Unit 9 Question Bank
In the exam: quote your lecturer's figures (3 and 2), but if asked to explain, give the proton-counting reason.TMU Lecture 9 Slide 27 · Harper's ch.13, p.131
Electrons pass down the respiratory chain in the inner mitochondrial membrane to their final reaction with oxygen to form water. The free energy released is used by Complexes I, III and IV, acting as proton pumps, to translocate H⁺ from the matrix into the intermembrane space; the resulting proton motive force drives a membrane-located ATP synthase which phosphorylates ADP.
It is the greatest quantitative source of high-energy phosphate in aerobic organisms.Harper's ch.13, pp.130–131
Its components are organised as four protein-lipid complexes spanning the membrane: I NADH-Q oxidoreductase, II succinate-Q reductase, III Q-cytochrome c oxidoreductase and IV cytochrome c oxidase. Ubiquinone (Q₁₀) and cytochrome c are the mobile components connecting the fixed complexes.Harper's ch.13, pp.126–130
The resulting proton motive force — an electrochemical potential difference, negative on the matrix side — drives the mechanism of ATP synthesis. Complexes I, III and IV act as proton pumps, and because the inner membrane is impermeable to protons they accumulate in the intermembrane space.Harper's ch.13, p.130
⚠️ Your sources disagree. TMU slide 16 gives P:O = 3 for substrates oxidised via an NAD-linked dehydrogenase and P:O = 2 via a flavoprotein-linked dehydrogenase. Harper's p.131 gives 2.5 and 1.5, because roughly 10 protons are pumped per NADH while about 4 are required per ATP exported, which does not divide into a whole number. Your own slide 27 concedes “possibly 2.5”.
Answer with the lecturer's figures; explain with the proton count.Harper's ch.13, p.131 vs TMU Lecture 9 Slides 16, 27
This arises because oxidation and phosphorylation are tightly coupled: oxidation cannot proceed via the respiratory chain without concomitant phosphorylation of ADP. Most cells in the resting state are in state 4, in which respiration is ADP-limited; when work is performed ATP is converted to ADP, allowing more respiration, which replenishes ATP.Harper's ch.13, pp.131–132
Uncouplers are toxic in vivo, causing respiration to become uncontrolled because its rate is no longer limited by the concentration of ADP or Pi; the energy is released as heat. The most frequently used is 2,4-dinitrophenol (DNP).
Contrast oligomycin, which blocks H⁺ conduction through F₀ and therefore stops both oxidation and phosphorylation.Harper's ch.13, pp.132–133
In the complete oxidation of glucose it accounts for the net two high-energy phosphates of glycolysis (at phosphoglycerate kinase and pyruvate kinase) and the phosphate generated in the citric acid cycle during the conversion of succinyl-CoA to succinate. All the remainder — the large majority — arises from oxidative phosphorylation at the respiratory chain level.Harper's ch.13, p.131
Location and purpose
The respiratory chain is a series of redox carriers in the inner mitochondrial membrane which collect and transport reducing equivalents (2H) to their final reaction with oxygen to form water, coupling the free energy liberated to the generation of ATP. The reducing equivalents come chiefly from β-oxidation and the citric acid cycle in the matrix. The inner membrane is selectively permeable and thrown into folds, or cristae; it also concentrates the phospholipid cardiolipin.
The carriers
NAD⁺ collects reducing equivalents from most dehydrogenases. Flavoproteins (FMN, FAD) follow — NADH dehydrogenase is a metalloflavoprotein containing FeS and FMN. Ubiquinone (Q₁₀) and cytochrome c are the mobile components; cytochrome c is the only soluble cytochrome. Iron-sulfur proteins in Complexes I, II and III carry out single-electron transfers, the iron cycling between Fe²⁺ and Fe³⁺.
The four complexes
| Complex | Name | Function | H⁺ pumped |
|---|---|---|---|
| I | NADH-Q oxidoreductase | NADH → FMN → Fe-S centres → Q | 4 |
| II | Succinate-Q reductase | FADH₂ from succinate → fumarate; electrons via Fe-S to Q | 0 |
| III | Q-cytochrome c oxidoreductase | QH₂ → cytochrome c, via the Q cycle using cyt c₁, bL, bH and a Rieske Fe-S | 4 |
| IV | Cytochrome c oxidase | Cytochrome c → O₂ → 2H₂O, via haems a and a₃ and CuA/CuB | 2 |
Complex IV catalyses the only irreversible reaction in the chain, which gives direction to the whole process; it has a very high affinity for oxygen and holds O₂ bound until fully reduced, minimising release of superoxide and peroxide.
The chemiosmotic theory
Peter Mitchell (1961) postulated that the energy of oxidation is coupled to the translocation of protons from the matrix to the intermembrane space. Complexes I, III and IV act as proton pumps; because the inner membrane is impermeable to protons, they accumulate, creating a proton motive force — an electrochemical potential difference, negative on the matrix side.
ATP synthase
The proton motive force drives a membrane-located ATP synthase. F₀ spans the membrane and forms the proton channel; proton flow causes F₀ and the attached γ-subunit to rotate. F₁, a ball of three α- and three β-subunits, projects into the matrix and is fixed. By the binding change mechanism, rotation of the γ-subunit squeezes each β-subunit in turn, changing its conformation from one that binds ATP tightly to one that releases ATP and binds ADP and Pi. Three ATP are generated per revolution.
Yield
For substrate oxidised via Complexes I, III and IV the P:O ratio is 3 by the lecture figures (2.5 by current Harper's); via Complexes II, III and IV it is 2 (Harper's 1.5). The difference arises because electrons entering at Complex II bypass Complex I and its four protons. Either way, the respiratory chain accounts for the large majority of ATP formed during catabolism, the remainder arising from substrate-level phosphorylation in glycolysis and the citric acid cycle.
Control
Because oxidation and phosphorylation are tightly coupled, the rate of respiration is controlled by the availability of ADP — respiratory control. Energy not captured as high-energy phosphate is liberated as heat, which keeps the system far from equilibrium and contributes to maintenance of body temperature.
The classification
Agents affecting oxidative phosphorylation are classified as inhibitors of the respiratory chain, inhibitors of oxidative phosphorylation, and uncouplers of oxidative phosphorylation. The distinction between the last two is the most examinable point in the topic.
1 · Inhibitors of the respiratory chain
| Agent | Site |
|---|---|
| Barbiturates (amobarbital) | Inhibit NAD-linked dehydrogenases by blocking transfer from FeS to Q — Complex I. At sufficient dosage they are fatal in vivo |
| Antimycin A, dimercaprol (BAL) | Between cytochrome b and cytochrome c — Complex III |
| H₂S, carbon monoxide, cyanide | Cytochrome oxidase (Complex IV); can totally arrest respiration |
| Malonate | Competitive inhibitor of succinate dehydrogenase — Complex II |
The classic poisons are so lethal because Complex IV catalyses the chain's only irreversible reaction: there is no bypass.
2 · Inhibitors of oxidative phosphorylation
Oligomycin completely blocks oxidation and phosphorylation by acting on a step in phosphorylation — specifically it blocks conduction of H⁺ through F₀.
Atractyloside inhibits the transporter of ADP into and ATP out of the mitochondrion — the adenine nucleotide transporter. Since respiration is controlled by ADP availability, blocking its entry is as effective as poisoning a complex.
3 · Uncouplers
Uncouplers dissociate oxidation in the respiratory chain from phosphorylation by allowing leakage of H⁺ across the membrane, collapsing the electrochemical proton gradient. They are toxic in vivo, causing respiration to become uncontrolled, since its rate is no longer limited by the concentration of ADP or Pi. The commonest is 2,4-dinitrophenol (DNP).
The crucial contrast
Both oligomycin and an uncoupler abolish ATP synthesis, but they have opposite effects on oxidation, and the reason is coupling:
- Oligomycin plugs the F₀ channel. Protons cannot return to the matrix, the gradient builds until the pumps can no longer work against it, and oxidation stops as well. Blocking the turbine backs up the whole dam.
- An uncoupler lets protons return without passing through ATP synthase. The gradient never builds, so the pumps run freely: oxidation accelerates and becomes uncontrolled while phosphorylation ceases, and the energy emerges as heat.
Clinical relevance
Cyanide and carbon monoxide kill by disrupting the haem proteins cytochrome oxidase and haemoglobin respectively. DNP was marketed as a slimming agent — fuel is burned without ATP production — but patients died of hyperthermia, since respiration was no longer ADP-limited and all the energy appeared as heat. The physiological version of the same mechanism operates in brown adipose tissue, which uncouples deliberately for thermogenesis.