Mitochondria & Electron Transport Chain
This interactive diagram covers 15 structures of the mitochondrion and the electron transport chain (AP Biology Unit 3). The upper section shows the overall mitochondrial architecture; the lower zoom reveals the five protein complexes of the inner membrane in order of electron flow: Complex I → CoQ → Complex III → Cytochrome c → Complex IV → ATP synthase, with Complex II shown as the alternate FADH₂ entry point.
Outer Membrane
A smooth, continuous bilayer enclosing the entire mitochondrion. Porins (VDACs) make it freely permeable to molecules up to ~5 kDa. Larger proteins cross via the TOM (Translocase of the Outer Membrane) complex.
Inner Membrane
A highly impermeable bilayer containing no porins — sealed to all ions including H⁺. Houses all five ETC complexes and ATP synthase. Contains the unique phospholipid cardiolipin and has an unusually high protein-to-lipid ratio (~80% protein). The site of oxidative phosphorylation.
Cristae
Extensive infoldings of the inner membrane that increase its surface area several-fold, concentrating the ETC complexes. Cristae shape is maintained by MICOS complexes and OPA1; their density correlates with a cell's energy demand.
Matrix
The aqueous interior enclosed by the inner membrane. Houses the citric acid cycle enzymes, pyruvate dehydrogenase, fatty acid oxidation enzymes, mitochondrial DNA (circular, ~16,569 bp), and mitochondrial ribosomes. NADH and FADH₂ are produced here and feed electrons into the ETC.
Intermembrane Space
The compartment between the outer and inner membranes. Small solutes (including H⁺) equilibrate with the cytoplasm via outer membrane porins, but the ETC pumps additional H⁺ into the IMS from the matrix, establishing the proton-motive force. The IMS is also the compartment from which cytochrome c is released during apoptosis.
Complex I (NADH dehydrogenase)
The largest ETC complex (~45 subunits). Oxidizes NADH → NAD⁺ in the matrix and reduces CoQ to CoQH₂. Pumps 4 H⁺ into the IMS per 2 electrons. Inhibited by rotenone. The entry point for electrons from NADH produced in the matrix by the citric acid cycle and pyruvate oxidation.
Complex II (succinate dehydrogenase)
The only ETC complex that is also a citric acid cycle enzyme: it oxidizes succinate → fumarate, producing enzyme-bound FADH₂. Electrons pass through FAD and iron-sulfur clusters to CoQ. Does NOT pump H⁺ into the IMS — the reason FADH₂ yields fewer ATP (~1.5) than NADH (~2.5).
Coenzyme Q / Ubiquinone (CoQ)
A small, hydrophobic mobile carrier that diffuses laterally within the inner membrane lipid bilayer. Collects electrons from both Complex I and Complex II (as CoQH₂) and delivers them to Complex III. The convergence point of NADH and FADH₂ electron inputs. Analogous to plastoquinone (PQ) in chloroplasts.
Complex III (cytochrome bc1)
Oxidizes CoQH₂ and reduces cytochrome c via the Q-cycle, pumping 4 H⁺ into the IMS per 2 electrons transferred. Contains cytochrome b, cytochrome c1, and the Rieske iron-sulfur protein. Inhibited by antimycin A. Analogous to the cytochrome b6f complex of the chloroplast thylakoid membrane.
Cytochrome c
A small, soluble heme protein (12 kDa) loosely bound to the outer face of the inner membrane. Shuttles one electron at a time from Complex III to Complex IV within the IMS. When released into the cytoplasm during apoptosis, it binds Apaf-1 to activate caspase-9. Analogous to plastocyanin in chloroplasts.
Complex IV (cytochrome c oxidase)
The terminal complex of the ETC. Accepts 4 electrons from 4 cytochrome c molecules and reduces \(\ce{O2 + 4H+ + 4e- -> 2H2O}\) in the matrix. Pumps 4 H⁺ into the IMS per O₂ reduced. Contains copper (CuA, CuB) and heme (cyt a, cyt a3) centers. Inhibited by cyanide, carbon monoxide, and azide.
ATP Synthase (Complex V)
Uses the proton-motive force — H⁺ flowing from IMS → matrix through the F₀ transmembrane channel — to synthesize ATP via the F₁ catalytic head in the matrix. The F₀ c-ring rotates as H⁺ passes through, driving conformational changes in F₁ β-subunits (binding change mechanism; ~2.7 H⁺ per ATP). Inhibited by oligomycin. Compare with CF₁ in chloroplasts: identical mechanism, opposite H⁺ flow direction (lumen → stroma vs. IMS → matrix).
NADH / FADH₂ Inputs
The electron-carrying products of glycolysis, pyruvate oxidation, and the citric acid cycle that feed the ETC. NADH delivers electrons to Complex I; FADH₂ delivers to Complex II. Per glucose: 10 NADH and 2 FADH₂ are produced across all stages. NADH yields ~2.5 ATP; FADH₂ yields ~1.5 ATP via oxidative phosphorylation.
H⁺ Proton Gradient
The proton-motive force (PMF) across the inner membrane has two components: a chemical gradient (ΔpH ≈ 1 unit) and an electrical potential (ΔΨ ≈ −180 mV, matrix negative). Complexes I, III, and IV each pump 4 H⁺ into the IMS per O₂ reduced (12 H⁺ total). H⁺ flows back through ATP synthase to drive ATP synthesis (chemiosmosis, Mitchell hypothesis).
O₂ → H₂O (Final Electron Acceptor)
Molecular oxygen is the terminal electron acceptor at Complex IV. \(\ce{O2 + 4H+ + 4e- -> 2H2O}\) — the very negative reduction potential of this reaction (\(E°' = +0.82\text{ V}\)) pulls electrons through the entire ETC. Without O₂, the chain backs up, NAD⁺ and FAD are depleted, and aerobic metabolism halts.