Pyruvate Metabolism and Enzyme Complexes

Thiamine Pyrophosphate (TPP)

• Thiamine (Vitamin B1) is a precursor to thiamine pyrophosphate (TPP).
• TPP has an amylopyrimidine ring and a thiazole ring.
• A key feature of TPP is a carbon atom on the thiazole ring that is acidic, allowing it to release a proton and form a carbanion (an ylide form), which is crucial for its catalytic activity.
• The carbanion acts as a nucleophile, attacking carbon-carbon bonds, leading to decarboxylation by stabilizing a tetragonal intermediate, facilitating the release of CO_2.

Role of TPP in Decarboxylation

• TPP is essential for decarboxylation reactions.
• TPP stabilizes the carbanion, which attacks the carbon-carbon bond, leading to the release of CO_2.
• Without TPP, this decarboxylation would not occur.

Alcohol Dehydrogenase

• Alcohol dehydrogenase facilitates the chemistry using a positively charged zinc ion (Zn^{+2}).
• The reaction involving alcohol dehydrogenase is reversible, with NADH releasing a hydride ion (H^-) and being oxidized to NAD^+.

Aerobic Conditions and Pyruvate Conversion

• Under aerobic conditions, pyruvate, produced during glycolysis, is converted into acetyl-CoA inside the mitochondria.
• The mitochondrial inner membrane is impermeable unless specific protein transporters are present.
• The energy for transport is derived from the proton gradient across the mitochondrial membrane.

Coenzyme A (CoA)

• CoA consists of pantothenic acid and a mercaptoethylamine moiety.
• It contains a thioester bond, the hydrolysis of which is highly exergonic, with a very negative \Delta G.

Pyruvate to Acetyl-CoA Conversion

• The conversion of pyruvate to acetyl-CoA is a complex reaction catalyzed by the pyruvate dehydrogenase complex.

Pyruvate Dehydrogenase Complex

• The pyruvate dehydrogenase complex is large enough to be seen via electron microscopy, unlike smaller enzymes such as isokinase.
• It exhibits supramolecular chemistry, involving interactions between numerous lipid molecules to form an ordered structure.
• The complex has a central cubic core with E2 units arranged with a non-cubic symmetry.
• The structure features a triangle at the vertex of the complex with internal voids.

Subunits and Active Sites

• The complex consists of E1, E2, and E3 types of units.
• The E2 unit has an internal domain and a carboxy-terminal domain.
• Multiple active sites within the complex facilitate the transfer of the substrate from one enzymatic site to another via a mobile domain (K).

Symmetry in Multi-Subunit Proteins

• Symmetry in multi-subunit proteins is mathematically complex, involving symmetry groups related to crystallography.
• Proteins like hemoglobin exhibit symmetry (e.g., D2 symmetry).

Allostery

• Allostery involves binding at one site affecting the conformation at a distant site.
• Hemoglobin exists in tense (T) and relaxed (R) states, differing in oxygen-binding affinity.
• Allosteric effects can occur without significant conformational changes, influenced by vibrational patterns within the protein.

Intrinsically Disordered Proteins

• Intrinsically disordered proteins or regions lack a well-defined three-dimensional structure.
• These disordered regions are crucial for protein function.

Release of CO_2 and Role of Lipoamide

• Following CO_2 release, the remaining fragment is transferred to lipoamide.
• Lipoamide accepts electrons through a redox reaction with a disulfide bond.

Irreversibility of Decarboxylation

• Decarboxylation reactions, such as the conversion of pyruvate to acetyl-CoA, are irreversible.
• Mammals cannot reverse this reaction to utilize carbon dioxide to synthesize glucose, unlike plants or green algae.

Similar Reactions in the Krebs Cycle

• A similar reaction scheme occurs in the Krebs cycle with the alpha-ketoglutarate dehydrogenase complex.
• This complex is structurally and functionally similar to the pyruvate dehydrogenase complex.
• Another analogous complex is involved in branched-chain amino acid metabolism.