Cellular Energetics
Unit 3 of AP Biology, worth 12–16% of the exam. 14 questions below, each with the working. Every answer was checked by a second pass before it was published.
Enzyme structure, catalysis and regulation; energy and coupled reactions; photosynthesis; cellular respiration and fermentation.
How this unit is tested
Start by anchoring everything to two ideas that repeat across this whole unit: free energy (ΔG) determines whether a reaction runs on its own, and cells couple exergonic reactions to endergonic ones (almost always via ATP) to get work done. Once that's solid, layer enzymes on top — they change rate (by lowering activation energy) but never change ΔG or equilibrium, and their regulation (competitive/noncompetitive inhibition, allosteric control, feedback inhibition) is tested constantly through Vmax/Km graph reasoning, so practice reading those graphs rather than memorizing definitions alone.
For photosynthesis and respiration, don't memorize the pathways as lists of names — trace three things through each: where carbon goes, where electrons go, and where the proton gradient forms. Photosynthesis pulls electrons from water and carbon from CO2 to build sugar; respiration reverses this, pulling electrons from sugar and depositing carbon as CO2. In both, electron transport chains build a proton gradient across a membrane, and chemiosmosis (ATP synthase) turns that gradient into ATP — this parallel structure is the single most exam-relevant insight in the unit.
Expect experimental and graph-based reasoning: the AP exam rarely just asks 'define enzyme' — it gives you inhibitor data, oxygen consumption graphs, or a poisoned pathway and asks you to predict what happens upstream or downstream. Practice explaining mechanism (why), not just stating the fact (what), since free-response scoring rewards causal reasoning.
Finally, resist memorizing exact ATP yield numbers (36 vs 38, etc.) — the current framework cares about relative comparisons (aerobic yields far more ATP than fermentation, and why), not precise counts.
What you have to know
Enzymes and Activation Energy
Enzymes are biological catalysts that lower the activation energy (Ea) required to reach the transition state, increasing reaction rate, but they do not change the free energy change (ΔG) or equilibrium of the reaction.
Free Energy and Spontaneity
A negative ΔG (exergonic) reaction releases free energy and proceeds spontaneously; a positive ΔG (endergonic) reaction requires energy input. Cells drive endergonic reactions by coupling them to exergonic ones.
Energy Coupling via ATP
Hydrolysis of ATP to ADP + Pi is exergonic; cells couple this reaction to endergonic processes (transport, synthesis, mechanical work), often by transferring the phosphate group to a substrate to activate it.
Redox Reactions in Metabolism
Oxidation is the loss of electrons and reduction is the gain of electrons (LEO the lion says GER). Electron carriers NAD+/NADH, NADP+/NADPH, and FAD/FADH2 shuttle electrons between redox reactions in respiration and photosynthesis.
Chemiosmosis
Electron transport chains use redox reactions to pump protons across a membrane, creating an electrochemical gradient; ATP synthase harnesses the energy of protons flowing back down this gradient to phosphorylate ADP into ATP.
14 practice questions
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A researcher adds a molecule to an enzymatic reaction. Data show the reaction's Vmax decreases while Km stays the same. What type of regulation does this molecule most likely represent?
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Answer. A noncompetitive (allosteric) inhibitor.
Noncompetitive inhibitors bind a site distinct from the active site, changing the enzyme's shape and reducing its maximum catalytic capacity (Vmax) regardless of substrate concentration. Because it doesn't compete for the active site, adding more substrate cannot restore full activity, so Km (substrate affinity) is unaffected. -
Explain, in terms of activation energy and free energy change (ΔG), why enzymes speed up reactions without changing whether a reaction is spontaneous.
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Answer. Enzymes lower the activation energy needed to reach the transition state, increasing the rate at which the reaction proceeds, but they do not alter the ΔG of the reaction.
Rate and spontaneity are separate properties: spontaneity is set by the intrinsic free energy difference between reactants and products, which enzymes cannot change. Enzymes only reduce the energy barrier (Ea) that must be overcome, so a reaction that was already spontaneous just happens faster, and a non-spontaneous one still won't proceed on its own. -
A cell uses ATP hydrolysis to phosphorylate a membrane transport protein, allowing it to pump ions against their concentration gradient. What term describes this linking of an exergonic process to an endergonic one?
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Answer. Energy coupling (a coupled reaction).
ATP hydrolysis (exergonic, releases free energy) is coupled to the endergonic process of pumping ions uphill against their gradient. The phosphate group transferred to the transport protein raises its energy state, allowing the otherwise unfavorable transport to proceed. -
Which statement correctly applies the second law of thermodynamics to a food chain?
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Answer. Some energy is lost as heat at each energy transformation, so entropy of the universe increases.
The second law states that every energy transformation increases the entropy of the universe, typically as unusable heat. This is why energy transfer efficiency between trophic levels is far from 100%, and why food chains lose usable energy at each step. -
Explain where the light-dependent reactions and the Calvin cycle occur within a chloroplast, and why the site of each is important.
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Answer. Light-dependent reactions occur in the thylakoid membranes; the Calvin cycle occurs in the stroma.
The thylakoid membrane houses photosystems, the electron transport chain, and ATP synthase needed to convert light energy into ATP and NADPH via chemiosmosis. The stroma, surrounding the thylakoids, contains the enzymes (like rubisco) that use that ATP and NADPH to fix CO2 into sugar during the Calvin cycle. -
During the light reactions, which sequence correctly traces the path of electrons under noncyclic (linear) electron flow?
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Answer. Water -> Photosystem II -> electron transport chain -> Photosystem I -> NADPH.
Water is split at Photosystem II to replace electrons excited by light and passed down an electron transport chain (pumping protons for chemiosmosis) to Photosystem I, where they are re-excited by light again and ultimately used to reduce NADP+ to NADPH. -
If CO2 supply to a photosynthesizing plant is suddenly cut off while light continues to shine, predict what happens to the relative levels of RuBP and G3P in the Calvin cycle, and explain why.
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Answer. RuBP levels rise and G3P levels fall.
Carbon fixation (RuBP + CO2 -> two molecules of 3-PGA, later reduced to G3P) stops without CO2, so RuBP is no longer being consumed but continues to be regenerated from existing G3P. As a result, G3P is depleted (used up regenerating RuBP without replenishment) while RuBP accumulates. -
Glycolysis converts one glucose molecule into two pyruvate molecules. If 2 ATP are invested and 4 ATP are produced by substrate-level phosphorylation, what is the net ATP yield per glucose, and what other energy-carrying molecule is also produced?
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Answer. Net yield is 2 ATP per glucose, plus 2 NADH.
Glycolysis invests 2 ATP early on to phosphorylate glucose intermediates, then produces 4 ATP later via substrate-level phosphorylation, giving a net gain of 2 ATP. Along the way, 2 NAD+ are reduced to 2 NADH, which can later feed electrons into the electron transport chain if oxygen is available. -
In eukaryotic cells, where do the citric acid (Krebs) cycle and the electron transport chain take place, respectively?
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Answer. Mitochondrial matrix; inner mitochondrial membrane.
The citric acid cycle's enzymes are dissolved in the mitochondrial matrix, where they oxidize acetyl-CoA and generate NADH, FADH2, and some ATP. The electron transport chain proteins are embedded in the inner mitochondrial membrane, where they use those electron carriers to build a proton gradient across that same membrane. -
Cyanide blocks the last protein complex of the electron transport chain. Predict the immediate effect on ATP production by chemiosmosis and explain why glycolysis alone cannot compensate long term without fermentation.
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Answer. Chemiosmotic ATP production stops because electrons can no longer be passed to oxygen, collapsing the proton gradient; without fermentation, glycolysis would also halt from lack of available NAD+.
With the ETC blocked, electrons back up and the chain stops pumping protons, so ATP synthase has no gradient to use. NADH from glycolysis cannot be reoxidized to NAD+ through the ETC, and without NAD+ regenerated (as fermentation would do), the oxidation step of glycolysis stalls, cutting off even that small ATP source. -
Compare the end products of lactic acid fermentation and alcoholic fermentation, and explain the shared purpose both serve for glycolysis.
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Answer. Lactic acid fermentation reduces pyruvate to lactate; alcoholic fermentation converts pyruvate to ethanol and CO2. Both regenerate NAD+ so glycolysis can continue.
In both pathways, NADH produced during glycolysis donates its electrons back to pyruvate or its derivative, restoring the pool of NAD+ needed for the oxidation step of glycolysis (G3P dehydrogenase reaction). This lets ATP production by substrate-level phosphorylation continue even without oxygen, despite yielding far less ATP than aerobic respiration. -
A plant's rate of photosynthesis increases with light intensity up to a point, after which further increases in light intensity have no effect. What most likely limits the rate at high light intensity?
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Answer. Availability of CO2 or the rate of the Calvin cycle enzymes.
Once light is no longer limiting, the light-independent reactions become the bottleneck: rubisco and other Calvin cycle enzymes can only fix CO2 at a certain maximum rate, so photosynthesis plateaus even if more light energy is supplied, unless CO2 concentration is also increased. -
In both mitochondria and chloroplasts, ATP synthase produces ATP as protons flow down their gradient into a specific compartment. Identify that compartment in each organelle.
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Answer. In mitochondria, protons flow from the intermembrane space into the matrix; in chloroplasts, protons flow from the thylakoid lumen into the stroma.
In both organelles, an electron transport chain pumps protons into a confined compartment (intermembrane space or thylakoid lumen), building up a high concentration there. ATP synthase then allows protons to flow back down this gradient into the larger compartment (matrix or stroma), and this flow powers ATP synthesis. -
In a metabolic pathway A -> B -> C -> D, the final product D binds to the first enzyme in the pathway and inhibits its activity. Name this regulatory mechanism and explain its adaptive significance.
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Answer. Feedback inhibition, a form of allosteric regulation.
When D accumulates, it binds an allosteric site on the first enzyme, reducing the pathway's activity and preventing wasteful overproduction of D. This self-limiting loop lets the cell conserve energy and raw materials, only running the pathway when more D is actually needed.
What people get wrong
- Thinking enzymes change whether a reaction is spontaneous. Fix: enzymes only lower activation energy and speed up the approach to equilibrium; ΔG and equilibrium position are unchanged.
- Mixing up competitive and noncompetitive inhibitor graphs. Fix: memorize that competitive inhibition raises Km only (Vmax unchanged, overcome by more substrate); noncompetitive/allosteric inhibition lowers Vmax only (Km unchanged, cannot be overcome by more substrate).
- Swapping the locations of the light reactions and the Calvin cycle. Fix: light reactions happen in the thylakoid membrane (photosystems, ETC, chemiosmosis); the Calvin cycle happens in the stroma (carbon fixation, reduction, RuBP regeneration).
- Assuming fermentation replaces cellular respiration entirely when oxygen is absent. Fix: fermentation only regenerates NAD+ so glycolysis (which always occurs in the cytoplasm) can continue; it does not run the Krebs cycle or ETC.
- Treating photosynthesis and respiration as belonging to different organisms. Fix: plants perform both — they photosynthesize to build sugar and respire (in mitochondria) to extract usable energy from that sugar, just like animals.
- Trying to memorize exact ATP yield numbers (e.g., 36 vs 38 ATP). Fix: focus on the relative comparison — aerobic respiration yields far more ATP per glucose than fermentation because of the ETC and chemiosmosis — the AP exam does not require an exact count.
Drill this unit until it sticks
These questions come back on a schedule built from what you get wrong, alongside the rest of AP Biology. Free, and no account needed to start.