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What is an enzyme?
Answer: A biological catalyst (usually a protein, sometimes RNA) that speeds up a chemical reaction by lowering its activation energy, without being consumed or permanently changed itself.
RNA enzymes are called ribozymes (e.g., in the ribosome, RNA splicing).
What is the active site of an enzyme?
Answer: The specific region of the enzyme, formed by its 3D folded shape, where the substrate binds and the reaction is catalyzed.
Shape depends on the enzyme's tertiary (and sometimes quaternary) structure.
Lock-and-key vs. induced-fit model of enzyme binding — difference?
Answer: Lock-and-key: active site shape exactly matches substrate shape, like a rigid lock. Induced fit: the active site changes shape slightly as it binds the substrate, molding around it for a tighter fit.
Induced fit is the currently accepted model and explains why enzymes can also bind closely related substrates.
What is a cofactor vs. a coenzyme?
Answer: Cofactor: a non-protein helper required for enzyme activity, often an inorganic ion (e.g., Mg²⁺, Zn²⁺). Coenzyme: an organic cofactor, often derived from a vitamin (e.g., NAD⁺, FAD, coenzyme A).
Without its required cofactor/coenzyme, many enzymes are inactive.
What is denaturation?
Answer: The loss of an enzyme's (or protein's) native 3D shape, usually due to extreme temperature or pH, which destroys the active site's function.
Denaturation is often irreversible and permanently inactivates the enzyme.
What is activation energy (Ea)?
Answer: The minimum amount of energy required for reactants to reach the transition state and proceed to products.
Enzymes speed up reactions by lowering Ea, not by changing the overall free energy change (ΔG) of the reaction.
Compare the energy diagram of a catalyzed vs. uncatalyzed reaction.
Answer: The catalyzed reaction reaches a much lower energy peak (transition state) than the uncatalyzed reaction, though both start and end at the same free energy levels.
Example: an uncatalyzed reaction may need to climb to 90 energy units, while the enzyme-catalyzed path only climbs to 50 — same reactant and product energy, lower peak.
Exergonic vs. endergonic reaction — define each.
Answer: Exergonic: releases free energy (ΔG < 0), spontaneous, products have less energy than reactants (e.g., cellular respiration). Endergonic: requires net input of free energy (ΔG > 0), nonspontaneous, products have more energy than reactants (e.g., photosynthesis).
ATP hydrolysis (exergonic) is often coupled to endergonic reactions to drive them forward.
How does temperature affect enzyme activity? Describe the general shape of the graph.
Answer: Enzyme activity rises with temperature up to an optimum (often ~37°C for human enzymes), then falls sharply as higher temperatures denature the enzyme — a bell-shaped curve.
Below the optimum, molecules move slower and collide less often; above it, the enzyme loses its functional shape.
How does pH affect enzyme activity?
Answer: Each enzyme has an optimal pH range where activity is maximal; activity drops off (bell-shaped curve) above or below this range because pH extremes disrupt the ionic/hydrogen bonds maintaining the enzyme's shape.
Optimal pH varies by location: pepsin (stomach) ~pH 2, trypsin (small intestine) ~pH 8.
How does substrate concentration affect reaction rate, with and without enzyme?
Answer: With enzyme: rate increases with substrate concentration, then plateaus at Vmax once all active sites are saturated. Without enzyme: rate increases much more slowly and roughly linearly, with no saturation plateau in the same range.
At saturation, adding more substrate has no effect unless more enzyme is added.
Competitive inhibitor vs. noncompetitive (allosteric) inhibitor — how do they differ?
Answer: Competitive inhibitor: binds directly to the active site, competing with the substrate — effect can be overcome by adding more substrate. Noncompetitive inhibitor: binds to an allosteric site elsewhere, changing the enzyme's shape so the active site no longer works — adding more substrate does not reverse it.
On a rate-vs-substrate graph: competitive inhibition raises the substrate concentration needed to reach the same rate (Km increases, Vmax unchanged); noncompetitive inhibition lowers Vmax itself.
What is allosteric regulation / feedback inhibition?
Answer: Binding of a regulatory molecule (often a pathway's end product) to an allosteric site changes enzyme shape, turning it on (activator) or off (inhibitor). Feedback inhibition: the final product of a metabolic pathway inhibits an early enzyme in that same pathway, shutting it down once enough product accumulates.
This prevents the cell from wasting resources overproducing a molecule it already has enough of.
What is the structure of ATP?
Answer: Adenosine triphosphate: an adenine base + a ribose sugar + three phosphate groups linked by two high-energy phosphoanhydride bonds.
The negatively charged phosphates repel each other, storing potential energy that is released when a phosphate bond is broken.
Write the hydrolysis reaction of ATP and explain why it releases energy.
Answer: ATP + H2O → ADP + Pi + energy. Energy is released because removing a phosphate relieves electrostatic repulsion between the negatively charged phosphate groups, and the products are more stable (lower free energy) than ATP.
This released energy and/or the transferred phosphate (phosphorylation) powers most endergonic cellular work.
How does the cell use ATP to drive unfavorable (endergonic) reactions?
Answer: Via energy coupling: the exergonic hydrolysis of ATP is paired with an endergonic reaction, often by transferring ATP's phosphate group to a substrate (phosphorylation), making the combined reaction spontaneous overall.
Example: phosphorylating a transport protein changes its shape to actively pump a molecule across a membrane.
Write the overall (summary) equation for photosynthesis.
Answer: 6CO2 + 6H2O + light energy → C6H12O6 + 6O2
This is the reverse, in net atoms, of cellular respiration's overall equation.
Where in the chloroplast do the light reactions and the Calvin cycle occur?
Answer: Light reactions occur in the thylakoid membrane (organized into stacks called grana). The Calvin cycle occurs in the stroma, the fluid surrounding the thylakoids.
The thylakoid lumen (interior space) is where H+ ions accumulate during chemiosmosis.
What are the two main stages of photosynthesis, and what does each produce?
Answer: 1) Light reactions (thylakoid): convert light energy into ATP and NADPH, and release O2 from water. 2) Calvin cycle (stroma): uses ATP and NADPH to fix CO2 into G3P/sugar.
The Calvin cycle depends on the ATP and NADPH supplied by the light reactions.
What happens at Photosystem II (PSII) during the light reactions?
Answer: Light excites electrons in chlorophyll; water is split (photolysis) to replace the lost electrons, releasing O2 and H+; the excited electrons pass into the electron transport chain.
PSII is the source of all the O2 released by photosynthesis.
What happens at Photosystem I (PSI) during the light reactions?
Answer: Light re-excites electrons (arriving from the ETC after PSII); these high-energy electrons are passed via ferredoxin to NADP+ reductase, which reduces NADP+ to NADPH.
NADPH carries the electrons/energy to the Calvin cycle.
Describe chemiosmosis in the light reactions.
Answer: The electron transport chain pumps H+ into the thylakoid lumen, creating a proton gradient. H+ flows back down its gradient through ATP synthase into the stroma, driving the synthesis of ATP (photophosphorylation).
This is mechanistically identical to chemiosmosis in oxidative phosphorylation, just across the thylakoid membrane instead of the inner mitochondrial membrane.
List the inputs and outputs of the light reactions.
Answer: Inputs: light energy, H2O, ADP + Pi, NADP+. Outputs: O2, ATP, NADPH.
ATP and NADPH then feed into the Calvin cycle.
List the inputs and outputs of the Calvin cycle.
Answer: Inputs: CO2, ATP, NADPH. Outputs: G3P (glyceraldehyde-3-phosphate, used to build glucose), ADP + Pi, NADP+.
ADP and NADP+ are recycled back to the light reactions to be reused.
What enzyme fixes CO2 in the Calvin cycle, and what are the three phases of the cycle?
Answer: RuBisCO fixes CO2 onto RuBP (carbon fixation). The three phases are: (1) carbon fixation, (2) reduction (using ATP and NADPH to form G3P), and (3) regeneration of RuBP (using more ATP).
RuBisCO is considered the most abundant enzyme on Earth and is relatively slow/inefficient, which is why plants need many copies of it.
Write the overall (summary) equation for cellular respiration.
Answer: C6H12O6 + 6O2 → 6CO2 + 6H2O + energy (ATP)
This is an exergonic, catabolic reaction that releases the energy stored in glucose.
What are the four stages of aerobic cellular respiration, in order?
Answer: 1) Glycolysis (cytoplasm) 2) Pyruvate oxidation (mitochondrial matrix) 3) Krebs/citric acid cycle (mitochondrial matrix) 4) Oxidative phosphorylation — electron transport chain + chemiosmosis (inner mitochondrial membrane).
Only glycolysis does not require a mitochondrion or oxygen.
Where does glycolysis occur, and what are its net products per glucose?
Answer: Occurs in the cytoplasm. Net products per glucose: 2 ATP (net; 4 made, 2 invested), 2 NADH, and 2 pyruvate molecules.
Glycolysis does not require oxygen, so it occurs in both aerobic and anaerobic conditions.
What happens during pyruvate oxidation?
Answer: In the mitochondrial matrix, each pyruvate (from glycolysis) loses a carbon as CO2 and is oxidized to form acetyl CoA, generating 1 NADH per pyruvate.
Since glycolysis makes 2 pyruvate per glucose, this step happens twice per glucose, yielding 2 NADH and 2 CO2 total.
What are the products of one turn of the Krebs (citric acid) cycle, from one acetyl CoA?
Answer: Per acetyl CoA: 3 NADH, 1 FADH2, 1 ATP (via GTP), and 2 CO2 released.
Since there are 2 acetyl CoA per glucose, the cycle turns twice, doubling these totals (6 NADH, 2 FADH2, 2 ATP, 4 CO2).
What happens during oxidative phosphorylation?
Answer: NADH and FADH2 donate electrons to the electron transport chain (inner mitochondrial membrane); as electrons move down the chain, energy is used to pump H+ into the intermembrane space, creating a gradient. H+ flows back through ATP synthase (chemiosmosis), producing most of the cell's ATP. Oxygen is the final electron acceptor, combining with electrons and H+ to form water.
Without oxygen as the final acceptor, electrons back up and the ETC stops, which is why oxidative phosphorylation cannot occur anaerobically.
Approximately how much ATP comes from each stage of cellular respiration per glucose molecule?
Answer: Glycolysis: ~2 ATP (substrate-level). Krebs cycle: ~2 ATP (substrate-level). Oxidative phosphorylation (from all the NADH/FADH2 generated): the large majority of total ATP, historically cited as ~34 ATP (modern estimates are lower, ~26–28), giving an approximate total of 30–32+ ATP per glucose.
The electron transport chain/chemiosmosis produces far more ATP than substrate-level phosphorylation in glycolysis or the Krebs cycle.
Why is fermentation necessary, and what does it accomplish?
Answer: Fermentation regenerates NAD+ from NADH without using the electron transport chain, allowing glycolysis to continue producing ATP when oxygen is unavailable.
Glycolysis requires a steady supply of NAD+ to keep running; without regeneration, NADH would accumulate and glycolysis would halt.
Compare lactic acid fermentation and alcoholic fermentation.
Answer: Lactic acid fermentation: pyruvate is directly reduced to lactate (lactic acid), regenerating NAD+ — occurs in muscle cells and some bacteria. Alcoholic fermentation: pyruvate is converted to acetaldehyde (releasing CO2), which is then reduced to ethanol, regenerating NAD+ — occurs in yeast and some bacteria.
Both pathways produce no additional ATP beyond glycolysis's net 2 ATP; their sole purpose is to regenerate NAD+.
Compare total ATP yield: fermentation vs. complete aerobic respiration, per glucose.
Answer: Fermentation yields only the 2 net ATP from glycolysis. Aerobic respiration yields roughly 30–32+ ATP total, because it can also run pyruvate oxidation, the Krebs cycle, and oxidative phosphorylation.
This illustrates why aerobic respiration is far more energy-efficient than fermentation.
Compare photosynthesis and cellular respiration: reactants/products and energy flow.
Answer: Photosynthesis: endergonic, converts light energy into chemical energy; CO2 + H2O → glucose + O2; occurs in chloroplasts. Cellular respiration: exergonic, releases chemical energy from glucose; glucose + O2 → CO2 + H2O + ATP; occurs in cytoplasm and mitochondria. The outputs of one process are the inputs of the other.
Both use electron transport chains and chemiosmosis to make ATP, but in different membranes (thylakoid vs. inner mitochondrial membrane) and for opposite overall purposes.
On the AP exam, how should you approach a graph showing enzyme reaction rate under different conditions (e.g., temperature, pH, inhibitor presence)?
Answer: Identify the independent variable (x-axis, what was manipulated) and dependent variable (y-axis, reaction rate/product formed); describe the trend in words (e.g., 'rate increases then plateaus'); connect the trend to the underlying mechanism (e.g., saturation of active sites, denaturation, inhibitor binding) rather than just restating the data.
AP free-response questions award points for correctly describing trends AND explaining the biological reason behind them.
What is a common AP exam strategy for comparing two experimental groups (e.g., enzyme with vs. without inhibitor, plant in light vs. dark)?
Answer: State which group had the higher/lower value, cite the specific data (numbers or trend) from the graph/table, and explain the mechanistic reason for the difference using correct vocabulary (e.g., competitive inhibition raises Km, or without light there is no ATP/NADPH to run the Calvin cycle).
Vague answers without citing specific data or mechanism lose points on AP free-response scoring.
How should you describe 'energy flow' through metabolic pathways on the AP exam?
Answer: Describe the sequence of energy carriers and transformations: e.g., light energy → excited electrons → ETC → proton gradient → ATP (chemiosmosis); or chemical energy in glucose → electron carriers (NADH/FADH2) → ETC → proton gradient → ATP. Emphasize that energy is transferred/transformed, not created, and that ATP is the usable energy currency for cellular work.
Many FRQs ask students to trace energy or electron flow step-by-step through a pathway diagram.
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