Electron Transport Chain & Oxidative Phosphorylation Vocabulary

Overview / Driving Force

• Electrons donated to the respiratory chain ultimately reduce O2 to H2O.
• The chain works because the standard reduction potential (E°’) rises step-wise from NADH (low) → O₂ (high).
  • Higher E°’ = more favorable reduction = lower free energy ((\Delta G = -nF\Delta E)).
  • Energy released is captured first as an electro-chemical proton gradient ((\Delta p)) and then as ATP.

Complex I – NADH:CoQ Oxidoreductase ((~1 MDa, 45 polypeptides))

• Entry point for most electrons (from NADH made in TCA, PDH, β-oxidation shuttles, etc.).
• First acceptor = FMN (flavin mononucleotide, riboflavin derivative).
  • FMN can accept either 1 e⁻ or 2 e⁻, unlike NAD⁺ (obligate 2 e⁻).
  • After 2 e⁻ uptake from NADH, FMNH₂ delivers electrons one-by-one to a relay of Fe-S clusters (([2Fe–2S], [4Fe–4S])).
• Terminal acceptor inside complex I = Coenzyme Q (ubiquinone) → partially reduced Q^{\bullet-} → fully reduced QH_2.
• Proton pumping: 4 H⁺/2 e⁻ are moved from matrix → inter-membrane space (IMS).
  • Mechanism: long range allosteric change; chains of protonatable residues (Asp/Glu) undergo sequential protonation–deprotonation cycles.
• Net stoichiometry (matrix side written left):
  \text{NADH} + H^+ + Q + 4H^+{(matrix)} \;\rightarrow\; \text{NAD}^+ + QH2 + 4H^+_{(IMS)}

Iron–Sulfur (Fe-S) Clusters – brief note

• Cannot leave iron free in cytosol (risk of Fenton chemistry/precipitation).
• Clusters are synthesized by dedicated biogenesis machinery, incorporated via Cys thiolates, and deeply buried in protein cores.

Coenzyme Q (Ubiquinone)

• Benzoquinone head (redox active) + poly-isoprenoid tail (10 units in humans → hydrophobic) ⇒ freely diffuses in inner-membrane core.
• Accepts 2 e⁻ + 2 H⁺:
  Q + e^- + H^+ \rightarrow Q^{\bullet-} (semiquinone)
  Q^{\bullet-} + e^- + H^+ \rightarrow QH_2 (ubiquinol)

Complex II – Succinate:CoQ Reductase (Succinate Dehydrogenase)

• Shared enzyme of TCA and ETC; 4 polypeptides.
• Succinate → Fumarate with reduction of FAD → FADH₂; e⁻ passed through 3 Fe-S clusters + a heme b to CoQ.
• No proton pumping! Therefore electrons entering via complex II yield less ATP (see stoichiometry).
• Net: \text{Succinate} + Q \rightarrow \text{Fumarate} + QH_2

Additional Q-Reducing Enzymes (mentioned)

• ETF–Q oxidoreductase (from β-oxidation), glycerol-3-P DH, cytosolic NADH shuttles, etc., all feed reduced Q directly → bypass complexes I/II.

Complex III – Q-Cytochrome c Oxidoreductase (bc₁ complex, ~250 kDa, 10–11 subunits)

• Proton pump (4 H⁺/2 e⁻ to IMS).
• Contains cyt b_{L,H}, Rieske Fe-S, cyt c₁.
• Operates via the Q cycle (two half-cycles):
  1. First QH₂ binds at Q_o site. • One e⁻ → Rieske Fe-S → cyt c₁ → soluble cyt c in IMS (1 e⁻ carrier). • Second e⁻ travels within cyt b to Q_i site, reducing a Q to semiquinone (Q^{\bullet-}). • 2 H⁺ from QH₂ are released to IMS.
  2. Second QH₂ repeats path; semiquinone at Q_i is fully reduced to QH₂, taking 2 matrix protons.
• Net per 2 e⁻:
  • 1 QH₂ oxidized (since one is re-formed),
  • 2 cyt c (reduced),
  • 4 H⁺ pumped (2 released, 2 translocated).

Cytochrome c (mobile, soluble)

• 104 aa protein with covalently bound heme c (Cys-heme thioether bonds).
• Shuttles on outer surface of inner membrane; each molecule carries 1 e⁻ from complex III → IV.
• Leakage into cytosol is apoptotic signal.

Complex IV – Cytochrome c Oxidase (CcO)

• 13 subunits; key redox centers: Cu_A, heme a, heme a₃–Cu_B binuclear center.
• Accepts 4 e⁻ (from 4 cyt c^{red}) to reduce O2 + 4H^+{(matrix)} → 2H_2O.
• Pumps 2 H⁺ per 2 e⁻ (i.e., 4 H⁺ per O₂).
• Contributes additional (\Delta p) by chemical consumption of 4 matrix protons for water formation.

Net reaction for 2 e⁻

2\,cyt\,c^{\text{(red)}} + \frac12 O2 + 2H^+{(matrix)} \rightarrow 2\,cyt\,c^{\text{(ox)}} + H_2O
(add 2 pumped H⁺ to IMS).

Reactive Oxygen Species (ROS)

• Partial reduction generates O2^{\bullet-} (superoxide), H2O_2, OH^{\bullet}.
• Controlled ROS act as signalling of mitochondrial status (new view vs. ‘damage only’ view).
• Detox enzymes: SOD (superoxide dismutase) 2O2^{\bullet-}+2H^+→O2+H2O2, then catalase/peroxidases 2H2O2→2H2O+O2.

Proton-Motive Force ((\Delta p))

• pH difference: (\Delta pH \approx 0.75) (matrix more alkaline).
• Membrane potential: (\Delta\psi ≈ 150\,\text{mV}).
• Combined, surface field ≈ 3×10^{7}\,V·m^{-1} ("lightning bolt inside mitochondria").

Stoichiometry Summary (per 2 e⁻)

Complex V (ATP Synthase) – F₀F₁ / Complex 5

Architecture

• F₁ head (matrix): 3 α + 3 β (catalytic), plus γ, δ, ε (rotor shaft).
• F₀ base (membrane): a-subunit + 8 c-subunit ring (human), b, d, F6, OSCP (stator).
• Overall ~550 kDa.

Binding-Change Mechanism (Paul Boyer's model)

1. Each β-subunit cycles through three conformations:
   • O (open / “empty”) – ATP release/ADP + Pi entry.
   • L (loose) – substrates bound, no catalysis.
   • T (tight) – ATP synthesized.
2. Rotation of γ (120° steps, counter-clockwise when driven by H⁺ influx) forces sequential O→L→T→O conversions.
3. One full 360° rotation ⇒ 3 ATP (one per β).

Proton-Driven Rotation (F₀)

• a-subunit presents two half-channels: IMS-side & matrix-side.
• Each c-subunit carries a protonatable Asp/Glu. Sequence:
  • Proton binds from IMS side (high [H⁺]) → neutralizes Asp → c-ring rotates to bury it in membrane.
  • After almost full circle, the same c faces matrix half-channel; lower [H⁺] + interaction with a-Arg → deprotonation → H⁺ released to matrix.
• 8 H⁺/turn (human). Coupled with 3 ATP ⇒ ≈2.7 H⁺/ATP for F₁; adding 1 H⁺/ATP for Pi/ADP symport gives global ~4 H⁺ per ATP.

Experimental Proof of Rotation

• Single-molecule microscopy: F₁ heads immobilized on glass; fluorescent actin filament or nanobead attached to γ.
• Upon ATP hydrolysis the bead is seen rotating clockwise in 120° jumps. Reverses under proton motive force.

Indirect Contributors to (\Delta p)

• Complex II & part of III consume matrix protons for Q reduction.
• Complex IV consumes 4 matrix H⁺/O₂ for water formation.

Electron Shuttles (preview)

• Malate–Aspartate Shuttle & Glycerol-3-Phosphate Shuttle move cytosolic NADH reducing power into matrix/Q pool without physically transporting NADH (avoids energetically costly uphill move).

Global ATP Yield from One Glucose (aerobic, textbook values)

1. Glycolysis: 2 ATP (net) + 2 NADH (cytosolic).
2. PDH: 2 NADH.
3. TCA (2 turns): 6 NADH + 2 FADH₂ + 2 GTP(ATP).
4. ETC/ATP synthase:
   • 8 matrix NADH × 2.5 = 20 ATP
   • 2 FADH₂ × 1.5 = 3 ATP
   • Cytosolic NADH → 3–5 ATP depending on shuttle.
5. Substrate-level: 2 (glycolysis) + 2 (TCA GTP) = 4 ATP.
   Total ≈ 30–32 ATP per glucose.

Key Concept Connections

• Redox chemistry ↔ proton translocation ↔ conformational mechanics ↔ ATP regeneration.
• Regulation involves membrane integrity, gradient maintenance, ROS signalling, substrate availability, and apoptotic release of cytochrome c.

Ethical / Practical Implications

• Electron-leak drugs (rotenone, antimycin A, cyanide, oligomycin) illustrate how targeting a single complex can induce neurodegeneration or death.
• Antioxidant therapy: simplistic ‘free-radical bad’ paradigm now nuanced by signalling roles of moderate ROS.
• Mitochondrial dysfunction at any complex or ATP synthase manifests in myopathies, neurodegeneration, aging phenotypes.