McGraw-Hill Education 500 Review Questions for the MCAT Biology 2nd

🧭 Overview

🧠 One-sentence thesis

This excerpt provides only copyright information, table of contents, and introduction material for an MCAT biology review book, with no substantive content about amino acids and proteins.

📌 Key points (3–5)

• The excerpt contains legal/copyright notices, author information, and a general table of contents.
• The introduction describes the book's purpose: 500 multiple-choice questions for MCAT biology preparation.
• A few partial questions from Chapter 2 (Molecular Biology) appear at the end, covering PCR and DNA manipulation techniques.
• No actual content from Chapter 1 (Amino Acids and Proteins) is present in this excerpt.
• The material is intended as independent practice to supplement textbooks and coursework.

📚 Book structure and purpose

📚 What this book offers

• 500 multiple-choice questions covering essential MCAT biology course material.
• Questions parallel the content and difficulty of actual MCAT exam questions.
• Each question includes a rationale explanation in the answer key.
• Covers 12 chapters spanning major biology topics (amino acids/proteins, molecular biology, genetics, metabolism, cells, viruses, reproduction, etc.).

🎯 Intended use

• Designed for final review in the weeks before the MCAT exam.
• Suitable for both students who study extra weeks in advance and those who prepare last-minute.
• Meant to supplement regular textbooks and classroom learning, not replace them.
• Goal: build skills and confidence for the actual exam.

🧬 Partial content visible (Chapter 2 fragments only)

🧬 PCR mechanism (Question 79)

The excerpt shows an incomplete question about polymerase chain reaction (PCR):

• The question asks: "What mechanism is used to separate complementary DNA strands from each other?"
• Answer choices include heating, DNA polymerase melting capability, bacterial ribosomes, restriction endonucleases, and sodium chloride.
• Note: This is from Chapter 2 (Molecular Biology), not Chapter 1.

🧬 DNA fragment isolation (Question 80)

Another incomplete question about gene isolation for cloning:

• Context: DNA is fragmented by enzymes; the question asks what is done next to purify fragments.
• Answer choices mention gradient ultracentrifugation, affinity chromatography, agarose gel electrophoresis, filtration, and bacterial incorporation.
• Note: Also from Chapter 2, not the amino acids/proteins chapter.

🧬 Translation (Question 81)

A third question begins but is cut off:

• Topic: "During translation, how is the..." (incomplete).
• Note: Translation relates to protein synthesis, which could connect to Chapter 1 topics, but the question is not complete in this excerpt.

⚠️ Limitation of this excerpt

⚠️ Missing substantive content

• The title references "Chapter 1 Amino Acids and Proteins Questions 1–42," but none of those questions appear in this excerpt.
• The excerpt consists primarily of:
  • Copyright and legal terms of use
  • ISBN and publication information
  • Author biography (Robert Stewart, PhD, Professor of Biology at Regent University)
  • Table of contents listing all 12 chapters
  • A brief introduction explaining the book's purpose
  • Fragments of 2–3 questions from Chapter 2 (not Chapter 1)
• No definitions, mechanisms, or concepts related to amino acids or proteins are present.

🧭 Overview

🧠 One-sentence thesis

This excerpt covers key molecular biology techniques and mechanisms—PCR strand separation, DNA fragment isolation, translation mechanics, and the proportion of protein-coding DNA in the human genome—that are essential for understanding genetic manipulation and gene expression.

📌 Key points (3–5)

• PCR mechanism: Heat is used to separate complementary DNA strands during the polymerase chain reaction.
• DNA fragment purification: After enzymatic fragmentation, agarose gel electrophoresis separates DNA fragments by size for isolation.
• Translation catalysis: Ribosomal RNA (rRNA) catalyzes the transfer of amino acids from tRNA to the growing polypeptide chain.
• tRNA synthesis: RNA polymerase III is responsible for synthesizing transfer RNA molecules.
• Common confusion: Only a small fraction (~3.6 cm out of 1.8 meters) of human DNA actually codes for proteins, not the majority.

🧬 PCR and DNA manipulation techniques

🔥 Strand separation in PCR

During PCR, heating is the mechanism used to separate complementary DNA strands from each other.

• Question 79 asks about the separation mechanism during polymerase chain reaction.
• The answer is heating (option A), not enzymatic activity or chemical additives.
• This is a physical denaturation process that breaks hydrogen bonds between base pairs.
• Don't confuse: DNA polymerase synthesizes new strands but does not separate existing ones through "melting capability."

🧪 DNA fragment isolation workflow

The excerpt describes a two-step process for gene isolation:

1. Fragmentation: Enzymes cut DNA into fragments
2. Purification: Agarose gel electrophoresis separates fragments (question 80, option C)

Method mentioned	Purpose	Why it works
Agarose gel electrophoresis	Separate DNA fragments	Fragments migrate based on size through the gel matrix
Gradient ultracentrifugation	Alternative separation	Not the standard method for this purpose
Affinity chromatography	Selective binding	Not typically used for size-based DNA separation

Example: After cutting genomic DNA with restriction enzymes, researchers load the mixture onto an agarose gel and apply electric current to separate fragments by size, allowing isolation of the desired gene.

🧬 Translation mechanisms

🔗 Amino acid transfer during translation

Question 81 addresses how amino acids move from tRNA to the growing protein chain.

The rRNA of the ribosome serves to catalyze the transfer from the tRNA to the polypeptide strand.

• This is a catalytic function of ribosomal RNA, not just structural support.
• The ribosome acts as a ribozyme (RNA enzyme) during peptide bond formation.
• Don't confuse: While proteins are part of the ribosome structure, the catalytic activity for peptide bond formation comes from rRNA (option C), not ribosomal proteins alone.

Key mechanism:

• The incoming tRNA brings an amino acid to the ribosome
• Ribosomal rRNA catalyzes the peptide bond formation
• The amino acid joins the nascent (growing) polypeptide chain
• No ATP is directly consumed in this transfer step (ruling out option B)

🧬 RNA synthesis and genome organization

📝 tRNA synthesis machinery

Question 82 asks which enzyme synthesizes transfer RNA.

RNA polymerase III is responsible for the synthesis of tRNA.

• Different RNA polymerases have specialized roles in eukaryotes
• RNA polymerase III specifically transcribes tRNA genes
• Don't confuse with:
  • RNA polymerase II: transcribes mRNA
  • DNA polymerase I or III: synthesize DNA, not RNA
  • RNase: degrades RNA rather than synthesizing it

📏 Protein-coding DNA proportion

Question 83 presents a striking fact about human genome organization:

• Total DNA length in one human nucleus: 1.8 meters (if laid end to end)
• Amount that codes for proteins: approximately 3.6 cm (option C)

This means:

• Only about 2% of human DNA codes for proteins (3.6 cm ÷ 180 cm = 0.02)
• The vast majority of genomic DNA is non-coding
• Common confusion: Students often assume most DNA codes for proteins, but the actual proportion is surprisingly small

Example: If you could stretch out all the DNA from a single cell nucleus, it would be nearly 2 meters long, yet a segment only as long as your thumb would contain all the protein-coding information.

🧭 Overview

🧠 One-sentence thesis

This chapter tests understanding of core genetics concepts including inheritance patterns, chromosomal abnormalities, meiosis, mutations, and how genetic variation drives evolutionary change in populations.

📌 Key points (3–5)

• Inheritance patterns: Simple dominance, codominance, incomplete dominance, sex-linked traits, and epistasis each produce distinct phenotypic ratios and expression patterns.
• Chromosomal mechanics: Meiosis produces haploid gametes through segregation and independent assortment; nondisjunction causes abnormal chromosome numbers (aneuploidy).
• Mutations and their effects: Mutations are any DNA sequence changes; effects range from silent (no protein change) to lethal, depending on location and type.
• Common confusion: Genotype vs phenotype—homozygous dominant and heterozygous individuals can share the same phenotype despite different genotypes; also, sex-linked recessive traits require different genotypes in males (hemizygous) vs females (homozygous).
• Population genetics and selection: Allele frequencies change over time through selection pressures, as demonstrated by the parrot color study showing directional selection favoring the yellow variant.

🧬 Chromosomes and Cell Division

🧬 Human chromosome numbers

• Diploid number: 46 chromosomes total in somatic cells (body cells)
• Haploid number: 23 chromosomes in gametes (sex cells)
• Organization: 23 pairs of chromosomes in somatic cells
• Don't confuse: Gametes contain one of each of the 23 chromosomes, not two of each (question 93 tests this).

🔄 Meiosis vs mitosis

Process	Starting cell	Daughter cells	Genetic variation
Meiosis	Diploid	4 haploid, genetically different	High (shuffling, recombination)
Mitosis	Diploid	2 diploid, genetically identical	None

Meiosis: the process by which a mother cell gives rise to four genetically different daughter cells.

• Meiosis changes chromosome number from diploid to haploid
• Alternate forms of genes (alleles) are shuffled
• Provides offspring with new gene combinations
• Occurs in both ovaries and testes (question 88 tests this misconception)

⚠️ Nondisjunction and chromosomal abnormalities

Nondisjunction: failure of chromosomes to separate properly during cell division, resulting in abnormal chromosome numbers.

• Example: XXY sex chromosome combination (Klinefelter syndrome) results from nondisjunction, not gene deletion, duplication, or translocation (question 86)
• Aneuploidy: having an abnormal number of chromosomes
• Trisomy 21 (Down syndrome) and cancer cells are both examples of aneuploid cells (question 118)

🧪 Karyotyping

• Colchicine is commonly added to collected cells to better observe chromosomes (question 121)
• Amniocentesis is the best cell collection method for fetal karyotyping (question 124)

🧬 Inheritance Patterns and Genotypes

🧬 Simple dominance

• Homozygous dominant (e.g., RR) and heterozygous (e.g., Rr) individuals have the same phenotype but different genotypes (question 98)
• Example: If brown hair is dominant over black hair, both RR and Rr animals have brown hair

Genotype RR indicates: homozygous dominant on any chromosome (question 92)

• Test cross with heterozygote produces 1:1 ratio (question 103)

🎨 Codominance

• ABO blood groups are under codominance inheritance control (question 87)
• Both alleles are fully expressed
• Example: Blood type AB expresses both A and B antigens (question 106 contrasts this with incomplete dominance)

🌈 Incomplete dominance

Incomplete dominance: a pattern where the heterozygote shows a blended or intermediate phenotype.

• Example: Having medium-thickness hair from a parent with thin hair and a parent with thick hair (question 106)
• Don't confuse with codominance: In incomplete dominance, the result is a blend; in codominance, both traits are fully expressed

🔗 Sex-linked traits

• X-linked recessive traits:
  • Males need only one copy (hemizygous) to express the trait
  • Females must be homozygous to express the trait (question 95)
  • If a daughter expresses an X-linked recessive trait, she inherited it from both parents (question 104)
• If all males in a family are afflicted but females rarely are, the pattern is likely X-linked recessive (question 112)

🎭 Epistasis

Epistasis: when one gene affects or masks the expression of another gene.

• Most probable expression: When offspring with one phenotype (e.g., brown hair) are afflicted, but those with another phenotype (e.g., black hair) are healthy (question 110)
• Different from simple dominance, which involves alleles of the same gene

🧬 Genes, Loci, and Alleles

📍 Locus

Locus: the location of an allele on a chromosome (question 97).

• Not the gene itself, but its physical position
• Different alleles of the same gene occupy the same locus

🎲 Independent assortment

• Genes on different chromosome pairs will sort independently (question 99)
• They are not sex-linked and will not appear together in gametes consistently
• Law of Segregation: Gametes receive only one copy of each gene (question 111)

🧮 Gamete diversity

• An individual with genotype AaBBCcDd produces 8 different forms of gametes (question 108)
• Calculation: 2^n where n = number of heterozygous gene pairs (here: A, C, D = 3 heterozygous pairs, so 2^3 = 8)

📏 Centimorgan

Centimorgan: a measure of gene linkage (question 109).

• Indicates how closely genes are located on the same chromosome
• Related to recombination frequency

🧬 Mutations and Their Effects

🧬 Definition and types

Mutation: any change in the DNA sequence (question 94).

• Not necessarily detrimental or lethal
• Can have neutral, beneficial, or harmful effects

🤫 Silent and neutral mutations

• Silent mutation: DNA change that does not alter any protein (question 102)
• Can occur within introns (non-coding regions)
• Can be a neutral mutation with no phenotypic effect
• Cannot be a deletion mutation if no protein is changed (deletions typically alter reading frames)

🧬 Mutation effects on tRNA

• A deletion mutation in a gene coding for a single tRNA would most likely result in no phenotypic changes because of wobble (question 107)
• Wobble: flexibility in base pairing at the third codon position allows multiple tRNAs to recognize the same amino acid

🧬 Mitochondrial genetics

• Human cells contain only maternal mitochondria (question 101)
• Mitochondria replicate and function independently of the nucleus
• Mitochondrial genes more closely resemble prokaryotic than eukaryotic genes (supporting endosymbiotic theory)

🩺 Genetic Disorders

🩺 Specific disorders mentioned

Disorder	Key characteristic
Cystic fibrosis	Mutation in an ion channel protein (question 89)
Tay-Sachs disease	Mutation in a gene controlling lipid production (question 96)
Sickle cell anemia	Confers both affliction and advantage (malaria resistance) (question 105)
Klinefelter syndrome (XXY)	Results from nondisjunction (question 86)

🧬 Syndrome definition

Syndrome: a group of signs and symptoms that tend to appear together (question 100).

• Not necessarily a genetic disorder (though many are)
• Not always undefined or rare

💊 Phenotypic cure

Phenotypic cure: can correct the defective expression (question 122).

• Does not eliminate the defective gene in parents
• Does not prevent the disorder from being passed to offspring
• Does not replace the defective gene in offspring
• Only addresses the symptoms or expression, not the underlying genetic cause

📊 Penetrance

Penetrance: any difference between the percentage of a population having a defective gene and the percentage expressing that gene (question 125).

• Measures how often a gene produces its expected phenotype
• Not the same as dominance, epistasis, or Hardy-Weinberg equilibrium calculations

🩸 Blood Type Genetics

🩸 ABO system

• Under codominance control (question 87)
• A father with type A and mother with type B can have children of all blood types (A, B, AB, O), depending on parental genotypes (question 91)
• Example: If both parents are heterozygous (IAi and IBi), offspring can be type A, B, AB, or O

🩸 Transfusion compatibility

• If transfusion from Jim to Bill causes death, but Bill to Jim is safe, then Jim has type O blood (question 119)
• Type O is the universal donor (can give to anyone)
• Type O individuals can only receive type O blood
• Don't confuse: The scenario rules out Bill having type O (he would be the universal donor)

🩸 Rh factor

• Rh+ blood transfused to Rh- recipient can cause problems
• However, the question scenario (119) points to ABO incompatibility as the best explanation

🧬 Crosses and Ratios

🧬 Monohybrid cross

• GGHH crossed with gghh produces F1 generation all GgHh
• F2 generation (crossing F1 × F1) most common genotype: GgHh (question 120)
• This is a dihybrid cross; the 9:3:3:1 ratio applies to phenotypes, but GgHh is the most frequent genotype

🧬 Sex chromosome nondisjunction

• If nondisjunction of X chromosomes occurs during ovum formation, two ova genotypes are produced
• If fertilized normally (by X or Y sperm), possible resulting genotypes: XXY, X0 (question 123)
• One ovum has XX (fertilized → XXY or XXX)
• One ovum has no sex chromosome (fertilized → X0 or Y0; Y0 is not viable)

🦜 Population Genetics and Evolution (Parrot Study)

🦜 Study overview

• Ornithologists discovered parrots with near-fluorescent yellow pigment (mutation) in a population normally red
• Yellow birds were more conspicuous (expected selection pressure against them)
• Study followed population for 10 years, tracking percentage of yellow vs red birds

🦜 Mutation timing

• The mutation most likely occurred before the study began (question 113)
• Yellow birds were already present at the start of observations

🦜 Population change between years 6 and 8

• Large change most likely due to: introduction of a strain of bird flu that increased mortality within the red group (question 114)
• This would explain a sudden increase in yellow percentage (red birds dying off)
• Not due to changes in yellow group directly, but to red group decline

🦜 Behavior and plumage

• None of the above conclusions can be drawn about behavior-plumage relationships (question 115)
• The excerpt provides no evidence that pigment is caused by food preference, sun exposure, or bathing habits

🦜 Mating preference

• In year 10, yellow females showed 2% mating bias for yellow males
• Conclusion: The bias is too small to produce significant change in color distribution (question 116)
• 2% preference is a weak selective force

🦜 Type of selection

• The change in population colors strongly suggests directional selection (question 117)
• One variant (yellow) is increasing in frequency over time
• Not stabilizing selection (which favors intermediate forms)
• Not allopatric speciation (no geographic isolation mentioned)
• Not behavioral isolation (though mating preference is noted, it's weak)

🧭 Overview

🧠 One-sentence thesis

This chapter tests understanding of cellular metabolism through questions covering energy production pathways (glycolysis, TCA cycle, electron transport), molecular structures (carbohydrates, lipids, nucleotides), enzyme mechanisms, and the relationships between metabolic intermediates.

📌 Key points (3–5)

• Core pathways tested: glycolysis, TCA (Krebs) cycle, oxidative phosphorylation, and fermentation as alternative respiration routes.
• Energy accounting: ATP yield from glucose oxidation, the role of NADH/FADH₂ in electron transport, and substrate-level vs oxidative phosphorylation.
• Molecular relationships: distinguishing isomers (glucose/galactose as epimers, glucose/fructose), polymers (starch/glycogen/cellulose), and functional groups (fatty acids, glycosidic bonds).
• Common confusion: NADH vs NADPH differ in function (catabolic vs anabolic), not just the phosphate group; carbon-14 vs carbon-12 in dating experiments depends on isotope presence, not survival.
• Regulatory mechanisms: feedback inhibition, equilibrium constants related to free energy, and homeostasis as biological equilibrium maintenance.

🌱 Plant metabolism and experimental design

🌱 Carbon isotope experiments (Q126–127)

The passage describes plants grown in controlled gas chambers with different carbon dioxide isotopes.

• Carbon-14 (¹⁴CO₂) atmosphere: Question 126 asks about carbon dating after two days of growth in radioactive ¹⁴CO₂.

  • Plants incorporate ¹⁴C through photosynthesis into their tissues.
  • Carbon dating measures ¹⁴C decay; newly incorporated ¹⁴C would make the plant material appear "younger" or recently formed compared to controls with atmospheric ¹⁴C ratios.
  • The question tests understanding that carbon dating reflects isotope ratios, not chronological age.

• Carbon-12 (¹²CO₂) atmosphere: Question 127 presents the same scenario with non-radioactive ¹²CO₂.

  • ¹²C is stable and does not decay; carbon dating relies on ¹⁴C presence.
  • Plants grown in pure ¹²CO₂ would have no ¹⁴C incorporated, making them "impossible to date" or appear extremely old (no detectable ¹⁴C).
  • Don't confuse: ¹²C is not harmful; plants do not require ¹⁴C to survive—it's merely a tracer isotope.

🌬️ Gas composition effects (Q128–130)

These questions test understanding of what plants actually need from the atmosphere.

• Pure nitrogen atmosphere (Q128): Despite nitrogen being "essential for amino acid and nucleic acid production," plants cannot use atmospheric N₂ directly.

  • Plants obtain nitrogen from soil (nitrates, ammonium), not from N₂ gas.
  • Without CO₂ and O₂, photosynthesis and respiration cannot occur → plants would die.
  • Example: Even with excellent soil nutrients (as stated in the passage), lack of atmospheric CO₂ is fatal.

• Pure carbon dioxide (Q129): Plants need CO₂ for photosynthesis but also require O₂ for cellular respiration.

  • Without O₂, mitochondrial respiration stops; plants cannot survive on photosynthesis alone (especially roots, non-green tissues).
  • The plants would die despite abundant CO₂.

• Low pressure, normal composition (Q130): One-tenth normal atmospheric pressure means one-tenth the partial pressure of each gas.

  • Gas exchange depends on partial pressure gradients; reduced pressure slows diffusion rates.
  • Plants would likely grow "near normally" but with reduced efficiency, not die immediately.

🔥 Cellular respiration pathways

🔥 TCA cycle components (Q131, Q159–160)

TCA cycle (tricarboxylic acid cycle): also called the Krebs cycle or citric acid cycle; a cyclic metabolic pathway that oxidizes acetyl-CoA to produce CO₂, ATP, NADH, and FADH₂.

• Products of the TCA cycle (Q131): CO₂, ATP (via GTP), NADH, and FADH₂ are all produced.

  • Acetyl-CoA is NOT a product; it is the input that "feeds into" the cycle (Q159).
  • Don't confuse: acetyl-CoA is consumed by the cycle, not generated by it.

• Cyclic vs linear processes (Q160): TCA, citric acid, Krebs, and tricarboxylic acid all refer to the same cyclic process.

  • Pyruvate is NOT cyclic; it is the linear end product of glycolysis that is then converted to acetyl-CoA before entering the TCA cycle.

⚡ Glycolysis details (Q135, Q163)

• Enzymatic steps (Q135): Glycolysis involves 10 enzymatic steps to convert glucose to pyruvate.

  • This is a specific factual detail about the pathway's complexity.

• Key enzyme and intermediate (Q163): Phosphofructokinase produces fructose 1,6-bisphosphate.

  • This is a major regulatory step in glycolysis (often subject to feedback inhibition).
  • Other pairings listed are incorrect enzyme-product matches.

🔋 Electron transport and ATP synthesis (Q136, Q141, Q145, Q152)

• Proton and electron transfer (Q136): Coenzyme Q (ubiquinone) transfers both protons and electrons.

  • Cytochromes typically transfer only electrons.
  • ATP synthase uses the proton gradient but doesn't transfer electrons itself.

• ATP yield in bacteria (Q141): Bacteria can produce 38 net ATP per glucose through oxidative phosphorylation.

  • The statement "the majority of ATP molecules are produced within the mitochondria" is NOT true for bacteria—bacteria lack mitochondria; they use their plasma membrane for electron transport.
  • This yield is greater than in human cells (which lose some efficiency transporting NADH into mitochondria).
  • The total includes substrate-level phosphorylation (glycolysis and TCA) and accounts for ATP invested in glycolysis.

• ATP per NADH (Q145): Each NADH through the electron transport chain produces approximately 3 ATP (though modern estimates are closer to 2.5).

  • This reflects the proton-motive force and ATP synthase efficiency.

• Chemiosmotic coupling (Q152): ATP synthase operates via chemiosmotic coupling.

  • The proton gradient across the membrane drives ATP synthesis as protons flow through ATP synthase.
  • This is distinct from symport (co-transport of two substances) or gated channels (which respond to ligands or mechanical stress).

🍷 Anaerobic processes (Q137–138, Q161)

• Final electron acceptors (Q137): In anaerobic respiration, sulfur, protons, iron, and nitrogen can serve as final electron acceptors.

  • Oxygen is NOT used in anaerobic respiration (by definition).
  • Example: Some bacteria use sulfate or nitrate when oxygen is unavailable.

• Fermentation (Q138): The process that results in buildup of organic waste compounds (like lactate or ethanol) is fermentation.

  • Fermentation regenerates NAD⁺ without a complete electron transport chain.
  • Organic waste accumulates because it is not fully oxidized to CO₂.

• Gluconeogenesis and fasting (Q161): Gluconeogenesis (synthesis of glucose from non-carbohydrate sources) is especially associated with fasting.

  • When dietary glucose is unavailable, the body synthesizes glucose from amino acids, lactate, or glycerol.
  • Don't confuse with fermentation or anaerobic respiration, which are about ATP production under low oxygen, not glucose synthesis.

🧪 Redox reactions and energy

🧪 Oxidation and reduction (Q132, Q143)

• NADH to NAD conversion (Q132): When NADH loses hydrogen (and electrons), it is oxidized.

  • Oxidation = loss of electrons/hydrogen; reduction = gain of electrons/hydrogen.
  • This process is also exergonic (releases energy), but the question asks for the categorization of the electron transfer itself.

• Negative free energy (Q143): A reaction with –ΔG is exergonic (releases energy).

  • Exergonic reactions are typically catabolic (breaking down molecules).
  • Both A (catabolic) and C (exergonic) are correct descriptors.
  • Don't confuse: endergonic reactions (+ΔG) require energy input and are typically anabolic.

🧪 NADH vs NADPH (Q164)

• Functional difference (Q164): NADH is used in catabolic (energy-releasing) reactions; NADPH is used in anabolic (biosynthetic) reactions.
  • The structural difference is the phosphate group, but the key distinction is their cellular roles.
  • Example: NADH feeds into the electron transport chain for ATP production; NADPH provides reducing power for fatty acid synthesis.

🧪 Free energy and equilibrium (Q155–156)

• Equilibrium constant purpose (Q155): The equilibrium constant (Kₑq) determines the composition of any system at equilibrium.

  • It does not calculate reaction rate (that's kinetics, not thermodynamics).
  • It reflects the ratio of products to reactants when the reaction is at equilibrium.

• Relationship to free energy (Q156): The natural logarithm of Kₑq equals –ΔG divided by RT.

  • Formula in words: ln(Kₑq) = –ΔG / (R × T), where R is the gas constant and T is temperature.
  • This links thermodynamics (free energy) to the equilibrium position.

🍬 Carbohydrate structures and relationships

🍬 Monosaccharides and isomers (Q153–154, Q157)

• Glucose and dextrose (Q153): Glucose and dextrose are the same molecule.

  • "Dextrose" is another name for D-glucose (the dextrorotatory form).
  • Don't confuse with fructose (a structural isomer) or starch/glycogen (polymers of glucose).

• Glucose and galactose (Q154): These are epimers.

  Epimers: isomers that differ in configuration at only one chiral carbon.

  • Glucose and galactose differ at the C-4 carbon.
  • Neither is a disaccharide; both are monosaccharides (single sugar units).

• Pentoses (Q157): Ribose and deoxyribose are pentoses (five-carbon sugars).

  • Glucose and lactose are hexoses or disaccharides, not pentoses.
  • DNA and RNA are polymers, not monosaccharides.
  • "Deoxyfructose" is not a standard biological molecule.

🍬 Polysaccharides and bonds (Q149, Q158)

• Glycosidic bonds (Q149): When monosaccharides polymerize, glycosidic bonds form.

  • Peptide bonds link amino acids; hydrogen bonds are non-covalent interactions.
  • Exergonic/endergonic describe energy changes, not bond types.

• Glycogen and starch analogy (Q158): "What glycogen is to starch, X is to Y" tests understanding of structural parallels.

  • Glycogen (animal storage polysaccharide) and starch (plant storage polysaccharide) are analogous.
  • The correct answer would pair similar structural or functional analogs (e.g., peptidoglycan/chitin as structural polymers in bacteria/fungi).

🍬 CO₂ origin and glucose oxidation (Q140, Q148)

• CO₂ in blood (Q140): CO₂ originates from glycolysis and the Krebs cycle in tissue cells.

  • It is NOT produced by conversion from O₂ or as the final electron acceptor (that's O₂'s role, producing H₂O).
  • CO₂ is a waste product of cellular respiration, transported in blood to the lungs.

• CO₂ from glucose (Q148): Fully oxidizing one glucose molecule releases 6 CO₂.

  • Glucose formula: C₆H₁₂O₆ → 6 CO₂ + 6 H₂O (plus energy).
  • This accounts for all six carbons in glucose.

🥩 Lipids and proteins

🥩 Fatty acids and lipids (Q146, Q165)

• Fatty acid definition (Q165): A carboxylic acid with a long aliphatic (hydrocarbon) tail describes a fatty acid.

  • Nucleic acids contain nucleotides; polysaccharides are carbohydrate polymers; peptides are amino acid chains.
  • Lipopolysaccharides are complex molecules in bacterial membranes, not simple fatty acids.

• Smoking point (Q146): Saturated fats have the highest burning (smoking) point.

  • Saturated fats lack double bonds, making them more stable at high temperatures.
  • Polyunsaturated fats and vegetable oils have lower smoking points due to double bonds that are more reactive.

🥩 Protein energy (Q139)

• Energy from protein oxidation (Q139): Proteins yield approximately 4 Calories per gram.
  • 6.5 g × 4 Cal/g = 26 Calories net energy.
  • This is lower than fats (9 Cal/g) but similar to carbohydrates (4 Cal/g).

🧬 Molecular bonds and structures

🧬 DNA structure (Q144)

• Hydrogen bonds in DNA (Q144): Hydrogen bonds hold the two strands of the DNA double helix together.
  • These must be broken for replication, transcription, and gene expression.
  • Covalent bonds form the sugar-phosphate backbone; hydrogen bonds are between complementary bases (A-T, G-C).

🧬 ATP hydrolysis (Q162)

• ATP hydrolysis products (Q162): Hydrolysis of ATP produces ADP, inorganic phosphate, and releases energy.
  • Water is a reactant in hydrolysis, not a product.
  • Glucose and ketone bodies are not produced by ATP hydrolysis.
  • Example: ATP + H₂O → ADP + Pᵢ + energy.

🔬 Enzymes and regulation

🔬 Feedback inhibition (Q142)

Feedback inhibition: a regulatory mechanism where the final product of a metabolic pathway inhibits an earlier enzyme in the pathway.

• This prevents overproduction and conserves resources.
• Example: If a cell has enough of a particular amino acid, that amino acid binds to and inhibits the first enzyme in its synthesis pathway.
• Don't confuse with competitive inhibition (a substrate analog blocks the active site) or noncompetitive inhibition (an inhibitor binds elsewhere on the enzyme).

🔬 Catalase in food industry (Q151)

• Catalase application (Q151): Catalase is used in cold pasteurization of milk.
  • Catalase breaks down hydrogen peroxide (H₂O₂), which is used as a sterilizing agent.
  • After sterilization, catalase removes residual H₂O₂ to prevent off-flavors.

🧫 Organism classification and processes

🧫 Heterotrophs and autotrophs (Q147)

• Heterotroph definition (Q147): An organism requiring organic compounds (like glucose) as its energy source is a heterotroph.
  • Autotrophs synthesize their own organic compounds from inorganic sources (e.g., plants via photosynthesis).
  • Chemotrophs obtain energy from chemical reactions; phototrophs from light.
  • Lithotrophs use inorganic substrates.

🧫 Homeostasis and Le Chatelier (Q133, Q150)

• Homeostasis enables steady state (Q133): Cells maintain homeostasis because they continually take up energy from the environment.

  • This allows them to maintain order and perform work despite the second law of thermodynamics.
  • Not all reactions are anabolic or exergonic; cells balance both types.

• Le Chatelier analogy (Q150): What Le Chatelier's principle (chemical equilibrium shifts) is to chemistry, homeostasis is to biology.

  • Both describe systems maintaining balance in response to changes.

🧫 Photosynthesis-related compounds (Q166)

• Fluorochromes, cytochromes, pigments (Q166): A compound associated with photosynthesis, bioluminescence, and apoptosis is likely a pigment or fluorochrome.
  • Pigments absorb and emit light (photosynthesis, bioluminescence).
  • Cytochromes are electron carriers in respiration.
  • Flavoproteins contain flavin cofactors; peptidoglycan is a bacterial cell wall component.

🧫 Apoptosis characteristics (Q167)

• Apoptosis features (Q167): Blebbing, DNA fragmentation, chromatin condensation, and cellular condensation are all associated with apoptosis (programmed cell death).
  • Inflammation is NOT characteristic of apoptosis; it is associated with necrosis (uncontrolled cell death).
  • Apoptosis is a clean, controlled process that does not trigger immune responses.

🧭 Overview

🧠 One-sentence thesis

This chapter tests understanding of eukaryotic cell structures, organelle functions, membrane transport mechanisms, and cellular processes through experimental scenarios and conceptual questions.

📌 Key points (3–5)

• Experimental design: Questions 168–172 analyze a yeast experiment measuring gas production from hydrogen peroxide breakdown, testing understanding of enzyme activity and experimental controls.
• Membrane transport mechanisms: Multiple questions distinguish between passive diffusion, channel-mediated transport, carrier-mediated transport, and active transport across membranes.
• Organelle structure and function: Questions cover the roles of mitochondria, endoplasmic reticulum, Golgi apparatus, nucleus, lysosomes, and other organelles in protein synthesis, transport, and cellular metabolism.
• Common confusion: Distinguishing between different transport types (gated vs. vesicular vs. transmembrane) and understanding which proteins move by which mechanism.
• Cytoskeleton and tissue types: Questions address microfilament functions, connective tissue classification, and epithelial tissue categories.

🧪 Experimental analysis: Yeast and hydrogen peroxide

🧪 The experimental setup

The passage describes three test tubes:

• Tube A: Yeast cells in 1% glucose solution + hydrogen peroxide
• Tube B: No cells, just glucose solution + hydrogen peroxide
• Tube C: Yeast cells in distilled water + hydrogen peroxide

All tubes were sealed with pressure sensors, then acid (HCl) was added after 5 minutes.

🔬 What the experiment measures

Question 168 asks what process produces the pressure. The correct interpretation involves:

• A cellular enzyme breaking down hydrogen peroxide
• Release of oxygen gas (O₂)
• Not CO₂ from respiration or acid degradation

🧫 Role of the acid addition

Question 169 examines the effect of adding HCl to tube A:

• The acid likely denatures the enzyme responsible for gas production
• This would stop further pressure increase
• The acid does not directly degrade cells or react with the gas

🎯 Purpose of control tubes

Question 171 asks about tube C (cells in distilled water):

• Helps determine the effect of cellular metabolism on gas production
• Distinguishes between glucose-dependent and glucose-independent processes
• Example: If tube C produces similar pressure to tube A, glucose is not required for the reaction

🧬 Enzyme identification

Question 172 asks which enzyme might be involved:

Catalase: an enzyme that breaks down hydrogen peroxide into water and oxygen

This fits the experimental observations of O₂ gas production.

🧱 Membrane structure and transport

🧱 Membrane composition and fluidity

Question 177 addresses what increases membrane fluidity:

• Shorter-chained phospholipids increase fluidity (less interaction between tails)
• Unsaturated fatty acids increase fluidity (kinks prevent tight packing)
• Don't confuse: Decreasing unsaturated fatty acids would decrease fluidity

Question 183 specifies the typical carbon chain length:

• Hydrophobic tails commonly range from 15–21 carbons
• This range ensures proper membrane characteristics

🚪 Types of membrane transport

Transport Type	Characteristics	Example from Questions
Simple diffusion	No protein needed, down gradient	Small nonpolar molecules
Channel-mediated passive	Through protein pores, down gradient	Ion channels (Q175)
Carrier-mediated passive	Protein carrier, down gradient	Facilitated diffusion
Carrier-mediated active	Protein carrier, against gradient, requires energy	Glucose against gradient (Q182)

Question 182 specifically asks about glucose moving against a gradient:

• Requires carrier-mediated active transport
• Cannot occur by simple or passive mechanisms
• Example: Moving glucose from low to high concentration requires energy input

🔄 Phospholipid movements

Question 179 lists motions phospholipids can perform:

• Lateral diffusion: moving sideways within the same layer
• Rotation: spinning around their axis
• Flexion: bending of the fatty acid tails
• Flip-flop: moving from one layer to the other (rare without enzymes)
• NOT inversion: this is not a recognized phospholipid motion

🧬 Glycosylated proteins

Question 189 addresses membrane proteins with attached sugars:

• Most frequently associated with cell signaling
• Serve as recognition markers
• Not primarily for permeability, anchoring, or limited to mitosis

🏭 Protein synthesis and transport

🏭 Protein transport mechanisms

Three major mechanisms are distinguished in questions 174, 180, and 184:

Vesicular transport (Q174):

• Movement from endoplasmic reticulum to Golgi apparatus
• Proteins packaged in membrane-bound vesicles
• Example: Secretory proteins moving through the endomembrane system

Gated transport (Q180):

• Movement through nuclear pores with specific protein accompaniment
• Example: Movement from cytosol into the nucleus
• Proteins remain folded during passage (Q195)

Transmembrane transport:

• Direct crossing of membranes
• Used for mitochondrial and peroxisomal import

🧬 Ribosomal protein synthesis

Question 185 traces ribosomal protein production:

• Synthesized in the cytosol
• Transported to the nucleus for subunit assembly
• Don't confuse: Not synthesized in rough ER, despite ribosomes being found there

🔧 Protein folding assistance

Question 190 identifies where chaperones function:

Chaperones: proteins that assist in proper folding of other proteins

• Best associated with protein folding within the endoplasmic reticulum lumen
• Also function in the cytosol
• Prevent misfolding and aggregation

📦 Chloroplast protein import sequence

Question 184 outlines the proper order:

1. Signal sequence binds to a receptor
2. Protein-receptor complex moves laterally
3. Signal sequence is removed
4. Protein refolds

This sequence ensures proper targeting and functional protein structure.

🏗️ Organelle structure and function

🏗️ Mitochondria

Question 197 asks about the primary mitochondrial function:

• Generates the bulk of ATP required for cellular functions
• Not the sole site of respiration or glycolysis
• Example: Glycolysis occurs in the cytosol, not mitochondria

Question 192 examines endosymbiotic theory evidence:

• Mitochondria have their own bacterial-like genome
• Carry out independent transcription and translation
• Surrounded by a double membrane
• NOT evidence: Having different RNA forms (this is actually true and supports the theory)

🧬 Nucleus structure and function

Question 195 describes nuclear features:

• Inner membrane lined with nuclear lamina binding chromosomes
• Outer membrane continuous with endoplasmic reticulum
• Incorrect statement: Pores are NOT composed of a single protein (they are multi-protein complexes)
• Proteins pass through in folded configuration

Question 202 identifies nucleolus function:

• Strongly associated with ribosomal construction
• Site of ribosomal RNA synthesis and ribosome assembly
• Not primarily for mRNA production or DNA synthesis

🧹 Lysosomes

Question 203 identifies the organelle for destroying phagocytosed materials:

Lysosome: organelle containing digestive enzymes that break down cellular waste and foreign materials

• Contains hydrolytic enzymes
• Functions in intracellular digestion
• Don't confuse with peroxisomes (which detoxify but don't digest phagocytosed materials)

📊 Peroxisomes

Question 200 asks which organelles can exceed 1,000 per cell:

• Peroxisomes can be present in such high numbers
• Also mitochondria in some cell types
• Not typically chloroplasts, endosomes, or Golgi apparatus

🔄 Endoplasmic reticulum

Question 201 examines RER vs. SER relationship:

• Correct: Ribosomes are concentrated near RER, lacking in SER
• Protein synthesis occurs on RER-bound ribosomes
• Proteins move from RER to SER and Golgi by vesicular transport
• Don't confuse: Glycosylation begins in RER, not exclusively in SER

🧬 Cytoskeleton and cell structure

🧬 Cytoskeletal components

Question 176 addresses cytoskeleton distribution:

• Found in eukaryotic and some prokaryotic cells
• Not exclusive to eukaryotes
• Present in both plant and animal cells
• Example: Even bacteria have cytoskeletal elements

Question 181 asks about microtubule subunits:

• Composed of α- and β-tubulin dimers
• Not actin, intermediate filaments, or antibody-like structures
• These dimers polymerize to form hollow tubes

🏃 Microfilament functions

Question 191 lists what microfilaments (actin) do:

• Amoeboid movement and cytoplasmic streaming
• Forming cleavage furrow during cytokinesis
• Maintaining cell shape
• Acting as contractile fibers in muscle
• NOT: Forming interior structure of flagella/cilia (that's microtubules)

🧱 Tissue types and cell specialization

🧱 Connective tissue

Question 178 asks what is NOT connective tissue:

• Collagenous tissue, cartilage, adipose, and blood are all connective
• Muscle is NOT connective tissue (it's muscle tissue)

Question 187 identifies embryonic origin:

• Fetal connective tissue derives from the mesoderm germinal layer
• Not ectoderm (nervous system, skin) or endoderm (gut lining)

Question 193 describes reticular connective tissue:

• Best associated with structural framework of soft organs
• Provides support for organs like spleen and lymph nodes
• Not for blood vessel lining or tendons

🧱 Epithelial tissue

Question 188 asks for an improper categorization:

• Stratified squamous, simple columnar, stratified cuboidal are proper
• Complex columnar is NOT a proper epithelial category
• Epithelia are classified as simple or stratified, not complex

Question 206 asks where M cells are found:

• Located in intestinal tissue
• Specialized epithelial cells in gut-associated lymphoid tissue
• Not in bone, cartilage, nervous, or muscle tissue

🩸 Cell repair capacity

Question 173 asks which cells have least repair ability:

• Muscle cells have limited regenerative capacity
• Hepatocytes (liver), fibroblasts, and chondrocytes have better repair abilities
• Example: Heart muscle damage is often permanent because cardiac muscle cells rarely divide

💀 Apoptosis (programmed cell death)

💀 Apoptosis characteristics

Question 167 asks what is NOT associated with apoptosis:

• Blebbing, DNA fragmentation, chromatin condensation, cellular condensation all occur
• Inflammation does NOT occur (distinguishes apoptosis from necrosis)
• Apoptosis is a "clean" death without inflammatory response

💀 Apoptosis sequence

Question 194 outlines the proper order:

1. Chromosome condensation
2. Nuclear fragmentation
3. DNA digestion
4. Cytoplasmic fragmentation
5. Bleb formation

💀 Apoptosis machinery

Question 204 identifies components involved:

• Cytochrome c (released from mitochondria)
• Death receptors (on cell surface)
• Caspases (proteases that execute cell death)
• Apoptosomes (protein complexes activating caspases)
• NOT peroxisomes: these are not part of apoptosis machinery

🔬 Additional cellular concepts

🔬 Ion gradients

Question 186 asks about calcium concentration:

• Calcium in body fluids is 10,000 times higher than inside cells
• This steep gradient is maintained by active transport
• Important for cell signaling when calcium enters cells

🔬 Glucose transport regulation

Question 196 asks what prevents glucose from leaving epithelial cells into the intestinal lumen:

• Glucose is imported with sodium symport
• Transporters are directional and located on specific membrane sides
• The sodium-potassium pump maintains the sodium gradient driving glucose import

🔬 Cancer traits

Question 199 asks what is NOT a common cancer trait:

• Evasion of apoptosis, self-production of growth signals, self-sustained angiogenesis, and insensitivity to tumor suppression are all common traits
• Mutagenesis by chemicals or radiation is a cause, not a trait of cancer cells

🔬 Membrane protein functions

Question 208 lists membrane protein functions:

• Transporting substances, anchoring structure, serving as receptors, enzymatic activity
• NOT storing materials: this is not a primary membrane protein function
• Example: Storage typically occurs in organelles or cytoplasm, not in membrane proteins themselves

🧭 Overview

🧠 One-sentence thesis

This chapter tests understanding of bacterial staining techniques (especially Gram stain), viral and bacterial structures and replication, genetic mechanisms in prokaryotes, and how to distinguish viruses from bacteria and other microorganisms.

📌 Key points (3–5)

• Gram stain mechanics: The procedure uses crystal violet, iodine, ethanol wash, and safranin to differentiate bacteria by cell wall thickness—thick-walled cells retain blue, thin-walled cells turn red.
• Viral vs bacterial structures: Viruses lack metabolism and cell walls but have capsids/envelopes; bacteria have cell walls (often peptidoglycan), ribosomes, and metabolize independently.
• Bacterial genetics: Bacteria exchange DNA horizontally via transformation (naked DNA uptake), transduction (phage-mediated), and conjugation (plasmid transfer); mutations can restore phenotype without restoring original genotype (suppressor mutations).
• Common confusion—obligate intracellular parasites: Both viruses and rickettsia are obligate intracellular parasites, but viruses lack metabolism while rickettsia do metabolize host resources.
• Growth and replication: Bacteria divide by binary fission with predictable generation times; viruses follow attachment → penetration → uncoating → biosynthesis → maturation → release.

🔬 Gram stain procedure and interpretation

🔬 The four-step staining process

The Gram stain differentiates bacteria based on cell wall structure:

1. Crystal violet (60 sec) — primary stain, colors all cells blue
2. Iodine (30 sec) — mordant, forms complex with crystal violet
3. Ethanol wash (10–15 sec) — decolorizer, removes stain from thin-walled cells
4. Safranin (60 sec) — counterstain, colors decolorized cells red

The Gram stain is the most common bacteriologic stain used in the clinical laboratory.

🧱 What determines final color

• Cells with thick cell walls (containing peptidoglycan) retain the crystal violet-iodine complex after ethanol wash → appear blue (Question 209: A or B).
• Cells with thin cell walls lose the complex during ethanol wash and take up safranin → appear red (Question 209: C).
• Cells lacking a cell wall would not retain stain effectively.

⚠️ What happens if steps are skipped

Step skipped	Effect	Reason
Iodine (Q210)	All cells stain red (D)	No mordant to lock crystal violet; ethanol removes it from all cells
Ethanol (Q211)	All cells stain blue (A)	No decolorization; all cells retain crystal violet
Heat fixation (Q212)	No cells on slide, no color (B)	Cells not adhered to slide, wash away
Extended crystal violet (Q213)	No effect on final colors (C)	Extra time doesn't change which cells retain stain after ethanol

Don't confuse: The iodine step is not optional—it forms the complex that thick-walled cells retain. Without it, even thick-walled cells lose the primary stain.

🦠 Bacterial structures and functions

🦠 Cell wall composition

What chitin is to a fungus, peptidoglycan is to a bacterium (Question 216: C).

• Peptidoglycan is the structural polymer in bacterial cell walls.
• The Gram stain (Question 233: E) differentiates the two major types of bacterial cell walls.

🏴 Flagella structure

The basal bodies of bacterial flagella are embedded into the cell membrane (Question 215: D).

• Not the cell wall, not the cytosol.
• This anchoring allows rotation for motility.

🛡️ Endospores

Endospores are a survival mechanism for bacteria that is formed when resources become limited or conditions hostile (Question 217: C).

• Not asexual reproduction (that's binary fission).
• Not sexual reproduction or post-conjugation structures.
• Not fully metabolizing—they are dormant, resistant structures.
• Example: When nutrients run out, some bacteria form endospores that can survive extreme conditions until conditions improve.

🧬 Binary fission

Bacteria divide by binary fission (Question 218: B), not mitosis or meiosis.

• Eukaryotic cells divide by mitosis; bacteria use a simpler process.
• Each daughter cell receives a copy of the circular chromosome.

🧬 Bacterial genetics and horizontal gene transfer

🧬 Types of mutations

Suppressor mutation (Question 221: C) restores a bacterial phenotype similar to wild type without restoring the original genotype.

• Reversion/back mutations restore the original DNA sequence.
• Frame-shift mutations alter the reading frame.
• Conditional mutations are expressed only under certain conditions.
• Example: A second mutation elsewhere compensates for the first mutation's effect, so the bacterium looks normal again but has two mutations instead of zero.

🔄 Horizontal gene transfer mechanisms

Mechanism	Description	Example from excerpt
Transformation (Q230, Q242)	Uptake of naked DNA from environment	A virus stripped of its capsid could infect via this process (Q230: B)
Transduction (Q242)	Phage-mediated DNA transfer	Generalized: lysogenic phage packages random DNA (Q242: E)
Conjugation (Q245)	Direct cell-to-cell transfer via pili	Most common mechanism for antibiotic resistance acquisition (Q245: C)

Don't confuse transformation with other processes: It is not the only mechanism for genetic mixing (conjugation and transduction also exist), and it is not related to mitochondrial function or endospore formation (Question 230).

🧰 Genetic engineering tools

• pBR322 (Question 223) is a plasmid (A) used in bacterial genetic engineering.
• Replica plating (Question 224) is used for detection of nutritionally deficient organisms (D).
• Metabolic plasmids (Question 225: C) convey extra degradative or nitrogen-fixing pathways.

🦠 Viruses: structure, replication, and classification

🦠 Viral structure basics

All viruses share certain features but differ in others:

• All viruses: crystallizable, incapable of metabolism, show eclipse period, do not grow or differentiate (Question 240).
• Not all viruses have a lipid bilayer membrane (Question 240: B)—only enveloped viruses do.

Polyhedral virus vs bacterial coccus (Question 214): The only similarity is the relative overall general shape (B). Their genomes, walls/coats, and lifestyles differ fundamentally.

🔄 Viral replication sequence

The proper sequence for viral replication is: attachment → penetration → uncoating → biosynthesis → maturation → release (Question 235: C).

• Attachment: virus binds to host cell receptors.
• Penetration: virus or its genome enters the cell.
• Uncoating: capsid is removed, releasing the genome.
• Biosynthesis: viral components are synthesized using host machinery.
• Maturation: new viral particles are assembled.
• Release: new viruses exit the host cell.

Don't confuse the order: Uncoating must happen before biosynthesis; maturation must happen before release.

🧬 Viral genome types

Genome type	Examples (from excerpt)
Double-stranded DNA (Q219)	Bacteriophage T4, variola (B)
Ambisense (Q238)	Can be translated in both 5′→3′ and 3′→5′ directions (A)
Positive sense	Can be directly translated
Negative sense	Must be transcribed to positive sense first

Multipartite viruses and viroids (Question 226) are both associated with plants (D).

🦠 Bacteriophages

An infectious agent with complex protein structure, often incorporating base plates or tail fibers, best describes a T-even bacteriophage (Question 244: A).

Why bacteriophages don't cause human disease (Question 246): Human cells do not have the proper phage receptors (C).

• Bacteriophages are specific to bacterial hosts.
• They can be used as "antibiotics" because they only infect bacteria.

🧫 Bacterial physiology and metabolism

🧫 Oxygen requirements

Facultative anaerobe (Question 227): Can grow with or without oxygen; no gas would be toxic to it. The question asks which gas would be toxic, but facultative anaerobes tolerate oxygen, so the answer is likely none of the common gases listed or a trick question. (The excerpt does not provide a clear answer; chlorine (E) might be toxic as a disinfectant, but that's not typical metabolism-related toxicity.)

Hydrogen peroxide test (Question 236): If bubbles form, the organism probably produces catalase or peroxidase, indicating it is likely aerobic (B).

• Aerobic organisms break down hydrogen peroxide (a toxic byproduct of aerobic metabolism) into water and oxygen.
• Bubbles = oxygen gas released.

📈 Bacterial growth phases

Bacterial cultures in closed systems progress through four phases (Question 232):

1. Lag phase: adaptation, little division
2. Log phase: exponential growth
3. Stationary phase: growth = death
4. Logarithmic decline phase: death > growth, greatest ratio of dead to living cells (D)

Generation time calculation (Question 231): If generation time is 20 minutes and you start with 10 cells, after 3 hours (180 min = 9 generations):

• Number of cells = 10 × 2⁹ = 10 × 512 = 5,120 (A).

🧪 Disinfection

Halogens (Question 243) provide disinfection by denaturing most organic materials (B).

• Not by osmotic imbalance, cell wall disruption, or pH changes.

🧬 Special topics: prions, mobile elements, and molecular biology

🧬 Prions

An infectious agent lacking both RNA and DNA suggests a prion (Question 241: E).

• Prions are misfolded proteins that cause disease without nucleic acids.
• Not a lab error, not a mutant virus, not a new genomic material.

🧬 Mobile genetic elements

LTR retrotransposon (Question 247: B) has great similarity to certain types of viruses.

• Retrotransposons use reverse transcriptase, similar to retroviruses.

🧬 RNA polymerase function

RNA polymerase reads a template DNA strand 3′ to 5′ and synthesizes an RNA strand 5′ to 3′ (Question 248: E).

Don't confuse: RNA polymerase synthesizes RNA, not DNA. It reads the template strand in the 3′→5′ direction to build the new RNA strand in the 5′→3′ direction.

🧬 Shine-Dalgarno sequence

The Shine-Dalgarno sequence is found in the leader sequence of mRNA (Question 249: D).

• Not in promoter or operator regions.
• Not on intron edges.
• It is a ribosome binding site in prokaryotic mRNA.

🩺 Clinical and applied microbiology

🩺 Specific pathogens and treatments

• Isoniazid (INH) (Question 222) is used to treat Mycobacterium sp. (A), e.g., tuberculosis.
• Genital warts (Question 228) are caused by a virus (A) (human papillomavirus).
• Inhalation anthrax (Question 237): Administer antibiotics immediately (D). Anthrax is bacterial (Bacillus anthracis), not viral, so antibiotics work.

🩺 Organism identification

Organism lacking cell wall but with 70S ribosomes and circular double-stranded genome (Question 239): This is a eubacterium (C), likely a Mycoplasma or similar.

• 70S ribosomes = prokaryotic.
• Circular dsDNA = bacterial.
• No cell wall = some bacteria naturally lack walls (e.g., Mycoplasma).

Don't confuse: Protozoa and animals are eukaryotic (80S ribosomes, linear chromosomes). Fungi have cell walls.

🩺 Mutant bacterium using DNA as carbon source

If a mutant bacterium could use DNA as a sole carbon source (Question 229), you would be unconcerned because most bacteria have this ability (C).

• Bacteria commonly degrade extracellular DNA for nutrients.
• It would not consume its own DNA (that would be lethal).
• Not inherently pathogenic or lethal to humans.

🧬 Comparisons: bacteria vs fungi vs viruses

🧬 Bacteria and fungi similarities

Bacteria and fungi are alike in that they both can exist in unicellular form (Question 234: A).

• Their cell walls are not composed of the same material (peptidoglycan vs chitin/cellulose).
• Their genomes and ribosomes differ (prokaryotic vs eukaryotic).
• Bacteria do not have sexual reproduction in the eukaryotic sense.

🧬 Viruses and rickettsia

Similarities (Question 220): Both are obligate intracellular parasites (D).

• Differences: Rickettsia metabolize host resources; viruses do not. Rickettsia are bacteria; viruses are acellular.

Don't confuse: Being an obligate intracellular parasite does not mean both metabolize or both spread by sexual contact. Only the dependency on a host cell is shared.

🧭 Overview

🧠 One-sentence thesis

This chapter tests understanding of cellular division, gene expression mechanisms, chromosome structure, and the processes that control cell differentiation and reproduction through a series of multiple-choice questions covering topics from organelle identification to mitosis, meiosis, and epigenetics.

📌 Key points (3–5)

• Cellular division structures: Questions focus on identifying and sequencing mitotic structures (centrioles, kinetochores, centromeres, spindle microtubules) and understanding their roles during metaphase and chromosome movement.
• Gene expression control: Multiple questions address mechanisms including epigenetics (histone methylation/acetylation), oncogenes, proto-oncogenes, and how mutations affect cellular growth regulation.
• Chromosome organization: Covers nucleosomes, chromatin packaging hierarchy, telomeres, centromeres, and DNA packaging from nucleosome to chromosome level.
• Common confusion: mitosis vs. meiosis: The excerpt distinguishes these by number of reduction divisions, genetic composition of resulting cells, amount of DNA, and involvement of genetic recombination—not by G₁ phase enzymes.
• Stem cells and differentiation: Questions explore pluripotent stem cells, terminal differentiation, and how genetically identical cells can produce diverse cell types through mechanisms like alternate splicing and mobile genetic elements.

🧬 Chromosome Structure and Organization

🧬 Nucleosome definition and composition

A nucleosome is described as "a cluster of four pairs of proteins supporting 146 nucleotide base pairs with attached linker DNA."

• Not eight identical proteins; it is four pairs of proteins (eight total histones, but in pairs).
• The DNA wraps around this protein core: 146 base pairs plus linker DNA connecting to the next nucleosome.
• Example: Think of nucleosomes as beads on a string, where each bead is the histone cluster and the string is the DNA.

🎯 Telomeres and centromeres

Telomeres are "repetitive sequences that are found on the ends of chromosomes."

• Telomeres protect chromosome ends; they are not coding sequences.
• Both telomeres and centromeres are "rich in simple-sequence repeated DNA."
• Microsatellites also share this repetitive DNA characteristic.
• Don't confuse: Centromeres are where spindle fibers attach during division; telomeres are protective caps at chromosome ends.

📦 Chromatin packaging hierarchy

The proper sequence is: nucleosome → chromatin fiber → heterochromatin → chromosome

• Nucleosome is the first level (DNA + histones).
• These coil into chromatin fibers.
• Chromatin fibers condense into heterochromatin (tightly packed regions).
• Heterochromatin further organizes into visible chromosomes during division.

🔬 Mitosis Structures and Mechanisms

🔬 Metaphase structure sequence

Scanning from one pole to the opposite during metaphase: Centriole → spindle microtubules → kinetochore → centromere → kinetochore → spindle microtubules → centriole

• Centrioles are at the poles (opposite ends of the cell).
• Spindle microtubules extend from centrioles toward the center.
• Kinetochores are protein structures that attach to centromeres.
• Centromere is the central point where sister chromatids join.
• The structure is symmetrical from pole to pole.

🔗 Centromere vs. kinetochore relationship

"A kinetochore attaches to the centromere during mitosis."

• The centromere is a DNA region on the chromosome.
• The kinetochore is a protein structure that forms at the centromere.
• Spindle microtubules attach to kinetochores, not directly to centromeres.
• Both are associated with cellular division, so options claiming only one is involved are incorrect.

⚙️ Chromosome movement requirements

"Molecular motors attached to microtubules" are required for chromosome movement.

• Not myosin at kinetochores (myosin is for muscle contraction).
• Not microfibril attachment to nuclear membrane.
• Not histone attachment to telomeres.
• Microtubules must attach to spindle poles, but the movement itself requires molecular motors (motor proteins like dynein and kinesin).

🌟 Asters in mitosis

"Asters form around both centrosomes."

• Asters are star-shaped microtubule arrays radiating from centrosomes.
• They do not attach to telomeres or manufacture molecular motors.
• Telomerases (which maintain telomeres) are unrelated to aster formation.

🆕 Five stages of mitosis

The new stage is called prometaphase.

• Traditional four stages: prophase, metaphase, anaphase, telophase.
• Prometaphase occurs between prophase and metaphase, when the nuclear envelope breaks down and kinetochores attach to spindle microtubules.

❓ Nuclear envelope during mitosis

"No; it remains intact in lower eukaryotes."

• In most eukaryotes, the nuclear envelope disassembles during mitosis.
• However, some lower eukaryotes (simpler organisms) keep the nuclear envelope intact throughout division.
• Don't assume all eukaryotes follow the same mitotic pattern.

🧪 Gene Expression and Regulation

🧪 Epigenetic mechanisms

The excerpt presents scenarios involving histone modifications:

• Histone acetylation: Can change gene expression between observations under identical environmental conditions.
• Histone methylation: Associated with cells that have extensive modifications affecting differentiation potential.
• These chemical modifications to histones alter gene accessibility without changing DNA sequence.

🔄 Pluripotent stem cells

A pluripotent stem cell is "a cell that can terminally differentiate into any of a number of final cell forms."

Key facts from the excerpt:

• "These cells can be produced from adult cells by genetic manipulation."
• They are not found only in embryos.
• They are not the same as cancer cells (though both involve growth regulation).
• Adult bone marrow contains stem cells, but the excerpt distinguishes pluripotent cells as producible through manipulation.

🧬 Proto-oncogenes and oncogenes

A proto-oncogene is "a normal important growth-regulating gene."

• Proto-oncogenes are normal, functional genes that regulate cell growth.
• When mutated, they can become oncogenes (cancer-causing genes).
• "A mutated oncogene often prevents apoptosis" (programmed cell death).
• Example: HPV's E7 oncogene protein binds to protein Rb, preventing the infected cell from controlling its own growth.

🛡️ The p53 protein

"It regulates the rate of cellular division."

• The p53 gene product controls cell cycle progression.
• HPV can cause cancer by interfering with p53 protein, leading to cell death dysregulation.
• Not primarily about triggering division or selecting gene expression order; it's about regulating the rate of division.

🧩 Gene expression control mechanisms

Mechanism	What it does	Example from excerpt
Alternate splicing	Produces different proteins from one mRNA	Two different proteins from a single lymphocyte mRNA strand
Mobile genetic elements	Creates genetic diversity in mature cells	Bone marrow stem cells → genetically unique lymphocytes via "random movement of DNA segments"
Epigenetic control	Changes expression without altering DNA sequence	Histone methylation/acetylation affecting differentiation

🔁 Cell Division Processes

🔁 Gamete formation summary

The simplest complete summary is: 2n → 4n → 2n → 1n

• Starts with diploid cell (2n).
• DNA replication creates 4n.
• First reduction division returns to 2n.
• Second reduction division produces haploid gametes (1n).
• Don't confuse with mitosis, which maintains chromosome number: effectively 2n → 2n.

🆚 Mitosis vs. meiosis differences

Feature	Mitosis	Meiosis
Amount of DNA in resulting cells	Same as parent (2n)	Half of parent (1n)
Genetic composition	Identical to parent	Genetically unique (recombination)
Number of reduction divisions	Zero (maintains ploidy)	Two (reduces ploidy)
Genetic recombination	No	Yes

NOT a difference: "The enzymes produced during the G₁ phase"—both processes use the same G₁ enzymes.

🔄 Cell cycle control

"The signal that initiates cell cycling through to the process of mitosis is controlled by cyclins."

• Cyclins are regulatory proteins that control cell cycle progression.
• They work with cyclin-dependent kinases (CDKs) to trigger mitosis.
• Not controlled by DNA polymerase, ribulose biphosphate, or general phosphoprotein levels alone.

🧬 Mitochondrial replication timing

Mitochondria replicate during the S phase.

• S phase is when DNA replication occurs in the nucleus.
• Mitochondria must replicate before cytokinesis to ensure both daughter cells receive sufficient numbers.
• Not during G₁, G₂, metaphase, or G₀ (resting phase).

🧫 Cellular Differentiation and Specialization

🧫 Cellular determination

The process whereby "a single cell will divide into two genetically identical daughter cells that will, in turn, differentiate into cells that will follow separate differentiation pathways is called cellular determination."

• Starts with identical cells (same genome).
• Through determination, cells commit to different fates.
• This is distinct from selection or transposition.

🔀 Genetic diversity in lymphocytes

"How is it that bone marrow stem cells all have the exact same genome, but mature lymphocytes derived from those stem cells, when released into circulation, are all genetically unique?"

Answer: Alternate DNA excision and splicing

• Also described as "random movement of DNA segments by mobile genetic elements."
• This is a somatic (body cell) genetic rearrangement, not inherited.
• Example: Antibody diversity arises from DNA rearrangement in developing B cells, not from alternate mRNA splicing alone.

🧬 Polycistronic vs. dicistronic messages

When a lymphocyte produces two different proteins from a single mRNA:

• The message can be dicistronic (codes for two proteins).
• Alternate splicing can also account for different products.
• Splicing may retain introns that are translated into separate protein domains.
• Not polycistronic in the bacterial sense (multiple independent genes on one mRNA).

🚫 Terminal differentiation

Cells that are NOT terminally differentiated (still capable of further differentiation):

• Monocyte (can differentiate into macrophages or dendritic cells).

Terminally differentiated cells (cannot differentiate further):

• Dendritic cells, platelets, megakaryocytes, NK cells.

🧬 DNA and RNA Processing

🧬 The replisome

"The replisome is best associated with replication within the nucleus."

• The replisome is the complex of proteins that carries out DNA replication.
• Not involved in transcription (mRNA, tRNA, rRNA production).
• Not involved in translation (protein synthesis).
• Not involved in cDNA transcription (reverse transcription).

✂️ Ribozymes

A ribozyme is "any RNA that is capable of cleaving itself."

• Ribozymes are catalytic RNA molecules.
• Not the enzyme that terminates translation (that's a protein).
• Not limited to spliceosomes; any self-cleaving RNA qualifies.
• Example: Some introns can self-splice without protein enzymes.

🔚 Eukaryotic transcription termination

"The eukaryotic equivalent of the bacterial hairpin terminator is the 3′ poly-A tail."

• Bacterial hairpin structures signal transcription termination.
• In eukaryotes, the poly-A tail (string of adenine nucleotides) is added to the 3′ end of mRNA.
• Not the 5′ cap (7-methylguanosine), leader sequence, or stop codon (which terminates translation, not transcription).

🧬 Gene duplication

"What alternative mechanism has been suggested as a viable alternative" to 200+ billion years of random point mutations for generating new functional genes?

Answer: Gene duplication

• Duplicating an existing gene provides raw material for evolution.
• One copy can maintain original function while the other mutates.
• Much faster than building a gene de novo from random mutations.

🧬 Specialized Topics

🧬 Barr body inactivation timing

"What evidence suggests that the random inactivation of the Barr body occurs very early in fetal development?"

Answer: Tortoiseshell cats

• Tortoiseshell cats have patches of different colors.
• Each patch represents a clone of cells with the same X chromosome inactivated.
• Early inactivation → larger patches; late inactivation → smaller patches.
• The large, distinct patches indicate very early developmental inactivation.

🦎 Mammalian regeneration limits

"What prevents mammals from regenerating limbs much as some salamanders can regenerate a new leg?"

Answer: Mammals trade regeneration for faster wound healing.

• This is a trade-off in evolutionary strategy.
• Not due to genome complexity or lack of specialized tissues.
• Regeneration is not unique to salamanders (some mammals have limited regeneration).

🧬 Homologous chromosomes

"When two same-sized chromosomes are found in a nucleus, one from the mother and one from the father, these are referred to as homologous chromosomes."

• Not sister chromatids (which are identical copies joined at the centromere).
• Not in synapsis (which is the pairing process during meiosis).
• Not duplicate chromosomes (imprecise term).
• Not sister chromatin (not a standard term).

☠️ Apoptosis initiation

Factors that initiate apoptosis (programmed cell death):

• Cell isolation
• Lack of nutrients
• NK cell contact
• Loss of survival signal
• T_CTL cell contact

The question asks what does NOT initiate apoptosis, but all listed options in the excerpt are known triggers, so this is a knowledge-check question without a clear answer provided in the excerpt.

🧬 Cellular senescence consequences

"If researchers could find a way to discourage or eliminate cellular senescence and aging, what would be a probable outcome?"

Answer: An increase in cancers

• Senescence limits cell division, preventing uncontrolled growth.
• Removing this limit would allow damaged cells to continue dividing.
• Telomerase expression would likely increase (not decrease) to maintain telomeres.
• This relates to the balance between aging and cancer risk.

🧬 Spacer DNA mutations

"An inversion mutation within spacer DNA would most likely do what to the resulting phenotype?"

Answer: It would have no effect.

• Spacer DNA is non-coding DNA between genes.
• Inversions (flipping a DNA segment) in non-coding regions typically don't affect protein production.
• Not lethal, not affecting nearby gene expression in most cases.
• Example: If the inversion is truly in "spacer" (non-regulatory) DNA, the cell machinery ignores it.

🧭 Overview

🧠 One-sentence thesis

Cellular communication in the nervous and endocrine systems relies on specialized structures, ion channels, neurotransmitters, and hormones to transmit signals rapidly via neurons and regulate long-term processes through glands.

📌 Key points (3–5)

• Nervous system signal transmission: action potentials propagate down neurons through voltage-gated ion channels, maintained by sodium-potassium pumps, and accelerated by myelin sheaths and nodes of Ranvier.
• Neurotransmitters and synapses: chemical messengers like acetylcholine, dopamine, serotonin, and GABA transmit signals across synapses; stimulatory neurons open sodium channels while inhibitory neurons open chloride channels.
• Endocrine system regulation: hormones from glands (pituitary, thyroid, parathyroid, adrenals, pancreas) control metabolism, calcium levels, blood glucose, stress responses, and water balance.
• Common confusion: distinguishing central nervous system (brain and spinal cord) from peripheral nervous system (nerves outside vertebrae); understanding that the hypothalamus bridges both nervous and endocrine systems.
• Two hormone mechanisms: hormones act either by binding surface receptors and producing second messengers (e.g., cAMP) or by passing through membranes to bind nuclear receptors (steroid hormones).

🧠 Nervous System Structure and Cells

🧠 Key cell types and components

• Schwann cells: major component of the nervous system; produce myelin in the peripheral nervous system.
• Oligodendrocytes: produce the "white matter" in the central nervous system (CNS).
• Glial cells: found specifically in nervous tissue.
• Neurons: the functional unit; nucleus resides in the cell body.

Nerve: a bundle of neurons (not a single cell).

🧩 Neuron anatomy

• Axon: conducts action potentials from the neuron body to the synapses.
• Dendrites: receive signals.
• Nodes of Ranvier: gaps in the myelin sheath that increase the rate of conduction down the axon.
• Myelin sheath: three primary functions:
  1. Provides insulation for the axon
  2. Increases the speed of signal propagation
  3. Assists in neuron regeneration

Example: Ion channels responsible for action potential propagation are located along the axon at the nodes of Ranvier, not between them.

🗺️ Nervous system organization

Division	Components	Location
Central nervous system (CNS)	Brain and spinal cord	Within vertebrae and skull
Peripheral nervous system	Nerves outside CNS	Outside vertebrae

• Meninges layers (outside to inside): dura mater → arachnoid → pia mater.
• Forebrain includes: cerebrum, thalamus, limbic system, hypothalamus (but NOT the pons).
• Hypothalamus: associated with both the nervous system and the endocrine system.

⚡ Action Potential Propagation

⚡ Mechanism of signal transmission

Action potential: propagated down a neuron by voltage-gated ion channels.

Sequence at a specific point along the neuron:

1. A flood of sodium into the cell
2. Potassium moves out of the cell
3. The action of the sodium-potassium pumps

🔋 Depolarization phase

• What happens: Sodium rapidly enters the cell, dropping the polarity to +30 mV (from resting –70 mV).
• Maintenance: The action potential is maintained by the vigorous activity of sodium-potassium pumps.
• Energy cost: The brain has only 2% of total body mass but consumes about 25% of available glucose because all neurons must generate huge amounts of energy to maintain membrane polarity.

Don't confuse: The sodium-potassium pumps work continuously to restore polarity after depolarization; they don't cause the initial depolarization.

🔗 Synaptic Transmission and Neurotransmitters

🔗 Neuromuscular synapse

• Primary neurotransmitter: acetylcholine.
• Nerve agents (VX and sarin): impair signal transduction by binding to cholinesterase, preventing the recycling of the neurotransmitter and greatly weakening muscle contraction.

🧪 Brain-specific neurotransmitters

• Found only in the brain: serotonin and GABA (gamma-aminobutyric acid).
• GABA: a neurotransmitter with a role in pain perception.
• Other neurotransmitters mentioned: dopamine, histamine, D-serine, norepinephrine, endorphins.

🎯 Stimulatory vs inhibitory neurons

Type	Mechanism	Effect
Stimulatory	Activates Na⁺ channels on postsynaptic cell	Depolarizes, increases likelihood of action potential
Inhibitory	Opens Cl⁻ channels on postsynaptic cell	Hyperpolarizes, decreases likelihood of action potential

Example: A stimulatory neuron opening sodium channels makes the postsynaptic cell more likely to fire; an inhibitory neuron opening chloride channels makes it less likely.

🏭 Endocrine System and Hormones

🏭 Major glands and their functions

• Master gland: anterior pituitary (controls other endocrine glands).
• Hypothalamus: bridges nervous and endocrine systems; regulates pituitary.
• Thyroid: best associated with regulation of metabolism; requires iodine for function.
• Parathyroid: responsible for raising calcium levels in the blood.
• Pancreas: secretes insulin (Type I diabetes is caused by inability to secrete insulin) and glucagon.
• Adrenals: produce epinephrine and norepinephrine ("fight-or-flight" response).
• Posterior pituitary: secretes oxytocin and ADH (antidiuretic hormone).

💧 Specific hormone functions

• Aldosterone: regulation of water concentration in the blood.
• ACTH (adrenocorticotropic hormone): secreted in response to a release of hormones from the anterior pituitary.
• Oxytocin: released when an infant suckles on its mother's breast.
• Calcitonin and thyroxine: thyroid hormones.
• Melatonin: regulates diurnal rhythms (sleep-wake cycle; rapid eye movement is best associated with the sleep-wake cycle).

Don't confuse: The anterior pituitary secretes FSH, LH, and ACTH; the posterior pituitary secretes oxytocin and ADH.

🔬 Two mechanisms of hormone action

1. Surface receptor pathway: Hormone binds to a receptor on the cell surface → produces cAMP as a second messenger → triggers intracellular changes.
2. Nuclear receptor pathway: Steroid hormones pass through the cell membrane → bind to a nuclear hormone receptor → control cell action by affecting gene expression.

Example: A steroid hormone like testosterone can cross the membrane and directly influence which genes are transcribed, while a peptide hormone like insulin must bind to a surface receptor and use a second messenger system.

🧬 Spinal Cord and Autonomic Functions

🧬 Spinal nerve regions

• Portions that stimulate digestion: sacral nerves.
• Portions that inhibit digestion: thoracic nerves.
• Other regions: cervical, lumbar, cranial.

🧪 Brain structures and fluids

• Choroid plexus: function is the production of CSF (cerebrospinal fluid).
• CSF flow: produced by choroid plexus → flows to the subarachnoid space.

🧪 Stress, Metabolism, and Other Topics

🧪 Long-term stress effects

Effects of long-term stress include:

• Organ exhaustion
• Ion imbalances
• Energy depletion
• Adrenal exhaustion

NOT an effect: Iodine insensitivity.

🧪 CNS depressants

• Alcohol is a CNS depressant.
• Not depressants: marijuana, PCP, nicotine, anabolic steroids.

🧪 Miscellaneous

• Terminally differentiated cells (cannot divide further): dendritic cells, platelets, NK cells, monocytes are mentioned; megakaryocyte is NOT terminally differentiated (it produces platelets).
• Apoptosis initiators: cell isolation, lack of nutrients, NK cell contact, loss of survival signal, T_CTL contact. (All listed options are known to initiate apoptosis.)

🧭 Overview

🧠 One-sentence thesis

This chapter tests understanding of immune system components, blood circulation, cardiovascular anatomy, and defense mechanisms through multiple-choice questions and a case study of variant Creutzfeldt-Jakob disease (vCJD) linked to prion-contaminated elk meat.

📌 Key points (3–5)

• Prion disease case study: Four hunters developed vCJD symptoms (memory loss, personality changes, seizures) after sharing elk meat, caused by abnormal PrP protein accumulation, not bacteria or viruses.
• Immune system organization: Primary lymphoid organs (thymus and bone marrow) vs. secondary structures (lymph nodes, spleen); different cell types have distinct roles (T CTL cells eliminate cancer, macrophages/neutrophils phagocytose).
• Cardiovascular flow sequences: Blood flows right atrium → right ventricle → lungs → left atrium → left ventricle; valves follow tricuspid → pulmonary semilunar → bicuspid → aortic semilunar.
• Common confusion—serum vs. plasma: Plasma contains clotting proteins; serum is plasma minus clotting proteins (not the other way around).
• Antibody responses: Primary response is slower and mainly IgM; secondary response is faster, stronger, and mainly IgG due to memory cells.

🦠 Prion Disease Case Study (Questions 333–337)

🦠 The disease agent

Variant Creutzfeldt-Jakob disease (vCJD): a spongiform encephalopathy caused by infectious prions, not bacteria, viruses, or parasites.

• What happened: Four elk hunters shared meals over 20+ years; one died in accident with autopsy showing spongiform encephalopathy and amyloid plaques; remaining three developed memory loss, personality changes, balance problems, speech difficulties, seizures, and depression.
• Why acquired, not inherited: The probability that all four unrelated friends would inherit the same rare genetic disease is extremely unlikely; the shared exposure (elk meat) points to acquired infection.
• Don't confuse with: Bacterial meningitis, viral encephalitis, or parasitic infections—these have different mechanisms and would respond to standard sterilization.

🧬 Biochemical mechanism

• Abnormal PrP protein accumulation: The disease involves progressive buildup of misfolded prion protein (PrP), forming amyloid plaques in brain tissue.
• How prions propagate: Abnormal PrP induces conformational changes in normal PrP proteins, converting them to the abnormal form—this is propagation by protein misfolding, not by DNA/RNA replication.
• Why heat-resistant: The infectious agent remains active even after autoclaving for an hour because it is already denatured protein; the infectious property comes from its abnormal shape, not from nucleic acids that would be destroyed by heat.

Example: Normal PrP protein in neurons encounters abnormal PrP from ingested elk tissue → abnormal form acts as a template, forcing normal PrP to misfold → newly misfolded proteins spread to more neurons → progressive brain damage.

🩹 Skin Structure and Wound Repair (Questions 338–342)

🩹 Wound healing sequence

Proper order after skin break: Clot formation → inflammation → fibroblast proliferation → debris removal → regeneration.

• Why this order matters: Clot must form first to stop bleeding; inflammation brings immune cells; fibroblasts rebuild tissue; debris is cleared; finally regeneration completes repair.
• Don't confuse: Debris removal comes after fibroblast proliferation begins, not before inflammation.

🌡️ Skin functions

Structure	Function	Notes
Arrector pili	Thermoregulation	Muscles that raise hair for insulation
Meissner's corpuscles	Sense movement of hair shaft	NOT thermoregulation
Merkel's disks	Touch sensation	Correct pairing
Pacinian corpuscles	Pressure sensation	Correct pairing
Free nerve endings	Temperature and pain	Correct pairing

💅 Nail growth and vitamin synthesis

• Nail growth mechanism: Epithelial cell division in the nail bed produces new nail tissue—not protein synthesis alone, not osteoclasts (those are bone cells), not hardened sebum.
• Dermal nutrition role: The skin synthesizes molecules (vitamin D precursors) that are later activated in the liver and aid calcium absorption in the intestine.
• Don't confuse: The dermis does not store significant energy as collagen, nor does it absorb essential minerals from outside, nor provide meaningful gas exchange.

🛡️ Immune System Components (Questions 343–348, 351, 355, 365, 369, 371)

🛡️ Structural organization

Size hierarchy (smallest to largest): Lymph nodule < lymph follicle < lymph node < thymus/spleen.

Primary vs. secondary lymphoid organs:

Type	Organs	Function
Primary	Thymus and bone marrow	Where lymphocytes mature
Secondary	Lymph nodes, spleen, nodules, follicles	Where immune responses occur

• Don't confuse: Thyroid is an endocrine gland, not a lymphoid organ; bone marrow is primary, not the spleen.

🔬 Cell types and functions

Cell Type	Primary Role	Notes
Macrophage	Greatest phagocytic responsibility	Derived from monocytes
Neutrophil	Phagocytosis	Most abundant leukocyte in healthy blood
T CTL cells	Eliminate cancer cells	Cytotoxic T lymphocytes
T-helper cells	Coordinate immune response	Not direct cancer killers
Plasma cells	Produce secreted antibodies	Differentiated from B-cells
Memory cells	Enable secondary response	Provide faster, stronger reaction

Example: A B-cell encounters its specific antigen → undergoes lymphoproliferation (clonal expansion) → differentiates into plasma cells (secrete antibodies) and memory cells (long-term protection).

🧬 Antibody specificity and classes

• How specificity is determined: Random gene rearrangements within B-cell progenitors create diverse antibody repertoires before antigen encounter.
• Don't confuse: Specificity is determined before antigen exposure, not by antigen selection in bone marrow or lymph nodes.

Antibody structure: Immunoglobulins are glycoproteins with complementary regions that bind antigens—NOT composed of three α-chains and one β-chain (that description is incorrect).

Antibody classes by function:

Class	Special Role
IgA	Best protection against microbial invasion through intestinal mucosa
IgM	Predominant in primary immune response
IgG	Predominant in secondary immune response
IgE	Involved in allergic reactions

🔄 Primary vs. secondary immune response

Key distinctions:

• Time to maximum response: Primary is slower; secondary is faster (due to memory cells).
• Antibody class: Primary mainly IgM; secondary mainly IgG.
• Response level: Secondary produces higher antibody levels.
• What does NOT distinguish them: Both can respond to the same antigen type; the difference is in timing, magnitude, and antibody class, not which antigen is used.

🫀 Cardiovascular System (Questions 349–350, 356–359, 367–368, 370)

🫀 Blood flow through the heart

Proper sequence starting at vena cava: Right atrium → right ventricle → left atrium → left ventricle.

Valve sequence: Tricuspid → pulmonary semilunar → bicuspid → aortic semilunar.

• Why this matters: Blood must flow through the right side to the lungs (for oxygenation) before entering the left side for systemic circulation.
• Don't confuse: The pulmonary veins (from lungs to left atrium) have the highest oxygen level, not pulmonary arteries (which carry deoxygenated blood to lungs).

🏗️ Heart tissue layers (outside to inside)

Proper sequence: Pericardium → epicardium → myocardium → endocardium.

• Pericardium: Outer protective sac.
• Epicardium: Outer heart wall layer.
• Myocardium: Thick muscular middle layer.
• Endocardium: Inner lining.

⚡ Cardiac conduction and blood supply

Conduction system components: SA node, AV node, AV bundle, Purkinje fibers—M cells are NOT part of the cardiac conduction system.

Myocardium oxygen/nutrient supply: Through two coronary arteries—NOT by diffusion through endocardium or pericardium, not from pericardial cavity, not from vena cava vessels.

💓 Diastole vs. systole

Diastole: the phase when both atria and both ventricles are relaxing.

• What happens: Heart chambers fill with blood; this is the lower number in blood pressure readings.
• Don't confuse: Not when valves snap shut (that's between phases), not when only one side relaxes, not when all valves are open simultaneously.

⚠️ Hypertension risk factors

Factors that increase risk: Obesity, smoking, advanced age, elevated sodium levels.

NOT a risk factor: Elevated HDL (high-density lipoprotein) levels—HDL is "good cholesterol" and protective, not a risk factor.

🩸 Blood Components and Processes (Questions 345–346, 353–354, 360–366, 372–373)

🩸 Blood cell types

Erythrocytes: degenerate cells that contain hemoglobin and carry oxygen.

• Not: Leukocytes (white blood cells), thrombocytes (platelets), lymphocytes, or bone marrow cells that carry only nutrients.
• Key feature: Erythrocytes lack nuclei (degenerate) but are packed with hemoglobin for oxygen transport.

Leukocyte relationships:

Pair	Relationship
Macrophage—monocyte	Most closely related; macrophages differentiate from monocytes
Eosinophil—basophil	Both granulocytes but different functions

Healthy leukocyte distribution: Neutrophils should always be at the highest level in a differential count from a healthy person.

🧪 Plasma vs. serum

Serum: the same thing as plasma but lacks clotting proteins.

• How to distinguish: Plasma = whole blood minus cells (includes clotting factors); serum = plasma minus clotting proteins (after clot forms).
• Don't confuse: Serum does NOT have higher protein concentration than plasma; plasma is NOT the same as whole blood; both contain antibodies.

🩹 Clotting sequence

Proper order: Calcium binds prothrombin activator → prothrombin activator produces thrombin → thrombin produces fibrin → fibrin produces clot.

• Why this sequence: Each step activates the next in a cascade; calcium is required early to activate prothrombin activator.
• Interference: Heparin interferes with platelet function and clotting; plasminogen is involved in clot breakdown, not formation.

🚶 Phagocyte recruitment sequence

Proper order from blood to infected tissue: Rolling adhesion → tight binding → diapedesis → migration.

• Rolling adhesion: Phagocytes loosely attach and roll along vessel walls.
• Tight binding: Firm attachment to endothelium.
• Diapedesis: Squeezing between endothelial cells to exit vessel.
• Migration: Moving through tissue toward infection site.

🏭 Hematopoiesis

Hematopoiesis: the process of blood cell formation that occurs in bone marrow.

• Not in: Spleen, thymus, lymph nodes, or general infection sites (though some immune activity occurs there).

🔗 Lymph-circulatory connection

Where lymph system connects to circulatory system: At the vena cava (lymph drains into venous circulation).

• Not: Within the spleen, in lymph nodes, at tissue capillaries, or within the lungs.

🦠 Blood Disorders and Immune Conditions (Questions 358, 361–363, 369)

🦠 Genetic blood disorders

Sickle cell anemia: a genetic disorder in which normally biconcave erythrocytes fold into sickle shapes under low oxygen conditions.

• Mechanism: Abnormal hemoglobin causes shape change when deoxygenated.
• Don't confuse with: Pernicious anemia (vitamin B12 deficiency), spherocytosis (sphere-shaped cells), hemophilia (clotting disorder), leukemia (white blood cell cancer).

🛡️ Autoimmune disorders

Which ARE autoimmune: Type I diabetes, rheumatoid arthritis, hemolytic anemia, pernicious anemia.

NOT autoimmune: Type II diabetes—this is a metabolic disorder related to insulin resistance, not autoimmune attack.

💉 Inflammatory mediators

Histamine: a substance that dilates blood vessels, increases tissue pressure, and can induce hypovolemic shock.

• Effects: Vasodilation, increased permeability, fluid shift from blood to tissues.
• Don't confuse with: SRS-A, γ-interferon, IL-2, or CD4 (which have different immune functions).

🧪 Lymph System Functions (Question 352)

🧪 What the lymph system does

Primary functions:

• Maintaining proper fluid balance (returns excess tissue fluid to blood).
• Transport of large triglycerides (absorbed from intestine).
• Movement of materials from tissues to blood.
• Transport of proteins.

NOT a primary function: Production of antibodies—antibodies are produced by plasma cells in lymphoid tissues, but antibody production itself is not a function of the lymph transport system.

🧭 Overview

🧠 One-sentence thesis

This chapter tests understanding of how organisms interact with their environment through cardiovascular, immune, digestive, renal, and respiratory systems, emphasizing the mechanisms by which these systems maintain homeostasis and respond to environmental conditions.

📌 Key points (3–5)

• Wood lice behavioral experiments (374–378): organisms demonstrate preferences for specific environmental conditions (moisture, light, pH) that can be tested through controlled experiments.
• Digestive system integration: multiple organs (liver, gallbladder, intestines) coordinate to digest and absorb nutrients through mechanical and chemical processes.
• Renal system function: kidneys regulate fluid balance, waste excretion, and homeostasis through filtration, reabsorption, and secretion mechanisms.
• Respiratory system mechanics: gas exchange depends on anatomical structures, pressure gradients, and chemical regulation of breathing rate.
• Common confusion: distinguishing between where substances are produced versus where they are stored or act (e.g., bile produced in liver but stored in gallbladder; ADH produced in hypothalamus but acts on kidneys).

🫀 Cardiovascular and Immune Systems

🫀 Myocardial oxygen supply

The myocardium receives oxygen and nutrients through two coronary arteries (Question 368, answer B).

• The heart muscle cannot rely on diffusion from the blood inside its chambers.
• Dedicated coronary circulation delivers oxygenated blood directly to heart tissue.
• Don't confuse: the endocardium (inner lining) and pericardium (outer sac) are structural layers, not nutrient delivery routes.

🛡️ Immune system components

🛡️ Antibody classes and mucosal immunity

• IgA provides the best protection against microbial invasion through the intestinal mucosa (Question 369, answer E).
• This antibody class is specialized for mucosal surfaces.
• Other classes (IgM, IgG, IgD, IgE) have different primary roles.

🛡️ Primary vs secondary immune responses

Question 371 asks what least distinguishes these responses:

• The antigen used to stimulate the responses (answer C) is the least distinguishing factor.
• Key differences include: timing of maximum response, predominant antibody class, antibody level, and memory cell involvement.

🩸 Blood components

🩸 Leukocyte differential counts

• Neutrophils should always be at the highest level in a healthy person (Question 372, answer E).
• Other white blood cells (monocytes, lymphocytes, eosinophils, basophils) are present in lower proportions.

🩸 Blood clotting sequence

The proper sequence (Question 373, answer A):

1. Calcium binds prothrombin activator
2. Prothrombin activator produces thrombin
3. Thrombin produces fibrin
4. Fibrin produces clot

🔬 Wood Lice Environmental Preference Study (Passage 9)

🔬 Experimental design

The study used three runs with 10 wood lice divided into two corrals (A and B):

• Run 1: Identical conditions for 5 minutes, then corral B darkened for 5 minutes.
• Run 2: Corral A moist, corral B dry; identical lighting for 5 minutes, then corral B darkened.
• Run 3: Both corrals moist; after 5 minutes, mild acid added to corral B and then darkened.

🔬 Environmental control

• The first half of the first run serves as the best environmental control (Question 374, answer A).
• This period had identical conditions in both corrals, establishing baseline behavior.

🔬 Moisture preference

• Animals prefer a moist environment when under lighted conditions (Question 375, answer D).
• The preference is condition-dependent, not absolute.

🔬 Acid preference

• Animals clearly prefer a nonacid environment (Question 376, answer A).
• They avoid acidic conditions when given a choice.

🔬 Light preference

• Animals prefer to be in the dark when other conditions are equal (Question 377, answer C).
• This preference can be overridden by other environmental factors.

🔬 Overall preference

Given all data, animals would prefer moist and dark conditions (Question 378, answer A).

• This combines the two positive preferences without the negative acid factor.

🍽️ Digestive System

🍽️ Gallbladder contents

α-amylase is NOT found within the gallbladder (Question 379, answer A).

• The gallbladder stores bile, which contains lipase, β-galactosidase, nucleases, and peptidases.
• Don't confuse: amylase is produced by salivary glands and pancreas, not stored in the gallbladder.

🍽️ Liver functions

The liver performs multiple functions (Question 384):

• Lipid metabolism
• Production of albumin and blood clotting proteins
• Carbohydrate metabolism
• Storage of iron and vitamin B₁₂
• NOT storage of water-soluble vitamins (answer D) – the liver stores fat-soluble vitamins.

🍽️ Bile composition and pathway

Bile is composed of water, bilirubin, and cholesterol (Question 388, answer B).

• When a gallstone is passed, it goes to the duodenum (Question 385, answer B).
• Bile salts, nitrogenous wastes, and bilirubin are also components mentioned in the options.

🍽️ Digestive enzyme locations

🍽️ Amylase release sites

Amylase is released in the small intestine and mouth (Question 386, answer D).

• Salivary amylase begins carbohydrate digestion in the mouth.
• Pancreatic amylase continues digestion in the small intestine.

🍽️ Parietal cell functions

Parietal cells in the stomach produce materials that:

• Activate pepsinogen
• Kill microorganisms
• Enable absorption of vitamin B₁₂
• Denature proteins
• Do NOT form gastric mucus (Question 389, answer C) – that is produced by other cells.

🍽️ Saliva characteristics

Question 390 asks what is NOT true about saliva:

• Answer E is false: there are three pairs of major salivary glands (parotid, submandibular, sublingual), not four; pharyngeal tonsils are not salivary glands.
• True facts: saliva contains antibodies and lysozymes, adults produce about one liter daily, it contains mucin/amylase/bicarbonate, and is about 99.5% water.

🍽️ Small intestine characteristics

Question 393 asks what is NOT descriptive:

• Answer E is false: digestion in the small intestine begins in the duodenum, not the jejunum.
• True characteristics: nutrient absorption occurs there, brush border cells digest carbohydrates, plica and villi increase absorption surface area, and peristalsis is under autonomic control.

🍽️ Nutrient absorption mechanisms

🍽️ Carbohydrate absorption

The correct process (Question 396, answer D):

1. Simple sugars enter epithelial cells by active transport
2. Exit these cells by facilitated diffusion
3. Enter capillaries by simple diffusion

• Don't confuse: polysaccharides must be broken down first; they don't enter cells intact.

🍽️ Lipid absorption sequence

The correct sequence (Question 397, answer E):

1. Emulsification by bile salts
2. Digestion by lipases
3. Formation of chylomicrons
4. Secretion by epithelial cells

🍽️ Intrinsic factor and vitamin B₁₂

Intrinsic factor allows the absorption of vitamin B₁₂ within the ileum (Question 382, answer D).

• Intrinsic factor is produced in the stomach but absorption occurs in the ileum.

🫘 Renal System

🫘 Nephron location and structure

• Nephrons can be found within the renal medulla (Question 383, answer E).
• Some sources also place nephrons in the cortex, but the medulla is the primary location mentioned.

🫘 Urine passage sequence

The correct sequence through a nephron (Question 387, answer A):

1. Bowman's capsule
2. Loop of Henle
3. Distal tubule
4. Collecting tubule

🫘 Filtration and reabsorption site

Materials exit the blood and enter the urine in the Bowman's capsule (Question 415, answer A).

• This is where initial filtration occurs.
• Other structures (proximal tubule, loop of Henle) primarily reabsorb materials back into blood.

🫘 Loop of Henle mechanisms

🫘 Countercurrent multiplier mechanism

The term refers to the mechanism used to create a concentration gradient within the loop of Henle (Question 391, answer C).

• This gradient is essential for concentrating urine.
• Don't confuse with laboratory techniques or other physiological processes.

🫘 Loop of Henle processes

What is true (Question 392, answer B):

• Sodium and chlorine leave the urine in the ascending loop.
• Water leaves the urine in the descending portion (not ascending).
• The ascending portion is impermeable to water.

🫘 Kidney functions

The kidneys have roles in all of the following EXCEPT (Question 398):

• Disposal of bilirubin through the urine (answer D) – bilirubin is primarily disposed through bile/feces, not urine.
• True functions: waste excretion, pH maintenance, homeostasis contribution, fluid balance, and blood pressure regulation.

🫘 Hormonal regulation of water balance

🫘 ADH and alcohol

Alcohol intake increases urination by interfering with the function of ADH (Question 394, answer B).

• ADH (antidiuretic hormone) normally promotes water reabsorption.
• Alcohol blocks this effect, leading to increased urine output.

🫘 Response to increased water intake

The physiologic response (Question 395, answer B):

• The hypothalamus and anterior pituitary decrease the rate of water reabsorption in the kidneys.
• This allows excess water to be excreted.
• Don't confuse: ADH is produced in the hypothalamus (not adrenals).

🫘 Chronic renal failure effects

What would likely be observed (Question 380, answer B):

• Generalized edema – fluid retention due to impaired kidney function.
• Not increased erythrocyte production (kidneys produce less EPO in failure).
• Not hyponatremia or hypouremia (levels would increase, not decrease).

🫁 Respiratory System

🫁 Respiratory anatomy

🫁 Airway sequence

The proper sequence of inspired air (Question 400, answer A):

1. Pharynx
2. Larynx
3. Trachea
4. Bronchi
5. Bronchioles
6. Alveoli

🫁 Lung anatomy

The correct description (Question 409, answer B):

• Three right lobes and two left lobes
• Surrounded by pleural membranes
• Resting upon the diaphragm

🫁 Structures lacking cartilage

The bronchioles lack cartilage (Question 403, answer E).

• The pharynx, trachea, and bronchi all contain cartilage for structural support.

🫁 Alveolar function

🫁 Septal cells

Septal cells secrete surfactants (Question 399, answer B).

• Surfactants reduce surface tension and prevent alveolar collapse.
• Don't confuse with other alveolar cell types that perform gas exchange or immune functions.

🫁 Conditions interfering with gas exchange

Question 406 asks what generally does NOT interfere:

• The question appears to have an error, as all listed conditions (tuberculosis, pneumonia, emphysema, lung cancer) typically interfere with gas exchange.

🫁 Breathing mechanics

🫁 Boyle's law

There is an inverse relationship between pressure and volume for a given amount of air (Question 402, answer C).

• This principle explains how changing chest volume creates pressure gradients that move air.
• Example: expanding the chest decreases pressure, drawing air in.

🫁 Inspiratory reserve volume

The difference between the amount of air in the lungs at rest and the amount brought in by the use of muscles (Question 401, answer D).

• This represents the extra air that can be inhaled beyond normal breathing.

🫁 Autonomic control

The autonomic control of breathing is centered in the medulla oblongata (Question 404, answer B).

• This brain region contains the respiratory control centers.
• Don't confuse with the cerebellum, hypothalamus, or cerebrum.

🫁 Gas transport and exchange

🫁 CO₂ fate in blood

What happens to CO₂ from tissue capillaries (Question 405, answer A):

• More than 90 percent enters erythrocytes
• About 25 percent of that binds to hemoglobin
• The remainder is converted to bicarbonate.

🫁 Nitrogen in blood

About what percentage of total blood gases is nitrogen (Question 407, answer D):

• Less than 2 percent
• Despite being 78% of atmospheric air, nitrogen is poorly soluble in blood.

🫁 Tissue partial pressures

The respective partial pressures in tissues (Question 411, answer A):

• pO₂ = 40 mm Hg
• pCO₂ = 45 mm Hg

🫁 Protective mechanisms

🫁 Mucus movement

What is true about respiratory mucus movement (Question 408, answer A):

• All of the mucus is swept upward in order to be swallowed or spit out.
• This mechanism helps clear pathogens and debris.

🫁 Cough reflex

Irritation of which area does NOT produce coughing (Question 412, answer B):

• Oropharynx – irritation here typically triggers swallowing or gagging, not coughing.
• Coughing is triggered by irritation of the larynx, trachea, and bronchi.

🫁 Nasal turbinate roles

The nasal turbinates do NOT (Question 414, answer C):

• Cool the air entering the lungs – they actually warm the air.
• True roles: moisten air, recover water during exhalation, carry air to olfactory centers, trap dust and infectious materials.

🫁 Chemoreceptor regulation

What does NOT occur when alveolar CO₂ levels get too high (Question 410, answer C):

• The elevated CO₂ levels produce the yawning reflex – yawning is not a direct CO₂ response.
• True responses: bronchodilation, increased respiration rate, proportionate pO₂ drop, increased gas exchange rate.

🫁 Chronic obstructive pulmonary disease (COPD)

COPD is defined as a condition representing a loss of more than 50 percent of expected breathing capacity (Question 413).

What is NOT included:

• Bacterial pneumonia (answer E) – this is typically acute, not chronic.
• Included conditions: chronic asthma, chronic bronchiolitis, pulmonary emphysema, chronic bronchitis.

🩺 Clinical Correlations

🩺 Hypertension risk factors

Which is NOT a risk factor (Question 370):

• Elevated HDL levels (answer D) – high HDL is actually protective.
• True risk factors: obesity, smoking, advanced age, elevated sodium levels.

🩺 Large intestine anatomy

Which is NOT a section of the large intestine (Question 381):

• Duodenum (answer E) – this is part of the small intestine.
• True sections: cecum, transverse colon, sigmoid colon, vermiform appendix.

🧭 Overview

🧠 One-sentence thesis

The musculoskeletal system integrates bone structure, muscle contraction mechanisms, and connective tissues to enable movement, support, mineral storage, and blood cell production.

📌 Key points (3–5)

• Muscle contraction fundamentals: thin filaments (actin, troponin, tropomyosin) and thick filaments (myosin) interact in sarcomeres; calcium is essential for contraction.
• Bone functions: support and movement, calcium/phosphate storage, hematopoiesis (blood cell formation), and organ protection.
• Bone structure and growth: spongy bone in epiphyses, compact bone in diaphysis; adolescent elongation occurs at the epiphyseal plate; repair follows hematoma → callus → osteoclast cleanup → osteoblast rebuilding.
• Common confusion—muscle types: skeletal muscle is voluntary and striated; smooth muscle is involuntary, non-striated, and provides slow sustained contractions; cardiac muscle is involuntary, striated, and connects via gap junctions.
• Joint and connective tissue distinctions: fibrous joints are immovable; tendons connect muscle to bone; ligaments connect bone to bone; osteoarthritis is mechanical wear vs. rheumatoid arthritis is autoimmune.

💪 Muscle structure and contraction

🧵 Thin filament composition

Thin filaments are composed of actin, troponin, tropomyosin, and myosin binding sites.

• Not myosin: myosin forms the thick filament, not the thin filament (Question 421).
• The thin filament provides the binding sites where myosin heads attach during contraction.

🔬 The sarcomere as contractile unit

A sarcomere is the contractile unit of the myofibril.

• It is not where bone attaches to muscle, not another name for a muscle cell, and not the postsynaptic receptor site (Question 429).
• The sarcomere contains overlapping thin and thick filaments that slide past each other during contraction.
• Actin is the primary component of the thin filament (Question 439).

🧪 Calcium's role in contraction

• If half the calcium leaks out of a muscle cell, the force of contraction decreases (Question 422).
• Calcium ions trigger the interaction between actin and myosin by binding to troponin, which moves tropomyosin off the myosin binding sites.
• Don't confuse: calcium affects contraction strength, not the action potential in the neuron or signal strength from neuron to muscle.

🏪 Sarcoplasmic reticulum function

• The sarcoplasmic reticulum is essential for muscle contraction (Question 431).
• It stores and releases calcium needed for the contraction cycle.
• It is not involved in protein synthesis/transport, not a joining structure, and not for ATP transport from mitochondria.

⚡ Energy sources for contraction

After the initial ATP supply is exhausted, muscle cells use creatine phosphate immediately (Question 434).

• Sequence: ATP → creatine phosphate → glucose/glycogen → fatty acids.
• Example: A person with McArdle's disease (glycogen storage deficiency) experiences rapid onset of fatigue during exercise because they cannot mobilize glycogen for sustained ATP production (Question 446).

🔄 Oxygen debt recovery

Following oxygen debt, the body converts lactic acid to glucose (Question 452).

• Oxygen levels and creatine phosphate levels return to normal, but do not rebound above preexercise levels.

🦴 Bone structure and function

🏗️ Primary functions of bone

The skeletal system provides (Question 430):

Function	Description
Support for movement	Framework for muscle attachment
Calcium and phosphate reservoir	Primary storage site for these minerals (Question 423)
Hematopoiesis	Blood cell formation
Organ protection	Shields vital organs

• Not essential for cellular metabolism in the sense described.

🧱 Bone tissue organization

• Spongy bone is best associated with the proximal epiphysis (Question 432), not bone loss, the diaphysis, the medullary cavity, or the periosteum.
• Compact bone forms the shaft (diaphysis).
• Periosteum is the connective tissue containing osteoclasts (Question 435).

📏 Adolescent bone elongation

During adolescent development, bones elongate by forming bone tissue under the cartilage epiphyseal plate (Question 437).

• This is the growth plate where cartilage is replaced by bone tissue.
• Not under joint cartilage, not spongy bone in the marrow cavity, not dense bone along the marrow cavity, not collagenous fibrocartilage at marrow cavity ends.

🩹 Bone fracture repair sequence

The correct sequence is (Question 442):

1. Hematoma forms (blood clot at fracture site)
2. Callus forms (fibrocartilage bridge)
3. Osteoclasts remove debris (clean up damaged bone)
4. Osteoblasts replace bone material (rebuild with new bone)

🧬 Cartilaginous bones

"Cartilaginous bones" refers to bone development within a cartilage framework (Question 451).

• This describes endochondral ossification, where cartilage models are gradually replaced by bone.
• Not bones that articulate with cartilage, not lack of ossification, not inappropriate cartilage deposits, not bone surrounded by cartilage.

🦴 Collagen in bone

Collagen is found at the highest levels in bone tissue (Question 458), providing tensile strength and flexibility.

🔗 Joints and connective tissues

🔒 Fibrous joints

A fibrous joint is best described as immovable (Question 428).

• Examples: sutures in the skull.
• Not like the knee or elbow (synovial joints), not slightly movable, not like sternum-cartilage connections.

🦵 The knee joint

The knee is closely associated with (Question 433):

• Ligaments

• Patella (kneecap)

• Meniscus (cartilage cushion)

• Femur (thigh bone)

• Not a fibrous joint—the knee is a synovial joint (highly movable).

🧷 Tendons vs. ligaments

A tendon is a connective tissue that connects bone to muscle (Question 438).

• Tendons are collagenous but not highly vascularized.
• Ligaments connect bone to bone (collagenous material).
• Don't confuse: tendons (muscle to bone) vs. ligaments (bone to bone).

🎯 Muscle attachment points

• Muscles connect through tendons to relatively immovable origins (Question 444).
• The insertion point is the more movable attachment.
• Muscles produce motion by pulling (not pushing) on the insertion point.

🏃 Muscle types and control

🔄 Smooth muscle characteristics

Smooth muscle (Question 424):

• Provides long-term slow contractions
• Is involuntary (not under voluntary control)
• Is non-striated (not striated)
• Is found throughout the body (not only in the digestive system)
• Is not best associated with bony structures (that's skeletal muscle)

🫀 Cardiac muscle synchronization

Cardiac muscle cells beat in synchronized fashion when they make contact because they connect via gap junctions (Question 441).

• Gap junctions allow electrical signals to pass directly between cells.
• Not because of nerve connections, ATP release, calcium release into medium, or physical gating.

🍽️ Digestive system muscle control

Muscles associated with peristalsis are controlled by the parasympathetic nervous system (Question 436).

• The parasympathetic system promotes "rest and digest" functions.
• Not the cerebrum, not the sympathetic system alone, not both sympathetic and parasympathetic, not cerebrum and cerebellum.

🏋️ Red muscle vs. white muscle

Red muscle is characterized by (Question 455):

• Rich in mitochondria

• High capillary density

• Rich in myoglobin (oxygen-binding protein)

• Best for sustained exertion

• Not fast twitch—red muscle is slow twitch for endurance.

🦴 Skeletal anatomy

💀 Skull bones

Skull bones include (Question 425):

• Maxilla and mandible

• Palatine and sphenoid

• Parietal and occipital

• Ethmoid and zygomatic

• Not tarsals and metatarsals—these are foot bones.

🦴 Vertebral column

The vertebrae (Question 427):

• Seven cervical vertebrae (neck)

• Thoracic region (upper back)

• Lumbar region (lower back, below thoracic)

• Sacrum (connects lumbar to coccyx)

• Protect portions of the CNS (spinal cord)

• Not seven fused bones in the coccyx—the coccyx typically has four fused bones.

🫁 Rib cage structure

The rib cage (Question 443):

• Ribs 8–10 are false ribs

• All ribs attach to thoracic vertebrae

• Ribs 11 and 12 are not connected to the sternum (floating ribs)

• Part of the respiratory system

• Not "intervertebral spaces"—the spaces between ribs are called intercostal spaces.

🦴 Axial vs. appendicular skeleton

The axial skeleton consists of (Question 445):

• Skull

• Ribs

• Vertebrae

• Sternum

• Not the femurs—femurs are part of the appendicular skeleton (limbs).

🦴 Analogous structures

The structures analogous to the tibia and fibula (lower leg bones) are the radius and ulna (forearm bones) (Question 447).

🤝 Muscle coordination and movement

🤸 Synergistic muscle combinations

Hamstring and gastrocnemius work synergistically (Question 426).

• Both are involved in leg flexion and movement.
• Not sartorius and hamstring, not biceps and triceps (antagonists), not pectoralis major and trapezius, not quadriceps and biceps.

🧘 Posture maintenance reflexes

Reflexes associated with posture maintenance include (Question 457):

• Myotatic reflex

• Knee-jerk reflex

• Deep tendon reflex

• Stretch reflex

• Not the flexor reflex—this is a withdrawal reflex, not for posture.

🧍 Backbone bending muscle

The muscle that bends the backbone is the rectus abdominis (Question 449).

• This is the "six-pack" muscle that flexes the spine forward.

🏥 Clinical conditions

🦴 Osteoarthritis vs. rheumatoid arthritis

Osteoarthritis differs from rheumatoid arthritis in that osteoarthritis (Question 440):

• Is initiated by mechanical mechanisms (wear and tear)
• Rheumatoid arthritis is an autoimmune disorder

Feature	Osteoarthritis	Rheumatoid Arthritis
Cause	Mechanical wear	Autoimmune
Joint integrity	Retained overall	Permanent deformation
Primary joints	Synovial joints	Synovial joints

🦴 Osteoporosis management

For someone with osteoporosis, appropriate measures include (Question 448):

• Calcium supplementation

• Moderate exercise

• Estrogen replacement for women

• Stretching

• Not contact sports—these pose high fracture risk.

🦴 Scoliosis

Scoliosis is the improper lateral curvature of the spine (Question 450).

• Not related to silicon incorporation, fontanel closure, allergic response to cold, or bone stenosis.

🌡️ Thermoregulation and muscle function

🔥 Why organisms thermoregulate

Organisms thermoregulate because cellular enzymes function within a narrow temperature range (Question 453).

• Enzymes denature or become inefficient outside their optimal temperature range.
• While other factors (fluid balance, electrolytes, immune function, metabolic rate) are affected by temperature, the primary reason is enzyme function.

🐝 Insect wing movement

Some insects (e.g., wasps) continually move their wings even when walking because they must keep their flight muscles warm (Question 456).

• Flight muscles require a specific temperature to function effectively.
• Not for warning predators, venom production, cooling, or no function.

🩸 Endocrine involvement in oxygen delivery

🫘 Erythropoietin production

The endocrine system is involved in oxygen delivery to muscles because the kidneys produce erythropoietin (Question 454).

• Erythropoietin stimulates red blood cell production, increasing oxygen-carrying capacity.
• Not atrial natriuretic peptide (fluid balance), cholecystokinin (digestion), or prostaglandins.

🧭 Overview

🧠 One-sentence thesis

Sexual reproduction in humans involves coordinated hormonal regulation of gamete production, fertilization, and embryonic development through distinct stages from gametogenesis through implantation and differentiation.

📌 Key points (3–5)

• Gamete formation differs by sex: males produce sperm continuously via spermatogenesis in seminiferous tubules; females are born with a fixed number of primary oocytes (~500,000), releasing only ~500 via ovulation.
• Hormonal cycles coordinate reproduction: FSH, LH, estrogen, and progesterone regulate the menstrual cycle's follicular and luteal phases, with the hypothalamus as the ultimate regulator.
• Embryonic development follows a sequence: fertilization → cleavage → morula → blastocyst → implantation (day 6) → gastrulation → differentiation into three germ layers (ectoderm, mesoderm, endoderm).
• Common confusion—polar bodies vs gametes: polar bodies are degenerate haploid cells from meiosis, not functional gametes; they result from unequal division during oocyte maturation.
• Extraembryonic membranes support development: amnion (cushioning fluid), chorion (gas exchange), allantois (umbilical cord formation), and yolk sac (early blood cell formation) each have distinct roles.

🧬 Sexual Dimorphism and Gamete Production

🎭 Sexual dimorphism

Sexual dimorphism: when males differ in appearance from females.

• This is distinct from primary sexual characteristics (reproductive organs themselves).
• Not to be confused with polymorphism (multiple forms within a species unrelated to sex) or being monoecious (having both male and female organs in one individual).

🥚 Oocyte development in females

• At birth: human females have approximately 500,000 primary oocytes.
• Released by ovulation: only about 500 will be released over a lifetime.
• The vast majority degenerate without being released.

Polar bodies:

Polar body: a degenerate haploid cell resulting from meiosis during oocyte maturation.

• Formed through unequal cell division during meiosis.
• Prior to the second meiotic division, the polar body is haploid (not diploid).
• It is not a functional gamete; it degenerates.
• Don't confuse: the polar body is a byproduct, not the mature female gamete (ovum).

🧵 Sperm development in males

Proper sequence of spermatogenesis:

Spermatogonium → primary spermatocyte → secondary spermatocyte → spermatid

• Location: sperm are formed in the seminiferous tubules (not the epididymis, prostate, vas deferens, or bulbourethral gland).
• Testosterone production: produced by interstitial cells (Leydig cells) of the seminiferous tubules, not by Sertoli cells or spermatogonia.

Sperm components:

• Include: microtubules, flagellum, acrosome, mitochondria.
• Do NOT include: endoplasmic reticulum (sperm are highly streamlined cells).

🔬 Acrosome function

Acrosome: structure on the tip of sperm that provides enzymes permitting tunneling through the zona pellucida.

• Not for energy (that comes from mitochondria).
• Not for molecular sensors (chemotaxis receptors are elsewhere).
• Not for flagellar power or protection.
• Example: the acrosome releases digestive enzymes to penetrate the egg's protective layer during fertilization.

🔄 Hormonal Regulation and Menstrual Cycle

🎛️ Hypothalamic-pituitary-gonadal axis

Ultimate regulator in males:

• The hypothalamus serves as the ultimate regulator of FSH and LH in males (not the anterior pituitary, interstitial cells, or Sertoli cells).
• Males do produce both LH and FSH.

🌙 Menstrual cycle phases

Follicular phase:

• Includes: the uterine proliferative phase, the menstrual phase, and the rise of estrogen and LH.
• Associated with ovarian follicle maturation.

Luteal phase:

• Best associated with the secretory phase of the uterine cycle.
• Characterized by rising progesterone levels (not progressively increasing FSH and LH).
• Not associated with menses, uterine proliferation, or the spike of estrogen/LH/FSH (those occur around ovulation).

Phase	Hormones	Uterine Activity	Ovarian Activity
Follicular	Rising estrogen and LH	Proliferative phase, menstrual phase	Follicle maturation
Ovulation	Spike of estrogen, LH, FSH	Transition	Egg release
Luteal	Rising progesterone	Secretory phase	Corpus luteum function

🍼 Lactation hormones

Hormones involved in lactation:

• Oxytocin (milk ejection)
• Estrogen
• Progesterone
• Prolactin (milk production)

NOT involved: Testosterone plays no role in a mother's lactation following birth.

🩺 Clinical considerations

Ectopic pregnancy:

• The tissue usually involved is the uterine tube (fallopian tube), not the vagina, perimetrium, endometrium, or ovary.

Endometriosis and infertility:

• The cause is uncertain (not definitively due to reduced LH, blocked FSH receptors, or pelvic pain preventing sexual activity).
• Fragmentation and scarring may block implantation, but the mechanism is not fully understood.

🧫 Fertilization and Preembryonic Development

🥼 Fertilization to implantation sequence

Proper sequence of preembryonic development:

Fertilization → cleavage of blastomeres → morula → blastocyst

• Implantation timing: normally takes place around day 6 following fertilization (not day 1, 2, 3, or 9).

👯 Twin formation

Identical twins:

• Result from division of a single fertilized ovum into two zygotes.
• Not from double fertilization of a single ovum, separate fertilization of two ova, fusion of two fertilized ova, or division of a single ovum with separate fertilization.

Tetragametic individuals:

Tetragametic: a person with the genetic composition of two once-separate individuals.

• Not related to armadillo litters, fraternal twins, meiosis products, or quadruplets.

🧪 Abnormal pregnancies

Molar pregnancy:

Molar pregnancy: a condition in which an ovum, after fertilization, forms a nonviable and undifferentiated cell mass that mimics a pregnancy.

• Not a miscarriage, ectopic pregnancy, chorionic pregnancy, or stromal pregnancy.

🌱 Embryonic Development and Germ Layers

📐 CNS development sequence

Correct sequence of CNS development during embryogenesis:

Notochord → neural groove → neural fold → neural tube

• The notochord forms first, inducing the neural structures.
• The neural groove deepens, edges fold up (neural folds), then fuse to form the neural tube.

🧬 Three germ layers and their derivatives

Ectoderm-derived tissues (include):

• Tooth enamel
• Posterior pituitary gland
• Skin epidermis
• Retina of the eye

NOT ectoderm: Thymus (derived from endoderm).

Mesoderm-derived tissues (include):

• Bone marrow
• Gonads
• Lymph vessels
• Connective tissue

NOT mesoderm: Digestive tract mucosa (derived from endoderm).

Endoderm-derived tissues (include):

• Anterior pituitary
• Lung alveoli
• Thyroid gland

NOT endoderm: Sweat glands and muscle tissue (sweat glands from ectoderm, muscle from mesoderm).

🧠 Neural crest cells

Cell types originating from neural crest:

• Neurons
• Epinephrine-producing cells of the adrenal glands
• Epidermal pigment cells
• Glial cells

NOT from neural crest: Lymphocytes (derived from mesoderm).

🔬 Cellular differentiation triggers

At the blastocoel stage:

• The significant event triggering cellular differentiation is the formation of tight junctions.
• Not increased division rate, increased cellular volume, metabolic rate drop, or onset of gluconeogenesis.

Signal response system for differentiation: Cells differentiate based on signals from nearby cells. The system includes:

• A signal protein
• A specific receptor protein
• A signal transport or translation mechanism
• A response that produces a gene regulatory product

NOT included: A lipid synthesizing mechanism.

🛡️ Extraembryonic Membranes and Fetal Support

🧷 Membrane functions

Correct pairings:

• Amnion: produces cushioning fluid for the fetus
• Allantois: helps form the umbilical cord
• Yolk sac: initially forms fetal blood cells
• Chorion: assists in gas exchange between mother and fetus

Incorrect pairing: Myometrium—this is uterine muscle tissue, not an extraembryonic membrane; it does not help form the placenta in the same way as true extraembryonic membranes.

🤰 Conceptus components

Conceptus: the products of conception, including the embryo and all extraembryonic structures.

Components include:

• Amnion
• Embryo
• Umbilical cord
• Yolk sac
• Chorion

(All listed options are part of the conceptus.)

🩸 Maternal-fetal exchange

Immune protection of newborns:

• A newborn has an immature immune system but is initially protected by antibodies passed on from the mother through the placenta.
• Additional protection comes from antibodies in breast milk.
• Not from T_H cells, antibody-producing cells from the umbilical cord, or maternal macrophages in fetal lymph nodes.

Rh incompatibility:

• Marked jaundice in the infant at birth is a sign of an Rh mismatch with the mother (not Rh incompatibility in general, ABO mismatch, autoimmune disorder, or inheriting the father's tissue type).

🧬 Maternal-fetal cell transfer

Can a child's cells reside in the mother's body?

• Yes, and these cells can even be passed on to subsequent children.
• They gain entry during pregnancy (not just at birth).
• They do not necessarily trigger immediate immune elimination or cause most autoimmune diseases, though their long-term effects are complex.

🕰️ Developmental Milestones and Apoptosis

💓 Fetal heartbeat detection

• A heartbeat can initially be detected at week 4 of fetal development (not month 3, week 8, month 4, or month 5).

✋ Syndactyly and apoptosis

Webbing between fingers:

• During development in utero, fingers are initially connected by weblike tissue.
• This tissue normally disappears prior to birth through programmed apoptosis (not lack of blood vessels, fetal urine, tearing from movement, or maternal antibodies).

When webbing persists:

Syndactyly: the condition when weblike tissue connecting fingers does not disappear prior to birth.

• Not polydactyly (extra digits), apoptosis (the normal process), cytokinesis (cell division), or dyslysis.

🐛 Protostomal vs Deuterostomal Development

🔄 Developmental distinction

Protostomes: gastrulate the mouth opening first.
Deuterostomes: gastrulate the anus first.

• Both groups go through the blastula stage (neither bypasses it).
• The key difference is which opening forms first during gastrulation.
• Don't confuse: this is about the order of gut opening formation, not about having a blind gut or skipping developmental stages.

🧱 Tissue Types and Cellular Junctions

🧱 Epithelial tissue types

Keratinized squamous epithelium:

• Describes cells that make up the skin.
• Not cells lining the small intestine lumen, stomach interior, covering nerve bundles, or comprising tendons.

🧪 Goblet cells

Goblet cells are found in:

• Trachea
• Eyes
• Intestine
• Bronchioles

NOT found in: Kidneys.

🔗 Cellular junctions

Highest concentration of spot desmosomes, tight junctions, and gap junctions:

• Found in skin (epithelial tissue with high structural integrity needs).
• Not in blood, fibroblasts, neurons, or alveoli at the same concentration.