Chapter 5: Mitochondrial Electron Transport

Part II — Core Metabolism

5.1 Complexes I–IV: Overview

The mitochondrial electron transport chain (ETC) transfers electrons from NADH and FADH₂ to molecular oxygen, coupling this thermodynamically favorable process to proton pumping across the inner mitochondrial membrane. The resulting proton electrochemical gradient drives ATP synthase (Complex V).

Complex I (NADH:ubiquinone oxidoreductase)

NADH (−0.32 V) → CoQ (+0.045 V)

L-shaped, 45 subunits. Pumps 4H⁺/2e⁻. FMN + 8 Fe–S clusters. Inhibited by rotenone.

Complex II (Succinate dehydrogenase)

FADH₂ (−0.031 V) → CoQ (+0.045 V)

TCA cycle enzyme also in ETC. 4 subunits, FAD + 3 Fe–S + cytochrome b. Does NOT pump protons.

Complex III (Cytochrome bc₁ complex)

CoQH₂ (+0.045 V) → Cyt c (+0.254 V)

Q-cycle doubles proton pumping: 4H⁺ pumped per 2e⁻. Inhibited by antimycin A.

Complex IV (Cytochrome c oxidase)

Cyt c (+0.254 V) → O₂ (+0.816 V)

Reduces O₂ to 2H₂O. Pumps 4H⁺/4e⁻. Contains CuA, CuB, heme a, heme a₃. Inhibited by CN⁻.

5.2 Proton Motive Force & P/O Ratio

The free energy change for electron transfer from NADH to O₂ drives proton translocation. Total ΔG from NADH oxidation:

\[\Delta G = -nF\,\Delta E_0' = -(2)(96.5)(0.816 - (-0.320)) = -219\text{ kJ mol}^{-1}\]

Proton pumping per NADH:

Complex I: 4H⁺
Complex III (Q-cycle): 4H⁺
Complex IV: 4H⁺
Total: 10H⁺ per NADH
FADH₂ bypasses Complex I → 6H⁺

ATP Synthesis:

With H⁺/ATP ratio of ~4.7 (plant mitochondria):

\[P/O_{NADH} = \frac{10}{4.7} \approx 2.13\]

\[P/O_{FADH_2} = \frac{6}{4.7} \approx 1.28\]

Total per glucose: ~30 ATP (P/O × 10 NADH + 2 FADH₂ + 2 substrate-level)

5.3 Plant-Specific: Alternative Oxidase (AOX)

Plants uniquely express alternative oxidase (AOX), which branches from the ubiquinone pool and reduces O₂ to water without pumping protons — thus bypassing Complexes III and IV. AOX dissipates excess reducing power as heat rather than ATP.

Functions of AOX:

Thermogenesis in aroids (Arum lily, voodoo lily) — volatilizes insect attractants
Overflow valve — prevents over-reduction of CoQ pool → reduces ROS
Maintains TCA/glycolysis flux when ATP demand is low
Stress response (cold, drought, pathogen attack)

Regulation of AOX:

Activated by pyruvate (allosteric) and α-keto acids
Regulated by thioredoxin reduction (active when reduced)
Inhibited by n-propyl gallate and salicylhydroxamic acid (SHAM)
AOX1 gene induced by cytochrome pathway inhibition (cyanide-resistant respiration)

5.4 ATP Synthase (Complex V): Rotary Mechanism

The mitochondrial F₀F₁-ATP synthase uses H⁺ flow to synthesize ATP via rotary catalysis — the γ-subunit rotation drives conformational changes in three β-subunits cycling through Open (O), Loose (L), and Tight (T) conformations (Boyer's binding change mechanism):

\[ADP + P_i + nH^+_{IMS} \xrightarrow{\text{ATP synthase}} ATP + H_2O + nH^+_{matrix}\quad (n \approx 4.7)\]

The c-ring of the F₀ subunit has 8 subunits in mammals and ~9–15 in plants depending on species, determining the H⁺/ATP stoichiometry. Each 360° rotation synthesizes 3 ATP.

Uncoupling proteins (UCPs) in plants:

Plant UCPs (StUCP in potato, AtUCP1/2 in Arabidopsis) dissipate the proton gradient without ATP synthesis, acting as a second alternative pathway alongside AOX. Induced by fatty acids, superoxide, and during stress. UCPs may play roles in seed germination thermogenesis and cold acclimation.

Simulation: Redox Tower & Complex Energetics

Standard reduction potentials of ETC components and free energy released / ATP equivalents per complex.

Python

script.py75 lines

import numpy as np
import matplotlib.pyplot as plt
import matplotlib.patches as mpatches
# output saved as output.png

fig, axes = plt.subplots(1, 2, figsize=(14, 7), facecolor='#0a0f0a')
fig.subplots_adjust(wspace=0.4)

# Panel 1: Standard reduction potentials - redox tower
ax1 = axes[0]
ax1.set_facecolor('#0d1a0d')
components = ['NAD+/NADH', 'FMN/FMNH2
(Cx I)', 'FAD/FADH2
(Cx II)', 'CoQ/CoQH2', 'Cyt b
(Cx III)', 'Cyt c1', 'Cyt c', 'Cyt a
(Cx IV)', 'Cyt a3', 'O2/H2O']
E0_prime = [-0.320, -0.300, -0.031, +0.045, +0.030, +0.220, +0.254, +0.290, +0.385, +0.816]
cols = ['#f87171','#fb923c','#fbbf24','#a3e635','#4ade80','#34d399','#22d3ee','#60a5fa','#818cf8','#c084fc']

for i, (comp, E0, col) in enumerate(zip(components, E0_prime, cols)):
    y = i * 0.9
    ax1.barh(y, E0, height=0.6, color=col, alpha=0.8, edgecolor='#0d1a0d')
    ax1.text(max(E0 + 0.02, 0.02), y, comp, va='center', color=col, fontsize=7.5, fontweight='bold')

ax1.axvline(0, color='white', lw=0.8, ls=':')
ax1.set_xlabel('Standard Reduction Potential E°' (V)', color='#a3e635', fontsize=9)
ax1.set_title('Mitochondrial ETC: Redox Tower', color='#d9f99d', fontsize=10)
ax1.set_yticks([])
ax1.tick_params(colors='#a3e635', labelsize=8)
ax1.grid(True, alpha=0.2, color='#4ade80', axis='x')
for sp in ax1.spines.values(): sp.set_edgecolor('#4ade80')

# Panel 2: Free energy released at each complex + ATP synthesis
ax2 = axes[1]
ax2.set_facecolor('#0d1a0d')
F = 96.485  # kJ/(mol V)
complexes = ['Cx I
NADH→CoQ', 'Cx II
FADH2→CoQ', 'Cx III
CoQ→Cyt c', 'Cx IV
Cyt c→O2']
delta_E = [0.320 + 0.045, 0.031 + 0.045, 0.254 - 0.045, 0.816 - 0.254]
n_electrons = [2, 2, 2, 4]
delta_G = [-n * F * dE for n, dE in zip(n_electrons, delta_E)]
protons_pumped = [4, 0, 4, 4]
atp_equivalent = [p / 4.7 for p in protons_pumped]  # assuming 4.7 H+/ATP

x = np.arange(len(complexes))
width = 0.35
bars1 = ax2.bar(x - width/2, [-g for g in delta_G], width, label='|deltaG| (kJ/mol)', color='#4ade80', edgecolor='#0d1a0d')
bars2 = ax2.bar(x + width/2, atp_equivalent, width, label='ATP equiv (H+/4.7)', color='#fbbf24', edgecolor='#0d1a0d', alpha=0.85)
ax2.set_xticks(x)
ax2.set_xticklabels(complexes, color='#a3e635', fontsize=9)
ax2.set_ylabel('Energy / ATP equivalents', color='#a3e635', fontsize=9)
ax2.set_title('Energy Released & ATP Synthesis per Complex', color='#d9f99d', fontsize=10)
ax2.legend(fontsize=8.5, labelcolor='#d9f99d', facecolor='#0d1a0d', edgecolor='#4ade80')
ax2.tick_params(colors='#a3e635', labelsize=8)
ax2.grid(True, alpha=0.2, color='#4ade80', axis='y')
for sp in ax2.spines.values(): sp.set_edgecolor('#4ade80')

# Annotations
for bar, dg in zip(bars1, delta_G):
    ax2.text(bar.get_x() + bar.get_width()/2, bar.get_height() + 0.5,
        f'{-dg:.0f}', ha='center', va='bottom', color='#d9f99d', fontsize=8)
for bar, h_ions in zip(bars2, protons_pumped):
    ax2.text(bar.get_x() + bar.get_width()/2, bar.get_height() + 0.02,
        f'{h_ions}H+', ha='center', va='bottom', color='#fbbf24', fontsize=8)

fig.suptitle('Mitochondrial Electron Transport Chain', color='#d9f99d', fontsize=13, fontweight='bold')

plt.savefig('output.png', bbox_inches='tight', facecolor=fig.get_facecolor(), dpi=120)
plt.close()
print('Simulation complete.')

Click Run to execute the Python code

Code will be executed with Python 3 on the server

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