Must-know sheet

Biology must-know sheet

The equations, processes, molecules and structures you should know cold for AP Biology, in short plain steps. The real exam gives you an equations and formulas sheet and lets you use a calculator, so this sheet focuses on when to use each equation, how to set it up and what the answer means.

Experiments, graphs and answer words

Units 1, 2, 3, 4, 5, 6, 7, 8

Independent variable: The factor the experimenter changes on purpose, such as temperature or light color. It goes on the x-axis.
Dependent variable: What you measure to see the effect of the independent variable, such as the rate of O₂ production. It goes on the y-axis.
Control group: A group that doesn't get the treatment (or gets a normal baseline), so you can compare it with the treated groups. It shows that a change was caused by the independent variable and not something else.
Negative and positive controls: A negative control should show no effect (for example, a tube with no enzyme), proving nothing else causes the result. A positive control should show a known effect, proving the setup can detect one.
Controlled (constant) variables: Everything besides the independent variable that's kept the same in every group, such as volume, temperature, light or time. On free-response questions, name a specific one that makes sense for that experiment.
Null and alternative hypotheses: The null hypothesis says there is no effect or no difference (for example, the treatment does not change growth). The alternative hypothesis says there is one. Statistics tell you whether you can reject the null.
Replication and sample size: Repeating trials and using many individuals makes chance results less likely to mislead you. A bigger sample makes the mean more reliable and shrinks the standard error.
Choosing a graph: Use a line graph or scatterplot when the independent variable is continuous (time, temperature, concentration), a bar graph when it's in categories (species, treatments), and a histogram to show how one measured variable is spread out.
Graphing checklist: Independent variable on the x-axis, dependent on the y-axis, both labeled with units; an even scale that fits the data; points plotted correctly; a key for more than one data set; and error bars when you're given SE or SD.
Claim, evidence, reasoning: Make a clear claim, point to specific data that support it, then explain the biology that links the evidence to the claim.
Identify or state: Give the answer directly; no explanation is needed.
Describe: Give the relevant features or say what happens, such as a trend in data.
Explain: Say how or why something happens, including the cause-and-effect link.
Justify: Back up a claim or prediction with evidence or a biological reason.
Predict: Say what will happen under new conditions; usually you'll then be asked to justify it.
Calculate: Show the equation, the numbers you plug in and the final answer with units, rounded as the question asks.

Statistics and probability

Units 1, 2, 3, 4, 5, 6, 7, 8

Mean: x̄ = Σx ÷ n: Add all values and divide by how many there are. It's the usual summary of a treatment group.
Median, mode and range: The median is the middle value when data are in order (less pulled by outliers), the mode is the most common value, and the range is the largest value minus the smallest.
Standard deviation: s = √[Σ(x − x̄)² ÷ (n − 1)]: Measures how spread out individual data points are around the mean. For bell-shaped data, about 68% of values fall within 1 SD of the mean and about 95% within 2 SD.
Standard error of the mean: SE = s ÷ √n: Measures how precisely your sample mean estimates the true mean. It gets smaller as the sample size n gets bigger.
Error bars of ±2 SE: Mean ± 2 SE is roughly a 95% confidence interval. If the ±2 SE bars of two groups don't overlap, the difference is likely statistically significant; if they overlap, you can't conclude the means differ.
Chi-square: χ² = Σ (o − e)² ÷ e: Compares observed counts (o) with the counts expected (e) under the null hypothesis, adding one term per category. Always use counts, never percentages.
Finding expected values: Use the null hypothesis to split the total: for a predicted 3:1 ratio with 200 offspring, expect 150 and 50; for no preference between two chambers with 20 animals, expect 10 and 10.
Degrees of freedom = number of categories − 1: Count the phenotype or outcome categories, not the individuals. Four phenotypes give 3 degrees of freedom.
Critical values at p = 0.05: 3.84 for 1 df, 5.99 for 2, 7.81 for 3, 9.49 for 4 and 11.07 for 5. The exam's formula sheet has the full table.
Chi-square conclusion: If χ² is greater than the critical value, reject the null hypothesis: the difference is too big to be chance alone (p < 0.05). If it's smaller, fail to reject the null; never say you proved or accepted it.
Multiplication rule (and): For independent events, P(A and B) = P(A) × P(B). From Aa × Aa, the chance of aa is ½ × ½ = ¼; from AaBbCc × AaBbCc, the chance of aabbcc is (¼)³ = 1/64.
Addition rule (or): For events that can't happen together, P(A or B) = P(A) + P(B). From Aa × Aa, a heterozygote can get A from the mother and a from the father (¼) or the reverse (¼), so P(Aa) = ½.
Percent change = (new − original) ÷ original × 100: Use it to compare growth or mass change across groups that started at different sizes. A negative answer means a decrease.
Rate = change in y ÷ change in x: The slope of a graph, with units such as mL O₂ per minute. The steepest part of a curve is where the rate is fastest; compare initial rates when a reaction slows as substrate runs out.
Metric prefixes: Kilo- = 10³, centi- = 10⁻², milli- = 10⁻³, micro- (µ) = 10⁻⁶ and nano- = 10⁻⁹. So 1 mm = 1,000 µm and 1 µm = 1,000 nm.

Cell size and water potential math

Unit 2

Surface area-to-volume ratio = SA ÷ V: As a cell grows, volume rises faster than surface area, so SA:V falls and the membrane can't exchange materials fast enough. Small size, thin or flat shapes, and folds or microvilli all raise SA:V.
Cube with side s: SA = 6s², V = s³, so SA:V = 6 ÷ s. A 2 µm cube has SA = 24 µm², V = 8 µm³ and SA:V = 3 per µm.
Sphere with radius r: SA = 4πr², V = (4/3)πr³, so SA:V = 3 ÷ r. Doubling the radius halves the ratio.
Cylinder and rectangular solid: Cylinder: SA = 2πrh + 2πr², V = πr²h. Rectangular solid: SA = 2lw + 2lh + 2wh, V = lwh.
Body size and heat loss: Small animals have a higher SA:V, so they lose heat faster and tend to have a higher metabolic rate per gram of body mass than large animals.
Water potential: Ψ = Ψp + Ψs: Total water potential is pressure potential plus solute potential, usually in bars (1 MPa = 10 bars). Water always moves from higher (less negative) Ψ to lower (more negative) Ψ.
Pure water: Ψ = 0: Pure water in an open container at normal air pressure has a water potential of zero. Adding solute always lowers Ψs below zero.
Solute potential: Ψs = −iCRT: i = ionization constant (1 for sucrose or glucose, 2 for NaCl), C = molar concentration in mol/L, R = 0.0831 L·bar/(mol·K), and T = temperature in kelvins (°C + 273). Forgetting to convert to kelvins is the most common mistake.
Worked setup for Ψs: 0.2 M sucrose at 20 °C: Ψs = −(1)(0.2 mol/L)(0.0831 L·bar/(mol·K))(293 K) ≈ −4.87 bars. In an open beaker Ψp = 0, so Ψ = −4.87 bars too.
Pressure potential (Ψp): Zero in an open container. Positive inside a plant cell full of water, because the cell wall pushes back (turgor pressure); it can be negative (tension) in xylem.
Hypertonic, hypotonic, isotonic: Compare solute concentrations: a hypertonic solution has more solute (lower Ψ) than the cell, a hypotonic one has less solute (higher Ψ), and an isotonic one has the same. Water moves toward the hypertonic side.
What happens to cells: In a hypotonic solution animal cells swell and may burst (lyse), while plant cells become firm (turgid), which is their healthy state. In a hypertonic solution animal cells shrivel and plant cell membranes pull away from the wall (plasmolysis); in isotonic, plant cells go limp (flaccid).
Finding a tissue's water potential from data: Soak tissue samples (like potato cores) in a range of sucrose solutions and graph percent mass change against molarity. Where the line crosses 0% change, the solution's Ψ equals the tissue's Ψ.
Osmoregulation: Organisms control water balance: freshwater protists pump extra water out with contractile vacuoles, and plant cells store water in a large central vacuole that keeps them turgid.

Hardy–Weinberg and population math

Units 7, 8

Allele frequencies: p + q = 1: For a gene with two alleles, p is the frequency of one allele (usually dominant) and q is the frequency of the other (usually recessive).
Genotype frequencies: p² + 2pq + q² = 1: p² is the homozygous dominant frequency, 2pq the heterozygous (carrier) frequency and q² the homozygous recessive frequency, assuming the population is in equilibrium.
The five Hardy–Weinberg conditions: A very large population, no migration (gene flow), no mutation, random mating and no natural selection. If any is broken, allele frequencies can change, which means the population is evolving.
Solving from phenotypes: Start with the recessive phenotype, the only group whose genotype you know: its frequency is q². Take the square root to get q, then p = 1 − q, and carriers = 2pq. Never start from the dominant phenotype, which mixes p² and 2pq.
Worked setup: 1 in 2,500 affected: q² = 1/2,500 = 0.0004, so q = 0.02, p = 0.98 and carriers = 2pq = 2(0.98)(0.02) ≈ 0.039, about 3.9% of the population.
Allele frequency from genotype counts: Each diploid individual has two copies, so p = (2 × number of AA + number of Aa) ÷ (2 × total individuals). This works whether or not the population is in equilibrium.
Hardy–Weinberg as a null hypothesis: Use the population's p and q to predict expected genotype counts, then compare them with observed counts using chi-square. A significant difference means at least one condition isn't met.
Population change: dN/dt = B − D: N is population size, B is the number of births and D the number of deaths in a time period (immigration and emigration ignored). If B > D, the population grows.
Exponential growth: dN/dt = rₘₐₓN: With unlimited resources, each individual reproduces at the maximum per capita rate rₘₐₓ, so growth speeds up as N grows and the graph is J-shaped.
Per capita growth rate: r = (dN/dt) ÷ N: Growth per individual. In exponential growth r stays constant while dN/dt keeps increasing; don't mix them up.
Logistic growth: dN/dt = rₘₐₓN(K − N)/K: K is carrying capacity and (K − N)/K is the share of K still unused. Growth is nearly exponential when N is small, fastest at N = K/2, zero at N = K and negative above K, giving an S-shaped curve.
Simpson's diversity index = 1 − Σ(n/N)²: n is the number of individuals of one species and N is the total of all species. It runs from 0 (one species) toward 1, and it's higher with more species and more even numbers; four species with 25 each give 0.75, while 85, 5, 5, 5 give 0.27.
Gross and net primary productivity: GPP is all the energy producers capture by photosynthesis; NPP = GPP − R, what's left after producers' own respiration, and it's the energy available to consumers.
Light and dark bottle setup: Measure dissolved O₂ at the start and after a set time in a light bottle and a dark bottle. Respiration = initial − dark, NPP = light − initial, and GPP = light − dark (= NPP + respiration).
About 10% of energy moves up each trophic level: Most energy is lost as heat from respiration or is never eaten or digested. So 10,000 kcal in producers supports about 1,000 kcal of primary consumers and about 100 kcal of secondary consumers, which is why food chains are short.

Water and the molecules of life

Unit 1

Water is polar: Oxygen pulls shared electrons harder than hydrogen, so oxygen is slightly negative and the hydrogens are slightly positive. Opposite partial charges on neighboring molecules form hydrogen bonds.
Cohesion and surface tension: Water molecules hydrogen-bond to each other, which creates surface tension and lets water be pulled up through xylem in a continuous column.
Adhesion and capillary action: Water hydrogen-bonds to other polar surfaces, such as the walls of xylem vessels, helping it climb against gravity.
High specific heat and heat of vaporization: Water must absorb a lot of energy to warm up or evaporate, so it keeps body and environmental temperatures steady and evaporation (like sweating) cools surfaces.
Ice floats, and water dissolves polar substances: Hydrogen bonds hold ice in an open lattice that's less dense than liquid water, so ice insulates lakes from the top. Water dissolves ions and polar molecules well, making it the medium for cell chemistry.
Elements and where they go: C, H and O make up most biological molecules. Nitrogen is in proteins and nucleic acids, phosphorus in nucleic acids and phospholipids (and ATP), and sulfur in some amino acids.
Dehydration synthesis and hydrolysis: Dehydration synthesis joins two monomers by removing a water molecule, building a polymer. Hydrolysis adds water to break that bond, as in digestion.
Carbohydrates: Monomers are monosaccharides such as glucose, linked by glycosidic bonds into polysaccharides. Starch stores energy in plants, glycogen (highly branched) stores it in animals, and cellulose builds plant cell walls.
Lipids: Mostly nonpolar and hydrophobic, and not true polymers. Fats (one glycerol plus three fatty acids) store energy, phospholipids build membranes, and steroids such as cholesterol and some hormones have four fused carbon rings.
Saturated vs unsaturated fatty acids: Saturated chains have only single C–C bonds and pack tightly, so they're solid at room temperature. Unsaturated chains have at least one double bond that kinks the chain, so they're usually liquid.
Phospholipids: A hydrophilic phosphate head and two hydrophobic fatty acid tails. In water they form a bilayer with heads facing out and tails facing in.
Nucleotides and nucleic acids: Each nucleotide has a five-carbon sugar, a phosphate and a nitrogenous base. Nucleotides join by covalent bonds between sugar and phosphate (phosphodiester bonds), forming a sugar-phosphate backbone with a 5′ phosphate end and a 3′ hydroxyl end.
New nucleotides join the 3′ end: Nucleic acids are always built in the 5′ to 3′ direction, because each new nucleotide attaches to the 3′ end of the growing strand.
DNA vs RNA: DNA has deoxyribose and thymine and is usually a double helix. RNA has ribose and uracil instead of thymine and is usually single-stranded.
Base pairing and antiparallel strands: A pairs with T (U in RNA) and G pairs with C, so in double-stranded DNA %A = %T and %G = %C. The two strands run in opposite directions, one 5′ to 3′ and the other 3′ to 5′.
Purines and pyrimidines: Purines (A and G) have two rings; pyrimidines (C, T and U) have one. Every base pair matches a purine with a pyrimidine, which keeps the helix the same width.
Amino acids: A central carbon bonded to an amino group, a carboxyl group, a hydrogen and an R group (side chain). The R group can be nonpolar (hydrophobic), polar or charged, and that sets how the amino acid behaves.
Peptide bonds and protein direction: Dehydration synthesis joins amino acids with peptide bonds. A polypeptide has an amino (N-terminal) end and a carboxyl (C-terminal) end, and ribosomes build it starting at the amino end.
Four levels of protein structure: Primary: the amino acid sequence; secondary: α-helices and β-pleated sheets held by hydrogen bonds along the backbone; tertiary: the overall 3D shape from R-group interactions (hydrophobic clustering, hydrogen and ionic bonds, disulfide bridges). Quaternary structure is two or more polypeptides working together, as in hemoglobin.
Structure decides function: A change in the amino acid sequence can change how a protein folds and what it can do. In sickle cell disease one amino acid change in hemoglobin makes the protein clump and deform red blood cells.

Cell structures

Unit 2

Ribosome: Built from rRNA and protein, with no membrane, and found in every living cell. It makes proteins by reading mRNA; free ribosomes make proteins for the cytosol, and ribosomes on the rough ER make proteins to be exported, put in membranes or sent to lysosomes.
Nucleus: Holds the eukaryotic cell's DNA inside a double membrane (nuclear envelope) with pores. Transcription and RNA processing happen here.
Rough ER: Membranes studded with ribosomes, where proteins for secretion or membranes are made and folded, then sent off in vesicles.
Smooth ER: No ribosomes. Makes lipids, breaks down toxins and stores calcium ions.
Golgi complex: Stacks of flattened sacs that receive proteins from the ER, modify them (for example, adding sugar chains), then sort and ship them in vesicles.
Lysosome: A membrane sac of hydrolytic enzymes that break down food, worn-out organelles and invaders; lysosomes also help with programmed cell death (apoptosis).
Vacuoles: Membrane sacs for storage. Plant cells have a large central vacuole that stores water and keeps the cell turgid; freshwater protists use contractile vacuoles to pump out extra water.
Mitochondrion: Double membrane: the smooth outer membrane and a highly folded inner membrane (cristae) that adds surface area for the electron transport chain. The Krebs cycle runs in the fluid inside, called the matrix.
Chloroplast: Double membrane around stacks of thylakoids, where the light reactions happen. The fluid around them, the stroma, is where the Calvin cycle builds sugar.
Cell wall: A rigid layer outside the plasma membrane that gives support and stops cells from bursting in hypotonic surroundings. Plant walls are mostly cellulose, fungal walls chitin and bacterial walls peptidoglycan; most archaea have walls made of other materials.
Fluid mosaic model: The membrane is a phospholipid bilayer with proteins floating in it. Cholesterol in animal membranes helps keep fluidity steady, and proteins and lipids with sugar chains (glycoproteins and glycolipids) act in cell recognition.
Membrane proteins: Integral proteins span or sit inside the bilayer: their nonpolar (hydrophobic) parts touch the lipid tails and their polar or charged parts face the water. Peripheral proteins are loosely attached to the surface. Together they act as channels, carriers, receptors, enzymes and attachment points.
Selective permeability: Small nonpolar molecules such as O₂ and CO₂ cross the hydrophobic core directly. Ions and large polar molecules need channel or carrier proteins, and most water crosses through aquaporins.
Prokaryotic vs eukaryotic cells: Prokaryotes (bacteria and archaea) usually lack a nucleus and membrane-bound organelles; their DNA is one circular chromosome in a nucleoid region, often with plasmids. Eukaryotes have a nucleus, linear chromosomes and membrane-bound organelles.
Compartmentalization: Internal membranes give each reaction its own space, so conflicting reactions don't interfere and conditions like pH can be set for each job. Folded membranes add surface area for reactions.
Endosymbiotic theory: Mitochondria and chloroplasts descend from prokaryotes engulfed by a host cell. Evidence: double membranes, their own circular DNA, bacteria-like ribosomes, and division by a process like binary fission.

Moving things across membranes

Unit 2

Concentration gradient: A difference in concentration across a space or membrane. Moving down the gradient (high to low) releases energy; moving up it (low to high) requires energy.
Simple diffusion: Passive movement of small nonpolar molecules (O₂, CO₂) straight through the bilayer, down their gradient, with no protein and no energy.
Facilitated diffusion: Passive movement down the gradient through proteins: channel proteins for ions such as Na⁺ and K⁺, and carrier proteins for larger polar molecules like glucose. No energy is used.
Osmosis and aquaporins: Osmosis is the diffusion of water across a membrane from higher to lower water potential. Large amounts of water move through aquaporin channels.
Active transport: Membrane proteins (pumps) use energy, usually from ATP, to move substances against their gradient, from low to high concentration.
Sodium-potassium pump: Each cycle uses one ATP to move 3 Na⁺ out and 2 K⁺ in. This builds the electrochemical gradient and helps make the inside of the cell negative compared with the outside (membrane potential).
Cotransport (secondary active transport): A protein lets one ion flow down a gradient made by a pump and uses that energy to drag another substance up its gradient, like a H⁺/sucrose cotransporter in plant cells.
Endocytosis: The membrane wraps around material and pinches off a vesicle to bring it in: phagocytosis takes in large particles, pinocytosis takes in fluid, and receptor-mediated endocytosis takes in specific molecules that bind receptors. It uses energy.
Exocytosis: A vesicle fuses with the plasma membrane and releases its contents outside, as when cells secrete hormones like insulin or neurotransmitters. It uses energy.

Enzymes and cellular energy

Unit 3

Enzymes lower activation energy: Enzymes are biological catalysts (most are proteins) that speed reactions by lowering activation energy. They aren't used up and don't change how much energy a reaction releases or absorbs.
Active site and specificity: The substrate binds only if its shape and charge fit the active site, forming an enzyme-substrate complex. The enzyme may shift shape slightly to grip the substrate (induced fit).
Substrate concentration: More substrate raises the rate until every active site is busy; then the rate levels off (saturation). Adding more enzyme raises that maximum.
Temperature: Warming speeds the reaction because molecules collide more often, up to the optimum. Past that, heat breaks hydrogen bonds and other interactions, the enzyme denatures and the rate drops quickly.
pH and pH = −log[H⁺]: Each enzyme has an optimum pH; too acidic or basic disrupts the bonds holding its shape. Each pH unit is a tenfold change in H⁺ concentration, so pH 4 has 1,000 times more H⁺ than pH 7.
Denaturation: Loss of a protein's 3D shape, and so its function, without breaking peptide bonds. It's sometimes reversible if normal conditions return.
Competitive inhibitor: Resembles the substrate and binds the active site, blocking it. Adding much more substrate can outcompete it and bring the rate back up.
Noncompetitive (allosteric) inhibitor: Binds somewhere other than the active site (an allosteric site) and changes the enzyme's shape so the active site works less well. Adding more substrate can't overcome it.
Feedback inhibition: The end product of a pathway inhibits an enzyme early in that pathway, so the cell stops making a product it already has enough of.
Cofactors and coenzymes: Non-protein helpers some enzymes need: cofactors are often metal ions, and coenzymes are organic molecules, many made from vitamins.
Laws of thermodynamics: Energy can't be created or destroyed, only converted (first law), and every energy transfer loses some energy as heat, increasing disorder (second law). So living things need a constant input of energy to stay organized.
ATP and energy coupling: ATP is adenine, ribose and three phosphates. Breaking off the last phosphate (ATP → ADP + Pᵢ) releases energy, and cells couple that energy-releasing (exergonic) reaction to energy-requiring (endergonic) ones, often by attaching the phosphate to another molecule.
Metabolic pathways: Reactions run in sequences where each product is the next step's reactant, each step with its own enzyme. Core pathways such as glycolysis are shared by all three domains, evidence of common ancestry.
Electron carriers: NAD⁺ and FAD pick up electrons in respiration to become NADH and FADH₂; NADP⁺ picks them up in photosynthesis to become NADPH. They deliver high-energy electrons to an electron transport chain or the Calvin cycle.

Photosynthesis and respiration in steps

Unit 3

Photosynthesis overall: 6CO₂ + 6H₂O + light energy → C₆H₁₂O₆ + 6O₂. Light energy ends up stored in the chemical bonds of sugar.
Light reactions (thylakoid membrane): 1) Light excites electrons in chlorophyll at photosystem II. 2) Water is split to replace them, releasing O₂ and H⁺. 3) Electrons pass along an electron transport chain to photosystem I, and the energy pumps H⁺ into the thylakoid space. 4) Photosystem I re-energizes the electrons, which reduce NADP⁺ to NADPH.
ATP synthase in the chloroplast: H⁺ built up inside the thylakoid flows back out into the stroma through ATP synthase, which makes ATP. This is chemiosmosis.
Calvin cycle (stroma): Uses ATP and NADPH from the light reactions to fix CO₂ into sugar. It returns ADP and NADP⁺ to the light reactions, so the Calvin cycle stops when the light reactions stop.
The O₂ comes from water: The oxygen released by photosynthesis comes from splitting water in the light reactions, not from CO₂.
Photosynthesis history: Photosynthesis first evolved in prokaryotes, and photosynthetic cyanobacteria are credited with giving Earth an oxygen-rich atmosphere. Chloroplasts descend from cyanobacteria-like cells.
Cellular respiration overall: C₆H₁₂O₆ + 6O₂ → 6CO₂ + 6H₂O + energy (captured as ATP). Its overall equation is the reverse of photosynthesis, though the steps are different.
1) Glycolysis (cytosol): One glucose is split into two pyruvate, for a net gain of 2 ATP and 2 NADH. It doesn't need oxygen and happens in nearly all organisms.
2) Pyruvate oxidation and the Krebs cycle (mitochondrial matrix): Pyruvate enters the mitochondrion and is broken down step by step. Its carbons leave as CO₂, and the energy is loaded onto NADH and FADH₂, with a small amount of ATP made directly.
3) Electron transport chain (inner mitochondrial membrane): NADH and FADH₂ hand their electrons to the chain. As electrons move down it, proteins pump H⁺ from the matrix into the intermembrane space, and oxygen, the final electron acceptor, combines with electrons and H⁺ to form water.
4) Chemiosmosis and ATP synthase: H⁺ flows back into the matrix through ATP synthase, which turns that flow into most of the cell's ATP (oxidative phosphorylation). No oxygen means the chain backs up and this ATP production stops.
Uncoupling the proton gradient: If H⁺ leaks back across the inner membrane without passing through ATP synthase, the energy is released as heat instead of ATP. Brown fat in some mammals does this on purpose to stay warm.
Fermentation: Without oxygen, cells turn pyruvate into lactic acid (animal muscle, some bacteria) or ethanol plus CO₂ (yeast). Its job is to regenerate NAD⁺ so glycolysis can keep making its 2 ATP per glucose.
Comparing chloroplasts and mitochondria: Both use an electron transport chain to build an H⁺ gradient and ATP synthase to make ATP. In chloroplasts H⁺ is pumped into the thylakoid space and electrons come from water; in mitochondria H⁺ is pumped into the intermembrane space and electrons come from food.

Cell signaling, feedback and the cell cycle

Unit 4

Three ways cells signal: Direct contact (touching cells or connections between them, as with immune cells), local signals that reach nearby cells (such as neurotransmitters), and hormones that travel long distances in the blood (such as insulin).
Quorum sensing: Bacteria release signal molecules and respond when the concentration shows enough neighbors are present, coordinating behavior such as forming biofilms.
Reception, transduction, response: 1) A ligand binds a specific receptor, which changes shape. 2) A relay of molecules inside the cell passes and amplifies the signal. 3) The cell responds, for example by changing gene expression, activating an enzyme or secreting a product.
Surface vs intracellular receptors: Polar or large ligands can't cross the membrane, so they bind receptors on the cell surface. Small nonpolar ligands such as steroid hormones cross the membrane and bind receptors inside, which often act directly on genes.
G protein-coupled receptor pathway: The ligand binds the receptor, which activates a G protein; the G protein turns on an enzyme that makes the second messenger cAMP, and cAMP switches on protein kinases. For example, epinephrine signals liver cells to break down glycogen this way.
Second messengers: Small, fast-spreading molecules inside the cell, such as cAMP and Ca²⁺ ions, that relay the signal from the receptor to other proteins.
Phosphorylation cascade: Protein kinases switch on other kinases by adding phosphate groups, one after another, amplifying the signal at each step. Phosphatases remove the phosphates to switch the pathway off.
When a pathway changes: Each step depends on the one before, so a mutated receptor, a relay protein stuck on or off, or a drug that blocks a step can stop the response or keep it running even with no signal.
Negative feedback: The response pushes a variable back toward its set point. High blood glucose triggers insulin, which helps cells take up glucose and the liver store it as glycogen; low blood glucose triggers glucagon, which makes the liver release glucose.
Positive feedback: The response pushes the change even further. Examples: oxytocin making contractions stronger during childbirth, and ripening fruit giving off ethylene that speeds up more ripening.
Cell cycle phases: Interphase is G₁ (growth), S (DNA copied, so each chromosome becomes two sister chromatids) and G₂ (preparing to divide), followed by mitosis and cytokinesis. Cells that stop dividing rest in G₀.
Mitosis in four stages: Prophase: chromosomes condense, the spindle forms and the nuclear envelope breaks down; metaphase: chromosomes line up in the middle; anaphase: sister chromatids separate to opposite poles; telophase: nuclear envelopes re-form around each set.
Cytokinesis: The cytoplasm divides: a cleavage furrow pinches animal cells in two, while plant cells build a cell plate that becomes a new wall.
Result of mitosis: Two daughter cells genetically identical to the parent, with the same chromosome number. It's used for growth, repair and asexual reproduction.
Checkpoints: G₁ checks cell size, nutrients and DNA damage before copying DNA; G₂ checks that DNA was copied correctly; the M (spindle) checkpoint checks that every chromosome is attached to the spindle before anaphase.
Cyclins and CDKs: Cyclin-dependent kinases (CDKs) are active only when bound to cyclins, whose levels rise and fall through the cycle. An active cyclin-CDK complex phosphorylates target proteins that push the cell into the next phase.
Cancer: Mutations in genes that control the cycle let cells divide without passing checkpoints, forming tumors. Typically, growth-promoting genes become stuck on and growth-stopping (tumor-suppressor) genes stop working.
Apoptosis: Programmed cell death, a controlled self-destruction that removes damaged or unneeded cells, such as the tissue between developing fingers.
Mitotic index: Cells in mitosis ÷ total cells counted. Because more cells are seen in longer phases, the fraction of cells in a phase × the total cycle length estimates how long that phase lasts.

Meiosis and inheritance

Unit 5

Haploid and diploid: Diploid (2n) cells have two sets of chromosomes, one from each parent; haploid (n) cells such as gametes have one. Humans have 2n = 46 and n = 23.
Homologous chromosomes vs sister chromatids: Homologs are a matching pair, one from each parent, with the same genes but possibly different alleles. Sister chromatids are the two identical copies of one chromosome made in S phase.
Meiosis I: Homologous chromosomes pair up (synapsis) and cross over in prophase I, line up as pairs in metaphase I, and separate in anaphase I. Each resulting cell is haploid, but each chromosome still has two chromatids.
Meiosis II: Works like mitosis: sister chromatids separate. The result is four haploid cells, each genetically different.
Mitosis vs meiosis: Mitosis: one division, two identical diploid cells, for growth and repair. Meiosis: two divisions, four genetically different haploid gametes, for sexual reproduction.
Crossing over: Homologous chromosomes swap segments in prophase I, making new combinations of alleles on each chromosome (recombination).
Independent assortment in meiosis: Each homologous pair lines up in a random orientation in metaphase I, so a gamete can get any mix of maternal and paternal chromosomes: 2ⁿ combinations, which is 2²³ ≈ 8.4 million for humans before crossing over.
Random fertilization: Any sperm can fertilize any egg, multiplying the variation from crossing over and independent assortment.
Nondisjunction: Homologs (in meiosis I) or sister chromatids (in meiosis II) fail to separate, so gametes get an extra or missing chromosome. Fertilization then gives trisomy (2n + 1, as in Down syndrome, trisomy 21) or monosomy (2n − 1, as in Turner syndrome, XO).
Law of segregation: The two alleles for a gene separate during meiosis, so each gamete carries only one of them.
Law of independent assortment: Alleles of genes on different chromosomes are sorted into gametes independently. It doesn't hold for genes close together on the same chromosome.
Monohybrid cross: Aa × Aa: Genotype ratio 1 AA : 2 Aa : 1 aa; phenotype ratio 3 dominant : 1 recessive with complete dominance.
Dihybrid cross: AaBb × AaBb: Phenotype ratio 9 : 3 : 3 : 1 for two unlinked genes with complete dominance. The chance of showing both dominant traits is ¾ × ¾ = 9/16.
Testcross: Cross an organism with the dominant phenotype to a homozygous recessive. All dominant offspring means it was homozygous; a 1:1 ratio means heterozygous. For AaBb × aabb with unlinked genes, expect 1:1:1:1.
Reading pedigrees: Autosomal recessive: can skip generations, and two unaffected parents can have an affected child (both carriers). Autosomal dominant: every affected person usually has an affected parent, and two affected parents can have an unaffected child.
X-linked recessive traits: More common in XY individuals, who have only one X. An affected father passes the allele to all his daughters (who are at least carriers) but never to his sons; a carrier mother passes it to about half her sons.
Linked genes and map distance: Genes close together on one chromosome are usually inherited together, so parental types outnumber recombinants. Recombination frequency = recombinant offspring ÷ total offspring × 100, and 1% equals 1 map unit; genes far apart approach 50%, like unlinked genes.
Incomplete dominance: The heterozygote shows an in-between phenotype, such as pink flowers from red × white. An F₂ gives a 1 : 2 : 1 phenotype ratio that matches the genotype ratio.
Codominance and multiple alleles: Both alleles show fully in the heterozygote. In ABO blood type, Iᴬ and Iᴮ are codominant (type AB), and i is recessive to both (type O = ii).
Pleiotropy and polygenic traits: Pleiotropy: one gene affects several traits. Polygenic: many genes add up to one trait, like height or skin color, giving a smooth range of phenotypes.
Non-nuclear inheritance: Genes in mitochondria and chloroplasts are usually passed on only through the egg, so these traits follow the mother, not Mendel's ratios.
Environment and phenotype: The same genotype can give different phenotypes in different environments (phenotypic plasticity): hydrangea flower color changes with soil pH, and in some reptiles nest temperature decides sex.

DNA to protein

Unit 6

Flow of genetic information: DNA is copied into RNA (transcription), and RNA is read to build protein (translation). Retroviruses such as HIV run part of this backward, using reverse transcriptase to copy their RNA into DNA.
How genomes are packed: Prokaryotes usually have one circular chromosome; eukaryotes have several linear chromosomes wrapped around histone proteins. Both can carry plasmids, small extra DNA circles that often hold genes like antibiotic resistance.
Semiconservative replication: Each new double helix keeps one original strand and gets one new strand, because each old strand serves as a template.
Replication steps: 1) Helicase unzips the helix at an origin of replication, and topoisomerase relieves the twisting ahead of it. 2) Primase lays down short RNA primers. 3) DNA polymerase adds nucleotides to the 3′ end, building 5′ to 3′ and proofreading. 4) The primers are replaced with DNA, and ligase seals the gaps.
Leading and lagging strands: Because DNA polymerase only builds 5′ to 3′, the leading strand is made continuously toward the fork, while the lagging strand is made in short pieces (Okazaki fragments) away from the fork, later joined by ligase.
Transcription: RNA polymerase binds a promoter, reads the template strand and builds a complementary RNA 5′ to 3′ (no primer needed). The RNA matches the non-template (coding) strand, with U in place of T.
Three kinds of RNA: mRNA carries the gene's message to the ribosome, tRNA carries amino acids and has the anticodon, and rRNA makes up the ribosome and catalyzes peptide bonds.
Eukaryotic RNA processing: Before leaving the nucleus, mRNA gets a cap on its 5′ end (called the GTP cap in AP materials) that helps ribosomes recognize it, a poly-A tail on its 3′ end that protects it, and splicing that removes introns and joins exons.
Alternative splicing: Exons can be joined in different combinations, so one gene can code for more than one protein.
Translation steps: 1) Initiation: the ribosome assembles on the mRNA and starts at the start codon AUG (methionine). 2) Elongation: tRNA anticodons pair with each codon, and the ribosome links their amino acids with peptide bonds as it moves 5′ to 3′ along the mRNA. 3) Termination: a stop codon (UAA, UAG or UGA) releases the finished polypeptide.
The genetic code: Codons are three bases long, so there are 4³ = 64 codons: 61 code for 20 amino acids and 3 are stops. The code is redundant (most amino acids have several codons) and nearly universal, evidence of common ancestry.
Reading a codon chart: Use mRNA codons, not DNA or tRNA: convert the template DNA to its complementary mRNA first, then read three bases at a time from the start codon.
Prokaryotes vs eukaryotes: In prokaryotes transcription and translation happen together in the cytoplasm, and mRNA usually isn't processed. In eukaryotes transcription and processing happen in the nucleus and translation happens in the cytoplasm.

Gene regulation, mutations and biotech

Unit 6

Operon parts: A bacterial cluster of related genes under one promoter, with an operator (an on-off switch) where a repressor protein can bind and block RNA polymerase. A separate regulatory gene makes the repressor.
lac operon (inducible): Usually off: the repressor sits on the operator. When lactose is present, a form of it (allolactose) binds and inactivates the repressor, so the genes for breaking down lactose are transcribed.
trp operon (repressible): Usually on, making the enzymes that build tryptophan. When tryptophan builds up, it binds and activates the repressor, which shuts the operon off.
Transcription factors, promoters and enhancers: In eukaryotes, transcription factors bind the promoter and enhancers (regulatory DNA that can be far away) to help RNA polymerase start; repressor proteins can block transcription. Different combinations of factors switch on different genes.
Epigenetic changes: Changes to DNA or histones that turn genes up or down without changing the sequence. Adding methyl groups to DNA usually silences genes; adding acetyl groups to histones loosens DNA and usually increases transcription.
Small regulatory RNAs: Short RNA molecules (such as microRNAs) bind matching mRNA and block its translation or mark it for breakdown, silencing the gene after transcription.
Cell specialization: Almost all cells in a body have the same DNA, but each cell type expresses a different set of genes (differential gene expression), mostly controlled by which transcription factors it has.
Substitution mutations: One base is swapped for another. It can be silent (same amino acid), missense (a different amino acid) or nonsense (an early stop codon that cuts the protein short).
Insertions, deletions and frameshifts: Adding or removing bases (not a multiple of 3) shifts the reading frame, changing every codon after it and usually ruining the protein.
Mutations are random: Mutations come from DNA copying errors or damage (like UV light or chemicals), not because an organism needs them. Whether one helps, harms or does nothing depends on its effect and the environment.
Changes in chromosome number: Errors in meiosis such as nondisjunction give trisomy or monosomy. Whole extra sets of chromosomes (polyploidy) are common in plants and can create new species in one generation.
Horizontal gene transfer in bacteria: Transformation: taking up DNA from the surroundings. Transduction: a virus carries DNA from one bacterium to another. Conjugation: one bacterium passes DNA, often a plasmid, to another through direct contact.
Viruses and variation: Viruses, especially RNA viruses, copy their genomes with many errors, so they mutate and evolve fast; that's why new flu vaccines are needed often.
PCR (polymerase chain reaction): Copies a chosen DNA segment over and over: heat to separate the strands (about 95 °C), cool so primers bind, then a heat-stable DNA polymerase extends them. Each cycle doubles the DNA, so n cycles give about 2ⁿ times as many copies.
Gel electrophoresis: DNA is negatively charged (from its phosphates), so it moves toward the positive electrode. Smaller fragments travel farther; compare bands with a ladder of known sizes to estimate fragment length.
Restriction enzymes: Bacterial enzymes that cut DNA at specific short sequences. Cutting a linear molecule in n places gives n + 1 pieces, but cutting a circular plasmid in n places gives n pieces.
Bacterial transformation in the lab: Bacteria take up a plasmid carrying a gene of interest plus an antibiotic-resistance gene. Growing them on antibiotic plates selects the cells that took up the plasmid.
DNA sequencing: Reads the exact order of bases. It's used to compare species and build evolutionary trees, identify disease mutations and match DNA in forensics.

Evolution, phylogeny and speciation

Unit 7

What natural selection needs: Variation among individuals, traits that are heritable, more offspring than can survive (competition for limited resources), and differences in survival and reproduction linked to those traits.
Fitness: Reproductive success: how many offspring an individual leaves, compared with others. It's not strength or size, and which traits raise fitness depends on the environment.
Individuals are selected, populations evolve: Selection acts on individuals' phenotypes, but evolution is a change in a population's allele frequencies over generations. An individual can't evolve.
Directional, stabilizing and disruptive selection: Directional favors one extreme and shifts the average; stabilizing favors the middle and narrows the range; disruptive favors both extremes and can split a population in two.
Artificial selection: Humans choose which individuals breed, as in dog breeds or broccoli, cabbage, kale and cauliflower from one wild mustard species. It shows how fast selection can change a population.
Genetic drift: Random changes in allele frequencies from chance events, strongest in small populations. It can remove alleles, even helpful ones, and lowers genetic diversity.
Bottleneck effect: A disaster leaves only a few survivors, so the new population's alleles reflect chance, not fitness, and diversity drops (for example, northern elephant seals).
Founder effect: A few individuals start a new population, so rare alleles they happen to carry can become common there.
Gene flow and mutation: Gene flow moves alleles between populations through migration and makes them more alike. Mutation is the only source of brand-new alleles.
Fossil evidence: Fossils show change over time. They are dated by their rock layers and by radiometric dating, which uses the known half-lives of radioactive isotopes: carbon-14 for remains up to about 50,000 years old, and isotopes with longer half-lives, such as potassium-40, for older rock.
Homologous structures: Same underlying structure from a common ancestor, even if used differently, such as the bones in a human arm, whale flipper and bat wing.
Analogous structures: Similar function but different origins, such as bird and insect wings. They come from convergent evolution under similar pressures, not common ancestry.
Vestigial structures: Reduced structures with little or no function that were useful in ancestors, such as the human tailbone or leg bones in whales.
Molecular evidence: The more similar two species' DNA or protein sequences are, the more recently they shared a common ancestor. Molecular data are usually more reliable than comparing body structures.
Common ancestry of all life: All living things use DNA, the same genetic code, ribosomes and core pathways like glycolysis. All eukaryotes also share membrane-bound organelles, linear chromosomes and genes with introns.
Evolution is still happening: Bacteria evolving antibiotic resistance, insects evolving pesticide resistance and pathogens causing new diseases are all evolution observed today.
Reading a cladogram or phylogenetic tree: Each node is a common ancestor, and two groups are most closely related if they share the most recent node. Branches can rotate around a node without changing relationships, and the outgroup is the least closely related group.
Shared derived characters and parsimony: Traits that appeared in a common ancestor and are shared by its descendants define each branch point. The best tree usually needs the fewest evolutionary changes (parsimony).
Cladogram vs phylogenetic tree: Both are testable hypotheses that can change with new evidence. Only a phylogenetic tree shows time or amount of change through its branch lengths.
Molecular clock: If mutations build up at a roughly steady rate, the number of sequence differences estimates time since two groups split. Time = differences ÷ rate; 24 differences at 2 per million years means about 12 million years.
Biological species concept: A species is a group whose members can interbreed in nature and produce fertile offspring. It doesn't work for asexual organisms or fossils.
Allopatric vs sympatric speciation: Allopatric: a geographic barrier splits a population and the parts diverge. Sympatric: new species form without a barrier, for example through polyploidy in plants or different habitats or mating times.
Prezygotic barriers: Stop mating or fertilization: habitat, temporal (breeding at different times), behavioral (different courtship), mechanical (parts don't fit) and gametic (egg and sperm can't fuse) isolation.
Postzygotic barriers: Act after a hybrid zygote forms: hybrids die early, are sterile (like a mule) or have weak, infertile offspring of their own.
Tempo of speciation: Gradualism: slow, steady change. Punctuated equilibrium: long stable periods broken by quick bursts of change. Adaptive radiation: one ancestor quickly branches into many species to fill open niches.
Genetic diversity and survival: A diverse population is more likely to include individuals that survive a new disease or environmental change. Populations with little variation, like the California condor, face higher extinction risk.
Origins of life timeline: Earth formed about 4.6 billion years ago, conditions may have allowed life by about 3.9 billion years ago, and the oldest known fossils are about 3.5 billion years old.
From chemicals to cells: Experiments such as Miller–Urey showed simple organic molecules can form from inorganic ones under early-Earth conditions. The RNA world hypothesis says RNA came first because it can store information and catalyze reactions (ribozymes).

Ecology

Unit 8

Taxis vs kinesis: Taxis is directed movement toward or away from a stimulus, like moving toward light. Kinesis is a change in speed or turning rate with no set direction, like pill bugs moving faster in dry areas.
Innate vs learned behavior: Innate behavior is inherited and done correctly the first time; learned behavior changes with experience. Behaviors that raise survival and reproduction are favored by natural selection.
Animal communication: Visual, sound, touch, electrical and chemical (pheromone) signals warn others, defend territory, find mates and coordinate groups. Cooperative behavior, especially toward relatives, can raise the fitness of the group's shared genes.
Endotherms vs ectotherms: Endotherms (birds, mammals) make body heat from their own metabolism and use more energy; ectotherms get heat mostly from their surroundings. Smaller endotherms have higher metabolic rates per gram.
Producers, consumers and decomposers: Producers (autotrophs) capture energy from sunlight or, in chemosynthesis, from chemicals. Consumers eat other organisms, and decomposers break down dead matter and return nutrients to the soil and water.
Energy flows, matter cycles: Energy enters as light, moves one way up trophic levels and leaves as heat, so ecosystems need constant input. Atoms like carbon and nitrogen are recycled between organisms and the environment.
Food chains, food webs and trophic levels: Producers form the first trophic level, primary consumers (herbivores) the second, and secondary and tertiary consumers the next. A food web links many chains, so removing one species can affect many others; energy pyramids always narrow toward the top.
Energy budgets: An organism that takes in more energy than it uses can grow, store energy or reproduce; one that takes in less loses mass and can die. Reproduction costs extra energy, so a drop in available energy can shrink populations and disrupt the ecosystem.
Carbon cycle: Photosynthesis removes CO₂ from the air; respiration, decomposition and burning fossil fuels return it. Carbon is stored in living things, fossil fuels, rocks and the ocean.
Nitrogen cycle: Nitrogen fixation: bacteria (some in root nodules) turn N₂ gas into ammonia or ammonium. Nitrification: bacteria turn ammonium into nitrite and then nitrate, which plants take up. Ammonification: decomposers release ammonium from dead matter. Denitrification: bacteria turn nitrate back into N₂.
Phosphorus cycle: No major gas phase: phosphate comes from weathering rock, moves through soil, organisms and water, and settles into sediments. It's needed for DNA, ATP and phospholipids and often limits growth, especially in water.
Water cycle: Water evaporates from surfaces and transpires from plants, condenses into clouds, falls as precipitation, then runs off or soaks into groundwater.
Carrying capacity (K): The largest population an environment can support long-term with its limited resources. Logistic growth levels off at K.
Density-dependent factors: Limits that get stronger as a population gets more crowded: competition for food, predation, disease and waste buildup.
Density-independent factors: Limits that affect a population regardless of crowding: floods, fires, freezes and other weather or natural disasters.
Species interactions: Competition (−/−), predation and herbivory (+/−), parasitism (+/−), mutualism (+/+) and commensalism (+/0). The signs show whether each species is helped, harmed or unaffected.
Competitive exclusion and niche partitioning: Two species can't share exactly the same niche for long; one will outcompete the other. Species often coexist by dividing resources, such as feeding at different heights or times.
Keystone species: A species with an effect far bigger than its numbers. Remove sea otters from a kelp forest and sea urchins multiply and wipe out the kelp.
Trophic cascade: A change at one trophic level ripples through others, as when removing a top predator lets herbivores boom and overeat plants.
Biodiversity and resilience: Ecosystems with more species and more genetic variety usually resist and recover from disturbances better.
Invasive species: Introduced species that spread fast because they lack natural predators or competitors, outcompeting native species and lowering diversity.
Biomagnification: Persistent toxins such as DDT and mercury become more concentrated at each higher trophic level, so top predators carry the most.
Eutrophication: Nutrient runoff (nitrogen and phosphorus from fertilizer or sewage) causes an algal bloom; when the algae die, decomposers use up dissolved oxygen, creating dead zones where fish die.
Disruptions and variation: Geological and weather events such as El Niño, plus human activity, change habitats. Which individuals survive depends on variation already present, because mutations don't happen on demand.
Heterozygote advantage: Sometimes heterozygotes have the highest fitness, keeping a harmful allele common. Carriers of one sickle cell allele resist malaria, so the allele stays frequent where malaria is common.