Lecture 29 Summary: Bridging glycolysis and the citric acid cycle

Pyruvate, the end product of glycolysis under aerobic conditions, is a metabolic branch point. As a preliminary to following the central path of aerobic metabolism from glycolysis to the citric acid cycle, we put pyruvate in perspective by considering its various possible fates. We also consider the broader context of common carboxylation and decarboxylation reactions in biochemistry.

The most important fate of pyruvate - at least for our present purposes - is its oxidative decarboxylation to acetyl CoA. This reaction is catalyzed by complex, multisubunit enzyme called the pyruvate dehydrogenase complex (PDH complex, or often simply "PDH"). This large supramolecular assembly contains multiple copies of three different types of subunit. These subunits catalyze different steps of the overall reaction. Central to the operation of the PDH complex is a key catalytic cofactor, thiamine pyrophosphate (TPP). We will examine closely the chemistry of this extraordinary and important cofactor.

Carboxylation and decarboxylation reactions

Let us define a carboxylation reaction as the addition of a CO₂ unit to a substrate molecule, and decarboxylation as loss of CO₂. Decarboxylation reaction reactions are typically quite thermodynamically favorable due to the entropic contribution of cleaving a single molecule into two, one of which is a gas. Conversely, we can expect carboxylation reactions to be energy-requiring, and we should not be surprised to learn ATP hydrolysis coupled to carboxylation. The most prominent carboxylation reactions in biochemistry are catalyzed by biotin-dependent carboxylases and RuBisCO.

The biochemistry of thiamine

Decarboxylations in metabolism can be either non-oxidative or oxidative. In contrast to the relatively facile decarboxylation of β-keto acids, the decarboxylation of α-keto acids presents a mechanistic challenge. Thiamine pyrophosphate (TPP) provides the biochemical and enzymological answer.

Thiamine deficiency underlies the disorder beriberi.

The pyruvate dehydrogenase (PDH) complex

The PDH complex carries out the oxidative decarboxylation process that generates acetyl CoA from pyruvate. The PDH complex serves as the link between glycolysis and the citric acid cycle, and is required for oxidative metabolism. The activity of PDH involves three distinct enzymes, four activities, and five different cofactors.

Steps of the PDH complex:

(1) decarboxylation (E1, formation of hydroxyethyl-TPP)

(2) oxidation (transfer of acetyl group to lipoamide)

(3) transfer of acetyl group from acetyllipoamide to CoA)

(4) oxidation of dihydrolipoamide to lipoamide (E3, FAD, NAD⁺)

The α-ketoglutarate dehydrogenase complex, which participates in the citric acid cycle, shows a close resemblance to PDH complex.

Learning objectives

• Draw the structure of the key metabolic intermediate pyruvate, recognize it as an α-keto acid.
• List the possible metabolic fates of pyruvate.
• Distinguish mechanistically between decarboxylation of an α- and a β-keto acid.
• Distinguish between nonoxidative and oxidative decarboxylation.
• Illustrate the mechanistic role of thiamine pyrophosphate (TPP) in decarboxylation of an α-keto acid.
• Write a chemical equation representing the net reaction catalyzed by pyruvate dehydrogenase (PDH) complex.
• Describe the components (enzyme subunits and cofactors) of PDH complex and their roles.

Page updated 07-21-2010

References

1. Staunton J. Primary Metabolism: A Mechanistic Approoach (1978, Oxford University Press)
2. Silverman RB. The Organic Chemistry of Enzyme-Catalyzed Reactions (Revised ed., 2002, Academic Press).

Cofactors that act as carriers in metabolism

"Redox" cofactors (electron carriers): NAD⁺ (or NADP⁺) and FAD

Acyl group carrier: Coenzyme A

Acetyl CoA and other thioesters

Learning objectives

• Describe the cofactors
  • Coenzyme A
  • NAD
  • FAD
• Explain how ATP, acetyl CoA, and NADPH illustrate the importance of kinetic stability in an activated carrier, and describe any structural similarities and their significance.

Page updated 12-17-06

References

1. Staunton J. Primary Metabolism: A Mechanistic Approoach (1978, Oxford University Press)