AP Biology study guide

The molecules that make living things possible: water, carbon compounds, macromolecules, and the enzymes that run metabolism.

What you need to know

Water makes life possible

Water is a polar molecule: the oxygen end carries a partial negative charge and the hydrogen ends carry partial positives, which lets neighboring molecules form hydrogen bonds. Those bonds explain most of water's remarkable properties.

Cohesion (water sticking to itself) creates surface tension and pulls water up narrow tubes, while adhesion (water sticking to other surfaces) helps that transport. Because of hydrogen bonding, water has a high specific heat, a high heat of vaporization, and ice floats (water expands as it freezes).

Water is also the solvent of life. Its polarity pulls ions and other polar molecules apart, so most biochemistry happens in aqueous solution. Nonpolar molecules like lipids are hydrophobic and are excluded from water.

Carbon and macromolecules

Carbon forms four covalent bonds and can chain into rings and long skeletons, which is why it is the backbone of biological molecules. The four major classes are carbohydrates, lipids, proteins, and nucleic acids.

Carbohydrates store energy (glucose, glycogen, starch) and build structure (cellulose, chitin). Lipids are hydrophobic: fats store energy, phospholipids make membranes, and steroids act as signaling molecules.

Proteins are chains of amino acids folded into shapes that do nearly all cellular work. Nucleic acids (DNA and RNA) store and express genetic information. All four classes are built by dehydration synthesis (removing water to link monomers) and broken down by hydrolysis (adding water).

Enzymes control the pace of reactions

Enzymes are proteins that speed reactions by lowering activation energy. Each enzyme has an active site whose shape fits specific substrates, so enzymes are highly specific.

Enzyme activity depends on temperature, pH, and concentration. Heat or wrong pH can denature the enzyme, unfolding it so the active site no longer fits the substrate. Inhibitors can block activity, and cells regulate enzymes to control metabolic pathways.

Key terms

• Hydrogen bond — A weak attraction between a partially positive hydrogen and a partially negative atom such as oxygen or nitrogen.
• Cohesion — The tendency of water molecules to stick to each other through hydrogen bonds.
• Adhesion — The tendency of water to stick to other polar surfaces.
• Hydrolysis — A reaction that breaks a polymer into monomers by adding water.
• Dehydration synthesis — A reaction that links monomers by removing a water molecule.
• Monomer — A single building-block molecule, such as an amino acid or glucose.
• Polymer — A chain of many monomers linked together.
• Denaturation — A change in an enzyme's shape that destroys its function, often caused by heat or wrong pH.
• Activation energy — The initial energy needed to start a chemical reaction.
• Active site — The region of an enzyme where a substrate binds and reacts.
• Hydrophobic — Water-fearing; molecules that do not mix with water.
• Hydrophilic — Water-loving; molecules that mix readily with water.

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How cells are organized: prokaryotes and eukaryotes, organelles and their jobs, and how materials move across membranes.

What you need to know

Two cell designs

Prokaryotic cells (bacteria and archaea) have no nucleus and no membrane-bound organelles; their DNA sits in the cytoplasm. Eukaryotic cells have a nucleus and a set of membrane-bound organelles, and they are generally larger and more complex.

Eukaryotes include single-celled protists and all multicellular organisms. The endosymbiotic theory explains that mitochondria and chloroplasts began as free-living bacteria engulfed by early cells, which is why they have their own DNA and double membranes.

Organelles and their jobs

The nucleus stores DNA and directs RNA synthesis. Ribosomes build proteins. The rough endoplasmic reticulum (with ribosomes) makes proteins for export; the smooth ER makes lipids and detoxifies chemicals. The Golgi apparatus sorts, modifies, and packages proteins.

Mitochondria carry out aerobic respiration and are the main ATP producers. Lysosomes digest wastes and worn-out parts. Vacuoles store water and solutes, and in plant cells maintain pressure. Plant cells add a cell wall and chloroplasts, while animal cells have centrioles and lysosomes.

The cytoskeleton gives shape, anchors organelles, and moves materials and chromosomes. Cilia and flagella are motile projections built on microtubules.

Membrane transport

The plasma membrane is a fluid mosaic of phospholipids, proteins, and cholesterol. Small nonpolar molecules diffuse freely; ions and large polar molecules need transport proteins.

Passive transport (diffusion, osmosis, facilitated diffusion) needs no energy and moves things down their gradient. Active transport and endo/exocytosis use ATP to move things against the gradient. The tonicity of the solution determines which way water moves: hypotonic solutions swell cells, hypertonic solutions shrink them.

Key terms

• Prokaryote — A cell without a nucleus or membrane-bound organelles, such as a bacterium.
• Eukaryote — A cell with a nucleus and membrane-bound organelles.
• Endosymbiotic theory — The idea that mitochondria and chloroplasts evolved from engulfed bacteria.
• Rough ER — ER studded with ribosomes, making proteins destined for export.
• Smooth ER — ER that makes lipids and detoxifies chemicals.
• Golgi apparatus — Organelle that modifies, sorts, and packages proteins.
• Lysosome — Vesicle of digestive enzymes that breaks down waste and cellular parts.
• Fluid mosaic model — The membrane concept: a flexible bilayer with embedded proteins.
• Osmosis — The diffusion of water across a selectively permeable membrane.
• Active transport — Movement of molecules against their gradient, requiring ATP.
• Hypotonic — A solution with lower solute concentration, causing water to enter the cell.
• Hypertonic — A solution with higher solute concentration, causing water to leave the cell.
• Cytoskeleton — A network of protein fibers that shapes and supports the cell.

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How cells capture and spend energy: enzymes, ATP, cellular respiration, and photosynthesis.

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Energy and enzymes

Energy can exist as heat (random motion) or as usable chemical energy. Organisms are open systems that exchange matter and energy with the environment, obeying the laws of thermodynamics: energy is conserved, and entropy tends to increase.

Cells run on ATP, the energy currency. ATP releases energy when a phosphate group is removed, becoming ADP. Coupled reactions use the energy released by exergonic reactions to drive endergonic ones, and enzymes control how fast those reactions go.

Cellular respiration

Aerobic respiration harvests energy from glucose in three stages: glycolysis (in the cytoplasm, no oxygen needed), the Krebs cycle, and oxidative phosphorylation in the mitochondria.

Glycolysis splits glucose into two pyruvates and yields a net 2 ATP. Pyruvate enters the Krebs cycle, which produces NADH, FADH2, and some ATP. Oxidative phosphorylation uses the electron transport chain and chemiosmosis to make the bulk of the ATP (~30 per glucose).

If oxygen is absent, fermentation regenerates NAD+ so glycolysis can continue, producing lactic acid or ethanol and just 2 ATP total.

Photosynthesis

Photosynthesis captures light energy and stores it in sugars. It happens in chloroplasts, whose thylakoid membranes hold the pigments and electron transport chains.

The light reactions split water, release oxygen, and make ATP and NADPH using light energy. The Calvin cycle (in the stroma) uses that ATP and NADPH to fix CO2 into sugar. Overall: 6 CO2 + 6 H2O become C6H12O6 + 6 O2, powered by light.

Key terms

• ATP — Adenosine triphosphate, the molecule cells use to transfer energy.
• Endergonic reaction — A reaction that absorbs energy, needing an input.
• Exergonic reaction — A reaction that releases energy.
• Glycolysis — The splitting of glucose into pyruvate, yielding 2 ATP, in the cytoplasm.
• Krebs cycle — A mitochondrial cycle that produces NADH, FADH2, and ATP from acetyl-CoA.
• Oxidative phosphorylation — ATP production via the electron transport chain and chemiosmosis.
• Chemiosmosis — ATP synthesis driven by proton flow through ATP synthase.
• Fermentation — Anaerobic regeneration of NAD+ from pyruvate, yielding 2 ATP.
• Electron transport chain — A series of membrane proteins that pass electrons and pump protons.
• Calvin cycle — The light-independent reactions that fix CO2 into sugar.
• Light reactions — Photosynthetic reactions that split water and make ATP and NADPH.
• NADH — An electron-carrying coenzyme produced during respiration and photosynthesis.

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How cells signal each other and how they regulate growth, division, and reproduction.

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Cell communication

Cells talk through signaling molecules. A signaling cell releases a ligand that binds a receptor on (or in) the target cell, which triggers a response. Direct contact, local signaling, and long-distance (hormonal) signaling are the main routes.

Most signaling uses a chain of events: reception, transduction, and response. Second messengers like cAMP and calcium amplify the signal inside the cell. Signal transduction can lead to gene expression changes, metabolic shifts, or even cell division.

The cell cycle

Eukaryotic cells divide through a cycle: interphase (G1, S, G2), then mitosis (prophase, metaphase, anaphase, telophase), then cytokinesis. During S phase DNA replicates; during mitosis the sister chromatids separate into two daughter nuclei.

Checkpoints (G1, G2, and M) verify the cell is ready to continue. If DNA is damaged or conditions are wrong, the cycle stops or triggers apoptosis. Cancer arises when these controls fail and cells divide uncontrollably.

Meiosis is the specialized division that produces gametes with half the chromosome number, creating genetic variety through crossing over and independent assortment.

Apoptosis and regulation

Apoptosis is programmed cell death, used to remove damaged or unneeded cells. It is triggered by internal or external signals and keeps tissues healthy. In development, it sculpts structures such as fingers by removing the webbing between them.

Cyclins and cyclin-dependent kinases (Cdks) drive the cell cycle forward at checkpoints. Growth factors from outside signal when division should happen; without them, cells typically remain in G1 or enter G0.

Key terms

• Ligand — A signaling molecule that binds a specific receptor.
• Signal transduction — The relay of a signal through a cell to produce a response.
• Second messenger — A small molecule, such as cAMP, that amplifies a signal inside the cell.
• Interphase — The G1, S, and G2 phases where the cell grows and replicates DNA.
• S phase — The synthesis phase when DNA is replicated.
• Mitosis — Division of the nucleus into two genetically identical nuclei.
• Cytokinesis — Division of the cytoplasm that completes cell division.
• Checkpoint — A control point where the cell verifies readiness to continue the cycle.
• Apoptosis — Programmed cell death.
• Meiosis — A division producing four genetically varied haploid gametes.
• Crossing over — Exchange of genetic material between homologous chromosomes in prophase I.
• Cyclin — A protein whose concentration cycles, activating Cdks to drive the cycle.
• Cyclin-dependent kinase (Cdk) — An enzyme that, when bound by cyclin, phosphorylates targets to advance the cell cycle.

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How traits pass between generations: meiosis, Mendelian genetics, non-Mendelian patterns, and linked genes.

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Meiosis and the rules of inheritance

Meiosis separates homologous chromosomes and, in the second division, sister chromatids, cutting the chromosome number in half. Independent assortment shuffles chromosomes, and crossing over mixes alleles between homologs, so each gamete is genetically unique.

Fertilization restores the diploid number. Mendel's laws follow from meiosis: the law of segregation says alleles separate into different gametes, and the law of independent assortment says genes on different chromosomes sort independently.

Mendelian patterns

A monohybrid cross of two heterozygotes (Aa × Aa) gives a 3:1 phenotype ratio, and a dihybrid cross of double heterozygotes gives 9:3:3:1. A Punnett square tracks possible gamete combinations.

Dominant alleles mask recessive ones, but many traits do not follow simple dominance. In incomplete dominance the heterozygote shows a blend; in codominance both alleles show. Sex-linked traits ride on the X chromosome, so males (XY) express recessive X-linked alleles more often than females.

Chromosomes and disease

Genes sit on chromosomes, and their locations can be mapped. Linked genes on the same chromosome travel together, but crossing over recombines them; the frequency of recombination reflects their distance apart.

Chromosomal errors cause disorders: nondisjunction produces aneuploidy such as trisomy 21 (Down syndrome) when a chromosome fails to separate. Karyotypes reveal such changes.

Key terms

• Allele — An alternative version of a gene.
• Homozygous — Having two identical alleles for a gene.
• Heterozygous — Having two different alleles for a gene.
• Law of segregation — Alleles separate into different gametes during meiosis.
• Law of independent assortment — Genes on different chromosomes sort into gametes independently.
• Phenotype — An organism's observable traits.
• Genotype — An organism's genetic makeup (alleles).
• Incomplete dominance — A pattern where the heterozygote shows an intermediate phenotype.
• Codominance — A pattern where both alleles are fully expressed in the heterozygote.
• Linked genes — Genes on the same chromosome that tend to be inherited together.
• Nondisjunction — Failure of chromosomes to separate during meiosis, causing aneuploidy.
• Karyotype — A photograph of an individual's chromosomes arranged in pairs.

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How DNA becomes protein, how genes are turned on and off, and how cells change without changing DNA.

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From DNA to protein

DNA stores the instructions; genes are expressed in two steps. Transcription copies a gene into messenger RNA (mRNA) in the nucleus. Translation reads the mRNA at a ribosome to build a protein from amino acids.

The genetic code uses three-letter codons; each codon specifies one amino acid. In eukaryotes, RNA processing adds a cap and tail and splices out introns to make mature mRNA. Mutations in DNA can change codons and therefore proteins.

Regulating gene expression

Cells do not express every gene at once. In prokaryotes, the lac operon turns on lactose-digesting genes only when lactose is present. In eukaryotes, regulatory proteins, transcription factors, and epigenetic marks (like DNA methylation and histone modification) control when and how strongly genes are read.

Regulation happens at many levels: chromatin structure, transcription, RNA processing, translation, and protein breakdown. This is why a liver cell and a nerve cell use the same genome but do different jobs.

Epigenetics and cell identity

Epigenetic changes alter gene activity without changing the DNA sequence. DNA methylation typically silences genes, while histone acetylation loosens chromatin and promotes expression.

During development, cells differentiate by switching different sets of genes on and off. These patterns can sometimes be inherited by daughter cells, which is how a stem cell becomes a committed tissue cell.

Key terms

• Transcription — Copying a DNA gene into mRNA.
• Translation — Building a protein from mRNA at a ribosome.
• Codon — A three-nucleotide mRNA sequence that codes for one amino acid.
• RNA polymerase — The enzyme that synthesizes mRNA from a DNA template.
• Intron — A noncoding RNA segment removed during processing.
• Exon — A coding RNA segment retained in mature mRNA.
• Operon — A cluster of prokaryotic genes with a shared promoter and operator.
• Transcription factor — A protein that regulates whether a gene is transcribed.
• DNA methylation — Addition of methyl groups to DNA, usually silencing genes.
• Histone acetylation — Addition of acetyl groups that loosen chromatin and promote expression.
• Mutation — A change in the DNA sequence.
• Epigenetics — Heritable changes in gene activity not caused by DNA sequence changes.

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How evolution works: variation, selection, adaptation, population genetics, and the origins of species.

What you need to know

Mechanisms of evolution

Natural selection acts on heritable variation: individuals with traits better suited to their environment survive and reproduce more, so those traits spread. Variation comes from mutation and sexual reproduction (crossing over and independent assortment).

Evolution is a change in allele frequencies in a population over time. The Hardy-Weinberg principle describes when allele frequencies stay constant: no mutation, random mating, no selection, no gene flow, and large population size. Deviation from those conditions drives evolution.

Other forces also change allele frequencies: genetic drift (random changes, powerful in small populations), gene flow (migration), and mutation.

Adaptation and fitness

An adaptation is a heritable trait that improves survival or reproduction in a given environment. Fitness is measured by reproductive success, not strength or size. Sexual selection favors traits that improve mating success.

Selection comes in forms: directional (favors one extreme), stabilizing (favors the middle), and disruptive (favors both extremes).

Speciation

Speciation occurs when populations become reproductively isolated. Allopatric speciation happens when a physical barrier separates populations; sympatric speciation happens without a barrier, often through polyploidy or habitat differences.

Gradualism says change accumulates slowly; punctuated equilibrium says long stable periods are interrupted by rapid bursts of change. Evidence for evolution includes fossils, comparative anatomy, DNA comparisons, and direct observation such as bacterial antibiotic resistance and beak changes in Darwin's finches.

Key terms

• Natural selection — Differential survival and reproduction of individuals with favorable heritable traits.
• Adaptation — A heritable trait that improves fitness in a given environment.
• Fitness — An organism's relative reproductive success.
• Genetic drift — Random changes in allele frequencies, strongest in small populations.
• Gene flow — Movement of alleles between populations through migration.
• Hardy-Weinberg principle — The rule that allele frequencies stay constant under five ideal conditions.
• Directional selection — Selection favoring one extreme phenotype.
• Stabilizing selection — Selection favoring the intermediate phenotype.
• Disruptive selection — Selection favoring both extremes over the middle.
• Speciation — The formation of new species from reproductive isolation.
• Allopatric speciation — Speciation caused by a physical barrier separating populations.
• Punctuated equilibrium — A model of evolution with long stable periods punctuated by rapid change.
• Sexual selection — Selection for traits that improve mating success.

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How organisms interact with each other and their environment: populations, communities, ecosystems, and biodiversity.

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Population ecology

A population grows exponentially when resources are unlimited (J-shaped curve). Real populations hit carrying capacity (K), the maximum the environment can support, producing an S-shaped logistic curve.

Growth is limited by density-dependent factors (competition, predation, disease) and density-independent factors (weather, natural disasters). Life histories vary: r-strategists produce many offspring quickly; K-strategists invest in fewer, well-cared-for offspring.

Community ecology

Species interact in several ways: competition (both harmed), predation, parasitism, mutualism (both benefit), and commensalism (one benefits, other unaffected). A niche is a species' role and requirements; competing species often divide resources to coexist.

Keystone species have outsized effects on community structure. Succession is the gradual change of a community: primary succession starts on bare rock, secondary succession after a disturbance that leaves soil.

Ecosystems and energy

Energy flows through ecosystems along food chains and webs, with only about 10% passing between trophic levels (the rest is lost as heat). Nutrients like carbon, nitrogen, and phosphorus cycle through the environment.

Human impacts reshape ecosystems: habitat loss, pollution, overharvesting, and climate change reduce biodiversity. Biodiversity is valuable because it provides resilience and ecosystem services.

Key terms

• Carrying capacity (K) — The maximum population size an environment can sustain.
• Logistic growth — Population growth that levels off at carrying capacity.
• Exponential growth — Unrestricted growth producing a J-shaped curve.
• Density-dependent factor — A limiting factor whose effect intensifies with population density.
• Density-independent factor — A factor that affects populations regardless of density.
• Niche — A species' role and resource use within its ecosystem.
• Mutualism — A relationship that benefits both species.
• Commensalism — A relationship that benefits one species without affecting the other.
• Keystone species — A species whose influence on community structure is far greater than its abundance.
• Primary succession — Succession beginning on surfaces with no soil, such as bare rock.
• Secondary succession — Succession after a disturbance that leaves soil intact.
• Trophic level — A step in a food chain, such as producer, consumer, or decomposer.
• Biomagnification — Increasing concentration of toxins as they move up the food chain.

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