Citric Acid Cycle

Carbohydrate Metabolism

Glycogen Metabolism

  • Polysaccharide Metabolism
    • Glycogen Breakdown (Catabolism)
    • Glycogen Synthesis (Anabolism)

Glucose Metabolism

  • Monosaccharide Metabolism
    • Glucose Breakdown (Catabolism)
    • Glycolysis
    • The Citric Acid Cycle (CAC)
    • Pentose Phosphate Pathway
    • Glucose Synthesis (Anabolism)
    • Gluconeogenesis
    • Photosynthesis
      • Light Reaction
      • Dark Reaction - Calvin Cycle

The Citric Acid Cycle (CAC)

  • Also referred to as Tricarboxylic Acid Cycle (TCA) or Krebs Cycle.
  • The citric acid cycle oxidizes a two-carbon unit, producing two molecules of CO$_{2}$.
  • Process Overview:
    • Pyruvate from glycolysis is converted into acetyl CoA (the C$_{2}$ unit).
    • Acetyl CoA is then degraded to CO$_{2}$ in the CAC.
    • Initiates the CAC by reacting with oxaloacetate (OAA) but is not an intermediate in the CAC.
    • Oxaloacetate (a C$_{4}$ unit) is the traditional start and finish point of the CAC.
  • ATP/GTP Production:
    • Produced by substrate-level phosphorylation.
    • Three NADH and one FADH$_{2}$ are generated; these go on to produce more ATP via oxidative phosphorylation.
  • Overall Reaction:
    • extAcetyl−CoA+3extNAD++extFAD+extGDP+extP<em>i+2extH</em>2extO<br/>ightarrow2extCO<em>2+3extNADH+extFADH</em>2+extGTP+extCoA+3extH+ext{Acetyl-CoA} + 3 ext{NAD}^+ + ext{FAD} + ext{GDP} + ext{P}<em>i + 2 ext{H}</em>2 ext{O} <br /> ightarrow 2 ext{CO}<em>2 + 3 ext{NADH} + ext{FADH}</em>2 + ext{GTP} + ext{CoA} + 3 ext{H}^+
  • Location:
    • In eukaryotes, the CAC occurs in the mitochondria; in bacteria, it takes place in the cytosol.
    • Glycolysis occurs in the cytoplasm, while the CAC occurs in the mitochondrial matrix, except for succinate dehydrogenase, which is located in the mitochondrial inner membrane.
  • Intermediates:
    • Citric acid cycle intermediates serve as precursors for the biosynthesis of amino acids, nucleotides, fatty acids, sterols, etc.

The Bridging Step: Oxidative Decarboxylation of Pyruvate

  • Energy from glucose breakdown to pyruvate in glycolysis is minimal.
  • Much more energy is released when pyruvate is degraded aerobically to CO$_{2}$.
  • The end product of glycolysis, pyruvate, is oxidative decarboxylated to acetyl-CoA, linking glycolysis to the TCA cycle.
  • Catalyst:
    • The reaction is catalyzed by the pyruvate dehydrogenase complex which requires 5 coenzymes: TPP, lipoic acid, and FAD as prosthetic groups, and NAD$^{+}$ and CoA-SH as co-substrates.
  • Regulation:
    • The primary regulation of the pyruvate dehydrogenase complex occurs via inhibition by phosphorylation.
  • Conversions:
    • The conversion of 1 mole of pyruvate to 3 moles of CO$_{2}$ via pyruvate dehydrogenase and the CAC yields:
    • _ moles of NADH,
    • moles of FADH${2}$,
    • _ moles of ATP (or GTP).

Citric Acid Cycle Steps

  • Enzymes: The citric acid cycle involves 8 enzymes and proceeds in 8 steps:

Step 1: C-C Bond Formation to Make Citrate

  • Catalyst: Citrate synthase.
  • Process: Catalyzes the condensation of acetyl-CoA and oxaloacetate to yield citrate.
  • Reaction Type: It is a condensation reaction.
  • CO${2}$ Origin: The two CO${2}$ produced in the first turn of the CAC originate from the two carboxyl groups derived from oxaloacetate, not from acetyl-CoA.

Step 2: Isomerization via Dehydration/Rehydration

  • Catalyst: Aconitase.
  • Process: Isomerizes citrate into isocitrate (easily oxidized form).
  • Mechanism: The conversion involves dehydration followed by hydration.
  • Regulation: The first isomerization step is irreversible and requires making it reactive.

Step 3: Oxidative Decarboxylation to Produce NADH and CO$_{2}$

  • Catalyst: Isocitrate dehydrogenase.
  • Process: Oxidizes isocitrate into oxalosuccinate while producing NADH.
  • Decarboxylation: Oxalosuccinate is decarboxylated to form α-ketoglutarate.

Step 4: Oxidative Decarboxylation to Produce Second NADH and CO$_{2}$

  • Catalyst: α-Ketoglutarate dehydrogenase.
  • Process: Oxidatively decarboxylates α-ketoglutarate to succinyl-CoA.
  • Comparison: This is similar to the pyruvate dehydrogenase complex-catalyzed reaction.
  • Properties: This reaction is thermodynamically favorable and irreversible.

Step 5: Substrate-Level Phosphorylation to Yield GTP

  • Catalyst: Succinyl-CoA synthetase.
  • Process: Converts succinyl-CoA to succinate, forming GTP.
  • Energy Equivalence: GTP is energetically equivalent to ATP in metabolism.
  • Nucleoside Diphosphokinase: Transfers a phosphoryl group from GTP to ADP:
    • extGTP+extADP<br/>ightarrowextGDP+extATPext{GTP} + ext{ADP} <br /> ightarrow ext{GDP} + ext{ATP}

Step 6: Dehydrogenation Forms FADH$_{2}$

  • Catalyst: Succinate dehydrogenase.
  • Reaction: Oxidizes succinate to fumarate, producing FADH$_{2}$.
  • Location: Bound to the mitochondrial inner membrane; Part of Complex II in the electron transport chain.
  • Equilibrium: The reaction near equilibrium and is reversible; product concentration is maintained low to favor forward reaction.

Step 7: Hydration Across a Double Bond

  • Catalyst: Fumarase.
  • Process: Catalyzes hydration of fumarate to produce malate.

Step 8: Dehydrogenation to Produce Third NADH

  • Catalyst: Malate dehydrogenase.
  • Process: Reforming oxaloacetate by oxidizing the secondary hydroxyl group to a ketone.
  • Characteristics: The final step of CAC, regenerates oxaloacetate for citrate synthase and is thermodynamically unfavorable but reversible.

Regulation of the Citric Acid Cycle

  • General Regulatory Mechanism:
    • Activated by substrate availability.
    • Inhibited by product accumulation.
    • Overall pathway products are NADH and ATP impacting all regulated enzymes.
  • Inhibitors: NADH and ATP.
  • Activators: NAD$^{+}$ and AMP.
  • Key Regulation Points:
    • The CAC is regulated at thermodynamically favorable and irreversible steps:
    • Citrate Synthase: Inhibited by ATP, NADH, and succinyl-CoA.
    • Isocitrate Dehydrogenase: Inhibited by ATP; activated by ADP and NAD$^{+}$.
    • α-Ketoglutarate Dehydrogenase: Inhibited by NADH and succinyl-CoA; activated by AMP.
  • Additional Regulation: The pyruvate dehydrogenase is a key regulatory site for CAC, primarily regulated by reversible phosphorylation of E1:
    • Phosphorylation performs the inactive state.
    • Dephosphorylation performs the active state.

The Glyoxylate Cycle

  • A process in which plants and some bacteria convert two-carbon acetyl units into four-carbon units (succinate) for glucose synthesis, energy production, and biosynthesis.
  • Allows plants and some microorganisms to grow on acetate by bypassing the decarboxylation steps of the CAC.
  • Enables net synthesis of glucose from acetyl-CoA.
  • Catalysts Specific to Glyoxylate Cycle: The reactions diverge from the CAC at isocitrate lyase and malate synthase, differing in structure but comparable in metabolism.