Unit 3: Cellular Energetics

AP Biology — 113 practice questions with detailed explanations.

Unit Study Guide

Unit 3: Cellular Energetics

Executive Summary

Unit 3 covers the biochemical pathways that cells use to capture, store, and transfer energy. The AP exam tests your ability to trace energy from sunlight through photosynthesis into chemical bonds of glucose, and then through cellular respiration back into ATP. Enzymes catalyze every step, and understanding how enzyme structure determines specificity and regulation is foundational. The key insight is that energy flows in one direction (sun to chemical to ATP to heat) while matter cycles. You must explain not just what happens in each pathway, but why each step occurs and how the cell regulates it.

Molecular Deep-Dive

Enzyme Structure and Catalysis

Enzymes are globular proteins (or ribozymes) that lower the activation energy of reactions without being consumed. The active site is a three-dimensional cleft formed by the protein's tertiary structure; its shape, charge distribution, and hydrophobicity are complementary to the substrate. The induced-fit model proposes that the enzyme undergoes a conformational change upon substrate binding, straining bonds in the substrate and stabilizing the transition state. Environmental factors affect enzyme function: temperature increases kinetic energy and collision frequency up to the point where hydrogen bonds and hydrophobic interactions in the protein denature; pH alters ionization states of amino acid R-groups in the active site; and substrate concentration affects reaction rate following Michaelis-Menten kinetics, with rate plateauing at Vmax when all active sites are saturated. Competitive inhibitors bind the active site (increasing apparent Km without affecting Vmax), while noncompetitive inhibitors bind allosteric sites (decreasing Vmax without changing Km). Allosteric regulation includes both activators and inhibitors, enabling feedback inhibition where the product of a metabolic pathway inhibits an enzyme early in the pathway.

Cellular Energy Currency: ATP

Adenosine triphosphate (ATP) is the primary energy currency of the cell. The three phosphate groups carry negative charges that repel each other; hydrolysis of the terminal phosphoanhydride bond releases 7.3 kcal/mol under standard conditions. The cell couples exergonic ATP hydrolysis to endergonic reactions through phosphorylation: a phosphate group is transferred to a substrate, increasing its potential energy and reactivity. ATP is continuously regenerated through cellular respiration and fermentation. The ATP/ADP ratio in a typical cell is about 10:1, maintaining a large free energy gradient.

Photosynthesis

Photosynthesis converts light energy into chemical energy stored in glucose. It occurs in two stages within the chloroplast: the light-dependent reactions in the thylakoid membrane and the Calvin Cycle in the stroma.

Light-Dependent Reactions: Photosystem II (P680) absorbs photons, exciting electrons that are passed through the electron transport chain. Water is split by the oxygen-evolving complex, releasing O2, H+ ions, and electrons. The energy released as electrons flow pumps H+ into the thylakoid lumen, creating a proton gradient. Photosystem I (P700) re-energizes electrons, which are transferred to NADP+ reductase, producing NADPH. ATP synthase uses the proton gradient to phosphorylate ADP (photophosphorylation). The net products are ATP, NADPH, and O2.

Calvin Cycle: Carbon fixation by RuBisCO attaches CO2 to ribulose-1,5-bisphosphate (RuBP), forming an unstable 6-carbon intermediate that splits into two molecules of 3-phosphoglycerate (3-PGA). ATP phosphorylates 3-PGA, and NADPH reduces it to glyceraldehyde-3-phosphate (G3P). For every 3 CO2 fixed, one net G3P is produced. RuBisCO can also react with O2 (photorespiration), which wastes energy and is favored in hot, dry conditions.

Cellular Respiration

Cellular respiration completely oxidizes glucose to CO2 and H2O, producing up to 36-38 ATP per glucose molecule.

Glycolysis occurs in the cytoplasm and does not require oxygen. One glucose (6C) is phosphorylated (consuming 2 ATP), then split into two G3P molecules. Each G3P is oxidized (NAD+ reduced to NADH), and substrate-level phosphorylation produces 4 ATP. Net yield: 2 ATP and 2 NADH per glucose.

Pyruvate Oxidation occurs in the mitochondrial matrix. Each pyruvate (3C) is oxidized, losing one carbon as CO2, and the remaining 2-carbon acetyl group binds CoA, forming acetyl-CoA. NAD+ is reduced to NADH.

Krebs Cycle occurs in the mitochondrial matrix. Acetyl-CoA (2C) combines with oxaloacetate (4C) to form citrate (6C). Through redox reactions, two carbons are released as CO2 per turn, generating 3 NADH, 1 FADH2, and 1 ATP. Two turns per glucose yield: 6 NADH, 2 FADH2, 2 ATP.

Oxidative Phosphorylation occurs across the inner mitochondrial membrane. NADH and FADH2 donate electrons to the electron transport chain. Protons are pumped from the matrix to the intermembrane space, creating a proton-motive force. Oxygen is the final electron acceptor, combining with H+ to form H2O. ATP synthase allows H+ to flow back, phosphorylating ADP. NADH yields approximately 2.5-3 ATP; FADH2 yields approximately 1.5-2 ATP.

Fermentation

When oxygen is unavailable, cells regenerate NAD+ through fermentation, allowing glycolysis to continue producing 2 ATP per glucose. In alcoholic fermentation (yeast), pyruvate is converted to acetaldehyde, then ethanol, releasing CO2. In lactic acid fermentation (animal muscle cells), pyruvate is reduced to lactate. Fermentation does not produce additional ATP beyond the 2 from glycolysis.

AP Exam Traps

Trap: Students claim plants undergo photosynthesis only and animals undergo respiration only. Correction: Plant cells perform both photosynthesis and cellular respiration. Plant cells contain both chloroplasts and mitochondria; photosynthesis produces glucose and O2, while respiration consumes glucose and O2 to generate ATP, even during daylight hours.

Trap: Students state that ATP is produced only in oxidative phosphorylation. Correction: ATP is also produced by substrate-level phosphorylation in glycolysis (net 2 ATP) and the Krebs cycle (2 ATP via GTP).

Trap: Students believe increasing light intensity always increases photosynthetic rate. Correction: Light intensity increases rate only up to the saturation point; beyond this, CO2 concentration or RuBisCO activity becomes the limiting factor.

Study Moves

  • Draw the complete chloroplast and mitochondrion, labeling every structure and tracing where every molecule enters and exits.
  • Build a comparison chart for glycolysis, pyruvate oxidation, Krebs cycle, and oxidative phosphorylation: location, inputs, outputs, ATP yield.
  • Practice explaining why cyanide kills: it blocks Complex IV, preventing oxygen from accepting electrons, collapsing the proton gradient, and halting ATP production.

    • Top 5 Concepts to Master

    1. 1Enzymes lower activation energy through induced-fit binding; temperature, pH, and inhibitors regulate activity and determine reaction rates.
    2. 2Photosynthesis converts light energy to chemical energy: light reactions (thylakoid) produce ATP, NADPH, and O2; the Calvin Cycle (stroma) fixes CO2 into G3P.
    3. 3Cellular respiration oxidizes glucose through glycolysis, pyruvate oxidation, the Krebs cycle, and oxidative phosphorylation to produce up to 36-38 ATP.
    4. 4Chemiosmosis couples electron transport to ATP synthesis in both chloroplasts and mitochondria via a proton gradient driving ATP synthase.
    5. 5Fermentation regenerates NAD+ anaerobically, allowing glycolysis to continue producing 2 ATP per glucose when oxygen is unavailable.

    Key Terms & Definitions

    Practice with Flashcards
    Enzyme

    A biological catalyst, typically a globular protein, that lowers the activation energy of a specific reaction by stabilizing the transition state through complementary active-site binding and induced fit.

    Activation Energy

    The minimum energy input required to initiate a chemical reaction by breaking existing bonds in the reactants before new bonds form in the products.

    Active Site

    The specific three-dimensional region of an enzyme where substrate molecules bind and catalysis occurs, determined by the folding of the polypeptide chain.

    Allosteric Regulation

    A form of enzyme regulation in which a molecule binds to a site other than the active site, causing a conformational change that either activates or inhibits enzyme activity.

    Competitive Inhibitor

    A molecule structurally similar to the substrate that binds reversibly to the active site, blocking substrate access and increasing apparent Km without changing Vmax.

    Noncompetitive Inhibitor

    A molecule that binds to an allosteric site, inducing a conformational change that reduces catalytic activity, decreasing Vmax without affecting Km.

    Feedback Inhibition

    A regulatory mechanism in which the end product of a metabolic pathway inhibits an enzyme early in the pathway, preventing overproduction.

    ATP

    The primary energy currency of the cell, consisting of adenine, ribose, and three phosphate groups; hydrolysis of the terminal phosphate bond releases energy for cellular work.

    Photosynthesis

    The process by which photoautotrophs convert light energy, CO2, and H2O into glucose and O2, occurring in two stages: light-dependent reactions and the Calvin Cycle.

    Light-Dependent Reactions

    The first stage of photosynthesis in the thylakoid membrane, where light energy is absorbed by photosystems, water is split, and ATP and NADPH are produced.

    Calvin Cycle

    The light-independent reactions in the stroma that fix CO2 into organic molecules using ATP and NADPH from the light reactions, producing G3P.

    RuBisCO

    Ribulose-1,5-bisphosphate carboxylase/oxygenase; the enzyme that catalyzes carbon fixation by attaching CO2 to RuBP. Also responsible for photorespiration when O2 competes with CO2.

    Glycolysis

    The anaerobic breakdown of glucose into two pyruvate molecules in the cytoplasm, producing a net 2 ATP and 2 NADH through substrate-level phosphorylation.

    Krebs Cycle

    A series of redox reactions in the mitochondrial matrix that completely oxidize acetyl-CoA to CO2, generating 3 NADH, 1 FADH2, and 1 ATP per turn.

    Oxidative Phosphorylation

    The production of ATP through chemiosmosis using the proton gradient generated by the electron transport chain, with oxygen as the final electron acceptor.

    Chemiosmosis

    The coupling of electron transport to ATP synthesis via a proton gradient across a membrane; protons flow through ATP synthase, driving phosphorylation of ADP.

    Electron Transport Chain

    A series of protein complexes in the inner mitochondrial membrane that transfer electrons from NADH and FADH2 to oxygen, pumping protons to create the proton-motive force.

    Fermentation

    An anaerobic pathway that regenerates NAD+ by reducing pyruvate to lactate or ethanol, allowing glycolysis to continue producing 2 ATP per glucose.

    Photorespiration

    A wasteful process where RuBisCO binds O2 instead of CO2, consuming ATP and releasing CO2 without producing sugar; favored in hot, dry conditions.

    Substrate-Level Phosphorylation

    The direct transfer of a phosphate group from a phosphorylated substrate to ADP, producing ATP without involving the electron transport chain.

    ⚠️ Common Misconceptions — Exam Traps

    ❌ ATP is only produced in mitochondria during oxidative phosphorylation.

    ✅ Correct: ATP is also produced by substrate-level phosphorylation in glycolysis (2 net ATP) and the Krebs cycle (2 ATP via GTP).

    ❌ Plants photosynthesize during the day and respire only at night.

    ✅ Correct: Plant cells respire continuously. During the day, photosynthesis typically exceeds respiration, so there is net O2 release and CO2 uptake.

    ❌ Fermentation produces additional ATP beyond glycolysis.

    ✅ Correct: Fermentation regenerates NAD+ so glycolysis can continue producing its net 2 ATP. No additional ATP is generated during fermentation itself.

    ❌ Increasing temperature always increases enzyme activity.

    ✅ Correct: Enzyme activity increases with temperature up to an optimum, beyond which the enzyme denatures as hydrogen bonds and hydrophobic interactions are disrupted.

    ❌ The Calvin Cycle does not require light at all.

    ✅ Correct: The Calvin Cycle depends on ATP and NADPH from the light-dependent reactions. If light is removed, these intermediates are depleted and the cycle stops.

    ❌ Oxygen is produced during the Calvin Cycle.

    ✅ Correct: O2 is produced only during the light-dependent reactions when water is split by photosystem II. The Calvin Cycle consumes CO2 and produces G3P.

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