Bioenergetics and Thermodynamics

Thermodynamic Principles - Energy's Ebb & Flow

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ATP - Cellular Power Coin

• Adenosine Triphosphate (ATP): Universal energy currency.
  • Structure: Adenine base, Ribose sugar, 3 Phosphate groups ($\alpha, \beta, \gamma$).
  • High-energy bonds: Two phosphoanhydride bonds (between $\gamma-\beta$ & $\beta-\alpha$ P).
• Hydrolysis & Energy Release:
  • $ATP \rightarrow ADP + P_i$; $\Delta G \approx \text{-30.5 kJ/mol}$ ($\text{-7.3 kcal/mol}$).
  • $ATP \rightarrow AMP + PP_i$; $\Delta G \approx \text{-45.6 kJ/mol}$ ($\text{-10.9 kcal/mol}$).
  • $PP_i$ hydrolysis to $2 P_i$ further drives reactions.
• Key Roles: Powers biosynthesis, active transport, muscle contraction.
• Major Synthesis Pathways:
  • Substrate-level phosphorylation.
  • Oxidative phosphorylation (primary).
• Regulation: ATP/ADP ratio influences metabolic flux.

⭐ A resting human turns over their body weight in ATP daily (approx. 50-75 kg).

Redox & Electron Carriers - Energy Baton Pass

• Redox: Coupled reactions.
  • Oxidation: Loss of e⁻ (LEO). Oxidizing agent accepts e⁻.
  • Reduction: Gain of e⁻ (GER). Reducing agent donates e⁻.
• Redox Potential ($E_0'$): Measure of e⁻ affinity.
  • e⁻ flow: more negative $E_0'$ → more positive $E_0'$.
  • $\Delta G^{0'} = -nF\Delta E_0'$.
• Key Electron Carriers:
  • NAD⁺/NADH: Carries 2e⁻, 1H⁺. From Niacin (B3). For ATP synthesis.
  • NADP⁺/NADPH: Anabolic reactions.
  • FAD/FADH₂: Carries 2e⁻, 2H⁺. From Riboflavin (B2).
  • FMN: Similar to FAD (Flavin Mononucleotide).
  • Coenzyme Q (Ubiquinone): Lipid-soluble.
  • Cytochromes: Heme proteins (Fe²⁺↔Fe³⁺).

⭐ NADH generates approx. 2.5 ATP; FADH₂ generates approx. 1.5 ATP via oxidative phosphorylation. 📌 LEO says GER: Loss Electrons Oxidation, Gain Electrons Reduction.

ATP Synthesis Mechanisms - Factory Blueprints

• Two main ATP factories:

  • Substrate-Level Phosphorylation (SLP)
  • Oxidative Phosphorylation (OxPhos)

• Substrate-Level Phosphorylation (SLP):

  • Direct $P_i$ transfer to ADP from high-energy substrate.
  • Enzymes: Kinases.
  • Locations: Cytosol (Glycolysis), Mitochondrial matrix (TCA cycle).
  • Key steps:
    • 1,3-BPG $\rightarrow$ 3-PG
    • PEP $\rightarrow$ Pyruvate
    • Succinyl CoA $\rightarrow$ Succinate (GTP mediated)
  • Rapid, O₂ not directly required.

• Oxidative Phosphorylation (OxPhos):

  • Major ATP yield; Inner mitochondrial membrane.
  • ETC: e⁻ flow (NADH, FADH₂) pumps H⁺ $\rightarrow$ proton motive force (PMF).
  • ATP Synthase (Complex V) uses PMF for ATP synthesis.
  • O₂: Final electron acceptor.
  • Yield: NADH ≈ 2.5 ATP; FADH₂ ≈ 1.5 ATP (P/O).

⭐ Uncouplers (DNP, Aspirin, Thermogenin) dissipate H⁺ gradient: ATP ↓, O₂ use ↑, heat ↑.

High‑Yield Points - ⚡ Biggest Takeaways

• Gibbs Free Energy (ΔG) dictates reaction spontaneity: negative ΔG for exergonic (releases energy), positive for endergonic (requires energy).
• ATP is the universal energy currency; its hydrolysis to ADP + Pi releases approx. -7.3 kcal/mol (or -30.5 kJ/mol).
• Standard Free Energy Change (ΔG°') is defined at pH 7, 25°C (298K), and 1M concentrations for all reactants and products.
• Coupled reactions enable thermodynamically unfavorable (endergonic) reactions to proceed by linking them to highly favorable (exergonic) reactions, often ATP hydrolysis.
• Electrons spontaneously flow from substances with a more negative reduction potential (E°') to those with a more positive E°'.
• Key high-energy phosphate compounds like phosphoenolpyruvate (PEP) and 1,3-bisphosphoglycerate (1,3-BPG) possess a higher phosphate transfer potential than ATP, meaning their hydrolysis releases more energy.
• The actual free energy change (ΔG) depends on ΔG°' and actual cellular concentrations of reactants and products (related by ΔG = ΔG°' + RT ln Q).