Biology

🧭 Overview

🧠 One-sentence thesis

Biology is the science that studies living organisms and their interactions through systematic observation, hypothesis testing, and reasoning, aiming to understand both the shared properties that define life and the diversity of life forms on Earth.

📌 Key points (3–5)

• What biology studies: living organisms, their interactions with each other and their environments, from microscopic cells to entire ecosystems.
• How science works: through the scientific method—observation, hypothesis formation, testing, and conclusion—combined with both inductive and deductive reasoning.
• Common confusion: inductive vs. deductive reasoning—inductive moves from specific observations to general conclusions; deductive moves from general principles to specific predictions.
• Two types of science: basic science seeks knowledge for its own sake, while applied science aims to solve real-world problems; both are interconnected and valuable.
• What defines life: nine shared characteristics including order, response to stimuli, reproduction, adaptation, growth, regulation, homeostasis, energy processing, and evolution.

🔬 What Biology Studies

🌍 The scope of biology

Biology: the study of living organisms and their interactions with one another and their environments.

• This is a very broad definition because biology's scope is vast.
• Biologists may study anything from the microscopic view of a cell to ecosystems and the whole living planet.
• Biology connects to daily life: disease outbreaks (E. coli, Salmonella), medical research (AIDS, Alzheimer's, cancer), and global issues (climate change, environmental protection).

🦠 Earth's life history

• The first life forms were microorganisms that existed for billions of years in the ocean before plants and animals appeared.
• Mammals, birds, and flowers are relatively recent, originating 130 to 250 million years ago.
• The earliest representatives of genus Homo inhabited Earth for only the last 2.5 million years; humans started looking like we do today only in the last 300,000 years.
• Example: Cyanobacteria (formerly called blue-green algae) are some of Earth's oldest life forms, forming ancient structures called stromatolites.

🔍 Biology's many branches

Biology has many subdisciplines because it studies diverse phenomena:

• Cell biologists study cell structure and function.
• Anatomists investigate the structure of entire organisms.
• Physiologists focus on internal functioning.
• Botanists explore plants; zoologists specialize in animals.

🧪 The Scientific Method

🎯 What science is

Science: knowledge that covers general truths or the operation of general laws, especially when acquired and tested by the scientific method.

• Science is better defined as fields of study that attempt to comprehend the nature of the universe.
• The scientific method is a method of research with defined steps that include experiments and careful observation.
• One of the most important aspects: testing hypotheses by means of repeatable experiments.
• Don't confuse: not all sciences can easily repeat experiments (archaeology, psychology, geology), but they are still sciences because they test hypotheses and seek to understand nature.

🔬 Natural sciences

Natural sciences: fields of science related to the physical world and its phenomena and processes.

• Include astronomy, biology, chemistry, earth science, and physics.
• Can be divided into:
  • Life sciences: study living things (biology).
  • Physical sciences: study nonliving matter (astronomy, geology, physics, chemistry).
• Some disciplines like biophysics and biochemistry are interdisciplinary, building on both life and physical sciences.
• Natural sciences are sometimes called "hard science" because they rely on quantitative data.

📋 Steps of the scientific method

The scientific method typically follows this sequence:

1. Observation: Notice something (often a problem to solve).
2. Question: Ask why or how.
3. Hypothesis: Propose a suggested explanation that can be tested.
4. Prediction: Format as "If... then..." statement.
5. Experiment: Test the hypothesis with controlled experiments.
6. Result: Analyze data and draw conclusions.

Hypothesis: a suggested explanation for an event, which one can test.

Theory: a tested and confirmed explanation for observations or phenomena.

• Example: A student observes the classroom is too warm (observation). Question: "Why is the classroom so warm?" Hypothesis: "The classroom is warm because no one turned on the air conditioning." Prediction: "If the student turns on the air conditioning, then the classroom will no longer be too warm."
• Important: Science does not claim to "prove" anything because scientific understandings are always subject to modification with further information.

🧪 Testing hypotheses properly

A valid hypothesis must be:

• Testable: can be examined through experiments.
• Falsifiable: experimental results can disprove it.

Variable: any part of the experiment that can vary or change during the experiment.

Control group: contains every feature of the experimental group except it is not given the manipulation that the researcher hypothesizes.

• If the experimental group's results differ from the control group, the difference must be due to the hypothesized manipulation, rather than some outside factor.
• Rejecting one hypothesis does not determine whether you can accept other hypotheses; it simply eliminates one hypothesis that is not valid.
• Don't confuse: The presence of the supernatural is neither testable nor falsifiable, which distinguishes sciences from non-sciences.

🧠 Two Types of Reasoning

🔼 Inductive reasoning

Inductive reasoning: a form of logical thinking that uses related observations to arrive at a general conclusion.

• This type of reasoning is common in descriptive science.
• Proceeds from the particular to the general.
• A scientist makes observations, records data (qualitative or quantitative), and infers conclusions based on evidence.
• Example: Brain studies—scientists observe many live brains while people view images of food. From many observations, they infer which part of the brain controls the response to food images (the part that "lights up").

🔽 Deductive reasoning

Deductive reasoning: a form of logical thinking that uses a general principle or law to forecast specific results.

• This is the type of logic used in hypothesis-based science.
• Proceeds from the general to the particular.
• From general principles, a scientist can extrapolate and predict specific results that would be valid as long as the general principles are valid.
• Example: Climate change studies—if the climate becomes warmer in a particular region, then scientists predict the distribution of plants and animals should change.

🔄 How they work together

• Both types of logical thinking are related to two main pathways: descriptive science (usually inductive) and hypothesis-based science (usually deductive).
• Descriptive (discovery) science: aims to observe, explore, and discover.
• Hypothesis-based science: begins with a specific question or problem and a potential answer that can be tested.
• The boundary between these two forms is often blurred; most scientific endeavors combine both approaches.
• Example: A gentleman in the 1940s observed burr seeds stuck to his clothes had tiny hook structures (observation/inductive). He experimented to find the best material that acted similarly (hypothesis-based/deductive), producing Velcro.

🔬 Two Types of Science

🎓 Basic science

Basic science or "pure" science: seeks to expand knowledge regardless of the short-term application of that knowledge.

• Not focused on developing a product or service of immediate public or commercial value.
• The immediate goal is knowledge for knowledge's sake.
• This does not mean it may not eventually result in a practical application.
• Example: Discovery of DNA structure led to understanding molecular mechanisms of DNA replication, which later enabled practical applications.

🛠️ Applied science

Applied science or "technology": aims to use science to solve real-world problems.

• Makes it possible to improve a crop yield, find a cure for a disease, or save animals threatened by disaster.
• The problem is usually defined for the researcher.
• Example: After Hurricane Irma in 2017, applied science knowledge enabled scientists to rehabilitate baby squirrels thrown from their nests.

🔗 How they connect

Aspect	Basic Science	Applied Science
Goal	Knowledge for knowledge's sake	Solve real-world problems
Focus	Expand understanding	Develop practical applications
Value	Foundation for future applications	Immediate practical benefit

• Don't confuse: Some perceive applied science as "useful" and basic science as "useless," but basic knowledge has resulted in many remarkable applications of great value.
• Applied science relies on results generated through basic science.
• Example: The Human Genome Project relied on basic research with simple organisms and later with the human genome. The end goal became using the data for applied research, seeking cures and early diagnoses for genetically related diseases.

🍀 Serendipity in science

Serendipity: a fortunate accident or lucky surprise.

• Some discoveries are made by serendipity, not just careful planning.
• Example: Alexander Fleming discovered penicillin when he accidentally left a petri dish of Staphylococcus bacteria open. An unwanted mold grew and killed the bacteria. His curiosity to investigate, followed by experiments, led to the discovery of the antibiotic penicillin.
• Even in organized science, luck—when combined with an observant, curious mind—can lead to unexpected breakthroughs.

📝 Communicating Scientific Work

📄 Why scientists share findings

• Scientists must share findings for other researchers to expand and build upon their discoveries.
• Collaboration when planning, conducting, and analyzing results is important.
• Most scientists present results in peer-reviewed manuscripts published in scientific journals.

🔍 Peer review process

Peer-reviewed manuscripts: scientific papers that a scientist's colleagues or peers review.

• Colleagues are qualified individuals, often experts in the same research area.
• They judge whether the scientist's work is suitable for publication.
• Peer review helps ensure research is original, significant, logical, and thorough.
• Grant proposals (requests for research funding) are also subject to peer review.
• Scientists publish work so others can reproduce experiments under similar or different conditions to expand on findings.

📋 Structure of scientific papers

Scientific papers follow a fixed structure, sometimes called the "IMRaD" format:

Section	Purpose
Abstract	Concise summary at the beginning
Introduction	Brief, broad background; rationale for the work; hypothesis or research question
Materials and Methods	Complete description of substances, methods, techniques, measurements, calculations
Results	Narrates findings with tables or graphs; no interpretation
Discussion	Interprets results, describes relationships, explains observations, cites literature
Conclusion	Summarizes importance of findings; suggests future questions

• Scientific writing must be brief, concise, and accurate.
• Detailed enough to allow peers to reproduce experiments.
• The introduction requires citations; using others' work or ideas without proper citation is plagiarism.
• The materials and methods section should be thorough enough for another researcher to repeat the experiment and obtain similar results.
• Don't confuse: Results section simply narrates findings; discussion section interprets them.

📚 Review articles

• Do not follow the IMRAD format because they do not present original scientific findings (primary literature).
• Instead, they summarize and comment on findings published as primary literature.
• Typically include extensive reference sections.

🌱 Properties of Life

🧬 Nine characteristics that define life

All living organisms share nine key characteristics or functions that, when viewed together, define life:

1. Order
2. Sensitivity or response to the environment
3. Reproduction
4. Adaptation
5. Growth and development
6. Regulation
7. Homeostasis
8. Energy processing
9. Evolution

🏗️ Order

• Organisms are highly organized, coordinated structures consisting of one or more cells.
• Even simple, single-celled organisms are remarkably complex.
• Inside each cell, atoms comprise molecules, which comprise cell organelles and other cellular inclusions.
• In multicellular organisms, similar cells form tissues; tissues collaborate to create organs (body structures with a distinct function); organs work together to form organ systems.
• Example: A toad represents a highly organized structure consisting of cells, tissues, organs, and organ systems.

👁️ Sensitivity or response to stimuli

• Organisms respond to diverse stimuli.
• Plants can bend toward light, climb on fences and walls, or respond to touch.
• Even tiny bacteria can move toward or away from chemicals (chemotaxis) or light (phototaxis).
• Movement toward a stimulus is a positive response; movement away is a negative response.
• Example: Leaves of the sensitive plant (Mimosa pudica) instantly droop and fold when touched, then return to normal after a few minutes.

🧬 Reproduction

• Single-celled organisms: reproduce by first duplicating their DNA, then dividing it equally as the cell prepares to divide to form two new cells.
• Multicellular organisms: often produce specialized reproductive cells (germline, gamete, oocyte, and sperm cells).
• After fertilization (fusion of an oocyte and a sperm cell), a new individual develops.
• When reproduction occurs, DNA containing genes are passed to offspring.
• These genes ensure offspring will belong to the same species and have similar characteristics.

🧭 Overview

🧠 One-sentence thesis

All biological processes obey the laws of physics and chemistry, so understanding the structure of atoms, the behavior of elements, and how they combine into molecules is essential for comprehending how living systems work.

📌 Key points (3–5)

• Why chemistry matters for biology: All matter—including living organisms—is built from atoms and molecules, and biological processes follow chemical and physical laws.
• What atoms are made of: Atoms contain protons (positive charge), neutrons (no charge), and electrons (negative charge); protons and neutrons sit in the nucleus, electrons orbit around it.
• Isotopes vs. elements: Elements are defined by the number of protons (atomic number), but isotopes of the same element have different numbers of neutrons, leading to different mass numbers.
• Common confusion—mass number vs. atomic mass: Mass number is the sum of protons and neutrons in one atom; atomic mass is the weighted average of all naturally occurring isotopes of an element.
• Application—radioisotopes: Unstable isotopes decay over time (radioactive decay), and their predictable half-lives allow scientists to date formerly living materials (e.g., carbon-14 dating).

🧱 Building blocks of matter

🧱 Matter and elements

Matter: any substance that occupies space and has mass.

Elements: unique forms of matter with specific chemical and physical properties that cannot break down into smaller substances by ordinary chemical reactions.

• There are 118 elements total, but only 98 occur naturally; the rest are synthesized in labs.
• Each element has a chemical symbol: a single capital letter (e.g., C for carbon) or two letters (e.g., Ca for calcium); some symbols come from Latin names (e.g., Na for sodium, from natrium).
• Four elements common to all living organisms: oxygen (O), carbon (C), hydrogen (H), and nitrogen (N).
• Distribution varies: Living organisms (e.g., humans) are ~65% oxygen, ~18% carbon, ~10% hydrogen, and ~3% nitrogen, but the atmosphere and Earth's crust have very different proportions (e.g., atmosphere is 78% nitrogen but has only trace carbon).

⚛️ What an atom is

Atom: the smallest unit of matter that retains all of the element's chemical properties.

• You cannot break an atom down further and still keep the element's properties.
• Example: A single gold atom has all the properties of gold (solid metal at room temperature); a gold coin is just many gold atoms molded together.
• Two regions:
  • Nucleus (center): contains protons and neutrons.
  • Electron orbitals (outer region): electrons orbit the nucleus.
• Exception: Hydrogen (H) has one proton and one electron, but no neutrons.

🔬 Inside the atom

⚡ Protons, neutrons, and electrons

Particle	Charge	Mass (amu)	Location
Proton	+1	1	Nucleus
Neutron	0	1	Nucleus
Electron	–1	~0 (1/1800 amu)	Orbitals

• Protons are positively charged; neutrons have no charge; electrons are negatively charged.
• Protons and neutrons have roughly the same mass (~1.67 × 10⁻²⁴ grams), defined as one atomic mass unit (amu) or one Dalton.
• Electrons are much lighter (~9.11 × 10⁻²⁸ grams), so they contribute almost nothing to the atom's mass but are crucial for charge.
• In a neutral atom: number of protons = number of electrons, so positive and negative charges cancel out.
• Why solid objects don't pass through each other: Electrons surrounding atoms are negatively charged, and negative charges repel each other, even though atoms are mostly empty space (>99% empty).

🔢 Atomic number and mass number

Atomic number: the number of protons in an atom; this defines which element it is.

Mass number: the sum of protons and neutrons in an atom (electrons are ignored because their mass is negligible).

• Atomic number distinguishes one element from another (e.g., carbon always has 6 protons).
• Mass number varies for the same element if the number of neutrons changes (these are called isotopes).
• How to find the number of neutrons: Subtract the atomic number from the mass number.
• Example: Carbon-12 has 6 protons and 6 neutrons (mass number 12); carbon-13 has 6 protons and 7 neutrons (mass number 13).

🧮 Atomic mass

Atomic mass: the calculated mean of the mass numbers for an element's naturally occurring isotopes.

• Because most elements exist as a mixture of isotopes in nature, the atomic mass is often a decimal (a weighted average).
• Example: Chlorine (Cl) has an atomic mass of 35.45 because it is mostly chlorine-35 (17 protons + 18 neutrons) with some chlorine-37 (17 protons + 20 neutrons).
• Don't confuse: Mass number is an integer for a single atom; atomic mass is an average across all isotopes.

☢️ Isotopes and radioactivity

🔄 What isotopes are

Isotopes: different forms of the same element that have the same number of protons but different numbers of neutrons.

• Same atomic number (same element), but different mass numbers.
• Example: Carbon-12 (6 protons, 6 neutrons) and carbon-14 (6 protons, 8 neutrons) are both carbon, but carbon-14 has two extra neutrons.
• Many elements (carbon, potassium, uranium) have naturally occurring isotopes.

⏳ Radioisotopes and half-life

Radioisotopes (radioactive isotopes): unstable isotopes that emit neutrons, protons, or electrons to reach a more stable configuration, releasing energy in the process (radioactive decay).

• Radioactive decay: the energy loss when an unstable nucleus releases radiation.
• Example: Carbon-14 decays to nitrogen-14 over time by emitting electrons (beta decay).
• Half-life: the time it takes for half of the original concentration of an isotope to decay.
  • Carbon-14 half-life: ~5,730 years.
  • Potassium-40 half-life: ~1.25 billion years.
  • Uranium-235 half-life: ~700 million years.

📅 Carbon dating application

• How it works:
  • Living organisms take in carbon-14 (¹⁴C) from the atmosphere (formed when cosmic rays hit nitrogen-14).
  • While alive, the ratio of ¹⁴C to ¹²C in the organism matches the atmosphere.
  • After death, the organism stops taking in ¹⁴C, so the ¹⁴C/¹²C ratio declines as ¹⁴C decays to ¹⁴N.
  • By comparing the remaining ¹⁴C to the atmospheric level, scientists can calculate how long ago the organism died.
• Limitation: Carbon dating is accurate for materials less than ~50,000 years old (because after many half-lives, too little ¹⁴C remains to measure).
• Example: Scientists used carbon dating to determine the age of pygmy mammoth remains.
• Other isotopes for older samples: Potassium-40 and uranium-235 have much longer half-lives, so they can date much older fossils and rocks (radiometric dating).

📊 The periodic table

🗂️ Organization of elements

Periodic table: a chart that organizes and displays elements, grouping those that share certain chemical properties.

• Devised by Russian chemist Dmitri Mendeleev in 1869.
• Elements in the same group (column) share chemical properties, even though each element is unique.
• The table reflects the physical state of elements at room temperature (solid, liquid, or gas) based on their properties.

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Note: The excerpt ends mid-sentence in the periodic table section, so no further details about the table's structure or element groupings are provided.

🧭 Overview

🧠 One-sentence thesis

Biological macromolecules—carbohydrates, lipids, proteins, and nucleic acids—are large carbon-based molecules built from smaller monomers through dehydration synthesis, and they perform essential functions that sustain life.

📌 Key points (3–5)

• What macromolecules are: large organic molecules necessary for life, built from smaller subunits called monomers that link together to form polymers.
• How they form: monomers join through dehydration synthesis (releasing water) and break apart through hydrolysis (adding water).
• Carbon's central role: carbon can bond with up to four other atoms, forming the backbone of all biological macromolecules.
• Common confusion: dehydration synthesis vs. hydrolysis—synthesis builds molecules by removing water; hydrolysis breaks them down by adding water.
• Why they matter: these four classes (carbohydrates, lipids, proteins, nucleic acids) make up the majority of a cell's dry mass and perform a wide array of life-sustaining functions.

🧱 Building blocks and structure

🧱 Monomers and polymers

Monomer: a single subunit or building block that can combine with others to form larger molecules.

Polymer: a larger molecule made from monomers combined using covalent bonds.

• Biological macromolecules are polymers constructed from monomers.
• The monomer-to-polymer relationship is like bricks (monomers) forming a wall (polymer).
• Example: glucose molecules (monomers) link together to form maltose (a polymer).

💎 Carbon as the backbone

• Carbon has an atomic number of 6, with four electrons in its outermost shell.
• This allows carbon to form up to four covalent bonds with other atoms, satisfying the octet rule.
• Carbon's versatility makes it ideal as the structural backbone of macromolecules.
• All biological macromolecules are organic molecules (carbon-containing).
• They may also contain hydrogen, oxygen, nitrogen, and minor elements.

🔄 Chemical reactions that build and break macromolecules

🔄 Dehydration synthesis (condensation)

Dehydration synthesis: a reaction that joins monomers by removing water molecules; literally "to put together while losing water."

How it works:

• The hydrogen (H) from one monomer combines with the hydroxyl group (OH) from another monomer.
• This releases a water molecule (H₂O) as a byproduct.
• The remaining parts of the two monomers form a covalent bond.

Example from the excerpt:

• Two glucose molecules link to form maltose (a disaccharide).
• In the process, one water molecule is released.

Why it matters:

• This is the primary mechanism cells use to build large macromolecules from smaller subunits.
• It applies to forming carbohydrates, proteins, and nucleic acids.

💧 Hydrolysis (breaking down)

Hydrolysis: a reaction that breaks polymers apart by adding water molecules.

How it works:

• Water is added to the bond between monomers.
• The bond breaks, with the hydrogen from water attaching to one monomer and the hydroxyl group attaching to the other.
• This reverses dehydration synthesis.

Don't confuse:

• Dehydration synthesis = building up, water removed.
• Hydrolysis = breaking down, water added.
• These are opposite processes.

Why it matters:

• Cells use hydrolysis to digest food and recycle macromolecules.
• Example: breaking down maltose back into two glucose molecules requires adding water.

🧬 The four major classes

🧬 Overview of macromolecule classes

The excerpt introduces four major classes:

Class	Building blocks	Key elements	Main functions (general)
Carbohydrates	Simple sugars	C, H, O	Energy, structure
Lipids	Fatty acids, glycerol	C, H, O	Energy storage, membranes
Proteins	Amino acids	C, H, O, N, S	Enzymes, structure, signaling
Nucleic acids	Nucleotides	C, H, O, N, P	Genetic information (DNA, RNA)

• Combined, these molecules make up the majority of a cell's dry mass.
• Water makes up the majority of a cell's complete mass, but macromolecules dominate the non-water portion.

🔬 Why carbon-based life

• Carbon's ability to form four covalent bonds allows it to create diverse, complex structures.
• It can form chains, rings, and branched structures.
• This versatility is why carbon is the foundation of all organic life.
• The excerpt emphasizes that carbon is "essential for organic life" because of this bonding flexibility.

🍞 Context and importance

🍞 Macromolecules in food

• The excerpt opens by noting that foods like bread, fruit, and cheese are rich sources of biological macromolecules.
• Food provides the body with nutrients it needs to survive, many of which are macromolecules.
• These molecules are necessary for life.

🔍 Key questions the chapter addresses

The excerpt states the chapter explores:

• What specific biological macromolecules do living things require?
• How do these molecules form?
• What functions do they serve?

🧪 Organic vs. inorganic

• Organic molecules: any carbon-containing liquid, solid, or gas.
• Biological macromolecules are a subset of organic molecules, especially important for life.
• The excerpt notes that macromolecules are organic, meaning they contain carbon, plus hydrogen, oxygen, nitrogen, and additional minor elements.

🧭 Overview

🧠 One-sentence thesis

The excerpt provided is a table of contents that lists the subsections of Chapter 4 (Cell Structure) but contains no substantive content about cell structure itself.

📌 Key points (3–5)

• The excerpt is only a table of contents listing six subsections: Studying Cells, Prokaryotic Cells, Eukaryotic Cells, The Endomembrane System and Proteins, The Cytoskeleton, and Connections between Cells and Cellular Activities.
• No definitions, explanations, mechanisms, or examples are provided in the excerpt.
• The excerpt also includes preface material about foundations and donors, which is not related to cell structure.
• To create meaningful review notes, the actual chapter content (pages 107–131) would be needed.

📋 Content summary

📋 What the excerpt contains

The provided text is a table of contents from a biology textbook. It shows that Chapter 4 is titled "Cell Structure" and appears on page 107. The chapter is divided into six numbered subsections:

• 4.1 Studying Cells (page 107)
• 4.2 Prokaryotic Cells (page 110)
• 4.3 Eukaryotic Cells (page 113)
• 4.4 The Endomembrane System and Proteins (page 121)
• 4.5 The Cytoskeleton (page 126)
• 4.6 Connections between Cells and Cellular Activities (page 131)

📋 What is missing

• No actual explanations of cell structure concepts.
• No definitions of prokaryotic vs eukaryotic cells.
• No descriptions of organelles, membranes, or cellular components.
• No mechanisms, processes, or functions.
• No comparisons or examples.

🔍 Note for review

🔍 Limitation of this excerpt

This excerpt cannot support a substantive review of cell structure because it contains only organizational metadata (chapter and section titles with page numbers). To study Chapter 4: Cell Structure, you would need to access the actual chapter text starting on page 107 of the source document.

🧭 Overview

🧠 One-sentence thesis

This excerpt presents the organizational structure and mission of an OpenStax biology textbook, emphasizing free access to high-quality educational materials through open licensing.

📌 Key points (3–5)

• What the excerpt contains: a detailed table of contents covering biology topics from fungi to conservation, plus a preface explaining the textbook's purpose.
• OpenStax mission: a nonprofit organization providing free, openly licensed college textbooks to remove barriers to education.
• Licensing model: Creative Commons Attribution 4.0 International (CC BY) license allows distribution, remixing, and building upon content with proper attribution.
• Common confusion: this excerpt is structural/navigational only—it lists chapter titles and page numbers but does not contain substantive biological content to review.

📚 Content structure

📚 What the table of contents covers

The excerpt lists chapters organized into major biology domains:

• Organismal diversity: fungi (Chapter 24), seedless plants (25), seed plants (26), animal diversity (27), invertebrates (28), vertebrates (29).
• Plant structure and function: plant form and physiology (30), soil and nutrition (31), reproduction (32).
• Animal structure and function: body form (33), digestion (34), nervous system (35), sensory systems (36), endocrine system (37), musculoskeletal system (38), respiratory system (39), circulatory system (40), excretion (41), immune system (42), reproduction and development (43).
• Ecology: biosphere (44), population and community ecology (45), ecosystems (46), conservation biology (47).

Each chapter is broken into numbered subsections (e.g., 24.1, 24.2).

📖 Appendices and supplementary material

• Appendix A: The Periodic Table of Elements
• Appendix B: Geological Time
• Appendix C: Measurements and the Metric System
• Index

🎓 About the textbook

🎓 Purpose and audience

This textbook was written to increase student access to high-quality learning materials, maintaining highest standards of academic rigor at little to no cost.

• The book is titled Biology 2e (2nd edition).
• It is an OpenStax resource, meaning it is freely available online.
• The goal is to remove cost barriers while preserving academic quality.

🏛️ OpenStax organization

OpenStax is a nonprofit based at Rice University, and it's our mission to improve student access to education.

• When it started: the first openly licensed college textbook was published in 2012.
• Current scale: the library has grown to over 25 books for college and Advanced Placement (AP) courses, used by hundreds of thousands of students.
• Additional tools: OpenStax Tutor is a low-cost personalized learning tool used in college courses.
• Partnerships: OpenStax works with philanthropic foundations and other educational resource organizations to break down learning barriers.

🔓 Licensing and customization

🔓 Creative Commons license

Biology 2e is licensed under a Creative Commons Attribution 4.0 International (CC BY) license, which means that you can distribute, remix, and build upon the content, as long as you provide attribution to OpenStax and its content contributors.

• What you can do: distribute, remix, and build upon the content.
• What you must do: provide attribution to OpenStax and its content contributors.
• The excerpt notes "Because our books" but the sentence is cut off, so the full implication is not stated.

🛠️ Customization

The preface mentions "Customization" as a heading, indicating that the textbook can be adapted, but the excerpt does not provide further details on how customization works.

⚠️ Note on this excerpt

This excerpt is primarily a table of contents and introductory preface. It does not contain substantive biological concepts, mechanisms, or explanations to review. The content is organizational and describes the textbook's structure, mission, and licensing rather than teaching biology itself.

🧭 Overview

🧠 One-sentence thesis

Biology 2e is a freely accessible, revised textbook designed to cover the full scope of a two-semester biology course through an evolutionary lens, with improved clarity, accessibility, and pedagogical features based on extensive user feedback.

📌 Key points (3–5)

• What this textbook is: an openly licensed, comprehensive biology resource covering eight major units from chemistry of life through ecology, organized around evolutionary principles.
• Key revision approach: the second edition focused on clarity, accuracy, currency, additional assessments (over 350 new questions), and substantially improved art and accessibility features.
• Pedagogical features: includes Evolution Connection, Scientific Method Connection, Career Connection, Everyday Connection, Visual Connection, and Link to Learning features to engage students.
• Common confusion: this is not a reorganization—the structure remains similar to the first edition, with targeted content revisions rather than wholesale chapter changes.
• Why it matters: provides high-quality, no-cost learning materials with built-in accessibility and flexibility for customization, supported by additional instructor and student resources.

📚 Textbook structure and scope

📚 Eight major units

The textbook is organized into eight units that build from foundational concepts to complex systems:

Unit	Coverage	Purpose
Unit 1: Chemistry of Life	Scientific method, chemistry, physics foundations	Framework for understanding biological processes
Unit 2: The Cell	Cell structures, functions, processes	Basic unit of life
Unit 3: Genetics	Early experiments through DNA to biotechnology/genomics	Basis of heredity and modern applications
Unit 4: Evolutionary Processes	Core evolution concepts with examples	Central organizing principle reinforced throughout
Unit 5: Biological Diversity	Viruses, bacteria, protists, plants, animals, phylogenetic relationships	Diversity of life
Unit 6: Plant Structure and Function	Fundamental plant biology	Essential plant knowledge
Unit 7: Animal Structure and Function	Body systems and processes, focus on human anatomy/physiology	Form and function with relatable examples
Unit 8: Ecology	Ecological concepts, conservation, biodiversity	Broad coverage with real-world issues

🎯 Evolutionary lens

• Evolution is not confined to one unit; it reappears throughout the textbook in general discussion.
• Special Evolution Connection features highlight specific evolution-based topics in various chapters.
• Example: "The Evolution of Metabolic Pathways" and "Algae and Evolutionary Paths to Photosynthesis."

🔄 Second edition revisions

🔄 Content updates

The revision plan was targeted rather than uniform:

• About twenty chapters: wholly revised with significant updates to conceptual coverage, research-informed data, and clearer language.
• About fifteen chapters: focused mostly on readability and clearer language with fewer conceptual and factual changes.
• Rationale: revisions were based on user feedback, surveys, focus groups, pre-revision reviews, and OpenStax Tutor data.
• Don't confuse: this is not a complete rewrite—the organization and chapter structure remain largely the same, with very targeted changes at the section level (mostly in biodiversity).

📊 Additional assessments

• Over 350 new end-of-chapter questions added to nearly every chapter.
• Includes both review questions and critical thinking questions.
• Purpose: help students understand and apply key concepts.

🎨 Art and illustration improvements

Changes were made to most of the art under the guidance of authors and expert scientific illustrators:

Revision category	What was done
Accuracy	Corrections to ensure scientific correctness
Understanding and impact	Redesigns to make concepts clearer
Consistency	Recoloring art for overall visual consistency
Accessibility	Improved color contrast for visually impaired students

♿ Accessibility improvements

• All alternative text was reviewed and revised for comprehensiveness and clarity to accommodate users of assistive technologies.
• Many illustrations were revised to improve color contrast, important for some visually impaired students.
• The OpenStax platform has been continually upgraded to improve accessibility.
• Example: the first edition already had an accessibility focus; the second edition emphasized and improved that approach.

🧩 Pedagogical features

🧬 Evolution Connection

Features that uphold the importance of evolution to all biological study through discussions.

• Appears throughout the textbook to reinforce evolutionary principles.
• Example topics: "The Evolution of Metabolic Pathways" and "Algae and Evolutionary Paths to Photosynthesis."

🔬 Scientific Method Connection

Call-outs that walk students through actual or thought experiments elucidating the steps of the scientific process.

• Applied to specific topics to show how science works in practice.
• Example features: "Determining the Time Spent in Cell Cycle Stages" and "Testing the Hypothesis of Independent Assortment."

💼 Career Connection

Features presenting information on a variety of careers in the biological sciences.

• Introduces students to educational requirements and day-to-day work life of various professions.
• Example careers: microbiologist, ecologist, neurologist, forensic scientist.

🌍 Everyday Connection

Features that tie biological concepts to emerging issues and discuss science in terms of everyday life.

• Makes biology relevant to students' lives.
• Example topics: "Chesapeake Bay" and "Can Snail Venom Be Used as a Pharmacological Pain Killer?"

👁️ Visual Connection

Features that call out core figures in each chapter for student study.

• Includes questions about key figures, including clicker questions for classroom use.
• Purpose: engage students' critical thinking and analytical abilities to ensure genuine understanding.

🔗 Link to Learning

Features that direct students to online interactive exercises and animations.

• Adds fuller context and examples to core content.
• Helps bring biology to life for students.

📖 OpenStax model and resources

📖 Open licensing and customization

Biology 2e is licensed under a Creative Commons Attribution 4.0 International (CC BY) license.

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🎓 About OpenStax

🎓 Mission and history

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📋 Development process

• The pedagogical choices, chapter arrangements, and learning objective fulfillment were developed and vetted with feedback from another one hundred reviewers.
• Reviewers thoroughly read the material and offered detailed critical commentary.
• User feedback from adopters, surveys, focus groups, pre-revision reviews, and OpenStax Tutor data all aided in planning the second edition revision.

🧭 Overview

🧠 One-sentence thesis

Biology encompasses the study of all living organisms from microscopic cells to entire ecosystems, and scientists use the scientific method to investigate the diversity of life that has evolved over billions of years on Earth.

📌 Key points (3–5)

• What biology studies: living organisms and their interactions with one another and their environments, from microscopic to planetary scale.
• Timeline of life: microorganisms existed for billions of years before plants and animals; mammals, birds, and flowers are relatively recent (130–250 million years ago); modern humans appeared only 300,000 years ago.
• Scope: biology is vast, covering everything from submicroscopic cell views to whole ecosystems and the living planet.
• Common confusion: the familiar life forms (mammals, birds, flowers) seem dominant but are actually recent arrivals; microorganisms dominated Earth's history for far longer.

🌍 Life on Earth through time

🦠 The dominance of microorganisms

• Scientists believe the first life forms on Earth were microorganisms.
• These microorganisms existed for billions of years in the ocean before plants and animals appeared.
• Example: cyanobacteria (formerly called blue-green algae) are some of Earth's oldest life forms, and ancient stromatolites formed by layering cyanobacteria in shallow waters still exist today.

🐦 Recent arrivals: complex life

• The mammals, birds, and flowers familiar to us are all relatively recent.
• They originated 130 to 250 million years ago—a short time compared to billions of years of microbial life.
• Don't confuse: what we see around us today represents only a tiny fraction of Earth's biological history.

👤 Human timeline

• The earliest representatives of the genus Homo (to which we belong) inhabited this planet for only the last 2.5 million years.
• Only in the last 300,000 years have humans started looking like we do today.
• This is an extremely recent development in the context of Earth's life history.

🔬 What biology studies

🔬 The definition of biology

Biology: the study of living organisms and their interactions with one another and their environments.

• This is a very broad definition because the scope of biology is vast.
• The excerpt emphasizes that biology covers interactions both between organisms and with their environments.

📏 The scale of biological study

Biologists may study anything across a huge range of scales:

Scale	What biologists study
Submicroscopic/microscopic	The view of a cell and its internal structures
Intermediate	Organisms, populations, communities
Large	Ecosystems and the whole living planet

• Example: a biologist might examine a single cell under a microscope or study how an entire ecosystem functions.
• The excerpt notes that biology spans from the smallest units of life to the entire biosphere.

🛰️ Observing life from space

🛰️ Earth from a distance

• Viewed from space, Earth offers no clues about the diversity of life forms that reside there.
• Scientists combine observations of different parts of the planet to create whole-Earth images.
• This perspective reminds us that life's complexity is not visible from afar—detailed study is required to understand biological diversity.

🧭 Overview

🧠 One-sentence thesis

Biology is the study of living organisms and their interactions, and it shares with other natural sciences a reliance on the scientific method—a process of testing hypotheses through observation and repeatable experiments to understand the natural world.

📌 Key points (3–5)

• What biology studies: living organisms, their interactions with one another, and their environments—from microscopic cells to entire ecosystems.
• What defines science: fields of study that attempt to comprehend the nature of the universe, especially through the scientific method (experiments and careful observation).
• Natural sciences vs other sciences: natural sciences focus on the physical world and its phenomena; they include astronomy, biology, chemistry, geology, and physics.
• Common confusion: not all sciences can use repeatable experiments equally—archaeology, psychology, and geology are still sciences even though repeating experiments is harder.
• Two types of reasoning: inductive reasoning moves from specific observations to general conclusions; deductive reasoning applies general principles to predict specific results.

🌍 What biology covers

🔬 The scope of biology

Biology: the study of living organisms and their interactions with one another and their environments.

• This definition is very broad because biology's scope is vast.
• Biologists may study anything from the submicroscopic view of a cell to ecosystems and the whole living planet.
• Example: daily news topics related to biology include bacterial outbreaks (E. coli in spinach, Salmonella in peanut butter), efforts to cure AIDS and cancer, and research on climate change and environmental protection.

🦠 Ancient and modern life

• The first life forms on Earth were microorganisms that existed for billions of years in the ocean before plants and animals appeared.
• Cyanobacteria (formerly called blue-green algae) are some of Earth's oldest life forms; stromatolites are ancient structures formed by layering cyanobacteria in shallow waters.
• Mammals, birds, and flowers are relatively recent, originating 130 to 250 million years ago.
• The earliest representatives of the genus Homo have inhabited Earth for only the last 2.5 million years; humans started looking like we do today only in the last 300,000 years.

🔍 What science is and how it works

🧪 Defining science

Science: knowledge that covers general truths or the operation of general laws, especially when acquired and tested by the scientific method.

• The scientific method is a method of research with defined steps that include experiments and careful observation.
• One of the most important aspects: testing hypotheses by means of repeatable experiments.
• However, defining science only by the scientific method is inadequate—some disciplines (archaeology, psychology, geology) find repeating experiments more difficult but are still sciences.
• Better definition: fields of study that attempt to comprehend the nature of the universe.

🧬 Key terms in the scientific method

Hypothesis: a suggested explanation for an event, which one can test.

Theory: a tested and confirmed explanation for observations or phenomena.

• A hypothesis may become a verified theory after continued testing and support.
• Example: an archaeologist can hypothesize that an ancient culture existed based on finding pottery, then make further hypotheses about characteristics of that culture—these can be supported or contradicted by other findings.

⚠️ Why repeatability is not always possible

• It is relatively easy to apply the scientific method to physics and chemistry.
• In disciplines like archaeology, psychology, and geology, repeating experiments becomes more difficult.
• Don't confuse: lack of repeatable experiments does not disqualify a field from being a science—hypotheses can still be supported through continued evidence.

🌌 Natural sciences and their branches

🌟 What natural sciences include

• Science includes diverse fields: astronomy, biology, computer sciences, geology, logic, physics, chemistry, and mathematics.
• Natural sciences: fields of science related to the physical world and its phenomena and processes.
• There is no complete agreement on what natural sciences include:
  • Some experts list: astronomy, biology, chemistry, earth science, and physics.
  • Others divide natural sciences into life sciences (study living things, include biology) and physical sciences (study nonliving matter, include astronomy, geology, physics, chemistry).
• Some disciplines (biophysics, biochemistry) build on both life and physical sciences and are interdisciplinary.
• Natural sciences are sometimes called "hard science" because they rely on quantitative data; social sciences are more likely to use qualitative assessments.

🧫 Branches within biology

• Biology has many branches or subdisciplines:
  • Cell biologists study cell structure and function.
  • Biologists studying anatomy investigate the structure of an entire organism.
  • Biologists studying physiology focus on the internal functioning of an organism.
• Some areas focus on particular types of living things:
  • Botanists explore plants.
  • Zoologists specialize in animals.

🧠 Two types of scientific reasoning

🔼 Inductive reasoning

Inductive reasoning: a form of logical thinking that uses related observations to arrive at a general conclusion.

• This type of reasoning is common in descriptive science.
• A life scientist makes observations and records them (data can be qualitative or quantitative, supplemented with drawings, pictures, photos, or videos).
• From many observations, the scientist can infer conclusions (inductions) based on evidence.
• Inductive reasoning involves formulating generalizations inferred from careful observation and analyzing a large amount of data.
• Example: brain studies—scientists observe many live brains while people view images of food; they predict the part of the brain that "lights up" during this activity controls the response to food images; then they can stimulate that part to see if similar responses result.

🔽 Deductive reasoning

Deductive reasoning: a form of logical thinking that uses a general principle or law to forecast specific results.

• This is the type of logic used in hypothesis-based science.
• The pattern of thinking moves in the opposite direction compared to inductive reasoning.
• From general principles, a scientist can extrapolate and predict specific results that would be valid as long as the general principles hold.

🔄 How to distinguish inductive vs deductive

Reasoning type	Direction	Use case
Inductive	Specific observations → general conclusion	Descriptive science; building generalizations from data
Deductive	General principle → specific predictions	Hypothesis-based science; testing predictions from laws

🎯 The ultimate goal of science

🎯 Curiosity and inquiry

• One thing is common to all forms of science: an ultimate goal "to know."
• Curiosity and inquiry are the driving forces for the development of science.
• Scientists seek to understand the world and the way it operates.

🧭 Overview

🧠 One-sentence thesis

The periodic table organizes elements by atomic number and electron configuration, and atoms achieve stability by filling their outermost electron shells through gaining, losing, or sharing electrons.

📌 Key points (3–5)

• Electron shells determine reactivity: the outermost electrons control how atoms bond and their chemical behavior.
• The octet rule: atoms are most stable when their valence (outermost) shell contains eight electrons (except the innermost shell, which holds two).
• Periodic table organization: columns (groups) share similar outer-shell electron counts, explaining why elements in the same group have similar chemical properties.
• Common confusion: the Bohr model shows electrons in circular orbits, but the orbital model is more accurate—electrons exist in probability regions (orbitals) with complex shapes, not fixed paths.
• Isotopes and half-life: isotopes of the same element differ in neutron count; radioactive isotopes decay at predictable rates (half-life), enabling dating of formerly living materials.

⚛️ Isotopes and radioactive decay

☢️ What isotopes are

Isotopes: atoms of the same element with different numbers of neutrons.

• Carbon-14 (¹⁴C) and Carbon-12 (¹²C) are both carbon, but ¹⁴C has more neutrons.
• The excerpt focuses on ¹⁴C, which decays to ¹⁴N through beta decay (emission of electrons or positrons).

⏳ Half-life and dating

Half-life: the time it takes for half of the original concentration of an isotope to decay back to its more stable form.

• ¹⁴C has a half-life of approximately 5,730 years.
• Scientists compare the ratio of ¹⁴C to ¹²C in a sample to the atmospheric ratio to calculate age.
• Limitation: carbon dating works for materials less than about 50,000 years old (e.g., pygmy mammoth bones).
• Other isotopes have different half-lives:
  • Potassium-40 (⁴⁰K): 1.25 billion years
  • Uranium-235 (²³⁵U): about 700 million years
• Example: radiometric dating helps scientists study fossils and understand how organisms evolved from earlier species.

📊 The periodic table and atomic structure

🗂️ How the periodic table is organized

Periodic table: organizes and displays elements by atomic number and shared chemical properties.

• Devised by Dmitri Mendeleev in 1869.
• Each element shows:
  • Atomic number (upper left): number of protons
  • Atomic mass (below symbol): approximate mass
  • Symbol and name
• Example: Carbon (C) has atomic number 6 and atomic mass 12.11.
• Elements are arranged in rows and columns based on shared chemical and physical properties.

⚡ Chemical reactivity

Chemical reactivity: the ability of elements to combine and chemically bond with each other.

• Reactivity differences arise from the number and spatial distribution of electrons.
• Physical state at room temperature (gas, solid, or liquid) also depends on element properties.

🔗 Molecules

Molecules: two or more atoms chemically bonded together.

• When atoms bond, their outermost electrons come together first to form the chemical bond.

🎯 Electron shells and the Bohr model

🌐 The Bohr model (1913)

• Developed by Niels Bohr.
• Shows the atom as a central nucleus (protons and neutrons) with electrons in circular orbitals at specific distances.
• Orbitals form electron shells (energy levels), designated by a number and "n" (e.g., 1n is the first shell closest to the nucleus).
• Electrons fill the lowest-energy shell first (closest to the nucleus), then move outward.

🔋 Energy levels and stability

• An electron normally exists in the lowest available energy shell.
• Energy from a photon can bump an electron to a higher shell, but this is unstable—the electron quickly decays back, releasing a photon.
• Filling order: electrons fill orbitals closest to the nucleus first, then continue to higher-energy orbitals.
• If multiple orbitals have equal energy, each gets one electron before any gets a second.

🛡️ The octet rule

Octet rule: atoms are more stable energetically when they have eight electrons in their valence shell (outermost shell), except the innermost shell, which holds a maximum of two electrons.

• Innermost shell: maximum 2 electrons
• Next two shells: maximum 8 electrons each
• Example:
  • Helium: 2 electrons fill its only shell (1n) → stable
  • Neon: 8 electrons fill its outer shell (2n) → stable
  • Chlorine: 7 electrons in outer shell → would be more stable with 8
  • Sodium: 1 electron in outer shell → would be more stable with 8

🔄 How atoms achieve stability

• Atoms may give, take, or share electrons to achieve a full valence shell.
• Example:
  • Group 1 elements (H, Li, Na) have 1 outer electron → donate or share it to become stable.
  • Losing an electron makes them positively charged ions.
  • Group 17 elements (F, Cl) have 7 outer electrons → gain 1 electron to fill the shell.
  • Gaining an electron makes them negatively charged ions.
  • Group 14 elements (including carbon) have 4 outer electrons → can make several covalent bonds.

🧲 Why periodic table columns matter

• Columns (groups) represent the potential shared state of outer electron shells.
• Elements in the same column have similar numbers of outer electrons → similar chemical characteristics.
• Example:
  • Group 18 (He, Ne, Ar): filled outer shells → highly stable, non-reactive → called inert gases or noble gases.
  • Group 1 (H, Li, Na): 1 outer electron → tend to donate it.
  • Group 17 (F, Cl): 7 outer electrons → tend to gain 1 electron.

🌀 Electron orbitals (beyond Bohr)

🌊 Why the Bohr model is incomplete

• The Bohr model is useful for explaining reactivity and bonding, but does not accurately reflect how electrons are spatially distributed.
• Electrons do not circle the nucleus like planets; they exist in electron orbitals.
• Electrons behave like both particles and waves.

📐 What orbitals are

Electron orbital: the area where an electron is most likely to be found, predicted by wave functions from quantum mechanics.

• Scientists cannot calculate an electron's exact location, only the probability of where it might be.
• Subshells exist within each electron shell, and each subshell has a specified number of orbitals.

🔤 Subshell types and shapes

Subshell	Shape	Number of orbitals	Electrons per subshell
s	Spherical	1	2
p	Dumbbell-shaped	3	6 (2 per orbital)
d	More complex	5	10
f	More complex	7	14

• Principal shell 1n: only 1s orbital → holds 2 electrons total.
• Principal shell 2n: 1s + 1p subshell → holds 8 electrons total.
• Principal shell 3n: s, p, and d subshells → holds 18 electrons total.
• Principal shell 4n: s, p, d, and f subshells → holds 32 electrons total.
• Moving away from the nucleus, the number of electrons and orbitals increases.

🎯 Filling orbitals: examples

• 1s orbital: closest to the nucleus, always fills first.
  • Hydrogen (H): 1 electron → 1s¹
  • Helium (He): 2 electrons → 1s² (completely fills the 1s orbital)
• Hydrogen and helium are the only elements in the first row of the periodic table because they only have electrons in the 1s orbital.
• Second shell: after 1s fills, the 2s orbital fills, then the three 2p orbitals.
• Example: the second shell can hold 8 electrons total (2 in 2s + 6 in 2p).

🚫 Don't confuse Bohr orbits with orbitals

• Bohr model: electrons in fixed circular paths (orbits) at specific distances.
• Orbital model: electrons in probability regions (orbitals) with specific shapes (spherical, dumbbell, etc.).
• The orbital model is more accurate but more complex.

🧭 Overview

🧠 One-sentence thesis

Atoms achieve stability by filling their outermost electron shells through chemical bonding—either by transferring electrons to form ionic bonds or by sharing electrons to form covalent bonds—and these bonds create molecules that participate in reversible or irreversible chemical reactions.

📌 Key points (3–5)

• Electron shells and orbitals: electrons occupy specific orbitals (s, p, d, f) arranged in shells around the nucleus; atoms are most stable when their outermost shell is filled according to the octet rule.
• Two main bond types: ionic bonds form when atoms transfer electrons (creating charged ions that attract), while covalent bonds form when atoms share electrons.
• Common confusion—ionic vs. covalent: ionic bonds involve complete electron transfer and opposite-charge attraction; covalent bonds involve electron sharing between atoms, with no net charge transfer.
• Chemical reactions: reactants bond or break apart to form products; reactions can be irreversible (one direction) or reversible (reaching equilibrium).
• Why bonding matters: atoms bond to achieve stable electron configurations, and the resulting molecules (like water, salts, and organic compounds) are essential for biological processes.

⚛️ Electron shells and orbitals

🔵 What orbitals are

Orbitals: specific regions around the nucleus where electrons may occupy, with different shapes (spherical s orbitals, dumbbell-shaped p orbitals) and capacities.

• Orbitals are arranged in shells (also called principal shells or energy levels) numbered 1, 2, 3, etc., moving outward from the nucleus.
• Each shell contains one or more types of orbitals (s, p, d, f), and each orbital can hold up to two electrons.
• The excerpt emphasizes that orbitals provide a more accurate depiction than simple "shells" because they specify shapes and orientations.

📐 Orbital types and capacities

Orbital type	Shape	Max electrons per orbital	Example shells
s	Spherical	2	1s, 2s, 3s
p	Dumbbell	2 (three p orbitals per shell = 6 total)	2p, 3p
d	(not detailed)	2 each	Higher shells
f	(not detailed)	2 each	Higher shells

• The first shell (1n) has only one s orbital (1s), holding up to 2 electrons.
• The second shell (2n) has one s orbital (2s) and three p orbitals (2p), holding up to 8 electrons total.
• Larger shells contain additional orbitals (d, f) and can hold more electrons.

🧩 Filling order and electron configuration

• Orbitals fill in order of increasing energy: 1s first, then 2s, then the three 2p orbitals.
• When filling p orbitals, each of the three takes one electron before any takes a second (this minimizes repulsion).
• Electron configuration notation: the number of electrons in each orbital is shown as a superscript.
  • Example: Hydrogen (1 electron) = 1s¹
  • Example: Helium (2 electrons) = 1s²
  • Example: Lithium (3 electrons) = 1s² 2s¹
  • Example: Neon (10 electrons) = 1s² 2s² 2p⁶ (completely filled second shell → very stable, inert gas)

🎯 The octet rule

Octet rule: atoms are most stable when their outermost shell is filled with electrons (typically 8 for shells beyond the first).

• This configuration is energetically favorable and makes atoms stable.
• Atoms that lack a full outer shell will form chemical bonds to obtain the needed electrons.
• Don't confuse: the first shell is full with 2 electrons (hydrogen and helium); larger shells follow the octet rule (8 electrons).

🔗 Chemical bonds: achieving stability

🔄 Why atoms bond

• Not all elements have enough electrons to fill their outermost shells on their own.
• Atoms form chemical bonds with other atoms to obtain electrons and achieve stable configurations.
• When two or more atoms bond, the result is a molecule.
• Example: Water (H₂O) consists of two hydrogen atoms and one oxygen atom bonded together.

⚡ Ionic bonds: electron transfer

Ionic bonds: bonds that form between ions with opposite charges after one atom donates electrons and another accepts them.

• Some atoms are more stable when they gain or lose electrons to fill their outer shell.
• Cations: positive ions formed by losing electrons.
• Anions: negative ions formed by gaining electrons (named with "-ide" ending: chlorine → chloride, sulfur → sulfide).
• The movement of electrons from one element to another is called electron transfer.

🧂 Example: sodium chloride (table salt)

• Sodium (Na) has 1 electron in its outer shell; it's easier to donate that 1 electron than accept 7 more.
  • After losing 1 electron: 11 protons, 10 electrons → net charge +1 → sodium ion (cation).
• Chlorine (Cl) has 7 electrons in its outer shell; it's easier to gain 1 electron than lose 7.
  • After gaining 1 electron: 17 protons, 18 electrons → net charge –1 → chloride ion (anion).
• The oppositely charged ions attract and bond, forming sodium chloride crystals with zero net charge.
• Note: these transactions normally occur simultaneously—sodium must be in the presence of a suitable recipient like chlorine.

💧 Electrolytes

Electrolytes: certain salts (including sodium, potassium, and calcium ions) necessary for nerve impulse conduction, muscle contractions, and water balance.

• Sports drinks and dietary supplements provide these ions to replace those lost through sweating.

🤝 Covalent bonds: electron sharing

Covalent bonds: bonds formed when atoms share electrons to fill their outer shells.

• Covalent bonds are stronger and much more common than ionic bonds in living organisms.
• Commonly found in carbon-based organic molecules (DNA, proteins) and inorganic molecules (H₂O, CO₂, O₂).
• Atoms may share one, two, or three pairs of electrons, forming single, double, or triple bonds.
• The more pairs shared, the stronger the bond: triple bonds are the strongest.

💧 Example: water (H₂O)

• Oxygen has 6 electrons in its outer shell but would be more stable with 8.
• Each hydrogen has 1 electron in its outer shell.
• Two hydrogen atoms each share their electron with the oxygen atom.
• The electrons split their time between the hydrogen and oxygen atoms' incomplete outer shells.
• Result: both hydrogen atoms and the oxygen atom have filled outer shells.

🧬 Example: molecular nitrogen (N₂)

• Molecular nitrogen consists of two nitrogen atoms triple bonded to each other.
• This strong triple bond makes the molecule very stable.
• The triple bond makes it difficult for living systems to break apart nitrogen for use in proteins and DNA, even though N₂ is the most abundant gas in the atmosphere.

🔍 Don't confuse: ionic vs. covalent

Feature	Ionic bonds	Covalent bonds
Mechanism	Electron transfer (donation/acceptance)	Electron sharing
Charge	Creates charged ions (cations and anions)	No net charge on atoms
Attraction	Opposite charges attract	Shared electrons hold atoms together
Strength	Generally weaker	Stronger; triple > double > single
Common in	Salts, electrolytes	Organic molecules, water, gases

⚗️ Chemical reactions

🧪 What happens in a reaction

Chemical reactions: processes that occur when two or more atoms bond together to form molecules or when bonded atoms break apart.

• Reactants: substances used at the beginning of a reaction (usually on the left side of the equation).
• Products: substances at the end of the reaction (usually on the right side of the equation).
• An arrow between reactants and products indicates the reaction's direction.
• Example: forming water from hydrogen and oxygen: 2H + O → H₂O

⚖️ Balanced chemical equations

Balanced chemical equation: an equation in which each element's number of atoms is the same on each side.

• According to the law of conservation of matter, the number of atoms before and after a reaction should be equal—no atoms are created or destroyed under normal circumstances.
• Example: breaking down hydrogen peroxide:
  • 2H₂O₂ (hydrogen peroxide) → 2H₂O (water) + O₂ (oxygen)
  • Each side has 4 hydrogen atoms and 4 oxygen atoms.

🔬 Compounds vs. molecules

• Compounds: molecules that contain atoms of more than one type of element.
  • Example: hydrogen peroxide (H₂O₂) and water (H₂O) are compounds.
• Homonuclear molecules: molecules made of only one type of element.
  • Example: molecular oxygen (O₂) consists of two doubly bonded oxygen atoms—not a compound.

↔️ Irreversible vs. reversible reactions

➡️ Irreversible reactions

• Proceed in one direction until all reactants are used up.
• Denoted by a unidirectional arrow (→).
• Example: some reactions that completely consume reactants to form products.

🔄 Reversible reactions

• Can go in either direction: reactants turn into products, and products can convert back into reactants.
• When product concentration exceeds a certain threshold, some products convert back to reactants.
• This back-and-forth continues until a relative balance is reached—a state called equilibrium.
• Denoted by a double-headed arrow (↔).

🩸 Example: bicarbonate buffer in blood

• Excess hydrogen ions (H⁺) bind to bicarbonate ions (HCO₃⁻) to form carbonic acid (H₂CO₃):
  • HCO₃⁻ + H⁺ ↔ H₂CO₃
• If carbonic acid is added, some converts to bicarbonate and hydrogen ions.
• However, biological reactions rarely reach true equilibrium because concentrations constantly change.
• Carbonic acid can also leave the body as carbon dioxide gas (CO₂) via exhalation, driving the reaction to the right by the law of mass action:
  • HCO₃⁻ + H⁺ ↔ H₂CO₃ ↔ CO₂ + H₂O
• These reactions are important for maintaining homeostasis in blood.

🧭 Overview

🧠 One-sentence thesis

The polarity of water molecules and the resulting hydrogen bonds create unique properties that are essential to life, including solvent ability, cohesion, adhesion, and temperature regulation.

📌 Key points (3–5)

• Polar vs nonpolar covalent bonds: unequal electron sharing creates partial charges (polar), while equal sharing creates no charge separation (nonpolar).
• Why water is polar: oxygen is more electronegative than hydrogen, pulling shared electrons closer and creating partial negative (oxygen) and partial positive (hydrogen) charges.
• Hydrogen bonds: weak attractions between slightly positive hydrogen atoms and slightly negative atoms in other molecules; individually weak but powerful in large numbers.
• Common confusion: bond type vs molecular polarity—carbon dioxide has polar bonds but is nonpolar overall because its linear shape cancels the partial charges.
• Hydrophilic vs hydrophobic: polar substances interact with water (hydrophilic = "water-loving"), while nonpolar substances do not (hydrophobic = "water-fearing").

🔗 Types of covalent bonds

⚡ Polar covalent bonds

Polar covalent bond: atoms unequally share electrons and are attracted more to one nucleus than the other.

• Because different elements have different electronegativities, electrons spend more time near one atom than the other.
• This unequal distribution creates partial charges: slightly positive (δ+) on one atom and slightly negative (δ–) on the other.
• The partial charges are crucial for water's properties and for forming hydrogen bonds.
• Example: In water, oxygen's nucleus attracts electrons more strongly than hydrogen's nucleus does, so oxygen becomes slightly negative and hydrogen becomes slightly positive.

🔄 Nonpolar covalent bonds

Nonpolar covalent bonds: form between two atoms of the same element or between different elements that share electrons equally.

• No partial charges develop because electrons are distributed equally.
• Example: Molecular oxygen (O₂) is nonpolar because electrons distribute equally between the two oxygen atoms.
• Example: Methane (CH₄) is nonpolar because carbon and hydrogen have similar electronegativity, so they share electrons equally.

🎯 Electronegativity and electron distribution

Electronegativity: the relative attraction an atom's nucleus has for electrons.

• Higher electronegativity means the atom pulls shared electrons closer.
• The probability of finding a shared electron near a more electronegative nucleus is higher.
• When one element is significantly more electronegative than another, partial charges develop.
• These partial charges can then be used to form hydrogen bonds based on attraction of opposite charges.

🧲 Weak bonds in biological systems

🧲 Hydrogen bonds

Hydrogen bond: a weak interaction between the slightly positive hydrogen (δ+) from one molecule and the slightly negative charge (δ–) on more electronegative atoms (usually oxygen or nitrogen) in another molecule or within the same molecule.

How they form:

• Polar covalent bonds containing hydrogen create a slightly positive charge on hydrogen.
• Hydrogen's electron is pulled toward the other element, away from hydrogen.
• The slightly positive hydrogen is attracted to neighboring negative charges.

Strength and importance:

• Individual hydrogen bonds are weak and easily broken.
• They occur in very large numbers in water and organic polymers, creating a major combined force.
• They provide many critical, life-sustaining properties of water.
• They stabilize the structures of proteins and DNA.
• They are responsible for "zipping together" the DNA double helix.

Example: Hydrogen bonds occur regularly between water molecules, where the slightly positive hydrogen of one molecule is attracted to the slightly negative oxygen of another.

🌀 Van der Waals interactions

Van der Waals interactions: weak attractions or interactions between molecules that depend on slight fluctuations of electron densities.

• Electron densities are not always symmetrical around an atom.
• These attractions require molecules to be very close to one another.
• They can occur between any two or more molecules.
• Along with ionic, covalent, and hydrogen bonds, they contribute to the three-dimensional structure of proteins necessary for proper function.

⚖️ Bond strength comparison

Bond type	Strength	Role in biological systems
Covalent	Strongest	Require energy to break; hold molecules together
Ionic	Strong (but not as strong as covalent)	Determines behavior in biological systems
Hydrogen	Weak individually, strong collectively	Life-sustaining properties; stabilize proteins and DNA
Van der Waals	Weak	Contribute to protein structure and function

Don't confuse: Individual weakness vs collective strength—hydrogen bonds are weak alone but create major forces when present in large numbers.

💧 Water's polarity and interactions

💧 Why water is polar

• Water molecules (H₂O) form polar covalent bonds between hydrogen and oxygen.
• Oxygen is more electronegative than hydrogen.
• Shared electrons spend more time near the oxygen nucleus than near hydrogen nuclei.
• This creates a slightly positive charge on hydrogen atoms and a slightly negative charge on oxygen.
• Key point: While there is no net charge to a water molecule overall, the polarity creates charge separation within the molecule.

🤝 Water's attraction properties

• Each water molecule attracts other water molecules because of opposite charges between them.
• This attraction forms hydrogen bonds between water molecules.
• Water also attracts or is attracted to other polar molecules and ions.

🧪 Hydrophilic vs hydrophobic substances

Hydrophilic ("water-loving"): a polar substance that interacts readily with or dissolves in water.

Hydrophobic ("water-fearing"): nonpolar compounds that do not interact well with water.

Property	Hydrophilic	Hydrophobic
Polarity	Polar	Nonpolar
Interaction with water	Dissolves or interacts readily	Does not interact well
Examples from excerpt	Polar molecules and ions	Oils and fats

Example: Vinegar and oil salad dressing—oil (nonpolar/hydrophobic) does not dissolve in the acidic water solution (polar) but forms droplets instead.

Don't confuse: Molecular shape matters—carbon dioxide has polar covalent bonds, but because it is linear, the partial charges cancel each other out, making the overall molecule nonpolar.

🌟 Why water is essential to life

🌟 Water's critical role

• Water comprises approximately 60–70 percent of the human body.
• Without water, life as we know it would not exist.
• Most of an organism's cellular chemistry and metabolism occur inside the watery contents of the cell's cytoplasm.
• Life originally evolved in a watery environment.

🔑 Special properties tied to polarity and hydrogen bonding

The excerpt identifies these special properties of water (all intimately tied to life processes):

• High heat capacity and heat of vaporization
• Ability to dissolve polar molecules (excellent solvent)
• Cohesive and adhesive properties
• Dissociation into ions that leads to generating pH

Why scientists look for water on other planets: Water is essential to life as we know it, so finding water elsewhere suggests the possibility of life.

🧬 Macromolecules and polar bonds

• Macromolecules often have atoms within them that differ in electronegativity.
• Polar bonds are often present in organic molecules.
• These polar bonds enable the formation of hydrogen bonds, which are critical for biological structure and function.

🧭 Overview

🧠 One-sentence thesis

Water's unique properties—polarity, hydrogen bonding, high heat capacity, heat of vaporization, solvent ability, and cohesion—make it essential for maintaining life by enabling cellular chemistry, temperature regulation, and molecular interactions.

📌 Key points (3–5)

• Polarity drives interactions: water molecules have partial positive (hydrogen) and negative (oxygen) charges that attract other polar molecules and ions, creating hydrogen bonds.
• Hydrogen bonding explains physical states: these bonds cause water's unusual behavior—ice floats because hydrogen bonds push molecules apart in solid form, unlike most liquids.
• High heat capacity and vaporization: water absorbs and releases large amounts of heat slowly, stabilizing temperatures in organisms and environments; evaporation cools by breaking hydrogen bonds.
• Solvent properties: water dissolves polar and ionic substances by forming hydration spheres around charged particles, enabling cellular chemistry.
• Common confusion—hydrophilic vs hydrophobic: polar substances ("water-loving") dissolve in water; nonpolar substances like oils ("water-fearing") do not interact with water and form separate droplets.

💧 Water's molecular structure and polarity

⚛️ Polar covalent bonds create charges

Polar molecules: molecules with unevenly distributed charges; in water, hydrogen carries a slight positive charge and oxygen a slight negative charge.

• Water (H₂O) forms polar covalent bonds because oxygen is more electronegative than hydrogen.
• Shared electrons spend more time near oxygen, creating a partial negative charge there and partial positive charges on hydrogen atoms.
• No net charge on the whole molecule, but the uneven distribution creates polarity.

🔗 Hydrogen bonding between water molecules

• The partial positive hydrogen of one water molecule attracts the partial negative oxygen of another.
• These attractions form hydrogen bonds, which hold water molecules together.
• Hydrogen bonds constantly form and break as molecules slide past each other in liquid water.

🧪 Hydrophilic vs hydrophobic substances

Hydrophilic (hydro- = "water"; -philic = "loving"): polar substances that interact readily with or dissolve in water.

Hydrophobic (hydro- = "water"; -phobic = "fearing"): nonpolar compounds that do not interact well with water.

Type	Interaction with water	Example from excerpt
Hydrophilic	Dissolves or mixes readily	Polar molecules and ions
Hydrophobic	Does not dissolve; forms separate droplets	Oils and fats (e.g., oil in vinegar-and-oil dressing)

Don't confuse: "hydrophobic" does not mean the substance repels water actively; it simply lacks the polar charges needed to form hydrogen bonds with water, so it stays separate.

🧊 Water's three states and the anomaly of ice

🌡️ How temperature affects hydrogen bonds

• Liquid water: hydrogen bonds constantly form and break as molecules move (kinetic energy from heat).
• Gas (steam/vapor): higher kinetic energy (boiling) breaks hydrogen bonds completely, allowing molecules to escape into the air.
• Solid (ice): lower temperature reduces kinetic energy; hydrogen bonds lock molecules into a crystalline structure.

❄️ Why ice floats—the density anomaly

• In most liquids, solidification increases density because molecules pack more tightly.
• Water is different: when freezing, hydrogen bonds orient in a way that pushes water molecules farther apart than in liquid form.
• Result: ice is less dense than liquid water, so it floats.

Example: Ice forms on the surface of lakes and ponds, creating an insulating layer that protects aquatic plants and animals from freezing solid.

Don't confuse: this is an anomaly—most substances become denser when they solidify, but water expands.

🧬 Biological impact of freezing

• Ice crystals rupture delicate cell membranes, irreversibly damaging them.
• Cells can only survive freezing if another liquid (like glycerol) temporarily replaces water.

🔥 Water's thermal properties

🌡️ High heat capacity

Specific heat capacity: the amount of heat one gram of a substance must absorb or lose to change its temperature by one degree Celsius.

• Water has the highest specific heat capacity of any liquid (one calorie per gram per degree Celsius).
• Water takes a long time to heat up and a long time to cool down—about five times longer than sand.
• Why it matters: this property explains why land cools faster than the sea.

Biological application: warm-blooded animals use water to distribute heat evenly throughout their bodies, like a car's cooling system, maintaining stable body temperature.

💨 High heat of vaporization

Heat of vaporization: the amount of energy required to change one gram of a liquid substance to a gas.

• Water requires 586 calories to vaporize one gram—a considerable amount.
• Hydrogen bonding makes it difficult to separate liquid water molecules, so much energy is needed to break the bonds.
• Water acts as a heat sink or heat reservoir, requiring much more heat to boil than liquids with weaker hydrogen bonding (e.g., ethanol).

💦 Evaporation as a cooling mechanism

Evaporation: the process by which individual water molecules at the surface acquire enough energy to escape and vaporize, even below boiling point.

• Breaking hydrogen bonds for evaporation uses substantial energy.
• As water evaporates, it takes up energy from the environment, cooling the area where evaporation occurs.

Example: In humans and many organisms, sweat (90 percent water) evaporates to cool the body and maintain homeostasis of body temperature.

🧪 Water as a solvent

🔬 Why water dissolves polar and ionic substances

Solvent: a substance capable of dissolving other polar molecules and ionic compounds.

• Water's partial charges allow it to interact with ions and polar molecules.
• The charges form hydrogen bonds with dissolved particles, surrounding them with water molecules.

Sphere of hydration (hydration shell): water molecules surrounding a dissolved particle, keeping it separated or dispersed in water.

⚡ Dissociation of ionic compounds

Dissociation: when atoms or groups of atoms break off from molecules and form ions.

• When ionic compounds (e.g., table salt, NaCl) are added to water, the polar water molecules disrupt ionic bonds.
• Example: NaCl dissociates into Na⁺ and Cl⁻ ions.
  • The partially negative oxygen of water surrounds the positively charged sodium ion.
  • The partially positive hydrogen of water surrounds the negatively charged chloride ion.
• Hydration spheres form around each ion, keeping them dispersed.

Why it matters: water's solvent properties enable the dissolution and transport of nutrients, ions, and molecules essential for cellular chemistry and metabolism.

🌊 Cohesive and adhesive properties

🤝 Cohesion and surface tension

Cohesion: the attraction of water molecules to each other (due to hydrogen bonding).

• Cohesion keeps water molecules together at the liquid-gas interface.
• Example: when a glass is filled to the very top, water forms a dome-like shape above the rim before overflowing.

Surface tension: the capacity of a substance to withstand rupturing when placed under tension or stress.

• Surface tension allows water to resist breaking when stress is applied.
• Example: a small scrap of paper can float on a water droplet even though paper is denser than water, because cohesion and surface tension support it.
• Example: a needle placed gently on water can float on the surface without sinking, creating an indentation in the water around it.

💧 Droplet formation

• Cohesion causes water to form droplets on a dry surface rather than flattening out due to gravity.
• Hydrogen bonds hold the molecules together, maintaining the droplet shape.

Don't confuse: cohesion is attraction between water molecules; adhesion (not detailed in this excerpt) would be attraction between water and other surfaces.

🧭 Overview

🧠 One-sentence thesis

Water's molecular properties—including its ability to dissolve substances, cohesion, adhesion, and buffering capacity—enable critical biological processes such as nutrient transport in plants, maintenance of stable pH in organisms, and survival in varying chemical environments.

📌 Key points (3–5)

• Hydration spheres: water molecules surround dissolved ions with their partial charges, enabling substances like salt to dissolve.
• Cohesion vs adhesion: cohesion is attraction between water molecules (creates surface tension); adhesion is attraction between water and other molecules (enables capillary action).
• pH scale: measures hydrogen ion concentration on an inverse logarithmic scale from 0 to 14, where 7.0 is neutral, below 7.0 is acidic, and above 7.0 is alkaline.
• Buffers prevent pH swings: buffers absorb excess H⁺ or OH⁻ ions to maintain pH within the narrow range required for survival.
• Common confusion: acids and bases—acids increase H⁺ concentration (lower pH), while bases either provide OH⁻ or remove H⁺ (raise pH).

💧 Water as a solvent

💧 Spheres of hydration

Spheres of hydration: arrangements of water molecules around dissolved ions, with the water's partial charges surrounding opposite charges on the ions.

• When table salt (NaCl) dissolves in water, it dissociates into Na⁺ and Cl⁻ ions.
• Water's partially negative oxygen surrounds the positively charged sodium ion.
• Water's partially positive hydrogen surrounds the negatively charged chloride ion.
• This property allows water to dissolve many ionic substances.

🔗 Cohesion and adhesion

🔗 Cohesion and surface tension

Cohesion: the attraction of water molecules to each other (due to hydrogen bonding).

• Cohesion keeps water molecules together at the liquid-gas interface.
• Example: water can form a dome-like shape above the rim of a full glass before overflowing.
• Surface tension: the capacity of a substance to withstand rupturing when placed under tension or stress.
  • Water forms droplets on dry surfaces rather than flattening.
  • A small piece of paper can float on a water droplet even though paper is denser than water.
  • A needle can be suspended on water's surface if placed gently without breaking surface tension.

🧲 Adhesion and capillary action

Adhesion: the attraction between water molecules and other molecules.

• Adhesion can be stronger than cohesion, especially when water contacts charged surfaces.
• Example: water "climbs" up the inside of thin glass tubes (capillary tubes), appearing higher on the sides than in the middle.
• Capillary action: adhesion to charged surfaces that exceeds cohesive forces between water molecules.
• Don't confuse: cohesion is water-to-water attraction; adhesion is water-to-other-substance attraction.

🌱 Biological importance

• Plant water transport: cohesive and adhesive forces create a "pull" on the water column from roots to leaves.
  • Water molecules evaporating from the plant surface stay connected to molecules below them.
  • This pull transports water and dissolved minerals upward.
  • Without these properties, plants could not receive necessary water and minerals.
• Insect survival: water striders use surface tension to stay afloat and even mate on the water's surface.

🧪 pH, acids, and bases

🧪 What pH measures

pH: indicates the acidity or alkalinity of a solution by measuring hydrogen ion concentration.

• Pure water spontaneously dissociates into equal numbers of H⁺ ions and OH⁻ ions.
• The concentration of hydrogen ions in pure water is 1 × 10⁻⁷ moles H⁺ per liter.
• pH is calculated as the negative of the base 10 logarithm of hydrogen ion concentration.
• For pure water: log₁₀ of 1 × 10⁻⁷ is -7.0, and the negative of this number yields pH 7.0 (neutral).
• The pH scale is an inverse logarithm: high H⁺ concentration = low pH number; low H⁺ concentration = high pH number.

⚗️ Acids and bases defined

Acid: a substance that increases hydrogen ion (H⁺) concentration in a solution, usually by having one of its hydrogen atoms dissociate.

Base: a substance that provides hydroxide ions (OH⁻) or other negatively charged ions that combine with hydrogen ions, reducing their concentration and raising pH.

Property	Acid	Base
Effect on H⁺	Increases H⁺ concentration	Decreases H⁺ concentration
Effect on pH	Lowers pH	Raises pH
Strong example	Hydrochloric acid (HCl) completely dissociates	Sodium hydroxide (NaOH) readily donates OH⁻
Weak example	Acids in tomato juice or vinegar do not completely dissociate	Seawater (pH near 8.0)

• When a base releases hydroxide ions, these ions bind to free hydrogen ions, generating new water molecules.
• Strong acids donate H⁺ more readily; strong bases donate OH⁻ or take up hydrogen ions more readily.

📏 The pH scale

• Ranges from 0 to 14.
• 0.0 to 6.9: acidic
• 7.0: neutral
• 7.1 to 14.0: alkaline (basic)
• Extremes in pH in either direction from 7.0 are usually inhospitable to life.

Examples of pH in the body:

• pH inside cells: 6.8 (close to neutral)
• pH in blood: 7.4 (close to neutral)
• pH in stomach: 1 to 2 (highly acidic)

🔄 Stomach survival mechanism

• The stomach environment is highly acidic (pH 1 to 2).
• Stomach cells cannot maintain near-neutral internal pH in this environment and are constantly dying.
• The stomach constantly produces new cells to replace dead ones, which stomach acids digest.
• Scientists estimate the human body completely replaces the stomach lining every seven to ten days.

🛡️ Buffers and pH regulation

🛡️ What buffers do

Buffers: substances that readily absorb excess H⁺ or OH⁻, keeping the body's pH carefully maintained in the narrow range required for survival.

• Buffers allow organisms to ingest acidic and basic substances (e.g., a human drinking orange juice) and survive.
• Example: a person can drink acidic orange juice without their blood pH dropping dangerously.

🩸 Blood pH buffering system

The buffer maintaining human blood pH involves three components:

1. Carbonic acid (H₂CO₃)
2. Bicarbonate ion (HCO₃⁻)
3. Carbon dioxide (CO₂)

How the buffer works:

Scenario	Mechanism	Result
Excess H⁺ in blood	Bicarbonate ions combine with free hydrogen ions to become carbonic acid	Removes hydrogen ions and moderates pH changes
Excess carbonic acid	Converts to carbon dioxide gas, which is exhaled through the lungs	Prevents too many free hydrogen ions from building up and dangerously reducing blood pH
Excess OH⁻ in blood	Carbonic acid combines with OH⁻ to create bicarbonate	Lowers the pH

• Maintaining constant blood pH is critical to a person's well-being.
• Without this buffer system, the body's pH would fluctuate enough to put survival in jeopardy.

💊 Other buffer examples

• Antacids: over-the-counter medications that combat excess stomach acid.
• Work in the same way as blood buffers, usually with at least one ion capable of absorbing hydrogen and moderating pH.
• Bring relief to those who suffer "heartburn" after eating.
• Water's unique properties contribute to this capacity to balance pH.

🧭 Overview

🧠 One-sentence thesis

Carbon's unique bonding capacity makes it the fundamental backbone of all macromolecules essential for life, while buffer systems maintain the narrow pH range organisms need to survive.

📌 Key points (3–5)

• Why pH stability matters: organisms require near-neutral pH to survive, even when consuming acidic or basic substances.
• How buffers work: they absorb excess H⁺ or OH⁻ ions to prevent dangerous pH fluctuations.
• Why carbon is special: it can form up to four covalent bonds, making it ideal as the structural backbone of macromolecules.
• Common confusion: isomers share the same chemical formula but differ in atom arrangement or bond placement, leading to different properties.
• How bond type affects shape: single, double, and triple carbon-carbon bonds create different three-dimensional geometries that determine molecular function.

🧪 Buffer Systems and pH Regulation

🩸 The blood buffer system

Buffers: substances that readily absorb excess H⁺ or OH⁻, keeping the body's pH carefully maintained in the narrow range required for survival.

• The human blood buffer involves three components: carbonic acid (H₂CO₃), bicarbonate ion (HCO₃⁻), and carbon dioxide (CO₂).
• How it raises pH: when bicarbonate ions combine with free hydrogen ions, they form carbonic acid, removing H⁺ and moderating pH changes.
• How it lowers pH: excess carbonic acid converts to CO₂ gas that we exhale through the lungs, preventing too many free hydrogen ions from building up.
• When pH is too high: if too much OH⁻ enters the system, carbonic acid combines with it to create bicarbonate, lowering the pH.
• Without this system, the body's pH would fluctuate enough to put survival in jeopardy.

💊 Other buffer examples

• Antacids work similarly to blood buffers to combat excess stomach acid.
• They usually contain at least one ion capable of absorbing hydrogen and moderating pH.
• Example: over-the-counter medications bring relief to those who suffer "heartburn" after eating by balancing stomach pH.

🔬 Carbon as the Foundation of Life

⚛️ Carbon's unique bonding properties

• Carbon has an atomic number of 6 (six electrons and six protons).
• The first two electrons fill the inner shell, leaving four in the second shell.
• Individual carbon atoms have an incomplete outermost electron shell.
• Key capability: carbon atoms can form up to four covalent bonds with other atoms to satisfy the octet rule.
• This versatile bonding makes carbon ideal to serve as the basic structural component, or "backbone," of macromolecules.

🧬 Macromolecules and organic molecules

Organic molecules: any carbon-containing liquid, solid, or gas.

• Many complex molecules called macromolecules comprise cells: proteins, nucleic acids (RNA and DNA), carbohydrates, and lipids.
• Macromolecules are a subset of organic molecules that are especially important for life.
• The fundamental component for all of these macromolecules is carbon.

🔥 Hydrocarbons

Hydrocarbons: organic molecules consisting entirely of carbon and hydrogen.

• Common uses: fuels like propane in a gas grill or butane in a lighter.
• The many covalent bonds between atoms in hydrocarbons store a great amount of energy, which releases when these molecules burn (oxidize).
• Methane example: the simplest hydrocarbon molecule (CH₄), with a central carbon atom bonded to four different hydrogen atoms.
• Methane has tetrahedral geometry, with the carbon and four hydrogen atoms forming a tetrahedron with four triangular faces, spaced 109.5° apart.

🏗️ Molecular Structure and Geometry

🔗 How bond type determines shape

• Individual carbon-to-carbon bonds may be single, double, or triple covalent bonds.
• Each type of bond affects the molecule's geometry in a specific way.
• This three-dimensional shape or conformation of macromolecules is critical to how they function.

Bond Type	Geometry	Rotation Allowed?	Example
Single	Tetrahedral	Yes, rotation along bond axis	Ethane
Double	Planar (flat)	No, atoms locked in place	Ethene
Triple	Linear	No	Ethyne

⛓️ Hydrocarbon chains

Aliphatic hydrocarbons: hydrocarbons that consist of linear chains of carbon atoms.

• Successive bonds between carbon atoms form hydrocarbon chains.
• These may be branched or unbranched.
• Naming pattern: the prefix indicates carbon number (eth- for two, prop- for three, but- for four), and the suffix indicates bond type (-ane for single, -ene for double, -yne for triple).
• Example: ethane (single bonds), ethene (double bonds), ethyne (triple bonds) all have two carbons but different geometries.

⭕ Hydrocarbon rings

Aromatic hydrocarbons: hydrocarbons that consist of closed rings of carbon atoms.

• Ring structures sometimes have double bonds present.
• Biological examples: some amino acids, cholesterol and its derivatives (including hormones estrogen and testosterone), and the herbicide 2,4-D all incorporate the benzene ring.
• Benzene is a natural component of crude oil and has been classified as a carcinogen.
• Some hydrocarbons have both aliphatic and aromatic portions (e.g., beta-carotene).
• Carbon can form five- and six-membered rings; nitrogen may be substituted for carbon.

🔄 Isomers

Isomers: molecules that share the same chemical formula but differ in the placement (structure) of their atoms and/or chemical bonds.

• The three-dimensional placement of atoms and chemical bonds within organic molecules is central to understanding their chemistry.

Two types of isomers:

1. Structural isomers: differ in the placement of their covalent bonds.

   • Example: butane and isobutene both have four carbons and ten hydrogens (C₄H₁₀), but different atom arrangement.
   • This leads to differences in chemical properties: butane is suited for use as fuel for cigarette lighters and torches, while isobutene is suited for use as a refrigerant and propellant in spray cans.

2. Geometric isomers: have similar placements of covalent bonds but differ in how these bonds are made to the surrounding atoms, especially in carbon-to-carbon double bonds.

   • Example: in butene (C₄H₈), the two methyl groups (CH₃) can be on either side of the double covalent bond central to the molecule.
   • When the carbons are bound on the same side of the double bond versus opposite sides, the molecules have different properties.

Don't confuse: isomers are not different molecules with different formulas—they have the same chemical formula but different structures, which changes their properties and functions.

🧭 Overview

🧠 One-sentence thesis

Organic molecules differ not only in their chemical formulas but also in the three-dimensional arrangement of atoms and the functional groups attached to their carbon backbones, which together determine their chemical properties and biological roles.

📌 Key points (3–5)

• Two types of hydrocarbons: aliphatic hydrocarbons form linear chains, while aromatic hydrocarbons form closed rings (like benzene).
• Isomers share formulas but differ in structure: structural isomers differ in bond placement, geometric isomers differ around double bonds (cis vs trans), and enantiomers are non-superimposable mirror images.
• Common confusion—cis vs trans: cis configuration places groups on the same side of a double bond (causing a bend), while trans places them on opposite sides (more linear); this affects physical properties like whether fats are liquid or solid.
• Functional groups confer specific properties: groups like hydroxyl, carboxyl, and amino attach to carbon backbones and determine whether molecules are hydrophobic or hydrophilic.
• Why structure matters: three-dimensional placement affects folding, hydrogen bonding, molecular recognition (e.g., DNA base pairing, enzyme-substrate binding), and biological function.

🔗 Hydrocarbon structures

🔗 Aliphatic vs aromatic hydrocarbons

Aliphatic hydrocarbons: hydrocarbons consisting of linear chains of carbon atoms.

Aromatic hydrocarbons: hydrocarbons consisting of closed rings of carbon atoms.

• Aliphatic hydrocarbons are straight or branched chains.
• Aromatic hydrocarbons form ring structures, sometimes with double bonds.
• Example: cyclohexane (ring without alternating double bonds) vs benzene (ring with alternating double bonds).

🧬 Benzene ring in biological molecules

• The benzene ring appears in:
  • Some amino acids
  • Cholesterol and its derivatives (including hormones estrogen and testosterone)
  • The herbicide 2,4-D
• Benzene is a natural component of crude oil and classified as a carcinogen.
• Some hydrocarbons (e.g., beta-carotene) have both aliphatic and aromatic portions.

🔢 Ring variations

• Carbon can form five- and six-membered rings.
• Single or double bonds may connect the carbons in the ring.
• Nitrogen may be substituted for carbon in rings.

🔄 Isomers: same formula, different arrangement

🔄 What isomers are

Isomers: molecules that share the same chemical formula but differ in the placement (structure) of their atoms and/or chemical bonds.

• The three-dimensional placement of atoms and chemical bonds is central to understanding organic chemistry.
• Different atom arrangements lead to differences in chemical properties.

🧱 Structural isomers

Structural isomers: isomers that differ in the placement of their covalent bonds.

• Example: butane and isobutene both have four carbons and ten hydrogens (C₄H₁₀), but different atom arrangements.
• Different structures → different chemical properties:
  • Butane is suited for use as fuel for cigarette lighters and torches.
  • Isobutene is suited for use as a refrigerant and propellant in spray cans.

🔀 Geometric isomers (cis-trans)

Geometric isomers: isomers with similar placements of covalent bonds but differing in how these bonds are made to surrounding atoms, especially around carbon-to-carbon double bonds.

• In butene (C₄H₈), two methyl groups (CH₃) can be on either side of the double bond.
• Cis configuration: carbons bound on the same side of the double bond → causes a bend (change in direction) in the carbon backbone.
• Trans configuration: carbons on opposite sides of the double bond → carbons form a more or less linear structure.

Don't confuse: cis means "same side" (bent), trans means "opposite sides" (linear).

🍔 Cis-trans in fats and oils

Configuration	Structure	Physical state at room temperature	Example
Cis	Bend in carbon backbone	Liquid (oil)	Oleic acid
Trans	Relatively linear fatty acids	Solid (trans fats)	Elaidic acid

• Unsaturated fats: triglycerides with at least one double bond between carbon atoms.
  • Cis double bonds → molecules cannot pack tightly → remain liquid (oil) at room temperature.
  • Trans double bonds → linear fatty acids pack tightly → form solid fats at room temperature.
• Saturated fats: triglycerides without double bonds between carbon atoms (contain all available hydrogen atoms) → solid at room temperature, usually of animal origin.
• Trans fats in the human diet are linked to increased cardiovascular disease risk; many manufacturers have reduced or eliminated their use.

🪞 Enantiomers (mirror images)

Enantiomers: molecules that share the same chemical structure and chemical bonds but differ in the three-dimensional placement of atoms so that they are non-superimposable mirror images.

• Example: D-alanine and L-alanine are mirror images.
• In nature:
  • Only L-forms of amino acids make proteins.
  • Some D-forms of amino acids appear in bacterial cell walls, but never in their proteins.
  • D-form of glucose is the main product of photosynthesis; the L-form is rarely seen in nature.

Don't confuse: enantiomers have the same bonds but are mirror images that cannot be superimposed, like left and right hands.

⚙️ Functional groups and chemical properties

⚙️ What functional groups are

Functional groups: groups of atoms that occur within molecules and confer specific chemical properties to those molecules.

• Found along the "carbon backbone" of macromolecules.
• Carbon backbone: chains and/or rings of carbon atoms with occasional substitution of elements like nitrogen or oxygen.
• Substituted hydrocarbons: molecules with other elements in their carbon backbone.
• Functional groups are usually attached to the carbon backbone at one or several places along its chain and/or ring structure.

🧪 Important functional groups in biological molecules

The excerpt lists these functional groups:

• Hydroxyl
• Methyl
• Carbonyl
• Carboxyl
• Amino
• Phosphate
• Sulfhydryl

These groups play an important role in forming molecules like DNA, proteins, carbohydrates, and lipids.

💧 Hydrophobic vs hydrophilic functional groups

Classification	Characteristics	Example
Hydrophobic	Nonpolar	Methyl molecule
Hydrophilic	Charged or polar; can form hydrogen bonds with water	Carboxyl group (ionizes to release H⁺, resulting in negatively charged COO⁻)

• Carboxyl group: found in amino acids, some amino acid side chains, and fatty acids that form triglycerides and phospholipids.
  • Ionizes to release hydrogen ions (H⁺) from COOH → negatively charged COO⁻ → contributes to hydrophilic nature.
• Carbonyl group: has a partially negatively charged oxygen atom that may form hydrogen bonds with water molecules → makes the molecule more hydrophilic.
• R-group (R): abbreviation for any group in which a carbon or hydrogen atom is attached to the rest of the molecule.

🔗 Hydrogen bonds and molecular function

• Hydrogen bonds between functional groups (within the same molecule or between different molecules) are important to the function of many macromolecules.
• Help molecules fold properly into and maintain the appropriate shape for functioning.
• Involved in various recognition processes:
  • DNA complementary base pairing (hydrogen bonds connect two strands of DNA to create the double-helix structure).
  • Binding of an enzyme to its substrate.

Why it matters: the three-dimensional structure and functional groups together determine how biological molecules interact, fold, and perform their roles in living organisms.

🧭 Overview

🧠 One-sentence thesis

Functional groups determine how biological molecules interact with water and each other through hydrogen bonding, which is essential for macromolecule structure and molecular recognition processes.

📌 Key points (3–5)

• Functional groups classified by water interaction: hydrophobic groups (nonpolar, like methyl) vs. hydrophilic groups (charged or polar, like carboxyl and carbonyl).
• Carboxyl groups ionize: they release hydrogen ions (H⁺) from COOH, becoming negatively charged COO⁻, which makes molecules more hydrophilic.
• Hydrogen bonds shape and function: these bonds between functional groups help macromolecules fold properly, maintain shape, and perform recognition tasks.
• Common confusion: hydrophilic vs. hydrophobic—hydrophilic groups interact well with water due to charge or polarity; hydrophobic groups are nonpolar and do not interact well with water.
• Why it matters: hydrogen bonding enables DNA base pairing and enzyme-substrate binding, critical for biological function.

🧪 Functional groups and water interaction

💧 Hydrophobic vs. hydrophilic classification

Functional groups are classified as hydrophobic or hydrophilic depending on their charge or polarity characteristics.

• Hydrophobic: nonpolar groups that do not interact well with water
  • Example: the methyl molecule is nonpolar and hydrophobic
• Hydrophilic: charged or polar groups that interact well with water
  • Example: carboxyl groups in amino acids, some amino acid side chains, and fatty acids

Don't confuse: Hydrophilic means "water-loving" (interacts with water); hydrophobic means "water-fearing" (does not interact with water). The distinction depends on charge or polarity, not the size or complexity of the group.

⚡ How carboxyl groups create hydrophilicity

• The carboxyl group (COOH) ionizes by releasing hydrogen ions (H⁺)
• This ionization results in a negatively charged COO⁻ group
• The negative charge contributes to the hydrophilic nature of the molecule
• Found in amino acids, fatty acids that form triglycerides, and phospholipids

🔋 How carbonyl groups attract water

• Carbonyl groups have a partially negatively charged oxygen atom
• This oxygen can form hydrogen bonds with water molecules
• The hydrogen bonding ability makes the molecule more hydrophilic

🔗 Hydrogen bonds in biological molecules

🧬 Role in macromolecule structure

Hydrogen bonds between functional groups (within the same molecule or between different molecules) are important to the function of many macromolecules and help them to fold properly into and maintain the appropriate shape for functioning.

• Hydrogen bonds can form:
  • Within the same molecule (intramolecular)
  • Between different molecules (intermolecular)
• These bonds are critical for:
  • Proper folding of macromolecules
  • Maintaining the appropriate shape for functioning

🔍 Role in molecular recognition

Hydrogen bonds are involved in various recognition processes:

Recognition process	How hydrogen bonds work
DNA base pairing	Hydrogen bonds connect two strands of DNA together to create the double-helix structure
Enzyme-substrate binding	Hydrogen bonds enable an enzyme to bind to its substrate

Example: In DNA, hydrogen bonds between complementary bases hold the two strands together in the characteristic double-helix shape, allowing genetic information to be stored and replicated.

Don't confuse: Hydrogen bonds are not the same as covalent bonds. Hydrogen bonds are weaker interactions between slightly charged atoms (often involving hydrogen), while covalent bonds involve sharing electrons between atoms.

🧭 Overview

🧠 One-sentence thesis

Water's unique chemical properties—polarity, hydrogen bonding, high heat capacity, and solvent ability—are critical to maintaining life, while carbon's bonding versatility makes it the central element in biological molecules.

📌 Key points (3–5)

• Water's polar nature enables hydrogen bonding, which underlies most of its life-supporting properties (solvent ability, temperature stability, cohesion/adhesion).
• Carbon's unique bonding: carbon can form four covalent bonds, creating diverse hydrocarbon chains, rings, and functional groups that define biological molecules.
• pH regulation: living organisms tightly regulate hydrogen ion concentration through acids, bases, and buffers to maintain homeostasis.
• Common confusion: hydrogen bonds vs covalent bonds—hydrogen bonds are weak chemical bonds between molecules; covalent bonds are strong bonds within molecules.
• Atoms and bonds: matter is built from atoms (protons, neutrons, electrons), which combine via ionic, covalent, hydrogen, and van der Waals bonds to form molecules, cells, and organisms.

🧪 Atoms and chemical bonds

⚛️ What matter is made of

Matter: anything that occupies space and has mass.

• All naturally occurring elements (98 total) have unique qualities that allow them to combine in various ways.
• Combinations create molecules → cells → tissues → organ systems → organisms.

⚛️ Atomic structure

Atom: the smallest unit of an element that retains all properties of that element.

• Components:
  • Proton: positively charged particle in the nucleus; mass = 1 amu, charge = +1.
  • Neutron: uncharged particle in the nucleus; mass = 1 amu.
  • Electron: resides in orbitals (regions surrounding the nucleus).
• Mass number: total number of protons and neutrons.
• Atomic number: number of protons (defines the element).

🔀 Isotopes and ions

Isotope: atoms that vary in the number of neutrons in their nuclei.

• Example: carbon-12 and carbon-13 have different numbers of neutrons.
• Radioisotope: an isotope that emits radiation to form more stable elements.
• Ion: an atom that has gained or lost electrons, creating a charge.

🔗 Types of chemical bonds

Electrons can transfer, share, or cause charge disparities to create bonds:

Bond type	Description	Strength
Ionic	Transfer of electrons between atoms	Strong
Covalent	Sharing of electrons between atoms	Strong
Nonpolar covalent	Electrons shared equally	Strong
Polar covalent	Electrons shared unequally, creating slightly positive and negative regions	Strong
Hydrogen bond	Weak attraction between polar molecules	Weak
Van der Waals interaction	Very weak interaction due to temporary charges between very close atoms	Very weak

• Octet rule: atoms are most stable when they hold eight electrons in their outermost (valence) shell.
• Don't confuse: hydrogen bonds are between molecules (weak); covalent bonds are within molecules (strong).

💧 Water's life-supporting properties

💧 Polarity and hydrogen bonding

Polar molecule: a molecule with slightly positive and negative regions due to unequal electron sharing.

• Water is polar, allowing it to form hydrogen bonds.
• Hydrogen bonds between water molecules underlie most of water's unique properties.
• These bonds continually break and reform as temperature changes.

🧪 Water as a solvent

Solvent: a substance capable of dissolving another substance.

• Water is an excellent solvent because hydrogen bonds allow ions and other polar molecules to dissolve.
• Sphere of hydration: when polar water molecules surround charged or polar molecules, keeping them dissolved in solution.
• Example: salts and sugars dissolve in water because water molecules surround and separate their ions or polar groups.

🌡️ Temperature stability

• High heat capacity: the amount of heat one gram of a substance must absorb or lose to change its temperature by one degree Celsius.
• Water has a high heat capacity, meaning it takes considerable added heat to raise its temperature.
• This allows overall temperature to remain stable even when energy is added to the system.
• High heat of vaporization: key to how organisms cool themselves by evaporating sweat.

🌊 Cohesion and adhesion

• Cohesive forces: attractive forces between water molecules create surface tension (tension at the surface of a liquid that prevents molecules from separating).
• Example: some insects can walk on water due to surface tension.
• Adhesive properties: water rises inside capillary tubes due to attraction to other surfaces.

🧬 pH and chemical balance

🧬 What pH measures

pH scale: a scale ranging from zero to 14 that is inversely proportional to the hydrogen ion concentration in a solution.

• pH is a measure of hydrogen ion (H⁺) concentration.
• It is one of many chemical characteristics highly regulated in living organisms through homeostasis.

⚖️ Acids, bases, and buffers

• Acid: donates hydrogen ions (H⁺); when added to a solution, pH decreases.
• Base: binds up excess hydrogen ions; when added to a solution, pH increases.
• Acids and bases can change pH values, but buffers tend to moderate the changes they cause.
• Buffers help prevent drastic swings in pH, maintaining stable conditions for life.
• Don't confuse: the excerpt states acids donate H⁺ (not that bases donate OH⁻, though that is implied by neutralization).

🔄 Neutralization

• Acids and bases will neutralize each other when mixed.
• This is critical for maintaining stable pH in biological systems.

🧱 Carbon and organic molecules

🧱 Why carbon is central to life

Organic molecule: any molecule containing carbon (except carbon dioxide).

• Carbon's unique properties make it a central part of biological molecules.
• Carbon can form four bonds: it has four electrons in its outermost shell and can bond with up to four other atoms or molecules.
• Carbon binds covalently to oxygen, hydrogen, and nitrogen to form many molecules important for cellular function.

🔗 Hydrocarbon structures

• Carbon and hydrogen can form hydrocarbon chains or rings.
• Substituted hydrocarbon: a hydrocarbon chain or ring containing an atom of another element in place of one of the backbone carbons.

🧩 Functional groups

Functional groups: groups of atoms that confer specific properties to hydrocarbon (or substituted hydrocarbon) chains or rings that define their overall chemical characteristics and function.

• Functional groups that can bond with carbon include:
  • Hydroxyl
  • Phosphate
  • Carbonyl
• Sodium is not a functional group (it is an element that forms ionic bonds, not a group attached to carbon).

🔄 Isomers

Structural isomers: molecules that share a chemical formula but differ in the placement of their chemical bonds.

• Different arrangements of the same atoms create molecules with different properties.
• Example: molecules with formulas CH₃CH₂COOH and C₃H₆O₂ could be structural isomers (same atoms, different arrangement).
• Cis-trans isomers: molecules must have a double bond to be cis-trans isomers.
• Enantiomers: a molecule must have at least four different atoms or groups connected to a central carbon to be enantiomers.

🔬 Chemical reactions

🔬 Reactants and products

Reactant: a molecule that takes part in a chemical reaction.

Product: a molecule that is the result of a chemical reaction.

• Chemical reactions transform reactants into products.

🔄 Reversible reactions

Reversible chemical reaction: a chemical reaction that functions bidirectionally, where products may turn into reactants if their concentration is great enough.

• Not all reactions go in only one direction; some can reverse depending on concentrations.

🧭 Overview

🧠 One-sentence thesis

Water's unique chemical properties—polarity, hydrogen bonding, high heat capacity, and solvent ability—are essential for maintaining life, while carbon's bonding versatility makes it the central element in biological molecules.

📌 Key points (3–5)

• Water's polarity and hydrogen bonds: water is polar, allowing it to form hydrogen bonds that enable dissolving ions and polar molecules, making it an excellent solvent.
• Temperature regulation: water's high heat capacity and high heat of vaporization help organisms maintain stable temperatures and cool themselves through evaporation.
• Carbon's bonding capacity: carbon can form four covalent bonds, creating diverse hydrocarbon chains and rings that are the basis of all biological molecules.
• pH and homeostasis: pH measures hydrogen ion concentration; acids and bases change pH, but buffers moderate these changes to maintain stable conditions in living organisms.
• Common confusion: hydrogen bonds vs. covalent bonds—hydrogen bonds are weak chemical bonds between molecules, while covalent bonds are strong bonds within molecules that involve electron sharing.

💧 Water's chemical properties

💧 Polarity and hydrogen bonding

Water is a polar molecule, allowing for forming hydrogen bonds.

• Polarity means water molecules have slightly positive and negative regions.
• Hydrogen bonds form between water molecules because of this polarity.
• These bonds are weak individually but collectively give water its unique properties.
• Don't confuse: hydrogen bonds (weak, between molecules) vs. covalent bonds (strong, within molecules).

🧪 Water as a solvent

• Hydrogen bonds allow ions and other polar molecules to dissolve in water.
• Therefore, water is an excellent solvent.
• When polar water molecules surround charged or polar molecules, they keep them dissolved and in solution (sphere of hydration).
• Example: salts and sugars dissolve in water because water molecules surround and separate their ions or polar regions.

🌡️ Temperature stability

High heat capacity:

• Water has a high heat capacity, meaning it takes considerable added heat to raise its temperature.
• As temperature rises, hydrogen bonds between water molecules continually break and form anew.
• This allows the overall temperature to remain stable, although energy is added to the system.

High heat of vaporization:

• Water exhibits a high heat of vaporization.
• This property is key to how organisms cool themselves by evaporating sweat.
• The amount of heat one gram of a substance must absorb or lose to change its temperature by one degree Celsius is called specific heat capacity.

🔗 Cohesion and adhesion

Property	Definition	Example
Cohesion	Attractive forces between water molecules	Surface tension—tension at the surface of a body of liquid that prevents molecules from separating
Adhesion	Attractive forces between water and other surfaces	Water rises inside capillary tubes

• Surface tension is created by the attractive cohesive forces between the liquid's molecules.
• Example: some insects can walk on water due to surface tension.

🧪 pH and chemical balance

🧪 What pH measures

pH scale: scale ranging from zero to 14 that is inversely proportional to the hydrogen ions' concentration in a solution.

• pH is a measure of hydrogen ion concentration in a solution.
• It is one of many chemical characteristics that is highly regulated in living organisms through homeostasis.
• Lower pH = more hydrogen ions (more acidic).
• Higher pH = fewer hydrogen ions (more basic).

⚖️ Acids, bases, and buffers

Acids:

• When acids are added to a solution, the pH should decrease.
• Acids donate hydrogen ions (H⁺).

Bases:

• A molecule that binds up excess hydrogen ions in a solution is called a base.
• Bases accept hydrogen ions.

Buffers:

• Acids and bases can change pH values, but buffers tend to moderate the changes they cause.
• Buffers help prevent drastic swings in pH by absorbing or releasing hydrogen ions as needed.
• This maintains stable conditions necessary for life.

Common confusion:

• Don't confuse: the excerpt states that acids donate H⁺ ions, not that "acids donate hydroxide ions (OH⁻); bases donate hydrogen ions (H⁺)"—that statement is marked as false in the review questions.

🔬 Atoms and chemical bonds

⚛️ Atomic structure

Atom: the smallest unit of an element that retains all of the properties of that element.

Components:

• Proton: positively charged particle that resides in the atom's nucleus; has a mass of one amu and a charge of +1.
• Neutron: uncharged particle that resides in an atom's nucleus; has a mass of one amu.
• Electron: resides in regions surrounding the nucleus called orbitals.
• Nucleus: core of an atom; contains protons and neutrons.

Key numbers:

• Atomic number = number of protons.
• Mass number = total number of protons and neutrons in an atom.
• Example: xenon with atomic number 54 and mass number 108 has 54 neutrons (108 - 54 = 54).

🔗 Types of chemical bonds

Bond type	Strength	Description
Covalent bond	Strong	Atoms share electrons; forms molecules
Nonpolar covalent bond	Strong	Electrons are shared equally between atoms
Polar covalent bond	Strong	Forms as a result of unequal electron sharing, creating slightly positive and negative charged molecule regions
Ionic bond	Strong	Electrons transfer between atoms, creating ions
Hydrogen bond	Weak	Forms between molecules due to polarity
Van der Waals interaction	Very weak	Temporary charges attracting atoms that are very close together

Electron configuration:

Octet rule: rule that atoms are most stable when they hold eight electrons in their outermost shells.

• The outermost shell of an atom is called the valence shell.
• Atoms may give, take, or share electrons with another atom to achieve a full valence shell, the most stable electron configuration.
• Example: potassium (atomic number 19) has shells 1, 2, and 3 full and shell 4 has one electron.

🧬 Isotopes and radioisotopes

Isotopes: atoms that vary in the number of neutrons found in their nuclei.

• Isotopes of the same element have the same atomic number but different mass numbers.
• Example: carbon-12 and carbon-13 are isotopes with different numbers of neutrons.

Radioisotope: isotope that emits radiation comprised of subatomic particles to form more stable elements.

🌿 Carbon and organic molecules

🌿 Carbon's unique properties

Organic molecule: any molecule containing carbon (except carbon dioxide).

• Carbon has four electrons in its outermost shell and can form four bonds.
• Each carbon molecule can bond with as many as four other atoms or molecules.
• The unique properties of carbon make it a central part of biological molecules.
• Carbon binds to oxygen, hydrogen, and nitrogen covalently to form the many molecules important for cellular function.

🔗 Hydrocarbon structures

• Carbon and hydrogen can form hydrocarbon chains or rings.
• Substituted hydrocarbon: hydrocarbon chain or ring containing an atom of another element in place of one of the backbone carbons.

Structural isomers:

Structural isomers: molecules that share a chemical formula but differ in the placement of their chemical bonds.

• Example: molecules with the formulas CH₃CH₂COOH and C₃H₆O₂ could be structural isomers.

🧩 Functional groups

Functional groups: groups of atoms that confer specific properties to hydrocarbon (or substituted hydrocarbon) chains or rings that define their overall chemical characteristics and function.

Common functional groups mentioned:

• Hydroxyl

• Phosphate

• Carbonyl

• Sodium is not a functional group that can bond with carbon (it's an element, not a group).

• Functional groups determine the overall chemical characteristics and function of organic molecules.

🧪 Chemical reactions

🧪 Reactants and products

Reactant: molecule that takes part in a chemical reaction.

Product: molecule that is result of chemical reaction.

↔️ Reversible reactions

Reversible chemical reaction: chemical reaction that functions bidirectionally, where products may turn into reactants if their concentration is great enough.

• Chemical reactions can proceed in both directions depending on the concentrations of reactants and products.

🌍 Matter and elements

🌍 Basic definitions

Matter: anything that has mass and occupies space.

Element: a substance that cannot be broken down into simpler substances by chemical means (implied by context).

• Matter is comprised of elements.
• All of the 98 elements that occur naturally have unique qualities.
• Elements can combine in various ways to create molecules.
• Molecules in turn combine to form cells, tissues, organ systems, and organisms.

Molecule: two or more atoms chemically bonded together.

📊 Periodic table

Periodic table: organizational chart of elements indicating each element's atomic number and atomic mass; provides key information about the elements' properties.

• The periodic table organizes elements by their properties.
• Groups (columns) in the periodic table share similar chemical behavior.
• Example: elements in group 1 need to lose one electron to achieve a stable electron configuration; elements in group 17 need to gain one electron.

🧭 Overview

🧠 One-sentence thesis

Biological macromolecules—carbohydrates, lipids, proteins, and nucleic acids—are built from smaller organic molecules through dehydration synthesis and broken down through hydrolysis, forming the essential building blocks that make up the majority of a cell's dry mass and enable life.

📌 Key points (3–5)

• What biological macromolecules are: large molecules necessary for life, built from smaller organic molecules (monomers) that combine into polymers; four major classes exist.
• How they are built and broken down: dehydration synthesis joins monomers by removing water; hydrolysis breaks polymers apart by adding water.
• Why water matters: water has unique properties (polarity, hydrogen bonding, high heat capacity, solvent ability) that are critical to maintaining life and biochemical processes.
• Common confusion: dehydration synthesis vs. hydrolysis—synthesis forms bonds and releases water (requires energy); hydrolysis breaks bonds and adds water (releases energy).
• Carbon's central role: carbon can form four bonds and binds to oxygen, hydrogen, and nitrogen to create the diverse molecules needed for cellular function.

🧱 Atoms and Chemical Bonds

⚛️ What matter is made of

Matter: anything that occupies space and has mass.

• Matter is composed of elements—98 occur naturally.
• Each element has unique qualities that allow combination into molecules, which form cells, tissues, organ systems, and organisms.

Atom: the smallest unit of an element that retains all properties of that element.

• Atoms consist of:
  • Protons: positively charged particles in the nucleus; mass of one amu, charge of +1.
  • Neutrons: uncharged particles in the nucleus; mass of one amu.
  • Electrons: found in orbitals (regions surrounding the nucleus).

🔢 Atomic structure terms

• Atomic number: the number of protons in an atom.
• Mass number: total number of protons and neutrons.
• Isotopes: atoms that vary in the number of neutrons (same element, different mass).
• Radioisotope: an isotope that emits radiation to form more stable elements.

Example: Xenon with atomic number 54 and mass number 108 has 54 neutrons (108 - 54 = 54).

🔗 Types of chemical bonds

Electrons can transfer, share, or cause charge differences between atoms to create bonds:

Bond type	How it forms	Strength
Ionic bond	Electrons transfer between atoms	Strong
Covalent bond	Electrons are shared between atoms	Strong
Nonpolar covalent bond	Electrons shared equally	Strong
Polar covalent bond	Electrons shared unequally, creating slightly positive and negative regions	Strong
Hydrogen bond	Weak attraction between molecules	Weak
van der Waals interaction	Very weak interaction due to temporary charges between very close atoms	Very weak

🎯 The octet rule and valence shell

Octet rule: atoms are most stable when they hold eight electrons in their outermost shells.

Valence shell: the outermost shell of an atom.

• Atoms give, take, or share electrons to achieve a full valence shell (most stable configuration).
• Example: Group 1 elements need to lose electrons; groups 14 and 17 need to gain electrons to achieve stability.

💧 Water's Life-Sustaining Properties

🧲 Why water is polar

• Water is a polar molecule: it has slightly positive and negative regions due to unequal electron sharing.
• This polarity allows water to form hydrogen bonds between molecules.

🌊 Key properties of water

Excellent solvent

• Hydrogen bonds allow ions and other polar molecules to dissolve in water.
• Sphere of hydration: when polar water molecules surround charged or polar molecules, keeping them dissolved in solution.

High heat capacity

Specific heat capacity: the amount of heat one gram of a substance must absorb or lose to change its temperature by one degree Celsius.

• Water has high heat capacity, meaning it takes considerable heat to raise its temperature.
• As temperature rises, hydrogen bonds continually break and reform, allowing overall temperature to remain stable even when energy is added.
• This helps organisms maintain stable internal temperatures.

High heat of vaporization

• Water requires significant energy to evaporate.
• This property is key to how organisms cool themselves by evaporating sweat.

Cohesion and adhesion

Surface tension: tension at the surface of a liquid that prevents molecules from separating; created by attractive cohesive forces between the liquid's molecules.

• Cohesive forces allow for surface tension (why some insects can walk on water).
• Adhesive properties cause water to rise inside capillary tubes.

🧪 pH and chemical balance

pH scale: scale ranging from zero to 14 that is inversely proportional to the hydrogen ion concentration in a solution.

• pH is a measure of hydrogen ion concentration in a solution.
• It is one of many chemical characteristics highly regulated in living organisms through homeostasis.

Acids and bases

• Acids: when added to a solution, pH decreases (more hydrogen ions).
• Bases: bind up excess hydrogen ions; when added, pH increases.
• Acids and bases can neutralize each other.

Buffer: a molecule that binds up excess hydrogen ions in a solution.

• Buffers tend to moderate pH changes caused by acids and bases.
• They help prevent drastic swings in pH, which is critical for life processes.

Don't confuse: The excerpt states that acids donate hydrogen ions (H⁺), not that "acids donate hydroxide ions"—that statement is false.

🔬 Carbon and Organic Molecules

💎 Carbon's unique properties

Organic molecule: any molecule containing carbon (except carbon dioxide).

• Carbon is central to biological molecules because of its unique bonding properties.
• Carbon has four electrons in its outermost shell and can form four bonds.
• This allows carbon to bond with oxygen, hydrogen, nitrogen, and other carbons in many configurations.

⛓️ Hydrocarbon structures

• Carbon and hydrogen can form hydrocarbon chains or rings.
• These serve as the backbone for many biological molecules.

Substituted hydrocarbon: a hydrocarbon chain or ring containing an atom of another element in place of one of the backbone carbons.

🧩 Functional groups

Functional groups: groups of atoms that confer specific properties to hydrocarbon (or substituted hydrocarbon) chains or rings that define their overall chemical characteristics and function.

Common functional groups that can bond with carbon include:

• Hydroxyl
• Phosphate
• Carbonyl

Note: Sodium is not a functional group that bonds with carbon.

🔄 Structural isomers

Structural isomers: molecules that share a chemical formula but differ in the placement of their chemical bonds.

• Different arrangements of the same atoms create molecules with different properties.
• Example: Molecules with formulas CH₃CH₂COOH and C₃H₆O₂ could be structural isomers.

🧬 Biological Macromolecules: Building and Breaking Down

🏗️ What biological macromolecules are

Biological macromolecules: large molecules, necessary for life, that are built from smaller organic molecules.

Four major classes:

1. Carbohydrates
2. Lipids
3. Proteins
4. Nucleic acids

• Each performs a wide array of functions and is an important cell component.
• Combined, these molecules make up the majority of a cell's dry mass (water makes up the majority of complete mass).
• All are organic (contain carbon) and may also contain hydrogen, oxygen, nitrogen, and additional minor elements.

🧱 Monomers and polymers

Monomer: single subunit or building block of macromolecules.

Polymer: larger molecule formed when monomers combine with each other using covalent bonds.

• Most macromolecules are made from monomers.
• Different monomer types can combine in many configurations, creating diverse macromolecules.
• Even one kind of monomer can combine in various ways to form several different polymers.

Example: Glucose monomers are the constituents of starch, glycogen, and cellulose—three different polymers from the same monomer.

🔨 Dehydration synthesis (building up)

Dehydration synthesis: a reaction that puts molecules together while losing water.

How it works:

• The hydrogen of one monomer combines with the hydroxyl group of another monomer.
• This releases a water molecule as a byproduct.
• At the same time, the monomers share electrons and form covalent bonds.
• As additional monomers join, a chain of repeating monomers forms a polymer.

Energy requirement:

• Dehydration reactions involve the formation of new bonds and require energy.
• Specific enzymes catalyze (speed up) these reactions.

Example: Two glucose molecules link to form the disaccharide maltose, releasing one water molecule in the process.

💧 Hydrolysis (breaking down)

Hydrolysis reaction: a reaction that breaks polymers down into monomers by adding water.

How it works:

• A water molecule is inserted across the bond between monomers.
• The polymer breaks into two components:
  • One part gains a hydrogen atom (H⁺).
  • The other gains a hydroxyl molecule (OH⁻) from the split water molecule.
• This breaks the covalent bond.

Energy release:

• Hydrolysis reactions break bonds and release energy.
• Specific enzymes catalyze these reactions.

Example: The disaccharide maltose breaks down to form two glucose monomers by adding a water molecule—the reverse of the synthesis reaction.

🍽️ Hydrolysis in digestion

• Catalytic enzymes in the digestive system hydrolyze (break down) food into smaller molecules.
• This allows cells in the intestine to easily absorb nutrients.
• Each macromolecule has a specific enzyme that breaks it down:

Macromolecule	Enzyme(s) that break it down
Carbohydrates	Amylase, sucrase, lactase, maltase
Proteins	Proteases (pepsin, peptidase), hydrochloric acid
Lipids	Lipases

• These broken-down macromolecules provide energy for cellular activities.

⚖️ Comparing synthesis and hydrolysis

Aspect	Dehydration Synthesis	Hydrolysis
Direction	Builds polymers from monomers	Breaks polymers into monomers
Water	Releases water	Adds water
Bonds	Forms new bonds	Breaks bonds
Energy	Requires energy	Releases energy
Catalysts	Specific enzymes	Specific enzymes

Don't confuse: Both reactions are enzyme-catalyzed and specific to each macromolecule class, but they are opposite processes.

🧪 Chemical Reactions and Products

🔄 Reactants and products

Reactant: molecule that takes part in a chemical reaction.

Product: molecule that is the result of a chemical reaction.

↔️ Reversible reactions

Reversible chemical reaction: a chemical reaction that functions bidirectionally, where products may turn into reactants if their concentration is great enough.

• Chemical reactions can proceed in both directions depending on concentrations.
• This is important for maintaining chemical balance in cells.

🧭 Overview

🧠 One-sentence thesis

Carbohydrates—built from simple sugar monomers through dehydration synthesis and broken down by hydrolysis—serve as essential energy sources and structural materials in living organisms, with their diverse functions determined by how monosaccharides link together into disaccharides and polysaccharides.

📌 Key points (3–5)

• Polymer formation and breakdown: dehydration synthesis joins monomers into polymers by removing water; hydrolysis breaks polymers apart by adding water.
• Carbohydrate classification: monosaccharides (simple sugars), disaccharides (two sugars), and polysaccharides (many sugars) differ in chain length and function.
• Structural diversity from linkage type: the same monomer (glucose) forms starch, glycogen, and cellulose depending on bond type (α vs β glycosidic bonds).
• Common confusion—α vs β bonds: α 1-4 linkages create digestible starches; β 1-4 linkages create indigestible cellulose (unless specialized enzymes are present).
• Why it matters: carbohydrates provide cellular energy (glucose, starch, glycogen) and structural support (cellulose in plants, chitin in arthropods).

🔗 Polymer chemistry fundamentals

🔗 Dehydration synthesis (building polymers)

Dehydration synthesis: monomers share electrons and form covalent bonds, releasing a water molecule as the polymer chain grows.

• How it works: as monomers join, one loses a hydroxyl group (OH⁻) and the other loses a hydrogen (H⁺), forming H₂O.
• Energy requirement: these reactions form new bonds and require energy.
• Catalysis: specific enzymes speed up dehydration reactions.
• Example: two glucose molecules join to form maltose (a disaccharide) by removing one water molecule.

💧 Hydrolysis (breaking down polymers)

Hydrolysis: a chemical reaction that breaks a polymer into monomers by inserting a water molecule across the covalent bond.

• How it works: the water molecule splits—one part of the polymer gains H⁺, the other gains OH⁻.
• Energy release: breaking bonds releases energy.
• Digestion example: enzymes in the digestive system hydrolyze food into smaller molecules for absorption:
  • Amylase, sucrase, lactase, maltase → break down carbohydrates
  • Proteases (pepsin, peptidase) + hydrochloric acid → break down proteins
  • Lipases → break down lipids
• Don't confuse: hydrolysis is the reverse of dehydration synthesis.

🍬 Monosaccharides: simple sugars

🍬 What monosaccharides are

Monosaccharides (mono- = "one"; sacchar- = "sweet"): simple sugars, the most common of which is glucose.

• General formula: (CH₂O)ₙ, where n is the number of carbons (ratio of carbon:hydrogen:oxygen = 1:2:1).
• Carbon count: usually 3–7 carbons.
• Naming: most names end in -ose.

🏷️ Classification by structure

Feature	Aldose	Ketose
Functional group	Aldehyde (R-CHO) at the end	Ketone (RC(=O)R') in the middle
Carbonyl position	End of carbon chain	Middle of carbon chain

Carbon count	Name	Example
3 carbons	Triose	(generic three-carbon sugar)
5 carbons	Pentose	Ribose
6 carbons	Hexose	Glucose, galactose, fructose

🔄 Isomers: same formula, different arrangement

• Glucose, galactose, and fructose all have the formula C₆H₁₂O₆ but differ in functional group arrangement around asymmetric carbons.
• They are structural isomers: same chemical formula, different atom arrangement.
• Glucose and galactose are aldoses; fructose is a ketose.
• Don't confuse: isomers have identical formulas but different structures and chemical properties.

🔵 Ring vs linear forms

• In aqueous solutions, monosaccharides usually exist as ring-shaped molecules (not linear chains).
• Anomeric carbon (carbon 1): becomes asymmetric when the ring forms.
  • α (alpha) position: hydroxyl group (OH) below carbon 1.
  • β (beta) position: hydroxyl group above the plane.
• Five-carbon sugars (e.g., ribose) and six-carbon sugars (e.g., glucose) form rings; fructose forms a five-membered ring.

⚡ Glucose: the key energy source

• Chemical formula: C₆H₁₂O₆.
• In humans: important energy source; during cellular respiration, glucose releases energy to make ATP.
• In plants: synthesized from CO₂ and water; provides energy for the plant; excess stored as starch.
• In animals: excess glucose stored as starch (in diet) or glycogen (in body).

🍭 Disaccharides: two sugars joined

🍭 How disaccharides form

Disaccharides (di- = "two"): form when two monosaccharides undergo a dehydration reaction, releasing water and forming a covalent bond.

• Glycosidic bond: the covalent bond between two carbohydrate molecules.
• Bond type:
  • Alpha bond: OH group on carbon-1 of the first glucose is below the ring plane.
  • Beta bond: OH group on carbon-1 is above the ring plane.

🥛 Common disaccharides

Disaccharide	Monomers	Where found
Lactose	Glucose + galactose	Milk (milk sugar)
Maltose	Glucose + glucose	Malt (grain sugar)
Sucrose	Glucose + fructose	Table sugar (most common disaccharide)

• Example: sucrose forms when glucose (carbon 1) links to fructose (carbon 2) via a glycosidic bond, releasing one water molecule.

🌾 Polysaccharides: many sugars, diverse functions

🌾 What polysaccharides are

Polysaccharide (poly- = "many"): a long chain of monosaccharides linked by glycosidic bonds.

• Structure: may be branched or unbranched; may contain different monosaccharide types.
• Molecular weight: 100,000 daltons or more.
• Primary examples: starch, glycogen, cellulose, chitin.

🌽 Starch: plant energy storage

• Composition: mixture of amylose and amylopectin (both glucose polymers).
• Function: plants store excess glucose as starch in roots and seeds; provides food for embryos and for humans/animals.
• Linkage types:
  • Amylose: unbranched chains with α 1-4 glycosidic bonds → helical structure.
  • Amylopectin: branched chains with α 1-4 bonds and α 1-6 bonds at branch points.
• Digestion: enzymes (e.g., amylase in saliva) break starch into maltose and glucose for absorption.

🥩 Glycogen: animal energy storage

• Composition: glucose monomers, highly branched.
• Function: storage form of glucose in humans and vertebrates; stored in liver and muscle cells.
• Glycogenolysis: when blood glucose drops, glycogen breaks down to release glucose.
• Don't confuse: glycogen is the animal equivalent of starch, but more highly branched.

🌳 Cellulose: plant structural support

• Composition: glucose monomers linked by β 1-4 glycosidic bonds.
• Function: most abundant natural biopolymer; main component of plant cell walls; provides structural support.
• Structure: every other glucose monomer is flipped over → linear, fibrous, tightly packed chains → rigidity and high tensile strength.
• Digestion challenge: human enzymes cannot break β 1-4 linkages.
  • Herbivores (cows, koalas, buffalos): specialized stomach flora secrete cellulase enzyme to digest cellulose.
  • Termites: harbor organisms that secrete cellulases.
  • Cellulase breaks cellulose into glucose monomers for energy.
• Don't confuse: α 1-4 bonds (starch) are digestible by humans; β 1-4 bonds (cellulose) are not, unless cellulase is present.

🐝 Chitin: arthropod exoskeleton

Chitin: a polysaccharide-containing nitrogen, made of repeating N-acetyl-β-d-glucosamine units (a modified sugar).

• Function: forms the hard outer exoskeleton of arthropods (insects, crustaceans) to protect internal body parts.
• Also found in: fungal cell walls (fungi form their own kingdom in domain Eukarya).
• Example: the hard outer shell of a bee is made of chitin.

📊 Carbohydrate roles summary

Carbohydrate	Type	Function	Key linkage
Glucose	Monosaccharide	Primary energy source (cellular respiration → ATP)	—
Starch	Polysaccharide	Plant energy storage	α 1-4, α 1-6 (amylopectin)
Glycogen	Polysaccharide	Animal energy storage	α 1-4, α 1-6 (highly branched)
Cellulose	Polysaccharide	Plant cell wall structure	β 1-4
Chitin	Polysaccharide	Arthropod exoskeleton, fungal cell walls	Modified sugar units

• Energy vs structure: digestible α-linked polymers (starch, glycogen) provide energy; indigestible β-linked polymers (cellulose, chitin) provide structural support.
• Common confusion: the same monomer (glucose) can form very different polymers depending on bond type and branching.

🧭 Overview

🧠 One-sentence thesis

Lipids serve critical roles in energy storage, membrane structure, and signaling despite their bad reputation, while proteins—built from amino acid sequences—perform the most diverse range of functions of all macromolecules.

📌 Key points (3–5)

• Trans fats vs other fats: artificially hydrogenated trans fats increase LDL cholesterol and heart disease risk, unlike omega-3 fatty acids which reduce cardiovascular problems.
• Phospholipid structure: amphipathic molecules with hydrophobic fatty acid tails and hydrophilic phosphate heads form the bilayer matrix of all cell membranes.
• Protein diversity: proteins have the most diverse functions of all macromolecules (structural, enzymatic, hormonal, transport, defense, etc.), all built from linear sequences of 20 amino acids.
• Common confusion: not all fats are bad—fats are essential for vitamin absorption, energy storage, and insulation; the key is consuming healthy fats in moderation.
• Shape determines function: protein shape is critical to function, and denaturation (permanent shape change from temperature, pH, or chemicals) leads to loss of function.

🧪 Types of lipids and their roles

🔄 Trans fats and health

Trans fats: fats where the hydrocarbon chain converts to double bonds in the trans-conformation through artificial hydrogenation.

• Found in margarine, some peanut butters, and shortening.
• Health impact: increase low-density lipoproteins (LDL or "bad" cholesterol), leading to plaque deposition in arteries and heart disease.
• Many fast food restaurants have banned trans fats; food labels must display trans fat content.
• Don't confuse: not all fats are harmful—trans fats are specifically problematic due to their artificial structure.

🐟 Omega-3 fatty acids

Essential fatty acids: those the human body requires but does not synthesize, so must be obtained through diet.

• Omega-3 structure: polyunsaturated fatty acids with a double bond connecting the third carbon from the hydrocarbon chain's end to its neighboring carbon.
• The farthest carbon from the carboxyl group is the omega (ω) carbon.
• Important types: alpha-linolenic acid (ALA), eicosapentaenoic acid (EPA), and docosahexaenoic acid (DHA).
• Sources: salmon, trout, and tuna.
• Health benefits:
  • Reduce sudden death risk from heart attacks
  • Lower blood triglycerides and blood pressure
  • Prevent thrombosis by inhibiting blood clotting
  • Reduce inflammation
  • May lower cancer risk in animals

🕯️ Waxes

• Long fatty acid chains esterified to long-chain alcohols.
• Cover some aquatic birds' feathers and plant leaf surfaces.
• Hydrophobic nature prevents water from sticking to surfaces.

🧱 Why fats matter despite bad publicity

Function	How it works
Vitamin absorption	Many vitamins are fat soluble
Energy storage	Long-term storage form of fatty acids
Insulation	Provide insulation for the body

• Eating excess fried and fatty foods does lead to weight gain.
• However, we should consume "healthy" fats in moderate amounts regularly.

🧬 Phospholipids and membrane structure

🧬 Phospholipid composition

Phospholipids: major plasma membrane constituents that comprise cells' outermost layer.

• Like fats, comprised of fatty acid chains attached to a glycerol or sphingosine backbone.
• Key difference from triglycerides: instead of three fatty acids, there are two fatty acids forming diacylglycerol, plus a modified phosphate group on the third carbon.
• A phosphate group alone does not qualify as a phospholipid—it is phosphatidate (the precursor).
• An alcohol modifies the phosphate group.
• Important examples: phosphatidylcholine and phosphatidylserine in plasma membranes.

💧 Amphipathic nature

Amphipathic molecule: has both a hydrophobic and a hydrophilic part.

• Hydrophobic part: fatty acid chains (the "tails") cannot interact with water.
• Hydrophilic part: phosphate-containing group (the "head") interacts with water.
• The head is hydrophilic; the tail contains hydrophobic fatty acids.

🏗️ Bilayer formation

• In a membrane, phospholipids form a bilayer structure.
• Arrangement: fatty acid tails face inside (away from water); phosphate groups face outside (toward aqueous solution).
• This bilayer is the major component of all cellular membranes.
• Phospholipids are responsible for the plasma membrane's dynamic nature.
• Micelle formation: if a drop of phospholipids is placed in water, it spontaneously forms a micelle with hydrophilic heads facing outside and fatty acids facing the interior.

💍 Steroids

💍 Steroid structure and classification

Steroids: lipids with a fused ring structure, grouped with lipids because they are hydrophobic and insoluble in water.

• Unlike phospholipids and fats, steroids have a fused ring structure.
• All steroids have four linked carbon rings.
• Several (like cholesterol) have a short tail.
• Many steroids have the –OH functional group, classifying them as alcohols (sterols).

🧪 Cholesterol functions

• Most common steroid, synthesized by the liver.
• Precursor roles:
  • Steroid hormones (testosterone, estradiol) secreted by gonads and endocrine glands
  • Vitamin D
  • Bile salts (help emulsify fats and their absorption by cells)
• Membrane component: sterols (cholesterol in animal cells, phytosterol in plants) are components of the plasma membrane, found within the phospholipid bilayer.
• Don't confuse: although often spoken of negatively, cholesterol is necessary for proper body functioning.

🧩 Protein structure and diversity

🧩 Protein functions overview

Proteins: one of the most abundant organic molecules in living systems with the most diverse range of functions of all macromolecules.

• May be structural, regulatory, contractile, or protective.
• May serve in transport, storage, or membranes.
• May be toxins or enzymes.
• Each cell may contain thousands of proteins, each with unique function.
• Structures vary greatly, like their functions.
• All are amino acid polymers arranged in a linear sequence.

🔧 Major protein types

Type	Examples	Functions
Digestive Enzymes	Amylase, lipase, pepsin, trypsin	Help in food digestion by catabolizing nutrients into monomeric units
Transport	Hemoglobin, albumin	Carry substances in blood or lymph throughout the body
Structural	Actin, tubulin, keratin	Construct different structures like the cytoskeleton
Hormones	Insulin, thyroxine	Coordinate different body systems' activity
Defense	Immunoglobulins	Protect the body from foreign pathogens
Contractile	Actin, myosin	Effect muscle contraction
Storage	Legume storage proteins, egg white (albumin)	Provide nourishment in early embryo development and seedling

🧬 Enzymes

Enzymes: catalysts in biochemical reactions produced by living cells, usually complex or conjugated proteins.

• Each enzyme is specific for the substrate (reactant that binds to the enzyme) upon which it acts.
• Types by function:
  • Catabolic enzymes: break down their substrates
  • Anabolic enzymes: build more complex molecules from substrates
  • Catalytic enzymes: affect the rate of reaction
• All enzymes increase reaction rate and are therefore organic catalysts.
• Example: salivary amylase hydrolyzes its substrate amylose (a starch component).

📡 Hormones

Hormones: chemical-signaling molecules, usually small proteins or steroids, secreted by endocrine cells to control or regulate specific physiological processes.

• Regulate growth, development, metabolism, and reproduction.
• Example: insulin (a protein hormone) helps regulate blood glucose level.

🎭 Protein shape

• Proteins have different shapes and molecular weights.
• Shape types: some are globular (e.g., hemoglobin); others are fibrous (e.g., collagen in skin).
• Shape is critical to function: many different types of chemical bonds maintain protein shape.

⚠️ Denaturation

Denaturation: permanent changes in protein shape leading to loss of function.

• Caused by changes in temperature, pH, and exposure to chemicals.
• Results in loss of function because shape is critical to protein function.

🧱 Amino acids: protein building blocks

🧱 Amino acid structure

Amino acids: the monomers that comprise proteins.

• Fundamental structure (same for all amino acids):
  • Central carbon atom (alpha carbon)
  • Bonded to an amino group (NH₂)
  • Bonded to a carboxyl group (COOH)
  • Bonded to a hydrogen atom
  • Bonded to an R group (side chain)
• The name "amino acid" reflects that these acids contain both amino group and carboxyl-acid-group.
• 20 common amino acids present in proteins.
• Two rare new amino acids discovered recently: selenocysteine and pyrrolysine.

🔤 R groups determine properties

• The R group (or side chain) is different for each amino acid.
• Chemical nature determined by side chain:
  • Nonpolar/hydrophobic: valine, methionine, alanine
  • Polar/hydrophilic: serine, threonine, cysteine
  • Positively charged (basic): lysine, arginine
  • Simple: glycine (hydrogen atom as R group)
• Special case: proline has an R group linked to the amino group, forming a ring-like structure (amino group not separate from side chain).
• Represented by single uppercase letter or three-letter abbreviation (e.g., V or val for valine).

🍽️ Essential amino acids

Essential amino acids: those necessary to build proteins in the body but not produced by the body.

• Must be obtained from diet.
• In humans include isoleucine, leucine, and cysteine.
• Which amino acids are essential varies from organism to organism.
• Similar concept to essential fatty acids.

🔗 Peptide bond formation

Peptide bond: covalent bond attaching amino acids, formed by dehydration reaction.

• One amino acid's carboxyl group combines with the incoming amino acid's amino group.
• Releases a water molecule in the process.
• Products: linkages form peptides; as more amino acids join, the chain becomes a polypeptide.
• Each polypeptide has a free amino group at one end (the N terminal or amino terminal).

🎯 Sequence determines function

• The sequence and number of amino acids ultimately determine the protein's shape, size, and function.
• Different arrangements of the same 20 amino acid types comprise all proteins.

🧭 Overview

🧠 One-sentence thesis

Biological macromolecules—carbohydrates, lipids, proteins, and nucleic acids—are large organic molecules built from smaller monomers through dehydration synthesis and broken down by hydrolysis, and they perform essential structural, storage, and functional roles in all living cells.

📌 Key points (3–5)

• What macromolecules are: large molecules necessary for life, built from smaller organic monomers; the four major classes are carbohydrates, lipids, proteins, and nucleic acids.
• How they form and break down: monomers join via dehydration synthesis (releasing water) to form polymers; hydrolysis (adding water) breaks polymers back into monomers.
• Carbohydrates: provide energy (especially glucose) and structural support (cellulose, chitin); classified as monosaccharides, disaccharides, or polysaccharides.
• Lipids: nonpolar, hydrophobic molecules including fats, oils, waxes, phospholipids, and steroids; store energy, insulate, and form cell membranes.
• Proteins: polymers of amino acids with diverse functions (enzymes, hormones, structure, transport); shape determines function, and denaturation destroys function.

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🔗 Synthesis and breakdown of macromolecules

🔗 Dehydration synthesis

Dehydration synthesis: a reaction in which monomers combine by releasing water molecules as byproducts, forming covalent bonds to create polymers.

• The hydrogen from one monomer combines with the hydroxyl group (OH) of another monomer, releasing H₂O.
• Monomers share electrons and form covalent bonds.
• Example: two glucose molecules link to form maltose (a disaccharide), releasing one water molecule.
• This process requires energy and is catalyzed by specific enzymes.

💧 Hydrolysis

Hydrolysis: a reaction that breaks polymers into monomers by inserting a water molecule across the bond.

• One part of the polymer gains a hydrogen atom (H⁺), the other gains a hydroxyl group (OH⁻) from the split water molecule.
• Example: maltose breaks down into two glucose monomers when water is added.
• Hydrolysis releases energy and is catalyzed by enzymes.
• Don't confuse: dehydration synthesis builds polymers and requires energy; hydrolysis breaks polymers and releases energy.

🧪 Enzyme specificity

• Different enzymes catalyze reactions for each macromolecule class.
• Carbohydrates: amylase, sucrase, lactase, maltase.
• Proteins: proteases (pepsin, peptidase) and hydrochloric acid.
• Lipids: lipases.
• These enzymes in the digestive system break down food into smaller molecules that cells can absorb.

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🍬 Carbohydrates: structure and classification

🍬 What carbohydrates are

Carbohydrates: organic molecules with the stoichiometric formula (CH₂O)ₙ, where the ratio of carbon to hydrogen to oxygen is 1:2:1.

• The name comes from "carbo" (carbon) and "hydrate" (water components).
• Classified into three subtypes: monosaccharides, disaccharides, and polysaccharides.

🔵 Monosaccharides

Monosaccharides: simple sugars, the most common being glucose.

• Carbon number usually ranges from three to seven.
• Names typically end in "-ose."
• Aldose vs ketose:
  • Aldose: has an aldehyde group (R-CHO) at the end of the carbon chain.
  • Ketose: has a ketone group (RC(=O)R') in the middle of the carbon chain.
• Trioses, pentoses, hexoses: three, five, or six carbons in the backbone.
• Example: glucose (C₆H₁₂O₆) is a hexose and an aldose; it is the primary energy source for cellular respiration and ATP production.
• Glucose, galactose, and fructose are all hexoses with the same chemical formula but different structures (structural isomers).
• Monosaccharides can exist as linear chains or ring forms; in aqueous solutions, they are usually in ring forms.
• Alpha (α) vs beta (β) position: in ring form, if the hydroxyl group on carbon 1 is below the ring plane, it is α; if above, it is β.

🔗 Disaccharides

Disaccharides: formed when two monosaccharides undergo a dehydration reaction, joining via a glycosidic bond.

• Glycosidic bond: a covalent bond between a carbohydrate molecule and another molecule (here, between two monosaccharides).
• Can be alpha or beta type depending on the position of the OH group on carbon-1.
• Common disaccharides:
  • Lactose: glucose + galactose (milk sugar).
  • Maltose: glucose + glucose (malt/grain sugar).
  • Sucrose: glucose + fructose (table sugar).
• Example: sucrose forms when glucose (carbon 1) and fructose (carbon 2) join, releasing water.

🌾 Polysaccharides

Polysaccharides: long chains of monosaccharides linked by glycosidic bonds; may be branched or unbranched.

• Molecular weight can be 100,000 daltons or more.
• Starch: plant storage form of glucose; mixture of amylose (unbranched, α 1-4 linkages) and amylopectin (branched, α 1-4 and α 1-6 linkages).
  • Plants synthesize glucose and store excess as starch in roots and seeds.
  • Enzymes (e.g., amylase in saliva) break down starch into maltose and glucose for absorption.
• Glycogen: animal storage form of glucose; highly branched, stored in liver and muscle cells.
  • Breaks down to release glucose when blood glucose levels decrease (glycogenolysis).
• Cellulose: most abundant natural biopolymer; main component of plant cell walls.
  • Glucose monomers linked by β 1-4 glycosidic bonds.
  • Every other glucose monomer is flipped, resulting in a linear, fibrous structure that provides rigidity and high tensile strength.
  • Human digestive enzymes cannot break β 1-4 linkages; herbivores (cows, koalas, buffalos) have specialized stomach flora that secrete cellulase to digest cellulose.
  • Termites also digest cellulose with the help of organisms in their bodies that secrete cellulases.
• Chitin: a polysaccharide containing nitrogen; made of repeating N-acetyl-β-d-glucosamine units (a modified sugar).
  • Major component of arthropod exoskeletons (insects, crustaceans) and fungal cell walls.

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🥑 Lipids: types and functions

🥑 What lipids are

Lipids: a diverse group of largely nonpolar compounds that are hydrophobic (water-fearing) or insoluble in water.

• Mostly hydrocarbons with nonpolar carbon–carbon or carbon–hydrogen bonds.
• Functions: energy storage, insulation, hormone building blocks, and cellular membrane components.
• Include fats, oils, waxes, phospholipids, and steroids.

🧈 Fats and oils

Fat molecule: consists of glycerol (an alcohol with three carbons, five hydrogens, and three hydroxyl groups) and fatty acids (long hydrocarbon chains with a carboxyl group attached).

• Triacylglycerol (triglyceride): three fatty acids attached to a glycerol backbone via ester bonds; three water molecules are released during formation.
• Fatty acids may be similar or different; number of carbons typically ranges from 4 to 36 (most common: 12–18).
• Saturated fatty acids: only single bonds between neighboring carbons; saturated with hydrogen; solid at room temperature.
  • Example: stearic acid (common in meat), palmitic acid (from palm trees), butyric acid (in butter).
  • Long straight chains pack tightly.
• Unsaturated fatty acids: contain one or more double bonds; liquid at room temperature (oils).
  • Monounsaturated: one double bond (e.g., oleic acid in olive oil).
  • Polyunsaturated: more than one double bond (e.g., canola oil).
  • Cis vs trans configuration:
    • Cis: hydrogens on the same side of the double bond; causes a kink that prevents tight packing, keeping fats liquid.
    • Trans: hydrogens on opposite sides; straighter chain.
  • Unsaturated fats are usually of plant origin and help lower blood cholesterol; saturated fats contribute to plaque formation in arteries.
• Trans fats: artificially hydrogenated oils (e.g., margarine, some peanut butters, shortening).
  • Hydrogen gas is bubbled through oils to solidify them; cis double bonds may convert to trans.
  • Increase LDL ("bad" cholesterol) and may lead to plaque deposition and heart disease.
  • Many fast food restaurants have banned trans fats; food labels must display trans fat content.

🐟 Omega fatty acids

Essential fatty acids: fatty acids the human body requires but does not synthesize; must be obtained from the diet.

• Omega-3 fatty acids: polyunsaturated fatty acids with a double bond between the third and fourth carbon from the omega (ω) end.
  • Examples: alpha-linolenic acid (ALA), eicosapentaenoic acid (EPA), docosahexaenoic acid (DHA).
  • Sources: salmon, trout, tuna.
  • Benefits: reduce risk of sudden death from heart attacks, lower triglycerides and blood pressure, prevent thrombosis, reduce inflammation, may lower risk of some cancers.
• Omega-6 fatty acid: the other essential fatty acid for humans.
• Don't confuse: omega-3 refers to the position of the double bond from the omega carbon, not the total number of double bonds.

🕯️ Waxes

Wax: long fatty acid chains esterified to long-chain alcohols.

• Hydrophobic; prevent water from sticking to surfaces.
• Cover some aquatic birds' feathers and some plants' leaf surfaces.

🧱 Phospholipids

Phospholipids: major constituents of the plasma membrane; comprise the outermost layer of cells.

• Structure: two fatty acids attached to a glycerol or sphingosine backbone, forming diacylglycerol; a modified phosphate group occupies the third carbon.
• The phosphate group is modified by an alcohol (e.g., phosphatidylcholine, phosphatidylserine).
• Amphipathic molecule: has both hydrophobic (fatty acid chains) and hydrophilic (phosphate-containing group) parts.
  • Hydrophilic head interacts with water; hydrophobic tails cannot.
• In a membrane, phospholipids form a bilayer:
  • Fatty acid tails face inside, away from water.
  • Phosphate heads face outside, toward the aqueous environment.
• Responsible for the plasma membrane's dynamic nature.
• In water, phospholipids spontaneously form micelles (heads face outside, tails face inside).

💊 Steroids

Steroids: lipids with a fused ring structure (four linked carbon rings); hydrophobic and insoluble in water.

• Do not resemble other lipids but are grouped with them due to hydrophobic nature.
• Many have a short tail and the –OH functional group (sterols).
• Cholesterol: the most common steroid; synthesized by the liver.
  • Precursor to steroid hormones (testosterone, estradiol), Vitamin D, and bile salts.
  • Bile salts help emulsify fats for absorption.
  • Component of the plasma membrane (sterols in animal cells, phytosterols in plants); found within the phospholipid bilayer.
  • Necessary for proper body functioning despite negative public perception.

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🧬 Proteins: structure and function

🧬 What proteins are

Proteins: one of the most abundant organic molecules in living systems; polymers of amino acids arranged in a linear sequence.

• Have the most diverse range of functions of all macromolecules.
• May be structural, regulatory, contractile, protective, transport, storage, membrane, toxins, or enzymes.
• Each cell may contain thousands of proteins, each with a unique function.

⚙️ Types and functions of proteins

Type	Examples	Functions
Digestive Enzymes	Amylase, lipase, pepsin, trypsin	Help digest food by breaking down nutrients into monomeric units
Transport	Hemoglobin, albumin	Carry substances in blood or lymph throughout the body
Structural	Actin, tubulin, keratin	Construct structures like the cytoskeleton
Hormones	Insulin, thyroxine	Coordinate activity of different body systems
Defense	Immunoglobulins	Protect the body from foreign pathogens
Contractile	Actin, myosin	Effect muscle contraction
Storage	Legume storage proteins, egg white (albumin)	Provide nourishment in early embryo development and seedlings

• Enzymes: catalysts in biochemical reactions; usually complex or conjugated proteins.
  • Each enzyme is specific for its substrate (the reactant it binds to).
  • Catabolic enzymes: break down substrates.
  • Anabolic enzymes: build more complex molecules from substrates.
  • Catalytic enzymes: affect the rate of reaction (all enzymes are organic catalysts).
  • Example: salivary amylase hydrolyzes amylose (a starch component).
• Hormones: chemical-signaling molecules (usually small proteins or steroids) secreted by endocrine cells.
  • Control or regulate physiological processes (growth, development, metabolism, reproduction).
  • Example: insulin regulates blood glucose levels.
• Proteins have different shapes (globular or fibrous) and molecular weights.
  • Example: hemoglobin is globular; collagen (in skin) is fibrous.
• Protein shape is critical to function; many chemical bonds maintain this shape.
• Denaturation: permanent changes in protein shape due to changes in temperature, pH, or chemical exposure, leading to loss of function.

🧱 Amino acids

Amino acids: the monomers that comprise proteins; all proteins are made from different arrangements of the same 20 types of amino acids.

• Basic structure: a central carbon atom (alpha carbon) bonded to:
  • An amino group (NH₂)
  • A carboxyl group (COOH)
  • A hydrogen atom
  • An R group (side chain)
• The R group is different for each amino acid and determines its chemical nature (acidic, basic, polar, or nonpolar).
• Examples:
  • Glycine: R group is a hydrogen atom.
  • Valine, methionine, alanine: nonpolar/hydrophobic.
  • Serine, threonine, cysteine: polar/hydrophilic.
  • Lysine, arginine: positively charged (basic).
  • Proline: R group linked to the amino group, forming a ring (exception to standard structure).
• Essential amino acids: necessary to build proteins but not produced by the body; must be obtained from the diet.
  • In humans: isoleucine, leucine, cysteine (among others).
  • Which amino acids are essential varies by organism.
• Amino acids are represented by a single uppercase letter or a three-letter abbreviation (e.g., V or val for valine).

🔗 Peptide bonds and polypeptides

Peptide bond: a covalent bond formed by a dehydration reaction that attaches amino acids to each other.

• One amino acid's carboxyl group combines with the incoming amino acid's amino group, releasing a water molecule.
• The resulting chain of linked amino acids is a peptide; longer chains are polypeptides.
• Each polypeptide has:
  • A free amino group at one end (N terminal or amino terminal).
  • A free carboxyl group at the other end (C terminal or carboxyl terminal).
• Polypeptide vs protein:
  • Polypeptide: technically a polymer of amino acids.
  • Protein: a polypeptide or polypeptides that have combined, often with bound non-peptide prosthetic groups, a distinct shape, and a unique function.
• Post-translational modifications: after protein synthesis (translation), most proteins are modified (e.g., cleavage, phosphorylation, addition of chemical groups) to become fully functional.

🧬 Protein structure and function

• The sequence and number of amino acids determine the protein's shape, size, and function.
• Protein shape is critical to function; changes in shape lead to loss of function (denaturation).
• Don't confuse: the terms "polypeptide" and "protein" are sometimes used interchangeably, but a protein is a functional, often modified polypeptide with a specific shape and role.

🧪 Cytochrome c and evolutionary significance

• Cytochrome c: an important component of the electron transport chain in cellular respiration; located in mitochondria.
  • Has a heme prosthetic group; the central ion alternately reduces and oxidizes during electron transfer.
  • Essential for producing cellular energy; has changed very little over millions of years.
• Protein sequencing and evolutionary kinship:
  • Human cytochrome c contains 104 amino acids.
  • 37 amino acids appear in the same position in all sequenced cytochrome c samples, indicating a possible common ancestor.
  • Human vs chimpanzee: no sequence difference.
  • Human vs rhesus monkey: one amino acid difference.
  • Human vs yeast: difference in the 44th position.
  • Evolutionary kinship can be assessed by measuring similarities or differences in DNA or protein sequences among species.

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🔍 Key comparisons and common confusions

🔍 Dehydration synthesis vs hydrolysis

Aspect	Dehydration synthesis	Hydrolysis
What it does	Builds polymers from monomers	Breaks polymers into monomers
Water	Releases water	Adds water
Energy	Requires energy	Releases energy
Bonds	Forms new covalent bonds	Breaks covalent bonds

🔍 Monosaccharides, disaccharides, polysaccharides

Type	Definition	Examples
Monosaccharides	Simple sugars (single unit)	Glucose, fructose, galactose
Disaccharides	Two monosaccharides joined	Lactose, maltose, sucrose
Polysaccharides	Long chains of monosaccharides	Starch, glycogen, cellulose, chitin

🔍 Saturated vs unsaturated fatty acids

Aspect	Saturated	Unsaturated
Bonds	Only single bonds	One or more double bonds
Hydrogen	Saturated with hydrogen	Not fully saturated
Physical state	Solid at room temperature	Liquid at room temperature (oils)
Packing	Pack tightly (straight chains)	Do not pack tightly (kinks from cis double bonds)
Health	Contribute to plaque formation	Help lower blood cholesterol
Origin	Usually animal fats	Usually plant oils

🔍 Cis vs trans fats

Aspect	Cis	Trans
Hydrogen position	Same side of double bond	Opposite sides of double bond
Shape	Kink in chain	Straighter chain
Physical state	Liquid at room temperature	More solid
Health	Generally healthier	Increase LDL ("bad" cholesterol), linked to heart disease
Origin	Natural (plant oils)	Artificially hydrogenated

🔍 Starch vs glycogen vs cellulose

Polysaccharide	Organism	Function	Linkage	Structure
Starch	Plants	Energy storage	α 1-4 (amylose); α 1-4 and α 1-6 (amylopectin)	Unbranched (amylose) or branched (amylopectin)
Glycogen	Animals	Energy storage	α 1-4 and α 1-6	Highly branched
Cellulose	Plants	Structural (cell walls)	β 1-4	Unbranched, linear, fibrous

• Common confusion: humans can digest starch (α linkages) but not cellulose (β linkages); herbivores have specialized flora that secrete cellulase to digest cellulose.

🔍 Phospholipids: amphipathic nature

• Amphipathic: has both hydrophobic and hydrophilic parts.
  • Hydrophilic head (phosphate group) faces water.
  • Hydrophobic tails (fatty acids) face away from water.
• In a bilayer, tails face inward (away from water), heads face outward (toward water).
• Don't confuse: a phosphate group alone attached to diacylglycerol is phosphatidate (the precursor), not a phospholipid; a phospholipid has an alcohol-modified phosphate group.

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📊 Why macromolecules matter

📊 Energy and nutrition

• Carbohydrates: provide 4.3 Kcal per gram; primary energy source (especially glucose for ATP production).
  • Fiber (insoluble cellulose) promotes regular bowel movement, regulates blood glucose consumption, removes excess cholesterol, and may reduce colon cancer risk.
  • Whole grains and vegetables provide a feeling of fullness.
  • Don't confuse: eliminating carbohydrates is not the best way to lose weight; a balanced diet with whole grains, fruits, vegetables, lean meat, exercise, and water is more sensible.
• Fats: provide 9 Kcal per gram (less desirable ratio than carbohydrates).
  • Long-term energy storage, insulation, and vitamin absorption (many vitamins are fat soluble).
  • "Healthy" fats should be consumed in moderate amounts regularly.
• Proteins: essential for structure, regulation, and catalysis; broken down by enzymes in digestion to provide energy for cellular activities.

📊 Structural and functional roles

• Carbohydrates: structural support in plants (cellulose in cell walls) and arthropods (chitin in exoskeletons and fungal cell walls).
• Lipids: insulation (e.g., aquatic mammals' fur), water repellency (waxes on bird feathers and plant leaves), and membrane structure (phospholipids form the bilayer).
• Proteins: diverse functions including enzymes (catalyze reactions), hormones (signaling), structural components (cytoskeleton, collagen), transport (hemoglobin), defense (antibodies), and muscle contraction (actin, myosin).
• Cholesterol: necessary for membrane fluidity, precursor to hormones and Vitamin D, and bile salt production.

📊 Digestion and absorption

• Enzymes hydrolyze macromolecules into smaller molecules for absorption:
  • Carbohydrates → glucose and other monosaccharides.
  • Proteins → amino acids.
  • Lipids → fatty acids and glycerol.
• Cells absorb these smaller molecules in the intestine to use for energy and building new macromolecules.

🧭 Overview

🧠 One-sentence thesis

A protein's unique amino acid sequence determines its three-dimensional structure through four levels of organization (primary, secondary, tertiary, and quaternary), and even a single amino acid change can dramatically alter function and cause disease.

📌 Key points (3–5)

• Four levels of structure: primary (sequence), secondary (local folding), tertiary (3D shape), and quaternary (multiple subunits) all contribute to final protein shape.
• Structure determines function: an enzyme's active site must maintain its shape to bind substrates; altered structure means lost function.
• Single amino acid substitutions matter: sickle cell anemia results from just one amino acid change out of ~600 in hemoglobin, showing how critical sequence is.
• Common confusion: polypeptide vs protein—a polypeptide is a polymer of amino acids, while a protein may include multiple polypeptides, prosthetic groups, and has a distinct shape and function.
• Denaturation can be reversible or irreversible: changes in temperature, pH, or chemicals can unfold proteins, sometimes permanently destroying function.

🧬 Primary structure: the amino acid sequence

🔤 What primary structure means

Primary structure: the unique sequence of amino acids in a polypeptide chain.

• The gene encoding the protein determines this sequence.
• Every polypeptide has an N-terminal (free amino group) and a C-terminal (free carboxyl group).
• Example: insulin has two chains (A and B) linked by disulfide bonds; chain A starts with glycine (N-terminal) and ends with asparagine (C-terminal).

🧬 Why sequence matters: sickle cell anemia

• Hemoglobin is made of two alpha and two beta chains, each ~150 amino acids (total ~600 amino acids).
• In sickle cell anemia, one amino acid substitution occurs in the beta chain: valine replaces glutamic acid at position 7.
• This single change (caused by one nucleotide point mutation out of 1800 bases) causes:
  • Hemoglobin molecules to form long fibers
  • Red blood cells to distort from disc-shaped to crescent "sickle" shape
  • Blood vessel clogging and serious health problems (breathlessness, dizziness, headaches, abdominal pain)
• Don't confuse: the structural difference is tiny (1 out of 600 amino acids), but the functional impact is enormous.

🧬 Evolutionary evidence from cytochrome c

• Cytochrome c is a protein in the electron transport chain (cellular respiration) located in mitochondria.
• It has changed very little over millions of years because its role in energy production is crucial.
• Human cytochrome c has 104 amino acids; 37 appear in the same position across all species studied, suggesting a common ancestor.
• Sequence differences reveal evolutionary relationships:
  • Human vs chimpanzee: zero amino acid differences
  • Human vs rhesus monkey: one amino acid difference
  • Human vs yeast: difference at position 44

🌀 Secondary structure: local folding patterns

🌀 Two main types

Secondary structure: the local folding of the polypeptide in some regions.

The most common secondary structures are:

Structure	Description	Key feature
α-helix	Helical coil	3.6 amino acid residues per turn; R groups protrude outward
β-pleated sheet	Folded sheet	Segments align parallel or antiparallel; R groups extend above and below folds

🔗 How they form

• Both structures are held together by hydrogen bonds.
• Hydrogen bonds form between:
  • The oxygen atom in the carbonyl group of one amino acid
  • Another amino acid that is four amino acids farther along the chain (in α-helix)
• In β-pleated sheets, hydrogen bonds form between the partially positive nitrogen in the amino group and the partially negative oxygen in the carbonyl group of the peptide backbone.
• These structures play important structural roles in most globular and fibrous proteins.

🎯 Tertiary structure: the 3D shape

🎯 What creates tertiary structure

Tertiary structure: the polypeptide's unique three-dimensional structure.

This structure results from chemical interactions among R groups (side chains):

Interaction type	Description	Role
Hydrophobic interactions	Nonpolar R groups cluster in protein interior	Keep water-fearing groups away from aqueous environment
Ionic bonds	Attraction between oppositely charged R groups	Stabilize structure through electrostatic forces
Hydrogen bonding	Between polar R groups	Weak but numerous stabilizing forces
Disulfide linkages	Covalent bonds between cysteine side chains	The only covalent bond formed during folding; requires oxygen

🎯 Inside vs outside

• Hydrophobic R groups (nonpolar amino acids) lie in the protein's interior.
• Hydrophilic R groups lie on the outside, interacting with the aqueous environment.
• R groups with like charges repel each other; unlike charges attract (ionic bonds).
• Don't confuse: most interactions are weak (hydrogen bonds, ionic, hydrophobic), but disulfide bonds are strong covalent bonds.

⚠️ Loss of shape means loss of function

• All interactions (weak and strong) determine the final 3D shape.
• When a protein loses its three-dimensional shape, it may no longer be functional.
• Example: an enzyme's active site must maintain its shape to bind substrates; if altered by local or overall structural changes, the enzyme cannot bind.

🧩 Quaternary structure: multiple subunits

🧩 When proteins team up

Quaternary structure: the interaction of multiple polypeptide subunits to form the functional protein.

• Some proteins in nature form from several polypeptides (subunits).
• Weak interactions between subunits stabilize the overall structure.

🧩 Examples of quaternary structure

• Insulin (globular protein):
  • Combination of hydrogen bonds and disulfide bonds cause it to clump into a ball shape
  • Starts as a single polypeptide
  • Loses some internal sequences after post-translational modification
  • Disulfide linkages hold remaining chains together
• Silk (fibrous protein):
  • Has a β-pleated sheet structure
  • Result of hydrogen bonding between different chains

🔄 Post-translational modifications and protein folding

✂️ After synthesis: modifications

• After protein synthesis (translation), most proteins are modified.
• These are called post-translational modifications.
• Common modifications include:
  • Cleavage (cutting)
  • Phosphorylation (adding phosphate groups)
  • Adding other chemical groups
• Only after these modifications is the protein completely functional.
• Don't confuse: the terms polypeptide and protein are sometimes used interchangeably, but technically a polypeptide is a polymer of amino acids, whereas protein refers to polypeptides that may have combined, have prosthetic groups, distinct shape, and unique function.

🧲 Protein folding and chaperones

Chaperones (or chaperonins): protein helpers that associate with the target protein during the folding process.

• Protein folding is critical to function.
• Scientists originally thought proteins folded themselves.
• Recently discovered that proteins often receive assistance from chaperones.
• Chaperones act by preventing polypeptide aggregation during folding.

🔥 Denaturation: losing the shape

Denaturation: when a protein loses its three-dimensional shape without losing its primary sequence.

Causes of denaturation:

• Changes in temperature
• Changes in pH
• Exposure to chemicals

Reversible denaturation:

• Often reversible because the primary structure (sequence) is conserved
• If the denaturing agent is removed, the protein can resume its function

Irreversible denaturation:

• Sometimes denaturation is irreversible, leading to permanent loss of function
• Example: frying an egg—albumin protein in liquid egg white denatures when placed in a hot pan and cannot refold

🌡️ Exceptions and special cases

• Not all proteins denature at high temperatures.
• Example: bacteria that survive in hot springs have proteins that function near boiling temperatures.
• The stomach is very acidic (low pH) and denatures proteins as part of digestion, but the stomach's digestive enzymes retain their activity under these conditions.

🧭 Overview

🧠 One-sentence thesis

Nucleic acids—DNA and RNA—are the most important macromolecules for life's continuity because they carry the cell's genetic blueprint and instructions for functioning, with DNA storing genetic information and RNA primarily involved in protein synthesis.

📌 Key points (3–5)

• What nucleic acids are: macromolecules built from nucleotide monomers; the two main types are DNA and RNA.
• DNA's role: stores genetic material in all living organisms and controls cellular activities by turning genes "on" or "off."
• RNA's role: mainly involved in protein synthesis; mRNA carries messages from DNA, while rRNA, tRNA, and microRNA participate in protein synthesis and regulation.
• Common confusion: DNA vs RNA structure—DNA uses deoxyribose sugar and thymine (T), while RNA uses ribose sugar and uracil (U) instead of thymine.
• Base pairing rule: in DNA, adenine pairs with thymine and guanine pairs with cytosine; this complementarity is critical for replication and function.

🧬 Nucleotide building blocks

🧩 What a nucleotide is

Nucleotide: the monomer unit of nucleic acids, composed of three components—a nitrogenous base, a pentose (five-carbon) sugar, and a phosphate group.

• Nucleotides combine to form a polynucleotide (DNA or RNA).
• The base attaches to the 1′ position of the sugar; the phosphate attaches to the 5′ position.
• When a polynucleotide forms, the incoming nucleotide's 5′ phosphate attaches to the 3′ hydroxyl group at the end of the growing chain, creating a 5′–3′ phosphodiester linkage.
• This linkage does not form by simple dehydration; it involves removing two phosphate groups.
• A polynucleotide may have thousands of such linkages.

🍬 The two pentose sugars

Sugar	Found in	Key difference
Deoxyribose	DNA	Has an H at the 2′ position
Ribose	RNA	Has an OH at the 2′ position

• The carbon atoms of the sugar are numbered 1′, 2′, 3′, 4′, and 5′ (read as "one prime," etc.).
• Don't confuse: the prime notation distinguishes sugar carbons from base carbons, which are numbered without primes.

🔬 Nitrogenous bases: purines and pyrimidines

Purines: nitrogenous bases with a double carbon-nitrogen ring structure (adenine and guanine).

Pyrimidines: nitrogenous bases with a single carbon-nitrogen ring structure (cytosine, thymine, and uracil).

• Bases are called "bases" because they contain an amino group that can bind an extra hydrogen, making the environment more basic.
• DNA contains: adenine (A), guanine (G), cytosine (C), and thymine (T).
• RNA contains: adenine (A), guanine (G), cytosine (C), and uracil (U).
• Example: RNA substitutes uracil for thymine; this is a key structural difference between DNA and RNA.

🧬 DNA structure and function

🌀 The double helix

• DNA has a double-helix structure with the sugar and phosphate on the outside (forming the backbone) and the nitrogenous bases stacked in the interior like staircase steps.
• Hydrogen bonds bind the base pairs to each other.
• Every base pair is separated from the next by 0.34 nm.
• The two strands run in opposite directions (antiparallel orientation): one strand's 5′ carbon end faces the other strand's 3′ carbon end.
• This antiparallel orientation is important for DNA replication and nucleic acid interactions.

🔗 Base complementary rule

Base complementary rule: only certain purines can pair with certain pyrimidines—adenine pairs with thymine, and guanine pairs with cytosine.

• This means the two DNA strands are complementary to each other.
• Example: if one strand is AATTGGCC, the complementary strand is TTAACCGG.
• During DNA replication, each strand copies itself, resulting in a daughter DNA double helix containing one parental strand and one newly synthesized strand.
• Don't confuse: complementary does not mean identical; it means the bases pair according to the rule (A with T, G with C).

🧬 DNA's role in the cell

• DNA is the genetic material in all living organisms, from single-celled bacteria to multicellular mammals.
• In eukaryotes, DNA is in the nucleus and in organelles (chloroplasts and mitochondria).
• In prokaryotes, DNA is not enclosed in a membranous envelope.
• The cell's entire genetic content is its genome; the study of genomes is genomics.
• In eukaryotic cells, DNA forms a complex with histone proteins to form chromatin, the substance of eukaryotic chromosomes.
• A chromosome may contain tens of thousands of genes.
• Many genes contain information to make protein products; other genes code for RNA products.
• DNA controls all cellular activities by turning genes "on" or "off."
• DNA molecules never leave the nucleus; they use an intermediary (messenger RNA) to communicate with the rest of the cell.

🧪 RNA structure and roles

🧬 RNA structure

• RNA is usually single-stranded and is made of ribonucleotides linked by phosphodiester bonds.
• A ribonucleotide contains ribose (the pentose sugar), one of four nitrogenous bases (A, U, G, C), and the phosphate group.
• RNA uses uracil (U) instead of thymine (T).
• Example: if a DNA strand has the sequence AATTGCGC, the complementary RNA sequence is UUAACGCG.

📬 Four major types of RNA

RNA type	Role
Messenger RNA (mRNA)	Carries the message from DNA; controls cellular activities
Ribosomal RNA (rRNA)	Involved in protein synthesis
Transfer RNA (tRNA)	Involved in protein synthesis
MicroRNA (miRNA)	Involved in protein synthesis regulation

🔄 How mRNA works

• If a cell needs to synthesize a certain protein, the gene for that product turns "on" and messenger RNA is synthesized in the nucleus.
• The RNA base sequence is complementary to the DNA's coding sequence from which it has been copied.
• In the cytoplasm, mRNA interacts with ribosomes and other cellular machinery.
• A ribosome has two parts: a large subunit and a small subunit; the mRNA sits between them.
• A tRNA molecule recognizes a codon (a set of three bases) on the mRNA, binds to it by complementary base pairing, and adds the correct amino acid to the growing peptide chain.
• Don't confuse: mRNA does not make proteins directly; it carries instructions that ribosomes and tRNA use to assemble proteins.

🧬 Nucleic acids and the continuity of life

🧬 Why nucleic acids are the most important macromolecules

• Nucleic acids carry the cell's genetic blueprint and carry instructions for its functioning.
• This makes them critical for the continuity of life—genetic information passes from one generation to the next through DNA.
• DNA stores the information; RNA executes the instructions by directing protein synthesis.
• Example: when a gene is turned "on," the DNA sequence is transcribed into mRNA, which then directs the synthesis of a specific protein needed by the cell.

🧭 Overview

🧠 One-sentence thesis

DNA carries genetic information in a double-stranded, antiparallel structure, while RNA—usually single-stranded—translates that information into proteins through transcription and translation, forming the Central Dogma of Life.

📌 Key points (3–5)

• DNA structure: double helix with antiparallel strands (one 5′→3′, the other 3′→5′), phosphate backbone outside, bases inside; adenine pairs with thymine, guanine pairs with cytosine.
• RNA structure and types: single-stranded, uses ribose and uracil (instead of thymine); four major types—mRNA, rRNA, tRNA, and miRNA—each with distinct roles in protein synthesis.
• Information flow: DNA → RNA → protein (Central Dogma); transcription produces RNA from DNA, translation produces protein from RNA.
• Common confusion: DNA vs RNA bases—DNA uses thymine (T), RNA uses uracil (U); both use adenine, guanine, and cytosine.
• Key mechanism: base pairing ensures complementary sequences; tRNA recognizes mRNA codons by complementary pairing to deliver the correct amino acid.

🧬 DNA structure and base pairing

🧬 Double helix architecture

DNA (deoxyribonucleic acid): a double-helical molecule that carries the cell's hereditary information.

• Antiparallel strands: the two strands run in opposite directions—one 5′ to 3′, the other 3′ to 5′.
• Backbone and bases: phosphate backbone is on the outside; nitrogenous bases are in the middle.
• The structure is stabilized by hydrogen bonds between complementary bases.

🔗 Base pairing rules

Base on one strand	Pairs with	Bond type
Adenine (A)	Thymine (T)	Hydrogen bonds
Guanine (G)	Cytosine (C)	Hydrogen bonds

• Why it matters: complementary pairing ensures accurate copying during replication and transcription.
• Example: if one strand is AATTGCGC, the complementary strand is TTAACGCG.
• Don't confuse: mutations can disrupt pairing—if adenine replaces cytosine, the normal G-C pairing is broken, potentially affecting DNA structure.

🧵 RNA structure and types

🧵 RNA vs DNA: key differences

Ribonucleic acid (RNA): mainly involved in the process of protein synthesis under the direction of DNA; usually single-stranded and comprised of ribonucleotides.

Feature	DNA	RNA
Function	Carries genetic information	Involved in protein synthesis
Location	Remains in the nucleus	Leaves the nucleus
Structure	Double helix	Usually single-stranded
Sugar	Deoxyribose	Ribose
Pyrimidines	Cytosine, thymine	Cytosine, uracil
Purines	Adenine, guanine	Adenine, guanine

• Key difference: RNA uses uracil (U) instead of thymine (T).
• Even though RNA is single-stranded, most types show intramolecular base pairing between complementary sequences, creating predictable three-dimensional structures essential for function.

📬 Messenger RNA (mRNA)

mRNA: carries the message from DNA, which controls all cellular activities in a cell.

• How it works: when a cell needs a certain protein, the gene "turns on" and mRNA is synthesized in the nucleus.
• The RNA base sequence is complementary to the DNA coding sequence from which it was copied.
• Example: if DNA has AATTGCGC, the complementary mRNA is UUAACGCG (note U replaces T).
• In the cytoplasm, mRNA interacts with ribosomes and other cellular machinery.
• Codon reading: mRNA is read in sets of three bases (codons); each codon codes for a single amino acid.

🏗️ Ribosomal RNA (rRNA)

rRNA: a major constituent of ribosomes on which the mRNA binds.

• Two key roles:
  1. Ensures proper alignment of mRNA and ribosomes.
  2. Has enzymatic activity (peptidyl transferase) that catalyzes peptide bond formation between two aligned amino acids.
• Example: rRNA acts as both structural scaffold and catalyst during protein synthesis.

🚚 Transfer RNA (tRNA)

tRNA: one of the smallest RNA types (usually 70–90 nucleotides long); carries the correct amino acid to the protein synthesis site.

• How it works: base pairing between tRNA and mRNA allows the correct amino acid to insert into the polypeptide chain.
• A tRNA molecule recognizes a codon on mRNA, binds by complementary base pairing, and adds the correct amino acid to the growing peptide chain.
• Don't confuse: tRNA does not carry genetic information; it delivers amino acids based on mRNA instructions.

🔬 MicroRNA (miRNA)

• The smallest RNA molecules.
• Role: regulate gene expression by interfering with the expression of certain mRNA messages.

🔄 Information flow: the Central Dogma

🔄 Transcription: DNA → RNA

Transcription: the process in which DNA dictates the structure of mRNA.

• DNA serves as a template; mRNA is synthesized with a complementary sequence.
• mRNA is synthesized in the nucleus, then leaves to the cytoplasm.
• Example: DNA sequence AATTGCGC → mRNA sequence UUAACGCG.

🔄 Translation: RNA → Protein

Translation: the process in which RNA dictates the protein's structure.

• mRNA sits between the large and small subunits of a ribosome.
• tRNA recognizes codons on mRNA by complementary base pairing.
• Each codon specifies one amino acid; the ribosome catalyzes peptide bond formation.
• The result is a growing polypeptide chain that folds into a functional protein.

🧬 The Central Dogma

Central Dogma of Life: information flow in an organism takes place from DNA to RNA to protein.

• This holds true for all organisms.
• Exception: the rule has exceptions in connection with viral infections (the excerpt notes this but does not elaborate).
• Why it matters: understanding this flow explains how genetic information is expressed as functional proteins that perform cellular activities.

🧩 Nucleotide building blocks

🧩 DNA nucleotide composition

Nucleotide: monomer of nucleic acids; contains a pentose sugar, one or more phosphate groups, and a nitrogenous base.

• In DNA: the sugar is deoxyribose.
• Nitrogenous bases: adenine (A), thymine (T), guanine (G), cytosine (C).
• Purines: adenine and guanine (larger, two-ring structures).
• Pyrimidines: cytosine and thymine (smaller, one-ring structures).

🧩 RNA nucleotide composition

• In RNA: the sugar is ribose.
• Nitrogenous bases: adenine (A), uracil (U), guanine (G), cytosine (C).
• Key difference: uracil replaces thymine.
• Ribonucleotides are linked by phosphodiester bonds to form the RNA chain.

🔗 Phosphodiester linkage

Phosphodiester: covalent chemical bond that holds together the polynucleotide chains with a phosphate group linking neighboring nucleotides' two pentose sugars.

• This linkage forms the backbone of both DNA and RNA.
• The phosphate backbone is on the outside of the DNA double helix.

🧭 Overview

🧠 One-sentence thesis

Biological macromolecules—carbohydrates, lipids, proteins, and nucleic acids—are built from smaller monomers through dehydration synthesis and broken down through hydrolysis, forming the essential building blocks that make up the majority of a cell's dry mass and enable life processes.

📌 Key points (3–5)

• What biological macromolecules are: large organic molecules necessary for life, built from smaller organic molecules (monomers) that combine into polymers.
• How they are built and broken down: dehydration synthesis joins monomers by removing water; hydrolysis breaks polymers apart by adding water.
• The four major classes: carbohydrates, lipids, proteins, and nucleic acids—each performs different functions in cells.
• Common confusion: dehydration synthesis vs hydrolysis—synthesis removes water to build bonds (requires energy); hydrolysis adds water to break bonds (releases energy).
• Why they matter: these molecules make up most of a cell's dry mass and provide energy, structure, and perform critical cellular functions.

🧱 Atoms and molecules: the building blocks

⚛️ What matter is made of

Matter: anything that occupies space and has mass.

• All matter is composed of elements—98 naturally occurring elements exist.
• Each element has unique qualities that allow them to combine in various ways.

⚛️ Atoms and their components

Atom: the smallest unit of an element that retains all properties of that element.

• Atoms consist of three subatomic particles:

  • Protons: positively charged particles in the nucleus; mass of one amu (atomic mass unit); charge of +1
  • Neutrons: uncharged particles in the nucleus; mass of one amu
  • Electrons: found in orbitals (regions surrounding the nucleus)

• Atomic number: the number of protons in an atom

• Mass number: total number of protons and neutrons in an atom

🔄 Isotopes and ions

Isotopes: atoms that vary in the number of neutrons found in their nuclei.

• Same element, different mass numbers
• Example: Carbon-12 and Carbon-13 have different numbers of neutrons
• Radioisotope: an isotope that emits radiation to form more stable elements

Ion: an atom that has gained or lost electrons, creating a charge.

🔗 Chemical bonds

Electrons can transfer, share, or cause charge disparities between atoms to create bonds:

Bond type	Description	Strength
Ionic bond	Electrons transferred between atoms	Strong
Covalent bond	Electrons shared between atoms	Strong
Nonpolar covalent bond	Electrons shared equally between atoms	Strong
Polar covalent bond	Electrons shared unequally, creating slightly positive and negative regions	Strong
Hydrogen bond	Weak attraction between molecules	Weak
Van der Waals interaction	Very weak interaction between molecules due to temporary charges	Very weak

🎯 Valence shell and the octet rule

Valence shell: the outermost shell of an atom.

Octet rule: atoms are most stable when they hold eight electrons in their outermost shells.

• Atoms may give, take, or share electrons with another atom to achieve a full valence shell
• This is the most stable electron configuration
• Example: Elements in group 1 need to lose electrons; elements in groups 14 and 17 need to gain electrons

💧 Water: essential properties for life

💧 Why water is special

Water has many properties that are critical to maintaining life:

• Polar molecule: allows for forming hydrogen bonds
• Hydrogen bonds allow ions and other polar molecules to dissolve in water
• Therefore, water is an excellent solvent

Solvent: a substance capable of dissolving another substance.

Sphere of hydration: when a polar water molecule surrounds charged or polar molecules, keeping them dissolved and in solution.

🌡️ Temperature regulation

• High heat capacity: it takes considerable added heat to raise water's temperature
  • As temperature rises, hydrogen bonds between water molecules continually break and form anew
  • This allows overall temperature to remain stable, although energy is added to the system

Specific heat capacity: the amount of heat one gram of a substance must absorb or lose to change its temperature by one degree Celsius.

• High heat of vaporization: key to how organisms cool themselves by evaporating sweat

🔗 Cohesion and adhesion

• Cohesive forces: water molecules attract each other

  • Creates surface tension: tension at the surface of a body of liquid that prevents molecules from separating
  • Example: This property allows some insects to walk on water

• Adhesive properties: water molecules attract other substances

  • Example: Water rises inside capillary tubes

🧪 pH and chemical balance

pH scale: scale ranging from zero to 14 that is inversely proportional to the hydrogen ion concentration in a solution.

pH value: a measure of hydrogen ion concentration in a solution.

• pH is one of many chemical characteristics highly regulated in living organisms through homeostasis
• Acids: donate hydrogen ions (H⁺); when added to a solution, pH decreases
• Bases: bind up excess hydrogen ions; when added to a solution, pH increases
• Buffers: molecules that moderate pH changes caused by acids and bases

Don't confuse: Acids donate H⁺ ions, not hydroxide ions (OH⁻); bases accept H⁺ ions or donate OH⁻ ions.

Litmus paper (pH paper): paper treated with a natural water-soluble dye that changes color as the pH of the environment changes, used as a pH indicator.

🌿 Carbon: the foundation of organic molecules

🌿 Why carbon is central to life

Organic molecule: any molecule containing carbon (except carbon dioxide).

The unique properties of carbon make it a central part of biological molecules:

• Carbon has four electrons in its outermost shell
• Can form four bonds with other atoms
• Binds to oxygen, hydrogen, and nitrogen covalently to form many molecules important for cellular function

🔗 Hydrocarbon structures

• Carbon and hydrogen can form hydrocarbon chains or rings
• Substituted hydrocarbon: a hydrocarbon chain or ring containing an atom of another element in place of one of the backbone carbons

🧩 Functional groups

Functional groups: groups of atoms that confer specific properties to hydrocarbon (or substituted hydrocarbon) chains or rings that define their overall chemical characteristics and function.

Common functional groups that can bond with carbon include:

• Hydroxyl
• Phosphate
• Carbonyl

Note: Sodium is not a functional group that bonds with carbon.

🔄 Isomers

Structural isomers: molecules that share a chemical formula but differ in the placement of their chemical bonds.

• Same atoms, different arrangements
• Different structural isomers can have different properties
• Example: Molecules with formulas CH₃CH₂COOH and C₃H₆O₂ could be structural isomers

Other types of isomers:

• Cis-trans isomers: molecules must have a double bond
• Enantiomers: a molecule must have at least four different atoms or groups connected to a central carbon

🧬 Biological macromolecules: the molecules of life

🧬 What biological macromolecules are

Biological macromolecules: large molecules, necessary for life, that are built from smaller organic molecules.

• Four major classes: carbohydrates, lipids, proteins, and nucleic acids
• Each is an important cell component and performs a wide array of functions
• Combined, these molecules make up the majority of a cell's dry mass
• All are organic (contain carbon)
• May also contain hydrogen, oxygen, nitrogen, and additional minor elements

🧱 Monomers and polymers

Monomer: single subunit or building block of a macromolecule.

Polymer: larger molecule formed when monomers combine with each other using covalent bonds.

• Most macromolecules are made from monomers
• Different monomer types can combine in many configurations, giving rise to a diverse group of macromolecules
• Even one kind of monomer can combine in a variety of ways to form several different polymers
• Example: Glucose monomers are the constituents of starch, glycogen, and cellulose

⚗️ Building and breaking down macromolecules

🔨 Dehydration synthesis: building polymers

Dehydration synthesis: a reaction that puts molecules together while losing water.

How it works:

• The hydrogen of one monomer combines with the hydroxyl group of another monomer
• This releases a water molecule as a byproduct
• At the same time, the monomers share electrons and form covalent bonds
• As additional monomers join, this chain of repeating monomers forms a polymer

Key characteristics:

• Involves the formation of new bonds
• Requires energy
• Catalyzed (sped up) by specific enzymes

Example: Two glucose molecules link to form the disaccharide maltose, forming a water molecule in the process.

💧 Hydrolysis: breaking down polymers

Hydrolysis reaction: a chemical reaction that breaks polymers down into monomers by inserting a water molecule across the bond.

How it works:

• A water molecule is inserted across the bond
• Breaking a covalent bond with this water molecule achieves polymer breakdown
• The polymer breaks into two components:
  • One part gains a hydrogen atom (H⁺)
  • The other gains a hydroxyl molecule (OH⁻) from the split water molecule

Key characteristics:

• Breaks bonds
• Releases energy
• Catalyzed by specific enzymes

Example: The disaccharide maltose breaks down to form two glucose monomers by adding a water molecule.

🔄 Dehydration synthesis vs hydrolysis: how to distinguish

Process	Water	Bonds	Energy	Result
Dehydration synthesis	Removes water	Forms new bonds	Requires energy	Builds polymers from monomers
Hydrolysis	Adds water	Breaks bonds	Releases energy	Breaks polymers into monomers

Don't confuse: These reactions are reverse processes—synthesis builds up, hydrolysis breaks down.

🍽️ Digestion: hydrolysis in action

• Catalytic enzymes in the digestive system hydrolyze or break down the food we ingest into smaller molecules
• This allows cells in our body to easily absorb nutrients in the intestine
• A specific enzyme breaks down each macromolecule:
  • Carbohydrates: broken down by amylase, sucrase, lactase, or maltase
  • Proteins: broken down by proteases (such as pepsin and peptidase) and hydrochloric acid
  • Lipids: broken down by lipases
• These broken down macromolecules provide energy for cellular activities

⚙️ Enzyme specificity

• Dehydration and hydrolysis reactions are similar for most macromolecules
• But each monomer and polymer reaction is specific for its class
• Each type of macromolecule requires its own specific enzyme

🧪 Chemical reactions and terminology

🧪 Reactants and products

Reactant: a molecule that takes part in a chemical reaction.

Product: a molecule that is the result of a chemical reaction.

🔄 Reversible reactions

Reversible chemical reaction: a chemical reaction that functions bidirectionally, where products may turn into reactants if their concentration is great enough.

• Reactions can proceed in both directions
• The direction depends on the relative concentrations of reactants and products

🧭 Overview

🧠 One-sentence thesis

Biological macromolecules are built from monomers through dehydration synthesis and broken down by hydrolysis, with carbohydrates serving as a major class that provides energy, structural support, and storage in living organisms.

📌 Key points (3–5)

• Polymer formation and breakdown: monomers join via dehydration synthesis (releasing water) to form polymers; hydrolysis (adding water) breaks polymers back into monomers.
• Carbohydrate classification: carbohydrates are classified into monosaccharides (simple sugars), disaccharides (two sugars), and polysaccharides (long chains).
• Structural vs functional roles: some carbohydrates provide energy (glucose, starch, glycogen), while others provide structural support (cellulose in plants, chitin in arthropods).
• Common confusion—alpha vs beta linkages: α and β refer to the position of the hydroxyl group on carbon-1; α linkages (starch, glycogen) are digestible by humans, but β linkages (cellulose) require specialized enzymes.
• Isomers matter: glucose, galactose, and fructose share the same formula (C₆H₁₂O₆) but differ in structure, leading to different properties and functions.

🔗 Polymer formation and breakdown

🔗 Dehydration synthesis (building polymers)

Dehydration synthesis: monomers share electrons and form covalent bonds, releasing a water molecule in the process.

• As monomers join, they form a repeating chain called a polymer.
• The reaction removes one hydrogen (H⁺) from one monomer and one hydroxyl group (OH⁻) from another, combining them into water (H₂O).
• Different monomer types and configurations produce diverse macromolecules.
• Example: glucose monomers can form starch, glycogen, or cellulose depending on how they link.

💧 Hydrolysis (breaking down polymers)

Hydrolysis: a chemical reaction that breaks a polymer into monomers by inserting a water molecule across the bond.

• The polymer splits into two parts: one gains H⁺, the other gains OH⁻ from the water molecule.
• Hydrolysis is the reverse of dehydration synthesis.
• Example: the disaccharide maltose breaks down into two glucose monomers by adding water.

⚡ Energy and enzymes

• Dehydration reactions require energy and form new bonds.
• Hydrolysis reactions break bonds and release energy.
• Specific enzymes catalyze (speed up) these reactions for each macromolecule class:
  • Amylase, sucrase, lactase, maltase → break down carbohydrates
  • Proteases (pepsin, peptidase) and hydrochloric acid → break down proteins
  • Lipases → break down lipids
• In digestion, enzymes hydrolyze food into smaller molecules that cells can absorb in the intestine, providing energy for cellular activities.

🍬 Monosaccharides: simple sugars

🍬 What monosaccharides are

Monosaccharides (mono- = "one"; sacchar- = "sweet"): simple sugars, the most common of which is glucose.

• The stoichiometric formula is (CH₂O)ₙ, where n is the number of carbons.
• The ratio of carbon to hydrogen to oxygen is 1:2:1.
• The term "carbohydrate" comes from carbon ("carbo") and water components ("hydrate").
• Most monosaccharide names end in -ose.

🔢 Classification by structure

Monosaccharides are classified by:

1. Carbonyl group position:

   • Aldose: aldehyde group (R-CHO) at the end of the carbon chain
   • Ketose: ketone group (RC(=O)R') in the middle of the carbon chain

2. Number of carbons:

   • Trioses: three carbons
   • Pentoses: five carbons
   • Hexoses: six carbons

🔄 Ring vs linear forms

• In aqueous solutions, monosaccharides usually exist in ring forms, though they can also be linear chains.
• When a five- or six-carbon sugar forms a ring, the hydroxyl group (OH) around carbon-1 (the anomeric carbon) can be in two positions:
  • Alpha (α): OH below the ring plane
  • Beta (β): OH above the ring plane
• Example: glucose forms a six-membered ring; fructose and ribose form five-membered rings.

🧬 Common monosaccharides and isomers

Monosaccharide	Formula	Type	Role
Glucose	C₆H₁₂O₆	Aldose, hexose	Main energy source; releases energy during cellular respiration to make ATP
Galactose	C₆H₁₂O₆	Aldose, hexose	Part of lactose (milk sugar)
Fructose	C₆H₁₂O₆	Ketose, hexose	Found in sucrose and fruit

• Isomers: glucose, galactose, and fructose all have the same chemical formula but differ in the arrangement of functional groups around asymmetric carbons.
• Don't confuse: same formula ≠ same structure or function.

🍭 Disaccharides: two-sugar units

🍭 Formation via glycosidic bonds

Disaccharides (di- = "two"): formed when two monosaccharides undergo a dehydration reaction.

• One monosaccharide's hydroxyl group (OH) combines with another's hydrogen (H), releasing water and forming a covalent bond.
• This bond is called a glycosidic bond (or glycosidic linkage).
• Glycosidic bonds can be alpha (OH on carbon-1 below the ring plane) or beta (OH on carbon-1 above the ring plane).

🥛 Common disaccharides

Disaccharide	Monomers	Where found
Lactose	Glucose + galactose	Milk (milk sugar)
Maltose	Glucose + glucose	Malt (grain sugar)
Sucrose	Glucose + fructose	Table sugar

• Example: sucrose forms when glucose (carbon-1) links to fructose (carbon-2) via a glycosidic bond, releasing water.

🌾 Polysaccharides: long chains for storage and structure

🌾 What polysaccharides are

Polysaccharide (poly- = "many"): a long chain of monosaccharides linked by glycosidic bonds.

• Chains may be branched or unbranched.
• Molecular weight can exceed 100,000 daltons depending on the number of monomers.
• Different types of monosaccharides can be included.

🌽 Starch: plant energy storage

• Starch is how plants store excess glucose beyond immediate energy needs.
• Stored in roots, seeds, and other plant parts.
• Composed of two glucose polymers:
  • Amylose: unbranched chains with α 1-4 glycosidic linkages (helical structure)
  • Amylopectin: branched chains with α 1-4 linkages and α 1-6 linkages at branch points
• Humans break down starch with enzymes (e.g., amylase in saliva) into maltose and glucose, which cells absorb for energy.
• Example: starch in seeds provides food for the plant embryo during germination and serves as a food source for humans and animals.

🥩 Glycogen: animal energy storage

• Glycogen is the animal equivalent of starch; it stores glucose in humans and other vertebrates.
• Highly branched molecule, usually stored in liver and muscle cells.
• When blood glucose levels drop, glycogen breaks down (glycogenolysis) to release glucose.

🌲 Cellulose: plant structural support

• Cellulose is the most abundant natural biopolymer; it makes up most of a plant's cell wall.
• Provides structural support; wood and paper are mostly cellulosic.
• Composed of glucose monomers linked by β 1-4 glycosidic bonds.
• Every other glucose monomer is flipped, resulting in a linear, fibrous structure with high tensile strength and rigidity.
• Human digestion: humans cannot break down β 1-4 linkages because we lack the enzyme cellulase.
• Herbivores: cows, koalas, buffalos, and termites have specialized bacteria/protists in their digestive systems that secrete cellulase, allowing them to digest cellulose and use it as an energy source.

🐝 Chitin: arthropod structural support

• Chitin is a polysaccharide containing nitrogen; it forms the exoskeleton of arthropods (insects, crustaceans).
• Made of repeating N-acetyl-β-d-glucosamine units (a modified sugar).
• Also a major component of fungal cell walls.
• Example: the hard outer shell of a bee is made of chitin.

🔍 Key distinctions and common confusions

🔍 Alpha vs beta linkages

Linkage type	Position of OH on carbon-1	Examples	Digestible by humans?
Alpha (α)	Below the ring plane	Starch, glycogen	Yes (with amylase)
Beta (β)	Above the ring plane	Cellulose	No (requires cellulase)

• Don't confuse: the same monomer (glucose) can form very different polymers depending on linkage type.
• α linkages → digestible energy sources; β linkages → structural materials humans cannot digest.

🔍 Isomers with the same formula

• Glucose, galactose, and fructose all have C₆H₁₂O₆ but differ in functional group arrangement.
• Glucose and galactose are aldoses; fructose is a ketose.
• This structural difference leads to different chemical properties and biological roles.

🔍 Storage vs structure

Function	Carbohydrate	Organism	Linkage
Energy storage	Starch	Plants	α 1-4, α 1-6
Energy storage	Glycogen	Animals	α 1-4, α 1-6 (more branched)
Structural support	Cellulose	Plants	β 1-4
Structural support	Chitin	Arthropods, fungi	β linkages with nitrogen

• Don't confuse: both starch and cellulose are made of glucose, but their linkages and functions are completely different.

🧭 Overview

🧠 One-sentence thesis

Cellulose and chitin are structural polysaccharides with specialized linkages that give them rigidity, while carbohydrates serve as energy sources and fiber, and lipids function as long-term energy storage, insulation, and membrane components.

📌 Key points (3–5)

• Cellulose structure: glucose monomers linked by β 1-4 glycosidic bonds in unbranched chains, with every other monomer flipped, creating rigidity and high tensile strength.
• Digestion distinction: human enzymes cannot break β 1-4 linkages, but herbivores use specialized bacteria/protists that secrete cellulase to digest cellulose.
• Carbohydrate benefits: provide 4.3 Kcal/g energy, fiber for bowel health and cholesterol removal, and immediate energy via glucose breakdown into ATP.
• Lipid diversity: fats store long-term energy, provide insulation, and include fats, oils, waxes, phospholipids, and steroids.
• Common confusion: saturated vs unsaturated fats—saturated have only single bonds and pack tightly (solid at room temperature), unsaturated have double bonds causing kinks (liquid at room temperature).

🧬 Structural polysaccharides

🧬 Cellulose structure and properties

Cellulose: glucose monomers linked in unbranched chains by β 1-4 glycosidic linkages, with every glucose monomer flipped relative to the next one, resulting in a linear, fibrous structure.

• The flipping pattern means every other glucose monomer is upside down.
• Monomers pack tightly as extended long chains.
• This arrangement gives cellulose its rigidity and high tensile strength—critical for plant cell structure.

🦠 Cellulose digestion mechanisms

Why humans cannot digest cellulose:

• Human digestive enzymes cannot break down the β 1-4 linkage.

How herbivores digest cellulose:

• Herbivores (cows, koalas, buffalos) have specialized flora in their stomach.
• Certain bacteria and protists in the rumen secrete the enzyme cellulase.
• The appendix of grazing animals also contains cellulose-digesting bacteria.
• Cellulases break cellulose into glucose monomers that animals use as an energy source.
• Termites also digest cellulose through other organisms in their bodies that secrete cellulases.

Example: A cow can digest plant material rich in cellulose because bacteria in its rumen produce cellulase, whereas a human eating the same plant material cannot extract glucose from the cellulose.

🦗 Chitin in arthropods and fungi

Chitin: a polysaccharide-containing nitrogen, made of repeating N-acetyl-β-d-glucosamine units (a modified sugar).

Functions:

• Forms the exoskeleton in arthropods (insects, crustaceans, etc.), protecting internal body parts.
• Major component of fungal cell walls.

Key distinction: Fungi are neither animals nor plants; they form their own kingdom in the domain Eukarya.

🍞 Carbohydrate functions and benefits

⚡ Energy provision

Caloric value:

• A gram of carbohydrate provides 4.3 Kcal.
• For comparison, fats provide 9 Kcal/g (a less desirable ratio for immediate energy needs).

Immediate energy source:

• Glucose breaks down during cellular respiration, producing ATP (the cell's energy currency).
• Without carbohydrates, availability of "instant energy" is reduced.

🧵 Fiber benefits

What fiber is:

• The insoluble part of carbohydrates, mostly cellulose.

Health functions:

Function	How it works
Bowel health	Promotes regular bowel movement by adding bulk
Blood glucose regulation	Regulates the rate of blood glucose consumption
Cholesterol removal	Binds to cholesterol in the small intestine, prevents entry into bloodstream, exits via feces
Cancer protection	Reduces occurrence of colon cancer
Satiety	Meals with whole grains and vegetables give a feeling of fullness

🥗 Dietary considerations

Common misconception about carbohydrates:

• Some diets claim carbohydrates are bad and should be avoided for weight loss.
• Some completely forbid carbohydrate consumption, claiming faster weight loss.

Why carbohydrates are important:

• Have been part of human diet for thousands of years (wheat, rice, corn in ancient civilizations).
• Should be part of a well-balanced diet supplemented with proteins, vitamins, and fats.
• Eliminating carbohydrates reduces instant energy availability.

Sensible approach to weight loss:

• Low-calorie diet rich in whole grains, fruits, vegetables, and lean meat.
• Combined with plenty of exercise and water.
• Not eliminating carbohydrates entirely.

🧈 Lipid structure and types

🧈 What lipids are

Lipids: a diverse group of compounds that are largely nonpolar in nature, including mostly nonpolar carbon–carbon or carbon–hydrogen bonds.

Key property:

• Nonpolar molecules are hydrophobic ("water fearing") or insoluble in water.

Major types:

• Fats, oils, waxes, phospholipids, and steroids.

🔋 Lipid functions

Function	Description
Energy storage	Cells store energy for long-term use in the form of fats
Insulation	Provide insulation from environment for plants and animals
Water protection	Help keep aquatic birds and mammals dry by forming protective layer over fur/feathers
Hormones	Building blocks of many hormones
Membranes	Important constituent of all cellular membranes

Example: Lipids in aquatic mammals' fur protect them from water because of their water-repellent hydrophobic nature.

🥑 Fats and oils composition

Basic structure:

A fat molecule consists of two main components—glycerol and fatty acids.

• Glycerol: an organic compound (alcohol) with three carbons, five hydrogens, and three hydroxyl (OH) groups.
• Fatty acids: have a long chain of hydrocarbons with a carboxyl group attached.
• Number of carbons in fatty acid: 4 to 36 (most common: 12–18 carbons).

How they join:

• Fatty acids attach to each of glycerol's three carbons with an ester bond through an oxygen atom.
• Three water molecules are released during this dehydration reaction.
• The result is called triacylglycerol or triglyceride.

🔗 Saturated vs unsaturated fatty acids

Saturated fatty acids:

If there are only single bonds between neighboring carbons in the hydrocarbon chain, the fatty acid is saturated.

• Saturated with hydrogen (maximum number of hydrogen atoms attached).
• Example: stearic acid, palmitic acid (common in meat), butyric acid (common in butter).
• Long straight fatty acids with single bonds pack tightly.
• Solid at room temperature.
• Usually animal fats.

Unsaturated fatty acids:

When the hydrocarbon chain contains a double bond, the fatty acid is unsaturated.

• Example: oleic acid.
• Most unsaturated fats are liquid at room temperature (called oils).
• Monounsaturated: one double bond (e.g., olive oil).
• Polyunsaturated: more than one double bond (e.g., canola oil).
• Usually of plant origin.

Don't confuse: The difference is not just physical state—it's about chemical structure (single vs double bonds) which determines packing and therefore physical state.

🔄 Cis vs trans configuration

Cis configuration:

• Hydrogens are present in the same plane around the double bond.
• Causes a bend or "kink" in the chain.
• Prevents fatty acids from packing tightly.
• Keeps them liquid at room temperature.
• Examples: olive oil, corn oil, canola oil, cod liver oil.

Trans configuration:

• Hydrogen atoms are on two different planes around the double bond.
• Straighter chain structure.

Health implications:

Fat type	Effect on health
Unsaturated (cis)	Help lower blood cholesterol levels
Saturated	Contribute to plaque formation in arteries
Trans fats	Increase LDL ("bad" cholesterol), lead to plaque deposition, result in heart disease

⚠️ Trans fats and hydrogenation

How trans fats are made:

• Food industry artificially hydrogenates oils to make them semi-solid.
• Hydrogen gas is bubbled through oils to solidify them.
• During hydrogenation, cis double bonds may convert to trans double bonds.
• Examples: margarine, some peanut butters, shortening.

Why they matter:

• Increase in trans fats may lead to higher LDL levels.
• Can lead to plaque deposition in arteries and heart disease.
• Many fast food restaurants have banned trans fats.
• Food labels are required to display trans fat content.

🐟 Omega fatty acids

Essential fatty acids: those that the human body requires but does not synthesize, so they must be supplemented through diet.

Omega-3 fatty acids:

• Polyunsaturated fatty acids.
• Called "omega-3" because a double bond connects the third carbon from the hydrocarbon chain's end to its neighboring carbon.
• The farthest carbon from the carboxyl group is the omega (ω) carbon.
• Examples: alpha-linolenic acid (ALA), eicosapentaenoic acid (EPA), docosahexaenoic acid (DHA).
• Good sources: salmon, trout, tuna.

Health benefits (from research):

• Reduce risk of sudden death from heart attacks.
• Lower triglycerides in blood.
• Decrease blood pressure.
• Prevent thrombosis by inhibiting blood clotting.
• Reduce inflammation.
• May help lower risk of some cancers in animals.

Note: The excerpt mentions omega-6 fatty acid as the only other essential fatty acid known for humans.

🏪 Energy storage in organisms

🐄 Fat storage in mammals

• Mammals store fats in specialized cells called adipocytes.
• In adipocytes, fat globules occupy most of the cell's volume.

🌱 Fat storage in plants

• Plants store fat or oil in many seeds.
• Used as a source of energy during seedling development.

🧭 Overview

🧠 One-sentence thesis

Lipids and proteins are diverse biological macromolecules: lipids serve as energy storage, membrane components, and signaling molecules despite their hydrophobic nature, while proteins perform the most varied functions of all macromolecules through their unique amino acid sequences and three-dimensional shapes.

📌 Key points (3–5)

• Trans fats vs omega fatty acids: artificially hydrogenated trans fats increase "bad" cholesterol and heart disease risk, while omega-3 fatty acids (which the body cannot synthesize) reduce cardiovascular risks and inflammation.
• Phospholipid structure: amphipathic molecules with hydrophobic fatty acid tails and hydrophilic phosphate heads spontaneously form bilayers that comprise cell membranes.
• Protein diversity: proteins have the most diverse range of functions of all macromolecules, including enzymatic, structural, transport, hormonal, and defense roles.
• Amino acid sequence determines function: the sequence and number of amino acids determine a protein's shape, size, and function; changes in temperature, pH, or chemical exposure can denature proteins and destroy function.
• Common confusion: not all lipids look alike—phospholipids and fats have glycerol backbones with fatty acids, but steroids have fused ring structures; they are grouped together because all are hydrophobic and water-insoluble.

🧪 Types of lipids and their roles

🔗 Trans fats and health risks

Trans fats: fats in which the hydrocarbon chain has converted to double bonds in the trans-conformation through artificial hydrogenation.

• Found in margarine, some peanut butters, and shortening.
• Health impact: increase low-density lipoproteins (LDL, "bad" cholesterol), leading to plaque deposition in arteries and heart disease.
• Many fast food restaurants have banned trans fats; food labels must display trans fat content.
• Don't confuse: trans fats are artificially created, not naturally occurring in most foods.

🐟 Omega-3 fatty acids

Essential fatty acids: fatty acids that the human body requires but does not synthesize, so they must be obtained through diet.

• Omega-3 definition: polyunsaturated fatty acids where a double bond connects the third carbon from the hydrocarbon chain's end to its neighboring carbon.
• The farthest carbon from the carboxyl group is the omega (ω) carbon.
• Important omega-3s: alpha-linolenic acid (ALA), eicosapentaenoic acid (EPA), and docosahexaenoic acid (DHA).
• Sources: salmon, trout, and tuna.
• Health benefits:
  • Reduce risk of sudden death from heart attacks
  • Lower blood triglycerides and blood pressure
  • Prevent thrombosis by inhibiting blood clotting
  • Reduce inflammation
  • May help lower risk of some cancers in animals
• Example: A person who does not eat fish must supplement omega-3s through diet because the body cannot make them.

🕯️ Waxes

Wax: lipids composed of long fatty acid chains esterified to long-chain alcohols.

• Cover some aquatic birds' feathers and some plants' leaf surfaces.
• Hydrophobic nature prevents water from sticking to surfaces.

🧱 Phospholipids and membrane structure

🧱 Phospholipid composition

Phospholipids: major plasma membrane constituents that comprise cells' outermost layer.

• Structure: two fatty acids attached to a glycerol or sphingosine backbone (forming diacylglycerol), plus a modified phosphate group on the third carbon.
• A phosphate group alone does not qualify as a phospholipid—it is phosphatidate, the precursor.
• An alcohol modifies the phosphate group.
• Important examples: phosphatidylcholine and phosphatidylserine in plasma membranes.

💧 Amphipathic nature

Amphipathic molecule: a molecule with both a hydrophobic and a hydrophilic part.

• Hydrophobic part: fatty acid chains (the "tail") cannot interact with water.
• Hydrophilic part: phosphate-containing group (the "head") interacts with water.
• This dual nature drives membrane formation.

🧬 Bilayer formation

• In a membrane bilayer:
  • Fatty acid tails face inside, away from water (sequestered in the middle)
  • Phosphate heads face the outside, aqueous side
  • This arrangement forms the matrix structure of all cellular membranes
• Spontaneous assembly: if phospholipids are placed in water, they spontaneously form micelles (hydrophilic heads face outside, fatty acids face interior).
• Phospholipids are responsible for the plasma membrane's dynamic nature.
• Don't confuse: the head is hydrophilic, the tail is hydrophobic—not the reverse.

💍 Steroids

💍 Steroid structure

Steroids: lipids with a fused ring structure, hydrophobic and insoluble in water.

• Structure: four linked carbon rings; many (like cholesterol) have a short tail.
• Do not resemble phospholipids or fats but are grouped with lipids because they are hydrophobic and water-insoluble.
• Many steroids have the –OH functional group, classifying them as alcohols (sterols).

🩺 Cholesterol functions

• Most common steroid: cholesterol.
• Synthesis: the liver synthesizes cholesterol.
• Roles:
  • Precursor to steroid hormones (testosterone, estradiol secreted by gonads and endocrine glands)
  • Precursor to Vitamin D
  • Precursor to bile salts (help emulsify fats for absorption by cells)
  • Component of plasma membranes (sterols in animal cells, phytosterol in plants) found within the phospholipid bilayer
• Despite negative public perception, cholesterol is necessary for proper body functioning.

🧬 Protein structure and diversity

🧬 Protein functions

Proteins: one of the most abundant organic molecules in living systems with the most diverse range of functions of all macromolecules.

Function	Examples	Role
Digestive enzymes	Amylase, lipase, pepsin, trypsin	Catabolize nutrients into monomeric units
Transport	Hemoglobin, albumin	Carry substances in blood or lymph
Structural	Actin, tubulin, keratin	Construct structures like the cytoskeleton
Hormones	Insulin, thyroxine	Coordinate different body systems' activity
Defense	Immunoglobulins	Protect body from foreign pathogens
Contractile	Actin, myosin	Effect muscle contraction
Storage	Legume storage proteins, egg white albumin	Provide nourishment in early development

• Each cell may contain thousands of proteins, each with a unique function.
• All proteins are amino acid polymers arranged in a linear sequence.

🔬 Protein shape and denaturation

• Shape variety: some proteins are globular (e.g., hemoglobin); others are fibrous (e.g., collagen in skin).
• Shape is critical: protein shape determines function.
• Bonds maintaining shape: many different types of chemical bonds maintain protein shape.

Denaturation: permanent changes in protein shape leading to loss of function.

• Causes: changes in temperature, pH, and exposure to chemicals.
• Example: heating an egg white denatures albumin, changing it from clear and liquid to white and solid, permanently destroying its original function.

🧩 Amino acids: protein building blocks

🧩 Amino acid structure

Amino acids: the monomers that comprise proteins.

• Fundamental structure: central carbon atom (alpha carbon) bonded to:
  • An amino group (NH₂)
  • A carboxyl group (COOH)
  • A hydrogen atom
  • An R group (side chain)
• The name "amino acid" reflects the presence of both amino group and carboxyl-acid-group.
• Diversity: 20 common amino acids in proteins, each with a different R group.
• Two rare amino acids discovered recently: selenocysteine and pyrrolysine.

🍽️ Essential amino acids

Essential amino acids: amino acids necessary to build proteins in the body but not produced by the body.

• Must be obtained from diet.
• In humans: nine essential amino acids, including isoleucine, leucine, and cysteine.
• Which amino acids are essential varies from organism to organism.
• Don't confuse: "essential" means "must be obtained from diet," not "most important for function."

⚗️ Chemical nature of amino acids

• The R group determines the amino acid's chemical nature:
  • Nonpolar/hydrophobic: valine, methionine, alanine
  • Polar/hydrophilic: serine, threonine, cysteine
  • Basic (positively charged): lysine, arginine
  • Simple: glycine (R group is just hydrogen)
• Exception: proline has an R group linked to the amino group, forming a ring-like structure—its amino group is not separate from the side chain.
• Notation: single uppercase letter (e.g., V) or three-letter abbreviation (e.g., val for valine).

🔗 Peptide bond formation

Peptide bond: a covalent bond that attaches amino acids to each other, formed by a dehydration reaction.

• Process: one amino acid's carboxyl group combines with the incoming amino acid's amino group, releasing a water molecule.
• Products: linkages form peptides; as more amino acids join, the chain becomes a polypeptide.
• Polypeptide ends: one end has a free amino group (N terminal or amino terminal); the other end has a free carboxyl group.
• Determines function: the sequence and number of amino acids ultimately determine the protein's shape, size, and function.

🧭 Overview

🧠 One-sentence thesis

A protein's function depends critically on its three-dimensional shape, which is determined by its amino acid sequence and stabilized by chemical interactions at four structural levels, and even a single amino acid change can cause serious disease.

📌 Key points (3–5)

• Four levels of structure: primary (amino acid sequence), secondary (local folding patterns), tertiary (3D shape), and quaternary (multiple subunit assembly).
• Shape determines function: enzymes must bind substrates at active sites; if shape changes, the protein may lose function.
• Single amino acid matters: sickle cell anemia results from just one amino acid substitution out of ~600 in hemoglobin—a single nucleotide change in DNA.
• Common confusion: polypeptide vs protein—polypeptide is the amino acid polymer; protein is the functional molecule (may include multiple polypeptides, prosthetic groups, and post-translational modifications).
• Denaturation: changes in temperature, pH, or chemicals can unfold proteins, sometimes reversibly, sometimes permanently destroying function.

🧬 Primary Structure: The Amino Acid Sequence

🔤 What primary structure is

Primary structure: the unique sequence of amino acids in a polypeptide chain.

• Every polypeptide has an N-terminal (free amino group) and a C-terminal (free carboxyl group).
• The gene encoding the protein determines this sequence.
• Example: insulin has two chains (A and B) linked by disulfide bonds; chain A starts with glycine (N-terminal) and ends with asparagine (C-terminal).

🧬 Why sequence matters: sickle cell anemia

• Hemoglobin is made of two alpha and two beta chains, each ~150 amino acids (total ~600 amino acids).
• In sickle cell anemia, one amino acid substitution occurs in the beta chain: valine replaces glutamic acid at position 7.
• This single change (caused by one nucleotide point mutation—1 base out of 1800) dramatically alters hemoglobin structure and function.
• Result: hemoglobin molecules form long fibers, distorting red blood cells into crescent "sickle" shapes that clog blood vessels, causing breathlessness, dizziness, headaches, and abdominal pain.

🧬 Evolutionary evidence: cytochrome c

• Cytochrome c is a protein in the electron transport chain (mitochondria) with a heme prosthetic group.
• It has changed very little over millions of years because its role in cellular energy is crucial.
• Human cytochrome c has 104 amino acids; 37 appear in the same position across all species sequenced—suggesting a common ancestor.
• Comparison shows:
  • Human vs chimpanzee: zero amino acid differences.
  • Human vs rhesus monkey: one amino acid difference.
  • Human vs yeast: difference at position 44.
• Don't confuse: sequence similarity measures evolutionary kinship, not just functional similarity.

🌀 Secondary Structure: Local Folding Patterns

🌀 What secondary structure is

Secondary structure: local folding of the polypeptide in some regions, held in shape by hydrogen bonds.

• The two most common patterns are the α-helix and β-pleated sheet.
• Hydrogen bonds form between the oxygen atom in the carbonyl group of one amino acid and the hydrogen in the amino group of another amino acid.

🌀 α-helix

• Every helical turn contains 3.6 amino acid residues.
• The R groups (side chains) protrude outward from the helix.
• Certain amino acids have a propensity to form α-helices.

🌀 β-pleated sheet

• Hydrogen bonds between atoms on the polypeptide backbone create "pleats."
• R groups extend above and below the folds.
• Pleated segments align parallel or antiparallel to each other.
• Hydrogen bonds form between the partially positive nitrogen (amino group) and partially negative oxygen (carbonyl group).
• Certain amino acids have a propensity to form β-pleated sheets.

🌀 Structural role

• Both α-helix and β-pleated sheet structures are present in most globular and fibrous proteins and play important structural roles.

🎯 Tertiary Structure: Three-Dimensional Shape

🎯 What tertiary structure is

Tertiary structure: the polypeptide's unique three-dimensional structure.

• This structure results from chemical interactions among R groups (side chains) on the amino acids.
• These interactions create the protein's complex 3D shape.

🔗 Types of interactions

Interaction type	Description	Strength
Hydrophobic interactions	Nonpolar R groups cluster in the protein's interior; hydrophilic R groups lie on the outside	Weak
Ionic bonds	R groups with opposite charges attract; like charges repel	Weak
Hydrogen bonds	Between polar R groups	Weak
Disulfide linkages	Covalent bonds between cysteine side chains in the presence of oxygen	Strong (only covalent bond formed during folding)

• All these interactions—weak and strong—determine the protein's final 3D shape.
• When a protein loses its 3D shape, it may no longer be functional.

🎯 Why tertiary structure matters

• The 3D shape is critical to function.
• Example: an enzyme must bind to a specific substrate at an active site; if the active site is altered by local or overall structural changes, the enzyme may be unable to bind the substrate.

🧩 Quaternary Structure and Post-Translational Modifications

🧩 What quaternary structure is

Quaternary structure: the interaction of multiple polypeptide subunits to form the functional protein.

• Some proteins in nature form from several polypeptides (subunits).
• Weak interactions between subunits stabilize the overall structure.
• Example: insulin (globular protein) has hydrogen and disulfide bonds causing it to clump into a ball shape; it starts as a single polypeptide and loses internal sequences after post-translational modification.
• Example: silk (fibrous protein) has a β-pleated sheet structure from hydrogen bonding between different chains.

🧩 Polypeptide vs protein

• Polypeptide: technically a polymer of amino acids.
• Protein: a polypeptide or polypeptides that have combined together, often with bound non-peptide prosthetic groups, a distinct shape, and a unique function.
• Don't confuse: the terms are sometimes used interchangeably, but protein implies functional completeness.

🧩 Post-translational modifications

• After protein synthesis (translation), most proteins are modified.
• Modifications include:
  • Cleavage (cutting).
  • Phosphorylation (adding phosphate groups).
  • Adding other chemical groups.
• Only after these modifications is the protein completely functional.

🔥 Denaturation and Protein Folding

🔥 What denaturation is

Denaturation: loss of protein shape (without losing primary sequence) due to changes in temperature, pH, or exposure to chemicals.

• The protein structure may change, losing its 3D shape while the amino acid sequence remains intact.
• Denaturation is often reversible if the denaturing agent is removed, because the primary structure is conserved—the protein can resume its function.
• Sometimes denaturation is irreversible, leading to permanent loss of function.

🔥 Examples of denaturation

• Irreversible: frying an egg—the albumin protein in liquid egg white denatures when placed in a hot pan and cannot refold.
• Reversible conditions: some proteins can refold if conditions return to normal.
• Exceptions: bacteria in hot springs have proteins that function near boiling temperatures; stomach digestive enzymes retain activity in very acidic (low pH) conditions even though the stomach denatures food proteins.

🧬 Protein folding helpers

• Scientists originally thought proteins folded themselves.
• Recent research shows proteins often receive assistance from chaperones (or chaperonins).
• Chaperones associate with the target protein during folding and prevent polypeptide aggregation.
• Don't confuse: chaperones assist folding but do not determine the final structure—the amino acid sequence does.

🧭 Overview

🧠 One-sentence thesis

Nucleic acids—DNA and RNA—are the most important macromolecules for life's continuity because they carry the cell's genetic blueprint and instructions for all cellular functions.

📌 Key points (3–5)

• What nucleic acids are: macromolecules built from nucleotide monomers that carry genetic information and direct protein synthesis.
• Two main types: DNA (deoxyribonucleic acid) stores genetic information; RNA (ribonucleic acid) mainly executes protein synthesis.
• Structural building blocks: every nucleotide has three components—a nitrogenous base, a pentose sugar, and a phosphate group.
• Common confusion: DNA vs RNA—DNA uses deoxyribose sugar and thymine (T); RNA uses ribose sugar and uracil (U) instead of T.
• Why structure matters: DNA's double-helix and base-pairing rules enable replication and information transfer; RNA's single-stranded structure allows it to carry messages and assist in protein synthesis.

🧬 Nucleotide building blocks

🧱 What a nucleotide contains

Nucleotide: the monomer unit of nucleic acids, composed of three parts—a nitrogenous base, a pentose (five-carbon) sugar, and one or more phosphate groups.

• The base attaches to the 1′ position of the sugar.
• The phosphate group attaches to the 5′ position of the sugar.
• When nucleotides link together, they form a polynucleotide (DNA or RNA).

🍬 Two types of pentose sugar

Sugar	Found in	Key difference
Deoxyribose	DNA	Has an H (hydrogen) at the 2′ position
Ribose	RNA	Has an OH (hydroxyl group) at the 2′ position

• The carbon atoms in the sugar are numbered 1′ through 5′ (the prime distinguishes them from the base's carbon numbering).
• Example: deoxyribose is "similar in structure to ribose, but it has an H instead of an OH at the 2′ position."

🔤 Nitrogenous bases: purines and pyrimidines

• Purines (double carbon-nitrogen ring structure): adenine (A) and guanine (G).
• Pyrimidines (single carbon-nitrogen ring structure): cytosine (C), thymine (T), and uracil (U).
• Bases are called "nitrogenous" because they contain carbon and nitrogen; they are "bases" because they have an amino group that can bind an extra hydrogen, making the environment more basic.

Base	Type	Found in
Adenine (A)	Purine	DNA and RNA
Guanine (G)	Purine	DNA and RNA
Cytosine (C)	Pyrimidine	DNA and RNA
Thymine (T)	Pyrimidine	DNA only
Uracil (U)	Pyrimidine	RNA only

• Don't confuse: DNA contains A, T, G, and C; RNA contains A, U, G, and C (uracil replaces thymine).

🔗 Phosphodiester linkage

• Nucleotides join by forming a 5′–3′ phosphodiester linkage.
• The 5′ phosphate of the incoming nucleotide attaches to the 3′ hydroxyl group at the end of the growing chain.
• This linkage is not a simple dehydration reaction; it involves removing two phosphate groups.
• A polynucleotide may have thousands of such linkages.

🧬 DNA structure and function

🌀 Double-helix structure

DNA has a double-helix structure with the sugar and phosphate on the outside (forming the backbone) and the nitrogenous bases stacked in the interior like staircase steps.

• The two strands run in opposite directions (antiparallel orientation): one strand runs 5′ to 3′, the other runs 3′ to 5′.
• Each base pair is separated from the next by 0.34 nm.
• Hydrogen bonds bind the base pairs to each other.
• Example: imagine a twisted ladder—the sides are the sugar-phosphate backbone, and the rungs are the base pairs.

🔐 Base complementary rule

• Only certain base pairings are allowed:
  • A (adenine) pairs with T (thymine)
  • G (guanine) pairs with C (cytosine)
• This is called the base complementary rule.
• The two DNA strands are complementary: if one strand is AATTGGCC, the complementary strand is TTAACCGG.
• Don't confuse: "complementary" means the bases match according to pairing rules, not that the sequences are identical.

🔄 DNA replication

• During replication, each strand copies itself.
• The result is a daughter DNA double helix containing one parental strand and one newly synthesized strand.
• The antiparallel orientation is important for replication and nucleic acid interactions.

🧬 DNA's role in the cell

• DNA is the genetic material in all living organisms (from single-celled bacteria to multicellular mammals).
• In eukaryotes, DNA is in the nucleus and in organelles (chloroplasts and mitochondria).
• In prokaryotes, DNA is not enclosed in a membranous envelope.
• The cell's entire genetic content is its genome; the study of genomes is genomics.
• In eukaryotic cells, DNA forms a complex with histone proteins to form chromatin, the substance of eukaryotic chromosomes.
• A chromosome may contain tens of thousands of genes.
• DNA controls all cellular activities by turning genes "on" or "off."

🧬 RNA structure and roles

🧵 RNA structure

• RNA is usually single-stranded (unlike DNA's double helix).
• RNA is composed of ribonucleotides linked by phosphodiester bonds.
• Each ribonucleotide contains:
  • Ribose (the pentose sugar)
  • One of four nitrogenous bases: A, U, G, and C
  • A phosphate group
• Don't confuse: RNA has uracil (U) instead of thymine (T); RNA uses ribose instead of deoxyribose.

📬 Four major types of RNA

RNA type	Full name	Role
mRNA	Messenger RNA	Carries the message from DNA; controls cellular activities
rRNA	Ribosomal RNA	Part of ribosome structure; involved in protein synthesis
tRNA	Transfer RNA	Recognizes codons on mRNA and adds correct amino acids to growing peptide chain
miRNA	MicroRNA	Involved in regulation of protein synthesis

📨 Messenger RNA (mRNA) function

• DNA molecules never leave the nucleus; instead, they use mRNA as an intermediary to communicate with the rest of the cell.
• If a cell needs to synthesize a certain protein, the gene for that product turns "on" and mRNA is synthesized in the nucleus.
• The RNA base sequence is complementary to the DNA coding sequence from which it was copied.
• Example: if the DNA strand is AATTGCGC, the complementary RNA sequence is UUAACGCG (note U replaces T).
• In the cytoplasm, mRNA interacts with ribosomes and other cellular machinery.

🏭 Ribosome and protein synthesis

• A ribosome has two parts: a large subunit and a small subunit.
• The mRNA sits between the two subunits.
• A tRNA molecule recognizes a codon (a set of three bases) on the mRNA.
• The tRNA binds to the codon by complementary base pairing and adds the correct amino acid to the growing peptide chain.
• The mRNA is read in sets of three bases (codons); each codon codes for a single amino acid.

🔬 Protein structure context

🧬 Protein structure levels

• Proteins have four levels of structure: primary, secondary, tertiary, and quaternary.
• Primary structure: the unique sequence of amino acids in a polypeptide chain.
• Secondary structure: local folding patterns (e.g., β-pleated sheets in silk) resulting from hydrogen bonding.
• Tertiary structure: overall three-dimensional shape (e.g., insulin's ball shape from hydrogen and disulfide bonds).
• Quaternary structure: arrangement of multiple polypeptide chains.
• Example: insulin starts as a single polypeptide and loses some internal sequences after forming disulfide linkages; silk has a β-pleated sheet structure from hydrogen bonding between different chains.

🔥 Denaturation and protein folding

Denaturation: the loss of a protein's shape (without losing its primary sequence) due to changes in temperature, pH, or exposure to chemicals.

• Denaturation is often reversible if the primary structure is conserved and the denaturing agent is removed.
• Sometimes denaturation is irreversible, leading to loss of function.
• Example: frying an egg—the albumin protein in liquid egg white denatures irreversibly when placed in a hot pan.
• Don't confuse: not all proteins denature at high temperatures—bacteria in hot springs have proteins that function near boiling; stomach digestive enzymes retain activity in very acidic conditions.

🤝 Chaperones assist folding

• Protein folding is critical to function.
• Scientists originally thought proteins folded themselves; recently they discovered that proteins often receive assistance from chaperones (or chaperonins).
• Chaperones associate with the target protein during folding, prevent polypeptide aggregation, and dissociate once the protein is folded.

🧭 Overview

🧠 One-sentence thesis

DNA carries genetic information in a double-stranded, antiparallel structure, while RNA—usually single-stranded—translates that information into proteins through transcription and translation, following the Central Dogma of Life.

📌 Key points (3–5)

• DNA structure: double helix with antiparallel strands (one 5′→3′, the other 3′→5′), phosphate backbone outside, bases inside; adenine pairs with thymine, guanine pairs with cytosine.
• RNA structure and types: usually single-stranded, contains ribose and uracil (instead of thymine); four major types—mRNA, rRNA, tRNA, and microRNA—each with distinct roles in protein synthesis.
• Information flow: DNA → RNA → protein (Central Dogma); transcription produces mRNA from DNA in the nucleus, translation produces protein from mRNA in the cytoplasm.
• Common confusion: DNA vs RNA bases—DNA has thymine (T), RNA has uracil (U); DNA is double-stranded and stays in the nucleus, RNA is usually single-stranded and leaves the nucleus.
• Key mechanism: base pairing ensures accurate information transfer—DNA to mRNA (complementary), mRNA codons to tRNA (complementary), tRNA to amino acids (correct insertion into polypeptide).

🧬 DNA Structure and Base Pairing

🧬 Double helix architecture

DNA (deoxyribonucleic acid): double-helical molecule that carries the cell's hereditary information.

• Antiparallel strands: the two strands run in opposite directions—one 5′ to 3′, the other 3′ to 5′.
• Backbone and bases: phosphate backbone is on the outside; nitrogenous bases are in the middle.
• The structure keeps genetic information protected inside while the stable backbone provides structural integrity.

🔗 Base pairing rules

• Adenine (A) pairs with thymine (T) via hydrogen bonds.
• Guanine (G) pairs with cytosine (C) via hydrogen bonds.
• These specific pairings ensure accurate replication and transcription.
• Example: if one strand reads AATTGCGC, the complementary strand must read TTAACGCG.

⚠️ Mutation impact

• The excerpt asks: "A mutation occurs, and adenine replaces cytosine. What impact do you think this will have on the DNA structure?"
• Changing a base disrupts normal pairing (e.g., A replacing C means the partner base no longer matches correctly), potentially altering the DNA structure and the information it encodes.

🧵 RNA Types and Roles

🧵 RNA structure basics

Ribonucleic acid (RNA): mainly involved in the process of protein synthesis under the direction of DNA.

• Usually single-stranded (unlike DNA's double helix).
• Composed of ribonucleotides linked by phosphodiester bonds.
• Each ribonucleotide contains:
  • Ribose (pentose sugar, not deoxyribose)
  • One of four nitrogenous bases: A, U, G, C (uracil replaces thymine)
  • Phosphate group
• Even though single-stranded, RNA often shows intramolecular base pairing between complementary sequences, creating predictable 3D structures essential for function.

📬 Messenger RNA (mRNA)

• Role: carries the message from DNA (in the nucleus) to the cytoplasm for protein synthesis.
• How it works:
  • When a cell needs a certain protein, the gene "turns on."
  • mRNA is synthesized in the nucleus with a base sequence complementary to the DNA coding sequence.
  • Example: DNA strand AATTGCGC → complementary mRNA UUAACGCG (note U instead of T).
• In the cytoplasm, mRNA interacts with ribosomes and other machinery to direct protein assembly.

🧩 Ribosomal RNA (rRNA)

Ribosomal RNA (rRNA): a major constituent of ribosomes on which the mRNA binds.

• Functions:
  • Ensures proper alignment of mRNA and ribosomes.
  • Has enzymatic activity (peptidyl transferase) that catalyzes peptide bond formation between two aligned amino acids.
• rRNA is structural and catalytic, not just a passive scaffold.

🚚 Transfer RNA (tRNA)

Transfer RNA (tRNA): one of the smallest RNA types, usually 70–90 nucleotides long; carries the correct amino acid to the protein synthesis site.

• Mechanism: base pairing between tRNA and mRNA allows the correct amino acid to insert into the growing polypeptide chain.
• Example: a tRNA molecule recognizes a codon on mRNA, binds by complementary base pairing, and adds the correct amino acid.
• Don't confuse: tRNA does not carry the genetic message; it translates the message into amino acids.

🔬 MicroRNA (miRNA)

• Smallest RNA molecules.
• Role: regulate gene expression by interfering with certain mRNA messages.
• They fine-tune protein production rather than directly participating in synthesis.

🔄 Information Flow: Central Dogma

🔄 Transcription (DNA → RNA)

Transcription: process in which messenger RNA forms on a template of DNA.

• DNA dictates the structure of mRNA.
• Occurs in the nucleus.
• The mRNA base sequence is complementary to the DNA coding sequence (with U replacing T).

🔄 Translation (RNA → Protein)

Translation: process through which RNA directs the protein's formation.

• RNA dictates the protein's structure.
• Occurs in the cytoplasm at ribosomes.
• Codons: mRNA is read in sets of three bases; each codon codes for a single amino acid.
• The ribosome has two parts (large and small subunits); mRNA sits between them.
• tRNA recognizes codons, binds by complementary base pairing, and adds amino acids to the growing peptide chain.

🧬 Central Dogma summary

• Information flow: DNA → RNA → Protein.
• Holds true for all organisms.
• Exception: viral infections can violate this rule (the excerpt notes this but does not elaborate).

📊 DNA vs RNA Comparison

Feature	DNA	RNA
Function	Carries genetic information	Involved in protein synthesis
Location	Remains in the nucleus	Leaves the nucleus
Structure	Double helix	Usually single-stranded
Sugar	Deoxyribose	Ribose
Pyrimidines	Cytosine, thymine	Cytosine, uracil
Purines	Adenine, guanine	Adenine, guanine

🔍 Key distinctions

• Thymine vs uracil: DNA uses T, RNA uses U.
• Strand number: DNA is double-stranded; RNA is typically single-stranded (though it can fold back on itself).
• Mobility: DNA stays in the nucleus; RNA travels to the cytoplasm to direct protein synthesis.
• Sugar difference: the "deoxy" in deoxyribose means one less oxygen atom compared to ribose.

🧪 Key Molecular Mechanisms

🧪 Complementary base pairing

• In DNA replication: each strand serves as a template; A pairs with T, G pairs with C.
• In transcription: DNA template → mRNA; A pairs with U (not T), G pairs with C.
• In translation: mRNA codon → tRNA anticodon; ensures correct amino acid delivery.
• This complementarity is the molecular basis for accurate information transfer.

🧪 Phosphodiester bonds

Phosphodiester: covalent chemical bond that holds together the polynucleotide chains with a phosphate group linking neighboring nucleotides' two pentose sugars.

• These bonds form the backbone of both DNA and RNA.
• They link nucleotides into long chains (polynucleotides).

🧪 Hydrogen bonds in base pairs

• Adenine–thymine (or adenine–uracil) and guanine–cytosine pairs are held together by hydrogen bonds.
• These are weaker than covalent bonds, allowing strands to separate during replication and transcription.
• The specificity of hydrogen bonding ensures fidelity in copying genetic information.

🧭 Overview

🧠 One-sentence thesis

Biological macromolecules—proteins, carbohydrates, nucleic acids, and lipids—are large molecules built from smaller monomers through dehydration reactions, and each class performs distinct vital functions in living organisms.

📌 Key points (3–5)

• What macromolecules are: large molecules necessary for life, built from smaller organic molecules (monomers) joined by covalent bonds to form polymers.
• How they're built and broken down: dehydration (condensation) reactions join monomers by releasing water; hydrolysis reactions break polymers apart by using water.
• Four major classes: proteins (amino acids), carbohydrates (sugars), nucleic acids (nucleotides), and lipids (nonpolar, hydrophobic molecules).
• Common confusion: the polymer is more than the sum of its parts—it acquires new characteristics and creates much lower osmotic pressure than its individual ingredients would.
• Why structure matters: shape and function are intricately linked; changes in temperature or pH can denature proteins and cause loss of function.

🔗 Building and Breaking Macromolecules

🔗 Monomers and polymers

Macromolecules: large molecules necessary for life that are built from smaller organic molecules.

Monomers: single units that are joined by covalent bonds to form larger polymers.

• The polymer acquires new characteristics beyond its individual parts.
• An important advantage: polymers create much lower osmotic pressure than their ingredients would, helping maintain cellular osmotic conditions.

💧 Dehydration (condensation) reactions

• How it works: a monomer joins with another monomer with water molecule release, leading to covalent bond formation.
• Energy requirement: dehydration reactions typically require an investment of energy for new bond formation.
• Example: linking two amino acids releases one water molecule and forms a peptide bond.

💦 Hydrolysis reactions

• How it works: when polymers break down into smaller units (monomers), they use a water molecule for each bond broken.
• Energy release: hydrolysis reactions typically release energy by breaking bonds.
• Similarity across classes: dehydration and hydrolysis reactions are similar for all macromolecules, but each monomer and polymer reaction is specific to its class.

🍬 Carbohydrates

🍬 What carbohydrates are

Carbohydrates: a group of macromolecules that are a vital energy source for the cell and provide structural support to plant cells, fungi, and all arthropods (lobsters, crabs, shrimp, insects, spiders).

• Scientists classify carbohydrates as monosaccharides, disaccharides, and polysaccharides depending on the number of monomers in the molecule.

🔵 Monosaccharides

• Common examples: glucose, galactose, and fructose.
• These are the basic building blocks of more complex carbohydrates.

🔗 Disaccharides

• How they form: monosaccharides are linked by glycosidic bonds that form as a result of dehydration reactions, eliminating a water molecule for each bond formed.
• Common examples: lactose, maltose, and sucrose.
• Example: lactose is formed by a glycosidic bond between glucose and galactose.

🌾 Polysaccharides

Type	Function	Structure	Examples
Storage	Store glucose	May be branched or unbranched	Starch (plants), glycogen (animals)
Structural	Provide support	Unbranched or highly branched	Cellulose (unbranched), amylopectin (highly branched)

• Why storage form matters: glucose storage in the form of polymers like starch or glycogen makes it slightly less accessible for metabolism; however, this prevents it from leaking out of the cell or creating high osmotic pressure that could cause the cell to uptake excessive water.
• Plant cell walls: contain cellulose in abundance.
• Extracellular matrix roles: protect insect internal organs from trauma, prevent plant cells from lysing after watering, maintain fungal spore shape.

🧈 Lipids

🧈 What lipids are

Lipids: a class of macromolecules that are nonpolar and hydrophobic in nature.

• Major types: fats and oils, waxes, phospholipids, and steroids.

🥓 Fats (triacylglycerols or triglycerides)

Fats: a stored form of energy; consist of three fatty acids linked to a glycerol molecule.

• Fats are comprised of fatty acids and either glycerol or sphingosine.

🔗 Fatty acids: saturated vs unsaturated

Type	Bond structure	Physical state	Common source
Saturated	Only single bonds in carbon chain	Solid at room temperature	Usually from animal sources
Unsaturated	One or more double bonds in hydrocarbon chain	Tend to be liquid	Various sources

• Don't confuse: saturated fats do NOT tend to dissolve in water easily (they are hydrophobic).
• Why it matters for storage: fatty acids are better than glycogen for storing large amounts of chemical energy.

🧱 Phospholipids

• Structure: have a glycerol or sphingosine backbone to which two fatty acid chains and a phosphate-containing group are attached.
• Function: comprise the membrane's matrix (the plasma membrane of cells).

💍 Steroids

• Basic structure: four fused carbon rings.
• Cholesterol: a type of steroid and an important constituent of the plasma membrane, where it helps maintain the membrane's fluid nature.
  • Location in membrane: embedded within the tail bilayer.
  • Also the precursor of steroid hormones such as testosterone.

🕯️ Waxes

Wax: lipid comprised of a long-chain fatty acid that is esterified to a long-chain alcohol.

• Function: serves as a protective coating on some feathers, aquatic mammal fur, and leaves.

🧬 Proteins

🧬 What proteins are

Proteins: a class of macromolecules that perform a diverse range of functions for the cell.

• Functions: help in metabolism by acting as enzymes, carriers, or hormones, and provide structural support.

🧱 Amino acids: the building blocks

Amino acids: the monomers (building blocks) of proteins.

• Structure: each amino acid has a central carbon that bonds to an amino group, a carboxyl group, a hydrogen atom, and an R group or side chain.
• Diversity: there are 20 commonly occurring amino acids, each of which differs in the R group.
• How they link: a peptide bond links each amino acid to its neighbors; a long amino acid chain is a polypeptide.

🏗️ Four levels of protein structure

Level	Description	Key features
Primary	Amino acids' unique sequence	The order of amino acids
Secondary	Local folding	Forms structures such as α-helix and β-pleated sheet
Tertiary	Overall three-dimensional structure	The complete 3D shape of one polypeptide
Quaternary (optional)	Multiple polypeptides combined	When two or more polypeptides combine to form the complete protein structure

⚠️ Shape and function are linked

• Key principle: protein shape and function are intricately linked.
• Denaturation: any change in shape caused by changes in temperature or pH may lead to protein denaturation and a loss in function.
• Impact of mutations: if even one amino acid is substituted for another in a polypeptide chain, it can affect the entire protein structure and function.
• Example: Mad cow disease is an infectious disease where one misfolded protein causes all other copies of the protein to begin misfolding—this impacts tertiary structure.

🔍 Amino acid distribution in proteins

• Soluble proteins: expect to find certain categories of amino acids on the surface and others in the interior.
• Membrane-embedded proteins: different distribution of amino acids expected in a protein embedded in a lipid bilayer.
• Example: Aquaporins are proteins embedded in the plasma membrane that allow water molecules to move between the extracellular matrix and the intracellular space—their shape and chemical characteristics of amino acids match their function and location.

🧬 Nucleic Acids

🧬 What nucleic acids are

Nucleic acids: molecules comprised of nucleotides that direct cellular activities such as cell division and protein synthesis.

Nucleotide: composed of a pentose sugar, a nitrogenous base, and a phosphate group.

• Two types: DNA and RNA.

🧬 DNA structure and function

• Function: carries the cell's genetic blueprint and passes it on from parents to offspring (in the form of chromosomes).
• Structure: has a double-helical structure with the two strands running in opposite directions, connected by hydrogen bonds, and complementary to each other.
• Components: deoxyribose sugar, nitrogenous bases (including thymine), and phosphate group.
• Why the structure matters: complementary base pairing creates a very stable structure, supporting DNA's role in encoding the genome.
• Mutation impact: if a mutation occurs and cytosine is replaced with adenine, it will impact the DNA structure.

🧬 RNA structure and function

RNA: a single-stranded polymer composed of linked nucleotides made up of a pentose sugar (ribose), a nitrogenous base, and a phosphate group.

• General function: involved in protein synthesis and its regulation.

🔤 Four types of RNA

Type	Full name	Function
mRNA	Messenger RNA	Copies from the DNA, exports itself from the nucleus to the cytoplasm, contains information for constructing proteins
rRNA	Ribosomal RNA	Part of the ribosomes at the site of protein synthesis
tRNA	Transfer RNA	Carries the amino acid to the site of protein synthesis
microRNA	MicroRNA	Regulates using mRNA for protein synthesis

🔄 Protein synthesis process

• Transcription: process through which messenger RNA forms on a template of DNA.
• Translation: RNA directs the protein's formation; tRNA carries activated amino acids to the site of protein synthesis on the ribosome.

🔍 Structural differences: DNA vs RNA

• Sugar: DNA has deoxyribose; RNA has ribose.
• Bases: DNA contains thymine; RNA contains uracil.
• Strands: DNA is double-stranded; RNA is single-stranded.
• Don't confuse: a DNA nucleotide contains deoxyribose, thymine, and a phosphate group; it does NOT contain ribose or uracil.

🧭 Overview

🧠 One-sentence thesis

Biological macromolecules—proteins, carbohydrates, nucleic acids, and lipids—are large molecules built from smaller monomers through dehydration reactions and broken down by hydrolysis, each class serving distinct structural, energy-storage, and regulatory roles in living cells.

📌 Key points (3–5)

• Building and breaking macromolecules: dehydration (condensation) reactions join monomers into polymers by releasing water and require energy; hydrolysis breaks polymers into monomers by adding water and releases energy.
• Four major classes: carbohydrates (energy and structure), lipids (energy storage, membranes, signaling), proteins (enzymes, structure, transport), and nucleic acids (genetic information and protein synthesis).
• Polymer advantage: polymers have new properties and lower osmotic pressure than their monomers, preventing cells from taking up excessive water.
• Common confusion: dehydration vs hydrolysis—dehydration removes water to build bonds (costs energy); hydrolysis adds water to break bonds (releases energy).
• Structure determines function: changes in temperature or pH can denature proteins and disrupt function; DNA's double helix stability supports its role in encoding the genome.

🔗 Synthesis and breakdown of macromolecules

🔗 Dehydration (condensation) reactions

Dehydration or condensation reactions: reactions in which monomers join with the release of a water molecule, forming a covalent bond.

• Each time a monomer links to another, one water molecule is released.
• These reactions typically require an investment of energy to form new bonds.
• The process is similar across all macromolecule classes, but the specific monomers and polymers differ.
• Example: linking two amino acids releases water and forms a peptide bond.

💧 Hydrolysis reactions

Hydrolysis reactions: reactions in which polymers break down into smaller units (monomers) by using a water molecule for each bond broken.

• One water molecule is consumed for each bond broken.
• These reactions typically release energy by breaking bonds.
• Hydrolysis is the reverse of dehydration synthesis.
• Don't confuse: dehydration builds polymers (removes water, costs energy); hydrolysis breaks polymers (adds water, releases energy).

🧩 Why polymers matter

• New characteristics: the polymer acquires properties beyond the sum of its parts.
• Lower osmotic pressure: polymers exert much lower osmotic pressure than their individual monomers, which is an important advantage in maintaining cellular osmotic conditions.
• Example: storing glucose as glycogen or starch prevents it from leaking out of the cell or causing excessive water uptake due to high osmotic pressure.

🍬 Carbohydrates

🍬 What carbohydrates are

Carbohydrates: a group of macromolecules that are a vital energy source for the cell and provide structural support to plant cells, fungi, and arthropods (lobsters, crabs, shrimp, insects, spiders).

• Scientists classify carbohydrates by the number of monomers: monosaccharides, disaccharides, and polysaccharides.

🔢 Classification of carbohydrates

Type	Description	Examples
Monosaccharides	Single sugar units	Glucose, galactose, fructose
Disaccharides	Two monosaccharides linked by glycosidic bonds	Lactose, maltose, sucrose
Polysaccharides	Long chains of monosaccharides; may be branched or unbranched	Starch, glycogen (branched); cellulose (unbranched)

• Glycosidic bonds form as a result of dehydration reactions, eliminating one water molecule for each bond formed.
• Example: lactose is formed by a glycosidic bond between glucose and galactose.

🌾 Storage polysaccharides

• Starch: the storage form of glucose in plants; contains amylopectin (highly branched) and other constituents.
• Glycogen: the storage form of glucose in animals.
• Storing glucose as polymers makes it slightly less accessible for metabolism but prevents leaking and high osmotic pressure.

🌿 Structural polysaccharides

• Cellulose: an unbranched polysaccharide that provides structural support to plant cell walls (present in abundance).
• Cellulose also maintains the shape of fungal spores and protects insect internal organs from external trauma.
• Humans cannot digest cellulose because they lack the enzymes to break its bonds.

🧈 Lipids

🧈 What lipids are

Lipids: a class of macromolecules that are nonpolar and hydrophobic in nature.

• Major types include fats and oils, waxes, phospholipids, and steroids.

🥓 Fats and oils

Fats (triacylglycerols or triglycerides): a stored form of energy consisting of three fatty acids linked to a glycerol molecule (or sphingosine).

• Fatty acids may be saturated or unsaturated:
  • Saturated fatty acids: contain only single bonds in the hydrocarbon chain; solid at room temperature; usually obtained from animal sources.
  • Unsaturated fatty acids: contain one or more double bonds in the hydrocarbon chain.
• Saturated fats do not dissolve in water easily (they are hydrophobic).

🧱 Phospholipids

Phospholipids: lipids that comprise the membrane's matrix; have a glycerol or sphingosine backbone to which two fatty acid chains and a phosphate-containing group are attached.

• Phospholipids are important components of the plasma membrane of cells.
• Their structure allows them to form bilayers with hydrophobic tails inside and hydrophilic heads outside.

💍 Steroids

• Basic structure: four fused carbon rings.
• Cholesterol: a type of steroid and an important constituent of the plasma membrane, where it helps maintain the membrane's fluid nature.
• Cholesterol is found within the tail bilayer (embedded with the phospholipid tails), not on the surface.
• Cholesterol is also the precursor of steroid hormones such as testosterone.

🕯️ Waxes

Waxes: lipids comprised of a long-chain fatty acid esterified to a long-chain alcohol; serve as a protective coating on some feathers, aquatic mammal fur, and leaves.

🧬 Proteins

🧬 What proteins are

Proteins: a class of macromolecules that perform a diverse range of functions for the cell, including metabolism (enzymes, carriers, hormones) and structural support.

• The building blocks (monomers) of proteins are amino acids.

🧱 Amino acid structure

• Each amino acid has a central carbon that bonds to:
  • An amino group
  • A carboxyl group
  • A hydrogen atom
  • An R group or side chain (which differs among the 20 commonly occurring amino acids)
• A peptide bond links each amino acid to its neighbors.
• A long amino acid chain is called a polypeptide.

🏗️ Protein structure levels

Level	Description
Primary	The unique sequence of amino acids
Secondary	Local folding to form structures such as the α-helix and β-pleated sheet
Tertiary	The overall three-dimensional structure of the polypeptide
Quaternary (optional)	The configuration when two or more polypeptides combine to form the complete protein

• Protein shape and function are intricately linked.
• Any change in shape caused by changes in temperature or pH may lead to protein denaturation and a loss in function.
• Example: Mad cow disease is caused by one misfolded protein causing all other copies to misfold—this impacts tertiary structure.

🔍 Structure-function relationship

• The amino acid sequence (primary structure) determines how the protein folds.
• The R groups allow amino acids to be linked into long peptide chains and influence folding.
• Soluble proteins typically have hydrophilic amino acids on the surface and hydrophobic amino acids in the interior.
• Proteins embedded in lipid bilayers have a different distribution suited to the membrane environment.

🧬 Nucleic Acids

🧬 What nucleic acids are

Nucleic acids: molecules comprised of nucleotides that direct cellular activities such as cell division and protein synthesis.

• Each nucleotide is comprised of:
  • A pentose sugar
  • A nitrogenous base
  • A phosphate group
• There are two types of nucleic acids: DNA and RNA.

🧬 DNA structure and function

DNA: carries the cell's genetic blueprint and passes it on from parents to offspring (in the form of chromosomes).

• Double-helical structure: two strands running in opposite directions, connected by hydrogen bonds, and complementary to each other.
• A DNA nucleotide contains deoxyribose, thymine (or other bases), and a phosphate group.
• Complementary base pairing creates a very stable structure, supporting DNA's role in encoding the genome.
• Example: if a mutation replaces cytosine with adenine, it disrupts the complementary pairing and can impact DNA structure.

🧬 RNA structure and function

RNA: a single-stranded polymer composed of linked nucleotides made up of a pentose sugar (ribose), a nitrogenous base, and a phosphate group; involved in protein synthesis and its regulation.

• Three main types of RNA:
  • Messenger RNA (mRNA): copies from DNA, exports itself from the nucleus to the cytoplasm, and contains information for constructing proteins (forms on a template of DNA).
  • Ribosomal RNA (rRNA): part of the ribosomes at the site of protein synthesis.
  • Transfer RNA (tRNA): carries activated amino acids to the site of protein synthesis on the ribosome.
  • MicroRNA: regulates the use of mRNA for protein synthesis.

🔄 RNA directs protein synthesis

• RNA directs the protein's formation through a process in which mRNA provides the template.
• tRNA brings amino acids to the ribosome, where rRNA facilitates assembly.
• This process translates the genetic information in DNA (via mRNA) into functional proteins.

🧭 Overview

🧠 One-sentence thesis

Cells are the fundamental building blocks of all organisms, and scientists study them using microscopes that vary in magnification and resolution to reveal structures invisible to the naked eye.

📌 Key points (3–5)

• Cells as building blocks: All organisms—whether single-celled bacteria or multi-celled humans—are made of cells, which are the smallest unit of life.
• Hierarchy of organization: Cells → tissues → organs → organ systems → organisms.
• Two broad cell categories: Prokaryotic (e.g., bacteria) and eukaryotic (e.g., animal and plant cells).
• Microscopy is essential: Most cells are too small to see with the naked eye; light microscopes and electron microscopes differ in magnification, resolution, and whether they can view living specimens.
• Common confusion: Light microscopes invert images (right-side up becomes upside-down) because of the two-lens system; also, light microscopes can view living cells but electron microscopes cannot.

🧱 Cells and biological organization

🧱 What is a cell?

Cell: the smallest unit of a living thing.

• An organism can be one cell (bacteria) or many cells (humans).
• Cells are the basic building blocks of all organisms, regardless of complexity.

🏗️ From cells to organisms

The excerpt describes a hierarchy:

Level	Definition	Example
Cell	Smallest unit of life	Individual epithelial cell, bone cell, immune cell
Tissue	Several cells of one kind that interconnect and share a function	Epithelial tissue
Organ	Tissues combine	Stomach, heart, brain
Organ system	Several organs working together	Digestive system, circulatory system, nervous system
Organism	Several systems functioning together	Human being

• Example: Epithelial cells protect the body's surface and cover organs; bone cells support and protect; immune cells fight bacteria; blood cells carry nutrients and oxygen.
• Each cell type plays a vital role in growth, development, and day-to-day maintenance.

🔬 Prokaryotic vs eukaryotic

• Scientists group cells into two broad categories: prokaryotic and eukaryotic.
• Bacterial cells are prokaryotic; animal and plant cells are eukaryotic.
• The excerpt mentions these categories but does not detail the criteria for distinguishing them here.

🔍 Microscopy fundamentals

🔍 Why microscopes are necessary

• With few exceptions, individual cells cannot be seen with the naked eye.
• Scientists use microscopes to study cells.

Microscope: an instrument that magnifies an object (micro- = "small"; -scope = "to look at").

• Most cells are photographed with a microscope; these images are called micrographs.

📏 Cell size perspective

• A typical human red blood cell is about 8 micrometers (8 μm) in diameter.
• A pin head is about 2 millimeters (2 mm) in diameter.
• About 250 red blood cells could fit on a pinhead.
• This illustrates how small cells are relative to everyday objects.

🔄 Image orientation quirk

• Microscope optics invert the image: right-side up becomes upside-down, and right becomes left.
• This happens because microscopes use two sets of lenses to magnify the image.
• If you move the slide left, it appears to move right; if you move it down, it appears to move up.
• Don't confuse: Binocular (dissecting) microscopes work similarly but include an additional magnification system that makes the final image appear upright.

💡 Light microscopy

💡 How light microscopes work

Light microscopes: microscopes in which visible light passes and bends through the lens system to enable the user to see the specimen.

• Most student microscopes are light microscopes.
• Visible light passes through lenses to magnify the specimen.

🎯 Magnification and resolution

Two important parameters:

• Magnification: the process of enlarging an object in appearance.
• Resolving power: the microscope's ability to distinguish two adjacent structures as separate; higher resolution = better clarity and detail.

Feature	Light microscope (undergraduate lab)	With oil immersion lenses
Magnification	Up to ~400 times	Up to ~1,000 times
Resolution	About 200 nanometers	Higher

🧪 Viewing living vs stained cells

• Advantage: Light microscopes can view living organisms.
• Challenge: Individual cells are generally transparent, so their components are not distinguishable unless colored with special stains.
• Trade-off: Staining usually kills the cells.
• Example: You can observe a living cell's movement under a light microscope, but to see internal structures clearly, you must stain (and kill) the cell.

⚡ Electron microscopy

⚡ How electron microscopes work

Electron microscopes: microscopes that use a beam of electrons instead of a beam of light.

• Electrons have shorter wavelengths than photons (light particles).
• Electrons move best in a vacuum.
• This allows for higher magnification and higher resolving power (more detail).

Feature	Light microscope	Electron microscope
Beam type	Visible light	Electrons
Magnification	Up to ~1,000×	Up to ~100,000×
Resolution	~200 nanometers	~50 picometers
Living specimens?	Yes	No (preparation kills the specimen)
Size/cost	Smaller, less expensive	Significantly bulkier and more expensive

🔬 Two types of electron microscopes

1. Scanning electron microscope (SEM):

   • A beam of electrons moves back and forth across a cell's surface.
   • Creates details of cell surface characteristics.

2. Transmission electron microscope (TEM):

   • The electron beam penetrates the cell.
   • Provides details of a cell's internal structures.

📸 Example comparison

The excerpt describes Salmonella bacteria viewed under different microscopes:

• (a) Light microscope: Bacteria appear as tiny purple dots.
• (b) Scanning electron microscope: Bacteria (red) invading human cells (yellow) show much greater magnification and detail.
• Even though the specimens differ, the comparative increase in magnification and detail is clear.

⚠️ Key limitation

• Preparing the specimen for electron microscopy kills the specimen.
• You cannot view living cells with an electron microscope because electrons require a vacuum.
• Don't confuse: Light microscopes can show living cells but with less detail; electron microscopes show much more detail but only of dead, prepared specimens.

🧬 Cell theory (introduction)

• The excerpt mentions that the microscopes used today are far more complex than those used by Antony van Leeuwenhoek, a Dutch shopkeeper.
• The text cuts off before elaborating on cell theory itself, but it sets the stage for understanding how microscopy enabled the development of cell theory.

🧭 Overview

🧠 One-sentence thesis

Electron microscopes provide far greater magnification and resolution than light microscopes, enabling scientists to observe cellular details that are invisible under light microscopy, though at the cost of being unable to view living specimens.

📌 Key points (3–5)

• Light vs. electron microscopes: Light microscopes magnify ~400× with 200 nm resolution; electron microscopes magnify ~100,000× with 50 pm resolution.
• Why electron microscopes see more: They use electron beams (shorter wavelengths than photons) instead of light, providing higher magnification and resolving power.
• Trade-off: Electron microscopy requires specimen preparation that kills the cell and a vacuum environment, so living cells cannot be observed.
• Common confusion: Scanning vs. transmission electron microscopes—scanning shows surface details; transmission reveals internal structures.
• Historical foundation: Early microscopes led van Leeuwenhoek to discover single-celled organisms and Hooke to coin "cell," eventually leading to unified cell theory.

🔬 Microscope types and capabilities

🔬 Light microscopes

• Magnification: Up to approximately 400 times.
• Resolution: About 200 nanometers.
• Use: Standard tool in college biology labs for viewing cells.
• Advantage: Can observe living specimens.

⚡ Electron microscopes

Electron microscopes: instruments that use a beam of electrons instead of a beam of light to achieve higher magnification and resolving power.

• Magnification: Up to 100,000 times.
• Resolution: 50 picometers (far superior to light microscopes).
• Why they work better: Electrons have shorter wavelengths than photons, allowing finer detail.
• Limitation: Electrons move best in a vacuum, and specimen preparation kills the cell—no living cells can be viewed.
• Cost and size: Significantly more bulky and expensive than light microscopes.

Example: Salmonella bacteria appear as tiny purple dots under a light microscope but show detailed surface invasion of human cells under electron microscopy, demonstrating the dramatic increase in observable detail.

🔍 Two types of electron microscopes

Type	What it shows	How it works
Scanning electron microscope	Cell surface characteristics	Electron beam moves back and forth across the cell's surface
Transmission electron microscope	Internal cell structures	Electron beam penetrates the cell

Don't confuse: Scanning reveals the outside (surface topology); transmission reveals the inside (internal organization).

📜 Historical development of cell biology

🕰️ Key milestones

• 1600s – Antony van Leeuwenhoek: Dutch shopkeeper skilled in lens crafting; observed movements of single-celled organisms, which he called "animalcules"; discovered bacteria and protozoa in the 1670s.
• 1665 – Robert Hooke: Published Micrographia; coined the term "cell" for box-like structures observed in cork tissue.
• Late 1830s – Matthias Schleiden and Theodor Schwann: Proposed the unified cell theory.
• Later – Rudolf Virchow: Made important contributions to cell theory.

🧬 Unified cell theory

Unified cell theory: states that one or more cells comprise all living things, the cell is the basic unit of life, and new cells arise from existing cells.

• This theory unified observations from botany (Schleiden) and zoology (Schwann).
• It established the cell as the fundamental unit of all life.

🏥 Practical application: Cytotechnology

🔬 What cytotechnologists do

Cytotechnologist (cyto- = "cell"): professionals who study cells via microscopic examinations and other laboratory tests.

• Training: Determine which cellular changes are normal and which are abnormal.
• Scope: Study cellular specimens from all organs, not just one type.
• Process: Stain cells and examine them under microscopes; consult a pathologist when abnormalities are noticed.

🩺 Medical importance

• Example: Pap smear test—a doctor takes cells from the uterine cervix; a cytotechnologist examines them for signs of cervical cancer or microbial infection.
• Why it matters: Early detection allows treatment to begin sooner, increasing chances of successful outcomes.
• Infected cells show visible changes: larger size, abnormal nucleus number (e.g., two nuclei instead of one in HPV-infected cervical cells).

🦠 Prokaryotic cells

🧫 Definition and classification

Prokaryote: a simple, mostly single-celled (unicellular) organism that lacks a nucleus or any other membrane-bound organelle.

• Only Bacteria and Archaea are classified as prokaryotes (pro- = "before"; -kary- = "nucleus").
• Predominantly single-celled organisms.
• Significantly different from eukaryotes (animals, plants, fungi, protists).

🧩 Common components of all cells

All cells share four components:

1. Plasma membrane: outer covering separating the cell's interior from its environment.
2. Cytoplasm: jelly-like cytosol containing other cellular components.
3. DNA: the cell's genetic material.
4. Ribosomes: synthesize proteins.

🗂️ Prokaryotic cell structure

Nucleoid: the central part of a prokaryotic cell where DNA is localized (not enclosed in a membrane).

Additional structures (present in some, not all, prokaryotes):

• Peptidoglycan cell wall (most prokaryotes): acts as extra protection, helps maintain shape, prevents dehydration.
• Polysaccharide capsule (many prokaryotes): enables attachment to surfaces.
• Flagella: used for locomotion.
• Pili: exchange genetic material during conjugation (direct transfer between bacteria).
• Fimbriae: attach to host cells.

Don't confuse: Pili are for genetic exchange; fimbriae are for attachment; flagella are for movement.

📏 Cell size and efficiency

📐 Size comparison

• Prokaryotic cells: 0.1 to 5.0 μm in diameter.
• Eukaryotic cells: 10 to 100 μm in diameter.
• Prokaryotic cells are significantly smaller than eukaryotic cells.

⚙️ Why small size matters

Advantages of small size in prokaryotes:

• Ions and organic molecules entering the cell can quickly diffuse to other parts.
• Wastes produced can quickly diffuse out.
• This is not the case in eukaryotic cells, which developed different structural adaptations (organelles) to enhance intracellular transport.

📊 Surface area-to-volume ratio

The mathematical principle:

• Surface area of a sphere = 4πr²
• Volume of a sphere = 4πr³/3
• As radius increases, surface area increases as the square of radius.
• Volume increases as the cube of radius (much more rapidly).
• Result: As a cell increases in size, its surface area-to-volume ratio decreases.

Cell dimension	Volume	Surface area	Ratio
1 mm	1 mm³	6 mm²	6:1
2 mm	8 mm³	24 mm²	3:1

Why this matters:

• If the cell grows too large, the plasma membrane will not have sufficient surface area to support the rate of diffusion required for the increased volume.
• As a cell grows, it becomes less efficient.

🔄 Solutions to size limitations

Two ways cells become more efficient:

1. Divide: Keep cells small by splitting.
2. Develop organelles: Specialized structures that perform specific tasks (leads to eukaryotic cells).

Don't confuse: Small size is necessary for all cells, but prokaryotes stay small and simple, while eukaryotes compensate for larger size with internal compartmentalization (organelles).

🧪 Microbiologists and their work

👨‍🔬 What microbiologists do

Microbes (microorganisms): organisms so tiny they can only be seen with microscopes; ubiquitous in the environment.

• Not all microbes cause disease; most are beneficial (e.g., gut microbes make vitamin K; others ferment beer and wine).
• Microbiologists study microbes and pursue diverse careers.

💼 Career applications

Field	Role
Food industry	Use microorganisms in production
Veterinary and medical	Study disease-causing microbes
Pharmaceutical	Research and development; identify new antibiotic sources
Environmental	Bioremediation—use microbes to remove pollutants from soil/groundwater or hazardous elements from contaminated sites
Bioinformatics	Design computer models (e.g., bacterial epidemics)

🧼 Practical hygiene insight

• Most effective action to prevent contagious illness: Wash hands.
• Why: Microbes live on doorknobs, money, hands, and many surfaces; they transfer through touch and can enter the body through mouth, nose, or eyes.

🧭 Overview

🧠 One-sentence thesis

As cells grow larger, their surface area-to-volume ratio decreases, limiting efficiency and driving adaptations like division or the development of specialized organelles found in eukaryotic cells.

📌 Key points (3–5)

• Surface area-to-volume problem: As cell radius increases, volume grows much faster (cubed) than surface area (squared), reducing efficiency.
• Why small size matters: Larger cells cannot support sufficient diffusion through their plasma membrane to meet internal volume needs.
• Eukaryotic vs prokaryotic: Eukaryotic cells are larger and more complex, with membrane-bound nucleus and organelles; prokaryotic cells are much smaller and simpler.
• Common confusion: "Form follows function"—structures like microvilli or abundant ribosomes reflect the cell's specialized role, not arbitrary design.
• Compartmentalization advantage: Organelles allow different functions to occur in separate areas, making eukaryotic cells more efficient despite larger size.

📏 Why cells must stay small

📐 The surface area-to-volume relationship

• Cell surface area grows as the square of the radius (formula: 4πr²).
• Cell volume grows as the cube of the radius (formula: 4πr³/3).
• Result: As radius increases, volume increases much more rapidly than surface area.
• This principle applies whether the cell is spherical or cube-shaped.

⚠️ The efficiency problem

As a cell increases in size, its surface area-to-volume ratio decreases.

• The plasma membrane must support diffusion for the entire internal volume.
• When volume grows faster than surface area, the membrane cannot keep up with the cell's needs.
• Consequence: The cell becomes less efficient; if it grows too large, it will either divide or die.
• Example: A cell with volume 1 mm³ and surface area 6 mm² has a 6:1 ratio; a cell with volume 8 mm³ and surface area 24 mm² has only a 3:1 ratio—less surface per unit volume.

🔧 Two solutions to the size problem

1. Divide: Keep cells small by splitting into two.
2. Develop organelles: Create specialized internal structures that perform specific tasks more efficiently.

• The second solution leads to the evolution of eukaryotic cells.

🧬 Eukaryotic cells: structure and complexity

🧬 Defining features of eukaryotic cells

Eukaryotic cells have three key characteristics not found in prokaryotes:

1. A membrane-bound nucleus (hence "true nucleus").
2. Numerous membrane-bound organelles (endoplasmic reticulum, Golgi apparatus, chloroplasts, mitochondria, etc.).
3. Several rod-shaped chromosomes.

Organelle: "little organ"—specialized structures with specific cellular functions, just as body organs have specialized roles.

• Organelles allow compartmentalization: different functions occur in different areas of the cell.
• This makes eukaryotic cells more complex but also more efficient than prokaryotic cells.

🌿 Animal vs plant cells

Feature	Animal cells	Plant cells
Cell wall	No	Yes
Chloroplasts	No	Yes
Central vacuole	No	Yes
Lysosomes	Rare	Rare
Centrosomes	Rare	Rare

• Both are eukaryotic and share most organelles.
• Plant cells have additional structures for photosynthesis and structural support.

🧱 Major cell components

🧱 The plasma membrane

Plasma membrane: a phospholipid bilayer with embedded proteins that separates the cell's internal contents from its surrounding environment.

• Phospholipid: a lipid molecule with two fatty acid chains and a phosphate-containing group.
• Function: Controls passage of organic molecules, ions, water, and oxygen into and out of the cell; also allows wastes (CO₂, ammonia) to exit.
• Present in both prokaryotic and eukaryotic cells.

🖐️ Microvilli: form follows function

• Some cells specialized for absorption have plasma membranes that fold into fingerlike projections called microvilli (singular: microvillus).
• Example: Cells lining the small intestine use microvilli to increase surface area for nutrient absorption.
• Don't confuse: Microvilli only appear on the side of the membrane facing the cavity from which substances are absorbed, not all around the cell.
• Real-world implication: In celiac disease, immune response to gluten damages microvilli, preventing nutrient absorption and causing malnutrition.

🧪 The cytoplasm

Cytoplasm: the entire region between the plasma membrane and the nuclear envelope.

• Comprised of:
  • Organelles suspended in the gel-like cytosol.
  • The cytoskeleton.
  • Various chemicals.
• Composition: 70–80% water, but has semi-solid consistency due to proteins.
• Also contains: glucose, sugars, polysaccharides, amino acids, nucleic acids, fatty acids, glycerol derivatives, and dissolved ions (sodium, potassium, calcium, etc.).
• Function: Many metabolic reactions, including protein synthesis, occur in the cytoplasm.

🧫 The nucleus and genetic material

🧫 The nucleus overview

Nucleus (plural: nuclei): typically the most prominent organelle in a cell; houses the cell's DNA and directs the synthesis of ribosomes and proteins.

• Surrounded by the nuclear envelope: a double-membrane structure (two phospholipid bilayers—inner and outer).
• The nuclear envelope is continuous with the endoplasmic reticulum.
• Nuclear pores punctuate the envelope, controlling passage of ions, molecules, and RNA between nucleoplasm and cytoplasm.

🧬 Chromatin and chromosomes

Chromosomes: structures within the nucleus made up of DNA (the hereditary material).

• In prokaryotes: DNA is a single circular chromosome.
• In eukaryotes: chromosomes are linear; each species has a specific number (humans: 46; fruit flies: 8).
• Chromosomes are only visible and distinguishable when the cell is preparing to divide.
• During growth and maintenance phases, proteins attach to chromosomes, forming an unwound, jumbled appearance.

Chromatin: the unwound protein-chromosome complexes; describes the material that makes up chromosomes both when condensed and decondensed.

• Nucleoplasm: the semi-solid fluid inside the nucleus where chromatin and the nucleolus are found.

🔵 The nucleolus

Nucleolus (plural: nucleoli): a darkly staining area within the nucleus that aggregates ribosomal RNA with associated proteins to assemble ribosomal subunits.

• Some chromosomes have DNA sections that encode ribosomal RNA.
• The nucleolus assembles ribosomal subunits, which are then transported through nuclear pores to the cytoplasm.
• Why it matters: If the nucleolus cannot function, ribosome production stops, affecting protein synthesis throughout the cell.

🏭 Protein synthesis machinery

🏭 Ribosomes

Ribosomes: cellular structures responsible for protein synthesis.

• Appearance: Under electron microscopy, they look like clusters (polyribosomes) or single tiny dots floating in the cytoplasm.
• Location: May be free-floating or attached to the plasma membrane, endoplasmic reticulum, or nuclear envelope's outer membrane.
• Structure: Large protein and RNA complexes consisting of two subunits (large and small).

🔄 How ribosomes work

1. The nucleus transcribes DNA into messenger RNA (mRNA).
2. mRNA travels to ribosomes.
3. Ribosomes translate the mRNA code (sequence of nitrogenous bases) into a specific order of amino acids.
4. Amino acids are assembled into proteins.

📊 Form follows function: ribosome abundance

• Protein synthesis is essential for all cells (enzymes, hormones, antibodies, pigments, structural components, surface receptors).
• Result: Ribosomes are found in practically every cell.
• Cells that synthesize large amounts of protein have particularly abundant ribosomes.
• Example: Pancreatic cells produce many digestive enzymes, so they contain many ribosomes.

⚡ Mitochondria

Mitochondria (singular: mitochondrion): often called the cell's "powerhouses" or "energy factories."

• Function: Responsible for making adenosine triphosphate (ATP), the cell's energy currency.
• (The excerpt cuts off here, so no further details are provided.)

🧭 Overview

🧠 One-sentence thesis

Eukaryotic cells contain specialized membrane-bound organelles—each with distinct structures and functions—that compartmentalize cellular processes such as protein synthesis, energy production, and waste breakdown, with plant and animal cells differing in key organelles like chloroplasts, cell walls, and lysosomes.

📌 Key points (3–5)

• Compartmentalization advantage: organelles separate incompatible chemical reactions (e.g., lysosomes maintain acidic pH while cytoplasm remains neutral).
• Form follows function: cells that perform specific tasks contain more of the relevant organelle (e.g., pancreas cells making digestive enzymes have many ribosomes; muscle cells have many mitochondria).
• Plant vs animal differences: plant cells have cell walls, chloroplasts, and large central vacuoles; animal cells have centrosomes with centrioles and lysosomes.
• Common confusion: vesicles vs vacuoles—vacuoles are larger, their membranes don't fuse with other cellular components, and they can break down macromolecules; vesicles are smaller and their membranes can fuse with plasma or other membranes.
• Endosymbiotic origin: mitochondria and chloroplasts have their own DNA and ribosomes because they likely originated as independent bacteria that formed mutually beneficial relationships with host cells.

🧬 The Nucleus and Protein Synthesis Machinery

🧬 Chromatin organization and the nucleolus

Nucleolus: a darkly staining area within the nucleus that aggregates ribosomal RNA with associated proteins to assemble ribosomal subunits.

• Chromosomes contain DNA organized with proteins into chromatin at various levels.
• Some chromosomes have DNA sections that encode ribosomal RNA.
• The nucleolus assembles ribosomal subunits, which are then transported through nuclear pores to the cytoplasm.
• This shows how the nucleus directs ribosome synthesis.

🔬 Ribosomes: the protein factories

Ribosomes: cellular structures responsible for protein synthesis, consisting of two subunits (large and small) made of protein and RNA complexes.

Where they're found:

• Free-floating in cytoplasm (as clusters called polyribosomes or single dots)
• Attached to plasma membrane's cytoplasmic side
• Attached to endoplasmic reticulum's cytoplasmic side
• Attached to nuclear envelope's outer membrane

How they work:

1. DNA in nucleus transcribes into messenger RNA (mRNA)
2. mRNA travels to ribosomes
3. Ribosomes translate the nitrogenous base sequence into a specific amino acid order
4. Amino acids assemble into proteins

Why abundance varies:

• Protein synthesis is essential for all cells (enzymes, hormones, antibodies, pigments, structural components, surface receptors)
• Cells that synthesize large amounts of protein have more ribosomes
• Example: pancreas cells producing digestive enzymes contain many ribosomes

⚡ Energy Production and Metabolism

⚡ Mitochondria: the powerhouses

Mitochondria: oval-shaped, double-membrane organelles responsible for making adenosine triphosphate (ATP), the cell's main energy-carrying molecule.

Structure:

• Outer membrane and inner membrane (both phospholipid bilayers with embedded proteins)
• Inner membrane has folds called cristae
• Space surrounded by folds = mitochondrial matrix
• Cristae and matrix have different roles in cellular respiration
• Have their own ribosomes and DNA

Function:

• Cellular respiration uses chemical energy in glucose and nutrients
• Process uses oxygen and produces carbon dioxide as waste
• The carbon dioxide you exhale comes from these cellular reactions
• ATP represents short-term stored energy

Form follows function:

• Muscle cells have very high concentrations of mitochondria because they need considerable energy for movement
• When cells lack oxygen, they produce little ATP and instead make lactic acid

🧪 Peroxisomes: detoxification specialists

Peroxisomes: small, round organelles enclosed by single membranes that carry out oxidation reactions.

Functions:

• Break down fatty acids and amino acids
• Detoxify many poisons that enter the body
• Oxidation reactions release hydrogen peroxide (H₂O₂), but enzymes safely break it down into oxygen and water when confined to peroxisomes
• Example: peroxisomes in liver cells detoxify alcohol

Specialized types:

• Glyoxysomes (in plants): convert stored fats into sugars
• Plant cells contain many peroxisome types for metabolism, pathogen defense, and stress response

🗑️ Storage, Transport, and Waste Management

📦 Vesicles and vacuoles

Vesicles and vacuoles: membrane-bound sacs that function in storage and transport.

Feature	Vesicles	Vacuoles
Size	Smaller	Somewhat larger
Membrane fusion	Can fuse with plasma membrane or other membrane systems	Do NOT fuse with other cellular component membranes
Additional function	Transport	Can contain enzymes that break down macromolecules (in plants)

Don't confuse: the distinction is subtle but important—vacuole membranes remain separate from other cellular membranes.

🗑️ Lysosomes: cellular garbage disposal

Lysosomes: organelles containing enzymes that break down proteins, polysaccharides, lipids, nucleic acids, and worn-out organelles.

Key characteristics:

• Present in animal cells; most plant cells lack them (digestive processes occur in vacuoles instead)
• Enzymes are active at much lower pH than cytoplasm
• Interior is more acidic than cytoplasm

Why compartmentalization matters:

• Many reactions in the cytoplasm could not occur at low pH
• Separating acidic breakdown processes from neutral cytoplasm demonstrates the advantage of organelles
• Example: this allows the cell to safely digest materials without damaging other cellular components

🌱 Plant-Specific vs Animal-Specific Structures

🐾 Animal cell specializations

The centrosome:

Centrosome: a microtubule-organizing center found near nuclei of animal cells, containing a pair of centrioles.

• Each centriole is a cylinder of nine triplets of microtubules
• Two centrioles lie perpendicular to each other
• Nontubulin proteins hold the microtubule triplets together
• The centrosome replicates before cell division
• Centrioles appear to help pull duplicated chromosomes to opposite ends during division

Important caveat:

• The exact function isn't clear because cells with removed centrosomes can still divide
• Plant cells lack centrosomes but are still capable of cell division

🌿 Plant cell specializations

The cell wall:

Cell wall: a rigid covering external to the plasma membrane that protects the cell, provides structural support, and gives shape.

• Also found in fungal and some protistan cells
• Major organic molecule is cellulose (a polysaccharide of glucose units)
• Prokaryotic cell walls use peptidoglycan instead
• Example: the crunch when biting raw celery comes from tearing rigid cell walls

Chloroplasts:

Chloroplasts: plant cell organelles that carry out photosynthesis—the series of reactions using carbon dioxide, water, and light energy to make glucose and oxygen.

Structure:

• Outer membrane and inner membrane
• Thylakoids: interconnected, stacked, fluid-filled membrane sacs
• Granum (plural = grana): each thylakoid stack
• Stroma: fluid enclosed by inner membrane surrounding the grana
• Thylakoid space: space inside thylakoid membranes
• Have their own DNA (single circular chromosome) and ribosomes

Function:

• Contain chlorophyll, a green pigment that captures light energy
• Light harvesting reactions occur in thylakoid membranes
• Sugar synthesis occurs in the stroma
• This allows plants (autotrophs) to make their own food

Key difference:

• Plants are autotrophs (make their own food like sugars)
• Animals are heterotrophs (must ingest food)
• Photosynthetic protists also have chloroplasts
• Some bacteria perform photosynthesis but their chlorophyll is not in an organelle

📊 Plant vs animal cell comparison

Feature	Animal Cells	Plant Cells
Centrosome with centrioles	✓ Present	✗ Absent (most)
Lysosomes	✓ Present	✗ Absent (most)
Cell wall	✗ Absent	✓ Present
Chloroplasts	✗ Absent	✓ Present
Large central vacuole	✗ Absent	✓ Present
Plasma membrane, cytoplasm, nucleus, ribosomes, mitochondria, peroxisomes	✓ Both have these	✓ Both have these

🔄 Endosymbiotic Theory

🤝 What endosymbiosis explains

Symbiosis: a relationship in which organisms from two separate species depend on each other for survival.

Endosymbiosis (endo- = "within"): a mutually beneficial relationship in which one organism lives inside the other.

Why mitochondria and chloroplasts have DNA and ribosomes:

• Strong evidence points to endosymbiosis as the explanation
• Scientists have long noticed bacteria, mitochondria, and chloroplasts are similar in size
• All three have DNA and ribosomes
• Scientists believe host cells and bacteria formed an endosymbiotic relationship when bacteria began living inside host cells

Endosymbiosis in nature:

• Endosymbiotic relationships are abundant
• Example: microbes producing vitamin K live inside the human gut
  • Beneficial for humans: we cannot synthesize vitamin K ourselves
  • Beneficial for microbes: protection from other organisms and drying out, plus abundant food from the large intestine environment

🧭 Overview

🧠 One-sentence thesis

The endomembrane system is a coordinated group of organelles in eukaryotic cells that work together to modify, package, and transport lipids and proteins to their proper destinations.

📌 Key points (3–5)

• What the endomembrane system includes: nuclear envelope, lysosomes, vesicles, endoplasmic reticulum (ER), Golgi apparatus, and plasma membrane—but excludes mitochondria and chloroplasts.
• Two specialized ER regions: rough ER (RER) modifies proteins and makes phospholipids; smooth ER (SER) synthesizes carbohydrates, lipids, steroid hormones, detoxifies substances, and stores calcium ions.
• How proteins travel: ribosomes synthesize proteins into the RER lumen, proteins are modified, then transport vesicles bud from the RER and carry cargo to the Golgi apparatus.
• Common confusion—RER vs SER: both are continuous, but RER has ribosomes on its surface and handles protein modification, while SER lacks ribosomes and handles lipid synthesis and detoxification.
• Why the Golgi matters: it sorts, tags, packages, and distributes proteins and lipids, ensuring they reach the correct cellular or extracellular destinations.

🏗️ Structure and components

🏗️ What the endomembrane system is

Endomembrane system (endo = "within"): a group of membranes and organelles in eukaryotic cells that works together to modify, package, and transport lipids and proteins.

• It is a coordinated network, not isolated parts.
• Components interact with each other through vesicle transport.
• The plasma membrane is included because it interacts with other endomembranous organelles, even though it is technically at the cell boundary.

🚫 What is excluded

• Mitochondria and chloroplast membranes are not part of the endomembrane system.
• The excerpt does not explain why, but explicitly states this exclusion.

🧬 The endoplasmic reticulum (ER)

🧬 Overall ER structure

Endoplasmic reticulum (ER): a series of interconnected membranous sacs and tubules that collectively modifies proteins and synthesizes lipids.

• The hollow portion inside the tubules is called the lumen or cisternal space.
• The ER membrane is a phospholipid bilayer embedded with proteins.
• It is continuous with the nuclear envelope.

🔬 Rough ER (RER)

Rough endoplasmic reticulum (RER): named for the ribosomes attached to its cytoplasmic surface, which give it a studded appearance under an electron microscope.

What the RER does:

• Ribosomes transfer newly synthesized proteins into the RER lumen.
• Proteins undergo structural modifications: folding or acquiring side chains.
• Modified proteins are incorporated into cellular membranes (ER itself or other organelles) or secreted from the cell (e.g., protein hormones, enzymes).
• The RER also makes phospholipids for cellular membranes.

Where RER is abundant:

• Cells that secrete proteins have abundant RER.
• Example: liver cells.

How proteins leave the RER:

• If proteins or phospholipids are not destined to stay in the RER, they travel via transport vesicles that bud from the RER membrane.

🧪 Smooth ER (SER)

Smooth endoplasmic reticulum (SER): continuous with the RER but has few or no ribosomes on its cytoplasmic surface.

SER functions include:

• Synthesis of carbohydrates, lipids, and steroid hormones.
• Detoxification of medications and poisons.
• Storing calcium ions.

Specialized SER in muscle cells:

• In muscle cells, a specialized SER called the sarcoplasmic reticulum stores calcium ions.
• These calcium ions trigger coordinated muscle contractions.

Don't confuse: RER and SER are continuous, but RER has ribosomes and handles protein work; SER lacks ribosomes and handles lipid/carbohydrate synthesis, detoxification, and calcium storage.

📦 The Golgi apparatus

📦 What the Golgi apparatus is

Golgi apparatus (also called the Golgi body): a series of flattened membranes responsible for sorting, tagging, packaging, and distributing lipids and proteins.

• Before reaching their final destination, lipids or proteins in transport vesicles need sorting, packaging, and tagging so they end up in the right place.
• The Golgi performs these tasks.

🔄 Golgi structure and orientation

Term	Meaning
Cis face	The side where transport vesicles from the ER arrive and fuse
Trans face	The opposite side, where modified and tagged cargo exits in secretory vesicles

🏷️ How the Golgi modifies and sorts cargo

Step-by-step process:

1. Transport vesicles bud from the ER and travel to the cis face of the Golgi.
2. Vesicles fuse with the cis face and empty their contents into the Golgi lumen.
3. As proteins and lipids travel through the Golgi, they undergo further modifications that allow them to be sorted.
   • Most frequent modification: adding short sugar molecule chains.
4. Proteins and lipids are then tagged with phosphate groups or other small molecules to travel to their proper destinations.
5. Modified and tagged cargo is packaged into secretory vesicles that bud from the trans face.

What happens to secretory vesicles:

• Some vesicles deposit their contents into other cell parts where they will be used.
• Other secretory vesicles fuse with the plasma membrane and release their contents outside the cell.

🌱 Additional Golgi roles in plant cells

• In plant cells, the Golgi apparatus synthesizes polysaccharides.
• Some polysaccharides are incorporated into the cell wall.
• Some are used by other cell parts.

📊 Where the Golgi is abundant

• Cells that engage in a great deal of secretory activity have an abundance of Golgi.
• Examples: salivary gland cells (secrete digestive enzymes), immune system cells (secrete antibodies).

🚚 Protein synthesis and transport pathway

🚚 The complete journey

From ribosome to destination:

1. Ribosomes synthesize proteins and transfer them into the RER lumen.
2. Proteins undergo structural modifications in the RER (folding, side chains).
3. Proteins may be incorporated into membranes or prepared for secretion.
4. Transport vesicles bud from the RER membrane carrying proteins and lipids.
5. Vesicles travel to and fuse with the Golgi's cis face.
6. Cargo travels through the Golgi, undergoing further modifications (e.g., addition of carbohydrate chains).
7. Cargo is tagged for proper destination.
8. Secretory vesicles bud from the Golgi's trans face.
9. Vesicles either deliver cargo to other cell parts or fuse with the plasma membrane to release contents outside the cell.

🖼️ Integral membrane protein example

The excerpt describes an illustration showing:

• A green integral membrane protein is modified in the ER by attachment of a purple carbohydrate.
• Vesicles with the integral protein bud from the ER and fuse with the Golgi's cis face.
• As the protein passes along the Golgi's cisternae, more carbohydrates are added.
• After synthesis is complete, it exits as an integral membrane protein in a vesicle that buds from the Golgi's trans face.
• When the vesicle fuses with the cell membrane, the protein becomes an integral portion of that cell membrane.

Don't confuse: Proteins synthesized in the ER lumen can end up in different membranes (ER, other organelles, or plasma membrane) or be secreted outside the cell—the Golgi's tagging determines the final destination.

💡 Functional examples

💡 Heart failure and the ER

• Heart failure does not mean the heart has stopped; it means the heart can't pump with sufficient force to transport oxygenated blood to all vital organs.
• Cardiac muscle tissue comprises the heart wall.
• Heart failure occurs when cardiac muscle cells' endoplasmic reticula do not function properly.
• Result: an insufficient number of calcium ions are available to trigger sufficient contractile force.
• Cardiologists (doctors who specialize in treating heart diseases) diagnose and treat heart failure.

💡 Form follows function

• Cells that secrete large amounts of protein have abundant RER (e.g., liver cells).
• Cells with high secretory activity have abundant Golgi (e.g., salivary gland cells, immune system cells).
• This pattern shows that organelle abundance matches the cell's functional needs.