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AP Biology

AP Biology Study Guide Expanded Edition

8 Units · 122 Quiz Questions · 64 Flashcards · Diagnostic · Full Reference Tables · Diagrams · Saved Progress

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Properties of water
Water's polarity and hydrogen bonding give it properties essential to life — cohesion, adhesion, high specific heat, and being a universal solvent.
  • Polarity: O is more electronegative than H → bent molecule with partial negative O and partial positive H's → forms hydrogen bonds between molecules
  • Cohesion: water molecules stick to each other via H-bonds → surface tension, allows water columns to move up xylem
  • Adhesion: water sticks to other polar surfaces → capillary action (water climbing a thin glass tube or plant cell walls)
  • High specific heat (1 cal/g°C): H-bonds absorb/release large amounts of heat with small temperature change → moderates climate and organism body temperature
  • Universal solvent: polar/charged solutes dissolve readily; ions become surrounded by water (hydration shells)
  • Density anomaly: ice is LESS dense than liquid water (H-bonds lock into a fixed hexagonal lattice) → ice floats, insulating water below
Macromolecules & functional groups
Life's four major macromolecule classes are built from monomers joined by dehydration synthesis and broken apart by hydrolysis.
  • Carbohydrates: monomer = monosaccharide (glucose, fructose); function = energy storage (starch, glycogen) and structure (cellulose, chitin)
  • Lipids: not true polymers; glycerol + 3 fatty acids = triglyceride; function = long-term energy storage, membranes (phospholipids), hormones (steroids)
  • Proteins: monomer = amino acid (20 types), joined by peptide bonds; function = enzymes, structure, transport, signaling, defense
  • Nucleic acids: monomer = nucleotide (sugar+phosphate+nitrogenous base); DNA stores genetic info, RNA involved in gene expression
  • Dehydration synthesis (condensation): monomers join, releasing one H₂O per bond formed
  • Hydrolysis: polymer broken into monomers by ADDING a water molecule across each bond (digestion uses hydrolysis)
Functional groups
Functional groups attached to carbon skeletons give organic molecules their specific chemical behavior.
  • Hydroxyl (-OH): polar, found in sugars and alcohols; enables hydrogen bonding, increases solubility
  • Carboxyl (-COOH): acidic, found in amino acids and fatty acids; can donate H⁺ (ionizes to -COO⁻)
  • Amino (-NH₂): basic, found in amino acids; can accept H⁺ (ionizes to -NH₃⁺)
  • Phosphate (-PO₄): found in nucleotides, ATP, phospholipids; negatively charged, involved in energy transfer
  • Methyl (-CH₃): nonpolar, affects gene expression via DNA methylation, affects molecular shape
Protein structure
A protein's function depends entirely on its 3D shape, built up through four levels of structure.
  • Primary structure: linear sequence of amino acids, determined by the gene's codon sequence; held by peptide bonds
  • Secondary structure: local folding into α-helices and β-pleated sheets, stabilized by hydrogen bonds between backbone atoms
  • Tertiary structure: overall 3D shape of one polypeptide, driven by R-group interactions (hydrophobic interactions, ionic bonds, hydrogen bonds, disulfide bridges)
  • Quaternary structure: two or more polypeptide subunits joined (e.g., hemoglobin = 4 subunits)
  • Denaturation: heat, pH change, or salt disrupts weak bonds → protein unfolds and loses function (primary structure usually intact)
Enzymes & activation energy
Enzymes are protein (or RNA) catalysts that speed up reactions by lowering the activation energy required to reach the transition state.
  • Activation energy (Ea): the energy barrier that must be overcome to start a reaction; enzymes lower Ea without changing ΔG (they don't change whether a reaction is spontaneous)
  • Active site: region of the enzyme where substrate binds; induced fit model — enzyme shape adjusts slightly around substrate for optimal fit
  • Enzymes are substrate-specific due to active site shape; each enzyme typically catalyzes one reaction or reaction type
  • Competitive inhibitor: binds the active site itself, blocking substrate; effect reduced by increasing substrate concentration
  • Noncompetitive (allosteric) inhibitor: binds a site other than the active site, changes enzyme shape so active site no longer works well; not overcome by more substrate
  • Enzyme activity affected by temperature (optimum, then denatures above it) and pH (each enzyme has an optimal pH range, e.g. pepsin ~2, trypsin ~8)
Enzymes lower activation energy — they do NOT change the free energy change (ΔG) of a reaction or make a nonspontaneous reaction spontaneous.
Dehydration synthesis RELEASES water; hydrolysis ADDS water — students often reverse these.
Ice floats because hydrogen bonds form a fixed, spaced-out lattice — this is LESS dense, not more.
Denaturation changes secondary/tertiary/quaternary structure, but primary structure (the amino acid sequence/peptide bonds) is unaffected.
Water: cohesion/adhesion via H-bonds
Dehydration synthesis: releases H₂O | Hydrolysis: adds H₂O
Prokaryotic vs eukaryotic cells
All cells share a plasma membrane, cytoplasm, ribosomes, and DNA, but eukaryotic cells add membrane-bound organelles and much greater internal compartmentalization.
  • Prokaryotes (bacteria, archaea): no nucleus, DNA is a single circular chromosome in the nucleoid region, no membrane-bound organelles, smaller (1-10 μm), 70S ribosomes
  • Eukaryotes (protists, fungi, plants, animals): true membrane-bound nucleus, linear DNA wound around histones, membrane-bound organelles, larger (10-100 μm), 80S ribosomes
  • Both have: plasma membrane, cytoplasm, ribosomes, DNA as genetic material
  • Surface area-to-volume ratio limits cell size: as a cell grows, volume increases faster (cubed) than surface area (squared) → limits nutrient/waste exchange rate → cells divide or fold membranes rather than grow indefinitely
Endosymbiotic theory
Mitochondria and chloroplasts likely originated as free-living prokaryotes engulfed by an ancestral eukaryotic cell, forming a mutualistic relationship.
  • Evidence: mitochondria and chloroplasts have their own circular DNA (like bacteria), their own 70S ribosomes, and double membranes (inner = original bacterial membrane, outer = from engulfing vesicle)
  • Both organelles replicate independently of the cell cycle by binary fission, similar to bacteria
  • Mitochondria likely derived from an aerobic heterotrophic bacterium; chloroplasts from a photosynthetic cyanobacterium
  • This theory explains why these organelles are semi-autonomous within eukaryotic cells
Organelles & their functions
Each organelle is structurally specialized for a particular function within the cell.
  • Nucleus: houses DNA, site of transcription and DNA replication; nucleolus makes ribosomal RNA/subunits
  • Rough ER: ribosomes attached, synthesizes and folds membrane/secreted proteins; Smooth ER: lipid synthesis, detoxification, calcium storage
  • Golgi apparatus: modifies, sorts, and packages proteins/lipids received from the ER (cis face receives, trans face ships)
  • Mitochondria: site of aerobic cellular respiration, produces most cellular ATP; cristae increase inner membrane surface area
  • Lysosome (animal cells): contains hydrolytic enzymes for digesting macromolecules, worn-out organelles (autophagy), and pathogens
  • Chloroplast (plant cells): site of photosynthesis; central vacuole (plants): storage, maintains turgor pressure, waste storage
Membrane structure
The fluid mosaic model describes the plasma membrane as a dynamic phospholipid bilayer studded with proteins that can move laterally.
  • Phospholipid bilayer: hydrophilic phosphate heads face the aqueous environments (inside/outside); hydrophobic fatty acid tails face each other in the middle
  • 'Fluid': phospholipids and proteins move laterally within the layer; fluidity increases with unsaturated fatty acids (kinks prevent tight packing) and decreases with cholesterol at high temps (buffers fluidity in both directions)
  • 'Mosaic': many different proteins embedded at varying depths — integral (span the membrane) vs peripheral (attached to surface)
  • Membrane proteins function as: channels/transporters, receptors, cell recognition markers (glycoproteins), enzymes, and cell junction anchors
Membrane transport & osmosis
Substances cross membranes passively (no ATP, down gradient) or actively (requires ATP, against gradient).
  • Simple diffusion: small/nonpolar molecules (O₂, CO₂) move directly through the bilayer down their concentration gradient
  • Facilitated diffusion: polar molecules/ions move through channel or carrier proteins down their gradient — still passive, no ATP
  • Active transport: moves solutes AGAINST their gradient, requires ATP (e.g., sodium-potassium pump moves 3 Na⁺ out, 2 K⁺ in per ATP)
  • Osmosis: diffusion of water across a selectively permeable membrane, from low solute (high water potential) to high solute (low water potential) concentration
  • Hypotonic solution (lower solute outside): water enters cell → animal cells lyse, plant cells become turgid (healthy)
  • Hypertonic solution (higher solute outside): water leaves cell → animal cells crenate/shrivel, plant cells plasmolyze
Both mitochondria AND chloroplasts have their own DNA and ribosomes — this is evidence for BOTH, not just chloroplasts.
Facilitated diffusion is still passive (no ATP) even though it requires a protein — don't confuse it with active transport.
A plant cell in a hypotonic solution becomes turgid (good) — it does NOT lyse because the cell wall resists expansion.
Osmosis moves water toward the side with MORE solute (lower water potential), not toward more water.
Surface area ∝ r² ; Volume ∝ r³ (SA:V decreases as cell size increases)
Na⁺/K⁺ pump: 3 Na⁺ out, 2 K⁺ in per ATP
ATP & energy coupling
ATP (adenosine triphosphate) is the cell's short-term energy currency, releasing energy when its terminal phosphate bond is hydrolyzed.
  • ATP → ADP + Pi releases ~7.3 kcal/mol; this exergonic reaction is coupled to endergonic cellular work (active transport, synthesis, mechanical work)
  • ATP is regenerated from ADP + Pi using energy released from cellular respiration (phosphorylation)
  • Energy coupling: the phosphate group is often transferred directly to a substrate (phosphorylation), providing energy and changing substrate shape/reactivity
Cellular respiration overview
Aerobic respiration breaks down glucose in stages to produce ATP, using O₂ as the final electron acceptor and releasing CO₂ and H₂O.
  • Glycolysis (cytoplasm, anaerobic): glucose (6C) split into 2 pyruvate (3C); net gain 2 ATP (substrate-level phosphorylation) + 2 NADH
  • Pyruvate oxidation (mitochondrial matrix): each pyruvate → acetyl-CoA + CO₂ + NADH (occurs twice per glucose)
  • Krebs/citric acid cycle (matrix): acetyl-CoA oxidized completely to CO₂; produces per glucose (2 turns): 6 NADH, 2 FADH₂, 2 ATP
  • Electron transport chain (inner mitochondrial membrane): NADH/FADH₂ donate electrons, which pass down the chain pumping H⁺ into intermembrane space, creating a gradient; O₂ is the final electron acceptor, forming H₂O
  • Chemiosmosis: H⁺ flows back through ATP synthase down its gradient, driving ATP synthesis (oxidative phosphorylation) — the majority of ATP (~26-28 of ~30-32 total) is made here
  • Total ATP yield per glucose: approximately 30-32 ATP (varies by shuttle system efficiency)
Fermentation
Without oxygen, cells regenerate NAD⁺ from NADH so glycolysis can continue, without using the ETC.
  • Purpose of fermentation: regenerate NAD⁺ (needed for glycolysis step 6) when O₂ is unavailable — only glycolysis's 2 ATP are produced (no Krebs or ETC)
  • Lactic acid fermentation: pyruvate → lactate directly (occurs in muscle cells during intense exercise, some bacteria/yogurt)
  • Alcoholic fermentation: pyruvate → acetaldehyde + CO₂ → ethanol (occurs in yeast; used in brewing, baking)
  • Anaerobic respiration (different from fermentation) uses an ETC but with a final electron acceptor other than O₂ (e.g., sulfate) — some prokaryotes only
Photosynthesis: light reactions
The light-dependent reactions occur in the thylakoid membrane, converting light energy into ATP and NADPH while splitting water.
  • Photosystem II (P680) absorbs light, excites electrons, which pass down an ETC to Photosystem I, pumping H⁺ into the thylakoid lumen (chemiosmosis, like mitochondria)
  • Water is split (photolysis) to replace electrons lost from PS II: 2H₂O → 4H⁺ + 4e⁻ + O₂ (this is the source of the O₂ released by photosynthesis)
  • Photosystem I (P700) re-excites electrons, which are passed to NADP⁺ + H⁺ → NADPH (via ferredoxin and NADP⁺ reductase)
  • ATP synthase uses the H⁺ gradient (lumen high, stroma low) to produce ATP via chemiosmosis — same mechanism as in mitochondria
  • Products of light reactions (ATP and NADPH) are used to power the Calvin cycle; O₂ is released as a byproduct
Photosynthesis: Calvin cycle
The Calvin cycle (light-independent reactions) occurs in the stroma, using ATP and NADPH to fix CO₂ into sugar.
  • Carbon fixation: CO₂ is attached to RuBP (5C) by the enzyme rubisco, forming an unstable 6C compound that splits into two 3-PG (3C) molecules
  • Reduction: ATP and NADPH (from light reactions) convert 3-PG into G3P (glyceraldehyde-3-phosphate)
  • Regeneration: most G3P molecules are used to regenerate RuBP (using more ATP) so the cycle continues; 1 out of every 6 G3P produced (net, after 3 turns) exits to build glucose
  • 3 turns of the cycle (fixing 3 CO₂) use 9 ATP and 6 NADPH to net one G3P, which can combine with another G3P to form one glucose
Most ATP from aerobic respiration comes from the electron transport chain/chemiosmosis, NOT substrate-level phosphorylation in glycolysis or Krebs.
Fermentation does NOT use an electron transport chain — its only job is regenerating NAD⁺ so glycolysis can keep running.
The O₂ released in photosynthesis comes from water (photolysis), NOT from CO₂.
The Calvin cycle does not directly require light, but it depends on ATP and NADPH that are made in the light reactions — so it stops without light within minutes.
Net ATP from glycolysis = 2 (substrate-level)
≈30–32 ATP per glucose (aerobic respiration total)
Calvin cycle: 3 CO₂ + 9 ATP + 6 NADPH → 1 G3P (net)
Signal transduction pathways
Cells communicate via signaling molecules that trigger a three-stage process: reception, transduction, and response.
  • Reception: a signaling molecule (ligand) binds a specific receptor protein, either on the cell surface (for polar/large ligands) or inside the cell (for lipid-soluble/nonpolar ligands like steroid hormones)
  • Transduction: receptor activation triggers a cascade of molecular changes, often via a series of relay proteins — a common mechanism is a phosphorylation cascade (kinases add phosphate groups, activating the next protein in line)
  • Second messengers (e.g., cyclic AMP, Ca²⁺) amplify the signal — one receptor activation can trigger production of many second messenger molecules, amplifying the response manyfold
  • Response: the pathway ultimately alters cell behavior — activating/deactivating enzymes, changing gene expression, altering cytoskeleton, or opening ion channels
  • G-protein coupled receptors: ligand binding activates a G protein, which activates an effector enzyme (e.g., adenylyl cyclase making cAMP)
Cell cycle phases
The cell cycle is divided into interphase (growth and DNA replication) and the mitotic phase (nuclear and cell division).
  • Interphase: G1 (cell growth, organelle production) → S (DNA replication, chromosomes become sister chromatids) → G2 (further growth, prep for division); interphase makes up ~90% of the cycle
  • Mitosis stages: prophase (chromosomes condense, spindle forms) → metaphase (chromosomes align at metaphase plate) → anaphase (sister chromatids separate, pulled to opposite poles) → telophase (nuclear envelopes reform, chromosomes decondense)
  • Cytokinesis: division of the cytoplasm — animal cells pinch via a cleavage furrow (actin ring); plant cells build a cell plate that becomes a new cell wall
  • G0 phase: non-dividing state that many differentiated cells (e.g., neurons) enter permanently, or temporarily until a signal triggers re-entry into G1
Cell cycle regulation
Checkpoints ensure the cell cycle proceeds only when conditions are correct, using regulatory proteins called cyclins and cyclin-dependent kinases (CDKs).
  • G1 checkpoint (restriction point): checks cell size, nutrients, and DNA integrity — the main 'go/no-go' point; without a go-ahead signal, cell enters G0
  • G2 checkpoint: verifies DNA replication completed correctly and without damage before entering mitosis
  • M checkpoint (spindle assembly checkpoint): verifies all chromosomes are properly attached to spindle fibers before anaphase begins
  • Cyclins bind and activate CDKs; cyclin levels rise and fall through the cycle, while CDK levels stay constant — together (cyclin-CDK complexes, e.g., MPF) they phosphorylate target proteins to trigger the next phase
Cancer & apoptosis
Cancer arises when mutations disrupt the normal genes that control cell division, leading to uncontrolled growth.
  • Proto-oncogenes: normal genes that promote cell division; a gain-of-function mutation turns them into oncogenes that overstimulate division (act like a stuck accelerator)
  • Tumor suppressor genes (e.g., p53, RB): normally inhibit cell division or trigger apoptosis when DNA is damaged; loss-of-function mutations remove this brake
  • p53 ('guardian of the genome'): detects DNA damage, halts the cell cycle for repair, or triggers apoptosis if damage is irreparable; mutated in over half of human cancers
  • Apoptosis: programmed cell death — a controlled process that removes damaged, infected, or unneeded cells without releasing harmful contents into surrounding tissue (unlike necrosis)
  • Metastasis: cancer cells lose contact inhibition and anchorage dependence, invade nearby tissue, and can spread to distant sites via blood/lymph
A mutated proto-oncogene becomes an oncogene through a GAIN of function; a mutated tumor suppressor loses its normal braking FUNCTION — the mutation types have opposite functional effects.
Interphase is NOT a resting phase — it's when the cell grows, functions normally, and replicates its DNA (S phase).
Cyclin levels oscillate through the cycle; CDK levels remain fairly constant — it's the cyclin binding that activates CDK activity at the right time.
Apoptosis is a controlled, beneficial process for the organism; necrosis is uncontrolled cell death that damages surrounding tissue.
Cell cycle order: G1 → S → G2 → M (mitosis + cytokinesis)
Cyclin + CDK → active complex → drives phase transition
Meiosis
Meiosis is a two-round division (meiosis I and II) that produces four genetically unique haploid gametes from one diploid cell.
  • Meiosis I (reductional division): homologous chromosomes separate — prophase I includes synapsis (homologs pair up) and crossing over (exchange of genetic material between non-sister chromatids), a major source of genetic variation
  • Independent assortment: homologous pairs align randomly at the metaphase I plate, so maternal/paternal chromosomes sort into gametes independently — for n chromosome pairs, 2ⁿ possible combinations
  • Meiosis II (equational division, like mitosis): sister chromatids separate — produces 4 haploid (n) cells from the 2 cells made in meiosis I
  • Sources of genetic variation: crossing over (prophase I), independent assortment (metaphase I), and random fertilization (any sperm can fertilize any egg)
  • Nondisjunction: failure of chromosomes/chromatids to separate properly → gametes with abnormal chromosome numbers (e.g., trisomy 21/Down syndrome from an extra chromosome 21)
Mendelian genetics
Gregor Mendel's laws of segregation and independent assortment describe how alleles are inherited.
  • Law of segregation: the two alleles for a gene separate during meiosis so each gamete gets only one allele
  • Law of independent assortment: alleles of different genes (on different chromosomes) assort independently into gametes
  • Genotype: the allele combination (e.g., Bb); Phenotype: the observable trait (e.g., brown eyes) resulting from genotype and environment
  • Homozygous: two identical alleles (BB or bb); Heterozygous: two different alleles (Bb)
  • Complete dominance: heterozygote shows only the dominant phenotype (Bb looks like BB)
Monohybrid & dihybrid crosses
Punnett squares predict offspring genotype/phenotype ratios from parental crosses.
  • Monohybrid cross (one gene): Bb × Bb → offspring ratio 1 BB : 2 Bb : 1 bb genotypically → 3:1 dominant:recessive phenotypically
  • Test cross: cross an unknown-genotype dominant phenotype individual with a homozygous recessive to reveal whether it's homozygous or heterozygous dominant
  • Dihybrid cross (two independently assorting genes): AaBb × AaBb → 9:3:3:1 phenotypic ratio (assuming independent assortment and no linkage)
  • Multiplication rule: for independent events (e.g., two separate gene crosses), multiply individual probabilities to get the combined probability
Non-Mendelian inheritance
Not all traits follow simple dominant/recessive patterns — several inheritance patterns deviate from classic Mendelian ratios.
  • Incomplete dominance: heterozygote phenotype is a BLENDED intermediate of both alleles (e.g., red × white snapdragon → pink; RR:Rr:rr gives 1:2:1 ratio phenotypically too)
  • Codominance: heterozygote shows BOTH parental phenotypes fully and simultaneously, not blended (e.g., AB blood type shows both A and B antigens; roan cattle with both red and white hairs)
  • Multiple alleles: more than 2 alleles exist for a gene in the population (e.g., ABO blood type has IA, IB, i alleles; only 2 present in any individual)
  • Sex-linked inheritance: genes on the X chromosome show different inheritance in males (XY, only one X allele expressed, hemizygous) vs females (XX) — e.g., red-green color blindness, hemophilia are X-linked recessive and more common in males
  • Linked genes: genes located close together on the same chromosome tend to be inherited together, violating independent assortment unless separated by crossing over (closer genes = less recombination)
  • Polygenic traits: controlled by multiple genes with additive effects, producing continuous variation (e.g., human height, skin color)
Independent assortment applies to genes on DIFFERENT chromosomes (or far apart on the same one) — linked genes on the same chromosome do NOT assort independently.
Incomplete dominance BLENDS the phenotype (pink); codominance shows BOTH traits fully and separately (spotted, AB blood) — these are commonly confused.
In X-linked recessive traits, a male needs only ONE recessive allele to express the trait (hemizygous); a female needs two.
A 9:3:3:1 ratio requires the two genes to assort independently — linked genes produce a skewed ratio instead.
Dihybrid ratio (independent genes): 9:3:3:1
Monohybrid ratio (Aa × Aa): 3:1 (phenotype), 1:2:1 (genotype)
2ⁿ = number of possible gamete combinations (n = # of chromosome pairs)
DNA replication
DNA replication is semiconservative — each new double helix contains one original (parental) strand and one newly synthesized strand.
  • Helicase unwinds and unzips the double helix at the origin of replication, creating a replication fork
  • DNA polymerase adds new nucleotides only in the 5'→3' direction, reading the template strand 3'→5'
  • Leading strand: synthesized continuously toward the replication fork; Lagging strand: synthesized discontinuously away from the fork in Okazaki fragments, later joined by DNA ligase
  • Primase lays down a short RNA primer to give DNA polymerase a starting 3'-OH group; primers are later replaced with DNA
  • DNA polymerase also proofreads, removing mismatched nucleotides — high fidelity replication with a very low error rate
Central dogma: transcription & translation
Genetic information flows from DNA → RNA (transcription) → protein (translation).
  • Transcription (in the nucleus of eukaryotes): RNA polymerase uses one DNA strand as a template to synthesize a complementary mRNA strand (5'→3'); in eukaryotes, pre-mRNA is processed — 5' cap and poly-A tail added, introns spliced out leaving only exons
  • Translation (at ribosomes): mRNA codons (3-nucleotide sequences) are read in the ribosome; tRNA molecules, each carrying a specific amino acid and complementary anticodon, pair with codons
  • Ribosome moves along mRNA, and peptide bonds form between amino acids, building a polypeptide chain until a stop codon is reached
  • Genetic code is degenerate (redundant, multiple codons can code for the same amino acid) but unambiguous (each codon specifies only one amino acid) and nearly universal across all life
  • Start codon AUG codes for methionine and sets the reading frame; stop codons (UAA, UAG, UGA) terminate translation without coding for an amino acid
Mutations
Mutations are changes in the DNA sequence; their effect depends on type and location.
  • Point mutation (substitution): one base is changed — silent (codes for same amino acid, no effect), missense (codes for different amino acid), or nonsense (creates a premature stop codon)
  • Frameshift mutation (insertion or deletion of bases not in multiples of 3): shifts the reading frame downstream of the mutation, usually causing a completely different, often nonfunctional protein
  • Insertions/deletions in multiples of 3 add/remove whole amino acids but don't shift the frame
  • Mutations in somatic cells affect only that organism (not heritable); mutations in germ-line cells (gametes) can be passed to offspring
  • Mutagens (UV light, chemicals, radiation) increase mutation rate; mutations are also the ultimate source of all new genetic variation for natural selection
Gene regulation
Cells control which genes are expressed, and when, largely through the operon system in prokaryotes and multiple layers of control in eukaryotes.
  • Lac operon (inducible, prokaryotic): in the absence of lactose, a repressor binds the operator, blocking transcription of lactose-digesting genes; when lactose is present, it binds the repressor, removing it from the operator, allowing transcription
  • Trp operon (repressible, prokaryotic): normally 'on'; when tryptophan is abundant, it acts as a co-repressor, activating the repressor to bind the operator and shut off transcription (negative feedback)
  • Eukaryotic gene regulation occurs at multiple levels: chromatin structure (heterochromatin = tightly packed/inactive vs euchromatin = loosely packed/active), transcription (transcription factors, enhancers/promoters), post-transcriptional (alternative splicing, mRNA stability), and post-translational (protein modification/degradation)
  • Epigenetics: heritable changes in gene expression without changing DNA sequence — DNA methylation (usually silences genes) and histone acetylation (usually activates genes by loosening chromatin)
Biotechnology basics
Modern techniques allow scientists to isolate, copy, and analyze specific DNA sequences.
  • PCR (polymerase chain reaction): amplifies a specific DNA sequence exponentially using primers, DNA polymerase (Taq), and repeated cycles of denaturation (heat separates strands), annealing (primers bind), and extension (polymerase synthesizes new strand)
  • Gel electrophoresis: separates DNA fragments by size using an electric field — DNA is negatively charged (phosphate backbone) and migrates toward the positive electrode; smaller fragments move farther/faster through the gel matrix
  • Restriction enzymes cut DNA at specific recognition sequences, producing fragments (often with 'sticky ends') used in cloning and creating restriction fragment patterns for comparison
  • Recombinant DNA/genetic engineering: a gene of interest is inserted into a plasmid vector (using the same restriction enzyme to create complementary sticky ends) and introduced into a host cell (e.g., bacteria producing human insulin)
DNA polymerase can only add nucleotides in the 5'→3' direction — this is why the lagging strand must be synthesized discontinuously in fragments.
A frameshift mutation (indel not a multiple of 3) usually has a much bigger effect than a single substitution because it shifts every codon downstream.
In gel electrophoresis, SMALLER DNA fragments travel FARTHER (faster) through the gel, not shorter distances.
The lac operon is induced (turned ON by lactose); the trp operon is repressed (turned OFF by tryptophan) — opposite regulatory logic, easy to mix up.
Codon = 3 mRNA bases → 1 amino acid
PCR cycle: denature → anneal → extend
DNA charge: negative (moves toward + electrode in electrophoresis)
Evidence for evolution
Multiple independent lines of evidence converge to support the theory that all life shares common ancestry and has evolved over time.
  • Fossil record: shows a chronological sequence of changing life forms and transitional forms between major groups
  • Comparative anatomy: homologous structures (same underlying structure, different function, e.g., forelimbs of humans/whales/bats) indicate common ancestry; analogous structures (different origin, similar function, e.g., wings of insects and birds) indicate convergent evolution, not common ancestry
  • Vestigial structures: reduced, functionless remnants of structures that were functional in an ancestor (e.g., human appendix, whale pelvic bones)
  • Molecular biology: the more similar the DNA/protein sequences (e.g., cytochrome c) between two species, the more recently they likely shared a common ancestor
  • Biogeography: geographic distribution of species reflects evolutionary history and geological events (e.g., continental drift, island colonization)
Hardy-Weinberg equilibrium
The Hardy-Weinberg model describes allele/genotype frequencies in a non-evolving population, serving as a null hypothesis to test whether evolution is occurring.
  • p + q = 1 (allele frequencies for a 2-allele gene: p = dominant allele frequency, q = recessive allele frequency)
  • p² + 2pq + q² = 1 (genotype frequencies: p² = homozygous dominant, 2pq = heterozygous, q² = homozygous recessive)
  • Five conditions required for equilibrium (no evolution): no mutation, no gene flow (migration), infinitely large population (no genetic drift), random mating, and no natural selection
  • If observed genotype frequencies differ significantly from Hardy-Weinberg predictions, one or more of these conditions is being violated, and the population is evolving
Mechanisms of evolution
Evolution is a change in allele frequencies in a population over time, driven by several mechanisms.
  • Natural selection: individuals with heritable traits better suited to the environment survive and reproduce at higher rates, increasing the frequency of favorable alleles
  • Genetic drift: random change in allele frequencies, with a larger effect in SMALL populations; bottleneck effect (population sharply reduced by a random event) and founder effect (small group establishes a new isolated population) are two types
  • Gene flow (migration): movement of alleles between populations via migrating individuals, tends to reduce genetic differences between populations
  • Types of selection: directional (favors one phenotypic extreme, shifts the mean), stabilizing (favors the intermediate phenotype, reduces variation, e.g., human birth weight), disruptive (favors both extremes over the intermediate, can increase variation/lead to speciation)
  • Sexual selection: a form of natural selection based on differential mating success — can produce traits that don't obviously aid survival (e.g., peacock tails)
Speciation & phylogenetics
Speciation is the formation of new, reproductively isolated species; phylogenetics organizes species based on evolutionary relationships.
  • Reproductive isolation prevents gene flow between populations, allowing them to diverge into separate species; mechanisms are prezygotic (prevent mating/fertilization, e.g., habitat, temporal, behavioral, mechanical, gametic isolation) or postzygotic (hybrid inviability, hybrid sterility, e.g., mules)
  • Allopatric speciation: geographic separation (e.g., river, mountain range) prevents gene flow, populations diverge independently — the most common mode of speciation
  • Sympatric speciation: new species arises without geographic separation, often via polyploidy (especially common in plants), habitat differentiation, or sexual selection
  • Phylogenetic trees/cladograms: branching diagrams showing hypothesized evolutionary relationships; a shared derived character (synapomorphy) defines a clade; the node represents the most recent common ancestor of the branches above it
  • More shared derived characteristics = more closely related; outgroup comparison helps root a tree and determine the direction of character change
Homologous structures indicate common ancestry (similar structure); analogous structures indicate convergent evolution (similar function only, NOT close relation) — often reversed by students.
Hardy-Weinberg describes a population that is NOT evolving — it's a null model to detect evolution, not a description of how evolution works.
Stabilizing selection REDUCES phenotypic variation (favors the average); disruptive selection INCREASES it (favors both extremes) — do not swap these.
Genetic drift has the LARGEST effect in SMALL populations, not large ones.
p + q = 1
p² + 2pq + q² = 1
q² = frequency of homozygous recessive genotype → q = √(q²)
Population growth models
Populations grow according to predictable mathematical models shaped by resource availability.
  • Exponential growth (J-curve): occurs with unlimited resources; rate of increase is proportional to population size; dN/dt = rN
  • Logistic growth (S-curve): growth slows as population approaches carrying capacity (K) due to density-dependent limiting factors; dN/dt = rN(K−N)/K
  • Carrying capacity (K): the maximum population size an environment can sustainably support given its resources
  • Density-dependent limiting factors: intensify as population density increases (competition for food/space, predation, disease, waste accumulation)
  • Density-independent limiting factors: affect population regardless of density (natural disasters, extreme weather, habitat destruction)
  • r-selected species: many small offspring, little parental care, fast maturation, thrive in unstable/exponential-growth conditions (insects, weeds); K-selected species: fewer offspring, more parental investment, thrive near carrying capacity (elephants, humans)
Community interactions
Species within a community interact through predation, competition, and symbiosis, shaping community structure.
  • Competition (−/−): both species harmed when using the same limited resource; competitive exclusion principle states two species cannot indefinitely occupy the exact same niche
  • Predation (+/−): predator benefits, prey is harmed/killed; can drive coevolutionary 'arms races' (e.g., cheetah speed vs gazelle speed)
  • Mutualism (+/+): both species benefit (e.g., mycorrhizae fungi and plant roots, gut bacteria and humans)
  • Commensalism (+/0): one species benefits, the other is unaffected (e.g., barnacles on a whale)
  • Parasitism (+/−): parasite benefits at the host's expense, usually without immediately killing the host
  • Resource partitioning: species divide a limited resource by using different parts of it (niche differentiation), reducing direct competition
Ecosystem energy flow
Energy flows one-way through ecosystems from producers to consumers, with substantial loss at each trophic level.
  • Producers (autotrophs, e.g., plants, algae, cyanobacteria) convert solar energy into chemical energy via photosynthesis, forming the base of the food chain
  • Primary consumers (herbivores) eat producers; secondary consumers (carnivores) eat primary consumers; tertiary consumers eat secondary consumers
  • Only about 10% of energy is transferred from one trophic level to the next (the rest is lost as heat via cellular respiration, or is unused/undigested) — the 10% rule
  • Trophic pyramid: energy, biomass, and typically numbers all decrease at higher trophic levels, limiting food chain length (usually 4-5 levels)
  • Gross primary productivity (GPP): total energy captured by producers; Net primary productivity (NPP) = GPP − energy producers use for their own respiration
Biogeochemical cycles
Essential elements cycle between living organisms and the physical (abiotic) environment.
  • Carbon cycle: CO₂ fixed by photosynthesis into organic carbon, returned to atmosphere via cellular respiration, decomposition, and combustion; also stored long-term in fossil fuels and dissolved in oceans
  • Nitrogen cycle: atmospheric N₂ is largely unusable by most organisms until nitrogen-fixing bacteria (e.g., Rhizobium in legume root nodules) convert it to ammonia/ammonium; nitrification converts this to nitrite then nitrate (usable by plants); denitrification returns N₂ to the atmosphere
  • Phosphorus cycle: has no significant atmospheric component — phosphorus cycles mainly through rock weathering, soil, water, and living organisms (a key component of DNA, ATP, phospholipids)
  • Water cycle: driven by solar energy — evaporation/transpiration, condensation, precipitation, and runoff/infiltration
Climate & biodiversity
Biodiversity and climate patterns interact, and human activity is altering both at an accelerating rate.
  • Biodiversity provides ecosystem services (e.g., pollination, water filtration, nutrient cycling) and increases ecosystem stability/resilience to disturbance
  • Greenhouse effect: greenhouse gases (CO₂, methane, water vapor) trap infrared radiation reflected from Earth's surface, warming the atmosphere — necessary for life, but human-caused excess is driving climate change
  • Ocean acidification: increased atmospheric CO₂ dissolves into oceans, forming carbonic acid, lowering pH, and threatening calcifying organisms (coral, shellfish)
  • Habitat fragmentation and loss reduce biodiversity by isolating populations, reducing gene flow, and shrinking available resources — currently the leading cause of species extinction
Only about 10% of energy passes to the next trophic level — the rest is lost as metabolic heat, NOT stored or passed on.
The phosphorus cycle has essentially no atmospheric gas phase, unlike carbon, nitrogen, and water cycles.
K-selected species are favored NEAR carrying capacity (density-dependent factors matter); r-selected species thrive when resources are abundant/uncrowded (early exponential growth).
Competitive exclusion means two species can't occupy the identical niche indefinitely — one will be excluded or the species will diverge (resource partitioning).
Logistic growth: dN/dt = rN(K−N)/K
Exponential growth: dN/dt = rN
10% rule: ~10% of energy transfers to the next trophic level
Practice Question Bank — 122 questions
Unit 1: Chemistry of Life (16)
  1. Water's high specific heat is primarily due to:

    • Its low molar mass
    • Extensive hydrogen bonding between molecules
    • Its nonpolar covalent bonds
    • High atmospheric pressure

    Hydrogen bonds must absorb significant energy to break before water's temperature rises, giving water its high specific heat.

  2. Ice floats on liquid water because:

    • Ice is chemically different from liquid water
    • Hydrogen bonds in ice form a rigid, spaced-out lattice that is less dense
    • Ice contains trapped air bubbles only
    • Cold water always rises

    The hexagonal hydrogen-bonded lattice in ice spaces molecules farther apart than in liquid water, making ice less dense.

  3. Which best describes dehydration synthesis?

    • Breaking a polymer using water
    • Joining monomers and releasing water
    • Denaturing a protein
    • Adding water to break a peptide bond

    Dehydration synthesis joins monomers into polymers, releasing one water molecule per bond formed.

  4. A carboxyl group (-COOH) found in amino acids and fatty acids is best described as:

    • Basic and able to accept a proton
    • Acidic and able to donate a proton
    • Nonpolar and hydrophobic
    • Uncharged at all pH levels

    The carboxyl group is acidic — it can ionize to -COO⁻, releasing an H⁺.

  5. Which level of protein structure is described as the linear sequence of amino acids?

    • Primary
    • Secondary
    • Tertiary
    • Quaternary

    Primary structure is simply the order of amino acids linked by peptide bonds.

  6. A protein loses its function after being placed in boiling water. This is best explained by:

    • Breaking of peptide bonds in the primary structure
    • Denaturation disrupting secondary/tertiary bonds while primary structure remains
    • Complete hydrolysis into amino acids
    • Conversion into a different type of macromolecule

    Heat denatures a protein by disrupting hydrogen bonds and other weak interactions, not the covalent peptide bonds of primary structure.

  7. Enzymes speed up reactions by:

    • Increasing the free energy change (ΔG) of the reaction
    • Lowering the activation energy required to reach the transition state
    • Making nonspontaneous reactions spontaneous
    • Increasing substrate concentration

    Enzymes lower activation energy; they do not change ΔG or reaction spontaneity.

  8. A noncompetitive inhibitor reduces enzyme activity by:

    • Binding the active site directly
    • Being chemically identical to the substrate
    • Binding a site other than the active site and changing enzyme shape
    • Increasing the enzyme's optimal temperature

    Noncompetitive (allosteric) inhibitors bind elsewhere and change the enzyme's shape so the active site functions poorly.

  9. Increasing substrate concentration would most effectively counteract the effect of a:

    • Noncompetitive inhibitor
    • Competitive inhibitor
    • Denaturing agent
    • Allosteric activator

    Competitive inhibitors compete with substrate for the same active site, so excess substrate can outcompete the inhibitor.

  10. Which macromolecule's monomer is a nucleotide?

    • Protein
    • Carbohydrate
    • Lipid
    • Nucleic acid

    Nucleic acids (DNA, RNA) are polymers of nucleotide monomers.

  11. Cohesion in water is responsible for:

    • Water's solvent properties
    • Surface tension and movement of water up plant xylem
    • Ice being less dense than liquid water
    • High boiling point alone

    Cohesion (water-water attraction via H-bonds) creates surface tension and allows continuous water columns in xylem.

  12. An enzyme functions best within a specific pH range because:

    • pH affects only the substrate, never the enzyme
    • Extreme pH can disrupt the ionic and hydrogen bonds maintaining the enzyme's shape
    • All enzymes require pH 7 to function
    • pH changes the enzyme's primary structure directly

    pH extremes disrupt the weak bonds that hold the enzyme's tertiary structure, altering the active site's shape.

  13. Which is an example of a phospholipid's role?

    • Long-term energy storage in fat cells
    • Forming the plasma membrane's structural bilayer
    • Catalyzing biochemical reactions
    • Carrying genetic information

    Phospholipids' amphipathic structure (polar head, nonpolar tails) makes them ideal for forming membrane bilayers.

  14. The induced fit model of enzyme action states that:

    • The active site is rigid and never changes shape
    • The active site changes shape slightly as the substrate binds, improving fit
    • Substrates change their own shape while the enzyme stays fixed
    • Enzymes bind any substrate equally well

    Induced fit describes a slight conformational change in the enzyme's active site upon substrate binding.

  15. Hydrolysis reactions are used by the digestive system to:

    • Build polymers from monomers
    • Break down polymers into monomers by adding water
    • Release oxygen from food
    • Denature all dietary proteins

    Digestion breaks polymers (starch, protein) into monomers via hydrolysis, adding a water molecule at each bond broken.

  16. Which functional group would most increase a molecule's water solubility?

    • Methyl group
    • Hydroxyl group
    • A long hydrocarbon chain
    • None of these affect solubility

    The polar hydroxyl group (-OH) can hydrogen bond with water, increasing solubility; methyl groups are nonpolar and decrease it.

Unit 2: Cell Structure & Function (16)
  1. Which structure is found in both prokaryotic and eukaryotic cells?

    • Nucleus
    • Mitochondria
    • Ribosomes
    • Endoplasmic reticulum

    Both cell types contain ribosomes (though prokaryotic 70S ribosomes are smaller than eukaryotic 80S), a plasma membrane, cytoplasm, and DNA.

  2. The best evidence for the endosymbiotic theory is that mitochondria and chloroplasts:

    • Are found only in plant cells
    • Contain their own circular DNA, 70S ribosomes, and double membranes
    • Are larger than the nucleus
    • Cannot produce ATP independently

    These features closely resemble free-living bacteria, supporting the idea that these organelles originated as engulfed prokaryotes.

  3. As a cell increases in size, its surface-area-to-volume ratio:

    • Increases, improving exchange efficiency
    • Decreases, limiting efficient exchange with the environment
    • Stays constant
    • Becomes irrelevant to cell function

    Volume increases faster (cubed) than surface area (squared) as size increases, so SA:V ratio decreases, limiting exchange.

  4. In the fluid mosaic model, membrane fluidity increases with:

    • More saturated fatty acid tails
    • More unsaturated fatty acid tails (kinks preventing tight packing)
    • More cholesterol at low temperatures
    • Thicker phospholipid heads

    Unsaturated fatty acids have kinks from double bonds that prevent tight packing, increasing membrane fluidity.

  5. Facilitated diffusion differs from active transport because facilitated diffusion:

    • Requires ATP and moves against the gradient
    • Requires no ATP and moves down the concentration gradient
    • Only works for nonpolar molecules
    • Always uses the sodium-potassium pump

    Facilitated diffusion is passive (no ATP) and moves solutes down their gradient via channel/carrier proteins.

  6. A red blood cell placed in a hypertonic solution will:

    • Swell and lyse
    • Shrivel (crenate) as water leaves the cell
    • Remain unchanged
    • Undergo mitosis

    In a hypertonic solution, water moves out of the cell (toward higher solute concentration), causing the cell to shrink/crenate.

  7. A plant cell placed in a hypotonic solution becomes:

    • Plasmolyzed
    • Turgid, due to the rigid cell wall resisting excess water entry
    • Crenated
    • Completely lysed

    Water enters the cell, but the cell wall prevents lysis, resulting in a firm, turgid cell — this is the healthy state for plant cells.

  8. The Golgi apparatus functions primarily to:

    • Synthesize ATP via cellular respiration
    • Modify, sort, and package proteins and lipids from the ER
    • Store the cell's genetic material
    • Break down worn-out organelles

    The Golgi receives products from the ER at its cis face and modifies/sorts/packages them, shipping them from its trans face.

  9. The sodium-potassium pump is an example of:

    • Simple diffusion
    • Facilitated diffusion
    • Active transport
    • Osmosis

    It moves Na⁺ and K⁺ against their gradients using ATP, making it active transport.

  10. Which is true of both mitochondria and chloroplasts?

    • Both are found only in animal cells
    • Both have double membranes and their own DNA
    • Both perform photosynthesis
    • Both lack ribosomes

    Both organelles have double membranes and circular DNA, consistent with endosymbiotic origin.

  11. Integral membrane proteins differ from peripheral membrane proteins in that integral proteins:

    • Are only found on the membrane's outer surface
    • Span or embed within the lipid bilayer
    • Cannot function as receptors
    • Are made of carbohydrates

    Integral proteins are embedded in or span the bilayer; peripheral proteins are attached to the membrane surface only.

  12. Which of the following would most likely increase the rate of facilitated diffusion?

    • Decreasing the number of transport proteins
    • Increasing the concentration gradient of the solute
    • Adding ATP to the system
    • Cooling the membrane to near-freezing

    A steeper concentration gradient increases the rate of passive transport processes like facilitated diffusion, up to a saturation point.

  13. Lysosomes primarily function to:

    • Produce ATP
    • Digest macromolecules, worn-out organelles, and pathogens using hydrolytic enzymes
    • Synthesize lipids
    • Store starch in plant cells

    Lysosomes contain hydrolytic enzymes for intracellular digestion (autophagy, pathogen destruction).

  14. Why can eukaryotic cells generally be larger than prokaryotic cells?

    • They lack a plasma membrane
    • Membrane-bound organelles increase internal surface area and compartmentalize functions
    • They do not need ribosomes
    • They reproduce more slowly

    Internal membranes (organelles) provide additional surface area for reactions, helping overcome surface-area-to-volume limitations.

  15. A cell surrounded by a solution with the same solute concentration as its cytoplasm is in a(n):

    • Hypotonic solution
    • Hypertonic solution
    • Isotonic solution
    • Osmotic solution

    Isotonic solutions have equal solute concentration, so there is no net water movement.

  16. Cholesterol embedded in the animal cell membrane functions to:

    • Buffer membrane fluidity, preventing it from becoming too fluid at high temperatures or too rigid at low temperatures
    • Only increase membrane rigidity at all temperatures
    • Actively transport ions across the membrane
    • Replace phospholipids entirely

    Cholesterol has a dual buffering role — it restrains excess fluidity at high temperatures and prevents excess rigidity at low temperatures.

Unit 3: Cellular Energetics (15)
  1. Which process directly produces the most ATP per glucose molecule?

    • Glycolysis
    • Pyruvate oxidation
    • Krebs cycle
    • Oxidative phosphorylation (chemiosmosis via the ETC)

    Oxidative phosphorylation via the electron transport chain and chemiosmosis produces roughly 26-28 of the ~30-32 total ATP per glucose.

  2. The main purpose of fermentation is to:

    • Produce large amounts of ATP directly
    • Regenerate NAD⁺ so glycolysis can continue without oxygen
    • Split water to release oxygen
    • Fix carbon dioxide into sugar

    Fermentation regenerates NAD⁺ from NADH, allowing glycolysis to continue producing its small net ATP yield in the absence of O₂.

  3. In the electron transport chain, the final electron acceptor in aerobic respiration is:

    • NAD⁺
    • Pyruvate
    • Oxygen
    • Carbon dioxide

    Oxygen accepts electrons at the end of the ETC, combining with H⁺ to form water.

  4. The oxygen released during photosynthesis comes from:

    • Carbon dioxide
    • Water, split during the light reactions
    • Glucose
    • The Calvin cycle

    Photolysis of water in Photosystem II releases O₂ as a byproduct; CO₂ becomes part of the sugar produced, not O₂.

  5. Which molecules directly power the Calvin cycle?

    • Glucose and oxygen
    • ATP and NADPH from the light reactions
    • CO₂ and H₂O only
    • FADH₂ and pyruvate

    The Calvin cycle uses ATP and NADPH (produced in the light reactions) to fix CO₂ into G3P/glucose.

  6. Chemiosmosis refers to:

    • Diffusion of chemicals across a membrane
    • ATP synthesis driven by H⁺ flowing through ATP synthase down its gradient
    • The breakdown of glucose in the cytoplasm
    • The splitting of water in photosynthesis

    Chemiosmosis is the process where a proton gradient drives ATP synthase to produce ATP, used in both respiration and photosynthesis.

  7. Glycolysis occurs in the:

    • Mitochondrial matrix
    • Inner mitochondrial membrane
    • Cytoplasm
    • Chloroplast stroma

    Glycolysis takes place in the cytoplasm and does not require oxygen.

  8. An athlete experiencing muscle burn during intense exercise is most likely undergoing:

    • Aerobic respiration only
    • Lactic acid fermentation due to insufficient oxygen supply
    • The Calvin cycle
    • Photosynthesis

    When oxygen delivery can't keep up with demand, muscle cells use lactic acid fermentation to regenerate NAD⁺.

  9. Rubisco catalyzes which step of the Calvin cycle?

    • Regeneration of RuBP
    • Reduction of 3-PG to G3P
    • Carbon fixation — attaching CO₂ to RuBP
    • Splitting of water

    Rubisco fixes atmospheric CO₂ onto the 5-carbon RuBP, the first step of the Calvin cycle.

  10. Which best describes the relationship between mitochondria and chloroplasts regarding ATP synthesis?

    • Only mitochondria use chemiosmosis
    • Both use chemiosmosis, driven by a proton gradient across an internal membrane
    • Only chloroplasts produce ATP
    • Neither uses a proton gradient

    Both organelles use ATP synthase and a proton gradient (chemiosmosis) to generate ATP, despite different electron sources.

  11. Alcoholic fermentation, used by yeast, converts pyruvate into:

    • Lactate
    • Ethanol and CO₂
    • Glucose
    • Oxygen and water

    Yeast converts pyruvate to acetaldehyde, releasing CO₂, then to ethanol, regenerating NAD⁺.

  12. During the Krebs cycle, most of the energy extracted from acetyl-CoA is stored in the form of:

    • ATP directly
    • NADH and FADH₂ (electron carriers)
    • Glucose
    • Free oxygen

    The Krebs cycle produces mostly NADH and FADH₂, which later fuel the ETC to make most of the cell's ATP; only 2 ATP form directly.

  13. If a poison blocked Photosystem II specifically, which process would be directly impaired first?

    • The Calvin cycle only
    • Splitting of water and the initial electron excitation for the light reactions
    • Cellular respiration
    • DNA replication

    PS II absorbs light and splits water; blocking it stops electron flow to PS I and halts water-splitting (O₂ release).

  14. The net ATP yield of glycolysis (before considering the electron transport chain) is:

    • 0 ATP
    • 2 ATP
    • 4 ATP
    • 36 ATP

    Glycolysis uses 2 ATP to invest and produces 4 ATP, for a net gain of 2 ATP via substrate-level phosphorylation.

  15. Which process produces ATP directly by substrate-level phosphorylation rather than chemiosmosis?

    • Oxidative phosphorylation in the ETC
    • Glycolysis and the Krebs cycle
    • Photophosphorylation in chloroplasts
    • Facilitated diffusion

    Glycolysis and the Krebs cycle each generate a small amount of ATP directly (substrate-level phosphorylation), unlike the ETC's chemiosmotic mechanism.

Unit 4: Cell Communication & Cell Cycle (15)
  1. In cell signaling, 'transduction' refers to:

    • The initial binding of a ligand to a receptor
    • The conversion of a received signal into a cellular response through a relay pathway
    • The final change in cell behavior
    • The diffusion of the ligand through the membrane

    Transduction is the relay/amplification stage that converts receptor activation into intracellular molecular changes.

  2. Which cell cycle checkpoint verifies that all chromosomes are properly attached to spindle fibers?

    • G1 checkpoint
    • G2 checkpoint
    • M checkpoint (spindle assembly checkpoint)
    • S checkpoint

    The M/spindle assembly checkpoint ensures proper chromosome attachment before anaphase proceeds.

  3. Cyclins differ from CDKs in that:

    • Cyclin levels oscillate through the cell cycle while CDK levels stay fairly constant
    • CDK levels oscillate while cyclin levels stay constant
    • Both remain constant throughout the cycle
    • Neither is involved in cell cycle regulation

    Cyclin concentration rises and falls at specific points in the cycle, binding and activating the constantly-present CDKs at the right time.

  4. A mutation that converts a proto-oncogene into an oncogene is best described as a:

    • Loss-of-function mutation that removes a cell cycle brake
    • Gain-of-function mutation that overstimulates cell division
    • Silent mutation with no effect
    • Mutation affecting only mitochondrial DNA

    Proto-oncogenes normally promote division; a gain-of-function mutation makes them overactive, driving excess division.

  5. The p53 gene is best classified as a:

    • Proto-oncogene
    • Tumor suppressor gene
    • Structural gene with no regulatory role
    • Mitochondrial gene

    p53 halts the cell cycle for repair or triggers apoptosis when DNA is damaged, functioning as a tumor suppressor.

  6. Apoptosis differs from necrosis in that apoptosis is:

    • Uncontrolled and damages surrounding tissue
    • A controlled, programmed process that avoids harming nearby cells
    • Only seen in cancer cells
    • The same process as mitosis

    Apoptosis is a regulated form of cell death that safely removes cells without releasing harmful contents, unlike necrosis.

  7. During which phase of the cell cycle does DNA replication occur?

    • G1
    • S
    • G2
    • M

    S phase (synthesis phase) is when DNA replication occurs, producing sister chromatids.

  8. A cell that permanently exits the cell cycle (e.g., a mature neuron) enters:

    • G0
    • Prophase
    • Metaphase
    • Telophase

    G0 is a non-dividing state that some differentiated cells enter permanently.

  9. Second messengers like cAMP function in signal transduction primarily to:

    • Directly transport the original ligand into the cell
    • Amplify the signal so one receptor activation triggers a large response
    • Replace the need for a receptor
    • Bind directly to DNA

    Second messengers amplify a small initial signal into a much larger intracellular response.

  10. Sister chromatids separate during which stage of mitosis?

    • Prophase
    • Metaphase
    • Anaphase
    • Telophase

    Anaphase is when sister chromatids are pulled apart to opposite poles of the cell.

  11. Loss of contact inhibition and anchorage dependence in a cell most directly suggests:

    • Normal, healthy tissue regeneration
    • A cancerous cell capable of uncontrolled growth and metastasis
    • A cell entering G0
    • Successful apoptosis

    Cancer cells typically ignore normal growth-limiting signals like contact inhibition, allowing invasive, uncontrolled growth.

  12. Which statement about the cell cycle checkpoints is correct?

    • The G1 checkpoint checks for proper spindle attachment
    • The G2 checkpoint verifies DNA replication was completed correctly before mitosis
    • The M checkpoint checks nutrient availability
    • Checkpoints only function in cancer cells

    The G2 checkpoint ensures DNA was replicated correctly and without damage before the cell proceeds into mitosis.

  13. A cell with damaged DNA that cannot be repaired is normally directed by p53 to:

    • Continue dividing regardless of damage
    • Undergo apoptosis
    • Immediately enter G0 permanently with no other effect
    • Convert into a stem cell

    When DNA damage is irreparable, functional p53 triggers apoptosis, eliminating the potentially dangerous cell.

  14. A phosphorylation cascade in a signal transduction pathway most directly:

    • Directly transports the ligand into the nucleus
    • Relays and amplifies the signal by sequentially activating a series of proteins via kinases
    • Immediately destroys the receptor
    • Has no effect on the eventual cellular response

    A phosphorylation cascade uses a chain of kinases, each activating the next, to relay and amplify the original signal.

  15. Chromosomes align at the metaphase plate during which stage of mitosis?

    • Prophase
    • Metaphase
    • Anaphase
    • Telophase

    During metaphase, chromosomes line up at the cell's equator (metaphase plate) before separating in anaphase.

Unit 5: Heredity (15)
  1. Crossing over occurs during which stage of meiosis?

    • Prophase I
    • Metaphase I
    • Anaphase II
    • Telophase II

    Crossing over occurs during prophase I, when homologous chromosomes synapse and exchange genetic material.

  2. For an organism with n=4 chromosome pairs, independent assortment alone can produce how many different chromosome combinations in gametes?

    • 4
    • 8
    • 16
    • 32

    2ⁿ = 2⁴ = 16 possible combinations from independent assortment of 4 chromosome pairs.

  3. A cross between a heterozygous (Rr) and a heterozygous (Rr) pea plant for a completely dominant trait produces what phenotypic ratio?

    • 1:1
    • 1:2:1
    • 3:1
    • 9:3:3:1

    Rr × Rr gives genotypes 1 RR : 2 Rr : 1 rr, which is 3 dominant : 1 recessive phenotypically.

  4. A cross between two heterozygous individuals for two independently assorting genes (AaBb × AaBb) produces which phenotypic ratio?

    • 3:1
    • 1:2:1
    • 9:3:3:1
    • 1:1:1:1

    Independent dihybrid crosses produce the classic 9:3:3:1 phenotypic ratio.

  5. Red (RR) crossed with white (WW) snapdragons produces all pink (RW) offspring. This demonstrates:

    • Codominance
    • Incomplete dominance
    • Complete dominance
    • Sex linkage

    The blended pink phenotype is the hallmark of incomplete dominance, unlike codominance where both traits appear fully and separately.

  6. AB blood type, where both A and B antigens appear on red blood cells, is an example of:

    • Incomplete dominance
    • Codominance
    • Polygenic inheritance
    • Sex linkage

    Both IA and IB alleles are expressed fully and simultaneously — this is codominance, not blending.

  7. A colorblind son is born to a mother who is a carrier (heterozygous) for the X-linked recessive trait and a father with normal vision. This is explained because the son:

    • Received the trait from his father's Y chromosome
    • Is hemizygous, so his single X-linked allele from his mother determines his phenotype
    • Cannot inherit X-linked traits from his mother
    • Must have a new mutation

    Males have only one X chromosome (hemizygous), so a single recessive allele inherited from the mother is enough to express an X-linked recessive trait.

  8. Two genes located very close together on the same chromosome will:

    • Always assort independently
    • Tend to be inherited together, violating independent assortment, unless separated by crossing over
    • Never be separated by any mechanism
    • Always produce a 9:3:3:1 ratio when crossed

    Linked genes tend to travel together during meiosis; only crossing over can separate them, and this happens more often the farther apart the genes are.

  9. Nondisjunction during meiosis I most directly leads to:

    • Normal haploid gametes
    • Gametes with an abnormal number of chromosomes (e.g., trisomy)
    • Increased crossing over
    • A completely new species

    Failure of homologous chromosomes to separate properly produces gametes with too many or too few chromosomes.

  10. A test cross is used to determine:

    • Whether an organism with a dominant phenotype is homozygous or heterozygous
    • The exact number of chromosomes in a species
    • Which parent contributed the Y chromosome
    • Whether a trait is codominant

    Crossing the unknown individual with a homozygous recessive reveals its genotype based on the offspring ratio produced.

  11. Which is a source of genetic variation unique to meiosis (not mitosis)?

    • DNA replication
    • Crossing over and independent assortment
    • Cytokinesis
    • Spindle fiber formation

    Crossing over (prophase I) and independent assortment (metaphase I) are meiosis-specific processes generating genetic variation.

  12. Human skin color, controlled by multiple genes with additive effects producing a continuous range of phenotypes, is an example of:

    • Codominance
    • Polygenic inheritance
    • Sex-linked inheritance
    • Incomplete dominance

    Polygenic traits are influenced by multiple genes, producing a continuous distribution of phenotypes rather than discrete categories.

  13. Meiosis II is most similar to mitosis because in both processes:

    • Homologous chromosomes separate
    • Sister chromatids separate, producing genetically identical daughter cells from each parent cell
    • Crossing over always occurs
    • The chromosome number is reduced by half

    Both meiosis II and mitosis separate sister chromatids; meiosis I (not II) is the reductional division that separates homologs.

  14. An offspring's blood type is O, meaning its genotype is ii. If one parent is IAi and the other is IBi, this outcome is:

    • Impossible under multiple allele inheritance
    • Possible — each parent could contribute the recessive i allele
    • Only possible if a mutation occurred
    • Evidence of codominance failing

    Each heterozygous parent carries one i allele; if both contribute i, the child is ii (type O), which is fully expected under multiple allele inheritance.

  15. Genes located far apart on the same chromosome are more likely to be separated by crossing over than genes located close together because:

    • Distance has no effect on recombination frequency
    • Greater physical distance increases the probability that a crossover event occurs between them
    • Close genes always cross over first
    • Far apart genes are on different chromosomes

    Recombination frequency increases with the physical distance between two linked genes, since there is more opportunity for a crossover to occur between them.

Unit 6: Gene Expression & Regulation (15)
  1. DNA replication is described as semiconservative because:

    • Both new strands are entirely new
    • Each new double helix has one original strand and one newly made strand
    • No original DNA is preserved
    • Replication only occurs in half the cell's DNA

    Semiconservative replication means each daughter molecule retains one parental strand paired with one new strand.

  2. Why is the lagging strand synthesized in short (Okazaki) fragments?

    • DNA polymerase can only add nucleotides in the 5'→3' direction, opposite to the replication fork's movement on that strand
    • DNA polymerase works faster on the lagging strand
    • The lagging strand template has no primers
    • Ligase cannot join DNA fragments

    Since DNA polymerase synthesizes only 5'→3', the lagging strand (running away from the fork direction) must be made discontinuously.

  3. A mutation that inserts 1 nucleotide into a gene's coding sequence would most likely:

    • Have no effect on the protein
    • Cause a frameshift, altering every amino acid downstream of the insertion
    • Only change one amino acid
    • Only affect the stop codon

    A single nucleotide insertion (not a multiple of 3) shifts the reading frame for all codons downstream, typically producing a nonfunctional protein.

  4. A silent mutation has no effect on the protein produced because:

    • It occurs outside the gene
    • The new codon still codes for the same amino acid, due to the redundancy of the genetic code
    • It always occurs in introns
    • It changes the start codon

    The genetic code is degenerate — several codons can specify the same amino acid, so some substitutions don't change the protein.

  5. In the lac operon, when lactose is present in the cell, it:

    • Binds the repressor, removing it from the operator and allowing transcription
    • Directly binds RNA polymerase
    • Binds the operator, blocking transcription
    • Has no effect on the operon

    Lactose acts as an inducer — it binds the repressor protein, changing its shape so it can no longer bind the operator, allowing transcription.

  6. In gel electrophoresis, DNA fragments migrate toward the positive electrode because:

    • DNA is positively charged
    • DNA's phosphate backbone gives it a negative charge
    • Smaller fragments are positively charged
    • The gel matrix repels the negative electrode

    DNA's phosphate groups give it an overall negative charge, so it migrates toward the positive electrode in an electric field.

  7. Which best describes the role of DNA polymerase's proofreading function?

    • It methylates DNA to silence genes
    • It detects and corrects mismatched nucleotides during replication, increasing fidelity
    • It splices introns from pre-mRNA
    • It attaches ribosomes to mRNA

    DNA polymerase proofreads newly added nucleotides, removing errors to keep the mutation rate very low.

  8. During eukaryotic mRNA processing, which of the following occurs?

    • Introns are added and exons are removed
    • A 5' cap and poly-A tail are added, and introns are spliced out
    • Ribosomes bind before transcription is complete
    • Nothing — mRNA is used immediately as made

    Eukaryotic pre-mRNA is processed by adding a 5' cap and poly-A tail and splicing out introns, leaving only exons in the mature mRNA.

  9. DNA methylation is an example of:

    • A point mutation
    • An epigenetic change that typically silences gene expression without altering the DNA sequence
    • A frameshift mutation
    • A step in PCR

    Epigenetic modifications like DNA methylation alter gene expression heritably without changing the underlying DNA sequence.

  10. PCR requires all of the following EXCEPT:

    • Primers complementary to the target sequence
    • Heat-stable DNA polymerase (Taq)
    • A ribosome
    • Repeated cycles of denaturation, annealing, and extension

    PCR amplifies DNA using primers and heat-stable polymerase through thermal cycling — ribosomes are involved in translation, not PCR.

  11. The trp operon is best described as:

    • Inducible — turned on by the presence of tryptophan
    • Repressible — normally on, turned off when tryptophan acts as a co-repressor
    • Identical in function to the lac operon
    • Only found in eukaryotes

    The trp operon is repressible: it's normally active, but abundant tryptophan activates the repressor to shut off transcription (negative feedback).

  12. Heterochromatin, compared to euchromatin, is:

    • Loosely packed and actively transcribed
    • Tightly packed and generally transcriptionally inactive
    • Found only in prokaryotes
    • The site of translation

    Heterochromatin is densely packed DNA that is generally inaccessible to transcription machinery, keeping those genes silent.

  13. A restriction enzyme used in genetic engineering functions to:

    • Join DNA fragments together
    • Cut DNA at a specific recognition sequence, often producing sticky ends
    • Synthesize new DNA strands
    • Translate mRNA into protein

    Restriction enzymes recognize specific sequences and cut DNA there, generating fragments (often with complementary sticky ends) for cloning.

  14. Which best describes the relationship between a gene's exons and introns in eukaryotic pre-mRNA processing?

    • Exons are removed and introns are joined into mature mRNA
    • Introns are removed by splicing, and exons are joined to form mature mRNA
    • Both are removed entirely
    • Neither is present in pre-mRNA

    Splicing removes noncoding introns, leaving only the coding exons joined together in the mature mRNA.

  15. A missense mutation results in:

    • No change in the amino acid sequence
    • A different amino acid being incorporated into the protein
    • A premature stop codon
    • No effect because the gene is not transcribed

    A missense mutation changes the codon so that it now codes for a different amino acid than the original.

Unit 7: Natural Selection (15)
  1. Homologous structures such as the forelimbs of humans, whales, and bats provide evidence for:

    • Convergent evolution from unrelated ancestors
    • Common ancestry, despite different current functions
    • Analogous adaptation to similar environments
    • Genetic drift only

    Homologous structures share the same underlying anatomical origin, indicating descent from a common ancestor even though functions differ.

  2. Bird wings and insect wings are considered analogous structures because they:

    • Share the same developmental origin
    • Serve a similar function (flight) but evolved independently (convergent evolution)
    • Prove birds and insects share a recent common ancestor
    • Are found in the fossil record only

    Analogous structures perform similar functions but arose independently, so they do NOT indicate a recent common ancestor.

  3. If observed genotype frequencies in a population differ substantially from those predicted by Hardy-Weinberg, this suggests:

    • The population is in equilibrium
    • The population is evolving (one or more HW assumptions is being violated)
    • No conclusion can be drawn
    • The population size is infinite

    Deviation from Hardy-Weinberg predictions indicates evolutionary forces (selection, drift, migration, mutation, or nonrandom mating) are acting.

  4. A population has an allele frequency q=0.2 for a recessive allele. What is the expected frequency of homozygous recessive individuals?

    • 0.2
    • 0.04
    • 0.4
    • 0.96

    q² = 0.2² = 0.04, so about 4% of the population is expected to be homozygous recessive.

  5. A population's allele frequencies change dramatically after a natural disaster kills most of its members randomly, unrelated to genotype. This illustrates:

    • Natural selection
    • The bottleneck effect (a type of genetic drift)
    • Gene flow
    • Directional selection

    The bottleneck effect is a form of genetic drift caused by a drastic, random reduction in population size.

  6. Stabilizing selection is best illustrated by:

    • Human birth weight favoring an intermediate value over extremes
    • Peppered moth coloration shifting toward darker forms during industrialization
    • Finch beak size splitting into two distinct extremes
    • Antibiotic resistance in bacteria increasing over time

    Stabilizing selection favors intermediate phenotypes and reduces variation — average birth weight has the highest survival rate.

  7. Disruptive selection tends to:

    • Reduce phenotypic variation by favoring the average
    • Increase phenotypic variation by favoring both extremes over the intermediate
    • Have no effect on allele frequencies
    • Only occur in asexual organisms

    Disruptive selection favors both phenotypic extremes, which can increase variation and sometimes drive speciation.

  8. Two populations of the same species become separated by a newly formed mountain range and evolve independently until they can no longer interbreed. This is an example of:

    • Sympatric speciation
    • Allopatric speciation
    • Genetic drift only
    • Convergent evolution

    Geographic separation preventing gene flow, leading to independent divergence, defines allopatric speciation.

  9. A mule (offspring of a horse and donkey) being sterile is an example of which reproductive isolating mechanism?

    • Prezygotic — behavioral isolation
    • Prezygotic — habitat isolation
    • Postzygotic — hybrid sterility
    • Postzygotic — hybrid inviability

    Hybrid sterility is a postzygotic barrier — the hybrid survives but cannot produce viable offspring.

  10. On a phylogenetic tree, a node represents:

    • A single living species
    • The most recent common ancestor of the lineages branching from that point
    • A mutation event only
    • The oldest fossil discovered

    Each node/branch point on a cladogram represents the most recent common ancestor shared by the descendant lineages.

  11. Which condition is NOT required for a population to remain in Hardy-Weinberg equilibrium?

    • No mutation
    • Random mating
    • Natural selection actively occurring
    • No gene flow

    Hardy-Weinberg equilibrium requires the ABSENCE of natural selection (along with no mutation, no gene flow, large population, and random mating).

  12. The high similarity of cytochrome c protein sequences between humans and chimpanzees compared to humans and yeast provides evidence that:

    • Humans and chimps share a more recent common ancestor than humans and yeast
    • Cytochrome c has no evolutionary significance
    • All organisms are identical genetically
    • Molecular data cannot be used to study evolution

    Greater molecular similarity generally indicates a more recent shared common ancestor.

  13. The human appendix, a reduced structure with little current function, is best classified as a:

    • Homologous structure
    • Analogous structure
    • Vestigial structure
    • Convergent structure

    Vestigial structures are reduced remnants of structures that were functional in an ancestral species.

  14. A new plant species arises instantly from a doubling of chromosome number (polyploidy) in a single generation, without any geographic separation. This is an example of:

    • Allopatric speciation
    • Sympatric speciation
    • Genetic drift only
    • Gene flow

    Sympatric speciation occurs without geographic isolation; polyploidy is a common mechanism, especially in plants.

  15. Sexual selection, a special case of natural selection based on mating success, can explain the evolution of traits like a peacock's tail because:

    • Such traits always improve survival against predators
    • Such traits can increase mating success even if they carry a survival cost
    • These traits arise only through genetic drift
    • These traits prevent gene flow

    Sexual selection favors traits that increase mating success, which can evolve even when they carry some survival cost (e.g., increased predation risk).

Unit 8: Ecology (15)
  1. Exponential population growth is best modeled by a curve that:

    • Levels off at carrying capacity
    • Rises in a J-shape with no resource limitation
    • Declines steadily over time
    • Oscillates around a fixed point

    Exponential growth produces a J-shaped curve because growth rate is proportional to population size, without resource limits.

  2. Logistic growth differs from exponential growth because logistic growth:

    • Never slows down
    • Slows as the population approaches carrying capacity due to limiting factors
    • Only applies to bacteria
    • Always produces a J-shaped curve

    Logistic growth incorporates carrying capacity (K), producing an S-shaped curve as density-dependent factors slow growth.

  3. Which is a density-dependent limiting factor?

    • A hurricane destroying habitat regardless of population size
    • Competition for food intensifying as population density increases
    • A volcanic eruption
    • Seasonal temperature drop unrelated to density

    Density-dependent factors like competition, predation, and disease intensify as population density increases.

  4. In a predator-prey relationship, this interaction is best classified as:

    • +/+ (mutualism)
    • +/− (predator benefits, prey harmed)
    • −/− (both harmed)
    • +/0 (commensalism)

    Predation benefits the predator (+) while harming the prey (−).

  5. Only about 10% of energy is transferred between trophic levels mainly because:

    • Producers absorb all remaining energy
    • Most energy is lost as heat through cellular respiration at each level
    • Energy is destroyed at each level, violating conservation of energy
    • Consumers refuse to eat all available food

    Metabolic processes (respiration) release most energy as heat rather than passing it on to the next trophic level, following the 10% rule.

  6. Nitrogen-fixing bacteria such as Rhizobium are important because they:

    • Convert atmospheric N₂ into a usable form (ammonia/ammonium) for plants
    • Break down organic nitrogen into N₂ gas
    • Only live in the ocean
    • Compete with plants for nitrogen

    Nitrogen-fixing bacteria convert unusable atmospheric N₂ into ammonia, which plants can use to build proteins and nucleic acids.

  7. Which biogeochemical cycle has essentially no significant atmospheric gas phase?

    • Carbon cycle
    • Nitrogen cycle
    • Water cycle
    • Phosphorus cycle

    Phosphorus cycles mainly through rock weathering, soil, and water — it lacks a major atmospheric gas component, unlike C, N, and water cycles.

  8. Two species of birds that feed on different parts of the same tree (one on insects in the bark, one on seeds in the canopy) illustrate:

    • Competitive exclusion leading to extinction
    • Resource partitioning, reducing direct competition
    • Predation
    • Parasitism

    Resource partitioning (niche differentiation) allows similar species to coexist by using different parts of a shared resource.

  9. An r-selected species is most likely to:

    • Produce few offspring with high parental investment
    • Produce many offspring, provide little parental care, and mature quickly
    • Only live near carrying capacity
    • Have a long lifespan and slow reproduction

    r-selected species prioritize rapid reproduction (many offspring, minimal care) suited to unstable or resource-rich environments.

  10. Ocean acidification, caused by increased atmospheric CO₂ dissolving into seawater, primarily threatens:

    • Nitrogen-fixing bacteria
    • Calcifying organisms such as coral and shellfish
    • Freshwater fish only
    • Terrestrial plants

    Increased CO₂ forms carbonic acid in seawater, lowering pH and interfering with calcium carbonate shell/skeleton formation.

  11. Habitat fragmentation reduces biodiversity primarily by:

    • Increasing gene flow between populations
    • Isolating populations, reducing gene flow, and shrinking available resources
    • Increasing carrying capacity
    • Eliminating all density-dependent factors

    Fragmentation splits habitats into smaller, isolated patches, reducing gene flow and resource availability, threatening population viability.

  12. Net primary productivity (NPP) is calculated as:

    • Gross primary productivity plus respiration
    • Gross primary productivity minus the energy producers use for their own respiration
    • Total energy at the top trophic level
    • The rate of decomposition only

    NPP = GPP − respiration by producers; it represents the energy actually available to consumers.

  13. Which best describes commensalism?

    • Both species benefit
    • One species benefits, the other is harmed
    • One species benefits, the other is unaffected
    • Both species are harmed

    Commensalism is a (+/0) relationship — one organism benefits while the other experiences neither benefit nor harm.

  14. A greater number of species and stronger species interactions in an ecosystem generally leads to:

    • Decreased ecosystem stability and resilience
    • Increased ecosystem stability and resilience to disturbance
    • No change in ecosystem function
    • Guaranteed extinction of keystone species

    Higher biodiversity is generally associated with greater ecosystem stability and resilience to environmental disturbances.

  15. The competitive exclusion principle states that:

    • Two species can indefinitely share the exact same ecological niche
    • Two species cannot indefinitely occupy the exact same niche in the same habitat — one will be excluded or niches will diverge
    • Competition always benefits both species
    • Predation is a form of competition

    When two species compete for the identical niche and resources, one typically outcompetes the other, or resource partitioning allows coexistence.

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Unit 1: Chemistry of Life

Hydrogen bond
Weak attraction between a partially positive H on one polar molecule and a partially negative atom (often O or N) on another; responsible for water's cohesion and high specific heat
Cohesion
Attraction between molecules of the SAME substance (water-water via H-bonds); produces surface tension and allows water columns to rise in plant xylem
Dehydration synthesis
Joins two monomers into a polymer, RELEASING one water molecule per bond formed
Hydrolysis
Breaks a polymer into monomers by ADDING a water molecule across each bond — how digestion works
Denaturation
Loss of a protein's 3D shape (and function) due to heat, pH change, or salt disrupting weak bonds; primary structure usually remains intact
Active site
Region on an enzyme where the substrate binds; shape determines the enzyme's specificity (induced fit model)
Activation energy (Ea)
Energy input needed to reach the transition state and start a reaction; enzymes speed reactions by lowering this, not by changing ΔG
Competitive inhibitor
Molecule that binds the enzyme's active site, blocking the substrate; effect can be reduced by increasing substrate concentration

Unit 2: Cell Structure & Function

Endosymbiotic theory
Mitochondria and chloroplasts arose from free-living prokaryotes engulfed by an ancestral eukaryotic cell; supported by their own DNA, 70S ribosomes, and double membranes
Fluid mosaic model
Describes the plasma membrane as a dynamic phospholipid bilayer with proteins that can move laterally through it
Facilitated diffusion
Passive movement of polar solutes/ions through channel or carrier proteins, down their concentration gradient; no ATP required
Active transport
Movement of a solute AGAINST its concentration gradient, requiring ATP (e.g., the sodium-potassium pump)
Hypotonic solution
Lower solute concentration outside the cell than inside; water enters the cell — animal cells may lyse, plant cells become turgid
Hypertonic solution
Higher solute concentration outside the cell than inside; water leaves the cell — animal cells crenate, plant cells plasmolyze
Surface area-to-volume ratio
Decreases as a cell grows larger (volume grows faster than surface area) — limits how large a cell can get before division is favored
Rough endoplasmic reticulum
ER studded with ribosomes; synthesizes and folds proteins destined for secretion or membranes

Unit 3: Cellular Energetics

Glycolysis
Splits glucose (6C) into 2 pyruvate (3C) in the cytoplasm; produces a net 2 ATP and 2 NADH; occurs with or without oxygen
Electron transport chain (ETC)
Series of membrane proteins that pass electrons from NADH/FADH₂ to O₂ (final acceptor), pumping H⁺ to build the gradient used for ATP synthesis
Chemiosmosis
ATP synthesis driven by H⁺ flowing down its gradient through ATP synthase; used in both mitochondria (respiration) and chloroplasts (photosynthesis)
Fermentation
Anaerobic process that regenerates NAD⁺ from NADH so glycolysis can continue; produces lactate (animals) or ethanol + CO₂ (yeast)
Photosystem II
Absorbs light (P680), splits water to replace lost electrons (releasing O₂), and starts the electron transport chain to Photosystem I
Calvin cycle
Light-independent reactions in the stroma; uses ATP and NADPH to fix CO₂ (via rubisco) into G3P, which builds glucose
Rubisco
Enzyme that catalyzes carbon fixation — attaching CO₂ to RuBP in the first step of the Calvin cycle
Substrate-level phosphorylation
Direct transfer of a phosphate group to ADP to form ATP, occurring in glycolysis and the Krebs cycle (as opposed to chemiosmotic phosphorylation)

Unit 4: Cell Communication & Cell Cycle

Signal transduction
Process by which a cell converts an extracellular signal (ligand binding a receptor) into a specific intracellular response, often via a phosphorylation cascade
G1 checkpoint
Main cell cycle checkpoint (restriction point); checks cell size, nutrients, and DNA integrity before committing to division
Cyclin-CDK complex
Regulatory protein pair that drives the cell cycle forward — cyclin levels oscillate, CDK levels stay constant; complex phosphorylates target proteins to trigger the next phase
Proto-oncogene
Normal gene promoting cell division; a gain-of-function mutation converts it into an oncogene that drives uncontrolled division
Tumor suppressor gene
Gene (e.g., p53) that normally halts the cell cycle or triggers apoptosis when DNA is damaged; loss-of-function mutation removes this control
Apoptosis
Programmed, controlled cell death that removes damaged or unneeded cells without harming surrounding tissue
Contact inhibition
Normal cells stop dividing when they contact neighboring cells; cancer cells lose this regulatory signal and keep growing
G2 checkpoint
Verifies DNA replication was completed correctly and without damage before the cell is allowed to enter mitosis

Unit 5: Heredity

Crossing over
Exchange of genetic material between non-sister chromatids of homologous chromosomes during prophase I of meiosis; a source of genetic variation
Independent assortment
Random orientation of homologous chromosome pairs at the metaphase I plate, leading to 2ⁿ possible gamete combinations
Incomplete dominance
Heterozygote phenotype is a BLEND of both alleles (e.g., red × white → pink)
Codominance
Heterozygote shows BOTH parental phenotypes fully and separately (e.g., AB blood type, roan coat color)
Sex-linked trait
Gene located on the X chromosome; males (XY) are hemizygous, so one recessive allele is enough to express the trait
Nondisjunction
Failure of homologous chromosomes or sister chromatids to separate properly during meiosis, producing gametes with abnormal chromosome numbers
Test cross
Cross between an individual of unknown genotype (dominant phenotype) and a homozygous recessive individual, used to determine the unknown genotype
Polygenic inheritance
Trait controlled by multiple genes with additive effects, producing continuous variation (e.g., human height, skin color)

Unit 6: Gene Expression & Regulation

Semiconservative replication
Each new DNA double helix contains one original (parental) strand and one newly synthesized strand
Leading vs lagging strand
Leading strand synthesized continuously toward the fork; lagging strand synthesized discontinuously (Okazaki fragments) away from the fork, joined by ligase
Frameshift mutation
Insertion or deletion of bases NOT in a multiple of 3, shifting the reading frame for every codon downstream — usually severely disrupts the protein
Lac operon
Inducible prokaryotic operon; normally off, turned ON when lactose binds and removes the repressor from the operator
PCR (polymerase chain reaction)
Technique that exponentially amplifies a specific DNA sequence via repeated cycles of denaturation, annealing, and extension
Gel electrophoresis
Separates DNA fragments by size using an electric field; smaller fragments migrate farther toward the positive electrode
Epigenetics
Heritable changes in gene expression without a change in DNA sequence, such as DNA methylation (silences genes) and histone acetylation (activates genes)
Restriction enzyme
Protein that cuts DNA at a specific recognition sequence, often producing 'sticky ends' used in cloning and recombinant DNA technology

Unit 7: Natural Selection

Homologous structures
Structures with the same underlying anatomy/origin but different function across species, indicating common ancestry (e.g., human arm, whale flipper)
Analogous structures
Structures with similar function but different evolutionary origin, resulting from convergent evolution, NOT common ancestry (e.g., bird wing, insect wing)
Hardy-Weinberg equilibrium
Model describing allele/genotype frequencies in a non-evolving population; used as a null hypothesis to detect evolution
Genetic drift
Random change in allele frequencies due to chance, with the largest effect in small populations (bottleneck and founder effects)
Allopatric speciation
Formation of new species due to geographic separation preventing gene flow between populations
Stabilizing selection
Favors intermediate phenotypes, reduces phenotypic variation (e.g., human birth weight)
Vestigial structure
Reduced, functionless remnant of a structure that was functional in an ancestor (e.g., human appendix, whale pelvic bones)
Reproductive isolation
Prezygotic or postzygotic mechanisms that prevent gene flow between populations, allowing them to diverge into separate species

Unit 8: Ecology

Carrying capacity (K)
Maximum population size an environment can sustainably support with available resources
Logistic growth
Population growth that slows as it approaches carrying capacity due to density-dependent limiting factors; produces an S-shaped curve
10% rule
Only about 10% of energy is transferred from one trophic level to the next; the rest is lost mainly as metabolic heat
Mutualism
Symbiotic interaction in which BOTH species benefit (e.g., mycorrhizae and plant roots)
Nitrogen fixation
Conversion of atmospheric N₂ into ammonia/ammonium by bacteria (e.g., Rhizobium), making nitrogen usable by plants
r-selected vs K-selected species
r-selected: many offspring, little care, fast growth in unstable environments; K-selected: few offspring, high parental investment, thrive near carrying capacity
Density-dependent limiting factor
A factor whose effect on population growth intensifies as population density increases, such as competition, predation, or disease
Trophic pyramid
Diagram showing energy, biomass, and typically numbers decreasing at each successive trophic level, limiting food chain length

Unit 1: Chemistry of Life

Properties of water
Water's polarity and hydrogen bonding give it properties essential to life — cohesion, adhesion, high specific heat, and being a universal solvent.
Macromolecules & functional groups
Life's four major macromolecule classes are built from monomers joined by dehydration synthesis and broken apart by hydrolysis.
Functional groups
Functional groups attached to carbon skeletons give organic molecules their specific chemical behavior.
Protein structure
A protein's function depends entirely on its 3D shape, built up through four levels of structure.
Enzymes & activation energy
Enzymes are protein (or RNA) catalysts that speed up reactions by lowering the activation energy required to reach the transition state.
Key fact
Water: cohesion/adhesion via H-bonds
Key fact
Dehydration synthesis: releases H₂O | Hydrolysis: adds H₂O

Unit 2: Cell Structure & Function

Prokaryotic vs eukaryotic cells
All cells share a plasma membrane, cytoplasm, ribosomes, and DNA, but eukaryotic cells add membrane-bound organelles and much greater internal compartmentalization.
Endosymbiotic theory
Mitochondria and chloroplasts likely originated as free-living prokaryotes engulfed by an ancestral eukaryotic cell, forming a mutualistic relationship.
Organelles & their functions
Each organelle is structurally specialized for a particular function within the cell.
Membrane structure
The fluid mosaic model describes the plasma membrane as a dynamic phospholipid bilayer studded with proteins that can move laterally.
Membrane transport & osmosis
Substances cross membranes passively (no ATP, down gradient) or actively (requires ATP, against gradient).
Key fact
Surface area ∝ r² ; Volume ∝ r³ (SA:V decreases as cell size increases)
Key fact
Na⁺/K⁺ pump: 3 Na⁺ out, 2 K⁺ in per ATP

Unit 3: Cellular Energetics

ATP & energy coupling
ATP (adenosine triphosphate) is the cell's short-term energy currency, releasing energy when its terminal phosphate bond is hydrolyzed.
Cellular respiration overview
Aerobic respiration breaks down glucose in stages to produce ATP, using O₂ as the final electron acceptor and releasing CO₂ and H₂O.
Fermentation
Without oxygen, cells regenerate NAD⁺ from NADH so glycolysis can continue, without using the ETC.
Photosynthesis: light reactions
The light-dependent reactions occur in the thylakoid membrane, converting light energy into ATP and NADPH while splitting water.
Photosynthesis: Calvin cycle
The Calvin cycle (light-independent reactions) occurs in the stroma, using ATP and NADPH to fix CO₂ into sugar.
Key fact
Net ATP from glycolysis = 2 (substrate-level)
Key fact
≈30–32 ATP per glucose (aerobic respiration total)
Key fact
Calvin cycle: 3 CO₂ + 9 ATP + 6 NADPH → 1 G3P (net)

Unit 4: Cell Communication & Cell Cycle

Signal transduction pathways
Cells communicate via signaling molecules that trigger a three-stage process: reception, transduction, and response.
Cell cycle phases
The cell cycle is divided into interphase (growth and DNA replication) and the mitotic phase (nuclear and cell division).
Cell cycle regulation
Checkpoints ensure the cell cycle proceeds only when conditions are correct, using regulatory proteins called cyclins and cyclin-dependent kinases (CDKs).
Cancer & apoptosis
Cancer arises when mutations disrupt the normal genes that control cell division, leading to uncontrolled growth.
Key fact
Cell cycle order: G1 → S → G2 → M (mitosis + cytokinesis)
Key fact
Cyclin + CDK → active complex → drives phase transition

Unit 5: Heredity

Meiosis
Meiosis is a two-round division (meiosis I and II) that produces four genetically unique haploid gametes from one diploid cell.
Mendelian genetics
Gregor Mendel's laws of segregation and independent assortment describe how alleles are inherited.
Monohybrid & dihybrid crosses
Punnett squares predict offspring genotype/phenotype ratios from parental crosses.
Non-Mendelian inheritance
Not all traits follow simple dominant/recessive patterns — several inheritance patterns deviate from classic Mendelian ratios.
Key fact
Dihybrid ratio (independent genes): 9:3:3:1
Key fact
Monohybrid ratio (Aa × Aa): 3:1 (phenotype), 1:2:1 (genotype)
Key fact
2ⁿ = number of possible gamete combinations (n = # of chromosome pairs)

Unit 6: Gene Expression & Regulation

DNA replication
DNA replication is semiconservative — each new double helix contains one original (parental) strand and one newly synthesized strand.
Central dogma: transcription & translation
Genetic information flows from DNA → RNA (transcription) → protein (translation).
Mutations
Mutations are changes in the DNA sequence; their effect depends on type and location.
Gene regulation
Cells control which genes are expressed, and when, largely through the operon system in prokaryotes and multiple layers of control in eukaryotes.
Biotechnology basics
Modern techniques allow scientists to isolate, copy, and analyze specific DNA sequences.
Key fact
Codon = 3 mRNA bases → 1 amino acid
Key fact
PCR cycle: denature → anneal → extend
Key fact
DNA charge: negative (moves toward + electrode in electrophoresis)

Unit 7: Natural Selection

Evidence for evolution
Multiple independent lines of evidence converge to support the theory that all life shares common ancestry and has evolved over time.
Hardy-Weinberg equilibrium
The Hardy-Weinberg model describes allele/genotype frequencies in a non-evolving population, serving as a null hypothesis to test whether evolution is occurring.
Mechanisms of evolution
Evolution is a change in allele frequencies in a population over time, driven by several mechanisms.
Speciation & phylogenetics
Speciation is the formation of new, reproductively isolated species; phylogenetics organizes species based on evolutionary relationships.
Key fact
p + q = 1
Key fact
p² + 2pq + q² = 1
Key fact
q² = frequency of homozygous recessive genotype → q = √(q²)

Unit 8: Ecology

Population growth models
Populations grow according to predictable mathematical models shaped by resource availability.
Community interactions
Species within a community interact through predation, competition, and symbiosis, shaping community structure.
Ecosystem energy flow
Energy flows one-way through ecosystems from producers to consumers, with substantial loss at each trophic level.
Biogeochemical cycles
Essential elements cycle between living organisms and the physical (abiotic) environment.
Climate & biodiversity
Biodiversity and climate patterns interact, and human activity is altering both at an accelerating rate.
Key fact
Logistic growth: dN/dt = rN(K−N)/K
Key fact
Exponential growth: dN/dt = rN
Key fact
10% rule: ~10% of energy transfers to the next trophic level
Common mistakes for each unit — read the mistake, then make sure you know why it's wrong.

Unit 1: Chemistry of Life

Watch out
Enzymes lower activation energy — they do NOT change the free energy change (ΔG) of a reaction or make a nonspontaneous reaction spontaneous.
Watch out
Dehydration synthesis RELEASES water; hydrolysis ADDS water — students often reverse these.
Watch out
Ice floats because hydrogen bonds form a fixed, spaced-out lattice — this is LESS dense, not more.
Watch out
Denaturation changes secondary/tertiary/quaternary structure, but primary structure (the amino acid sequence/peptide bonds) is unaffected.

Unit 2: Cell Structure & Function

Watch out
Both mitochondria AND chloroplasts have their own DNA and ribosomes — this is evidence for BOTH, not just chloroplasts.
Watch out
Facilitated diffusion is still passive (no ATP) even though it requires a protein — don't confuse it with active transport.
Watch out
A plant cell in a hypotonic solution becomes turgid (good) — it does NOT lyse because the cell wall resists expansion.
Watch out
Osmosis moves water toward the side with MORE solute (lower water potential), not toward more water.

Unit 3: Cellular Energetics

Watch out
Most ATP from aerobic respiration comes from the electron transport chain/chemiosmosis, NOT substrate-level phosphorylation in glycolysis or Krebs.
Watch out
Fermentation does NOT use an electron transport chain — its only job is regenerating NAD⁺ so glycolysis can keep running.
Watch out
The O₂ released in photosynthesis comes from water (photolysis), NOT from CO₂.
Watch out
The Calvin cycle does not directly require light, but it depends on ATP and NADPH that are made in the light reactions — so it stops without light within minutes.

Unit 4: Cell Communication & Cell Cycle

Watch out
A mutated proto-oncogene becomes an oncogene through a GAIN of function; a mutated tumor suppressor loses its normal braking FUNCTION — the mutation types have opposite functional effects.
Watch out
Interphase is NOT a resting phase — it's when the cell grows, functions normally, and replicates its DNA (S phase).
Watch out
Cyclin levels oscillate through the cycle; CDK levels remain fairly constant — it's the cyclin binding that activates CDK activity at the right time.
Watch out
Apoptosis is a controlled, beneficial process for the organism; necrosis is uncontrolled cell death that damages surrounding tissue.

Unit 5: Heredity

Watch out
Independent assortment applies to genes on DIFFERENT chromosomes (or far apart on the same one) — linked genes on the same chromosome do NOT assort independently.
Watch out
Incomplete dominance BLENDS the phenotype (pink); codominance shows BOTH traits fully and separately (spotted, AB blood) — these are commonly confused.
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In X-linked recessive traits, a male needs only ONE recessive allele to express the trait (hemizygous); a female needs two.
Watch out
A 9:3:3:1 ratio requires the two genes to assort independently — linked genes produce a skewed ratio instead.

Unit 6: Gene Expression & Regulation

Watch out
DNA polymerase can only add nucleotides in the 5'→3' direction — this is why the lagging strand must be synthesized discontinuously in fragments.
Watch out
A frameshift mutation (indel not a multiple of 3) usually has a much bigger effect than a single substitution because it shifts every codon downstream.
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In gel electrophoresis, SMALLER DNA fragments travel FARTHER (faster) through the gel, not shorter distances.
Watch out
The lac operon is induced (turned ON by lactose); the trp operon is repressed (turned OFF by tryptophan) — opposite regulatory logic, easy to mix up.

Unit 7: Natural Selection

Watch out
Homologous structures indicate common ancestry (similar structure); analogous structures indicate convergent evolution (similar function only, NOT close relation) — often reversed by students.
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Hardy-Weinberg describes a population that is NOT evolving — it's a null model to detect evolution, not a description of how evolution works.
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Stabilizing selection REDUCES phenotypic variation (favors the average); disruptive selection INCREASES it (favors both extremes) — do not swap these.
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Genetic drift has the LARGEST effect in SMALL populations, not large ones.

Unit 8: Ecology

Watch out
Only about 10% of energy passes to the next trophic level — the rest is lost as metabolic heat, NOT stored or passed on.
Watch out
The phosphorus cycle has essentially no atmospheric gas phase, unlike carbon, nitrogen, and water cycles.
Watch out
K-selected species are favored NEAR carrying capacity (density-dependent factors matter); r-selected species thrive when resources are abundant/uncrowded (early exponential growth).
Watch out
Competitive exclusion means two species can't occupy the identical niche indefinitely — one will be excluded or the species will diverge (resource partitioning).
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