

🧪 The four compound families

🧪 Carboxylic acids

Carboxylic acid: an organic compound that has a carboxyl group.

Carboxyl group: a functional group that contains a carbon–oxygen double bond and an OH group also attached to the same carbon atom.

  • General formula: RCOOH, where R is a hydrocarbon group.
  • The carboxyl group has characteristic properties of its own, distinct from simple carbonyl groups.
  • The carbon-to-oxygen double bond can be written explicitly or in condensed form (RCOOH).
  • Historical note: acetic acid (vinegar), formic acid (red ant sting), and citric acid (citrus fruits) all belong to this family.

🧪 Esters

Ester: an organic compound derived from a carboxylic acid and an alcohol in which the OH of the acid is replaced by an OR group.

  • General formula: RCOOR', where R and R' are hydrocarbon groups.
  • Looks somewhat like an ether and somewhat like a carboxylic acid, but reacts like neither.
  • Key difference from ethers: esters have a carbonyl group.
  • Key difference from carboxylic acids: esters have no acidic hydrogen atom; they have a hydrocarbon group in its place.
  • Biological examples: fats, oils, and many important fragrances and flavors are esters.

🧪 Amines

Amine: a compound derived from ammonia (NH₃); it has one, two, or all three of the hydrogen atoms of NH₃ replaced by an alkyl (or an aryl) group.

  • The functional group is a nitrogen atom with a lone pair of electrons and with one, two, or three alkyl or aryl groups attached.
  • Like ammonia, amines are weak bases.
  • Historical note: amines are the organic bases produced when animal tissue decays.

🧪 Amides

Amide: an organic compound with a carbonyl group joined to a nitrogen atom from ammonia or an amine.

  • The amide functional group has properties that differ from those of the simple carbonyl group, NH₃, and amines.
  • Biological significance: proteins, often called "the stuff of life," are polyamides.

🔗 How derivatives relate to carboxylic acids

🔗 The derivative concept

  • Esters and amides are considered derivatives of carboxylic acids.
  • The defining transformation: the OH in the carboxyl group is replaced with another group.
  • For esters: OH is replaced by OR (from an alcohol).
  • For amides: OH is replaced by a nitrogen-containing group (from ammonia or an amine).

🔗 The carbonyl connection

  • Carboxylic acids, esters, and amides all contain the carbonyl group (C=O).
  • However, the carbonyl group is only part of the functional group in these compounds.
  • This partial presence gives them characteristic properties distinct from aldehydes and ketones (where the carbonyl is the entire functional group).

🔍 Key distinctions and common confusions

🔍 Ester vs ether vs carboxylic acid

FeatureEsterEtherCarboxylic acid
Carbonyl group?YesNoYes
Acidic hydrogen?NoNoYes
General formulaRCOOR'ROR'RCOOH
ReactivityDistinctive familyDifferentDifferent
  • Don't confuse: Even though esters look like a hybrid of ethers and carboxylic acids, they form a distinctive family with unique reactivity.
  • The presence of the carbonyl group distinguishes esters from ethers.
  • The absence of acidic hydrogen distinguishes esters from carboxylic acids.

🔍 Carboxyl vs carbonyl

  • Carboxyl group: carbon–oxygen double bond plus an OH group attached to the same carbon.
  • Carbonyl group: just the carbon–oxygen double bond (C=O).
  • The carboxyl group has the carbonyl group as a component, but adds the OH group, creating characteristic properties of its own.

📊 Summary table of functional groups

FamilyFunctional Group StructureGeneral FormulaExample (Common Name)Example (IUPAC Name)
Carboxylic acidCarboxyl group (C=O + OH on same carbon)RCOOHAcetic acidEthanoic acid
EsterCarbonyl + OR groupRCOOR'Methyl acetateMethyl ethanoate
AmineNitrogen with lone pair + 1–3 alkyl/aryl groupsRNH₂, R₂NH, R₃NMethylamineMethanamine
AmideCarbonyl + nitrogen from ammonia/amineRCONH₂ (and variants)AcetamideEthanamide

📊 Pattern in nature

  • Most familiar carboxylic acids have an even number of carbon atoms.
  • These acids (called fatty acids) are synthesized in nature by adding two carbon atoms at a time.
89

Carboxylic Acids: Structures and Names

Carboxylic Acids: Structures and Names

🧭 Overview

🧠 One-sentence thesis

Carboxylic acids are widespread in nature and can be named either by common names derived from their historical sources or by systematic IUPAC rules based on the parent hydrocarbon chain.

📌 Key points (3–5)

  • What carboxylic acids are: organic compounds with a carboxyl group (carbon doubly bonded to oxygen and joined to an OH group), found in many foods, medicines, and household products.
  • Two naming systems exist: common names based on Latin/Greek words describing the source (e.g., formic acid from Latin formica meaning "ant") and IUPAC systematic names.
  • Common confusion: Greek letters vs numbers: common names use Greek letters (α, β, γ, δ) to show substituent positions relative to the carboxyl carbon; IUPAC names use numbers on the longest continuous chain.
  • IUPAC naming rule: replace the -e ending of the parent alkane with -oic and add "acid"; the carboxyl carbon is always counted first.
  • How they form: carboxylic acids are produced by oxidizing aldehydes or primary alcohols.

🏷️ Common names and natural sources

🐜 Formic acid (simplest carboxylic acid)

Formic acid (HCOOH): the simplest carboxylic acid, first obtained by distillation of ants.

  • Latin formica means "ant."
  • Found in ant bites and wasp/bee stings along with other poisonous materials.
  • Example: When certain ants bite, they inject formic acid into the skin.

🍯 Acetic acid (vinegar acid)

  • Made by fermenting cider and honey in the presence of oxygen.
  • Vinegar is a solution containing 4%–10% acetic acid plus flavor compounds.
  • The most familiar weak acid in educational and industrial labs.
  • Historical note: Pure acetic acid solidifies at 16.6°C (just below room temperature), so it would freeze on shelves in poorly heated old laboratories—hence the name "glacial acetic acid" for pure/concentrated acetic acid.

🧈 Higher homologs

AcidFormulaNotable characteristics
Propionic acidCH₃CH₂COOHSeldom encountered in everyday life
Butyric acidCH₃CH₂CH₂COOHOne of the most foul-smelling substances; found in rancid butter and body odor; bloodhounds can track it
Benzoic acidC₆H₅COOHCarboxyl group attached directly to a benzene ring

📐 IUPAC systematic naming

📏 Basic IUPAC rules

IUPAC naming: the parent hydrocarbon corresponds to the longest continuous chain (LCC) containing the carboxyl group; replace the -e ending with -oic and add "acid."

  • The carboxyl carbon atom is always counted first (position 1).
  • Numbers indicate positions of substituent groups.
  • Example: The carboxylic acid derived from pentane is pentanoic acid (CH₃CH₂CH₂CH₂COOH).

🔢 Numbering vs Greek letters

Don't confuse:

  • Common names use Greek letters (α, β, γ, δ) to designate positions relative to the carboxyl carbon.
  • IUPAC names use numbers (1, 2, 3, 4) on the longest chain.

Example from the excerpt:

  • ClCH₂CH₂CH₂COOH can be named:
    • Common: γ-chlorobutyric acid (chlorine at the γ position)
    • IUPAC: 4-chlorobutanoic acid (chlorine at carbon 4)

🔧 Naming procedure

  1. Identify the longest continuous chain containing the carboxyl group.
  2. Count the carboxyl carbon as position 1.
  3. Replace the parent alkane's -e with -oic acid.
  4. Number and name any substituents.

Example: For a six-carbon straight chain with a carboxyl group → hexanoic acid.

🧪 Formation of carboxylic acids

🔄 Oxidation reactions

Carboxylic acids form through oxidation of:

  • Primary alcohols → aldehydes → carboxylic acids
  • Aldehydes → carboxylic acids

Example from the excerpt:

  • Ethanol (CH₃CH₂OH) → acetaldehyde (CH₃CHO) → acetic acid (CH₃COOH)

🫀 Biological oxidation

  • This oxidation process occurs in the liver.
  • Enzymes (alcohol dehydrogenase) catalyze the oxidation of ethanol to acetic acid.
  • Acetic acid can be further oxidized to carbon dioxide and water.

Example: Caproic acid (hexanoic acid) can be prepared by oxidizing:

  • The corresponding primary alcohol: CH₃CH₂CH₂CH₂CH₂CH₂OH
  • The corresponding aldehyde: CH₃CH₂CH₂CH₂CH₂CHO
90

The Formation of Carboxylic Acids

The Formation of Carboxylic Acids

🧭 Overview

🧠 One-sentence thesis

Carboxylic acids are formed through the oxidation of aldehydes or primary alcohols, a process that occurs both in laboratory settings and in biological systems like the liver.

📌 Key points (3–5)

  • Core preparation method: oxidation of aldehydes or primary alcohols produces carboxylic acids.
  • Two-step pathway from alcohols: primary alcohols first oxidize to aldehydes, then aldehydes oxidize to carboxylic acids.
  • Biological relevance: the same oxidation process happens in the liver, where enzymes catalyze ethanol oxidation to acetic acid.
  • Common confusion: the oxidation is a two-stage process—alcohol → aldehyde → carboxylic acid—not a single direct conversion.
  • Further oxidation possible: carboxylic acids can be oxidized further to carbon dioxide and water.

🔬 Oxidation pathways to carboxylic acids

🧪 Starting materials

The excerpt identifies two types of starting compounds:

  • Primary alcohols: compounds with an -OH group attached to a carbon that has at least two hydrogen atoms.
  • Aldehydes: compounds with a -CHO group (carbonyl with one hydrogen).

Both can be oxidized to form carboxylic acids in the presence of an oxidizing agent.

⚗️ The two-step oxidation sequence

When starting from a primary alcohol, the process occurs in two stages:

  1. Alcohol to aldehyde: the primary alcohol is first oxidized to an aldehyde.
  2. Aldehyde to carboxylic acid: the aldehyde is then oxidized to a carboxylic acid.

Example: Ethanol (a primary alcohol) is oxidized to acetaldehyde, which is then oxidized to acetic acid.

The oxidation of aldehydes or primary alcohols forms carboxylic acids.

Don't confuse: This is not a single-step reaction. The alcohol must pass through the aldehyde stage before becoming a carboxylic acid.

🧬 Biological oxidation in the liver

The same chemical transformation occurs in living organisms:

  • Where: in the liver.
  • How: enzymes called alcohol dehydrogenase catalyze the oxidation.
  • Sequence: ethanol → acetaldehyde → acetic acid (using the same two-step pathway).
  • Beyond: acetic acid can be further oxidized to carbon dioxide and water.

This shows that laboratory and biological oxidation follow the same fundamental chemistry, though biological systems use enzyme catalysts instead of chemical oxidizing agents.

🔄 Reverse-engineering carboxylic acid synthesis

🎯 Identifying precursors

The excerpt provides practice in working backward from a carboxylic acid to identify what alcohol or aldehyde could produce it:

  • To find the alcohol precursor: replace the -COOH group with -CH₂OH.
  • To find the aldehyde precursor: replace the -COOH group with -CHO.

Example: Caproic acid (hexanoic acid) can be prepared from:

  • The alcohol: a compound with -CH₂OH at the same position.
  • The aldehyde: a compound with -CHO at the same position.

🧮 Multiple functional groups

When the starting material has more than one functional group, each oxidizable position follows the same rules:

Example: 1,4-butanediol (with -OH groups at both ends) will produce:

  • An aldehyde intermediate (with -CHO at the oxidized position).
  • A carboxylic acid product (with -COOH at the fully oxidized position).

📋 Summary comparison

Starting materialIntermediateFinal productConditions
Primary alcoholAldehydeCarboxylic acidOxidizing agent
Aldehyde(none)Carboxylic acidOxidizing agent
Ethanol (in liver)AcetaldehydeAcetic acidEnzyme-catalyzed
Acetic acid(none)CO₂ + H₂OFurther oxidation

The key takeaway from the excerpt: whether in the laboratory or in the body, the oxidation of aldehydes or primary alcohols forms carboxylic acids.

91

Physical Properties of Carboxylic Acids

Physical Properties of Carboxylic Acids

🧭 Overview

🧠 One-sentence thesis

Carboxylic acids have unusually high boiling points due to hydrogen bonding, and their water solubility decreases as the carbon chain lengthens.

📌 Key points (3–5)

  • Boiling point trend: carboxylic acids have higher boiling points than other substances of comparable molar mass, and boiling points increase with molar mass.
  • Why boiling points are high: extensive intermolecular hydrogen bonding between carboxylic acid molecules.
  • Solubility pattern: acids with one to four carbons are completely miscible with water; solubility decreases as molar mass increases.
  • Common confusion: melting points show no regular pattern with molar mass, unlike boiling points which increase predictably.
  • How to distinguish from similar compounds: carboxylic acids have higher boiling points than alcohols or ethers of similar molar mass because of more extensive hydrogen bonding.

🌡️ Boiling point behavior

🔗 Why carboxylic acids boil at high temperatures

Carboxylic acids have high boiling points compared to other substances of comparable molar mass.

  • The key reason is intermolecular hydrogen bonding between carboxylic acid molecules.
  • This bonding requires more energy to break, so more heat is needed to convert the liquid to gas.
  • Example: butyric acid (molar mass 88) has a higher boiling point than 2-pentanone (molar mass 86) because the acid can form hydrogen bonds while the ketone cannot.

📈 Boiling points increase with molar mass

  • As the carbon chain gets longer, the molar mass increases, and so does the boiling point.
  • The excerpt shows this pattern in the table: formic acid (100°C) → acetic acid (118°C) → propionic acid (141°C) → butyric acid (163°C) → valeric acid (187°C) → caproic acid (205°C).
  • This is a regular, predictable pattern for the first six homologs.

❄️ Melting points show no pattern

  • Unlike boiling points, melting points do not follow a regular trend with increasing molar mass.
  • The excerpt explicitly states "melting points show no regular pattern."
  • Don't confuse: boiling points are predictable; melting points are not.

💧 Water solubility patterns

🌊 Small carboxylic acids are highly soluble

Carboxylic acids having one to four carbon atoms are completely miscible with water.

  • "Miscible" means they dissolve in water in any proportion.
  • The reason is hydrogen bonding with water molecules.
  • The table shows formic, acetic, propionic, and butyric acids are all miscible.

📉 Solubility decreases with molar mass

  • As the carbon chain lengthens, the acid becomes less soluble in water.
  • The excerpt states: "Solubility decreases with molar mass."
  • The table illustrates this:
AcidCarbon atomsSolubility (g/100 g water)
Butyric acid4miscible
Valeric acid55
Caproic acid61.1
Benzoic acid7 (aromatic)0.29
  • Example: butyric acid (butanoic acid) is more soluble than 1-butanol in water because there is more extensive hydrogen bonding with the carboxylic acid group.

🔍 Why hydrogen bonding matters

  • The carboxylic acid group (–COOH) can both donate and accept hydrogen bonds with water.
  • This makes carboxylic acids more soluble than hydrocarbons or ethers of similar size.
  • Example: acetic acid (CH₃COOH) is soluble in water because it engages in hydrogen bonding, while butane (CH₃CH₂CH₂CH₃) is not soluble because it cannot form hydrogen bonds.

🔬 Comparing carboxylic acids to similar compounds

⚖️ Carboxylic acids vs. alcohols and ethers

  • Carboxylic acids have higher boiling points than alcohols or ethers of comparable molar mass.
  • The reason: carboxylic acids form more extensive hydrogen bonding networks.
  • Example: CH₃CH₂CH₂COOH (carboxylic acid) has a higher boiling point than both CH₃CH₂CH₂OCH₂CH₃ (ether, no intermolecular hydrogen bonding) and CH₃CH₂CH₂CH₂CH₂OH (alcohol, less extensive hydrogen bonding).

🧪 Key structural feature

  • The –COOH group contains both a carbonyl (C=O) and a hydroxyl (–OH).
  • This dual structure allows for stronger and more extensive hydrogen bonding than alcohols (which only have –OH) or ketones (which only have C=O).
  • Don't confuse: ethers (R–O–R) cannot form intermolecular hydrogen bonds at all because they lack an H attached to oxygen.
92

Chemical Properties of Carboxylic Acids: Ionization and Neutralization

Chemical Properties of Carboxylic Acids: Ionization and Neutralization

🧭 Overview

🧠 One-sentence thesis

Carboxylic acids behave as weak acids in water and neutralize bases to form salts, just like inorganic acids but with the added feature that insoluble carboxylic acids can form soluble salts.

📌 Key points (3–5)

  • Ionization behavior: Water-soluble carboxylic acids ionize slightly in water to form moderately acidic solutions and produce carboxylate anions (RCOO⁻).
  • Neutralization reactions: Carboxylic acids react with bases (NaOH), carbonates (Na₂CO₃), and bicarbonates (NaHCO₃) to form salts and water.
  • Gas production: Reactions with carbonates and bicarbonates also produce carbon dioxide gas.
  • Salt naming: Carboxylate salts are named by replacing the "-ic" ending of the acid with "-ate" and adding the cation name first.
  • Common confusion: Unlike inorganic acids, insoluble carboxylic acids can form soluble carboxylate salts, making them useful as preservatives.

🧪 Ionization in water

💧 How carboxylic acids ionize

Carboxylic acids ionize slightly in water to form moderately acidic solutions.

  • The general ionization equation: RCOOH + H₂O ⇄ RCOO⁻ + H₃O⁺
  • The product anion is called the carboxylate anion (RCOO⁻).
  • These solutions show typical acid properties, such as changing litmus from blue to red.
  • Example: Propionic acid (CH₃CH₂COOH) ionizes in water to form a propionate ion (CH₃CH₂COO⁻) and a hydronium ion (H₃O⁺).

⚖️ Weak acid character

  • The excerpt emphasizes "slightly" ionize and "moderately acidic," indicating these are weak acids.
  • The equilibrium arrow (⇄) shows the ionization is reversible and incomplete.
  • Don't confuse: This is different from strong acids that ionize completely.

🔄 Neutralization reactions

🧂 Reaction with sodium hydroxide

  • Carboxylic acids react with aqueous NaOH to form a salt and water.
  • General equation: RCOOH + NaOH(aq) → RCOO⁻Na⁺(aq) + H₂O
  • Example: Propionic acid reacts with NaOH to form sodium propionate and water: CH₃CH₂COOH(aq) + NaOH(aq) → CH₃CH₂COO⁻Na⁺(aq) + H₂O(ℓ)
  • This is similar to how inorganic acids neutralize bases.

💨 Reactions with carbonates and bicarbonates

Carboxylic acids react with carbonate and bicarbonate ions to produce additional carbon dioxide gas:

ReactantProductsKey difference
Na₂CO₃2RCOO⁻Na⁺ + H₂O + CO₂(g)Two acid molecules react; CO₂ released
NaHCO₃RCOO⁻Na⁺ + H₂O + CO₂(g)One-to-one ratio; CO₂ released
  • Example: Decanoic acid with NaHCO₃ produces sodium decanoate, water, and carbon dioxide gas.
  • The CO₂ gas production distinguishes these reactions from simple neutralization with NaOH.

🔬 Behavior like inorganic acids

  • The excerpt states: "In these reactions, the carboxylic acids act like inorganic acids: they neutralize basic compounds."
  • Key similarity: Both form salts and water.
  • Key difference: Insoluble carboxylic acids often form soluble carboxylate salts, which is useful in practical applications.

📝 Naming carboxylate salts

🏷️ Naming convention

The name of the cation is followed by the name of the organic anion. The name of the anion is obtained by dropping the "-ic" ending of the acid name and replacing it with the suffix "-ate."

  • This rule applies to both common names and IUPAC names.
  • The cation name comes first, then the anion name.

🔤 Examples of salt names

Acid nameSalt cationSalt name
Propionic acidSodium (Na⁺)Sodium propionate
Butyric acidLithium (Li⁺)Lithium butyrate
Acetic acidPotassium (K⁺)Potassium acetate
Butanoic acidAmmonium (NH₄⁺)Ammonium butanoate
  • Don't confuse: The "-ic" ending changes to "-ate" for the anion, not the whole salt name.

🍞 Practical applications

🛡️ Organic salts as preservatives

The excerpt mentions that some organic salts are used as food preservatives:

  • How they work: They prevent spoilage by inhibiting the growth of bacteria and fungi.
  • Examples given:
    • Calcium and sodium propionate: added to processed cheese and bakery goods
    • Sodium benzoate: added to cider, jellies, pickles, and syrups
    • Sodium and potassium sorbate: added to fruit juices, sauerkraut, soft drinks, and wine

🧼 Long-chain carboxylate salts

  • The excerpt notes that "salts of long-chain carboxylic acids are called soaps."
  • This connects the chemistry of carboxylic acids to everyday products.
  • The excerpt references further discussion in another chapter on lipids.
93

Esters: Structures and Names

Esters: Structures and Names

🧭 Overview

🧠 One-sentence thesis

Esters are organic compounds with a characteristic carbon-oxygen structure that are named by combining the alkyl/aryl group name with the acid-derived name ending in "-ate," and they are responsible for many pleasant natural fragrances.

📌 Key points (3–5)

  • General structure: Esters have the formula RCOOR′, featuring a carbon-to-oxygen double bond also singly bonded to a second oxygen atom joined to an alkyl or aryl group.
  • Naming convention: Named similarly to salts—the alkyl/aryl portion comes first, followed by the acid portion with "-ic" replaced by "-ate."
  • Natural occurrence: Widely found in nature, responsible for characteristic fragrances of fruits and flowers, unlike carboxylic acids which lack pleasant odors.
  • Common confusion: The R′ group in RCOOR′ cannot be hydrogen (that would make it a carboxylic acid, not an ester).
  • Practical applications: Used in perfumes, flavoring agents, and include important biological molecules like fats and oils.

🔬 Structure and Definition

🧪 What defines an ester

Ester general formula: RCOOR′, where R may be a hydrogen atom, an alkyl group, or an aryl group, and R′ may be an alkyl group or an aryl group but not a hydrogen atom.

  • The key structural feature: a carbon-to-oxygen double bond that is also singly bonded to a second oxygen atom.
  • This second oxygen is then joined to an alkyl or aryl group.
  • Example structures mentioned: ethyl acetate and methyl butyrate.

⚠️ Distinguishing from carboxylic acids

  • If R′ were a hydrogen atom, the compound would be a carboxylic acid, not an ester.
  • This is the critical structural difference between the two functional groups.
  • Don't confuse: the presence of the alkyl/aryl group on the second oxygen (not hydrogen) makes it an ester.

🏷️ Naming System

📝 Two-part naming approach

The naming follows a pattern similar to ionic salts, even though esters are covalent compounds:

  1. First part: Name of the alkyl or aryl group attached to the single-bonded oxygen
  2. Second part: Name of the acid portion with "-ic" changed to "-ate"

🔤 Common vs IUPAC names

Condensed FormulaCommon NameIUPAC Name
HCOOCH₃methyl formatemethyl methanoate
CH₃COOCH₃methyl acetatemethyl ethanoate
CH₃COOCH₂CH₃ethyl acetateethyl ethanoate
CH₃CH₂COOCH₂CH₃ethyl propionateethyl propanoate
  • Both systems follow the same two-part structure.
  • The difference lies in whether the acid portion uses common names (formate, acetate, propionate, butyrate) or systematic IUPAC names (methanoate, ethanoate, propanoate, butanoate).

🎯 Naming process step-by-step

Step 1: Identify the alkyl/aryl group directly attached to the oxygen atom.

  • Example: In a structure with a butyl group attached to oxygen → "butyl"

Step 2: Identify the acid-derived portion (the part with the carbonyl group).

  • Count the carbon atoms in this portion.
  • Example: Three carbon atoms → "propionate" (common) or "propanoate" (IUPAC)

Step 3: Combine the names.

  • Example: butyl propionate or butyl propanoate

🖼️ Special cases

  • Isopropyl groups: When the alkyl group is attached by its middle carbon atom, use "isopropyl."
    • Example: isopropyl benzoate
  • Aromatic esters: When derived from benzoic acid, use "benzoate" (same in both common and IUPAC).
    • Example: ethyl benzoate

🌸 Natural Occurrence and Applications

🌺 Where esters are found

  • Occur widely in nature.
  • Responsible for characteristic fragrances of fruits and flowers.
  • Generally have pleasant odors, unlike carboxylic acids.

🧴 Practical uses

  • Perfumes: Both natural and synthetic esters used for fragrance.
  • Flavoring agents: Flavor chemists duplicate natural odors/tastes after chemical analysis.
  • Biological importance: Fats and vegetable oils are esters of long-chain fatty acids and glycerol; esters of phosphoric acid are critical to life.

🔄 Drawing Structures from Names

✏️ Construction method

When given a name like "ethyl pentanoate":

Step 1: Draw the acid-derived portion first.

  • For pentanoate: draw five carbon atoms, remembering the last carbon is part of the carboxyl group.

Step 2: Attach the alkyl group.

  • Attach the ethyl group to the bond that would ordinarily hold the hydrogen atom in the carboxyl group.

🔍 Reverse process: from structure to components

To identify the parent acid and alcohol:

  • The acid portion includes the carbonyl carbon and everything attached to it (except the OR′ group).
  • The alcohol portion is the OR′ group plus a hydrogen.
  • Example: isopropyl hexanoate can be made from hexanoic acid and isopropyl alcohol.
94

Physical Properties of Esters

Physical Properties of Esters

🧭 Overview

🧠 One-sentence thesis

Esters occupy an intermediate position in boiling points and solubility because they have polar bonds but cannot form hydrogen bonds with themselves, only with water.

📌 Key points (3–5)

  • Boiling point position: Esters fall between nonpolar alkanes (lowest) and alcohols (highest) because they have polar bonds but no intermolecular hydrogen bonding.
  • Why esters can't hydrogen-bond with themselves: Esters lack a hydrogen atom bonded to oxygen or nitrogen, so ester molecules cannot form hydrogen bonds with each other.
  • Water solubility pattern: Low-molar-mass esters (roughly five or fewer carbons) are somewhat soluble in water because they can accept hydrogen bonds from water molecules.
  • Common confusion: Esters vs alcohols—both contain oxygen, but alcohols have an O–H group that allows self-hydrogen-bonding, while esters have a C=O and C–O but no H on oxygen.
  • Practical implication: The intermediate properties make esters useful as solvents and fragrance compounds.

🌡️ Boiling point comparisons

🌡️ Where esters fit

Esters have polar bonds but do not engage in hydrogen bonding and are therefore intermediate in boiling points between the nonpolar alkanes and the alcohols, which engage in hydrogen bonding.

  • Nonpolar alkanes: lowest boiling points (no polarity, no hydrogen bonding).
  • Esters: intermediate boiling points (polar C=O and C–O bonds, but no H-bonding between ester molecules).
  • Alcohols: highest boiling points (polar O–H bonds plus strong intermolecular hydrogen bonding).

🔗 Why esters cannot self-hydrogen-bond

  • Hydrogen bonding requires a hydrogen atom attached to a highly electronegative atom (O, N, or F) and a lone pair on another electronegative atom.
  • Esters have the carbonyl oxygen (C=O) and ether oxygen (C–O–C), but no hydrogen is bonded to oxygen.
  • Therefore, one ester molecule cannot donate a hydrogen to another ester molecule.
  • Example: Compare CH₃CH₂CH₂CH₂OH (butanol, boiling point 118 °C) with CH₃COOCH₃ (methyl acetate, boiling point 57 °C)—the alcohol boils much higher because of intermolecular hydrogen bonding.

📋 Comparison table

Compound typeExampleBoiling point (°C)Reason
AlcoholCH₃CH₂CH₂CH₂OH118Intermolecular H-bonding
EsterCH₃COOCH₃57Polar bonds, no self H-bonding
AlkaneSimilar molar massLower than esterNonpolar, no H-bonding

Don't confuse: The presence of oxygen does not automatically mean hydrogen bonding—only O–H, N–H, or F–H bonds allow a molecule to donate hydrogen bonds.

💧 Water solubility

💧 Low-molar-mass esters dissolve

Ester molecules can engage in hydrogen bonding with water, so esters of low molar mass are therefore somewhat soluble in water.

  • Water molecules have O–H bonds and can donate hydrogen bonds to the carbonyl oxygen (C=O) in the ester.
  • The ester oxygen atoms can accept hydrogen bonds from water.
  • This interaction allows smaller esters to dissolve.

💧 Solubility cutoff

  • The excerpt states that esters of low molar mass are "somewhat soluble."
  • As the hydrocarbon portion of the ester grows larger, the nonpolar character dominates and water solubility decreases.
  • Example: Methyl acetate (low molar mass) is more soluble than octyl acetate (higher molar mass, longer hydrocarbon chain).

🔍 How to distinguish ester solubility from alcohol solubility

  • Both esters and alcohols can hydrogen-bond with water.
  • Alcohols can also hydrogen-bond with each other, making them more strongly associated and often more soluble in water at comparable sizes.
  • The excerpt's answer to a review exercise confirms: butyric acid (which has an O–H group) is more soluble in water than methyl butyrate (an ester) because of hydrogen bonding with water.

🧪 Key takeaways from the excerpt

🧪 Summary statements

The excerpt provides two explicit key takeaways:

  1. Boiling points: Esters have polar bonds but do not engage in hydrogen bonding (with themselves) and are therefore intermediate in boiling points between the nonpolar alkanes and the alcohols, which engage in hydrogen bonding.
  2. Solubility: Ester molecules can engage in hydrogen bonding with water, so esters of low molar mass are therefore somewhat soluble in water.

🧪 Practice exercise logic

  • The exercises ask students to compare esters with carboxylic acids and alcohols.
  • The answer pattern: carboxylic acids and alcohols have intermolecular hydrogen bonding (because of O–H groups), so they have higher boiling points than esters of similar size.
  • Example from the excerpt: CH₃CH₂CH₂COOH (butanoic acid) has a higher boiling point than CH₃CH₂CH₂COOCH₃ (methyl butyrate) because there is intermolecular hydrogen bonding in the acid but not in the ester.

Don't confuse: "No intermolecular hydrogen bonding" in the ester means no H-bonding between ester molecules; esters can still H-bond with water molecules.

95

Preparation of Esters

Preparation of Esters

🧭 Overview

🧠 One-sentence thesis

Amides are formed by reacting a carboxylic acid with ammonia or an amine, splitting out water to create a bond between the nitrogen atom and the carbonyl carbon atom.

📌 Key points (3–5)

  • Formation mechanism: ammonia or an amine adds to a carboxylic acid, water is split out, and a nitrogen-to-carbonyl-carbon bond forms.
  • Reaction speed: the laboratory reaction at room temperature is very slow; in living cells, enzymes catalyze amide formation.
  • Polyamides: a diacid reacting with a diamine yields a polyamide polymer (e.g., nylons) by splitting out water repeatedly.
  • Biological importance: in proteins, the amide functional group is called a peptide bond, and proteins are polyamides formed by joining amino acids.
  • Common confusion: amide formation vs ester formation—both split out water, but amides use ammonia/amines (nitrogen source) while esters use alcohols (oxygen source).

🔬 Formation mechanism and conditions

🔬 Basic reaction

Amide formation: the addition of ammonia (NH₃) to a carboxylic acid forms an amide.

  • Water molecules are split out during the reaction.
  • A bond is formed between the nitrogen atom (from ammonia or amine) and the carbonyl carbon atom (from the carboxylic acid).
  • Example: butanoic acid (CH₃CH₂CH₂COOH) + ammonia (NH₃) → butanamide (CH₃CH₂CH₂CONH₂) + water.

⏱️ Reaction speed

  • At room temperature in the laboratory, the reaction is very slow.
  • In living cells, enzymes catalyze the reaction, making it much faster.
  • This explains why amide formation is efficient in biological systems despite being sluggish under ordinary lab conditions.

🧪 General pattern

  • The excerpt shows that any carboxylic acid can react with ammonia or an amine.
  • Example: hexanoic acid (CH₃CH₂CH₂CH₂CH₂COOH) + propylamine (CH₃CH₂CH₂NH₂) → CH₃CH₂CH₂CH₂CH₂CONHCH₂CH₂CH₃ + water.
  • The nitrogen from the amine replaces the hydroxyl group of the acid, forming the amide linkage.

🧬 Biological and polymer applications

🧬 Peptide bonds and proteins

  • In proteins, the amide functional group is called a peptide bond.
  • Proteins are polyamides: long chains formed by joining amino acids.
  • Each amino acid linkage involves splitting out water and forming an amide bond.
  • This is the same chemistry as laboratory amide formation, but catalyzed by enzymes in cells.

🧵 Polyamides (nylons)

Polyamide: a condensation polymer in which the monomer units are joined by an amide linkage.

  • Formed by reacting a diacid (a molecule with two carboxylic acid groups) with a diamine (a molecule with two amine groups).
  • The excerpt gives adipic acid and 1,6-hexanediamine as common monomers.
  • The monomers condense by splitting out water to form a new product that is still difunctional (has reactive groups at both ends), so it can react further to yield a long polymer chain.

🏭 Practical uses of nylons

  • Synthetic fibers: ropes, sails, carpets, clothing, tires, brushes, parachutes.
  • Molded blocks: electrical equipment, gears, bearings, valves.
  • The wide range of applications reflects the strength and versatility of polyamide materials.

🔄 Comparison with ester formation

🔄 Parallel chemistry

FeatureEster formationAmide formation
ReactantsCarboxylic acid + alcoholCarboxylic acid + ammonia/amine
Key atomOxygen (from alcohol)Nitrogen (from ammonia/amine)
Water split outYesYes
Polymer typePolyester (diol + diacid)Polyamide (diamine + diacid)
  • Both reactions are condensation reactions: small molecules (water) are eliminated.
  • The excerpt explicitly compares polyamide formation to polyester formation (mentioned as Section 15.8).
  • Don't confuse: esters have an oxygen atom bonded to the carbonyl carbon; amides have a nitrogen atom bonded to the carbonyl carbon.

🧩 Difunctional monomers

  • A diol (two alcohol groups) + diacid → polyester.
  • A diamine (two amine groups) + diacid → polyamide.
  • In both cases, the product remains difunctional after the first reaction, allowing the chain to grow into a polymer.

🧪 Physical properties context

🧪 Hydrogen bonding in amides

  • The excerpt mentions that nitrogen-to-hydrogen (N–H) and carbon-to-oxygen double (C=O) bonds in amides can engage in hydrogen bonding.
  • This explains why amides have much higher boiling points than esters of similar molar mass.
  • Example: butyramide has a higher boiling point than ethyl acetate because butyramide can hydrogen bond, but ethyl acetate cannot.

💧 Water solubility

  • Amides of five or fewer carbon atoms are soluble in water.
  • The N–H and C=O bonds can engage in hydrogen bonding with water molecules.
  • Example: acetamide (CH₃CONH₂) is more soluble in water than 1-butene (CH₂=CHCH₂CH₃) because acetamide can hydrogen bond with water, but 1-butene cannot.
  • Don't confuse: solubility depends on the ability to form hydrogen bonds with water, not just the presence of polar bonds.
96

Hydrolysis of Esters

Hydrolysis of Esters

🧭 Overview

🧠 One-sentence thesis

Ester hydrolysis—splitting an ester with water—can proceed under acidic conditions (reversible, yielding a carboxylic acid and alcohol) or basic conditions (going to completion, yielding a carboxylate salt and alcohol).

📌 Key points (3–5)

  • What hydrolysis is: a reaction in which water splits the ester bond, replacing the alkoxy (OR′) group with another group.
  • Acidic hydrolysis: reversible, catalyzed by strong acid, produces a carboxylic acid and an alcohol; does not go to completion.
  • Basic hydrolysis (saponification): uses a base as a reactant (not just a catalyst), goes to completion, produces a carboxylate salt and an alcohol.
  • Common confusion: acidic vs basic hydrolysis—acidic is reversible and incomplete; basic is irreversible and complete.
  • Why it matters: basic hydrolysis is the process used to make soap from fats and oils (saponification).

🔬 What happens in ester hydrolysis

🔬 The general mechanism

Hydrolysis: literally "splitting with water."

  • In typical ester reactions, the alkoxy (OR′) group of the ester is replaced by another group.
  • Hydrolysis specifically involves water breaking the ester bond.
  • The reaction can be catalyzed by either an acid or a base, leading to different products and outcomes.

🧪 How water splits the ester

  • Water (HOH) splits the ester linkage.
  • The H from water joins to the oxygen atom in the OR part of the ester.
  • The OH from water joins to the carbonyl carbon atom.
  • Example: In acidic hydrolysis of ethyl butyrate, water splits the bond so that H attaches to the ethoxy oxygen and OH attaches to the carbonyl carbon, forming butyric acid and ethanol.

⚗️ Acidic hydrolysis

⚗️ Conditions and reversibility

  • The ester is heated with a large excess of water containing a strong-acid catalyst.
  • The reaction is reversible and does not go to completion.
  • Acidic hydrolysis is simply the reverse of esterification (the formation of esters from carboxylic acids and alcohols).

🧴 Products of acidic hydrolysis

  • Products: a carboxylic acid and an alcohol.
  • Example: Butyl acetate and water react to form acetic acid and 1-butanol, but the reaction is reversible and incomplete.
  • Example: Ethyl butyrate (CH₃CH₂CH₂COOCH₂CH₃) hydrolyzes to butyric acid (butanoic acid) and ethanol.

🔄 Why it doesn't go to completion

  • Because acidic hydrolysis is the reverse of esterification, the forward and reverse reactions compete.
  • The reaction reaches an equilibrium rather than converting all ester to products.
  • Don't confuse: acidic hydrolysis is incomplete; basic hydrolysis (below) goes to completion.

🧼 Basic hydrolysis (saponification)

🧼 What saponification means

Saponification: the hydrolysis of fats and oils in the presence of a base to make soap (from Latin sapon, "soap," and facere, "to make").

  • When a base such as sodium hydroxide (NaOH) or potassium hydroxide (KOH) is used to hydrolyze an ester, the process is called saponification.
  • Soaps are prepared by the alkaline hydrolysis of fats and oils, which are esters.

🧪 Conditions and completeness

  • In saponification, the base is a reactant, not simply a catalyst.
  • The reaction goes to completion (irreversible).
  • This is a key difference from acidic hydrolysis, which is reversible and incomplete.

🧴 Products of basic hydrolysis

  • Products: a carboxylate salt and an alcohol.
  • The acid portion of the ester becomes the salt of the acid (e.g., sodium acetate, potassium benzoate).
  • The alcohol portion of the ester is released as the free alcohol.
  • Example: Ethyl acetate and NaOH react to form sodium acetate and ethanol.
  • Example: Methyl benzoate in potassium hydroxide solution yields potassium benzoate (the salt) and methanol (the alcohol).

🔄 Why it goes to completion

  • The base splits the ester linkage and consumes the acid product by forming a stable salt.
  • The salt does not re-form the ester, so the reaction is driven forward to completion.
  • Don't confuse: basic hydrolysis is complete; acidic hydrolysis is incomplete.

📊 Comparing acidic and basic hydrolysis

FeatureAcidic hydrolysisBasic hydrolysis (saponification)
Catalyst or reactantStrong acid (catalyst)Base (reactant, not just catalyst)
ProductsCarboxylic acid + alcoholCarboxylate salt + alcohol
ReversibilityReversible (does not go to completion)Irreversible (goes to completion)
Relationship to esterificationReverse of esterificationNot the reverse; driven by salt formation
ExampleButyl acetate → acetic acid + 1-butanolEthyl acetate + NaOH → sodium acetate + ethanol
  • The excerpt emphasizes that the extent of reaction differs: basic hydrolysis is complete, acidic hydrolysis is incomplete.
  • The products differ in the acid form: free carboxylic acid (acidic) vs carboxylate salt (basic).
97

Esters of Phosphoric Acid

Esters of Phosphoric Acid

🧭 Overview

🧠 One-sentence thesis

Phosphoric acid esters are crucial biochemical molecules that store and transfer energy in cells and serve as structural components of membranes and genetic material.

📌 Key points (3–5)

  • What they are: esters formed when phosphoric acid (or related acids like pyrophosphoric or triphosphoric acid) reacts with alcohols.
  • How they form: phosphoric acid can react with one, two, or three alcohol molecules to form monoalkyl, dialkyl, or trialkyl esters.
  • Energy storage: phosphoanhydride bonds in molecules like ATP store high-energy bonds from food metabolism and release energy when hydrolyzed.
  • Biological roles: present in every plant and animal cell as energy intermediates and structural components of phospholipids and nucleic acids.
  • Common confusion: phosphoric acid esters are not unique to carboxylic acids—inorganic acids like nitric, sulfuric, and phosphoric acid also form esters.

🧪 Formation and structure

🧪 What phosphoric acid esters are

Phosphoric acid esters: compounds formed when phosphoric acid (H₃PO₄) or related inorganic acids react with alcohols.

  • Just as carboxylic acids form esters with alcohols, inorganic acids (nitric acid, sulfuric acid, phosphoric acid) also form esters.
  • The excerpt emphasizes that phosphoric acid esters are "especially important in biochemistry."

🔢 Types by degree of substitution

Phosphoric acid can form three types of esters depending on how many alcohol molecules react:

TypeNumber of alcohol moleculesResult
Monoalkyl esterOneOne alcohol group attached
Dialkyl esterTwoTwo alcohol groups attached
Trialkyl esterThreeThree alcohol groups attached
  • Example: diethyl hydrogen phosphate has two alcohol groups; methyl dihydrogen phosphate has one.

🔗 Related phosphoric acids

  • Pyrophosphoric acid and triphosphoric acid also form esters.
  • These esters are present in every plant and animal cell.
  • They function as biochemical intermediates in transforming food into usable energy.

⚡ Energy storage and release

⚡ Phosphoanhydride bonds in ATP

Phosphoanhydride bonds: the bonds between phosphate units in molecules like adenosine triphosphate (ATP).

  • These are described as "high-energy bonds."
  • They store energy obtained from the metabolism of foods.
  • When ATP is hydrolyzed (broken down by water), energy is released.

🔋 How energy is used

  • The energy released from ATP hydrolysis is used for biochemical processes.
  • Example: muscle contraction requires energy released from ATP hydrolysis.
  • The excerpt describes this as releasing energy "as it is needed."

🏗️ Structural roles in cells

🏗️ Components of cell structures

Phosphate esters serve as important structural building blocks:

  • Phospholipids: structural constituents of cell membranes.
  • Nucleic acids: structural constituents of genetic material (DNA and RNA).
  • The excerpt notes these are covered in more detail in other chapters (Chapter 17 for phospholipids, Chapter 19 for nucleic acids).

🧬 Ubiquity in living systems

  • Esters of phosphoric, pyrophosphoric, and triphosphoric acids are present in every plant and animal cell.
  • This universal presence underscores their fundamental importance to life.

💊 Additional context

💊 Other inorganic acid esters

  • The excerpt mentions nitroglycerin (glyceryl trinitrate) as an example of an ester formed from glycerol and nitric acid.
  • It is described as "explosive" but also used in medicine to relieve chest pain in heart disease.
  • Don't confuse: this is an example of a nitric acid ester, not a phosphoric acid ester, showing that multiple inorganic acids form biologically or medically relevant esters.
98

Amines: Structures and Names

Amines: Structures and Names

🧭 Overview

🧠 One-sentence thesis

Amines are classified by the number of carbon-containing groups bonded directly to the nitrogen atom, and this classification determines both their naming and their structural properties.

📌 Key points (3–5)

  • What amines are: derivatives of ammonia (NH₃) in which one, two, or all three hydrogen atoms are replaced by hydrocarbon groups.
  • How to classify: primary (1°) = one alkyl/aryl group on nitrogen; secondary (2°) = two groups; tertiary (3°) = three groups.
  • Common confusion: For alcohols, classification depends on the carbon atom bearing the OH group, but for amines, classification depends on the nitrogen atom itself—so isopropylamine is primary even though isopropyl alcohol is secondary.
  • Naming simple amines: list the alkyl groups alphabetically, then add the suffix "-amine."
  • Special case: aniline is the primary amine with nitrogen attached directly to a benzene ring; other aryl amines are named as derivatives of aniline.

🔬 What amines are and how they're classified

🔬 The amine functional group

An amine is a derivative of ammonia in which one, two, or all three hydrogen atoms are replaced by hydrocarbon groups.

  • The functional group is the amino group (NH₂) or nitrogen with attached hydrocarbon groups.
  • Amines are related to the inorganic compound ammonia.
  • The nitrogen atom is the key structural feature.

🔢 Primary, secondary, and tertiary amines

The classification depends on how many carbon atoms are bonded directly to the nitrogen atom:

ClassificationNumber of alkyl/aryl groups on nitrogenExample structure
Primary (1°)OneCH₃CH₂CH₂NH₂ (propylamine)
Secondary (2°)TwoCH₃CH₂NHCH₂CH₃ (diethylamine)
Tertiary (3°)Three(CH₃)₂NCH₂CH₃ (ethyldimethylamine)
  • Example: CH₃CH₂CH₂NHCH₃ has one methyl and one propyl group on nitrogen → secondary amine (methylpropylamine).
  • Don't confuse: For alcohols, you count carbons bonded to the carbon bearing OH; for amines, you count groups bonded to nitrogen itself.

⚠️ Alcohol vs amine classification

  • Isopropylamine has one alkyl group on nitrogen → primary amine.
  • Isopropyl alcohol has the OH group on a secondary carbon → secondary alcohol.
  • The excerpt emphasizes: "we look at the number of carbon atoms bonded to the carbon atom bearing the OH group, not the oxygen atom itself" for alcohols, but for amines we look at the nitrogen atom.

📝 Naming simple aliphatic amines

📝 Common naming system

  • List the alkyl groups attached to nitrogen alphabetically.
  • Add the suffix -amine.
  • Example: two ethyl groups → diethylamine; one methyl and one propyl → methylpropylamine.

🧩 More complex amines

  • When the amine incorporates other functional groups or the alkyl groups cannot be simply named, the amino group (NH₂) is named as a substituent.
  • Example: 2-amino-3-methylpentane → start with the pentane chain, attach a methyl group at carbon 3 and an amino group at carbon 2.

🌸 Aromatic amines and aniline

🌸 Aniline as the parent compound

Aniline: the primary amine in which the nitrogen atom is attached directly to a benzene ring.

  • Aryl amines are named as derivatives of aniline.
  • Example: a benzene ring with NH₂ and a bromine at the 3-position (or meta position) → 3-bromoaniline or m-bromoaniline.

🎨 Drawing and classifying aniline derivatives

  • Example: p-ethylaniline → aniline with an ethyl group at the para position → primary amine (because nitrogen has only one aryl group and two hydrogens).
  • The excerpt shows that aniline derivatives are still classified by the number of groups on nitrogen: aniline itself is primary.

⚡ Ammonium ions

⚡ Naming ammonium ions

  • Ammonium (NH₄⁺) ions with alkyl groups replacing hydrogen atoms are named analogously to simple amines.
  • The parent species is regarded as the NH₄⁺ ion.
  • Alkyl groups are named as substituents.

🧪 Examples of ammonium ion names

Ion formulaName
CH₃NH₃⁺methylammonium ion
(CH₃)₂NH₂⁺dimethylammonium ion
(CH₃)₃NH⁺trimethylammonium ion
(CH₃)₄N⁺tetramethylammonium ion
  • The ion from aniline (C₆H₅NH₃⁺) is called the anilinium ion.
  • Example: [(CH₃CH₂)₃NH]⁺ I⁻ → triethylammonium iodide.
99

Physical Properties of Amines

Physical Properties of Amines

🧭 Overview

🧠 One-sentence thesis

Amines exhibit distinct boiling points and water solubility patterns determined by their ability to engage in hydrogen bonding, which varies by amine class and molecular structure.

📌 Key points (3–5)

  • Hydrogen bonding capability: Primary and secondary amines can hydrogen bond through N–H bonds; tertiary amines cannot because they lack hydrogen on nitrogen.
  • Boiling point hierarchy: Primary and secondary amines have higher boiling points than alkanes/ethers of similar molar mass but lower than alcohols; tertiary amines are comparable to alkanes/ethers.
  • Water solubility: All three amine classes can hydrogen bond with water, making low-molar-mass amines quite soluble; solubility borderline is at five or six carbon atoms.
  • Common confusion: Don't confuse tertiary amines with primary/secondary—tertiary amines cannot hydrogen bond with each other (no N–H), but they can still hydrogen bond with water (through the lone pair on nitrogen).
  • Structural impact: Higher molar mass increases boiling point within the same amine class; more carbon atoms decrease water solubility.

🔗 Hydrogen Bonding and Amine Classes

🔗 What determines hydrogen bonding in amines

Hydrogen bonding in amines: the ability of nitrogen-to-hydrogen (N–H) bonds to form intermolecular attractions.

  • Primary (1°) and secondary (2°) amines have at least one hydrogen atom bonded to nitrogen, so they can form N–H···N hydrogen bonds with each other.
  • Tertiary (3°) amines have no hydrogen on nitrogen (all three bonds go to carbon groups), so they cannot hydrogen bond with other amine molecules.
  • All three classes retain a lone pair on nitrogen, which allows them to accept hydrogen bonds from water (O–H···N).

🧪 Why this matters for physical properties

  • Hydrogen bonding between molecules increases intermolecular forces.
  • Stronger intermolecular forces → higher energy needed to separate molecules → higher boiling point.
  • Example: Butylamine (1°) has N–H bonds and can hydrogen bond, so it boils higher than pentane (an alkane of similar molar mass that cannot hydrogen bond).

🌡️ Boiling Point Patterns

🌡️ Primary and secondary amines vs alkanes and ethers

ComparisonBoiling pointReason
1° or 2° amine vs alkane (similar molar mass)Amine higherAmines can hydrogen bond; alkanes cannot
1° or 2° amine vs ether (similar molar mass)Amine higherN–H bonds form stronger hydrogen bonds than the lone pairs on ether oxygen
  • The excerpt emphasizes that primary and secondary amines have higher boiling points than alkanes or ethers of similar molar mass.
  • Example: Diethylamine (2°, molar mass 73) has a boiling point of 55°C, while dipropyl ether (molar mass 102) has a boiling point of 91°C—but when comparing similar molar masses, the amine is higher.

🍷 Primary and secondary amines vs alcohols

  • Alcohols have higher boiling points than amines of similar molar mass.
  • Reason: Oxygen is more electronegative than nitrogen, so O–H bonds form stronger hydrogen bonds than N–H bonds.
  • Example: Butyl alcohol (molar mass 74) boils at 118°C, while butylamine (molar mass 73) boils at 78°C.

🔺 Tertiary amines

  • Tertiary amines cannot engage in hydrogen bonding with each other because they lack N–H bonds.
  • Their boiling points are comparable to alkanes and ethers of similar molar mass.
  • Example: Triethylamine (3°, molar mass 101) boils at 90°C, close to dipropyl ether (molar mass 102) at 91°C.
  • Don't confuse: tertiary amines still have a lone pair, so they can hydrogen bond with water—just not with other tertiary amine molecules.

⚖️ Molar mass within the same class

  • Within the same amine class, higher molar mass → higher boiling point.
  • Example: CH₃NH₂ (methylamine) has a lower boiling point than CH₃CH₂CH₂CH₂CH₂NH₂ (pentylamine) because pentylamine has greater molar mass.

💧 Water Solubility

💧 All three classes can dissolve in water

  • All three amine classes (primary, secondary, tertiary) can engage in hydrogen bonding with water.
  • Mechanism: The lone pair on nitrogen accepts a hydrogen bond from water's O–H, and (for 1° and 2° amines) the N–H can donate a hydrogen bond to water's oxygen.
  • Result: Amines of low molar mass are quite soluble in water.

🧱 Solubility borderline

  • The excerpt states that the borderline of solubility in water is at five or six carbon atoms.
  • As the carbon chain lengthens, the nonpolar hydrocarbon portion dominates, reducing solubility.
  • Example: Ethylamine (CH₃CH₂NH₂) is miscible with water, but longer-chain amines like dipropylamine (101 molar mass) have limited solubility (4 g per 100 mL).

🔄 Comparing solubility to alkanes

  • Amines are more soluble in water than alkanes of similar size.
  • Reason: Alkanes cannot engage in hydrogen bonding; amines can.
  • Example: CH₃CH₂NH₂ (ethylamine) is more soluble in water than CH₃CH₂CH₃ (propane) because the amine can hydrogen bond with water.

🧬 Additional Context

🦠 Odor and biological amines

  • Simple amines smell like ammonia; higher aliphatic amines smell like decaying fish.
  • The stench of rotting fish comes from diamines such as putrescine and cadaverine, which arise from decarboxylation of amino acids (ornithine and lysine) in animal cells.

⚠️ Toxicity of aromatic amines

  • Aromatic amines are generally quite toxic and readily absorbed through the skin.
  • Several aromatic amines, including β-naphthylamine, are potent carcinogens.
  • Workers must exercise caution when handling these compounds.
100

Amines as Bases

Amines as Bases

🧭 Overview

🧠 One-sentence thesis

Amines act as bases because their nitrogen atoms have lone electron pairs that can accept protons, forming salts that are typically water-soluble and important in pharmaceutical applications.

📌 Key points (3–5)

  • Why amines are basic: the nitrogen atom has a lone pair of electrons that can accept a proton, just like ammonia.
  • Typical reaction: amines react with acids (especially strong acids) to form substituted ammonium salts that are soluble in water.
  • Naming convention: amine salts are named with the cation name followed by the anion name; drugs often use an older system (e.g., "hydrochloride").
  • Heterocyclic amines: ring compounds with nitrogen atoms in the ring; many are alkaloids with physiological activity.
  • Common confusion: even water-insoluble amines will react with strong acids to form water-soluble salts.

🧪 Basic behavior of amines

🔬 Why amines accept protons

Amines act as bases because the nitrogen atom has a lone pair of electrons that can accept a proton.

  • This is the same mechanism as ammonia (NH₃).
  • The lone pair on nitrogen is the key structural feature enabling basicity.
  • When an amine accepts a proton, it forms a substituted ammonium ion.

⚗️ Reaction with water

  • Amines react with water to form substituted ammonium ions and hydroxide ions.
  • Example: methylamine reacts with water to form the methylammonium ion and OH⁻ ion.
  • This demonstrates the base behavior in aqueous solution.

💧 Reaction with strong acids

  • Nearly all amines react with strong acids to form salts.
  • These salts are soluble in water, even if the original amine was not very soluble.
  • Don't confuse: water solubility of the amine itself versus the salt—the salt is typically much more soluble.

🧂 Amine salts and naming

📝 How to name amine salts

  • Amine salts follow standard salt naming: cation name + anion name.
  • Example from the excerpt: the salt [CH₃NH₂CH₂CH₃]⁺ CH₃COO⁻ comes from ethylmethylamine (the base) and acetic acid (the acid).
  • The cation is the protonated amine; the anion comes from the acid.

💊 Pharmaceutical applications

  • Many amine drugs are converted to hydrochloride salts to increase water solubility.
  • An older naming system for drugs: salts of aniline and hydrochloric acid are called "aniline hydrochloride."
  • These compounds are ionic (salts), so their properties—especially solubility—reflect salt characteristics.
  • Why it matters: increased solubility in aqueous solution makes the drug more bioavailable.

🔄 Heterocyclic amines and alkaloids

🔗 What heterocyclic compounds are

Heterocyclic compounds: cyclic compounds in which one or more atoms in the ring is an element other than carbon (such as nitrogen, oxygen, or sulfur).

  • Contrast with hydrocarbon rings, where all ring atoms are carbon.
  • The name comes from Greek "heteros" meaning "other."
  • Many are important in medicine and biochemistry.

🌿 Alkaloids

Alkaloid: a nitrogen-containing organic compound obtained from plants that has physiological properties.

  • The name means "like alkalis" because these compounds are basic.
  • Many heterocyclic amines occur naturally in plants.
  • Like other amines, they are basic due to the nitrogen lone pair.

🧠 Examples of physiologically active alkaloids

The excerpt mentions three well-known alkaloids:

AlkaloidSourceMechanism/Effect
CaffeineCoffee, tea, soft drinksBlocks adenosine (a neurotransmitter); stimulant effect
NicotineTobaccoMimics acetylcholine; stimulant followed by depression; highly toxic
CocainePlantsPrevents dopamine reuptake; stimulates pleasure centers; addictive
  • Caffeine effective dose: about 200 mg (two cups of strong coffee or tea).
  • Nicotine lethal dose: estimated at about 50 mg when injected; also used as an insecticide.
  • Cocaine forms: cocaine hydrochloride (water-soluble, snorted) and crack cocaine (free base, volatile, smoked).
  • Don't confuse the salt form with the free base—they have different physical properties and routes of administration.
101

Amides: Structures and Names

Amides: Structures and Names

🧭 Overview

🧠 One-sentence thesis

Amides are organic compounds characterized by a nitrogen atom bonded to a carbonyl carbon, and they are named by replacing the acid ending of the parent carboxylic acid with "-amide."

📌 Key points (3–5)

  • Functional group definition: an amide has a nitrogen atom attached to a carbonyl carbon atom.
  • Simple vs substituted amides: simple amides have hydrogen atoms on the remaining nitrogen bonds; substituted amides have alkyl or aryl groups instead.
  • Naming rule: replace the "-ic" (common) or "-oic" (IUPAC) ending of the parent carboxylic acid with "-amide."
  • Common confusion: the amide linkage (carbonyl-carbon-to-nitrogen bond) is also called a peptide linkage in proteins—don't confuse the general functional group with its biological context.
  • Stability note: the amide linkage is quite stable and appears in protein structures.

🔬 Structure and functional group

🔬 What defines an amide

The amide functional group has a nitrogen atom attached to a carbonyl carbon atom.

  • The key structural feature is the carbonyl carbon (C=O) bonded directly to nitrogen (N).
  • This bond is called an amide linkage (or peptide linkage in proteins).
  • The excerpt emphasizes that this bond is quite stable.

🧪 Simple vs substituted amides

TypeDefinitionWhat's on the nitrogen
Simple amideBoth remaining nitrogen bonds attached to hydrogen atomsTwo H atoms
Substituted amideOne or both remaining nitrogen bonds attached to alkyl or aryl groupsAlkyl or aryl groups (not H)
  • Example: If nitrogen has two H atoms, it's a simple amide; if one H is replaced by a methyl group, it's a substituted amide.
  • Don't confuse: "simple" refers only to what is attached to nitrogen, not the size of the carbonyl side.

📝 Naming amides

📝 The core naming rule

  • Start with the name of the parent carboxylic acid (the acid from which the amide is derived).
  • Common name system: drop the "-ic" ending from the acid name and add "-amide."
  • IUPAC system: drop the "-oic" ending from the acid name and add "-amide."

🔤 Naming examples from the excerpt

Example 1: Two-carbon amide

  • Parent acid: acetic acid (common) or ethanoic acid (IUPAC).
  • The OH of the acid is replaced by an NH₂ group.
  • Drop "-ic" from "acetic" → add "-amide" → acetamide (common).
  • Drop "-oic" from "ethanoic" → add "-amide" → ethanamide (IUPAC).

Example 2: Aromatic amide

  • Parent acid: benzoic acid.
  • Drop "-oic" → add "-amide" → benzamide.

🔢 Naming with substituents

  • The excerpt mentions "β-bromobutyramide" (common) or "3-bromobutanamide" (IUPAC).
  • The position of substituents (like bromine) is indicated by Greek letters (α, β, γ...) in common names or by numbers in IUPAC names.
  • Example: "α-methylbutyramide" means a methyl group is on the carbon adjacent to the carbonyl; "2-methylbutanamide" uses the IUPAC numbering.

🧬 Biological significance

🧬 Amide linkage in proteins

  • The carbonyl-carbon-to-nitrogen bond is called an amide linkage in general chemistry.
  • In protein molecules, this same bond is called a peptide linkage.
  • The excerpt notes that this bond is found in the repeating units of proteins.
  • Don't confuse: the functional group is the same; the name changes depending on the biological context (peptide linkage is just the amide linkage in proteins).

🔗 Stability

  • The amide linkage is described as "quite stable."
  • This stability is important for the structural integrity of proteins.
102

Physical Properties of Amides

Physical Properties of Amides

🧭 Overview

🧠 One-sentence thesis

Amides exhibit high melting and boiling points due to extensive hydrogen bonding, making most simple amides solid at room temperature and soluble in water when they contain five or fewer carbon atoms.

📌 Key points (3–5)

  • Physical state: Most simple amides are solids at room temperature (except formamide), contrasting with comparable alkanes and alcohols
  • Solubility pattern: Amides with five or fewer carbons are water-soluble; borderline solubility occurs at 5-6 carbons
  • High melting/boiling points: Amides have much higher melting and boiling points than alcohols of similar molar mass due to hydrogen bonding
  • Neutral in solution: Aqueous amide solutions are typically neither acidic nor basic, unlike carboxylic acids
  • Common confusion: Don't confuse amides with esters—amides can engage in hydrogen bonding through N–H and C=O bonds, while esters cannot

🔥 Thermal properties and physical state

🧊 Solid state dominance

Most simple amides are solids at room temperature.

  • Formamide (HCONH₂) is the only liquid among simple amides
  • All other simple amides listed (acetamide, propionamide, butyramide, benzamide) are crystalline solids
  • Melting points range from 2°C (formamide) to 132°C (benzamide)
  • This contrasts sharply with comparable alkanes and alcohols, which are often liquids or gases

Why this matters: The solid state reflects strong intermolecular forces that must be overcome for melting.

🌡️ Exceptionally high melting and boiling points

Amides have much higher boiling and melting points than alcohols of similar molar mass.

Example comparison (from exercises):

  • Pentanamide (CH₃CH₂CH₂CH₂CONH₂) has a higher boiling point than propyl acetate (CH₃COOCH₂CH₂CH₃)
  • Butyramide has a higher boiling point than ethyl acetate

The reason: Amides can engage in extensive hydrogen bonding through both N–H and C=O bonds, while esters lack N–H bonds and cannot participate in hydrogen bonding to the same extent.

💧 Solubility characteristics

🌊 Water solubility pattern

  • Lower members (five or fewer carbon atoms): soluble in water
  • Borderline: five to six carbon atoms show borderline solubility
  • Higher members: decreasing solubility as carbon chain lengthens

Why the pattern exists: The polar amide group (–CONH₂) can form hydrogen bonds with water, but as the nonpolar hydrocarbon chain grows longer, the molecule becomes increasingly hydrophobic.

🔄 Neutral solutions

Amide solutions in water are usually neutral—neither acidic nor basic.

  • This distinguishes amides from carboxylic acids (which are acidic) and amines (which are basic)
  • The amide functional group does not readily donate or accept protons in aqueous solution
  • Don't confuse: Esters also form neutral solutions, but for different structural reasons

🔗 Hydrogen bonding networks

🤝 Hydrogen bonding with water

Amide molecules can engage in hydrogen bonding with water molecules.

  • The carbonyl oxygen (C=O) acts as a hydrogen bond acceptor
  • The N–H hydrogen acts as a hydrogen bond donor (when present)
  • These interactions explain the water solubility of lower-molecular-weight amides

Example: Propanamide (CH₃CH₂CONH₂) is more soluble in water than 1-pentene (CH₂=CHCH₂CH₂CH₃) because the N–H and C=O bonds can engage in hydrogen bonding with water, while 1-pentene cannot.

🔗 Amide-to-amide hydrogen bonding

Amides with a hydrogen atom on the nitrogen can engage in hydrogen bonding with each other.

  • This creates extended hydrogen bonding networks in all directions
  • Both the N–H···O=C pattern allows for multiple hydrogen bonds per molecule
  • This extensive network is responsible for the high melting and boiling points

Biological significance: Similar hydrogen bonding plays a critical role in determining the structure and properties of proteins, DNA, and RNA—the excerpt notes these are "giant molecules so important to life processes."

📊 Comparison table

PropertyAmidesEstersAlcohols (similar mass)
Physical state (room temp)Mostly solidLiquidLiquid
Boiling pointHighModerateLower than amides
Water solubility (low MW)HighModerateHigh
Hydrogen bonding capabilityYes (N–H and C=O)Limited (C=O only)Yes (O–H)
Solution pHNeutralNeutralNeutral

Key distinction for exercises: When comparing boiling points, amides with N–H bonds will have higher boiling points than esters or other compounds that cannot form extensive hydrogen bonding networks.


Note: The excerpt references that this hydrogen bonding pattern is crucial for biological macromolecules (proteins, DNA, RNA) discussed in later chapters, emphasizing that understanding amide properties is foundational for biochemistry.

103

Formation of Amides

Formation of Amides

🧭 Overview

🧠 One-sentence thesis

Amino acids join together through amide linkages called peptide bonds to form chains that can grow into peptides and proteins, with the specific sequence of amino acids being critical for biological activity.

📌 Key points (3–5)

  • How peptide bonds form: the amino group of one amino acid reacts with the carboxyl group of another, releasing water and creating an amide linkage.
  • Chain growth mechanism: the product retains reactive amino and carboxyl groups at opposite ends, allowing continuous addition of more amino acids.
  • Naming by length: two units = dipeptide, three = tripeptide, ~50 or more = protein or polypeptide.
  • Sequence matters: not just which amino acids are present, but their order determines whether a peptide or protein is physiologically active.
  • Common confusion: peptide bond vs general amide bond—a peptide bond is specifically the amide linkage joining amino acid units.

🔗 How peptide bonds form

🔗 The basic reaction mechanism

Peptide bond: the amide bond joining two amino acid units in a peptide or protein.

  • The amino group (–NH₂) on one amino acid reacts with the carboxyl group (–COOH) on another.
  • This reaction releases one molecule of water (H₂O).
  • The result is an amide linkage connecting the two amino acids.
  • This is similar to the general reaction between ammonia and a carboxylic acid to form an amide (discussed in Chapter 15).

⚙️ Why the chain can keep growing

  • After two amino acids join, the product molecule still has:
    • A reactive amino group on one end (the left end by convention).
    • A reactive carboxyl group on the other end (the right end by convention).
  • These free functional groups can react with additional amino acids.
  • The process can continue until thousands of units have joined together.
  • Example: Start with two amino acids → dipeptide. Add a third → tripeptide. Continue adding → eventually a large protein.

📏 Naming and structure conventions

📏 Chain length terminology

TermNumber of amino acidsNotes
Dipeptide2Two amino acid units
Tripeptide3Three amino acid units
PeptideUnspecified lengthGeneral term for any amino acid chain
Protein or polypeptide~50 or moreLonger chains; physiologically active proteins may contain one or more polypeptide chains

🧭 Directional convention

  • Peptide and protein structures are always drawn with:
    • N-terminal end (amino group free) on the left.
    • C-terminal end (carboxyl group free) on the right.
  • This convention helps standardize how sequences are read and compared.

🧬 Why sequence is critical

🧬 Order matters for function

  • It is not enough for a peptide or protein to contain certain amounts of specific amino acids.
  • The order (sequence) in which the amino acids are connected is also of critical importance.
  • For peptides and proteins to be physiologically active, the sequence must be correct.

🧪 Example: Bradykinin

  • Bradykinin is a nine-amino acid peptide produced in the blood.
  • Its sequence is: arg-pro-pro-gly-phe-ser-pro-phe-arg.
  • Changing the order of these amino acids would produce a different molecule with different (or no) biological activity.
  • Don't confuse: having the same amino acids in different order ≠ the same peptide. Sequence defines identity and function.
104

Chemical Properties of Amides: Hydrolysis

Chemical Properties of Amides: Hydrolysis

🧭 Overview

🧠 One-sentence thesis

Amides resist hydrolysis in plain water but break down into a carboxylic acid and ammonia (or an amine) when heated with added acid or base, or when catalyzed by enzymes in living cells.

📌 Key points (3–5)

  • Amides are unusually stable: they resist hydrolysis in plain water, even after prolonged heating.
  • Acid or base enables hydrolysis: added acid or base causes amides to hydrolyze at a moderate rate.
  • Products depend on conditions: acid hydrolysis gives a carboxylic acid and an ammonium salt; base hydrolysis gives a carboxylate salt and ammonia (or amine).
  • Common confusion: the immediate product vs. the final product—in acid, ammonia or amine is neutralized to form a salt; in base, the carboxylic acid is neutralized to form a salt.
  • Biological relevance: in living cells, enzymes catalyze amide hydrolysis.

🛡️ Stability and resistance to hydrolysis

🛡️ Plain water does not hydrolyze amides

Generally, amides resist hydrolysis in plain water, even after prolonged heating.

  • Amides are much more stable than esters or other carbonyl derivatives.
  • Water alone, even with heat, cannot break the amide linkage at a practical rate.
  • This stability is important for biological molecules like proteins, which contain many amide (peptide) linkages.

⚗️ Acid or base is required

  • In the presence of added acid or base, hydrolysis proceeds at a moderate rate.
  • The excerpt emphasizes that acid or base must be added—it is not spontaneous.
  • Example: heating an amide with hydrochloric acid or sodium hydroxide solution will cause it to break down.

🧬 Enzyme catalysis in living cells

  • In living cells, amide hydrolysis is catalyzed by enzymes.
  • Enzymes allow the reaction to occur under mild biological conditions (body temperature, neutral pH).
  • This is how proteins are broken down into amino acids during digestion.

🧪 Hydrolysis products under different conditions

🧪 Acid hydrolysis products

Hydrolysis of an amide in acid solution actually gives a carboxylic acid and the salt of ammonia or an amine (the ammonia or amine initially formed is neutralized by the acid).

  • The amide bond breaks to form a carboxylic acid and ammonia (or an amine).
  • However, because the reaction occurs in acid solution, the ammonia or amine is immediately neutralized.
  • Final products: carboxylic acid + ammonium salt (or amine salt).
  • Example: when butyramide is hydrolyzed in hydrochloric acid, the products are butyric acid (CH₃CH₂CH₂COOH) and ammonium chloride (NH₄Cl), not free ammonia.

🧪 Base hydrolysis products

Basic hydrolysis gives a salt of the carboxylic acid and ammonia or an amine.

  • The amide bond breaks to form a carboxylic acid and ammonia (or an amine).
  • Because the reaction occurs in base solution, the carboxylic acid is neutralized.
  • Final products: carboxylate salt + ammonia (or amine).
  • Example: when pentanamide (CH₃CH₂CH₂CH₂CONH₂) is hydrolyzed in NaOH solution, the products are sodium pentanoate (CH₃CH₂CH₂CH₂COO⁻Na⁺) and ammonia (NH₃).

🔄 Don't confuse immediate and final products

  • The immediate product of breaking the amide bond is always a carboxylic acid and ammonia (or amine).
  • The final products depend on whether acid or base is present:
    • Acid neutralizes the ammonia/amine → you get an ammonium/amine salt.
    • Base neutralizes the carboxylic acid → you get a carboxylate salt.
  • The excerpt's note emphasizes this distinction to avoid confusion.

📝 Worked examples

📝 Hydrolysis of simple amides

The excerpt provides two examples:

Example 1: Butyramide

  • Butyramide is a simple amide (contains NH₂ group).
  • Hydrolysis produces butyric acid and ammonia.
  • Equation (in words): butyramide + water → butyric acid + ammonia.

Example 2: Benzamide

  • Benzamide is an aromatic amide (amide group attached to a benzene ring).
  • Hydrolysis produces benzoic acid and ammonia.
  • Equation (in words): benzamide + water → benzoic acid + ammonia.

📝 Predicting products in acid vs. base

ConditionStarting amideProducts
Base (NaOH)CH₃CH₂CH₂CH₂CONH₂CH₃CH₂CH₂CH₂COO⁻Na⁺ + NH₃
Acid (HCl)CH₃CH₂CH₂CH₂CONH₂CH₃CH₂CH₂CH₂COOH + NH₄Cl
  • Same starting material, different conditions → different final products.
  • The carboxylic acid part and the ammonia part are both present, but their forms differ.

🔑 Key takeaway

The hydrolysis of an amide produces a carboxylic acid and ammonia or an amine.

  • This is the fundamental transformation: amide → carboxylic acid + nitrogen compound.
  • The exact form of the products (free acid vs. salt, free ammonia vs. ammonium salt) depends on whether acid or base is present.
  • Remember: plain water is not enough; you need acid, base, or an enzyme to make hydrolysis happen at a useful rate.
105

Carbohydrates

Carbohydrates

🧭 Overview

🧠 One-sentence thesis

Carbohydrates are essential biological molecules composed of carbon, hydrogen, and oxygen that serve as energy sources and structural materials, synthesized by plants through photosynthesis and classified by their complexity into monosaccharides, disaccharides, and polysaccharides.

📌 Key points (3–5)

  • Chemical composition: Carbohydrates consist of carbon, hydrogen, and oxygen atoms and are polyhydroxy aldehydes or ketones (or compounds that break down into them).
  • Plant synthesis: Green plants produce glucose from carbon dioxide and water using solar energy through photosynthesis; animals depend on plants for carbohydrates.
  • Classification system: Carbohydrates are categorized as monosaccharides (simplest, cannot be hydrolyzed), disaccharides (two units), or polysaccharides (many units).
  • Common confusion: The term "carbohydrate" originated from a misinterpretation—glucose (C₆H₁₂O₆) was mistakenly thought to be a "carbon hydrate" with structure C₆·6H₂O, but it's actually a polyhydroxy aldehyde.
  • Biological importance: Carbohydrates make up 60–65% of the average diet and are needed for energy, nucleic acid synthesis, and many proteins and lipids.

🧪 Chemical structure and definition

🔬 What qualifies as a carbohydrate

Carbohydrate: A compound composed of carbon, hydrogen, and oxygen atoms that is a polyhydroxy aldehyde or ketone or a compound that can be broken down to form such a compound.

  • The key structural requirement is having an aldehyde or ketone functional group with OH (hydroxyl) groups on the other carbon atoms.
  • Not every molecule with C, H, and O is a carbohydrate—the functional groups matter.

✅ Recognition criteria

To identify a carbohydrate, check for:

  • An aldehyde functional group with OH groups on other carbon atoms, OR
  • A ketone functional group with OH groups on other carbon atoms

Don't confuse: A molecule with a ketone but lacking OH groups on other carbons is NOT a carbohydrate, even though it contains the right elements.

Example: A three-carbon molecule with a ketone and OH groups on the other two carbons qualifies; a three-carbon molecule with a ketone but only one OH group does not.

🌱 Photosynthesis and biological origin

☀️ How plants make carbohydrates

Photosynthesis: The process by which plants use solar energy to convert carbon dioxide and water to glucose.

The reaction: 6CO₂ + 6H₂O + 686 kcal → C₆H₁₂O₆ + 6O₂

  • The 686 kilocalories come from solar energy
  • Plants convert the simple glucose into larger carbohydrates like starch (for energy storage) or cellulose (for structure)

🔄 Why photosynthesis matters

  • Plants can synthesize glucose from inorganic materials; animals cannot
  • Humans and other animals are dependent on the plant kingdom for carbohydrates
  • We obtain carbohydrates by eating plant parts that store energy: seeds, roots, tubers, and fruits

🍽️ Human uses of carbohydrates

Use categoryExamples from excerpt
Food60–65% by mass of average diet
ClothingCotton, linen, rayon
ShelterWood
FuelWood
PaperWood

📊 Classification by complexity

🔹 Monosaccharides

Monosaccharide: The simplest carbohydrate that cannot be hydrolyzed to produce smaller carbohydrate molecules.

  • These are the building blocks—they cannot be broken down further by reaction with water
  • Glucose (C₆H₁₂O₆) is the key example mentioned

🔸 Disaccharides

Disaccharide: A carbohydrate containing two monosaccharide units.

  • Formed when two monosaccharides link together
  • Can be hydrolyzed (broken down with water) back into two monosaccharide units

Example: When trehalose solution is heated, it produces two glucose molecules, proving trehalose is a disaccharide.

🔶 Polysaccharides

Polysaccharide: A carbohydrate containing many monosaccharide units.

  • Chains with many monosaccharide units joined together
  • Can contain from several hundred to several thousand units
  • Examples include starch and cellulose
  • All can be hydrolyzed back to their constituent monosaccharides

🔢 Naming by unit count

The excerpt mentions prefixes indicate the number of units:

  • Mono-: one unit (cannot be broken down)
  • Di-: two units
  • Tri-: three units
  • Poly-: many units

Key distinction: Compounds that cannot be hydrolyzed will not react with water to form smaller compounds—this is what makes monosaccharides "simple."

🩺 Biological significance

⚡ Energy and metabolism

  • Glucose is needed by the body for energy
  • Carbohydrates provide energy for immediate use or storage
  • Plants store energy as starch; animals obtain this energy by consuming plants

🧬 Synthesis of other molecules

Carbohydrates are needed for:

  • Synthesis of nucleic acids
  • Production of many proteins
  • Formation of lipids

Don't confuse: Carbohydrates are not just "fuel"—they are also building blocks for other essential biological molecules.

106

Classes of Monosaccharides

Classes of Monosaccharides

🧭 Overview

🧠 One-sentence thesis

Monosaccharides are classified by both the number of carbon atoms they contain (triose through hexose) and the type of carbonyl group they possess (aldose or ketose), and most contain chiral carbons that allow them to exist as mirror-image enantiomers designated as D or L sugars.

📌 Key points (3–5)

  • Dual classification system: monosaccharides are named by carbon count (triose, tetrose, pentose, hexose) and carbonyl type (aldose for aldehyde, ketose for ketone).
  • Chiral carbons create stereoisomers: a carbon with four different groups attached is chiral, and molecules with chiral carbons exist as non-superimposable mirror images called enantiomers.
  • D vs L designation: sugars are classified as D or L based on the configuration of the penultimate (next-to-last) carbon atom, matching either D-glyceraldehyde or L-glyceraldehyde.
  • Common confusion: stereoisomers vs enantiomers—enantiomers are a specific type of stereoisomer that are mirror images; not all stereoisomers are enantiomers (e.g., cis-trans isomers are stereoisomers but not enantiomers).
  • Fischer projections: a two-dimensional convention for drawing monosaccharides where vertical lines point away and horizontal lines point toward the viewer, with the aldehyde or ketone group at the top.

🏷️ Naming by size and carbonyl type

🔢 Carbon atom count

Monosaccharides are named by a stem indicating the number of carbon atoms plus the suffix "-ose":

TermNumber of carbons
Triose3
Tetrose4
Pentose5
Hexose6
  • The excerpt notes that naturally occurring monosaccharides contain three to seven carbon atoms per molecule.
  • Example: a five-carbon sugar is a pentose; a six-carbon sugar is a hexose.

🧪 Carbonyl group type

Aldoses: monosaccharides that contain an aldehyde functional group.

Ketoses: monosaccharides that contain a ketone functional group on the second carbon atom.

  • The aldehyde group is on the first carbon; the ketone group is on the second carbon.
  • This distinction is independent of size—you can have aldoses and ketoses of any carbon count.

🔗 Combined naming system

The two classification systems combine to give names indicating both features:

  • Aldotetroses: aldehyde group + four carbons
  • Ketopentoses: ketone group + five carbons
  • Aldohexoses: aldehyde group + six carbons (e.g., glucose)
  • Ketohexoses: ketone group + six carbons (e.g., fructose)

Example: If you need to draw a ketopentose, the structure must have five carbon atoms with the second carbon being a carbonyl (ketone) group and the other four carbons each having an OH group attached.

🪞 Stereoisomers and enantiomers

🧬 What stereoisomers are

Stereoisomers: isomers having the same structural formula but differing in the arrangement of atoms or groups of atoms in three-dimensional space.

  • They have the same atoms connected in the same order, but the spatial arrangement differs.
  • The excerpt contrasts stereoisomers with other types of isomers (e.g., cis-trans geometric isomers are another type of stereoisomer).

🔄 Enantiomers as mirror images

Enantiomers: stereoisomers that are nonsuperimposable mirror images of each other.

  • If you make models of two enantiomers, you cannot place one on top of the other and have each functional group point in the same direction.
  • However, if you place one model in front of a mirror, the mirror image is identical to the other enantiomer.
  • Example: The two forms of glyceraldehyde (D-glyceraldehyde and L-glyceraldehyde) are enantiomers—they are mirror images and cannot be superimposed.

Don't confuse: Not all stereoisomers are enantiomers. Enantiomers are specifically mirror-image pairs; other stereoisomers (like cis-trans isomers) differ in spatial arrangement but are not mirror images.

⚛️ Chiral carbons

Chiral carbon: a carbon atom that has four different groups attached to it.

  • If a molecule contains one or more chiral carbons, it is likely to exist as two or more stereoisomers.
  • Example: Glyceraldehyde has a chiral carbon (the central carbon with four different groups: H, OH, CHO, and CH₂OH), so it exists as a pair of enantiomers.
  • Dihydroxyacetone does not contain a chiral carbon and thus does not exist as a pair of stereoisomers.

🌟 Physical properties of enantiomers

  • Enantiomers have identical physical properties except for the direction in which they rotate plane-polarized light.
  • One enantiomer of glyceraldehyde has a specific rotation of +8.7°, while the other has −8.7°.
  • Substances that rotate light to the right (clockwise) are dextrorotatory (denoted with +); those that rotate light to the left (counterclockwise) are levorotatory (denoted with −).

📐 Fischer projections and D/L designation

📝 Fischer projection convention

Fischer projections: formulas of chiral molecules where vertical lines represent bonds pointing away from you and horizontal lines represent bonds coming toward you.

  • Developed by H. Emil Fischer for writing two-dimensional representations of monosaccharides.
  • The aldehyde group is written at the top (or the ketone functional group at the second carbon for ketoses).
  • Hydrogen atoms and OH groups attached to each chiral carbon are written to the right or left.

🔠 D and L sugars

D sugars: sugars whose Fischer projections terminate in the same configuration as D-glyceraldehyde.

L sugars: sugars whose Fischer projections terminate in the same configuration as L-glyceraldehyde.

  • D- and L-glyceraldehyde serve as reference points for designating all other monosaccharides.
  • By convention, the penultimate (next-to-last) carbon atom determines whether a sugar is D or L—it is the chiral carbon farthest from the aldehyde or ketone functional group.
  • Example: D-glucose is a D sugar because the OH group on the fifth carbon atom (the chiral center farthest from the carbonyl group) is on the right, matching the configuration of D-glyceraldehyde.

Don't confuse: The D/L designation is based on structural configuration (the arrangement around the penultimate carbon), not on the direction of light rotation. A D sugar may rotate light to the left or right; the D refers to its structural similarity to D-glyceraldehyde.

🔬 Optical activity and polarized light

💡 What plane-polarized light is

  • Ordinary light is a bundle of waves vibrating in all directions.
  • Plane-polarized light: light altered so that all waves vibrate in a single plane.
  • Polaroid sheets can polarize ordinary light by permitting only light vibrating in a single plane to pass through.

🔄 Optically active substances

  • Optically active substances: substances that rotate the plane of vibration of polarized light.
  • The extent of optical activity is measured by a polarimeter, an instrument with two polarizing lenses separated by a sample tube.
  • When an optically active substance is placed in the sample tube, it rotates the plane of polarization, so the observer must rotate one lens to see maximum light.

➕➖ Dextrorotatory and levorotatory

  • Dextrorotatory: substances that rotate plane-polarized light to the right (clockwise), denoted with a positive sign (+).
  • Levorotatory: substances that rotate plane-polarized light to the left (counterclockwise), denoted with a negative sign (−).
  • Example: One enantiomer of glyceraldehyde is dextrorotatory (+8.7°), the other is levorotatory (−8.7°).

Don't confuse: The direction of light rotation (dextrorotatory/levorotatory, +/−) is a physical property measured in the lab; the D/L designation is a structural classification based on Fischer projection configuration. They are independent—D-sugars can be either + or −.

🧪 The trioses as foundational examples

🔺 Glyceraldehyde and dihydroxyacetone

The simplest sugars are the trioses (three-carbon monosaccharides):

TrioseTypeChiral carbon?Enantiomers?
GlyceraldehydeAldotrioseYesYes (D- and L-glyceraldehyde)
DihydroxyacetoneKetotrioseNoNo
  • Glyceraldehyde has a chiral carbon (the central carbon with four different groups), so it exists as two enantiomers: D-glyceraldehyde and L-glyceraldehyde.
  • Dihydroxyacetone does not have a chiral carbon, so it does not exist as stereoisomers.

🌱 Reference points for larger sugars

  • D- and L-glyceraldehyde are especially important because monosaccharides with more than three carbon atoms can be considered as being derived from them.
  • All other monosaccharides are designated as D or L based on whether their penultimate carbon matches D-glyceraldehyde or L-glyceraldehyde.
107

Important Hexoses

Important Hexoses

🧭 Overview

🧠 One-sentence thesis

Three hexoses—D-glucose, D-galactose, and D-fructose—are the most abundant monosaccharides in living organisms, each with distinct structures and biological roles that make them essential to metabolism and cellular function.

📌 Key points (3–5)

  • The three major hexoses: D-glucose and D-galactose are aldohexoses; D-fructose is a ketohexose.
  • Structural relationships: glucose and galactose differ only at the fourth carbon; glucose and fructose share the same structure from carbons 3–6.
  • Common confusion: all three are hexoses (six carbons), but they differ in functional group placement (aldehyde vs ketone) and stereochemistry (spatial arrangement of OH groups).
  • Multiple names for the same sugar: glucose is also called dextrose, corn sugar, and blood sugar; fructose is also called levulose; galactose is also called brain sugar.
  • Why they matter: glucose is the primary energy source for cells; galactose is essential for brain lipids; fructose is the sweetest natural sugar.

🍬 D-Glucose: The Primary Energy Sugar

🔬 What glucose is

D-Glucose: the most abundant sugar found in nature; most carbohydrates we eat are eventually converted to it in biochemical reactions that produce energy for cells.

  • It is a D sugar because the OH group on the fifth carbon atom (the chiral center farthest from the carbonyl group) is on the right.
  • All OH groups except the one on the third carbon are positioned to the right in the Fischer projection.

🏷️ Alternative names for glucose

Glucose has three other common names, each reflecting a different property or source:

NameWhy it's called that
DextroseRotates plane-polarized light in a clockwise (dextrorotatory) direction
Corn sugarIn the United States, cornstarch is used commercially to produce glucose from starch hydrolysis
Blood sugarIt is the carbohydrate found in the circulatory system of animals

📊 Normal glucose levels

  • Blood: 70 to 105 mg glucose per dL plasma
  • Urine: trace to 20 mg glucose per dL urine

Don't confuse: "blood sugar" refers specifically to glucose, not to all sugars found in blood.

🧠 D-Galactose: The Brain Sugar

🔬 What galactose is

D-Galactose: a hexose that does not occur in nature in the uncombined state; released when lactose (a disaccharide found in milk) is hydrolyzed.

  • Also known as brain sugar because it is an important constituent of glycolipids in the brain and myelin sheath of nerve cells.
  • The human body obtains needed galactose by metabolically converting D-glucose to D-galactose for lactose synthesis.

🔄 How galactose differs from glucose

  • Both are aldohexoses (aldehyde functional group, six carbons).
  • The configuration differs from glucose only at the fourth carbon atom.
  • Example: if you compare their Fischer projections side by side, all OH groups match except at carbon 4.

🍯 D-Fructose: The Sweetest Sugar

🔬 What fructose is

D-Fructose: the most abundant ketohexose; occurs along with glucose and sucrose in honey (which is 40% fructose) and sweet fruits.

  • From the third through the sixth carbon atoms, its structure is the same as that of glucose.
  • The key difference: fructose has a ketone functional group (making it a ketohexose), while glucose has an aldehyde (making it an aldohexose).

🏷️ Alternative name and properties

  • Also called levulose (from Latin fructus, meaning "fruit") because it has a specific rotation that is strongly levorotatory (−92.4°).
  • It is the sweetest natural sugar: 1.7 times sweeter than sucrose.

Don't confuse: fructose rotates light to the left (levorotatory), while glucose rotates it to the right (dextrorotatory)—this is why they have different alternative names (levulose vs dextrose).

🍭 Sweetness Comparison

📊 Relative sweetness scale

The excerpt provides a table showing how different compounds compare to sucrose (set at 100):

CompoundRelative Sweetness
Lactose16
Maltose32
Glucose74
Sucrose100 (reference)
Fructose173
Aspartame18,000
Acesulfame K20,000
Saccharin30,000
Sucralose60,000
  • Natural sugars range from 16 to 173 times the sweetness of a reference point.
  • Artificial sweeteners are several hundred to several thousand times sweeter than sucrose.
  • Example: fructose at 173 means it tastes 1.73 times sweeter than the same amount of table sugar; saccharin at 30,000 means it is 300 times sweeter.

🧪 Artificial sweeteners overview

The excerpt notes that sweetness is not limited to mono- and disaccharides:

  • Several synthetic organic compounds have been created as high-intensity sweeteners.
  • Useful for people with diabetes or those controlling carbohydrate intake.
  • They are noncaloric or used in such small quantities that they don't add significant calories.

Don't confuse: "high-intensity" refers to sweetness per unit mass, not to the intensity of flavor or chemical reactivity.

108

Cyclic Structures of Monosaccharides

Cyclic Structures of Monosaccharides

🧭 Overview

🧠 One-sentence thesis

Monosaccharides with five or more carbon atoms predominantly exist as cyclic ring structures in aqueous solution, continuously interconverting between two stereoisomeric forms (anomers) through a dynamic equilibrium process called mutarotation.

📌 Key points (3–5)

  • Why cyclization happens: aldehydes and ketones on monosaccharides react with hydroxyl groups on the same molecule to form stable five- or six-membered rings.
  • Two anomers form: the cyclic structure creates alpha (α) and beta (β) stereoisomers that differ in the orientation of the OH group on the anomeric carbon.
  • Mutarotation occurs: in solution, the α and β forms continuously interconvert through the open-chain form, reaching a dynamic equilibrium mixture.
  • Common confusion: even though less than 0.02% of molecules are in the open-chain aldehyde form at any time, the solution still exhibits aldehyde reactions because equilibrium shifts to replace reacted molecules.
  • Why small differences matter: the distinction between α and β forms is biochemically crucial—it explains why we can digest starch but not cellulose, even though both are glucose polymers.

🔄 From Linear to Cyclic Forms

🔄 How cyclization occurs

  • Monosaccharides larger than tetroses exist mainly as cyclic compounds rather than linear chains.
  • The process is an intramolecular reaction: the carbonyl group (aldehyde or ketone) reacts with a hydroxyl (OH) group on the same molecule.
  • Example: In D-glucose, the aldehyde group reacts with the OH group on the fifth carbon atom, not the second carbon.

🔗 Why five- or six-membered rings

  • Rings with five or six carbon atoms are the most stable, just as cyclic alkanes with five or six carbons are most stable.
  • This stability explains why the aldehyde reacts with the more distant OH group (fifth carbon) rather than the nearest one (second carbon).

⚛️ Anomers and the Anomeric Carbon

⚛️ What anomers are

Anomers: Stereoisomers that differ in structure around what was the carbonyl carbon atom in the straight-chain form of a monosaccharide.

Anomeric carbon: The carbon atom that was the carbonyl carbon atom in the straight-chain form of a monosaccharide.

  • When the straight-chain form closes into a ring, the carbonyl oxygen may be pushed either up or down.
  • This creates two distinct stereoisomers around the anomeric carbon.

🔼🔽 Alpha vs beta forms

FormOH group orientationExample (D-glucose)
α (alpha)OH on first carbon points downwardMelts at 146°C, specific rotation +112°
β (beta)OH on first carbon points upwardMelts at 150°C, specific rotation +18.7°
  • In Fischer projections: groups on the right appear below the ring plane; groups on the left appear above the ring plane (Haworth convention).
  • Don't confuse: these are not simply mirror images—they are stereoisomers differing only at the anomeric carbon position.

🔁 Mutarotation and Dynamic Equilibrium

🔁 What mutarotation means

Mutarotation: The ongoing interconversion between anomeric forms of a monosaccharide to form an equilibrium mixture (from Latin mutare, meaning "to change").

  • When pure crystalline α or β glucose dissolves in water, the molecules don't stay in one form.
  • They continuously open to the straight-chain form, then reclose as either α or β anomer.
  • This opening and closing repeats continuously.

⚖️ Equilibrium composition

  • At equilibrium in aqueous solution, D-glucose exists as:
    • About 36% α-D-glucose
    • About 64% β-D-glucose
    • Less than 0.02% open-chain aldehyde form
  • The observed rotation of this equilibrium mixture is +52.7°.
  • Example: You can start with pure α-glucose (rotation +112°) or pure β-glucose (rotation +18.7°), but once dissolved, both reach the same equilibrium mixture with rotation +52.7°.

🧪 Why aldehyde reactions still occur

  • Even though less than 0.02% of molecules are in the open-chain aldehyde form at any time, the solution still exhibits characteristic aldehyde reactions.
  • How this works: As the small amount of free aldehyde reacts, equilibrium shifts to produce more aldehyde from the cyclic forms.
  • Result: Eventually all molecules may react, even though very little free aldehyde exists at any given moment.
  • Don't confuse: "very little aldehyde present" does not mean "aldehyde reactions won't happen"—the dynamic equilibrium ensures continuous supply.

🔬 Biochemical Significance

🔬 Why α vs β matters

  • The difference between α and β forms may seem trivial structurally, but these differences are often crucial in biochemical reactions.
  • Real-world impact: This structural difference explains why humans can digest starch (which contains α linkages) but not cellulose (which contains β linkages), even though both are polysaccharides made entirely of glucose.
  • The specificity of enzymes depends on recognizing these precise structural differences.

📐 Haworth projection convention

  • Cyclic sugars are depicted as planar hexagons with a darkened edge showing the side facing the viewer.
  • The structure is simplified to show only functional groups attached to carbon atoms.
  • This convention (suggested by Walter N. Haworth) makes it easier to visualize three-dimensional sugar structures.
109

Properties of Monosaccharides

Properties of Monosaccharides

🧭 Overview

🧠 One-sentence thesis

Monosaccharides are highly water-soluble crystalline solids that act as reducing sugars because their aldehyde groups readily undergo oxidation with mild oxidizing agents.

📌 Key points (3–5)

  • Physical properties: monosaccharides are crystalline solids at room temperature and very soluble in water due to multiple OH groups that hydrogen-bond with water.
  • Key chemical behavior: the aldehyde group is easily oxidized by mild oxidizing agents like Tollens' or Benedict's reagents.
  • Reducing sugar definition: any carbohydrate that can reduce mild oxidizing agents without first undergoing hydrolysis.
  • Common confusion: ketoses (like fructose) also give positive oxidation tests even though they lack aldehyde groups, because they equilibrate with aldoses through tautomerism.
  • Practical application: these oxidation reactions serve as diagnostic tests for glucose in blood or urine.

💧 Physical characteristics

💧 Solubility and structure

  • Monosaccharides are crystalline solids at room temperature.
  • They are quite soluble in water.
  • The high solubility comes from the numerous OH (hydroxyl) groups on each molecule.

Monosaccharides are quite soluble in water because of the numerous OH groups that readily engage in hydrogen bonding with water.

  • Each OH group can form hydrogen bonds with water molecules, making the sugar dissolve easily.
  • Example: when you add table sugar to water, the multiple OH groups on each sugar molecule interact with water molecules, pulling the sugar into solution.

🔬 Chemical reactivity

🔬 Oxidation of the aldehyde group

  • The aldehyde group is one of the most easily oxidized organic functional groups.
  • Monosaccharides' chemical behavior is determined by their functional groups, especially the aldehyde.
  • Oxidation can be accomplished with mild oxidizing agents:
    • Tollens' reagent
    • Benedict's reagent

🧪 Benedict's test mechanism

  • Benedict's reagent contains complexed copper(II) ions.
  • During oxidation, copper(II) ions are reduced to copper(I) ions.
  • Copper(I) ions form a brick-red precipitate [copper(I) oxide].
  • The color change provides a visual indicator:
    • Green color → very little sugar
    • Brick-red color → sugar in excess of 2 g/100 mL of urine

Example: Benedict's test performed on three carbohydrates shows fructose and glucose producing the brick-red precipitate, while sucrose remains blue (because sucrose is a nonreducing sugar).

🔄 Reducing sugars

🔄 What makes a reducing sugar

Reducing sugar: any carbohydrate capable of reducing a mild oxidizing agent, such as Tollens' or Benedict's reagents, without first undergoing hydrolysis.

  • The key criterion is the ability to reduce (donate electrons to) the oxidizing agent.
  • "Without first undergoing hydrolysis" means the sugar itself, in its current form, can perform the reduction.
  • Monosaccharides are reducing sugars because they can reduce mild oxidizing agents.

🍬 Ketoses and tautomerism

  • Don't confuse: ketoses (such as fructose) also give positive tests even though they have a ketone group, not an aldehyde group.
  • Both Tollens' and Benedict's reagents are basic solutions.
  • In basic conditions, an equilibrium exists between ketoses and aldoses through a reaction called tautomerism.
  • This equilibrium allows ketoses to convert to aldoses, which then undergo oxidation.

Example: fructose (a ketose) gives a positive Benedict's test because it can rearrange to an aldose form in the basic solution, which then reduces the copper(II) ions.

🏥 Diagnostic applications

🏥 Testing for glucose

  • These oxidation reactions have been used as simple and rapid diagnostic tests for glucose in blood or urine.
  • Clinitest tablets are used to test for sugar in urine:
    • Contain copper(II) ions
    • Based on Benedict's test
    • Color interpretation:
      • Green → very little sugar
      • Brick-red → excess sugar (more than 2 g/100 mL of urine)

🔍 Which sugars test positive

All monosaccharides give positive Benedict's tests, including:

  • L-galactose
  • Levulose (another name for fructose)
  • D-glucose
  • D-glyceraldehyde
  • Corn sugar (another name for glucose)
  • L-fructose
110

Disaccharides

Disaccharides

🧭 Overview

🧠 One-sentence thesis

Disaccharides are two-monosaccharide sugars joined by glycosidic linkages, and their different structures determine whether they can reduce oxidizing agents and how the body digests them.

📌 Key points (3–5)

  • What disaccharides are: sugars composed of two monosaccharide units joined by a carbon–oxygen-carbon glycosidic linkage formed between an anomeric carbon and an OH group.
  • The three common disaccharides: maltose (two glucose units), lactose (galactose + glucose), and sucrose (glucose + fructose), all white crystalline solids soluble in water.
  • Reducing vs nonreducing: maltose and lactose are reducing sugars (one free anomeric carbon can open to an aldehyde); sucrose is nonreducing (both anomeric carbons are locked in the linkage).
  • Common confusion—linkage types: α-linkages point downward from the anomeric carbon; β-linkages point upward; the linkage type affects digestibility and properties.
  • Why digestion matters: the body cannot absorb disaccharides directly—enzymes (maltase, lactase, sucrase) must hydrolyze them into monosaccharides first; deficiencies cause lactose intolerance or galactosemia.

🔗 Structure and formation

🔗 What a glycosidic linkage is

Glycosidic linkage: the carbon–oxygen-carbon linkage between monosaccharide units in disaccharides or more complex carbohydrates.

  • Formed when the anomeric carbon of one cyclic monosaccharide reacts with the OH group of a second monosaccharide.
  • The excerpt states that cyclic monosaccharides (formed when a carbonyl group reacts with an OH group) can then react with another alcohol to create this linkage.
  • Example: one glucose molecule's anomeric carbon bonds to another glucose's fourth carbon → maltose.

🔄 α vs β linkages

  • α-glycosidic linkage: the bond from the anomeric carbon is directed downward.
  • β-glycosidic linkage: the bond from the anomeric carbon is directed upward.
  • The excerpt emphasizes checking the direction of the bond at the anomeric carbon to distinguish the two types.
  • Don't confuse: the α or β designation refers to the bond direction at the first monosaccharide's anomeric carbon in the linkage, not the free anomeric carbon (if present) at the other end.

🧪 Physical properties

  • All three common disaccharides are white crystalline solids at room temperature.
  • All are soluble in water (similar to monosaccharides, which are "quite soluble" due to numerous OH groups for hydrogen bonding).

🍬 The three common disaccharides

🌾 Maltose (malt sugar)

  • Composition: two D-glucose molecules.
  • Linkage: α-1,4-glycosidic linkage (head-to-tail fashion, first carbon of one glucose to fourth carbon of the second).
  • Source: occurs in sprouting grain; formed by partial hydrolysis of starch and glycogen; liberated in beer manufacture by malt (germinating barley) acting on starch.
  • Sweetness: about 30% as sweet as sucrose.
  • Reducing sugar: yes—one anomeric carbon remains free and can open to form an aldehyde group.
  • Hydrolysis: maltose + H⁺ (or maltase enzyme) → 2 D-glucose.
  • The excerpt notes that the OH group on the second glucose's anomeric carbon can be in either α or β position (equilibrium mixture).

🥛 Lactose (milk sugar)

  • Composition: one D-galactose + one D-glucose.
  • Linkage: β-1,4-glycosidic bond (bond directed upward from the anomeric carbon).
  • Source: occurs in milk of humans, cows, and other mammals; human milk ~7.5% lactose, cow's milk ~4.5%; natural synthesis occurs only in mammary tissue.
  • Sweetness: one of the lowest, about one-sixth as sweet as sucrose.
  • Reducing sugar: yes.
  • Hydrolysis: lactose + H⁺ (or lactase enzyme) → D-galactose + D-glucose.
  • Commercial production: from whey, a by-product of cheese manufacture; important as infant food and in penicillin production.

🍭 Sucrose (table sugar, cane sugar, beet sugar)

  • Composition: one α-D-glucose + one β-D-fructose.
  • Linkage: α-1,β-2-glycosidic linkage (head-to-head)—unique among common disaccharides.
  • Source: sugar cane and sugar beets (juices are 14–20% sucrose); obtained by evaporation and recrystallization; molasses is the dark brown liquid remaining after recrystallization.
  • Nonreducing sugar: the linkage ties up the anomeric carbons of both glucose and fructose, so neither can open to an aldehyde or ketone form.
  • No mutarotation: because neither monosaccharide can "uncyclize," sucrose exists in only one form in solid state and solution.
  • Hydrolysis: sucrose + H⁺ (or sucrase/invertase enzyme) → equimolar mixture of glucose and fructose (called "invert sugar" because it rotates plane-polarized light in the opposite direction from sucrose).
  • Sweetness and use: probably the largest-selling pure organic compound in the world; average American consumes more than 100 lb/year; fructose is sweeter than sucrose, so hydrolysis increases sweetness (bees make honey this way).
DisaccharideMonosaccharidesLinkage typeReducing?Source
Maltose2 glucoseα-1,4YesSprouting grain, starch hydrolysis
LactoseGalactose + glucoseβ-1,4YesMilk
SucroseGlucose + fructoseα-1,β-2NoSugar cane, sugar beets

🧬 Digestion and health

🧬 Why hydrolysis is necessary

  • Disaccharide molecules are too large to pass through the cell membranes of the intestinal wall.
  • The body cannot metabolize any disaccharide directly from the diet.
  • An ingested disaccharide must first be broken down by hydrolysis into its two constituent monosaccharide units.
  • In the body, hydrolysis reactions are catalyzed by specific enzymes: maltase (for maltose), lactase (for lactose), sucrase/invertase (for sucrose).
  • The same reactions can occur in the laboratory with dilute acid, but the rate is much slower and requires high temperatures.

🩺 Lactose intolerance

  • Cause: deficiency of the enzyme lactase.
  • Who is affected: many adults and some children; about 70% of the world's adult population has some deficiency; up to 20% of the US population suffers some degree of lactose intolerance.
  • Mechanism: infants and small children have an active form of lactase and can digest lactose easily; adults usually have a less active form; for some people, the inability to synthesize sufficient enzyme increases with age.
  • What happens: unhydrolyzed lactose passes into the colon, draws water into the intestinal lumen by osmosis, and intestinal bacteria produce organic acids and gases from the lactose.
  • Symptoms: abdominal distention, cramps, and diarrhea.
  • Management: exclude milk or consume sparingly; use lactase-pretreated milk; cooking or fermenting milk causes partial hydrolysis (cheese, yogurt may be tolerable); take lactase preparations (e.g., Lactaid) orally with dairy foods.

🧬 Galactosemia

  • Cause: absence of an enzyme needed to convert galactose to glucose (genetic disease).
  • Consequences: markedly elevated blood galactose level; galactose in urine; lack of appetite, weight loss, diarrhea, jaundice; may result in impaired liver function, cataracts, mental retardation, and even death.
  • Management: if recognized in early infancy, effects can be prevented by excluding milk and all other sources of galactose from the diet; as the child grows older, an alternate pathway for metabolizing galactose usually develops, so milk restriction is not permanent.
  • Incidence: 1 in every 65,000 newborn babies in the United States.
  • Don't confuse with lactose intolerance: galactosemia is a genetic enzyme deficiency for galactose metabolism, not just lactose digestion.

🍬 Sucrose and health concerns

  • Consumption: average American consumes more than 100 lb/year; about two-thirds ingested in soft drinks, presweetened cereals, and other highly processed foods.
  • Health effects: contributing factor to obesity (converted to fat when caloric intake exceeds body's requirements) and tooth decay (promotes plaque formation that sticks to teeth).

🔬 Practical applications

🔬 Invert sugar in food processing

  • What it is: the 1:1 mixture of glucose and fructose produced by sucrose hydrolysis.
  • Why it's called "invert": rotates plane-polarized light in the opposite direction from sucrose.
  • Why it's useful: sucrose readily recrystallizes from solution, but invert sugar has a much greater tendency to remain in solution; in jelly, candy manufacture, and fruit canning, recrystallization of sugar is undesirable, so conditions leading to sucrose hydrolysis are employed.
  • Added benefit: fructose is sweeter than sucrose, so hydrolysis adds to the sweetening effect.
  • Example: bees carry out this hydrolysis reaction when they make honey.

🦠 Bacterial metabolism of lactose

  • Certain bacteria can metabolize lactose, forming lactic acid as one of the products.
  • This reaction is responsible for the "souring" of milk.
111

Polysaccharides

Polysaccharides

🧭 Overview

🧠 One-sentence thesis

Polysaccharides—starch, glycogen, and cellulose—are large glucose polymers that serve distinct roles as energy storage in plants, energy storage in animals, and structural support in plants, respectively, with their different functions arising from variations in glycosidic linkage type and branching patterns.

📌 Key points (3–5)

  • What polysaccharides are: very large polymers composed of tens to thousands of monosaccharides joined by glycosidic linkages; the three most abundant (starch, glycogen, cellulose) are homopolymers that yield only glucose upon hydrolysis.
  • Energy storage vs. structure: starch and glycogen store energy in plants and animals; cellulose provides structural support in plant cell walls.
  • How linkage type determines function: α-1,4-glycosidic linkages (starch, glycogen) allow digestion by human enzymes; β-1,4-glycosidic linkages (cellulose) cannot be broken down by humans but can be digested by microorganisms with cellulase.
  • Common confusion—branching patterns: amylopectin (plant starch) and glycogen (animal starch) are both branched, but glycogen branches more frequently (every 8–12 units vs. every 25–30 units).
  • Why humans can't digest cellulose: our digestive enzymes are stereospecific and cannot hydrolyze β-glycosidic linkages, only α-linkages.

🌾 Starch: plant energy storage

🌾 What starch is and where it's found

Starch: the most important source of carbohydrates in the human diet, accounting for more than 50% of carbohydrate intake; occurs in plants as granules, particularly abundant in seeds (cereal grains) and tubers.

  • Starch serves as a storage form of carbohydrates in plants.
  • The breakdown of starch to glucose nourishes plants during periods of reduced photosynthetic activity.
  • Common sources: potatoes (15% starch), wheat (55%), corn (65%), rice (75%).
  • Commercial starch appears as a white powder.

🧬 Two components: amylose and amylopectin

Amylose (10–30% of natural starch):

  • A linear polysaccharide composed entirely of D-glucose units joined by α-1,4-glycosidic linkages (the same linkage found in maltose).
  • Not actually a straight chain—coiled like a spring with six glucose monomers per turn.
  • The coiled structure has just enough room in its core to accommodate an iodine molecule, producing a characteristic blue-violet color (sensitive starch test).

Amylopectin (70–90% of natural starch):

  • A branched-chain polysaccharide with glucose units linked primarily by α-1,4-glycosidic bonds.
  • Occasional α-1,6-glycosidic bonds create branch points approximately every 25–30 glucose units.
  • The branching disrupts the helical structure, so amylopectin produces a less intense reddish-brown color with iodine (not the deep blue-violet of amylose).

🔄 Starch digestion and dextrins

  • Complete hydrolysis of starch proceeds in stages: starch → dextrins → maltose → glucose.
  • In the human body, enzymes called amylases degrade starch sequentially into usable glucose units.
  • Dextrins: glucose polysaccharides of intermediate size; more easily digested than starch; used in infant foods, as adhesives (stamps, envelopes), binders (pills), and pastes; responsible for shine and stiffness in ironed clothing.

🐄 Glycogen: animal energy storage

🐄 What glycogen is and where it's stored

Glycogen: the energy reserve carbohydrate of animals; found as granules in liver (4–8% by weight) and skeletal muscle cells (0.5–1.0%).

  • Practically all mammalian cells contain some stored glycogen.
  • About 70% of total body glycogen is stored in muscle cells (because muscle mass is much greater than liver mass, even though liver has a higher percentage by weight).
  • During fasting, animals draw on glycogen reserves during the first day without food to maintain metabolic balance.

🌳 Structure: more highly branched than amylopectin

FeatureAmylopectin (plant)Glycogen (animal)
Basic structureBranched glucose polymerBranched glucose polymer
Branch frequencyEvery 25–30 glucose unitsEvery 8–12 glucose units (more frequent)
Iodine color testReddish brownReddish brown
Linkagesα-1,4 (main chain); α-1,6 (branches)α-1,4 (main chain); α-1,6 (branches)
  • Glycogen is structurally quite similar to amylopectin but more highly branched, with shorter branches.
  • Don't confuse: both are branched, but glycogen's more frequent branching allows faster mobilization of glucose when animals need energy.

⚙️ Breakdown of glycogen

  • Glycogen can be broken down into D-glucose subunits by acid hydrolysis or by the same enzymes that catalyze starch breakdown.
  • In animals, the enzyme phosphorylase catalyzes the breakdown of glycogen to phosphate esters of glucose.

🌿 Cellulose: plant structural support

🌿 What cellulose is and where it's found

Cellulose: a fibrous carbohydrate found in all plants; the structural component of plant cell walls; the most abundant of all carbohydrates, accounting for over 50% of all carbon in the vegetable kingdom.

  • Cotton fibrils and filter paper are almost entirely cellulose (about 95%).
  • Wood is about 50% cellulose.
  • Dry weight of leaves is about 10–20% cellulose.
  • Largest use: manufacture of paper and paper products.
  • Rayon (made from cellulose) and cotton account for over 70% of textile production.

🔗 Structure: linear polymer with β-linkages

  • Like amylose, cellulose is a linear polymer of glucose.
  • Key difference: glucose units are joined by β-1,4-glycosidic linkages (not α-1,4).
  • This produces a more extended structure than amylose.
  • The extreme linearity allows extensive hydrogen bonding between OH groups on adjacent chains, causing them to pack closely into fibers.
  • Result: cellulose exhibits little interaction with water or any other solvent; cotton and wood are completely insoluble in water and have considerable mechanical strength.
  • Because cellulose does not have a helical structure, it does not bind to iodine to form a colored product.

🚫 Why humans cannot digest cellulose

  • Cellulose yields D-glucose after complete acid hydrolysis, yet humans cannot metabolize cellulose as a glucose source.
  • Our digestive juices lack enzymes that can hydrolyze β-glycosidic linkages (we can only hydrolyze α-linkages).
  • Example: we can eat potatoes (starch with α-linkages) but not grass (cellulose with β-linkages).

Microorganisms and cellulase:

  • Certain microorganisms make the enzyme cellulase, which catalyzes the hydrolysis of cellulose.
  • Herbivorous animals (cows, horses, sheep) have cellulase-secreting microorganisms in their digestive tracts, allowing them to degrade cellulose from plant material into glucose for energy.
  • Termites also contain cellulase-secreting microorganisms and can subsist on a wood diet.
  • This demonstrates the extreme stereospecificity of biochemical processes: the same molecule (glucose polymer) can be digestible or indigestible depending solely on the stereochemistry of the linkage (α vs. β).

🔬 General properties of polysaccharides

🔬 Homopolymers vs. heteropolymers

  • Homopolymers: yield only one type of monosaccharide after complete hydrolysis; starch, glycogen, and cellulose are homopolymers (all yield only glucose).
  • Heteropolymers: may contain sugar acids, amino sugars, or noncarbohydrate substances in addition to monosaccharides; common in nature (gums, pectins) but not covered in detail in the excerpt.

🔬 Chemical behavior

  • Polysaccharides are nonreducing carbohydrates (no free anomeric carbon that can convert to an aldehyde).
  • They are not sweet tasting.
  • They do not undergo mutarotation (because they lack a free anomeric carbon that can open and close).
112

Fatty Acids

Fatty Acids

🧭 Overview

🧠 One-sentence thesis

Fatty acids are carboxylic acid building blocks of lipids that differ in carbon chain length and the number of carbon-to-carbon double bonds, which determines their physical properties and biological roles.

📌 Key points (3–5)

  • What fatty acids are: carboxylic acids that form the structural components of fats, oils, and most lipid categories (except steroids).
  • Classification by saturation: saturated (no double bonds), monounsaturated (one double bond), or polyunsaturated (two or more double bonds).
  • Essential fatty acids: linoleic and α-linolenic acids must come from the diet because the human body cannot synthesize them, yet they are required for normal growth and development.
  • Common confusion—structure vs. melting point: saturated fatty acids pack tightly and have higher melting points; unsaturated fatty acids have bends (cis double bonds) that prevent tight packing, resulting in lower melting points and liquid state at room temperature.
  • Why it matters: fatty acids determine the physical properties of fats and oils, support vitamin absorption, and serve as precursors for signaling molecules like prostaglandins.

🧪 What fatty acids are and how they are classified

🧪 Definition and general structure

Fatty acids: carboxylic acids that are structural components of fats, oils, and all other categories of lipids, except steroids.

  • More than 70 fatty acids have been identified in nature.
  • Typical characteristics:
    • Even number of carbon atoms (typically 12–20)
    • Generally unbranched chains
    • Classified by the presence and number of carbon-to-carbon double bonds

🔢 Three categories by saturation

The excerpt classifies fatty acids by double bonds:

CategoryDefinitionNumber of double bonds
Saturated fatty acidsContain no carbon-to-carbon double bonds0
Monounsaturated fatty acidsContain one carbon-to-carbon double bond1
Polyunsaturated fatty acidsContain two or more carbon-to-carbon double bonds2 or more

Example from the table:

  • Saturated: palmitic acid (16 carbons, no double bonds, melting point 63°C)
  • Monounsaturated: oleic acid (18 carbons, one double bond, melting point 16°C)
  • Polyunsaturated: linoleic acid (18 carbons, two double bonds, melting point −5°C)

🔄 Cis vs trans configuration

  • The atoms or groups around double bonds in unsaturated fatty acids can be arranged in either cis or trans isomeric form.
  • Naturally occurring fatty acids are generally in the cis configuration.
  • Don't confuse: the excerpt emphasizes that the natural form is cis, not trans.

🍽️ Essential fatty acids and their roles

🍽️ What makes a fatty acid "essential"

Essential fatty acids: fatty acids that must be obtained from the diet because they cannot be synthesized by the human body.

  • Two polyunsaturated fatty acids are essential: linoleic acid and α-linolenic acid.
  • Both are required for normal growth and development.
  • The average daily diet should contain about 4–6 grams of essential fatty acids.

🔧 Why essential fatty acids matter

  • Synthesis of other fatty acids: The body uses linoleic acid to synthesize many other unsaturated fatty acids, such as arachidonic acid.
  • Precursor for signaling molecules: Arachidonic acid is a precursor for the synthesis of prostaglandins.
  • Cholesterol metabolism: Essential fatty acids are necessary for the efficient transport and metabolism of cholesterol.
  • Example: Without dietary linoleic acid, the body cannot produce arachidonic acid, which is needed for prostaglandin synthesis.

💊 Prostaglandins—biological messengers from fatty acids

  • Prostaglandins are unsaturated fatty acids containing 20 carbon atoms, synthesized from arachidonic acid when needed by a particular cell.
  • Originally isolated from semen in the prostate gland, but now known to be synthesized in nearly all mammalian tissues.
  • Five major classes: PGA, PGB, PGE, PGF, and PGI.
  • Potency and effects: Among the most potent biological substances known; slight structural differences give highly distinct biological effects.
  • Common activities: induce smooth muscle contraction, lower blood pressure, contribute to inflammatory response.
  • Clinical relevance: Derivatives are used to induce labor, regulate blood pressure, inhibit stomach secretions, relieve nasal congestion and asthma, and prevent blood clots associated with heart attacks and strokes.
  • How aspirin works: Aspirin and other nonsteroidal anti-inflammatory agents (e.g., ibuprofen) obstruct prostaglandin synthesis by inhibiting cyclooxygenase, the enzyme needed for the initial step in converting arachidonic acid to prostaglandins.

🧊 Structure and physical properties

🧊 Saturated fatty acids—straight and tightly packed

  • Although carbon atoms are often drawn in a straight line, they actually have a zigzag configuration.
  • Overall shape: Viewed as a whole, the saturated fatty acid molecule is relatively straight.
  • Packing: Such molecules pack closely together into a crystal lattice, maximizing the strength of dispersion forces.
  • Result: Saturated fatty acids and the fats derived from them have relatively high melting points.
  • Example: Stearic acid (18 carbons, saturated) has a melting point of 70°C.

🌊 Unsaturated fatty acids—bent and loosely packed

  • Key structural feature: Each cis carbon-to-carbon double bond produces a pronounced bend in the molecule.
  • Packing: These molecules do not stack neatly because of the bends.
  • Result: The intermolecular attractions of unsaturated fatty acids (and unsaturated fats) are weaker, causing these substances to have lower melting points.
  • Physical state: Most are liquids at room temperature.
  • Example: Oleic acid (18 carbons, one cis double bond) has a melting point of 16°C, much lower than stearic acid.
  • Don't confuse: The difference in melting point is due to molecular shape (straight vs. bent), not just the presence of double bonds—the cis configuration creates the bend that prevents tight packing.

🕯️ Waxes—esters from long-chain components

Waxes: esters formed from long-chain fatty acids and long-chain alcohols.

  • Most natural waxes are mixtures of such esters.
  • Plant waxes: Found on surfaces of leaves, stems, flowers, and fruits; protect the plant from dehydration and invasion by harmful microorganisms.
  • Example: Carnauba wax (used in floor waxes, automobile waxes, and furniture polish) is largely myricyl cerotate, obtained from the leaves of certain Brazilian palm trees.
  • Animal waxes: Serve as protective coatings, keeping the surfaces of feathers, skin, and hair pliable and water repellent.
  • Example: If the waxy coating on the feathers of a water bird is dissolved (e.g., by swimming in an oil slick), the feathers become wet and heavy, and the bird, unable to maintain its buoyancy, drowns.

🥑 Lipids and dietary context

🥑 What lipids are and why fatty acids matter

Lipids: compounds isolated from body tissues that are more soluble in organic solvents (such as dichloromethane) than in water.

  • Lipids are not defined by specific functional groups (as carbohydrates are), but by a physical property—solubility.
  • The lipid category includes:
    • Fats and oils (esters of glycerol and fatty acids)
    • Compounds with functional groups from phosphoric acid, carbohydrates, or amino alcohols
    • Steroid compounds such as cholesterol
  • Dietary importance: Without lipids in our diets, we would be deficient in the fat-soluble vitamins A, D, E, and K.
  • Fatty acids are the structural components of fats, oils, and most other lipid categories (except steroids).
113

Fats and Oils

Fats and Oils

🧭 Overview

🧠 One-sentence thesis

Fats and oils are triglycerides whose physical state and properties depend on the degree of saturation and chain length of their constituent fatty acids, and they undergo key reactions—hydrolysis, hydrogenation, and oxidation—that determine their uses and stability.

📌 Key points (3–5)

  • What triglycerides are: esters composed of three fatty acid units joined to glycerol; called fats if solid at 25°C, oils if liquid.
  • What determines physical state: the degree of unsaturation and number of carbon atoms in the fatty acids; more unsaturation and shorter chains → lower melting point → oils.
  • Key reactions: saponification (hydrolysis in base to make soap), hydrogenation (converting oils to semi-solid fats), and oxidation (causing rancidity).
  • Common confusion: fats vs oils—both are triglycerides; the difference is melting point, which reflects fatty acid composition (saturated vs unsaturated).
  • Why composition matters: saturated fats raise health risks; unsaturated oils are healthier but can oxidize; trans fats (from hydrogenation) also raise cholesterol.

🧪 Structure and nomenclature

🧪 What triglycerides are

Triglycerides (or triacylglycerols): esters composed of three fatty acid units joined to glycerol, a trihydroxy alcohol.

  • Glycerol has three OH groups; each can form an ester bond with a fatty acid.
  • If all three fatty acids are the same, the result is a simple triglyceride (rare in nature).
  • If two or three different fatty acids are present, it is a mixed triglyceride (typical in natural fats and oils).
  • Example: A triglyceride might have palmitic, oleic, and linoleic acids attached to the same glycerol backbone.

🔍 Fat vs oil distinction

Fat: a triglyceride that is solid at 25°C.
Oil: a triglyceride that is liquid at 25°C.

  • The distinction is purely physical state at room temperature.
  • Fats are typically from animal sources (e.g., butter, lard, tallow).
  • Oils are typically from plant sources (e.g., canola, corn, olive, soybean oil).
  • Don't confuse: both are triglycerides; the difference lies in the fatty acid composition, not the glycerol backbone.

🔬 What determines melting point

🔬 Degree of unsaturation

  • Saturated fatty acids have straight chains that pack closely together in a crystal lattice, maximizing dispersion forces → higher melting points.
  • Unsaturated fatty acids have cis double bonds that produce pronounced bends in the molecule → molecules do not stack neatly → weaker intermolecular attractions → lower melting points.
  • Example: Stearic acid (saturated, 18 carbons) is solid at room temperature; oleic acid (one double bond, 18 carbons) is liquid.

📏 Chain length

  • Shorter-chain fatty acids also lower melting points.
  • The excerpt notes that coconut oil (highly saturated but with many C₈, C₁₀, C₁₂ fatty acids) has a lower melting point than expected for a saturated fat.

📊 Composition of common fats and oils

SourceSaturated (%)Unsaturated (%)Notes
Butter~53 (lauric, myristic, palmitic, stearic)~32 (oleic, linoleic, linolenic)Animal fat; solid
Lard~44 (myristic, palmitic, stearic)~54 (oleic, linoleic)Animal fat; semi-solid
Canola oil~6 (palmitic, stearic)~94 (oleic, linoleic, linolenic)Plant oil; liquid
Coconut oil~91 (high lauric, myristic, palmitic)~11 (oleic, linoleic)Plant oil; solid due to short chains
  • Palmitic acid is the most abundant saturated fatty acid; oleic acid is the most abundant unsaturated fatty acid.
  • Composition varies with species, diet, and climate (e.g., corn-fed hogs produce more saturated lard than peanut-fed hogs).

⚗️ Chemical reactions of triglycerides

🧼 Saponification (hydrolysis in base)

Saponification: the hydrolysis of fats and oils in the presence of a base to make soap.

  • Triglycerides are esters, so they can be hydrolyzed by acid, base, or enzymes (lipases).
  • In base (e.g., sodium hydroxide or sodium carbonate), the reaction produces glycerol and three carboxylate anions (soap molecules).
  • Industrial process: high pressure (~50 atm) and temperature (200°C) with water, then sodium carbonate or hydroxide to convert fatty acids to sodium salts.
  • Example: Treating tallow or coconut oil with alkali yields soap (sodium salts of fatty acids) plus glycerol.

How soap works:

  • Soap molecules have a hydrophilic head (ionic carboxylate) and a hydrophobic tail (hydrocarbon chain).
  • The tails dissolve in oils/grease; the heads remain in water.
  • Soap breaks oil into tiny droplets called micelles, which disperse in water and can be rinsed away.
  • Don't confuse: soap is not the triglyceride itself; it is the sodium (or potassium) salt of the fatty acids released by hydrolysis.

🔄 Hydrogenation

  • Hydrogenation: adding hydrogen (H₂) across carbon-to-carbon double bonds in the presence of a catalyst, converting unsaturated fatty acids to saturated ones.
  • This is the same reaction as for alkenes.
  • Partial hydrogenation is carefully controlled to produce fats with desired consistency (soft, pliable).
  • Example: Vegetable oils (canola, corn, soybean) are hydrogenated to make margarine and shortening.
  • Why it matters: Hydrogenation converts liquid oils into semi-solid fats that spread like butter.

Trans fats:

  • During hydrogenation, an isomerization reaction occurs, producing trans fatty acids (instead of the natural cis configuration).
  • Trans fatty acids lack the bend in their structure, so they pack closely like saturated fats.
  • Studies show trans fats raise cholesterol levels and increase heart disease risk, similar to saturated fats.
  • Don't confuse: hydrogenation reduces unsaturation (good for texture) but creates trans fats (bad for health).

🧪 Oxidation and rancidity

  • Fats and oils exposed to moist air at room temperature undergo oxidation and hydrolysis, causing them to turn rancid (disagreeable odor).
  • Hydrolytic rancidity: Lipases (enzymes from microorganisms in air) catalyze hydrolysis of ester bonds, releasing volatile fatty acids (e.g., butyric, caprylic, capric acids in butter).
  • Oxidative rancidity: Unsaturated fatty acids (especially polyunsaturated ones like linoleic and linolenic) are readily oxidized. One offensive product is malonaldehyde, formed by oxidative cleavage of double bonds.
  • Prevention: Cover the fat/oil and refrigerate (slows hydrolysis and oxidation).

🛡️ Antioxidants

Antioxidants: substances added in very small amounts (0.001%–0.01%) to prevent oxidation and suppress rancidity.

  • Antioxidants have a greater affinity for oxygen than the lipids, so they preferentially react with oxygen, protecting the lipids.
  • Example: Vitamin E is a natural antioxidant that helps reduce damage to unsaturated fatty acids in cell membranes.

🍽️ Physical properties and biological roles

🍽️ Physical properties

  • Pure fats and oils are colorless, odorless, and tasteless; characteristic colors, odors, and flavors come from absorbed foreign substances.
  • Example: Butter's yellow color is from carotene; its taste comes from diacetyl and 3-hydroxy-2-butanone (produced by bacteria in ripening cream).
  • Fats and oils are lighter than water (density ~0.8 g/cm³).
  • They are poor conductors of heat and electricity, so they insulate the body and slow heat loss through the skin.

🧬 Biological functions

  • Energy: Fats and oils are the most abundant lipids in nature and provide energy for living organisms.
  • Insulation: They insulate body organs.
  • Transport: They transport fat-soluble vitamins through the blood.

🥗 Dietary and health considerations

🥗 Saturated vs unsaturated fats

  • Saturated fats contain a high proportion of saturated fatty acids (e.g., butter, tallow, lard).
  • Unsaturated oils contain a high proportion of unsaturated fatty acids (e.g., canola, olive, soybean oil).
  • High consumption of saturated fats (along with cholesterol) is linked to increased risk of heart disease.
  • Recommendation: Use polyunsaturated oils and soft/liquid margarine; reduce total fat consumption to <30% of daily calories.

⚠️ Trans fats

  • Produced during hydrogenation of vegetable oils.
  • Raise cholesterol levels and increase heart disease incidence, similar to saturated fats.
  • Don't confuse: unsaturated oils are healthier than saturated fats, but partially hydrogenated oils (with trans fats) are not healthier.

🧴 Waxes

Waxes: esters formed from long-chain fatty acids and long-chain alcohols.

  • Most natural waxes are mixtures of such esters.
  • Plant waxes (on leaves, stems, flowers, fruits) protect against dehydration and harmful microorganisms.
  • Example: Carnauba wax (from Brazilian palm leaves) is used in floor waxes, automobile waxes, and furniture polish.
  • Animal waxes keep surfaces of feathers, skin, and hair pliable and water-repellent.
  • Example: If a water bird's waxy feather coating dissolves (e.g., in an oil slick), feathers become wet and heavy, and the bird drowns.
114

Membranes and Membrane Lipids

Membranes and Membrane Lipids

🧭 Overview

🧠 One-sentence thesis

Cell membranes are lipid bilayers whose structure arises from the dual hydrophilic-hydrophobic character of membrane lipids, enabling them to spontaneously form barriers that control what enters and leaves cells.

📌 Key points (3–5)

  • Dual character of membrane lipids: part is hydrophilic ("water loving") and part is hydrophobic ("water fearing"), which drives spontaneous assembly into membranes.
  • Three spontaneous arrangements: polar lipids in water form micelles, monolayers, or bilayers; bilayers make up all cell membranes.
  • Three main lipid categories: phospholipids (contain phosphorus), glycolipids (contain sugars), and sphingolipids (contain sphingosine instead of glycerol).
  • Common confusion: phospholipids vs sphingolipids—both can contain phosphate groups, but sphingolipids use sphingosine as the backbone instead of glycerol.
  • Proteins enable transport: integral proteins span the bilayer and create channels; peripheral proteins associate with the surface; together they allow ions and polar molecules to cross the hydrophobic interior.

🧱 Cell membrane structure and organization

🧱 What surrounds all living cells

  • Every living cell is surrounded by a cell membrane.
  • Plant and animal cells also have a nuclear membrane around the cell nucleus (which holds genetic information).
  • Everything between the cell membrane and nuclear membrane is called the cytoplasm (includes intracellular fluids, mitochondria, ribosomes, etc.).

Cytoplasm: Everything between the cell membrane and the nuclear membrane.

🔄 Fundamentally similar but functionally diverse

  • All cell membranes share a fundamentally similar structure.
  • Membrane function varies tremendously across organisms and even among cells in the same organism.
  • This diversity arises mainly from different proteins and lipids present in the membrane.

💧 Dual character of membrane lipids

💧 Hydrophilic and hydrophobic regions

  • Membrane lipids are highly polar but have dual characteristics:
    • Part of the lipid is ionic and dissolves in water.
    • The rest has a hydrocarbon structure and dissolves in nonpolar substances.

Hydrophilic: "water loving"—the ionic part that dissolves in water.

Hydrophobic: "water fearing"—the nonpolar part that is repelled by water.

  • This dual character is critical: it enables lipids to form the bilayer structure that creates a barrier while keeping the aqueous environments inside and outside the cell in contact with the hydrophilic heads.

🌀 Three spontaneous arrangements in water

When polar lipids float freely in water, they spontaneously cluster into one of three arrangements:

ArrangementStructureKey features
MicelleSpherical aggregationHydrophobic tails directed toward the center, away from water; hydrophilic heads directed outward in contact with water; may contain thousands of lipid molecules
MonolayerSingle layer on water surfacePolar heads face into water; nonpolar tails stick up into the air
BilayerDouble layerHydrophobic tails sandwiched between inner and outer surfaces of hydrophilic heads; heads in contact with water on both sides; tails sequestered inside, prevented from water contact

Micelle: An aggregation in which a nonpolar tail is directed toward the center of the structure and the polar head is directed outward.

Bilayer: A double layer of lipids arranged so that nonpolar tails are found between an inner surface and outer surface consisting of hydrophilic heads.

  • Bilayers make up every cell membrane.

🧈 Fluid nature of the membrane

  • In the bilayer interior, hydrophobic tails (fatty acid portions) interact via dispersion forces.
  • These interactions are weakened by unsaturated fatty acids.
  • As a result, membrane components are free to move around to some extent.
  • The membrane is described as fluid (components can "mill about").

Example: The presence of unsaturated fatty acids in the lipid tails allows more movement, making the membrane more flexible and dynamic.

🧬 Categories of membrane lipids

🧬 Three main classification schemes

Membrane lipids can be categorized in various ways:

Phospholipids: Lipids containing phosphorus.

Glycolipids: Sugar-containing lipids.

Sphingolipids: Phospholipids or glycolipids that contain the unsaturated amino alcohol sphingosine rather than glycerol.

  • Don't confuse: A single lipid can belong to more than one category (e.g., sphingomyelins are both sphingolipids and phospholipids).

🍬 Glycolipids and cell recognition

  • Glycolipids are found exclusively on the outer surface of the cell membrane.
  • They act as distinguishing surface markers for the cell.
  • They serve in cellular recognition and cell-to-cell communication.

🧪 Phosphoglycerides (glycerophospholipids)

🧪 Most abundant phospholipids

Phosphoglycerides (also known as glycerophospholipids): The most abundant phospholipids in cell membranes.

  • Structure:
    • A glycerol unit with fatty acids attached to the first two carbon atoms.
    • A phosphoric acid unit, esterified with an alcohol molecule (usually an amino alcohol), attached to the third carbon atom of glycerol.
  • The phosphoglyceride molecule is identical to a triglyceride up to the phosphoric acid unit.

🧠 Two common types

TypeAmino alcoholAlso calledFound inFunction/role
PhosphatidylethanolaminesEthanolamineCephalinsBrain tissue, nervesRole in blood clotting
PhosphatidylcholinesCholineLecithinsAll living organisms; egg yolks especially richImportant in nerve and brain tissue; used as emulsifying agents in foods

🥚 Lecithins as emulsifying agents

Emulsion: A dispersion of two liquids that do not normally mix, such as oil and water.

  • Commercial-grade lecithins isolated from soybeans are widely used in foods as emulsifying agents.
  • An emulsifying agent stabilizes an emulsion.
  • Many foods are emulsions:
    • Milk: emulsion of butterfat in water; emulsifying agent is casein (a protein).
    • Mayonnaise: emulsion of salad oil in water; stabilized by lecithins in egg yolk.

Example: Lecithins are often added to processed foods like hot cocoa mix to help the cocoa mix blend with water and stay evenly distributed after stirring.

🧬 Sphingolipids

🧬 Sphingomyelins

Sphingomyelins: The simplest sphingolipids; each contains a fatty acid, a phosphoric acid, sphingosine, and choline.

  • Because they contain phosphoric acid, they are also classified as phospholipids.
  • Important constituents of the myelin sheath surrounding the axon of a nerve cell.
  • Multiple sclerosis is one of several diseases resulting from damage to the myelin sheath.

🧠 Cerebrosides

Cerebrosides: Sphingolipids composed of sphingosine, a fatty acid, and galactose or glucose.

  • They resemble sphingomyelins but have a sugar unit in place of the choline phosphate group.
  • Important constituents of the membranes of nerve and brain cells.
  • Because they contain sugar groups, they are also classified as glycolipids.
  • Found in most animal cells.

🔗 Gangliosides

Gangliosides: More complex sphingolipids, usually containing a branched chain of three to eight monosaccharides and/or substituted sugars.

  • About 130 varieties have been identified due to variation in sugar components.
  • Most cell-to-cell recognition and communication processes (e.g., blood group antigens) depend on differences in the sequences of sugars in these compounds.
  • Most prevalent in the outer membranes of nerve cells, but also occur in smaller quantities in most other cells.
  • Also classified as glycolipids because they contain sugar groups.

🚪 Membrane proteins

🚪 Why proteins are needed

  • If membranes were composed only of lipids, very few ions or polar molecules could pass through the hydrophobic "sandwich filling" to enter or leave any cell.
  • Certain charged and polar species do cross the membrane, aided by proteins that move about in the lipid bilayer.

🔑 Two major classes

Integral proteins: Proteins that span the hydrophobic interior of the bilayer.

Peripheral proteins: Proteins more loosely associated with the surface of the lipid bilayer.

Protein typeLocationAttachment
IntegralSpan the entire bilayerEmbedded in the membrane
PeripheralSurface of the bilayerAttached to integral proteins, to polar head groups of phospholipids, or both (via hydrogen bonding and electrostatic forces)

🚂 Functions of integral proteins

  • Small ions and molecules soluble in water enter and leave the cell by way of channels through the integral proteins.
  • Some proteins, called carrier proteins, facilitate the passage of certain molecules (e.g., hormones, neurotransmitters) by specific interactions between the protein and the molecule being transported.

Example: A hormone molecule binds to a carrier protein, which then changes shape to move the hormone across the membrane—this is more selective than a simple open channel.

Don't confuse: Integral proteins vs peripheral proteins—integral proteins span the entire bilayer and create channels for transport; peripheral proteins are on the surface and do not create channels themselves.

115

Steroids

Steroids

🧭 Overview

🧠 One-sentence thesis

Steroids are nonsaponifiable lipids with a characteristic four-fused-ring structure that serve critical roles in mammals, including forming cell membranes, aiding fat digestion, and regulating metabolism and reproduction through hormones.

📌 Key points (3–5)

  • What makes steroids unique: They are nonsaponifiable lipids (do not react with alkali) with a four-fused-ring core structure.
  • Cholesterol's dual role: Essential for cell membranes and hormone synthesis, but excess levels increase heart disease risk.
  • Steroid hormones: Synthesized from cholesterol and include adrenocortical hormones (regulate metabolism and salt balance) and sex hormones (control reproductive characteristics).
  • Bile salts function: Act as emulsifying agents to break down dietary fats for digestion.
  • Common confusion: HDL vs. LDL cholesterol—high HDL reduces heart disease risk while high LDL increases it; the ratio matters more than total cholesterol alone.

🧬 What steroids are

🔬 Nonsaponifiable structure

Steroids: lipids with a four-fused-ring structure that do not react with aqueous alkali.

  • Unlike fats and phospholipids, steroids cannot be broken down by saponification (reaction with alkali).
  • All steroids share a core skeleton of four fused rings, labeled with letters and numbered carbon atoms.
  • Slight variations in this structure or attached groups produce dramatically different biological activities.

🌍 Where steroids occur

  • Found in plants, animals, yeasts, and molds—but not in bacteria.
  • May exist free or combined with fatty acids or carbohydrates.

🧪 Cholesterol

💊 What cholesterol is and where it's found

Cholesterol: a steroid found in mammals (not in plants); the most abundant steroid in the human body (typically ~240 g).

  • About half is embedded in cell membrane lipid bilayers.
  • Much of the rest converts to cholic acid for bile salt formation.
  • Also serves as a precursor for sex hormones, adrenal hormones, and vitamin D.

⚠️ Cholesterol and disease

  • Excess cholesterol is a primary factor in atherosclerosis and heart disease development.
  • Cholesterol not metabolized is transported to the gallbladder and normally secreted into the intestine via bile.
  • Sometimes precipitates as gallstones in the gallbladder.
  • The name derives from Greek chole (bile) and stereos (solid).

🩺 LDL vs. HDL—the critical distinction

Lipoprotein typeEffect on heart diseaseRole
LDL (low-density)High levels increase riskDelivers cholesterol to tissues
HDL (high-density)High levels reduce riskTransports excess cholesterol to liver for metabolism
  • Don't confuse: Total cholesterol level alone is less predictive than the LDL:HDL ratio.
  • HDLs help remove cholesterol from blood and arterial walls.
  • High LDL:HDL ratios correlate with higher heart disease incidence.

🍽️ Dietary and biosynthesis feedback

  • Average American consumes ~600 mg cholesterol daily and synthesizes ~1 g daily (mostly in liver).
  • When blood cholesterol exceeds 150 mg/100 mL, biosynthesis rate is halved.
  • However, dietary intake does not suppress synthesis on a 1:1 basis.
  • Recommendation: Replace saturated fats with unsaturated fats and reduce trans fatty acids to lower serum cholesterol.

🧬 Steroid hormones

📡 What hormones are

Hormones: chemical messengers released in one tissue and transported through the circulatory system to other tissues.

  • Steroid hormones are synthesized from cholesterol.
  • Two main groups: adrenocortical hormones and sex hormones.

🫘 Adrenocortical hormones

HormoneSourceFunction
AldosteroneAdrenal gland (next to kidneys)Enhances sodium reabsorption in kidney tubules; increases potassium/hydrogen secretion; promotes water retention and reduces urine output
CortisolAdrenal glandRegulates metabolic reactions (increases glucose production, mobilizes fatty acids and amino acids); inhibits inflammatory response
  • Cortisol and analogs used pharmacologically as immunosuppressants after transplants and for severe allergies, rheumatoid arthritis, and autoimmune diseases.

🚻 Sex hormones

Androgens (male sex hormones):

  • Testosterone and androstenedione are primary androgens.
  • Control development of male genital organs and continuous sperm production (primary characteristics).
  • Responsible for secondary characteristics: facial hair, deep voice, muscle strength.

Female sex hormones:

  • Progesterone: Prepares uterus for pregnancy; prevents further egg release during pregnancy.
  • Estrogens: Responsible for secondary female characteristics (breast development, fat deposition in breasts, buttocks, thighs).

Don't confuse: Both males and females produce androgens and estrogens—they differ in amounts secreted, not presence/absence.

💊 Therapeutic uses

  • Hormone replacement (e.g., after ovary removal).
  • Cancer chemotherapy (e.g., estrogens block testosterone activity in prostate cancer).
  • Preparation for sex-change operations.
  • Oral contraceptives (synthetic derivatives that prevent ovulation).

🧴 Bile salts

🟡 What bile is

Bile: a yellowish-green liquid (pH 7.8–8.6) produced in the liver, stored in the gallbladder, and secreted into the small intestine.

  • Composition gradually changes in the gallbladder as water is absorbed and other components concentrate.

🧼 Bile salt structure and function

  • Bile salts are sodium salts combining bile acids (e.g., cholic acid) with an amine (e.g., glycine).
  • Synthesized from cholesterol in the liver.
  • Contain both hydrophobic and hydrophilic groups, making them highly effective detergents and emulsifying agents.

How they work:

  • Break down large fat globules into smaller ones.
  • Keep smaller globules suspended in the aqueous digestive environment.
  • Enable enzymes to hydrolyze fat molecules more efficiently.

Major function: Aid in digestion of dietary lipids.

🏥 Clinical note

  • Gallbladder removal (for infection, inflammation, or perforation) does not seriously affect digestion.
  • Bile is still produced by the liver, though more dilute and secretion is less closely tied to food arrival.
116

Properties of Amino Acids

Properties of Amino Acids

🧭 Overview

🧠 One-sentence thesis

Amino acids—the building blocks of all proteins—share a common α-amino acid structure but differ in their side chains, which determine their classification, properties, and biological roles.

📌 Key points (3–5)

  • What amino acids are: molecules containing both an amino group and a carboxyl group attached to the same α-carbon, plus a distinctive side chain (R group).
  • The 20 standard amino acids: all living species construct proteins from the same set of 20 amino acids; humans can synthesize only about half and must obtain the rest (essential amino acids) from diet.
  • Classification by side chain: amino acids are grouped by whether their R group at neutral pH is nonpolar, polar but uncharged, negatively charged, or positively charged.
  • Common confusion—chirality and configuration: all amino acids except glycine have a chiral α-carbon; nearly all natural proteins use L-amino acids, even though D-amino acids exist in some bacteria and antibiotics.
  • Zwitterion structure: in solid state and neutral solution, amino acids exist as zwitterions (molecules with both positive and negative charges), explaining their high melting points similar to inorganic salts.

🧱 Structure and fundamental properties

🧱 The α-amino acid framework

Amino acid: a molecule that contains an amino group and a carboxyl group.

α-amino acid: an amino acid in which the amino group is attached to the α-carbon of the carboxylic acid.

  • Every amino acid has:
    • An amino group (–NH₂)
    • A carboxyl group (–COOH)
    • Both attached to the same carbon (the α-carbon)
    • A side chain or R group also attached to the α-carbon
  • The side chain is what makes each amino acid unique.

⚡ Zwitterion form

Zwitterion: an electrically neutral compound that contains both negatively and positively charged groups.

  • Amino acids are colorless, nonvolatile, crystalline solids.
  • They melt and decompose above 200°C—much higher than typical amines or organic acids.
  • These high melting temperatures indicate that amino acids exist as zwitterions (both a positively charged amino group and a negatively charged carboxyl group) in the solid state and neutral solution.
  • Example: the structure is best represented with –NH₃⁺ and –COO⁻ groups rather than neutral –NH₂ and –COOH.

🍽️ Essential vs. nonessential amino acids

Essential amino acid: an amino acid that must be obtained from the diet because it cannot be synthesized in sufficient quantities by the body.

  • Humans can synthesize only about half of the 20 amino acids.
  • The remainder must come from food.
  • Example: isoleucine is essential because most animals cannot synthesize branched-chain amino acids.

🗂️ Classification by side chain properties

🗂️ Four main categories

The excerpt classifies amino acids by the characteristics of their R group at neutral pH:

CategoryKey featureEffect on protein
Nonpolar R groupHydrophobic; no charge or polarityAffects solubility and structure
Polar but uncharged R groupContains –OH, –SH, or amide groupsCan form hydrogen bonds
Negatively charged R groupContains ionized carboxyl groups at physiological pHAcidic; participates in ionic interactions
Positively charged R groupContains ionized amino or other basic groupsBasic; participates in ionic interactions
  • The side chain's size, shape, solubility, and ionization properties determine each amino acid's unique characteristics.
  • These properties exert a profound effect on protein structure and biological activity.

🔬 Nonpolar amino acids

Examples from the excerpt:

  • Glycine (gly, G): the only amino acid lacking a chiral carbon.
  • Valine (val, V) and leucine (leu, L): branched-chain amino acids.
  • Phenylalanine (phe, F) and tryptophan (trp, W): also classified as aromatic amino acids.
  • Methionine (met, M): side chain functions as a methyl group donor.
  • Proline (pro, P): contains a secondary amine group; referred to as an α-imino acid.

💧 Polar but uncharged amino acids

Examples from the excerpt:

  • Serine (ser, S): found at the active site of many enzymes.
  • Cysteine (cys, C): oxidation of two cysteine molecules yields cystine.
  • Tyrosine (tyr, Y): also classified as an aromatic amino acid.
  • Asparagine (asn, N): the amide of aspartic acid.
  • Glutamine (gln, Q): the amide of glutamic acid.

⚡ Charged amino acids

Negatively charged (at physiological pH):

  • Aspartic acid (asp, D): carboxyl groups are ionized at physiological pH; also known as aspartate.
  • Glutamic acid (glu, E): carboxyl groups are ionized at physiological pH; also known as glutamate.

Positively charged (at physiological pH):

  • Histidine (his, H): the only amino acid whose R group has a pKₐ (6.0) near physiological pH.
  • Lysine (lys, K): positively charged at neutral pH.
  • Arginine (arg, R): almost as strong a base as sodium hydroxide.

🔄 Stereochemistry and configuration

🔄 Chirality of the α-carbon

  • With the exception of glycine, all amino acids have a chiral α-carbon.
  • This means they could theoretically exist in either D- or L-enantiomeric forms and rotate plane-polarized light.
  • Chemists use glyceraldehyde as the reference compound for assigning configuration to amino acids.
  • An amino acid structure closely resembles glyceraldehyde, except an amino group replaces the –OH group on the chiral carbon.

🌿 L-amino acids in nature

  • Nearly all known plant and animal proteins are composed entirely of L-amino acids.
  • This is the opposite of sugars, which all naturally occur in the D series.
  • Don't confuse: D-amino acids do exist in nature—certain bacteria contain D-amino acids in their cell walls, and several antibiotics contain D-leucine, D-phenylalanine, and D-valine.

🧪 Acid-base behavior

🧪 Dual acid-base nature

  • An amino acid can act as both an acid and a base because of its zwitterion structure.
  • At a certain pH value (different for each amino acid), nearly all amino acid molecules exist as zwitterions.

⚖️ Response to pH changes

When acid is added:

  • The carboxylate group (–COO⁻) captures a hydrogen ion (H⁺).
  • The amino acid becomes positively charged.

When base is added:

  • Removal of the H⁺ ion from the amino group (–NH₃⁺) produces a negatively charged amino acid.

  • In both cases, the amino acid acts to maintain the pH of the system by removing added acid (H⁺) or base (OH⁻).

  • This buffering capacity is important for biological systems.

📚 Historical and special notes

📚 Discovery and naming

  • The first amino acid isolated was asparagine in 1806, obtained from protein in asparagus juice (hence the name).
  • Glycine, the major amino acid in gelatin, was named for its sweet taste (Greek glykys, meaning "sweet").

🔧 Modified amino acids

  • In some cases, an amino acid found in a protein is actually a derivative of one of the common 20 amino acids.
  • Example: hydroxyproline is a derivative.
  • The modification occurs after the amino acid has been assembled into a protein.

🆕 Recently discovered amino acids

  • Two more amino acids have been found in limited quantities in proteins:
    • Selenocysteine (discovered in 1986)
    • Pyrrolysine (discovered in 2002)
117

Reactions of Amino Acids

Reactions of Amino Acids

🧭 Overview

🧠 One-sentence thesis

Amino acids can act as both acids and bases because they contain both amino and carboxyl functional groups, and they exist as electrically neutral zwitterions at a specific pH called the isoelectric point.

📌 Key points (3–5)

  • Dual reactivity: Amino acids react with both acids and bases due to their amino and carboxyl functional groups.
  • Zwitterion behavior: At neutral pH, amino acids exist as zwitterions with both positive and negative charges that balance each other.
  • Isoelectric point (pI): Each amino acid has a specific pH at which it exists as an electrically neutral zwitterion; this pH varies by amino acid type.
  • Common confusion: Different amino acid types have very different pIs—basic amino acids have high pIs (~8–11), acidic amino acids have low pIs (~3), and neutral amino acids fall in between (~5–6.5).
  • Functional group reactivity: The reactivity of amino and carboxyl groups is essential for linking amino acids into peptides and proteins, and for chemical detection tests.

⚡ Acid-Base Reactions

⚡ Reaction with bases

When an amino acid at neutral pH reacts with a base:

  • The base removes H⁺ from the protonated amine group (the positively charged NH₃⁺).
  • This produces an anion (negatively charged species).
  • The carboxylate group (COO⁻) remains negatively charged, while the amine becomes neutral (NH₂).
  • Example: Glycine reacting with base loses the positive charge on its amino group, leaving only the negative carboxylate charge.

⚡ Reaction with acids

When an amino acid at neutral pH reacts with an acid:

  • The acid adds H⁺ to the carboxylate group (the negatively charged COO⁻).
  • This produces a cation (positively charged species).
  • The amine group (NH₃⁺) remains positively charged, while the carboxyl becomes neutral (COOH).
  • Example: Glycine reacting with acid gains a proton on its carboxylate group, leaving only the positive amine charge.

🔄 Why dual reactivity matters

  • Amino acids contain both an amino group (basic) and a carboxyl group (acidic).
  • This dual nature allows them to respond to pH changes in solution.
  • The reactivity is particularly important for forming peptide bonds between amino acids.

🔋 Zwitterions and Isoelectric Point

🔋 What is a zwitterion

Zwitterion: an electrically neutral compound that contains both negatively and positively charged groups.

  • At neutral pH, amino acids exist as zwitterions.
  • The amino group is protonated (NH₃⁺, positive charge).
  • The carboxyl group is deprotonated (COO⁻, negative charge).
  • The positive and negative charges balance each other, making the molecule electrically neutral overall.
  • Don't confuse: "neutral" means net charge is zero, not that the molecule lacks charged groups.

📍 Isoelectric point (pI)

Isoelectric point (pI): the pH at which a given amino acid exists in solution as a zwitterion.

  • At the pI, the amino acid is electrically neutral as a whole.
  • Each amino acid has its own characteristic pI value.
  • The pI depends on the side chain properties of the amino acid.

📊 pI values by amino acid type

Amino Acid ClassificationpI RangeExamplesExplanation
Nonpolar~6.0Alanine (6.0), Valine (6.0)Neutral side chains; moderate pI
Polar, uncharged5.7–6.5Serine (5.7), Threonine (6.5)Neutral side chains; moderate pI
Positively charged (basic)7.6–10.8Histidine (7.6), Lysine (9.8), Arginine (10.8)Positively charged side chains at neutral pH; relatively high pI
Negatively charged (acidic)3.0–3.2Aspartic acid (3.0), Glutamic acid (3.2)Negatively charged side chains at neutral pH; quite low pI
  • Key pattern: Basic amino acids have high pIs because they have extra positive charges; acidic amino acids have low pIs because they have extra negative charges.
  • Amino acids with neutral side chains have pIs in the middle range (5.0–6.5).

🧪 Chemical Reactivity and Detection

🧪 Functional group reactivity

  • Amino acids undergo reactions characteristic of carboxylic acids (from the COOH group).
  • Amino acids also undergo reactions characteristic of amines (from the NH₂ group).
  • This reactivity is particularly important for linking amino acids together to form peptides and proteins.

🔬 Ninhydrin test

  • Simple chemical tests detect amino acids by taking advantage of functional group reactivity.
  • The ninhydrin test targets the amine functional group of α-amino acids.
  • The amine group reacts with ninhydrin to form purple-colored compounds.
  • Example application: Ninhydrin is used to detect fingerprints because it reacts with amino acids from proteins in skin cells transferred to surfaces.

🎯 Why detection matters

  • Chemical tests allow identification and quantification of amino acids in samples.
  • The reactivity of amino and carboxyl groups makes these tests possible.
118

Peptides

Peptides

🧭 Overview

🧠 One-sentence thesis

Peptides are chains formed when amino acids link together through peptide bonds, and the specific sequence of amino acids determines whether the resulting peptide or protein will function correctly.

📌 Key points (3–5)

  • How peptides form: amino acids join by reacting an amino group from one with a carboxyl group from another, releasing water and creating a peptide bond (amide linkage).
  • Naming by length: two amino acids = dipeptide; three = tripeptide; about 50+ = protein or polypeptide.
  • Sequence matters critically: the order of amino acids determines function—reversing the sequence can eliminate all biological activity.
  • Common confusion: it's not just which amino acids are present, but the exact order they appear in; even a single wrong amino acid can cause serious disease.
  • Convention: peptide structures are written with the N-terminal (free amino group) on the left and C-terminal (free carboxyl group) on the right.

🔗 How peptides form

🔗 The peptide bond reaction

A peptide bond: an amide bond joining two amino acid units.

  • The amino group (–NH₂) of one amino acid reacts with the carboxyl group (–COOH) of another.
  • This reaction releases one molecule of water (H₂O).
  • The result is an amide linkage connecting the two amino acids.
  • The product still has a reactive amino group on one end and a reactive carboxyl group on the other, allowing the chain to grow.

⛓️ Building longer chains

  • Additional amino acids can attach through more peptide bond formations.
  • The process can continue until thousands of units join together.
  • This produces large proteins from simple amino acid building blocks.

📏 Classification by length

📏 Naming conventions

TermNumber of amino acidsNotes
Dipeptide2Shortest peptide chain
Tripeptide3Three amino acid units
PeptideUnspecified lengthGeneral term for any amino acid chain
Protein / Polypeptide~50 or moreLarger chains; physiologically active proteins may contain one or more polypeptide chains

🧭 N-terminal and C-terminal ends

  • N-terminal end: the amino acid with a free amino group (not involved in a peptide bond).
  • C-terminal end: the amino acid with a free carboxyl group.
  • Convention: always write/draw peptides with N-terminal on the left, C-terminal on the right.
  • Example: in "arg-pro-gly," arg is N-terminal and gly is C-terminal.

🧬 Why sequence is critical

🧬 Order determines function

  • It's not enough for a peptide to contain the right amino acids; they must be in the correct order.
  • The excerpt compares this to spelling: the 26 letters of the English alphabet can spell millions of words, but rearranging letters creates gibberish.
  • Similarly, the 20 common amino acids can form millions of different proteins, but wrong sequences produce nonfunctional proteins.

🔄 Bradykinin example

  • Correct sequence: arg-pro-pro-gly-phe-ser-pro-phe-arg
    • Lowers blood pressure, stimulates smooth muscle, increases capillary permeability, causes pain.
  • Reversed sequence: arg-phe-pro-ser-phe-gly-pro-pro-arg
    • Shows none of the biological activity of bradykinin.
  • This demonstrates that reversing the order completely eliminates function.

⚠️ Small errors can be catastrophic

  • Sometimes a protein with a small percentage of incorrect amino acids may still function, though usually not as well.
  • However, even a single wrong amino acid can have disastrous effects.
  • Example from the excerpt: In some people, hemoglobin (a blood protein that transports oxygen) has one incorrect amino acid out of about 300—a single valine replaces a glutamic acid.
    • This "minor" error causes sickle cell anemia, an inherited condition that is usually fatal.
  • Don't confuse: "small error" in number doesn't mean "small effect"—location and role of that amino acid matter enormously.

🧪 Key terminology review

🧪 Distinguishing related concepts

  • Amino acid: a single building block containing both an amino group and a carboxyl group.
  • Peptide: two or more amino acids linked by peptide bonds.
  • Peptide bond: the specific name for the amide bond that joins amino acids in a chain.
  • Protein: typically a chain of about 50 or more amino acids; may consist of one or more polypeptide chains in its active form.

🧪 Functional group identity

  • A peptide bond is also called an amide bond.
  • This is the same functional group discussed in organic chemistry when ammonia reacts with a carboxylic acid.
  • In peptides, the amide linkage specifically connects amino acid units.
119

Proteins

Proteins

🧭 Overview

🧠 One-sentence thesis

Proteins are complex chains of amino acids that fold into unique three-dimensional structures, and these structures determine their specific biological functions, which can be disrupted by denaturation.

📌 Key points (3–5)

  • Two major structural classes: fibrous proteins (fiberlike, insoluble, structural roles) vs. globular proteins (spherical, soluble, diverse functions).
  • Four levels of structure: primary (amino acid sequence), secondary (α-helix or β-pleated sheet), tertiary (3D folding), and quaternary (multiple subunit arrangement).
  • Four stabilizing forces: ionic bonding, hydrogen bonding, disulfide linkages, and dispersion forces hold the folded protein together.
  • Common confusion: denaturation disrupts secondary, tertiary, and quaternary structure but leaves primary structure intact—the amino acid sequence itself is not broken.
  • Why structure matters: the three-dimensional shape is intimately tied to biochemical function; denatured proteins cannot perform their jobs.

🧱 Major structural classes

🧵 Fibrous proteins

Fibrous proteins: proteins that are elongated or fiberlike and insoluble in water.

  • These proteins are insoluble in water and usually serve structural, connective, and protective functions.
  • Examples from the excerpt: keratins (hair, outer skin), collagens (connective tissues), myosins (muscle proteins capable of contraction and extension), elastins (ligaments and artery walls).
  • They are tough and resistant to denaturation compared to globular proteins.

🌐 Globular proteins

Globular proteins: proteins that are generally spherical in structure and soluble in water.

  • The polypeptide chains fold so the molecule is roughly spherical.
  • These proteins are soluble in aqueous media.
  • Examples from the excerpt: egg albumin (egg whites), serum albumin (transports fatty acids and maintains osmotic pressure), hemoglobin and myoglobin (bind oxygen).
  • Globular proteins are much easier to denature than fibrous proteins.

🏗️ Four levels of protein structure

🔗 Primary structure

Primary structure: the sequence of amino acids in a polypeptide chain or protein.

  • This is the number and sequence of amino acids, beginning with the free amino group and maintained by peptide bonds.
  • Example from the excerpt: insulin is composed of 51 amino acids in a specific sequence.
  • Primary structure is not disrupted by denaturation—only the sequence itself defines this level.
  • The excerpt suggests that for at least some proteins, the primary structure determines the secondary and tertiary structure naturally if conditions are right.

🌀 Secondary structure

Secondary structure: the fixed arrangement of the polypeptide backbone.

  • Two main types are described:
    • α-helix: a spiral or helix stabilized by intrachain hydrogen bonding between a carbonyl oxygen and an amide hydrogen four amino acids up the chain. The helix makes one turn for every 3.6 amino acids, and side chains project outward.
    • β-pleated sheet: a sheetlike arrangement where two or more extended chains (or regions on the same chain) align side by side, connected by interchain hydrogen bonding. Chains can run parallel or antiparallel.
  • Example: α-keratins (hair, wool) are exclusively α-helical; silk fibroin has β-pleated sheet structure.
  • Some proteins (e.g., hemoglobin, myoglobin) are helical in certain regions but not others; others (e.g., gamma globulin) have little or no helical structure.

🎨 Tertiary structure

Tertiary structure: the unique three-dimensional shape of a polypeptide chain as a whole.

  • Results from the folding and bending of the protein backbone.
  • This level is intimately tied to the proper biochemical functioning of the protein.
  • The excerpt emphasizes that the tertiary structure is what gives the protein its specific biological role.
  • Example: insulin's three-dimensional ribbon model shows spiral regions (α-helix) and broad arrows (β-pleated sheet) folded into a compact shape.

🧩 Quaternary structure

Quaternary structure: the arrangement of multiple subunits in a protein.

  • When a protein contains more than one polypeptide chain, each chain is called a subunit.
  • Example: hemoglobin has four polypeptide chains (subunits).
  • Quaternary structure is produced and stabilized by the same interactions that maintain tertiary structure.
  • Not all proteins have quaternary structure—only those with multiple subunits.

🔗 Forces stabilizing protein structure

⚡ Ionic bonding

Ionic bonding: bonding that results from electrostatic attractions between positively and negatively charged groups.

  • Occurs between positively and negatively charged side chains of amino acids.
  • Example: mutual attraction between an aspartic acid carboxylate ion (negative) and a lysine ammonium ion (positive) helps maintain a folded region.

🌊 Hydrogen bonding

Hydrogen bonding: bonding between a highly electronegative oxygen atom or nitrogen atom and a hydrogen atom attached to another oxygen atom or nitrogen atom.

  • Forms between polar amino acid side chains.
  • Extremely important in both intra- and intermolecular interactions of proteins.
  • This is the predominant force stabilizing secondary structure (α-helix and β-pleated sheet).

🔗 Disulfide linkages

Disulfide linkages: a covalent bond that forms by the oxidation and linkage of two sulfur atoms from the side chains of two cysteine residues.

  • Two cysteine units are brought close together as the protein folds; oxidation links the sulfur atoms in their sulfhydryl (SH) groups to form cystine.
  • Intrachain disulfide linkages have a strong stabilizing effect on tertiary structure.
  • Example: insulin has disulfide linkages (shown as yellow bars in the primary structure figure).

🌫️ Dispersion forces

Dispersion forces: a force caused by the instantaneous imbalance of electrons about a molecule.

  • Arise when a normally nonpolar atom becomes momentarily polar, inducing a shift in a neighboring nonpolar atom.
  • Weak but important when other interactions are missing or minimal.
  • Example: fibroin (silk protein) has a high proportion of nonpolar side chains, so dispersion forces are significant.
  • Don't confuse: "hydrophobic interaction" is often misused as a synonym. Hydrophobic interactions actually refer to the protein folding so that nonpolar groups are buried in the interior, minimizing contact with water (which prefers hydrogen bonding with itself).
Interaction typeKey featureStrength
Ionic bondingElectrostatic attraction between charged side chainsStrong
Hydrogen bondingBetween electronegative O/N and H attached to O/NModerate; critical for secondary structure
Disulfide linkagesCovalent bond between two cysteine sulfur atomsVery strong; stabilizes tertiary structure
Dispersion forcesInstantaneous dipole between nonpolar groupsWeak; important when others are minimal

🔥 Denaturation of proteins

💥 What denaturation is

Denaturation: any change in the three-dimensional structure of a macromolecule that renders it incapable of performing its assigned function.

  • A denatured protein cannot do its job.
  • Denaturation is sometimes equated with precipitation or coagulation, but the excerpt defines it more broadly as any loss of functional three-dimensional structure.
  • Example: frying an egg—the clear egg white (albumin) turns opaque as it denatures and coagulates. No one has reversed that process.

🧪 How proteins are denatured

A wide variety of reagents and conditions can cause denaturation:

MethodEffect on protein structure
Heat above 50°C or UV radiationSupplies kinetic energy, causing atoms to vibrate more rapidly and disrupting weak hydrogen bonding and dispersion forces
Organic compounds (e.g., ethyl alcohol)Engage in intermolecular hydrogen bonding with the protein, disrupting intramolecular hydrogen bonding within the protein
Salts of heavy metal ions (mercury, silver, lead)Form strong bonds with carboxylate anions of acidic amino acids or SH groups of cysteine, disrupting ionic bonds and disulfide linkages
Alkaloid reagents (e.g., tannic acid)Combine with positively charged amino groups, disrupting ionic bonds

🔄 Renaturation is sometimes possible

  • Under sufficiently gentle conditions and with enough time, a protein that has unfolded can refold and may again exhibit biological activity.
  • This suggests that the primary structure (amino acid sequence) determines the secondary and tertiary structure naturally if conditions are right.
  • Don't confuse: denaturation disrupts secondary, tertiary, and quaternary levels but not primary structure. The peptide bonds linking amino acids remain intact; only the folding is lost.

🛡️ Vulnerability varies

  • Globular proteins (delicately folded) are much easier to denature than fibrous proteins (tough, structural).
  • Primary structures are quite sturdy—fairly vigorous conditions are needed to hydrolyze peptide bonds.
  • At secondary through quaternary levels, proteins are quite vulnerable to attack.
120

Enzymes

Enzymes

🧭 Overview

🧠 One-sentence thesis

Enzymes are biological catalysts that dramatically accelerate chemical reactions at body temperature and pH with remarkable specificity, and they are systematically classified according to the type of reaction they catalyze.

📌 Key points (3–5)

  • What enzymes do: increase reaction rates by a million times or more without being consumed, working at body temperature and physiological pH.
  • Substrate specificity: each enzyme catalyzes only one type of reaction in one compound or a group of structurally related compounds.
  • Systematic classification: enzymes are grouped into six classes based on reaction type and assigned four-digit EC numbers.
  • Naming convention: enzyme names typically combine the substrate name with the "-ase" suffix (e.g., urease hydrolyzes urea).
  • Common confusion: early enzymes were named by source (pepsin, papain), but modern enzymes follow a systematic scheme based on function.

🧪 What enzymes are and how they work

🔬 Definition and function

Catalyst: any substance that increases the rate or speed of a chemical reaction without being changed or consumed in the reaction.

Enzymes: biological catalysts, nearly all of which are proteins.

  • Enzymes achieve reaction rates that are a million (10⁶) or more times faster than reactions without them.
  • They work at body temperature (~37°C) and physiological pH (~7), not the extreme conditions (high temperature, pressure, strong acids/bases) typically needed to speed reactions.
  • Example: Without an enzyme, a reaction might take hours; with the enzyme, it completes in seconds at normal body conditions.

🎯 Substrate specificity

Substrates: the compound or compounds on which an enzyme acts.

  • Each enzyme is highly specific: it catalyzes only one type of reaction in one compound or structurally related compounds.
  • This specificity allows precise control of biochemical pathways.
  • Example: An enzyme that breaks down one type of sugar will not work on a different sugar molecule.
  • Don't confuse: specificity means the enzyme is selective about its substrate, not that it works slowly or on many different molecules.

🏷️ Enzyme classification and naming

📋 The six enzyme classes

Enzymes are grouped into six classes based on the general type of reaction they catalyze:

ClassType of ReactionExamples
OxidoreductasesOxidation-reduction reactionsDehydrogenases (oxidation-reduction with hydrogen); reductases (substrate reduction)
TransferasesTransfer of groups (methyl, amino, acetyl)Transaminases (transfer amino groups); kinases (transfer phosphate groups)
HydrolasesHydrolysis reactionsLipases (hydrolyze lipids); proteases (hydrolyze proteins)
LyasesRemove groups without hydrolysis or add groups to double bondsDecarboxylases (remove carboxyl groups)
IsomerasesConvert compound to its isomerIsomerases (aldose to ketose); mutases (transfer functional group within molecule)
LigasesForm new bonds between carbon and another atom; require energySynthetases (link two smaller molecules into larger one)

🔢 EC numbering system

  • Each enzyme receives a four-digit EC number (EC = enzyme classification).
  • The digits specify: (1) class, (2) subgroup, (3) secondary subgroup, (4) specific enzyme.
  • Example: Alcohol dehydrogenase = EC 1.1.1.1
    • First digit (1): oxidoreductase
    • Second digit (1): acts on primary or secondary alcohol
    • Third digit (1): requires NAD⁺ or NADP⁺ coenzyme
    • Fourth digit (1): first enzyme isolated and named in this category
  • Systematic name: alcohol:NAD⁺ oxidoreductase
  • Common name: alcohol dehydrogenase

🏷️ Naming conventions

  • Modern naming: substrate root + "-ase" suffix.
    • Urease → hydrolyzes urea
    • Sucrase → hydrolyzes sucrose
  • Historical naming: based on source or discovery method.
    • Pepsin → from stomach digestive juices (Greek pepsis = digestion)
    • Papain → isolated from papayas
  • Why the change: as more enzymes were discovered, a systematic, chemically informative scheme became necessary.

🔬 Enzyme mechanism basics

🧩 The enzyme-substrate complex

Enzyme-catalyzed reactions occur in at least two steps:

  1. Formation of E–S complex: enzyme (E) and substrate (S) collide and react to form an intermediate called the enzyme-substrate (E–S) complex.
    • This step is reversible: the complex can break apart back into free enzyme and substrate.
  2. Product formation and release: the E–S complex enables the enzyme to catalyze formation of product (P), which is then released from the enzyme surface.

Overall process:

  • S + E → E–S complex → E + P
  • The enzyme is not consumed—it is free to catalyze another reaction after releasing the product.

💊 Practical applications

  • Hundreds of enzymes have been studied to understand their effectiveness and specificity.
  • This knowledge is used to design drugs that inhibit or activate specific enzymes.
  • Example: AIDS research focuses on enzymes produced by HIV; drugs are developed to block viral enzymes without interfering with human enzymes.
  • Several such drugs have been approved for use by AIDS patients.
  • Don't confuse: inhibiting an enzyme means stopping its activity, not destroying the enzyme itself; the goal is selective inhibition of harmful enzymes while preserving beneficial ones.
121

Enzyme Action

Enzyme Action

🧭 Overview

🧠 One-sentence thesis

Enzymes bind substrates at their active sites through a flexible, shape-complementary interaction that enables highly specific catalysis, with activity influenced by substrate concentration, pH, and temperature.

📌 Key points (3–5)

  • How enzyme-substrate binding works: Enzymes and substrates collide to form an enzyme-substrate (E–S) complex at the active site, where catalysis occurs before product release.
  • Two models of binding: The lock-and-key model (rigid fit) vs. the induced-fit model (enzyme changes shape upon substrate binding).
  • Common confusion: The active site is not always rigid—modern understanding shows enzymes undergo conformational changes when binding substrates.
  • Substrate specificity varies: Some enzymes catalyze only one substrate (e.g., urease), while others act on many related molecules (e.g., carboxypeptidase).
  • What holds enzyme and substrate together: Hydrogen bonding and electrostatic interactions between functional groups in the active site and substrate.

🔗 The enzyme-substrate complex

🔗 Two-step reaction mechanism

Enzyme-catalyzed reactions occur in at least two steps:

  1. Formation of E–S complex: Enzyme (E) and substrate (S) collide and react to form an intermediate enzyme-substrate complex

    • This step is reversible—the complex can break apart back into free enzyme and substrate
    • Formula in words: Substrate plus Enzyme yields Enzyme-Substrate complex
  2. Product formation and release: The enzyme catalyzes formation of product (P), which is then released

    • Formula in words: Enzyme-Substrate complex yields Product plus Enzyme

🧲 What holds them together

  • Hydrogen bonding and other electrostatic interactions bind the enzyme and substrate in the complex
  • These interactions occur at specific structural features or functional groups on the enzyme surface
  • The binding brings reactants close together and aligns them properly—equivalent to increasing the concentration of reacting compounds

🎯 The active site

🎯 What the active site is

Active site: The location on an enzyme where a substrate binds and is transformed to product.

  • Located in a cleft or pocket on the enzyme surface
  • Contains specific structural features and functional groups that interact with the substrate
  • Has a unique conformation with correctly positioned bonding groups

🔧 How the active site works

The active site enables catalysis by:

  • Bringing specific parts of the substrate into alignment with specific parts of the enzyme
  • Positioning amino acid side chains to act as acid or base catalysts
  • Providing binding sites for transfer of functional groups
  • Aiding in substrate rearrangement

Important detail: The participating amino acids are usually widely separated in the primary sequence but brought close together when the protein folds into its tertiary and quaternary structure.

🔑 Models of enzyme action

🔑 Lock-and-key model (earlier model)

Lock-and-key model: A model that portrays an enzyme as conformationally rigid and able to bond only to a substrate or substrates that exactly fit the active site.

  • Enzyme and substrate fit together like a key fits into a tumbler lock
  • The enzyme is viewed as rigid and unchanging
  • The active site has a complementary structure to the substrate from the start

🧩 Induced-fit model (current theory)

Induced-fit model: A model that says an enzyme can undergo a conformational change when it binds substrate molecules.

Key differences from lock-and-key:

  • Binding of substrate leads to a large conformational change in both enzyme and substrate
  • The active site has a shape complementary to the substrate only after the substrate is bound
  • After catalysis, the enzyme resumes its original structure

Example: The enzyme hexokinase undergoes dramatic conformational changes when glucose binds, resulting in additional interactions between the enzyme and substrate.

Don't confuse: The lock-and-key model assumes a pre-formed perfect fit; the induced-fit model shows the enzyme actively changes shape to accommodate the substrate.

🎪 Substrate specificity

🎪 What substrate specificity means

Substrate specificity: A characteristic that distinguishes an enzyme from all other types of catalysts—its selectivity for particular substrates.

Contrast with non-biological catalysts:

  • Inorganic acids (like sulfuric acid) catalyze many different reactions with complete impartiality
  • Enzymes are much more specific and selective

🎯 Range of specificity

Enzymes exhibit varying degrees of specificity:

Specificity levelExampleWhat it catalyzes
Single substrateUreaseOnly urea hydrolysis; not methyl urea, thiourea, or biuret
Group of related moleculesCarboxypeptidaseRemoval of nearly any amino acid from the carboxyl end of any peptide or protein
Stereoisomer-specific(General case)Some enzymes distinguish between D- and L-stereoisomers, binding one but not the other

🧬 Why specificity matters

  • Results from the uniqueness of the active site in each enzyme
  • Depends on identity, charge, and spatial orientation of functional groups in the active site
  • Regulates cell chemistry so proper reactions occur in the proper place at the proper time
  • Crucial to proper functioning of the living cell

🔬 Types of interactions at the active site

🔬 Interaction types

The excerpt provides examples of substrate-enzyme interactions:

Substrate groupType of interactionExample amino acid in active site
OH (hydroxyl)Hydrogen bondingAsparagine (has amide functional group)
COOH (carboxyl)Hydrogen bondingSerine (polar side chain)
NH₃⁺ (protonated amine)Ionic bondingAspartic acid (negatively charged side chain)
COO⁻ (carboxylate)Ionic bonding(Amino acid with positive charge)
CH(CH₃)₂ (nonpolar)Dispersion forcesIsoleucine (nonpolar side chain)

These interactions hold the substrate in the correct position for catalysis to occur.

122

Enzyme Activity

Enzyme Activity

🧭 Overview

🧠 One-sentence thesis

Enzyme activity depends on substrate and enzyme concentrations, temperature, and pH, with activity increasing under optimal conditions until enzymes become saturated or denatured.

📌 Key points (3–5)

  • Catalytic activity: enzymes increase reaction rates in living organisms, and this activity can be measured by tracking substrate disappearance or product formation.
  • Substrate saturation: increasing substrate concentration raises reaction rate until all enzyme active sites are occupied, after which the rate plateaus.
  • Temperature effects: reaction rate roughly doubles per 10°C rise until denaturation occurs (typically 45–55°C), after which activity drops sharply.
  • pH sensitivity: enzymes have an optimum pH where they exhibit maximum activity; deviations alter ionization of active-site groups and reduce activity.
  • Common confusion: enzyme vs. non-enzyme reactions—enzyme-catalyzed reactions level off at high substrate concentrations due to saturation, while non-enzyme reactions keep increasing with more reactant.

🔬 How substrate concentration affects enzyme activity

📈 The saturation curve

Catalytic activity: the ability of enzymes to increase the rates of reactions occurring in living organisms.

  • When substrate concentration is low, increasing it raises the reaction rate proportionally.
  • As substrate increases further, the rate of increase slows and eventually plateaus (reaches a limiting rate).
  • At the plateau, essentially all enzyme active sites have substrate bound—the enzyme molecules are saturated.
  • Excess substrate molecules must wait until bound substrate reacts and is released before they can bind.

🚕 The taxi analogy

The excerpt provides a concrete analogy:

  • 10 taxis (enzymes) take passengers (substrate) on 10-minute trips, one at a time.
  • With 5 passengers: rate = 5 arrivals in 10 minutes.
  • With 10 passengers: rate = 10 arrivals in 10 minutes.
  • With 20 passengers: rate still = 10 arrivals in 10 minutes (taxis are saturated).
  • If taxis could carry 2–3 passengers each, the rate would be higher (20–30 per 10 minutes) but would still level off.

Don't confuse: This saturation behavior is unique to enzyme-catalyzed reactions; in non-enzyme reactions, rate continues to increase with reactant concentration because there is no "binding site" limit.

⚙️ How enzyme concentration affects activity

🔢 Direct dependence on enzyme amount

  • When enzyme concentration is significantly lower than substrate concentration (analogous to far fewer taxis than waiting passengers), reaction rate is directly dependent on enzyme concentration.
  • Increasing enzyme concentration increases the reaction rate, provided sufficient substrate is present.
  • This principle applies to all catalysts: more catalyst → faster reaction.
ConditionEffect on rateReason
Low substrate, increase substrateRate increasesMore substrate molecules available to bind
High substrate (saturated), increase substrateNo changeAll active sites already occupied
Low enzyme, increase enzymeRate increasesMore active sites available

🌡️ Temperature effects on enzyme activity

🔥 The dual nature of temperature

  • General rule of thumb: a 10°C temperature rise approximately doubles the reaction rate for most chemical reactions, including enzymatic ones.
  • This rule holds only up to a certain point.
  • Beyond that point, further temperature increase causes reaction rate to decrease due to denaturation of the protein structure and disruption of the active site.

❄️ Practical temperature ranges

  • Denaturation typically occurs between 45°C and 55°C for many proteins.
  • Maximum reaction rate may appear between 40°C and 50°C, but most biochemical reactions occur at lower temperatures because enzymes are unstable at higher temperatures and denature after a few minutes.
  • At 0°C and 100°C, enzyme-catalyzed reaction rate is nearly zero.

🧊 Real-world applications

The excerpt lists practical uses of temperature effects:

  • Sterilization: boiling water denatures bacterial enzymes.
  • Food preservation: refrigeration or freezing slows enzyme activity.
  • Hibernation: body temperature drops, decreasing metabolic process rates to levels sustainable by stored fat energy.

🧪 pH effects on enzyme activity

⚡ Why pH matters

Optimum pH: the median value of the pH range in which an enzyme exhibits maximum activity.

  • Most enzymes are proteins, so they are sensitive to hydrogen ion concentration (pH).
  • Extreme pH levels (high or low) can denature enzymes.
  • Even small pH changes alter the degree of ionization of:
    • The enzyme's acidic and basic side groups
    • The substrate components

🎯 Active site charge requirements

  • Ionizable side groups in the active site must have a certain charge for the enzyme to bind its substrate.
  • Neutralization of even one of these charges alters catalytic activity.
  • An enzyme exhibits maximum activity over a narrow pH range where the molecule exists in its properly charged form.

📊 Typical pH ranges

ContextpH rangeExample
Most body fluids6–8Most enzymes have optimum pH in this range
Gastric juice (stomach)~2Pepsin has optimum pH of 2.0

Example: An enzyme with optimum pH 7.4 will decrease in activity if pH drops to 6.3 (more acidic), because one or more key groups in the active site may bind a hydrogen ion, changing the charge on that group.

📋 Summary of factors

🔑 Key relationships

The excerpt emphasizes that enzyme activity is affected by:

  1. Factors that disrupt protein structure: temperature and pH
  2. Factors that affect catalysts in general: substrate concentration and enzyme concentration

📏 Measurement

Enzyme activity can be measured by monitoring either:

  • The rate at which substrate disappears, or
  • The rate at which product forms

Don't confuse: Substrate saturation (leveling off) vs. enzyme amount effects—saturation happens when all active sites are full; increasing enzyme concentration when substrate is abundant will still increase rate because more active sites become available.

123

Enzyme Inhibition

Enzyme Inhibition

🧭 Overview

🧠 One-sentence thesis

Enzyme inhibitors regulate enzyme activity through different mechanisms—irreversible inhibitors bond covalently to destroy function permanently, while reversible inhibitors (competitive and noncompetitive) bind temporarily and can be displaced or alter enzyme shape to control biochemical processes.

📌 Key points (3–5)

  • Irreversible inhibitors: bond covalently to the active site and permanently inactivate the enzyme; cannot be reversed by adding more substrate.
  • Reversible inhibitors: bind through weaker noncovalent interactions and can dissociate from the enzyme.
  • Competitive vs noncompetitive: competitive inhibitors resemble the substrate and compete for the active site; noncompetitive inhibitors bind elsewhere and change enzyme shape.
  • Common confusion: adding more substrate can reverse competitive inhibition (by displacing the inhibitor) but cannot reverse noncompetitive inhibition (because the inhibitor binds at a different site).
  • Why it matters: inhibition mechanisms are used by poisons, drugs like penicillin, and natural feedback control systems in cells.

🔒 Irreversible inhibition

🔒 What irreversible inhibitors do

Irreversible inhibitor: a substance that inactivates an enzyme by bonding covalently to a specific group at the active site.

  • The bond is so strong that the inhibition cannot be reversed by adding excess substrate.
  • The enzyme is permanently inactivated.
  • Example: nerve gases like DIFP form covalent bonds with a serine OH group at the active site of enzymes such as acetylcholinesterase, trypsin, and chymotrypsin.

☠️ Poisons as irreversible inhibitors

The excerpt provides a table of poisons that act as irreversible inhibitors:

PoisonExample enzyme inhibitedAction
Arsenate (AsO₄³⁻)Glyceraldehyde 3-phosphate dehydrogenaseSubstitutes for phosphate
Iodoacetate (ICH₂COO⁻)Triose phosphate dehydrogenaseBinds to cysteine SH group
DIFP (nerve poison)AcetylcholinesteraseBinds to serine OH group
  • These compounds bind covalently to particular enzymes or kinds of enzymes.
  • Many compounds are poisons precisely because they inactivate enzymes in this way.

🔄 Reversible inhibition

🔄 What reversible inhibitors do

Reversible inhibitor: a substance that inactivates an enzyme by binding at the active site through noncovalent, reversible interactions.

  • Unlike irreversible inhibitors, reversible inhibitors can dissociate from the enzyme.
  • The interactions are weaker (noncovalent) and more easily reversed.
  • There are two main types: competitive and noncompetitive inhibitors.

🏁 Competitive inhibitors

Competitive inhibitor: a compound that resembles a particular substrate and competes with the substrate for binding at the active site of an enzyme to slow the rate of the reaction.

How competitive inhibition works:

  • The inhibitor bears a structural resemblance to the substrate.
  • It competes with the substrate for binding at the active site.
  • The inhibitor is not acted on by the enzyme but prevents the substrate from approaching the active site.

Concentration matters:

  • If the inhibitor is present in relatively large quantities, it will initially block most of the active sites.
  • Because binding is reversible, some substrate molecules will eventually bind to the active site and be converted to product.
  • Increasing the substrate concentration promotes displacement of the inhibitor from the active site.
  • Competitive inhibition can be completely reversed by adding substrate so that it reaches a much higher concentration than that of the inhibitor.

Example: Malonate and succinate dehydrogenase

  • Succinate dehydrogenase normally catalyzes the conversion of succinate to fumarate (a dehydrogenation reaction).
  • Malonate and succinate are both anions of dicarboxylic acids (three and four carbon atoms, respectively).
  • Malonate binds to the active site because the spacing of its carboxyl groups is not greatly different from that of succinate.
  • However, no catalytic reaction occurs because malonate does not have a CH₂CH₂ group to convert to CH=CH.
  • Malonate remains bound to the enzyme, blocking the active site.

Don't confuse: Competitive inhibition can be overcome by adding more substrate; noncompetitive inhibition cannot.

🔀 Noncompetitive inhibitors

Noncompetitive inhibitor: a compound that can combine with either the free enzyme or the enzyme-substrate complex at a site distinct from the active site to slow the rate of the reaction.

How noncompetitive inhibition works:

  • The inhibitor's binding site on the enzyme is distinct from the active site.
  • It can bind to either the free enzyme or the enzyme-substrate complex.
  • Binding alters the three-dimensional conformation of the enzyme, changing the configuration of the active site.

Two possible results:

  1. The enzyme-substrate complex does not form at its normal rate.
  2. Once formed, the complex does not yield products at the normal rate.

Key difference from competitive inhibition:

  • Because the inhibitor does not structurally resemble the substrate, adding excess substrate does not reverse the inhibitory effect.
  • The inhibitor binds at a different location, so substrate and inhibitor are not competing for the same site.

🔁 Feedback inhibition

🔁 Natural regulation through noncompetitive inhibition

Feedback inhibition: a normal biochemical process that makes use of noncompetitive inhibitors to control some enzymatic activity.

How feedback inhibition works:

  • The final product of a series of reactions inhibits the enzyme that catalyzes the first step.
  • This is a natural control mechanism in cells.

Example: Isoleucine synthesis from threonine

  • Bacteria synthesize isoleucine from threonine in a series of five enzyme-catalyzed steps.
  • The first enzyme in the series is threonine deaminase.
  • As the concentration of isoleucine (the final product) increases, some of it binds as a noncompetitive inhibitor to threonine deaminase.
  • This brings about a decrease in the amount of isoleucine being formed.
  • The process prevents overproduction of isoleucine.

💊 Medical applications

💊 Drugs as competitive inhibitors

  • Pharmaceutical companies have synthesized drugs that competitively inhibit metabolic processes in bacteria and certain cancer cells.
  • Many drugs are competitive inhibitors of specific enzymes.
  • Studies of competitive inhibition have provided helpful information about enzyme-substrate complexes and the interactions of specific groups at the active sites.

💊 Penicillin as an enzyme inhibitor

What penicillin does:

  • Penicillin interferes with the synthesis of cell walls of reproducing bacteria.
  • It inhibits an enzyme called transpeptidase, which catalyzes the last step in bacterial cell-wall biosynthesis.
  • The defective walls cause bacterial cells to burst.
  • Human cells are not affected because they have cell membranes, not cell walls.

Structure and types:

  • Several naturally occurring penicillins have been isolated.
  • They share a common structure: a four-member cyclic amide (lactam ring) fused to a five-member ring.
  • Different R groups distinguish the different penicillins.

Effectiveness:

  • Effective against gram-positive bacteria and a few gram-negative bacteria (including Escherichia coli).
  • Used to treat diphtheria, gonorrhea, pneumonia, syphilis, pus infections, and certain types of boils.

Limitations:

  • Penicillin G cannot be administered orally because stomach acid converts it to an inactive derivative.
  • Oral penicillins (penicillin V, ampicillin, amoxicillin) are acid stable.
  • Some bacterial strains produce penicillinase, an enzyme that breaks down penicillin by cleaving the amide linkage in the lactam ring.
  • Scientists have synthesized penicillin analogs (such as methicillin) that are not inactivated by penicillinase.
  • About 5% of the population is allergic to penicillin and must be treated with other antibiotics.

Bacterial resistance:

  • Disease organisms began to develop strains resistant to antibiotics not long after the drugs were first used.
  • Scientists continue to seek new antibiotics to stay ahead of resistant bacterial strains.
  • Penicillins have been partially displaced by related compounds such as cephalosporins and vancomycin.
  • Some strains of bacteria have already shown resistance to these newer antibiotics.

📊 Comparison of inhibitor types

Inhibitor typeBindingReversibilityEffect of adding substrateBinding site
IrreversibleCovalentCannot be reversedNo effectActive site
CompetitiveNoncovalentReversibleCan displace inhibitorActive site (competes with substrate)
NoncompetitiveNoncovalentReversibleNo effectDistinct from active site

Key distinction:

  • Competitive inhibitors structurally resemble the substrate and compete for the same binding site.
  • Noncompetitive inhibitors do not resemble the substrate and bind at a different site, altering enzyme shape.
  • Only competitive inhibition can be overcome by increasing substrate concentration.
124

Enzyme Cofactors and Vitamins

Enzyme Cofactors and Vitamins

🧭 Overview

🧠 One-sentence thesis

Vitamins are essential trace nutrients that the body cannot synthesize in adequate amounts, and most water-soluble vitamins function as or are needed to synthesize coenzymes that enable enzyme activity.

📌 Key points (3–5)

  • Cofactors vs coenzymes: Cofactors are nonprotein components required by some enzymes; coenzymes are the organic molecule type of cofactor, while inorganic ions are the other type.
  • Vitamins defined: Organic compounds essential in trace amounts for normal metabolism that generally cannot be synthesized adequately by the body and must come from the diet.
  • Two vitamin categories: Fat-soluble vitamins (A, D, E, K) have high hydrocarbon content and serve various physiological roles; water-soluble vitamins (B complex and C) contain many electronegative atoms and mostly act as or form coenzymes.
  • Common confusion: Not all vitamins are coenzymes—water-soluble vitamins are used for coenzyme synthesis, but fat-soluble vitamins serve other physiological functions like vision, bone health, and blood clotting.
  • Antioxidant role: Some vitamins (C, E, and provitamin β-carotene) prevent free radical damage by stopping chain reactions that degrade lipoproteins and unsaturated fatty acids.

🧬 Enzyme cofactors and their types

🧬 What cofactors are

Cofactor: A nonprotein component of an enzyme that is necessary for the enzyme's proper functioning.

  • Many enzymes are simple proteins made entirely of amino acid chains, but others require additional nonprotein components to function.
  • Cofactors are these essential nonprotein helpers.
  • Without the cofactor, the enzyme cannot carry out its catalytic activity properly.

🔬 Two types of cofactors

TypeDescriptionExamples
Inorganic ionsMetal ions needed for enzyme functionZinc, Cu(I) ions
CoenzymesOrganic molecules required by enzymesDerived from vitamins

Coenzyme: A cofactor that is an organic molecule.

  • Don't confuse: All coenzymes are cofactors, but not all cofactors are coenzymes—some are simply inorganic ions.
  • Most coenzymes are vitamins or are derived from vitamins.

🍎 Vitamins: essential trace nutrients

🍎 Definition and necessity

Vitamin: An organic compound that is essential in very small (trace) amounts for the maintenance of normal metabolism.

  • The body generally cannot synthesize vitamins at adequate levels, so they must be obtained from the diet.
  • Absence or shortage leads to vitamin-deficiency diseases.
  • Why trace amounts matter: Even though needed in tiny quantities, vitamins are critical for normal growth and health.

🧪 Historical context

  • Early 1900s: Research established the need for trace nutrients beyond just carbohydrates, fats, and proteins.
  • First half of the 20th century: Major biochemistry focus was identifying, isolating, and characterizing vitamins.
  • Scientists have identified 13 vitamins required in the human diet.
  • Species variation: A substance that is a vitamin for one species may not be for another, depending on synthetic abilities.

💧 Two vitamin categories

💧 Fat-soluble vitamins (A, D, E, K)

  • Structural characteristic: High proportion of hydrocarbon components with one or two oxygen atoms; nonpolar overall.
  • Solubility: Do not dissolve well in water due to nonpolar nature.
  • Function: Important for various physiological functions, not primarily for coenzyme synthesis.
VitaminPhysiological FunctionDeficiency Effect
A (retinol)Formation of vision pigments; epithelial cell differentiationNight blindness; total blindness if continued
D (cholecalciferol)Increases calcium and phosphorus absorptionOsteomalacia (rickets in children)
E (tocopherol)Fat-soluble antioxidantCell membrane damage
K (phylloquinone)Formation of prothrombin for blood clottingIncreased blood clotting time

💦 Water-soluble vitamins (B complex and C)

  • Structural characteristic: Large numbers of electronegative oxygen and nitrogen atoms that can hydrogen bond with water.
  • Solubility: Dissolve readily in water.
  • Primary function: Most act as coenzymes or are required for coenzyme synthesis.
VitaminCoenzyme FormedFunctionDeficiency Disease
B₁ (thiamine)Thiamine pyrophosphateDecarboxylation reactionsBeri-beri
B₂ (riboflavin)Flavin mononucleotide or flavin adenine dinucleotideOxidation-reduction (two H atoms)
B₃ (niacin)Nicotinamide adenine dinucleotide (NAD) or NADPOxidation-reduction (hydride ion H⁻)Pellagra
B₆ (pyridoxine)Pyridoxal phosphateAmino group transfer reactions
B₁₂ (cyanocobalamin)Methylcobalamin or deoxyadenoxylcobalaminIntramolecular rearrangementsPernicious anemia
BiotinBiotinCarboxylation reactions
Folic acidTetrahydrofolateOne-carbon unit carrier (e.g., formyl group)Anemia
Pantothenic acidCoenzyme AAcyl group carrier
C (ascorbic acid)NoneAntioxidant; collagen formationScurvy

Example: Vitamin B₃ (niacin) is converted into NAD, which then helps enzymes catalyze oxidation-reduction reactions by carrying hydride ions.

🛡️ Antioxidant vitamins

🛡️ What antioxidants do

Antioxidant: A substance that prevents oxidation.

  • Vitamins C and E, plus provitamin β-carotene, can act as antioxidants in the body.
  • Provitamin note: β-carotene is called a provitamin because it can be converted to vitamin A in the body.

⚡ Free radical damage mechanism

  • Free radicals: Molecules that are highly reactive because they have unpaired electrons.
  • Sources: Formed through metabolic reactions involving oxygen and environmental factors (radiation, pollution).
  • Damage process:
    1. Free radicals most commonly attack lipoproteins and unsaturated fatty acids in cell membranes.
    2. They remove an electron, generating a new free radical.
    3. This becomes a chain reaction leading to oxidative degradation of affected compounds.

🔒 How antioxidants stop damage

  • Antioxidants react with free radicals to stop chain reactions.
  • Two mechanisms:
    1. Form a more stable molecule that cannot continue the chain.
    2. Form a much less reactive free radical (vitamin E does this).
  • Vitamin E regeneration: Vitamin E is converted back to its original form through interaction with vitamin C.

Example: When a free radical attacks a cell membrane lipid, vitamin E can intercept it, becoming a less reactive radical itself, then vitamin C restores vitamin E to its active form—breaking the destructive chain.

125

Nucleotides

Nucleotides

🧭 Overview

🧠 One-sentence thesis

Nucleotides are the monomer building blocks of nucleic acids (DNA and RNA), each composed of three parts—phosphoric acid, a pentose sugar, and a nitrogenous base—that together carry and express genetic information in all living organisms.

📌 Key points (3–5)

  • What nucleotides are: repeating monomer units that link together to form nucleic acids (DNA and RNA).
  • Three components: every nucleotide breaks down into phosphoric acid (H₃PO₄), a pentose sugar (ribose or deoxyribose), and a nitrogenous base.
  • Two types of nucleotides: ribonucleotides (contain ribose, form RNA) vs. deoxyribonucleotides (contain deoxyribose, form DNA).
  • Common confusion—bases: pyrimidines (six-member ring: uracil, thymine, cytosine) vs. purines (fused ring structure: adenine, guanine); DNA uses thymine while RNA uses uracil.
  • Beyond genetics: nucleotides also function in cell metabolism (ATP, ADP) and as components of coenzymes (FAD, NAD⁺, coenzyme A).

🧱 The three building blocks

🧪 Phosphoric acid

  • Every nucleotide contains phosphoric acid (H₃PO₄) as one of its three components.
  • This inorganic acid is the same in both DNA and RNA nucleotides.

🍬 Pentose sugar

The pentose sugar is a five-carbon sugar that differs between DNA and RNA.

  • Ribose: found in ribonucleotides, which form RNA.
  • 2-Deoxyribose: found in deoxyribonucleotides, which form DNA.
  • The sugar type determines whether the resulting nucleic acid is RNA or DNA.
  • Don't confuse: the only difference is the presence or absence of one oxygen atom at the 2' position.

🧬 Nitrogenous base

  • The nitrogen-containing base is the third component.
  • Bases are classified into two categories based on their ring structure.

🔷 Two types of nitrogenous bases

🔷 Pyrimidines

Pyrimidines are heterocyclic amines with two nitrogen atoms in a six-member ring.

  • Three pyrimidines: uracil, thymine, and cytosine.
  • Key distinction:
    • DNA contains cytosine and thymine
    • RNA contains cytosine and uracil (not thymine)

🔶 Purines

Purines are heterocyclic amines consisting of a pyrimidine ring fused to a five-member ring with two nitrogen atoms.

  • Two major purines: adenine and guanine.
  • Both DNA and RNA contain the same purines (adenine and guanine).
  • Purines have a larger, double-ring structure compared to pyrimidines.

🔗 How nucleotides connect

🔗 Bond formation

  • The pentose sugar bonds to the nitrogenous base through a specific connection:
    • C1' of the pentose sugar connects to N1 of pyrimidine bases
    • C1' of the pentose sugar connects to N9 of purine bases
  • A molecule of water is removed when this bond forms.

🔢 Numbering convention

  • Primed numbers (1', 2', etc.): designate atoms of the pentose sugar ring.
  • Unprimed numbers (1, 9, etc.): designate atoms of the purine or pyrimidine ring.
  • This convention helps distinguish which part of the nucleotide is being referenced.

📊 DNA vs RNA nucleotides

ComponentDNARNA
Purine basesAdenine and guanineAdenine and guanine
Pyrimidine basesCytosine and thymineCytosine and uracil
Pentose sugar2-deoxyriboseRibose
Inorganic acidH₃PO₄H₃PO₄

Key difference to remember: The sugar and one pyrimidine base differ; thymine appears only in DNA, while uracil appears only in RNA.

⚡ Functions beyond genetics

⚡ Energy metabolism

  • ATP (adenosine triphosphate) and ADP (adenosine diphosphate): nucleotide derivatives that play roles in cell metabolism.
  • These molecules are based on adenine nucleotides.

🔧 Coenzyme components

  • Several coenzymes contain adenine nucleotides as structural components:
    • FAD (flavin adenine dinucleotide)
    • NAD⁺ (nicotinamide adenine dinucleotide)
    • Coenzyme A
  • Example: These molecules help enzymes carry out chemical reactions in cells, showing that nucleotides have functions beyond storing genetic information.

🧮 Scale and quantity

🧮 Massive numbers

  • A typical mammalian cell contains about 3 × 10⁹ (3 billion) nucleotides in its DNA.
  • Human body cells have 23 pairs of chromosomes containing 20,000–40,000 different genes.
  • Each gene is defined as a segment of DNA that codes for a specific polypeptide.

🧬 Chromosomes and heredity

Chromosomes are elongated, threadlike structures composed of protein and DNA that contain the genetic blueprint.

Genes are the basic units of heredity.

  • Sperm and egg cells contain only one copy of each chromosome (one member of each pair).
  • In sexual reproduction, offspring receive half their hereditary material from each parent, achieving the full complement of chromosomes only when egg and sperm combine.
126

Nucleic Acid Structure

Nucleic Acid Structure

🧭 Overview

🧠 One-sentence thesis

DNA's double helix structure, with its complementary base pairing between purines and pyrimidines, enables cells to store genetic information and replicate it accurately.

📌 Key points (3–5)

  • Two types of nucleic acids: DNA stores genetic information; RNA uses that information to produce proteins.
  • How nucleotides link: phosphate group of one nucleotide forms an ester linkage to the OH group on the third carbon of another nucleotide's sugar, creating a backbone of alternating phosphate and sugar units.
  • Complementary base pairing: adenine always pairs with thymine (2 hydrogen bonds), guanine always pairs with cytosine (3 hydrogen bonds).
  • Common confusion: purine must pair with pyrimidine—not purine-purine or pyrimidine-pyrimidine—to keep the DNA double helix at constant width.
  • Why structure matters: the specific base pairing enables DNA replication, genetic transmission, and protein synthesis.

🧬 The two nucleic acids and their roles

🧬 DNA: genetic storage

Deoxyribonucleic acid (DNA): the nucleic acid that stores genetic information.

  • DNA in a typical mammalian cell, if stretched end to end, would extend more than 2 meters.
  • The excerpt emphasizes DNA's role as the storage molecule for genetic data.

🧬 RNA: genetic expression

Ribonucleic acid (RNA): the nucleic acid responsible for using the genetic information encoded in DNA to produce the thousands of proteins found in living organisms.

  • RNA does not store information; it uses the information stored in DNA.
  • The excerpt positions RNA as the intermediary between DNA and protein production.

🔗 Primary structure: how nucleotides link

🔗 The linkage mechanism

  • Nucleotides join through the phosphate group of one nucleotide connecting in an ester linkage to the OH group on the third carbon atom of the sugar unit of a second nucleotide.
  • This process repeats to produce a long nucleic acid chain.
  • The backbone consists of alternating phosphate and sugar units (deoxyribose in DNA, ribose in RNA).
  • The purine and pyrimidine bases branch off this backbone.

🔗 Why "nucleic acids"

  • Each phosphate group has one acidic hydrogen atom that is ionized at physiological pH.
  • This is the reason these compounds are called nucleic acids.

📝 Writing nucleotide sequences

  • Convention: write nucleotides starting with the nucleotide having a free phosphate group, known as the 5′ end.
  • The final nucleotide has a free OH group on the 3′ carbon atom and is called the 3′ end.
  • Example: the sequence in the excerpt's DNA segment is written 5′-dG-dT-dA-dC-3′, abbreviated to dGTAC or GTAC.
  • For DNA, a lowercase "d" is often written in front to indicate deoxyribonucleotides.
  • Unlike proteins (which have 20 different amino acids), nucleic acids have only 4 different kinds of nucleotides.

🌀 Secondary structure: the DNA double helix

🌀 Discovery and key features

  • In 1953, James D. Watson and Francis Crick announced their model for DNA's secondary structure.
  • They used information from Erwin Chargaff's experiments (1950) showing that the molar amount of adenine (A) always equals thymine (T), and guanine (G) always equals cytosine (C).
  • They also used X-ray data from Rosalind Franklin.

Double helix: the secondary structure of DNA, in which two nucleic acid chains run antiparallel to one another and are twisted together.

  • Antiparallel arrangement: the two chains run side-by-side with the 5′ end of one chain next to the 3′ end of the other.
  • Spiral staircase analogy: the phosphate and sugar groups (the backbone) represent the outside edges; the purine and pyrimidine bases face the inside and form the steps.

🧩 Complementary base pairing

Complementary bases: specific base pairings in the DNA double helix.

  • Guanine always pairs with cytosine (3 hydrogen bonds).
  • Adenine always pairs with thymine (2 hydrogen bonds).
  • The excerpt emphasizes that these specific pairings are the "steps" or "treads" in the staircase analogy.

🔍 Why purine must pair with pyrimidine

The excerpt explains two structural reasons for this pairing rule:

  1. Constant width: A pyrimidine paired with a purine in each case ensures that the long dimensions of both pairs are identical (1.08 nm).

    • If two pyrimidines were paired, they would take up less space than a purine and a pyrimidine.
    • If two purines were paired, they would take up more space.
    • The structure of DNA would be like a staircase made with stairs of different widths if these incorrect pairings occurred.
    • For the two strands to fit neatly, a pyrimidine must always be paired with a purine.
  2. Hydrogen bonding stability: The correct pairing enables formation of three instances of hydrogen bonding between guanine and cytosine and two between adenine and thymine.

    • The additive contribution of this hydrogen bonding imparts great stability to the DNA double helix.

Don't confuse: The width constraint is structural (keeping the helix uniform), while the hydrogen bonding is about stability. Both depend on purine-pyrimidine pairing.

🔬 Functional significance

🔬 What the structure enables

The excerpt states that the structure proposed by Watson and Crick provided clues to:

  • How cells divide into two identical, functioning daughter cells.
  • How genetic data are passed to new generations.
  • How proteins are built to required specifications.

All these abilities depend on the pairing of complementary bases.

🔬 Replication overview

The excerpt introduces replication briefly:

Replication: the process in which new copies of DNA are made.

  • New cells continuously form through cell division, requiring DNA to be copied.
  • The complementary base pairing of the double helix provides a model for how genetic replication occurs.
  • If the two chains of the double helix are pulled apart (disrupting the hydrogen bonding between base pairs), each chain can act as a template for the synthesis of a new complementary DNA chain.
  • The nucleus contains all the necessary enzymes, proteins, and nucleotides required for this synthesis.

📊 Comparison summary

FeatureDNARNA
Sugar unitDeoxyriboseRibose
FunctionStores genetic informationUses genetic information to produce proteins
BasesAdenine, thymine, guanine, cytosineAdenine, uracil, guanine, cytosine
StructureDouble helix (two antiparallel strands)(Not detailed in this excerpt)
Base pairingPartnerNumber of hydrogen bonds
Adenine (A)Thymine (T)2
Guanine (G)Cytosine (C)3
127

Replication and Expression of Genetic Information

Replication and Expression of Genetic Information

🧭 Overview

🧠 One-sentence thesis

DNA replication copies genetic information into new cells, while transcription and translation express that information by synthesizing RNA and proteins through complementary base pairing and template mechanisms.

📌 Key points (3–5)

  • Three core processes: replication (copying DNA), transcription (DNA → RNA), and translation (RNA → protein) are all required to store and express genetic information.
  • Template mechanism: both replication and transcription use complementary base pairing—each strand serves as a pattern for building a new complementary strand.
  • Key enzymes: DNA polymerase catalyzes replication; RNA polymerase catalyzes transcription.
  • Three types of RNA: mRNA carries the genetic message (codons), tRNA brings amino acids (anticodons), and rRNA is a component of ribosomes where proteins are made.
  • Common confusion: replication vs transcription—replication copies the entire DNA double helix and produces two DNA molecules; transcription copies only a segment of one DNA strand and produces a single RNA strand that does not remain bound to DNA.

🔄 DNA Replication

🧬 What replication does

Replication: the process in which the DNA in a dividing cell is copied.

  • New cells form continuously through cell division, and each new cell needs a complete copy of the parent cell's DNA.
  • The complementary base pairing of the double helix provides the model: if the two chains are pulled apart, each can act as a template (pattern) for synthesizing a new complementary DNA chain.
  • The nucleus contains all necessary enzymes, proteins, and nucleotides for this synthesis.

⚙️ How replication works

  • A short segment of DNA is "unzipped" so the two strands separate and serve as templates.
  • DNA polymerase (an enzyme) recognizes each base in a template strand and matches it to the complementary base in a free nucleotide.
  • The enzyme catalyzes formation of an ester bond between the 5′ phosphate group of the incoming nucleotide and the 3′ OH end of the growing DNA chain.
  • Each strand of the original DNA produces a duplicate of its former partner → two double helices form from one.
  • Semiconservative replication: each new double helix consists of one old strand and one new strand.
  • When the cell divides, each daughter cell gets one replicate helix and thus all the information originally possessed by the parent cell.

🧩 Base pairing rules in replication

  • T (thymine) pairs with A (adenine)
  • C (cytosine) pairs with G (guanine)
  • The two strands are antiparallel (run in opposite directions: 5′ to 3′ and 3′ to 5′).

Example: If one strand is 5′-TCCATGAGTTGA-3′, the complementary strand is 3′-AGGTACTCAACT-5′ (or written as TCAACTCATGGA).

💾 Information encoding in DNA

  • DNA sequences encode directions for building an organism, like letters forming words in assembly instructions.
  • There are only four "letters" (the four nucleotides), but their sequencing along DNA strands can vary so widely that information storage is essentially unlimited.
  • Example: the sequence CGT means one thing; TGC means something different.

📝 Transcription: DNA → RNA

📝 What transcription does

Transcription: the process in which RNA is synthesized from a DNA template.

  • Transcription is the first step in expressing hereditary information in DNA.
  • It is analogous to replication but produces RNA instead of DNA.
  • The RNA synthesized is a complementary copy of information in DNA.

🔀 Key differences: replication vs transcription

FeatureReplicationTranscription
ProductDNA (two full double helices)RNA (single strand, much shorter)
Building blocksDeoxyribonucleotidesRibonucleotides
TemplateEntire DNA molecule unzipsOnly a portion of one DNA strand is copied
Product associationNew DNA remains paired with templateRNA does not remain associated with DNA template
Base pairingT pairs with AT (in DNA) pairs with A (in RNA); A (in DNA) pairs with U (in RNA)

⚙️ How transcription works

  • The DNA sequence transcribed to make RNA is called the template strand; the complementary DNA sequence is the coding or informational strand.
  • The two DNA strands unwind at specific sites.
  • Ribonucleotides are attracted to the uncoiling region, beginning at the 3′ end of the template strand, according to base pairing rules:
    • Thymine (DNA) → Adenine (RNA)
    • Cytosine (DNA) → Guanine (RNA)
    • Guanine (DNA) → Cytosine (RNA)
    • Adenine (DNA) → Uracil (RNA)
  • RNA polymerase binds the complementary ribonucleotide and catalyzes formation of the ester linkage between ribonucleotides.
  • RNA synthesis proceeds in the 5′ to 3′ direction, antiparallel to the template strand.
  • Only a short segment of RNA is hydrogen-bonded to the template at any time.
  • When transcription is completed, the RNA is released and the DNA helix reforms.
  • The nucleotide sequence of the RNA is identical to the coding strand of DNA, except U replaces T.

Example: If the template strand is 5′-TCCATGAGTTGA-3′, the RNA formed is 3′-AGGUACUCAACU-5′ (or 5′-UCAACUCAUGGA-3′).

🧬 Don't confuse: template vs coding strand

  • The template strand is the DNA strand that is actually read by RNA polymerase (antiparallel to the RNA being made).
  • The coding strand has the same sequence as the RNA (except T instead of U) but is not directly used as the template.

🧵 Three Types of RNA

📋 Overview of RNA types

Three types of RNA are formed during transcription: messenger RNA (mRNA), ribosomal RNA (rRNA), and transfer RNA (tRNA). They differ in function, size, and percentage of total cell RNA.

TypeFunctionApproximate Number of NucleotidesPercentage of Total Cell RNA
mRNACodes for proteins100–6,000~3%
rRNAComponent of ribosomes120–2,90083%
tRNAAdapter molecule that brings amino acids to the ribosome75–9014%

📨 Messenger RNA (mRNA)

  • mRNA makes up only a small percent of total cell RNA because each mRNA molecule exists for a relatively short time—it is continuously degraded and resynthesized.
  • Molecular size varies according to the amount of genetic information the molecule contains.
  • After transcription in the nucleus, mRNA passes into the cytoplasm, carrying the genetic message from DNA to the ribosomes (sites of protein synthesis).
  • mRNA directly determines the sequence of amino acids during protein synthesis.

🏭 Ribosomal RNA (rRNA)

Ribosomes: cellular substructures where proteins are synthesized.

  • Ribosomes contain about 65% rRNA and 35% protein, held together by noncovalent interactions (e.g., hydrogen bonding).
  • Overall structure consists of two globular particles of unequal size.

🚚 Transfer RNA (tRNA)

  • tRNA molecules bring amino acids (one at a time) to the ribosomes for protein construction.
  • Each tRNA differs in the kind of amino acid it is designed to carry.
  • Each of the 20 amino acids found in proteins has at least one corresponding tRNA; most amino acids have more than one.

🔗 Codons and anticodons

Codon: a set of three nucleotides on the mRNA that specifies a particular amino acid.

Anticodon: a set of three nucleotides on the tRNA that is complementary to, and pairs with, the codon on the mRNA.

  • A codon on the mRNA determines which kind of tRNA will add its amino acid to the growing protein chain.
  • The anticodon is located on one loop of the tRNA molecule.
  • At the opposite end of the tRNA is the acceptor stem, where the amino acid is attached.

🍀 tRNA structure

  • Two-dimensional structure has three distinctive loops, reminiscent of a cloverleaf.
  • One loop contains the anticodon (three nucleotides that vary for each kind of tRNA).
  • The acceptor stem (at the 3′ end) is where the amino acid binds.
  • Example: yeast tRNA for phenylalanine has the anticodon loop at the bottom and the acceptor stem at the top in its three-dimensional structure.

🔑 Key Similarities and Differences

🤝 Similarities between replication and transcription

  • Both require a template from which a complementary strand is synthesized.
  • Both use complementary base pairing.
  • Both synthesize in the 5′ to 3′ direction.

⚖️ Critical distinctions

  • Replication: entire DNA molecule is copied; product is DNA; new strand remains paired with template; produces two identical double helices.
  • Transcription: only a segment of DNA is copied; product is RNA; RNA is released from template; produces a single RNA strand.
  • Base pairing difference: in replication, A pairs with T; in transcription, A (in DNA) pairs with U (in RNA).
128

Protein Synthesis and the Genetic Code

Protein Synthesis and the Genetic Code

🧭 Overview

🧠 One-sentence thesis

The genetic code translates groups of three nucleotides (codons) in mRNA into specific amino acids, directing the synthesis of proteins through the process of translation.

📌 Key points (3–5)

  • Why triplets: Groups of three nucleotides provide 64 combinations (4³), enough to code for all 20 amino acids, whereas pairs would only give 16 (4²).
  • Translation process: mRNA carries genetic instructions from the nucleus to ribosomes, where tRNA molecules deliver amino acids in the correct sequence to build proteins.
  • Code characteristics: The genetic code is universal, degenerate (most amino acids have multiple codons), continuous, and nonoverlapping.
  • Special codons: AUG serves as both the start codon (methionine) and the initiation signal; three stop codons (UAA, UAG, UGA) terminate synthesis.
  • Common confusion: The first two bases of a codon are most critical—the third "wobble" base can often vary without changing the amino acid, so not all mutations affect the protein.

🧬 The genetic code structure

🔢 Why three nucleotides per amino acid

Genetic code: the identification of each group of three nucleotides and its particular amino acid.

  • A single nucleotide can only specify 4 amino acids (one per base).
  • Pairs of nucleotides give 4² = 16 combinations—still not enough for 20 amino acids.
  • Triplets (codons) provide 4³ = 64 combinations—more than sufficient.
  • This triplet system allows redundancy while covering all amino acids.

📖 The codon dictionary

The excerpt describes how researchers (Har Khorana, Marshall Nirenberg, Philip Leder, Severo Ochoa) cracked the genetic code between 1961–1964:

  • 61 codons code for amino acids.
  • 3 codons (UAA, UAG, UGA) signal termination (like a period ending a sentence).
  • Only methionine (AUG) and tryptophan (UGG) have single codons; all other amino acids have two or more.

Example: The mRNA sequence 5′-AUGCCACGAGUUGAC-3′ codes for met-pro-arg-val-asp (read from the 5′ end, matching the N-terminal to C-terminal direction of protein synthesis).

🔄 Translation: from mRNA to protein

🚚 Role of tRNA and aminoacyl-tRNA synthetase

Translation: the process in which the information encoded in mRNA is used to direct the sequencing of amino acids to synthesize a protein.

Before an amino acid can be added to a growing protein chain:

  1. It must be attached to its unique tRNA molecule.
  2. Aminoacyl-tRNA synthetase enzymes perform this attachment—there is one specific enzyme for each amino acid.
  3. This specificity is vital to ensure the correct amino acid is incorporated.

Don't confuse: tRNA does not directly "read" mRNA; instead, its anticodon pairs with the mRNA codon, and the attached amino acid is added to the protein.

🏭 The translation machinery

ComponentRole
mRNACarries the genetic instructions (codon sequence) from nucleus to cytoplasm
tRNATransports amino acids to the ribosome; anticodon pairs with mRNA codon
rRNAPart of the ribosome structure (formed during transcription)
RibosomeThe site where protein synthesis occurs
EnzymesOver 100 enzymes coordinate the process
  • mRNA is transcribed in the nucleus, then transported across the nuclear membrane to ribosomes in the cytoplasm.
  • The ribosome reads the mRNA sequence and coordinates tRNA binding and amino acid linkage.

🔗 Elongation steps

The excerpt references a stepwise process (Figure 19.13):

  • Each codon on mRNA is read in sequence (5′ to 3′ direction).
  • The corresponding tRNA (with the correct anticodon) brings its amino acid.
  • Amino acids are joined in order to form the polypeptide chain.
  • The process continues until a stop codon is reached.

🧩 Key properties of the genetic code

🌍 Universal and degenerate

Universal: Animal, plant, and bacterial cells use the same codons for each amino acid (with rare exceptions).

Degenerate: Most amino acids are coded by more than one codon.

  • Only methionine and tryptophan have a single codon each.
  • This redundancy provides a buffer against some mutations.

🎯 The "wobble" base

  • The first two bases of each codon are most significant.
  • The third base often varies without changing the amino acid—called the "wobble" base.
  • Implication: A mutation in the third position may still allow correct amino acid incorporation, reducing the impact of some DNA changes.

Example: Multiple codons for the same amino acid often differ only in the third position.

📏 Continuous and nonoverlapping

  • No nucleotides between codons: the code is read continuously without gaps.
  • Adjacent codons do not overlap: each nucleotide belongs to exactly one codon.
  • This ensures unambiguous reading of the genetic message.

Don't confuse: "Continuous" does not mean the entire mRNA is one long codon; it means codons are read sequentially without skipping bases.

🚦 Start and stop signals

🟢 Initiation codon (AUG)

  • AUG codes for methionine and also serves as the start signal.
  • Every newly synthesized polypeptide begins with methionine.
  • This first methionine is usually removed enzymatically before the protein is completed, so most finished proteins do not start with methionine.

🔴 Termination codons

  • Three stop codons: UAA, UAG, UGA.
  • These do not code for amino acids.
  • Release factors (special proteins) recognize stop codons and signal the end of translation.
  • This terminates polypeptide synthesis, like a period ending a sentence.

🧪 Practical application: reading the code

🧮 Calculating nucleotide requirements

The excerpt provides examples:

  • Oxytocin (9 amino acids) requires a minimum of 27 nucleotides (9 amino acids × 3 nucleotides per codon).
  • Myoglobin (153 amino acids) requires at least 459 nucleotides (153 × 3).

Note: These are minimum numbers; actual mRNA may be longer due to untranslated regions.

🔍 Translating sequences

To determine the amino acid sequence from an mRNA sequence:

  1. Start at the 5′ end.
  2. Read in groups of three (codons).
  3. Use the genetic code table to find each amino acid.

Example from the excerpt: 5′-AUGAGCGACUUUGCGGGAUUA-3′ translates to met-ser-asp-phe-ala-gly-leu.

Remember: The sequence is read 5′ to 3′, matching the N-terminal to C-terminal direction of the protein.

129

Mutations and Genetic Diseases

Mutations and Genetic Diseases

🧭 Overview

🧠 One-sentence thesis

Mutations—changes in DNA nucleotide sequences caused by errors or external agents—can lead to genetic diseases when they disrupt critical genes, but most can be managed or prevented through early detection and treatment.

📌 Key points (3–5)

  • What mutations are: chemical or physical changes that alter the nucleotide sequence in DNA, occurring spontaneously (rarely) or from exposure to heat, radiation, or chemicals.
  • Three main types of point mutations: substitution (one nucleotide replaced), insertion (nucleotide added), and deletion (nucleotide removed)—insertions and deletions are usually more harmful because they shift the reading frame.
  • Common confusion: not all mutations are equally harmful—substitutions change only one amino acid, while insertions/deletions alter the entire amino acid sequence downstream, making them more damaging.
  • What causes mutations: mutagens (physical agents like UV/gamma radiation or chemical agents) that damage DNA, for example by creating thymine dimers.
  • Genetic diseases result from mutations: most involve a failure to synthesize a particular enzyme, leading to metabolic abnormalities that can often be detected early and managed through dietary or other interventions.

🧬 What mutations are and how they happen

🧬 Definition and frequency

Mutation: any chemical or physical change that alters the nucleotide sequence in DNA.

  • DNA normally determines the amino acid sequence in proteins, which is critical for proper cell function.
  • Mutations are rare: spontaneous replication errors occur approximately once per 10 billion nucleotides.
  • External causes include heat, radiation, and certain chemicals.
  • When a mutation occurs in egg or sperm cells, it will be inherited by all offspring.

🔀 Three types of point mutations

Point mutation: a change in which one nucleotide is substituted, added, or deleted.

TypeWhat happensImpact
SubstitutionA different nucleotide replaces the originalOnly one amino acid is altered
InsertionA new nucleotide is addedFrame-shift: changes reading of all subsequent codons
DeletionA nucleotide is lostFrame-shift: alters entire amino acid sequence downstream
  • Why insertions and deletions are worse: they cause a frame-shift that changes how all subsequent codons are read, altering the entire amino acid sequence after the mutation point.
  • Substitutions affect only a single amino acid, so they are usually less harmful.
  • Example: if a substitution changes one codon, only that one position in the protein changes; if an insertion adds one nucleotide, every codon after that point is read differently.

☢️ What causes mutations

☢️ Mutagens

Mutagen: a chemical or physical agent that causes mutations.

  • Physical mutagens include ultraviolet (UV) and gamma radiation.
  • Radiation works either directly or by creating free radicals that have mutagenic effects.

🔗 How radiation damages DNA

  • Radiation and free radicals can cause bonds to form between nitrogenous bases in DNA.
  • Example: UV light exposure can create a covalent bond between two adjacent thymines on a DNA strand, producing a thymine dimer.
  • If not repaired, the dimer prevents the double helix from forming at that point.
  • Normal cells have enzyme systems that cut out thymine dimers and repair the region.

🩺 Xeroderma pigmentosum

  • A genetic disease caused by lack of the enzyme that removes thymine dimers from damaged DNA.
  • People with this condition are abnormally sensitive to light and more prone to skin cancer.
  • This shows that both the original mutation and the inability to repair mutations can cause disease.

🧪 Genetic diseases

🧪 What genetic diseases are

Genetic diseases (also called inborn errors of metabolism): hereditary conditions caused by an altered DNA sequence.

  • Most mutations are detrimental; some are beneficial, but many are harmful.
  • If a point mutation occurs at a crucial position, the affected protein will lack biological activity, possibly causing cell death.
  • Nonlethal mutations in egg or sperm cells may lead to metabolic abnormalities or hereditary diseases.
  • In most cases, the defective gene results in a failure to synthesize a particular enzyme.

📋 Representative genetic diseases

The excerpt provides a table listing diseases and their responsible proteins/enzymes, including:

  • Phenylketonuria (PKU): phenylalanine hydroxylase
  • Tay-Sachs disease: hexosaminidase A
  • Sickle cell anemia: hemoglobin
  • Hemophilia: clotting factors
  • Many others involving enzyme deficiencies

🍼 Phenylketonuria (PKU)

🍼 What PKU is and what causes it

  • PKU results from the absence of the enzyme phenylalanine hydroxylase.
  • Without this enzyme, a person cannot convert phenylalanine to tyrosine.
  • Tyrosine is the precursor of neurotransmitters (dopamine and norepinephrine) and the skin pigment melanin.

⚠️ What happens in PKU

  • When the conversion cannot occur, phenylalanine accumulates.
  • Phenylalanine is then converted to higher-than-normal quantities of phenylpyruvate (a phenyl ketone).
  • The disease name comes from high levels of phenylpyruvate in urine.
  • Excessive phenylpyruvate impairs normal brain development, causing severe mental retardation.

🩺 Detection and treatment

Detection:

  • PKU can be diagnosed by testing blood or urine for phenylalanine or its metabolites.
  • Medical authorities recommend testing every newborn's blood within 24 hours to 3 weeks after birth.
  • Every state mandates screening for PKU in all newborns.

Treatment:

  • If detected, mental retardation can be prevented by immediately placing the infant on a diet containing little or no phenylalanine.
  • Because phenylalanine is plentiful in natural proteins, the diet depends on a synthetic protein substitute plus very small measured amounts of natural foods.

Outcomes:

  • Before dietary treatment (introduced early 1960s), severe mental retardation was common: 85% of PKU patients had IQ < 40; 37% had IQ < 10.
  • Since dietary treatment, over 95% of children with PKU have developed normal or near-normal intelligence.
  • Incidence: about 1 in 12,000 newborns in North America.

🧠 Tay-Sachs disease

🧠 What Tay-Sachs is

  • Tay-Sachs is one of several lipid-storage diseases.
  • Lipids are constantly synthesized and broken down; if degradation enzymes are missing, lipids accumulate and cause medical problems.

🔬 Cause and mechanism

  • Caused by a genetic mutation in the gene for the enzyme hexosaminidase A.
  • Without this enzyme, gangliosides cannot be degraded but accumulate in brain tissue.
  • Ganglion cells of the brain become greatly enlarged and nonfunctional.

😢 Symptoms and prognosis

  • Leads to regression in development, dementia, paralysis, and blindness.
  • Death usually occurs before age three.
  • There is currently no treatment.

🧬 Detection and carriers

Detection:

  • Can be diagnosed in a fetus by testing amniotic fluid (amniocentesis) for hexosaminidase A.

Carriers:

  • A blood test can identify Tay-Sachs carriers—people who inherit a defective gene from only one parent (not both).
  • Carriers produce only half the normal amount of hexosaminidase A.
  • Carriers do not exhibit symptoms of the disease.

🔧 Recombinant DNA technology (overview)

🔧 What it is and why it matters

Recombinant DNA technology: techniques for identifying and isolating genes with specific biological functions and placing them in another organism (such as bacteria) that can be easily grown in culture.

  • More than 3,000 human diseases have a genetic component.
  • Researchers have identified many genes and mutations responsible for specific genetic diseases.
  • This technology offers the potential to cure many serious genetic diseases.

🧰 Key tools and concepts

Restriction enzymes:

  • Also called restriction endonucleases; discovered in 1970.
  • Cut DNA at specific, known nucleotide sequences, yielding shorter fragments.
  • Example: the enzyme EcoRI recognizes a specific sequence and cuts both DNA strands at that point.
  • Named after the bacterium of origin (e.g., EcoRI from the R strain of E. coli; roman numeral I indicates it was the first enzyme from that strain).

Cloning:

  • Multiple identical copies of each DNA fragment are produced.
  • Accomplished by inserting DNA fragments into phages (bacterial viruses) that enter bacterial cells and replicate.
  • When an infected bacterial cell is cultured, it forms a colony containing copies of the original DNA fragment.

DNA library:

  • A collection of bacterial colonies that together contain the entire genome of a particular organism.

Hybridization probe:

  • A short piece of DNA with a nucleotide sequence complementary to a known sequence in the target gene.
  • A radioactive phosphate group is added as a "tag" to identify colonies containing the desired gene.

Plasmids:

  • Tiny mini-chromosomes found in many bacteria, such as Escherichia coli (E. coli).
  • Used as vectors to insert recombined DNA into host organisms.

💊 Applications and benefits

Current achievements:

  • Production of human growth hormone (formerly available only in tiny amounts from cadavers; now readily available).
  • Epidermal growth factor to speed healing of burns and skin wounds.
  • Insulin for diabetes, clotting factors for hemophilia, missing enzymes, hormones, vitamins, antibodies, vaccines.
  • Tissue plasminogen activator (clot-dissolving enzyme for heart attack victims).
  • Vaccines against hepatitis B (humans) and hoof-and-mouth disease (cattle).

Research tool:

  • Helps scientists map and sequence genes and determine functions of different DNA segments.

Beyond bacteria:

  • Scientists use yeast, fungi, and plant systems.
  • Example: Agrobacterium tumefaciens plasmids can introduce foreign genes into plants to enhance nutritional value (e.g., transferring the methionine synthesis gene into pinto beans, which normally lack high methionine levels).

Potential for cures:

  • When appropriate genes are inserted into E. coli, the bacteria become miniature pharmaceutical factories producing large quantities of therapeutic proteins.
130

Viruses

Viruses

🧭 Overview

🧠 One-sentence thesis

Viruses are simple infectious agents that must invade host cells to reproduce, and they can be targeted by drugs that block specific viral enzymes needed for replication.

📌 Key points (3–5)

  • What viruses are: infectious agents smaller and simpler than bacteria, composed of nucleic acids (DNA or RNA, never both) enclosed in a protein shell.
  • How viruses reproduce: they invade host cells and force the cells to replicate viral genetic material and produce viral proteins, which assemble into new viruses that are released (often killing the host cell).
  • DNA vs RNA viruses: DNA viruses contain DNA; RNA viruses contain RNA; retroviruses (a type of RNA virus) synthesize DNA from their RNA template inside the host cell.
  • Common confusion: retroviruses reverse the normal DNA-to-RNA transcription process by making DNA from RNA using reverse transcriptase.
  • Why it matters: understanding viral reproduction mechanisms allows development of drugs that inhibit specific viral enzymes (reverse transcriptase, protease, integrase) to treat diseases like AIDS.

🦠 Virus structure and classification

🧬 Basic structure

Viruses: infectious agents far smaller and simpler than bacteria that are composed of a tightly packed central core of nucleic acids enclosed in a protective shell.

  • The shell consists of layers of one or more proteins.
  • May also have lipid or carbohydrate molecules on the surface.
  • Visible only under an electron microscope.
  • Come in a variety of shapes, ranging from spherical to rod shaped.

🔀 Two major classes

Viruses are divided based on their genetic material:

ClassGenetic materialKey characteristic
DNA virusesDNA onlyContain deoxyribonucleic acid
RNA virusesRNA onlyContain ribonucleic acid
  • A virus contains either DNA or RNA—but never both.
  • This fundamental difference determines how the virus reproduces inside host cells.

🔑 Why simplicity matters

  • Because of their simplicity, viruses must invade the cells of other organisms to be able to reproduce.
  • They lack the machinery to replicate on their own.
  • Example: A virus cannot make copies of itself floating freely; it needs a host cell's resources.

🔄 How viruses reproduce

🧬 DNA virus reproduction

The excerpt describes a straightforward process:

  1. A DNA virus enters a host cell.
  2. The virus induces the cell to replicate the viral DNA and produce viral proteins.
  3. These proteins and DNA assemble into new viruses.
  4. New viruses are released by the host cell, which may die in the process.
  5. The new viruses can then invade other cells and repeat the cycle.

Why symptoms occur: Cell death and the production of new viruses account for the symptoms of viral infections.

🧬 RNA virus reproduction

Most RNA viruses work similarly to DNA viruses:

  • They penetrate a host cell.
  • They induce the cell to replicate the viral RNA and synthesize viral proteins.
  • The new RNA strands and viral proteins are then assembled into new viruses.

Don't confuse: While the genetic material is different (RNA vs DNA), the overall strategy is the same for most RNA viruses.

🔄 Retroviruses: the reverse process

Retroviruses: RNA viruses that direct the synthesis of a DNA copy in the host cell.

Some RNA viruses work differently:

  • Called retroviruses.
  • They synthesize DNA in the host cell.
  • This is the reverse of the DNA-to-RNA transcription that normally occurs in cells.
  • The synthesis of DNA from an RNA template is catalyzed by the enzyme reverse transcriptase.

Why "retro": The name reflects the reversal of the normal transcription direction (normally DNA → RNA; retroviruses do RNA → DNA).

Example: In a normal cell, DNA serves as the template to make RNA. A retrovirus flips this: its RNA serves as the template to make DNA.

💊 HIV and AIDS treatment strategies

🦠 HIV as a retrovirus

The human immunodeficiency virus (HIV) is the best-known retrovirus:

  • Causes AIDS (acquired immunodeficiency syndrome).
  • Estimated 33 million people worldwide testing positive for HIV infections.
  • In 2007: 2.7 million new infections; approximately 2 million deaths from AIDS.

How HIV attacks:

  • Uses glycoproteins on its outer surface to attach to receptors on the surface of T cells (a group of white blood cells that normally help protect the body from infections).
  • Enters the T cell, replicates, and eventually destroys the cell.
  • With T cells destroyed, the AIDS victim is at increased risk of succumbing to pneumonia or other infectious diseases.

🔬 Reverse transcriptase inhibitors

The first class of anti-HIV drugs:

AZT (azidothymidine):

  • Also known as zidovudine or brand name Retrovir.
  • Became the first drug approved for the treatment of AIDS in 1987.
  • How it works: Binds to reverse transcriptase in place of deoxythymidine triphosphate; because AZT does not have a 3′ OH group, further replication is blocked.

Other drugs: Several other drugs approved in the past 10 years also act by inhibiting the viral reverse transcriptase.

✂️ Protease inhibitors

A second class of anti-HIV drugs:

Why proteases matter: As part of HIV reproduction in an infected cell, newly synthesized viral proteins must be cut by a specific viral-induced HIV protease to form shorter proteins.

Drug development strategy: Design drugs that specifically inhibit this proteolytic enzyme, without affecting the proteolytic enzymes (like trypsin) that are needed by the host.

First protease inhibitor:

  • Saquinavir (brand names Invirase and Fortovase) approved in December 1995.
  • Represented a new class of drugs.

Other protease inhibitors that gained FDA approval:

  • Ritonavir (Norvir)
  • Indinavir (Crixivan)
  • Nelfinavir (Viracept)

🧩 Integrase inhibitors

A third class of anti-HIV drugs:

Raltegravir (Isentress):

  • Approved by the FDA in October 2007.
  • Inhibits the integrase enzyme that is needed to integrate the HIV DNA into cellular DNA.
  • This integration is an essential step in the production of more HIV particles.

🧪 Combination therapy

The resistance problem: A major problem in treating HIV infections is that the virus can become resistant to any of these drugs.

The solution: Administer a "cocktail" of drugs, typically:

  • Two reverse transcriptase inhibitors
  • Plus one protease inhibitor

Result: These treatments can significantly reduce the amount of HIV in an infected person.

Don't confuse: Using multiple drugs together is not redundancy; it's a strategy to prevent the virus from developing resistance to any single drug.

📊 Summary of viral enzyme targets

EnzymeFunction in HIV reproductionDrug classExample drug
Reverse transcriptaseSynthesizes DNA from RNA templateReverse transcriptase inhibitorsAZT (azidothymidine)
ProteaseCuts viral proteins into shorter functional proteinsProtease inhibitorsSaquinavir
IntegraseIntegrates HIV DNA into cellular DNAIntegrase inhibitorsRaltegravir

Each enzyme represents a critical step in the viral life cycle, and blocking any one of them can disrupt viral reproduction.

131

ATP—the Universal Energy Currency

ATP—the Universal Energy Currency

🧭 Overview

🧠 One-sentence thesis

ATP serves as the principal medium of energy exchange in biological systems because its hydrolysis releases energy at a level that allows it to both accept energy from high-energy compounds and donate energy to drive cellular processes.

📌 Key points (3–5)

  • What ATP hydrolysis does: breaks the pyrophosphate bond to release energy (>7 kcal/mol) by relieving electron-electron repulsions between negatively charged phosphate groups.
  • Energy currency role: ATP is produced by energy-supplying processes (photosynthesis, food breakdown) and hydrolyzed by energy-requiring processes (biosynthesis, nerve transmission, muscle contraction).
  • ATP's intermediate energy position: ATP releases ~7.5 kcal/mol, which is midway between high-energy compounds (e.g., creatine phosphate at −10.3) and low-energy compounds (e.g., glucose 6-phosphate at −3.3).
  • Common confusion: ATP is not the only high-energy compound—several others exist, but ATP's intermediate energy level makes it uniquely suited as a universal energy transfer molecule.
  • Reversibility principle: hydrolysis of compounds above ATP in energy can resynthesize ATP from ADP; ATP hydrolysis can phosphorylate compounds below it.

⚡ The hydrolysis reaction and energy release

⚡ What happens structurally

The pyrophosphate bond (symbolized by ~) is hydrolyzed when ATP is converted to adenosine diphosphate (ADP).

  • ATP contains a phosphoric acid anhydride (pyrophosphate) linkage.
  • The general equation: ATP + H₂O → ADP + Pᵢ + 7.4 kcal/mol
  • Pᵢ represents inorganic phosphate anions (H₂PO₄⁻ and HPO₄²⁻).
  • The structural difference between ATP and ADP: ATP has a triphosphate group; ADP has only a diphosphate group.

🔋 Why energy is released

  • Electron repulsion relief: the negatively charged phosphate groups repel each other when bonded together.
  • When the bond is broken, the products (ADP and phosphate ion) have less energy than the reactants (ATP and water).
  • This energy difference (>7 kcal/mol) is released during hydrolysis.
  • Example: Think of compressed springs pushing apart—breaking the bond releases the "tension" stored in the electron repulsions.

🔄 The reverse process requires energy

  • If hydrolysis releases energy, synthesis from ADP requires energy input.
  • Energy-supplying processes drive ATP synthesis:
    • Green plants: absorption of radiant energy from the sun
    • Animals: breakdown of food
  • Energy-requiring processes consume ATP:
    • Synthesis of carbohydrates, lipids, proteins
    • Transmission of nerve impulses
    • Muscle contractions

💰 ATP as the energy currency

💰 Why "currency" is the right metaphor

  • ATP is the principal medium of energy exchange in biological systems.
  • Just as money facilitates transactions, ATP transfers energy between different cellular processes.
  • It acts as an intermediary: energy-releasing processes "deposit" energy into ATP; energy-requiring processes "withdraw" energy by hydrolyzing ATP.

🎯 ATP's strategic energy position

Compound typeExampleEnergy released (kcal/mol)Position relative to ATP
High-energyCreatine phosphate−10.3Above ATP
High-energy1,3-bisphosphoglycerate−11.8Above ATP
ATPATP → ADP + Pᵢ−7.5Middle
Low-energyGlucose 6-phosphate−3.3Below ATP
Low-energyGlucose 1-phosphate−5.0Below ATP
  • ATP's energy release (~7.5 kcal/mol) is approximately midway between high-energy and low-energy phosphate compounds.
  • This intermediate position is functionally critical (see next section).

🔁 Energy transfer mechanisms

🔁 ATP can accept energy from above

  • Compounds that appear above ATP in the energy table can provide energy to resynthesize ATP from ADP.
  • Example: Creatine phosphate (−10.3 kcal/mol) releases more energy than needed to form ATP (−7.5 kcal/mol), so its hydrolysis can drive ATP synthesis.
  • This allows cells to store energy in high-energy compounds and regenerate ATP as needed.

🔁 ATP can donate energy to below

  • The hydrolysis of ATP provides sufficient energy for the phosphorylation of compounds below it in the table.
  • Example: ATP hydrolysis (−7.5 kcal/mol) releases enough energy to phosphorylate glucose to form glucose 1-phosphate (which requires only 5.0 kcal/mol).
  • This enables ATP to drive biosynthetic reactions that would not occur spontaneously.

⚖️ Don't confuse: ATP is not the highest-energy compound

  • ATP is not the only high-energy compound needed for metabolism.
  • Several others (creatine phosphate, 1,3-bisphosphoglycerate, acetyl phosphate) release more energy upon hydrolysis.
  • ATP's role is not to be the "strongest" energy source but to be the universal intermediary that can interact with both high- and low-energy compounds.

📋 Other high-energy phosphate compounds

📋 Classification by energy level

The excerpt provides a table of phosphate compounds grouped by type:

High-energy compounds (above or near ATP):

  • Acyl phosphates: 1,3-bisphosphoglycerate (−11.8), acetyl phosphate (−11.3)
  • Guanidine phosphates: creatine phosphate (−10.3), arginine phosphate (−9.1)
  • Pyrophosphates: PPᵢ → 2Pᵢ (−7.8), ATP → AMP + PPᵢ (−7.7)

ATP and ADP:

  • ATP → ADP + Pᵢ (−7.5)
  • ADP → AMP + Pᵢ (−7.5)

Low-energy compounds (below ATP):

  • Sugar phosphates: glucose 1-phosphate (−5.0), fructose 6-phosphate (−3.8), glucose 6-phosphate (−3.3), glycerol 3-phosphate (−2.2)
  • AMP → adenosine + Pᵢ (−3.4)

📋 Functional implications

  • Compounds are not arbitrarily "high" or "low" energy—their position determines their role in metabolism.
  • High-energy compounds can drive ATP synthesis.
  • Low-energy compounds require ATP (or similar) for their formation.
  • Example classification: creatine phosphate is a high-energy compound; glucose 6-phosphate is not.
132

Stage I of Catabolism

Stage I of Catabolism

🧭 Overview

🧠 One-sentence thesis

Stage I of catabolism breaks down food macromolecules—carbohydrates, fats, and proteins—into their individual monomer units through digestion, primarily in the small intestine, so that these building blocks can be further processed to produce cellular energy.

📌 Key points (3–5)

  • What Stage I accomplishes: breaks down carbohydrates into simple sugars, fats into fatty acids and glycerol, and proteins into amino acids.
  • Where digestion occurs: begins in the mouth (carbohydrates) or stomach (proteins), but most digestion happens in the small intestine.
  • How digestion works: hydrolysis reactions cleave large food molecules into smaller monomer units.
  • Common confusion: digestion is only the first stage of catabolism; the monomer units must still undergo Stage II and Stage III to produce ATP.
  • Why it matters: Stage I prepares nutrients for absorption into the bloodstream and for further breakdown in later stages that generate ATP.

🍞 Carbohydrate digestion

🦷 Mouth and stomach

  • Digestion begins in the mouth with salivary α-amylase, which attacks α-glycosidic linkages in starch.
  • Cleavage produces a mixture of dextrins, maltose, and glucose.
  • The enzyme remains active as food passes through the esophagus but is rapidly inactivated in the acidic stomach environment.
  • Don't confuse: carbohydrate digestion starts in the mouth, but protein digestion starts in the stomach.

🔬 Small intestine (primary site)

The primary site of carbohydrate digestion is the small intestine.

  • α-amylase secreted in the small intestine converts remaining starch and dextrins to maltose.
  • Maltase cleaves maltose into two glucose molecules.
  • Sucrase and lactase act on disaccharides sucrose and lactose, respectively, which are not digested until they reach the small intestine.
  • Example: lactose (a disaccharide) is not broken down in the mouth or stomach; it waits until lactase in the small intestine cleaves it.

🍬 End products

  • The major products of complete hydrolysis are three monosaccharides: glucose, fructose, and galactose.
  • These are absorbed through the wall of the small intestine into the bloodstream.

🥩 Protein digestion

🧪 Stomach (initial breakdown)

Gastric juice: a mixture of water, inorganic ions, hydrochloric acid, and various enzymes and proteins found in the stomach.

  • Protein digestion begins in the stomach, where gastric juice hydrolyzes about 10% of peptide bonds.
  • Hydrochloric acid (HCl) in gastric juice has a pH of about 1.0–2.5 and helps denature food proteins (unfolds them) to expose their chains for enzyme action.
  • Pepsinogen (inactive enzyme) is converted to pepsin (active form) when food enters the stomach and pH drops.
  • Pepsin catalyzes hydrolysis of peptide linkages, preferentially acting on linkages involving aromatic amino acids (tryptophan, tyrosine, phenylalanine) and methionine and leucine.
  • Example: pepsin cleaves peptide bonds near aromatic amino acids, breaking large proteins into smaller peptide fragments.

🔬 Small intestine (completion)

  • Protein digestion is completed in the small intestine.
  • Pancreatic juice contains inactive enzymes (trypsinogen, chymotrypsinogen, procarboxypeptidase) that are activated in the small intestine.
EnzymeActivationSpecificity
TrypsinTrypsinogen → trypsin (by enteropeptidase)Attacks peptide bonds involving carboxyl groups of basic amino acids (lysine, arginine)
ChymotrypsinChymotrypsinogen → chymotrypsin (by trypsin)Attacks peptide bonds involving carboxyl groups of aromatic amino acids (phenylalanine, tryptophan, tyrosine)
CarboxypeptidaseProcarboxypeptidase → carboxypeptidase (by trypsin)Hydrolyzes peptide linkages at the free carboxyl end, liberating amino acids stepwise from the C-terminal end
Aminopeptidase(in intestinal juice)Removes amino acids from the N-terminal end of peptides with a free amino group
  • Don't confuse: chymotrypsin and trypsin both break peptide bonds, but chymotrypsin acts after aromatic amino acids while trypsin acts after basic amino acids.

🧬 End products

  • The amino acids released by protein digestion are absorbed across the intestinal wall into the circulatory system, where they can be used for protein synthesis.

🥑 Lipid digestion

🔬 Small intestine (upper portion)

  • Lipid digestion begins in the upper portion of the small intestine.
  • A hormone stimulates the gallbladder to discharge bile into the duodenum.

🧼 Role of bile salts

Bile salts emulsify large, water-insoluble lipid droplets, disrupting hydrophobic interactions and suspending smaller globules (micelles) in the aqueous digestive medium.

  • Emulsification greatly increases the surface area of lipid particles, allowing more intimate contact with lipases and thus rapid digestion.
  • Example: large fat droplets are broken into tiny micelles, making it easier for enzymes to access and break down the fats.
  • Don't confuse: bile salts do not digest fats themselves; they prepare fats for digestion by lipases.

⚙️ Enzymatic breakdown

  • Another hormone promotes secretion of pancreatic juice, which contains lipases.
  • Lipases catalyze the digestion of triglycerides:
    • First to diglycerides
    • Then to 2-monoglycerides and fatty acids
  • The monoglycerides and fatty acids cross the intestinal lining into the bloodstream, where they are resynthesized into triglycerides and transported as lipoprotein complexes (chylomicrons).
  • Phospholipids and cholesteryl esters undergo similar hydrolysis in the small intestine; their component molecules are also absorbed through the intestinal lining.

🧬 End products

  • Monoglycerides and fatty acids (which are later resynthesized into triglycerides for transport).

🔄 Summary of Stage I

📍 Where digestion happens

  • Mouth: carbohydrate digestion begins (salivary α-amylase).
  • Stomach: protein digestion begins (pepsin); acidic environment inactivates salivary enzymes.
  • Small intestine: primary site for digestion of all three macromolecules (carbohydrates, proteins, lipids).

🧩 End products by macromolecule type

MacromoleculeEnd Products
CarbohydratesGlucose, fructose, galactose (monosaccharides)
ProteinsAmino acids
Lipids (triglycerides)Monoglycerides and fatty acids

🔗 Connection to later stages

  • The monomer units produced in Stage I (monosaccharides, fatty acids, amino acids) are absorbed into the bloodstream.
  • These building blocks undergo further breakdown in Stage II and Stage III of catabolism to produce ATP.
  • Don't confuse: digestion (Stage I) only breaks down food into absorbable units; it does not directly produce ATP—that happens in later stages.
133

Overview of Stage II of Catabolism

Overview of Stage II of Catabolism

🧭 Overview

🧠 One-sentence thesis

Stage II of catabolism converts the breakdown products of carbohydrates, triglycerides, and proteins into a common reactive intermediate, acetyl-CoA, which then serves as a hub for both energy production and biosynthesis.

📌 Key points (3–5)

  • What Stage II accomplishes: specific metabolic pathways (different for each macronutrient) break down Stage I products (monosaccharides, fatty acids, amino acids) to produce acetyl-CoA.
  • Why acetyl-CoA is central: the acetyl unit is attached to coenzyme A, making it more reactive and enabling it to participate in many biochemical pathways.
  • Two major fates of acetyl-CoA: it can be used to build new molecules (lipids, cholesterol, steroids) or enter the citric acid cycle to generate energy when oxygen is available.
  • Common confusion: acetyl-CoA is not just an energy molecule—it is a versatile intermediate that can be directed toward biosynthesis or energy production depending on the cell's needs.

🔄 The role of metabolic pathways in Stage II

🛤️ What a metabolic pathway is

A metabolic pathway: a series of biochemical reactions by which an organism converts a given reactant to a specific end product.

  • Stage II consists of multiple pathways, each tailored to a different macronutrient class.
  • These pathways are distinct for carbohydrates, triglycerides, and proteins, but they all converge on the same endpoint: acetyl-CoA.

🔗 How Stage I products become acetyl-CoA

  • Stage I outputs are monosaccharides (from carbohydrates), fatty acids (from triglycerides), and amino acids (from proteins).
  • Stage II pathways take these diverse molecules and process them through different reaction sequences.
  • The result is a single, common molecule: acetyl-CoA.
  • Example: a monosaccharide follows one pathway, a fatty acid follows another, but both yield acetyl-CoA at the end.

🧬 Structure and reactivity of acetyl-CoA

🧪 What makes acetyl-CoA reactive

  • The acetyl unit (a two-carbon fragment) is derived from the breakdown of all three macronutrient classes.
  • It is attached to coenzyme A, which increases the reactivity of the acetyl group.
  • This attachment is what allows acetyl-CoA to participate in so many different biochemical reactions.

🔑 Coenzyme A and its vitamin requirement

  • Coenzyme A is built from pantothenic acid (a vitamin).
  • Without this vitamin, the cell cannot synthesize coenzyme A, and acetyl-CoA formation is impaired.

🌐 The multiple fates of acetyl-CoA

🏗️ Biosynthesis pathways

Acetyl-CoA can serve as the starting material for building new molecules:

  • Triglycerides: storage lipids.
  • Phospholipids: membrane components.
  • Cholesterol and other steroids: signaling molecules and membrane constituents.

This biosynthetic role shows that acetyl-CoA is not only about breaking down molecules for energy—it is also a building block for synthesis.

⚡ Energy generation via the citric acid cycle

  • When the cell needs energy and oxygen is available, acetyl-CoA enters the citric acid cycle.
  • In the citric acid cycle, the acetyl unit is oxidized, releasing energy.
  • This is the "most important" fate for energy generation, according to the excerpt.

🧭 Decision point: build or burn

ConditionFate of acetyl-CoAOutcome
Cell needs building blocksBiosynthesisLipids, cholesterol, steroids
Cell needs energy + oxygen availableCitric acid cycleEnergy production (Stage III)
  • Don't confuse: acetyl-CoA is not automatically burned for energy. The cell can redirect it toward synthesis if that is what is needed.
  • Example: if an organism has sufficient energy but needs to build membranes, acetyl-CoA will be channeled into phospholipid synthesis rather than the citric acid cycle.

🔄 Summary of acetyl-CoA's central role

🎯 Why acetyl-CoA is called a "hub"

  • It is the common end product of Stage II, regardless of whether the original nutrient was a carbohydrate, lipid, or protein.
  • It is the starting point for both energy extraction (Stage III) and biosynthesis.
  • This dual role makes acetyl-CoA a critical junction in metabolism: it links catabolism (breakdown) and anabolism (building up).

📊 Acetyl-CoA in the bigger picture

  • Stage I: digestion breaks macronutrients into smaller units (monosaccharides, fatty acids, amino acids).
  • Stage II: these units are converted to acetyl-CoA through specific pathways.
  • Stage III: acetyl-CoA enters the citric acid cycle (if energy is needed and oxygen is present), leading to further oxidation and ATP production.
  • The excerpt emphasizes that acetyl-CoA's entrance into the citric acid cycle marks the beginning of Stage III of catabolism.
134

Stage III of Catabolism

Stage III of Catabolism

🧭 Overview

🧠 One-sentence thesis

Stage III of catabolism oxidizes acetyl-CoA to carbon dioxide and water through the citric acid cycle, electron transport chain, and oxidative phosphorylation, producing most of the cell's ATP by reoxidizing reduced coenzymes with oxygen.

📌 Key points (3–5)

  • What Stage III accomplishes: acetyl-CoA enters the citric acid cycle and is completely oxidized to CO₂, producing reduced coenzymes (NADH and FADH₂), ATP, and metabolic intermediates.
  • Where oxygen is actually used: not in the citric acid cycle itself, but in the electron transport chain to reoxidize NADH and FADH₂ back to NAD⁺ and FAD.
  • How ATP is made: the electron transport chain creates an H⁺ gradient across the inner mitochondrial membrane; ATP synthase uses this gradient to synthesize ATP (oxidative phosphorylation).
  • Common confusion—direct vs indirect ATP production: the citric acid cycle produces only 1 ATP (as GTP) directly; the bulk of ATP (9 from NADH, 2 from FADH₂) comes from reoxidizing the reduced coenzymes in the electron transport chain.
  • Maximum yield: complete oxidation of 1 acetyl-CoA yields approximately 12 ATP molecules total.

🔄 The citric acid cycle

🔄 What the citric acid cycle does

Citric acid cycle (also called Krebs cycle or tricarboxylic acid [TCA] cycle): a cyclic sequence of reactions that brings about the oxidation of a two-carbon unit to carbon dioxide and water.

  • Acetyl-CoA enters the cycle; the two-carbon acetyl group is transferred onto a four-carbon molecule (oxaloacetate) to form citrate (six carbons).
  • Through a series of reactions, two carbon atoms are released as CO₂, and the four-carbon oxaloacetate is regenerated to accept another acetyl group.
  • The cycle is the beginning of Stage III of catabolism.
  • Proposed by Hans Krebs in 1937 (awarded the 1953 Nobel Prize).

🧪 Types of reactions in the cycle

All reactions are familiar organic chemistry types:

  • Hydration: adding water to a double bond (e.g., fumarate → malate).
  • Oxidation: removing electrons/hydrogen atoms (e.g., malate → oxaloacetate).
  • Decarboxylation: releasing CO₂ (e.g., isocitrate → α-ketoglutarate).
  • Hydrolysis: breaking a bond with water (e.g., succinyl-CoA → succinate).

🏭 Where the cycle occurs

  • All reactions occur within mitochondria, small organelles in plant and animal cells.
  • The mitochondria have two membranes: outer and inner.
  • The matrix (inside the inner membrane) contains all citric acid cycle enzymes except succinate dehydrogenase, which is embedded in the inner membrane.

🔢 Key steps and products

StepReactionEnzymeProduct(s)
1Acetyl-CoA + oxaloacetate → citrateCitrate synthaseCitrate + CoA released
2Citrate → isocitrateAconitaseIsocitrate (tertiary → secondary alcohol)
3Isocitrate → α-ketoglutarate + CO₂Isocitrate dehydrogenaseα-ketoglutarate + NADH + CO₂
4α-ketoglutarate → succinyl-CoA + CO₂α-ketoglutarate dehydrogenase complexSuccinyl-CoA + NADH + CO₂ (irreversible)
5Succinyl-CoA → succinateSuccinyl-CoA synthetaseSuccinate + GTP (→ ATP)
6Succinate → fumarateSuccinate dehydrogenaseFumarate + FADH₂
7Fumarate → malateFumaraseMalate
8Malate → oxaloacetateMalate dehydrogenaseOxaloacetate + NADH

Net products per acetyl-CoA:

  • 2 CO₂
  • 3 NADH
  • 1 FADH₂
  • 1 GTP (equivalent to 1 ATP)

⚠️ Don't confuse: carbon atoms in vs out

  • Two carbon atoms enter as the acetyl group (step 1).
  • Two carbon atoms exit as CO₂ (steps 3 and 4).
  • However, the two carbon atoms released are not the same as the two that entered; the cycle mixes all carbons.

🔐 The only irreversible step

  • Step 4 (α-ketoglutarate → succinyl-CoA) is the only irreversible reaction.
  • This prevents the cycle from running backward and synthesizing acetyl-CoA from CO₂.

🔋 Cellular respiration and mitochondria

🫁 What cellular respiration means

Respiration: the process by which cells oxidize organic molecules in the presence of gaseous oxygen to produce carbon dioxide, water, and energy in the form of ATP.

  • The citric acid cycle itself does not directly use oxygen.
  • Oxygen is needed to reoxidize the reduced coenzymes (NADH and FADH₂) produced by the cycle.
  • Oxygen participation and significant ATP production occur after the citric acid cycle, in the electron transport chain and oxidative phosphorylation.

🏭 Mitochondrial structure

Mitochondria: small, oval organelles with double membranes; the "power plants" of a cell.

  • A cell may contain 100–5,000 mitochondria, depending on its energy needs.
  • Mitochondria can reproduce themselves if energy requirements increase.

Two membranes:

  • Outer membrane: permeable to most small molecules.
  • Inner membrane: impermeable to most molecules and ions (except water, O₂, and CO₂); extensively folded into internal ridges called cristae.

Two compartments:

  • Intermembrane space: between the two membranes.
  • Matrix: inside the inner membrane; contains citric acid cycle enzymes (except succinate dehydrogenase).

🧬 Where the machinery is located

  • Citric acid cycle enzymes: in the matrix (except succinate dehydrogenase, in the inner membrane).
  • Electron transport chain and ATP synthesis enzymes: embedded in the inner membrane, arranged in a specific "bucket brigade" sequence.

⚡ The electron transport chain

⚡ What the electron transport chain does

Electron transport chain (or respiratory chain): an organized sequence of oxidation-reduction reactions that ultimately transports electrons to oxygen, reducing it to water.

  • The chain is organized into four complexes (I, II, III, IV) in the inner mitochondrial membrane.
  • Each complex contains enzymes, proteins, and metal ions that can be repeatedly reduced and oxidized.
  • Electrons pass from one component to the next, releasing energy at each step.

🚪 Two entry points for electrons

Complex I entry (from NADH):

  • NADH is formed in three reactions of the citric acid cycle (steps 3, 4, and 8).
  • NADH donates two electrons to flavin mononucleotide (FMN) in complex I.
  • FMN is reduced to FMNH₂, then passes electrons to iron-sulfur (Fe·S) proteins.
  • Each Fe·S center transfers one electron by cycling between Fe(III) and Fe(II).

Complex II entry (from FADH₂):

  • FADH₂ is formed in step 6 of the citric acid cycle (succinate → fumarate).
  • Succinate dehydrogenase (part of complex II) catalyzes this reaction.
  • FADH₂ donates electrons to Fe·S proteins in complex II.

🔀 Electron shuttles

  • Coenzyme Q (CoQ, also called ubiquinone): mobile carrier that shuttles electrons from complexes I or II to complex III.
  • Cytochrome c: shuttles electrons from complex III to complex IV.

🧲 Cytochromes and iron porphyrins

Cytochromes: proteins that contain an iron porphyrin in which iron can alternate between Fe(II) and Fe(III).

  • Complexes III and IV contain several cytochromes (b, c, a, a₃).
  • Each cytochrome can accept one electron (Fe(III) → Fe(II)) and donate it to the next cytochrome.
  • This reversible change in oxidation state allows electrons to pass down the chain.

💧 Final electron acceptor

  • Complex IV (cytochrome oxidase) contains cytochromes a and a₃.
  • It transfers electrons to molecular oxygen (O₂), the last electron acceptor.
  • Oxygen is reduced to water (H₂O).

Final reduction half-reaction:
O₂ + 4H⁺ + 4e⁻ → 2H₂O

🔄 Don't confuse: where oxygen is used

  • Oxygen is not consumed in the citric acid cycle.
  • Oxygen is consumed only at the end of the electron transport chain (complex IV).
  • Without oxygen, NADH and FADH₂ cannot be reoxidized, and the citric acid cycle stops.

🔋 Oxidative phosphorylation and ATP synthesis

🔋 What oxidative phosphorylation means

Oxidative phosphorylation: the process that links ATP synthesis to the operation of the electron transport chain.

  • Electron transport is tightly coupled to ATP synthesis: NADH and FADH₂ are oxidized by the respiratory chain only if ADP is simultaneously phosphorylated to ATP.
  • This coupling ensures that energy from electron transport is captured as ATP.

🌊 The chemiosmotic hypothesis

  • Proposed by Peter Mitchell (awarded the 1978 Nobel Prize in Chemistry).
  • As electrons move through the electron transport chain, H⁺ ions are pumped from the matrix across the inner membrane into the intermembrane space.
  • This creates an H⁺ gradient: high concentration in the intermembrane space, low in the matrix.
  • The gradient stores energy, like water behind a dam.

⚙️ ATP synthase

  • A fifth enzyme complex embedded in the inner membrane.
  • H⁺ ions flow down the concentration gradient through ATP synthase, from the intermembrane space back into the matrix.
  • This flow causes a structural change in ATP synthase, driving the synthesis and release of ATP from ADP and inorganic phosphate.

📊 ATP yield from reduced coenzymes

Reduced coenzymeATP yield per molecule
NADH2.5–3 ATP
FADH₂1.5–2 ATP

Why the difference?

  • FADH₂ enters the chain at complex II, bypassing complex I.
  • Fewer H⁺ ions are pumped, so less ATP is synthesized.

🧮 Total ATP from one acetyl-CoA

SourceProductATP yield
Citric acid cycle (step 5)1 GTP (→ ATP)+1
Citric acid cycle (step 6)1 FADH₂+2
Citric acid cycle (steps 3, 4, 8)3 NADH+9 (3 × 3)
Net yield+12 ATP

🏃 Energy demand and oxygen consumption

  • Cells using energy have high ADP levels and must consume large amounts of oxygen to phosphorylate ADP to ATP.
  • Example: resting skeletal muscles use ~30% of an adult's oxygen; strenuously working muscles use ~90%.
  • High oxygen consumption reflects high ATP turnover.

⚠️ Don't confuse: direct vs indirect ATP production

  • The citric acid cycle produces only 1 ATP directly (as GTP in step 5).
  • The bulk of ATP (11 out of 12) comes from reoxidizing NADH and FADH₂ in the electron transport chain and oxidative phosphorylation.
  • This is why oxygen is essential: without it, the reduced coenzymes cannot be reoxidized, and ATP production drops dramatically.
135

Stage II of Carbohydrate Catabolism

Stage II of Carbohydrate Catabolism

🧭 Overview

🧠 One-sentence thesis

Glycolysis breaks down glucose into pyruvate with a net production of ATP, and the fate of pyruvate—complete oxidation or conversion to lactate/ethanol—depends on oxygen availability, determining whether cells extract a small fraction or a large fraction of glucose's total energy.

📌 Key points (3–5)

  • What glycolysis does: converts one glucose molecule into two pyruvate molecules, producing ATP and NADH in the process.
  • Two phases of glycolysis: Phase I consumes ATP to break glucose into two three-carbon molecules; Phase II generates ATP and NADH from those molecules.
  • Oxygen determines pyruvate's fate: with oxygen, pyruvate enters the citric acid cycle for complete oxidation; without oxygen, pyruvate is converted to lactate (vertebrates) or ethanol (yeast), allowing NADH to be reoxidized.
  • Common confusion—aerobic vs anaerobic yield: anaerobic glycolysis produces only 2 net ATP per glucose (about 2% efficiency), while complete aerobic oxidation yields 36–38 ATP (about 42% efficiency).
  • Why it matters: glycolysis is the first metabolic pathway elucidated and is essential for energy production in all cells, with efficiency varying dramatically based on oxygen availability.

🔬 What glycolysis is and how it works

🔬 Definition and discovery

Glycolysis: the metabolic pathway in which glucose is broken down to two molecules of pyruvate with the corresponding production of ATP.

  • It was the first metabolic pathway to be fully understood (early 20th century).
  • The enzymes are found in soluble form in the cell, making them easy to isolate and purify.
  • The pathway is structured so that the product of one enzyme-catalyzed reaction becomes the substrate of the next; intermediates transfer between enzymes by diffusion.
  • All intermediates in glycolysis are phosphorylated and contain either six or three carbon atoms.

🧩 Overall outcome

From one molecule of glucose, glycolysis produces:

  • Two molecules of pyruvate (three-carbon compounds)
  • Two molecules of ATP (net production)
  • Two molecules of NADH

⚙️ The two phases of glycolysis

⚙️ Phase I: Energy investment (glucose → two glyceraldehyde 3-phosphate)

What happens: Glucose is broken down into two molecules of glyceraldehyde 3-phosphate.

Key steps:

  1. Glucose → glucose 6-phosphate (enzyme: hexokinase; consumes 1 ATP)

    • ATP is the phosphate donor; magnesium ions required.
    • This reaction activates the glucose molecule.
    • It is essentially irreversible, keeping the process moving forward.
    • The added negative phosphate group prevents intermediates from diffusing out of the cell (unlike neutral glucose).
  2. Glucose 6-phosphate → fructose 6-phosphate (enzyme: phosphoglucose isomerase)

    • Isomerization reaction.
    • Creates a primary alcohol that can be readily phosphorylated.
  3. Fructose 6-phosphate → fructose 1,6-bisphosphate (enzyme: phosphofructokinase; consumes 1 ATP)

    • ATP is again the phosphate donor; magnesium ions required.
  4. Fructose 1,6-bisphosphate → two triose phosphates (enzyme: aldolase)

    • Cleaves into dihydroxyacetone phosphate and glyceraldehyde 3-phosphate.
  5. Dihydroxyacetone phosphate → glyceraldehyde 3-phosphate (enzyme: triose phosphate isomerase)

    • Isomerization converts one triose into the other.

Net result of Phase I: One molecule of fructose 1,6-bisphosphate is effectively converted into two molecules of glyceraldehyde 3-phosphate. Phase I requires 2 ATP and releases none of the energy stored in glucose.

Don't confuse: The prefix "bis-" means two phosphate groups on different carbon atoms; "di-" means two phosphate groups bonded to each other on the same carbon atom (e.g., ADP).

⚙️ Phase II: Energy payoff (glyceraldehyde 3-phosphate → pyruvate)

What happens: Each glyceraldehyde 3-phosphate is converted into pyruvate, generating ATP and NADH.

Key steps (remember: two molecules of glyceraldehyde 3-phosphate enter Phase II per glucose):

  1. Glyceraldehyde 3-phosphate → 1,3-bisphosphoglycerate (BPG) (enzyme: glyceraldehyde-3-phosphate dehydrogenase)

    • Oxidation and phosphorylation occur simultaneously.
    • NAD⁺ is the oxidizing agent (reduced to NADH).
    • Inorganic phosphate is the phosphate donor (not ATP).
    • BPG has a high-energy phosphate bond at C1.
  2. BPG → 3-phosphoglycerate (enzyme: phosphoglycerate kinase; produces 2 ATP per glucose)

    • The high-energy phosphate group is transferred directly to ADP, forming ATP.
    • This is substrate-level phosphorylation: direct transfer of a phosphate group from a metabolite to ADP (not oxidative phosphorylation).
    • Magnesium ions required.
  3. 3-phosphoglycerate → 2-phosphoglycerate (enzyme: phosphoglyceromutase)

    • The phosphate group moves from C3 to C2.
  4. 2-phosphoglycerate → phosphoenolpyruvate (PEP) (enzyme: enolase)

    • Dehydration reaction.
    • PEP has a high-energy phosphate group.
  5. PEP → pyruvate (enzyme: pyruvate kinase; produces 2 ATP per glucose)

    • Second substrate-level phosphorylation.
    • Phosphate group transferred to ADP, producing ATP.
    • Irreversible reaction.
    • Requires magnesium and potassium ions.

Net result of Phase II: Two molecules of glyceraldehyde 3-phosphate are converted to two molecules of pyruvate, producing 4 ATP and 2 NADH.

🔀 What happens to pyruvate and NADH

🔀 Oxygen determines the fate

The presence or absence of oxygen determines what happens to the pyruvate and NADH produced in glycolysis.

ConditionFate of pyruvateFate of NADHLocation/organism
Oxygen present (aerobic)Completely oxidized to CO₂ via citric acid cycle, electron transport chain, and oxidative phosphorylationEnters electron transport chain for ATP productionAll aerobic cells
Oxygen absent (anaerobic)Converted to lactateReoxidized to NAD⁺ (allows glycolysis to continue)Vertebrates (muscle, brain)
Oxygen absent (anaerobic)Converted to ethanol + CO₂Reoxidized to NAD⁺ (allows glycolysis to continue)Yeast and some microorganisms

Why NADH reoxidation matters: Glycolysis requires NAD⁺ as an oxidizing agent. Under anaerobic conditions, converting pyruvate to lactate or ethanol allows NADH to be reoxidized to NAD⁺, so glycolysis can continue even without oxygen.

Don't confuse: Substrate-level phosphorylation (direct transfer from metabolite to ADP, occurs in glycolysis) vs. oxidative phosphorylation (ATP synthesis coupled to the electron transport chain, occurs in mitochondria with oxygen).

📊 ATP yield and energy efficiency

📊 Anaerobic glycolysis (glucose → lactate or ethanol)

ATP accounting per mole of glucose:

  • Phase I: –2 ATP consumed (steps 1 and 3)
  • Phase II: +4 ATP produced (steps 7 and 10, each producing 2 ATP)
  • Net production: 2 ATP per glucose

Energy efficiency:

  • If 7.4 kcal is conserved per mole of ATP, and total energy from complete glucose oxidation is 670 kcal:
  • Energy conserved = 2 ATP × 7.4 kcal = 14.8 kcal
  • Efficiency = 14.8 ÷ 670 × 100 = 2.2%

Interpretation: Anaerobic cells extract only a very small fraction of the total energy in glucose.

📊 Aerobic oxidation (glucose → CO₂ + H₂O)

Total ATP yield: 36–38 ATP per glucose (depending on tissue type)

Breakdown by process:

ProcessATP yieldNotes
Glycolysis (net)+2Substrate-level phosphorylation
Pyruvate → acetyl-CoA0 direct; +6 from 2 NADH2 NADH × 3 ATP each
Citric acid cycle+2 from 2 GTP; +6 from 2 FADH₂; +18 from 6 NADH2 FADH₂ × 2 ATP; 6 NADH × 3 ATP
Cytoplasmic NADH from glycolysis+4 to +6Variable depending on tissue
Total36–38 ATP

Why the variable yield from cytoplasmic NADH:

  • NADH produced in the cytoplasm during glycolysis cannot cross the inner mitochondrial membrane directly.
  • Brain and muscle cells: use a transport mechanism that passes electrons to FAD inside mitochondria, forming FADH₂, which yields only 1.5–2 ATP per cytoplasmic NADH.
  • Liver, heart, and kidney cells: use a more efficient transport system where one cytoplasmic NADH → one mitochondrial NADH → 2.5–3 ATP.

Energy efficiency:

  • Energy conserved = 38 ATP × 7.4 kcal = 281.2 kcal
  • Efficiency = 281.2 ÷ 670 × 100 = 42%

Comparison: This 42% efficiency compares favorably with machines (automobiles are only 20–25% efficient). The remaining 58% of energy is released as heat, which helps maintain body temperature.

Example: During strenuous exercise, metabolism speeds up to provide energy for muscle contraction, producing more heat. Perspiration helps dissipate excess heat as water vapor evaporates.

📊 Aerobic vs anaerobic comparison

ConditionNet ATP per glucoseEfficiencyKey limitation
Anaerobic2~2%Cannot fully oxidize pyruvate
Aerobic36–38~42%Requires oxygen for electron transport

Don't confuse: The total ATP produced (4 in Phase II) vs. the net ATP produced by glycolysis (2, after subtracting the 2 consumed in Phase I).

🏥 Clinical relevance: Diabetes

🏥 What diabetes does to glucose metabolism

  • People with diabetes cannot use glucose properly, leading to excessive accumulation in blood and urine.
  • Characteristic symptoms: constant hunger, weight loss, extreme thirst, frequent urination (kidneys try to remove excess sugar).

🏥 Type 1 vs Type 2 diabetes

FeatureType 1 diabetesType 2 diabetes
Also known asInsulin-dependent; juvenile-onsetNoninsulin-dependent; adult-onset
CauseInsufficient insulin production; immune system destroys insulin-producing pancreas cellsInsulin-producing cells don't release enough, or defective/lacking insulin receptors on target cells
Prevalence~5% of cases~95% of cases (~16 million Americans)
TreatmentInsulin injections (cannot be taken orally because it's digested)Diet and exercise alone may suffice; oral antidiabetic drugs (e.g., glyburide) stimulate insulin release and increase receptor sensitivity; some require insulin
PredictionBlood test can detect antibodies years before symptoms appear

🏥 Serious complications

  • Leading cause of lower limb amputations in the United States.
  • Leading cause of blindness in adults over age 20.
  • Leading cause of kidney failure.
  • Increases heart attack or stroke risk by 2–4 times.

Management: Blood sugar must be carefully monitored and kept in the normal range (70–120 mg/dL) through diet or medication adjustments.

136

Stage II of Lipid Catabolism

Stage II of Lipid Catabolism

🧭 Overview

🧠 One-sentence thesis

Fatty acids are broken down through β-oxidation in the mitochondria, producing acetyl-CoA, NADH, and FADH₂ that ultimately generate large amounts of ATP with approximately 41% efficiency.

📌 Key points (3–5)

  • Activation is required first: fatty acids must be converted to fatty acyl-CoA (using one ATP) before they can be transported into the mitochondria and oxidized.
  • β-oxidation is a repeating cycle: four sequential reactions progressively remove two-carbon units (as acetyl-CoA) from the carboxyl end of the fatty acid.
  • Each cycle produces three key molecules: one acetyl-CoA, one FADH₂, and one NADH, which are then used in Stage III to generate ATP.
  • Common confusion—how many cycles?: for a fatty acid with n carbons, β-oxidation repeats n/2 – 1 times (not n/2), because the final turn yields two acetyl-CoA molecules at once.
  • High energy yield: complete oxidation of one palmitic acid (16 carbons) produces a net of 129 ATP molecules, comparable in efficiency to carbohydrate metabolism.

🔧 Activation and transport

🔧 Fatty acid activation

  • Fatty acids are relatively inert and must first be activated before catabolism can begin.
  • Activation occurs on the outer mitochondrial membrane.
  • The enzyme acyl-CoA synthetase catalyzes the reaction:
    • One molecule of coenzyme A (CoA) + one molecule of ATP → fatty acyl-CoA + AMP + 2 inorganic phosphates.
    • This consumes the equivalent of two high-energy bonds (ATP is converted to AMP, not ADP).
  • Example: a 16-carbon fatty acid (palmitic acid) is converted to palmitoyl-CoA before it can enter the mitochondrial matrix.

🚪 Transport into the mitochondrial matrix

  • The fatty acyl-CoA cannot cross the inner mitochondrial membrane directly.
  • It combines with a carrier molecule called carnitine in a reaction catalyzed by carnitine acyltransferase.
  • The acyl-carnitine derivative is transported into the mitochondrial matrix.
  • Once inside, the derivative is converted back to fatty acyl-CoA.
  • Further oxidation then occurs in the mitochondrial matrix.

🔄 The β-oxidation cycle

🔄 What β-oxidation means

β-oxidation: a sequence of four reactions in which fatty acyl-CoA molecules are oxidized, leading to the removal of acetyl-CoA molecules.

  • The name comes from the fact that the β-carbon (the second carbon from the carboxyl end) undergoes successive oxidations.
  • Each cycle removes two carbon atoms from the carboxyl end of the fatty acyl-CoA.
  • The cycle repeats until the entire fatty acid is broken down into acetyl-CoA units.
  • Don't confuse: β-oxidation is sometimes called the "fatty acid spiral" because each shortened fatty acyl-CoA cycles back to the beginning of the pathway.

🧪 The four reactions of each cycle

StepReaction typeEnzymeCoenzyme/productWhat happens
1OxidationAcyl-CoA dehydrogenaseFAD → FADH₂An alkene (double bond) is formed; hydrogen atoms are removed from the α- and β-carbons
2HydrationEnoyl-CoA hydrataseWater addedThe trans-alkene is hydrated to form a secondary alcohol (L-isomer only)
3Oxidationβ-Hydroxyacyl-CoA dehydrogenaseNAD⁺ → NADHThe secondary alcohol is oxidized to a ketone
4CleavageThiolaseCoA addedThe β-ketoacyl-CoA is cleaved by coenzyme A, producing one acetyl-CoA and a fatty acyl-CoA shortened by two carbons
  • The shortened fatty acyl-CoA becomes the substrate for the next round of β-oxidation.
  • The cycle continues until the final step produces two acetyl-CoA molecules.

🔁 How many cycles?

  • For a fatty acid with n carbon atoms, β-oxidation repeats (n/2) – 1 times.
  • Example: palmitic acid has 16 carbons, so β-oxidation repeats 7 times (not 8).
  • Why? The final turn of the cycle yields two acetyl-CoA molecules at once, so one fewer cycle is needed.

⚡ Energy yield and efficiency

⚡ Products from β-oxidation

Each complete breakdown of a fatty acid produces:

  • Multiple molecules of acetyl-CoA (one per two-carbon unit).
  • Multiple molecules of FADH₂ (one per cycle).
  • Multiple molecules of NADH (one per cycle).

These products enter Stage III:

  • Acetyl-CoA enters the citric acid cycle and is oxidized to produce energy.
  • FADH₂ is reoxidized via the electron transport chain, supplying energy to form 1.5–2 ATP per molecule.
  • NADH is reoxidized via the electron transport chain, furnishing 2.5–3 ATP per molecule.

🧮 ATP yield from palmitic acid (16 carbons)

The excerpt provides a detailed calculation for one mole of palmitic acid:

SourceCalculationATP yield
Activation cost1 ATP → AMP + 2Pᵢ–2 ATP
Acetyl-CoA formed8 mol × 12 ATP each (from citric acid cycle)+96 ATP
FADH₂ formed7 mol × 2 ATP each+14 ATP
NADH formed7 mol × 3 ATP each+21 ATP
Net total129 ATP
  • Note: the excerpt uses approximate values (e.g., 2.5–3 ATP per NADH; the table uses 3 for simplicity).

📊 Efficiency calculation

  • Combustion of 1 mol of palmitic acid releases 2,340 kcal of energy.
  • Energy conserved in ATP: 129 ATP × 7.4 kcal/ATP = 954.6 kcal.
  • Efficiency: (954.6 / 2,340) × 100 ≈ 41%.
  • This is comparable to the 42% efficiency of carbohydrate metabolism.

💧 Metabolic water production

  • The oxidation of fatty acids produces large quantities of water.
  • This water sustains migratory birds and animals (such as camels) for long periods of time.

🧬 Fate of acetyl-CoA and special conditions

🧬 What happens to acetyl-CoA

The fate of acetyl-CoA obtained from fatty acid oxidation depends on the organism's needs:

  • Enter the citric acid cycle and be oxidized to produce energy.
  • Form ketone bodies (water-soluble derivatives) in the liver.
  • Serve as starting material for the synthesis of new fatty acids.

🩺 Ketone bodies (special topic)

Ketone bodies: a group of compounds—acetoacetate, β-hydroxybutyrate, and acetone—synthesized in the liver from acetyl-CoA.

Normal conditions:

  • In the liver, most acetyl-CoA from fatty acid oxidation is oxidized by the citric acid cycle.
  • Some acetyl-CoA is used to synthesize ketone bodies.
  • Two acetyl-CoA molecules combine (in a reversal of the final β-oxidation step) to produce acetoacetyl-CoA.
  • Further reactions produce acetoacetate; most is reduced to β-hydroxybutyrate, and a small amount is decarboxylated to acetone.
  • The liver releases acetoacetate and β-hydroxybutyrate into the blood for use as metabolic fuel by other tissues (kidney, heart).
  • During prolonged starvation, ketone bodies provide about 70% of the brain's energy requirements.
  • Normal blood levels: about 1 mg per 100 mL; kidneys excrete about 20 mg per day.

Abnormal conditions (ketosis and acidosis):

  • In starvation, diabetes mellitus, and other conditions where cells do not receive sufficient carbohydrate, fatty acid oxidation increases.
  • Acetyl-CoA concentration rises but cannot be fully oxidized by the citric acid cycle (because oxaloacetate is diverted to glucose synthesis).
  • The liver produces ketone bodies at a rate much higher than other tissues can use.
  • Excess ketone bodies accumulate in the blood and urine—a condition called ketosis.
  • Acetone is expelled in the breath, causing a characteristic sweet smell (often noticed in severely diabetic patients).
  • Two of the three ketone bodies are weak acids; their excessive accumulation overwhelms blood buffers and causes blood pH to drop (from 7.4 to 6.9)—a condition called acidosis.
  • Effects of acidosis:
    • Decreased ability of hemoglobin to transport oxygen.
    • Labored and painful breathing.
    • Dehydration (kidneys eliminate large quantities of water to get rid of acids).
    • Depression, lethargy, loss of appetite, run-down feeling.
    • In severe cases, coma; prompt treatment is necessary to save the person's life.

🔬 Enzyme localization and efficiency

🔬 Why mitochondria matter

  • The enzymes for fatty acid catabolism are located in the mitochondria.
  • The enzymes for the citric acid cycle, electron transport chain, and oxidative phosphorylation are also in the mitochondria.
  • This localization is of utmost importance because it facilitates efficient utilization of energy stored in fatty acids and other molecules.
  • All the products of β-oxidation (acetyl-CoA, NADH, FADH₂) are immediately available for Stage III reactions in the same cellular compartment.

🔬 Overall equation for palmitoyl-CoA oxidation

The excerpt provides the overall equation for the β-oxidation of palmitoyl-CoA (16 carbons):

  • Palmitoyl-CoA + 7 CoA + 7 FAD + 7 NAD⁺ + 7 H₂O → 8 acetyl-CoA + 7 FADH₂ + 7 NADH + 7 H⁺
  • (This does not include the subsequent citric acid cycle and electron transport chain reactions.)
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Stage II of Protein Catabolism

Stage II of Protein Catabolism

🧭 Overview

🧠 One-sentence thesis

Amino acid breakdown begins with removing the amino group (usually by transamination), after which the remaining carbon skeletons are converted into intermediates that can either form glucose or ketone bodies depending on the metabolic pathway.

📌 Key points

  • Where it happens: The liver is the main site of amino acid metabolism, though kidneys, intestines, muscles, and adipose tissue also participate.
  • First step: Amino groups are separated from carbon skeletons, typically through transamination reactions (except for lysine, proline, and threonine).
  • Two fates for carbon skeletons: They can be converted to glucose (glucogenic amino acids) or to ketone bodies (ketogenic amino acids); some amino acids are both.
  • Common confusion: Transamination vs oxidative deamination—transamination transfers amino groups between molecules, while oxidative deamination removes the amino group as ammonium ion for excretion.
  • When it occurs: Amino acid catabolism is more likely when glucose levels are low, such as during fasting or starvation.

🔄 Amino group removal

🔄 Transamination mechanism

Transamination: an exchange of functional groups between any amino acid (except lysine, proline, and threonine) and an α-keto acid.

  • The amino group transfers to the keto carbon of pyruvate, oxaloacetate, or α-ketoglutarate.
  • This converts the α-keto acid to alanine, aspartate, or glutamate, respectively.
  • Requires specific transaminases (also called aminotransferases) with pyridoxal phosphate as a coenzyme.
  • Example: Alanine and aspartate undergo a second transamination, transferring their amino groups to α-ketoglutarate to form glutamate.

⚡ Oxidative deamination

Oxidative deamination: a reaction in which glutamate loses its amino group as an ammonium ion and is oxidized back to α-ketoglutarate.

  • The final acceptor of the α-amino group during amino acid breakdown is α-ketoglutarate, forming glutamate.
  • Glutamate then loses its amino group as NH₄⁺ (ammonium ion) and regenerates α-ketoglutarate.
  • Occurs primarily in liver mitochondria.
  • Most NH₄⁺ formed is converted to urea and excreted in urine through the urea cycle.
  • Don't confuse: Transamination only transfers amino groups between molecules; oxidative deamination actually removes the amino group from the body as waste.

🔁 Glutamate synthesis

  • Animal cells can reverse the glutamate dehydrogenase reaction using NADPH as the reducing agent.
  • This is significant because it is one of the few reactions in animals that can incorporate inorganic nitrogen (NH₄⁺) into an α-keto acid to form an amino acid.
  • The amino group can then be distributed to other amino acids through transamination reactions.

🧬 Carbon skeleton fate

🧬 Conversion to citric acid cycle intermediates

  • After amino group removal (usually by transamination), the remaining α-keto acid is catabolized by a pathway unique to that acid.
  • Each pathway consists of one or more reactions specific to that amino acid.
  • Example: Phenylalanine undergoes six reactions before splitting into fumarate (a citric acid cycle intermediate) and acetoacetate (which must be converted to acetyl-CoA before entering the cycle).

🍞 Glucogenic amino acids

Glucogenic amino acids: amino acids that can form any of the intermediates of carbohydrate metabolism and subsequently be converted to glucose.

  • These amino acids can form intermediates of carbohydrate metabolism.
  • They are converted to glucose via gluconeogenesis.
  • Most amino acids fall into this category.

🔥 Ketogenic amino acids

Ketogenic amino acids: amino acids that are converted to acetoacetyl-CoA or acetyl-CoA, which can be used for the synthesis of ketone bodies but not glucose.

  • These form acetoacetyl-CoA or acetyl-CoA.
  • Can be used for ketone body synthesis but not glucose synthesis.
  • Leucine and lysine are the only exclusively ketogenic amino acids.
  • Some amino acids are both glucogenic and ketogenic.

📊 Classification summary

CategoryWhat they formCan make glucose?Examples
GlucogenicCarbohydrate metabolism intermediatesYesMost amino acids
KetogenicAcetoacetyl-CoA or acetyl-CoANoLeucine, lysine (exclusively)
BothEither type of intermediateYes (via one pathway)Phenylalanine, tyrosine

🎯 Metabolic context

🎯 When amino acid catabolism increases

  • More likely to occur when glucose levels are low.
  • Happens during fasting or starvation.
  • The body uses amino acid carbon skeletons as alternative energy sources or glucose precursors.

🏥 Tissue distribution

  • Primary site: Liver handles most amino acid metabolism.
  • Secondary sites: Kidney, small intestine, muscles, and adipose tissue also participate.
  • The liver's mitochondria are especially important for oxidative deamination reactions.