The Citric Acid Cycle II and the Pentose Phosphate Pathway

The Citric Acid Cycle and the Pentose Phosphate Pathway

Overview

  • Main metabolic pathways discussed are:

    • The Citric Acid Cycle (Krebs Cycle)

    • The Pentose Phosphate Pathway

The Citric Acid Cycle

  • Overall Reaction:

    • 3 ext{ NAD}^+ + ext{ FAD} + ext{ GDP} + ext{ Pi} + ext{ acetyl-CoA}
      ightarrow 3 ext{ NADH} + ext{ FADH}2 + ext{ GTP} + ext{ CoA} + 2 ext{ CO}2

Key Intermediates and Reaction Steps

  • Key Compounds:

    • Pyruvate ⇒ Acetyl-CoA

    • Acetyl-CoA + Oxaloacetate ⇒ Citrate (via Citrate Synthase)

    • Conversion Process:

    • Pyruvate + CoA + NAD+ → Acetyl-CoA + CO2 + NADH

  • Subsequent Reactions:

    1. Citrate Synthase: Combines Acetyl-CoA and Oxaloacetate to form Citrate.

    2. Aconitase: Converts Citrate to Isocitrate; involves cis-Aconitate as an intermediate.

    3. Isocitrate Dehydrogenase: Converts Isocitrate to Alpha-Ketoglutarate; reduces NAD+ to NADH and releases CO2.

    4. Alpha-Ketoglutarate Dehydrogenase: Converts Alpha-Ketoglutarate to Succinyl-CoA; produces NADH and CO2.

    5. Succinyl-CoA Synthetase: Converts Succinyl-CoA to Succinate; generates GTP from GDP and Pi.

    6. Succinate Dehydrogenase: Converts Succinate to Fumarate; reduces FAD to FADH2.

    7. Fumarase: Converts Fumarate to Malate; involves the addition of H2O.

    8. Malate Dehydrogenase: Converts Malate back to Oxaloacetate; produces NADH.

Enzyme Properties and Mechanisms

  • E2 Subunits: 24 E2 subunits, 24 E1, and 12 E3 (from yeast pyruvate dehydrogenase).

  • Domain Structure of Dihydrolipoyl Transacetylase E2:

    • Composed of several domains including Lipoyl, E3 binding, and catalytic domains.

  • Induced Fit Mechanism:

    • Binding of oxaloacetate is necessary before Acetyl-CoA can bind.

  • Key Catalysts:

    • Enzymes like pyruvate dehydrogenase and alpha-ketoglutarate dehydrogenase act as multi-enzyme complexes.

Regulation of the Citric Acid Cycle

  • Standard Free Energy Changes ($ ext{DG}^ ext{°}$):

    • Citrate Synthase: -31.5 (Negative)

    • Aconitase: ~5

    • Isocitrate Dehydrogenase: -21 (Negative)

    • Alpha-Ketoglutarate Dehydrogenase: -33 (Negative)

    • Succinyl-CoA Synthetase: -20.1 (Near Zero)

    • Succinate Dehydrogenase: +6

    • Fumarase: -3.4 (Near Zero)

    • Malate Dehydrogenase: +29.7 (Positive)

  • Entrances of Regulation:

    • Pyruvate, Oxaloacetate, Acetyl-CoA, NADH, and Ca2+.

Citric Acid Cycle Intermediates

  • The intermediates are continuously being modified and fluxed, which includes:

    • Pyruvate, Acetyl-CoA, Citrate, Isocitrate, Alpha-ketoglutarate, Succinyl-CoA, Succinate, Fumarate, Malate, and Oxaloacetate.

Energy Yield from Glucose

  • A single glucose molecule can yield approximately 38 molecules of ATP through:

    • Glycolysis (2 ATP, 2 NADH yielding 6 ATP)

    • Citric Acid Cycle (6 NADH yielding 18 ATP, 2 FADH2 yielding 4 ATP, and 2 GTP yielding 2 ATP).

  • Total: 38 ATP per glucose molecule.

The Pentose Phosphate Pathway

  • Key Products:

    • Produces NADPH and Ribose-5-Phosphate, which are crucial for anabolic pathways.

    • The reaction:

    • 3 ext{ G-6-P} + 6 ext{ NADP}^+ + 3 ext{ H}2 ext{O} ightarrow 6 ext{ NADPH} + 3 ext{ CO}2 + 2 ext{ F-6-P} + ext{GAP}

Three Parts of the Pathway

  1. Oxidative Reactions:

    • 3 ext{ G-6-P} + 6 ext{ NADP}^+ + 3 ext{ H}2 ext{O} ightarrow 6 ext{ NADPH} + 3 ext{ CO}2 + 3 ext{ Ribulose-5-PO}_4

  2. Isomerization and Epimerization Reactions:

    • 3 ext{ Ribulose-5-PO}4 ightarrow ext{ Ribose-5-PO}4 + 2 ext{ Xylulose-5-PO}_4

  3. C-C Bond Cleavage and Formation:

    • ext{ Ribose-5-PO}4 + 2 ext{ Xylulose-5-PO}4
      ightarrow 2 ext{ F-6-P} + ext{GAP}

Enzymatic Reactions Involved

  • Key enzymes include:

    • Glucose-6-phosphate dehydrogenase, Gluconolactonase, Phosphogluconate dehydrogenase, Ribulose-5-phosphate isomerase and epimerase.

  • Transketolase and Transaldolase:

    • Transketolase transfers 2-carbon units and relies on Thiamine Pyrophosphate (TPP).

    • Transaldolase transfers 3-carbon units and uses a Shiff's base with an active lysine group.

Glutathione and its Role in Cellular Integrity

  • Role of NADPH:

    • Used for Glutathione Reductase to convert oxidized glutathione (GSSG) to reduced form (GSH).

  • Importance of GSH:

    • Protects against oxidative stress, maintains protein sulfhydryls in reduced state, and prevents cellular damage from peroxides.

  • Mechanism of Action:

    • ext{2 GSH} + ext{ R-A-O-O-H}
      ightarrow ext{ GS-SG} + ext{ ROH} + ext{ H}_2 ext{O}

Clinical Correlations

  • Glutathione deficiency especially in individuals with glucose-6-phosphate dehydrogenase deficiency leads to hemolytic anemia under oxidative stress or drug influence (e.g., Primaquine).

  • Individuals heterozygous for G-6-P deficiency may have a selective advantage against malaria (Plasmodium falciparum) due to the inability of the parasite to adapt to oxidative stress.