The Krebs Cycle and Oxidative Phosphorylation Revision Notes | A Level AQA Biology

1. The Big Picture: Where Does All That ATP Come From?

Glycolysis splits glucose in the cytoplasm and nets a modest two ATP. Yet aerobic respiration can yield around 30-32 ATP per glucose molecule. The vast majority of that energy is harvested deep inside the mitochondrion — first in the Krebs cycle, then through oxidative phosphorylation. These two stages are the engine room of aerobic respiration.

Think of the Krebs cycle as a carbon-processing factory: it strips electrons from carbon compounds, loads them onto carrier molecules, and releases carbon dioxide as waste. Oxidative phosphorylation then uses those loaded carriers to drive a molecular turbine — ATP synthase — producing the bulk of the cell's ATP. Understanding how these two stages connect is the key to the whole topic.

2. Acetylcoenzyme A: The Entry Ticket to the Krebs Cycle

Before the Krebs cycle can begin, pyruvate from glycolysis is converted to acetylcoenzyme A (acetyl-CoA) during the link reaction inside the mitochondrial matrix. The two-carbon acetyl group is carried into the cycle by coenzyme A, which is then released and recycled — it acts purely as a carrier, not a substrate.

The condensation of acetyl-CoA with oxaloacetate is the entry point of the Krebs cycle. Citrate (six carbons) is the first product. From here, a series of oxidation-reduction reactions progressively strips carbons and electrons from the molecule, regenerating oxaloacetate at the end of each turn so the cycle can continue.

3. The Krebs Cycle: Oxidation, Reduced Coenzymes, and Carbon Dioxide

Once citrate forms, it undergoes a sequence of enzyme-controlled reactions in the mitochondrial matrix. Two carbon atoms are lost as carbon dioxide — this is decarboxylation. At the same time, hydrogen atoms are removed from intermediates — this is oxidation — and transferred to the coenzymes NAD and FAD, reducing them to NADH and FADH2.

One molecule of ATP is also produced directly per turn by substrate-level phosphorylation, where a phosphate group is transferred from a phosphorylated intermediate directly to ADP. After a full turn, oxaloacetate is regenerated, ready to accept another acetyl group. Because one glucose yields two pyruvate molecules (and therefore two acetyl-CoA), the cycle turns twice per glucose.

Notice that the Krebs cycle itself produces relatively little ATP directly. Its primary function is to generate large quantities of reduced coenzymes — NADH and FADH2 — which carry high-energy electrons to the next stage. The real ATP bonanza comes from oxidative phosphorylation.

4. Oxidative Phosphorylation: The Electron Transfer Chain and Chemiosmosis

The reduced coenzymes produced in the Krebs cycle (and the link reaction) now deliver their electrons to the electron transfer chain — a series of protein complexes embedded in the inner mitochondrial membrane. This is where the term 'oxidative phosphorylation' comes from: electrons are passed along the chain (oxidation of NADH and FADH2), and this drives the phosphorylation of ADP to ATP.

As electrons move down the chain from higher to lower energy levels, the energy released is used to pump protons (H⁺ ions) from the mitochondrial matrix across the inner membrane into the intermembrane space. This pumping is not driven by ATP, but by the energy released from electron transfer. The result is a steep electrochemical gradient — a high concentration of protons on one side of the membrane.

Picture the inner mitochondrial membrane as a dam. Protons are pumped to one side, building up pressure. ATP synthase acts like a turbine in that dam — protons flow back through it, down their gradient, and the energy of that flow spins the enzyme's rotor, synthesising ATP. Oxygen acts as the final electron acceptor at the end of the chain, combining with electrons and protons to form water. Without oxygen, the chain stalls and ATP synthesis stops.

Worked example: Tracing the Journey: From NADH to ATP

Describe, in sequence, how the electrons carried by one NADH molecule ultimately lead to ATP synthesis during oxidative phosphorylation.

1. NADH → NAD⁺ + H⁺ + 2e⁻ — NADH is oxidised at the first protein complex of the electron transfer chain (complex I), releasing its electrons and a proton. NAD⁺ is regenerated and returns to the Krebs cycle or link reaction to pick up more hydrogen.
2. Electrons move through protein complexes I → III → IV (via ubiquinone and cytochrome c) — Each transfer releases energy. This energy is used to pump H⁺ ions from the matrix into the intermembrane space at complexes I, III, and IV. Note: FADH₂, another reduced coenzyme produced in the Krebs cycle, enters the electron transfer chain via complex II (succinate dehydrogenase). FADH₂ donates electrons to ubiquinone, bypassing complex I, and as a result, fewer protons are pumped per FADH₂ than per NADH.
3. H⁺ concentration in intermembrane space >> H⁺ concentration in matrix — The inner mitochondrial membrane is impermeable to protons except through ATP synthase, so the gradient is maintained. This electrochemical gradient stores potential energy.
4. H⁺ flows from intermembrane space → matrix through ATP synthase — Protons move down their electrochemical gradient (chemiosmosis). The flow drives rotation of the ATP synthase rotor — this is the mechanical basis of ATP synthesis.
5. ADP + Pi → ATP (catalysed by ATP synthase) — The rotational energy of ATP synthase drives the condensation of ADP and inorganic phosphate. This is oxidative phosphorylation — phosphorylation of ADP driven by the oxidation of reduced coenzymes.
6. 4e⁻ + 4H⁺ + O₂ → 2H₂O — Oxygen is the terminal electron acceptor. Without it, electrons cannot leave the chain, the chain stalls, protons cannot be pumped, and ATP synthesis stops. This is why aerobic respiration requires oxygen.

Answer: NADH is oxidised at the electron transfer chain → electrons pass along protein complexes → energy pumps H⁺ into the intermembrane space → H⁺ flows back through ATP synthase (chemiosmosis) → ATP is synthesised → oxygen accepts the final electrons, forming water.

5. Other Respiratory Substrates: Lipids and Amino Acids

Glucose is not the only fuel the cell can respire. Lipids and amino acids can also be broken down and fed into the same aerobic pathway — a key point that AQA examiners test regularly. The entry points differ, but the destination is the same: the Krebs cycle.

Lipids are first hydrolysed to glycerol and fatty acids. Glycerol is converted to glycerate-3-phosphate (G3P), which enters glycolysis. Fatty acids undergo beta-oxidation, a process that repeatedly cleaves two-carbon units from the fatty acid chain, each unit forming an acetyl-CoA molecule. These acetyl-CoA molecules then enter the Krebs cycle directly — the same entry point as acetyl-CoA from glucose.

Amino acids, the building blocks of proteins, can also be used as respiratory substrates when carbohydrate and lipid supplies are low. They are first deaminated — the amino group is removed and excreted as urea. The remaining carbon skeleton is then converted into one of several Krebs cycle intermediates (such as pyruvate, acetyl-CoA, or oxaloacetate), depending on the specific amino acid, and enters the cycle at that point.

6. Exam Technique: Scoring Full Marks on Krebs Cycle and Oxidative Phosphorylation Questions

AQA questions on this topic tend to fall into a few predictable patterns. 'Describe' questions want a sequential account of what happens — no 'because', no explanation, just the events in order. 'Explain' questions want cause and effect: state what happens, then link it to the underlying mechanism using 'because' or 'therefore'.

For oxidative phosphorylation questions, the word 'chemiosmosis' is expected and will often earn a mark on its own. Similarly, naming 'ATP synthase' as the enzyme that catalyses ATP synthesis from ADP and Pi is a reliable mark-winner. Avoid vague phrases like 'energy is released' — specify that energy from electron transfer is used to pump protons, and that proton flow through ATP synthase drives ATP synthesis.

A common trap on 'explain why cyanide inhibits ATP synthesis' questions: students write that cyanide 'stops the Krebs cycle'. Cyanide blocks the electron transfer chain (specifically the final cytochrome oxidase complex), not the Krebs cycle directly. The Krebs cycle can still turn, but without the chain running, NADH and FADH2 cannot be reoxidised, so the cycle quickly stalls due to a lack of NAD⁺ and FAD. Make the chain the primary target in your answer.

Together, the Krebs cycle and oxidative phosphorylation account for the overwhelming majority of ATP produced in aerobic respiration — the Krebs cycle supplies the reduced coenzymes, and oxidative phosphorylation converts their stored energy into ATP through the chemiosmotic mechanism of ATP synthase. Mastering the link between these two stages, and being able to describe where alternative substrates enter the pathway, covers the core of what AQA requires from this topic.