PDH and TCA Cycle: Carbohydrate Metabolism

Topic 7.2: PDH and TCA Cycle - Unit II: Carbohydrate Metabolism

• Eight enzymes participate in the nine reactions of the TCA cycle.
• Synthesis of citrate, oxidative decarboxylation, and condensation are irreversible reactions in the TCA cycle.

1. PDH Complex

• The PDH complex converts pyruvate into acetyl-CoA, linking glycolysis to the TCA cycle.

2. The TCA Cycle

• Citrate synthase catalyzes condensation, where acetyl-CoA donates an acetate molecule to oxaloacetate, producing citrate and releasing coenzyme A; it is irreversible.
• Aconitase performs dehydration and hydration in sequence, converting citrate to isocitrate via a cis-aconitate intermediate; this is reversible and an isomerization.
• Isocitrate dehydrogenase catalyzes oxidative decarboxylation, decarboxylating isocitrate into α-ketoglutarate, reducing NAD+ to NADH; it is irreversible.
• α-ketoglutarate dehydrogenase catalyzes oxidative decarboxylation, converting α-ketoglutarate to succinyl-CoA, reducing NAD+ to NADH; it is irreversible.
• Succinyl-CoA synthetase catalyzes substrate-level phosphorylation, converting succinyl-CoA to succinate, releasing coenzyme A and phosphorylating GDP to GTP (ATP equivalent).
• Succinate dehydrogenase oxidizes succinate into fumarate, with electrons transferred to FADH2; succinate dehydrogenase is complex II of the ETC.
• Fumarase catalyzes hydration, hydrating fumarate to produce malate.
• Malate dehydrogenase catalyzes dehydrogenation, oxidizing malate to oxaloacetate and reducing NAD+ to NADH.
• 2C are added via oxaloacetate, then two decarboxylations occur, thus obtaining succinyl-CoA, next reactions facilitate transformation of 4C molecule into oxaloacetate again.
• There are three irreversible reactions:
  • Initial condensation
  • Two oxidative decarboxylations.
• Enzyme 6 in the TCA cycle is complex 2 of the ETC.
• Two carbons released at not the same carbons just introduced.

The Stoichiometry of the Cycle

• Acetyl-CoA + 3 NAD+ + FAD + GDP + Pi + 2H2O → 2 CO2 + CoA-SH + 3 NADH + FADH2 + GTP + 2H+

Energy Yield

• Two pyruvate molecules enter the PDH-TCA cycle pathway.
• Glycolysis yields 2 ATP and 2 NADH.
• PDH yields 2 NADH.
• The TCA cycle yields 2 ATP, 6 NADH, and 2 FADH2.
• The 2 ATPs of the TCA Cycle are actually GTPs
• Note on NADH: depending on the matrix, the energy yield of NADH generated in the cytosol may vary.

3. Regulation of the TCA Cycle

• Main regulatory factors include the NAD+/NADH ratio and adenylate energy charge (balance between ATP, AMP, and ADP).

3.1. Regulation of PDH (Pyruvate Dehydrogenase)

• PDH regulation controls the cycle's feeding by regulating acetyl-CoA production.
  • ATP inhibits, while AMP activates PDH.
  • NADH inhibits, while NAD+ activates PDH.
  • Acetyl-CoA inhibits PDH.
  • Coenzyme A induces the TCA cycle.
  • High muscular Calcium induces the TCA cycle.
• PDH regulation occurs at two levels:
  • Allosteric regulation:
  • Positive regulators: AMP, CoA, NAD⁺
  • Negative regulators: ATP, acetyl-CoA, NADH.
  • Phosphorylation state regulation:
  • PDH kinase phosphorylates and inactivates PDH.
  • PDH phosphatase dephosphorylates and activates PDH.

3.2. Regulation of the 3 Irreversible Reactions of the TCA Cycle

• Citrate synthase, isocitrate dehydrogenase, and α-ketoglutarate dehydrogenase are regulated allosterically by NAD⁺, NADH, ATP, ADP, AMP, acetyl-CoA, CoA, Ca2+, succinyl-CoA, and citrate.
• NADH and ATP inhibit citrate synthase, while ADP activates it.
• Some TCA cycle intermediates, such as succinyl-CoA and citrate, inhibit the first step too.
• ATP inhibits isocitrate dehydrogenase, while ADP and Ca2+ activate it.
• NADH and succinyl-CoA inhibit α-ketoglutarate dehydrogenase, while Ca2+ induces the reaction.

4. The TCA Cycle Is Amphibolic

• The TCA cycle has both catabolic and anabolic functions, utilizing intermediates to synthesize other biomolecules.
• It is catabolic because acetyl-CoA (acetate) is degraded to CO2.
• It is anabolic because many intermediates are used to produce other biomolecules (e.g., oxaloacetate).
• Oxaloacetate: a precursor for amino acids, which is turn, precursors of pyrimidine nucleic acids.
• PEP: precursor for several amino acids.
• α-ketoglutarate: a precursor of some amino acids synthesis (Used for purines).
• Citrate: a precursor for fatty acids and sterol (PRODUCTION of LIPIDS).
• Succinyl CoA: a precursor of porphyrins

4.1. Anaplerotic Reactions

• Anaplerotic reactions replenish TCA cycle intermediates by introducing new intermediates derived from glycolytic products.
• Pyruvate carboxylase: Catalyzes oxaloacetate formation from pyruvate, bicarbonate, and ATP.
• PEP carboxykinase: Produces oxaloacetate from phosphoenolpyruvate (PEP), CO2, and GDP.
• Malic enzyme: Forms malate from pyruvate, bicarbonate, and NADH/NADPH.
• The three anaplerotic reactions are reversible.