Chemistry 501 Handout 16 The Citric Acid Cycle Chapter 16

1. Dep. of Chemistry & Biochemistry Prof. Indig Chemistry 501 Handout 16The Citric Acid CycleChapter 16 Lehninger. Principles of Biochemistry. by Nelson and Cox, 5th Edition; W.H. Freeman and Company

2. Catabolism of proteins, fats and carbohydrates in the three stages of cellular respiration Oxidation of fatty acids, glucose, and some amino acids yields acetyl-CoA Oxidation of acetyl groups in the citric acid cycle includes four steps in which electrons are abstracted Electrons carried by NADH and FADH2 are funneled into a chain of mitochondrial (or, in bacteria, plasma membrane-bound) electrons carriers - the respiratory chain - ultimately reducing O2 to H2O.

3. Overall reaction catalyzed by the pyruvate dehydrogenase complex

4. The pyruvate dehydrogenase (PDH) complex consists of three distinct enzymes Pyruvate dehydrogenase (E1) (thiamine pyrophosphate, TPP) Dihydrolipoyl transacetylase (E2) (lipoate, Coenzyme A) Dihydrolipoyl dehydrogenase (E3) (FAD, NAD+) Each present in multiple copies Cryoelectron micrograph

5. Five cofactors (four derived from vitamins) participate in the reaction mechanism Cofactor Vitamin (required in human nutrition) Thiamine pyrophosphate (TPP) (E1)thiamine Lipoate (E2)- Coenzyme A (CoA-SH) (E2)pantothenate Flavin adenine dinucleotide (FAD) (E3)riboflavin Nicotinamide adenine dinucleotide (NAD+) (E3)niacin

6. A few types of coenzymes and proteins serve as universal electron carriers Nicotinamide adenine dinucleotide

7. A few types of coenzymes and proteins serve as universal electron carriers

8. E2 (dihydrolipoil transacetylase) has three functionally distinct domains The active site of E1 has bound TPP (pyruvate dehydrogenase) The active site of E3 has bound FAD (dihydrolipoyl dehydrogenase) Long flexible arm that can move from the active site of E1 to the active sites of E2 and E3 dithiol The prostetic group lipoate is attached to E2 through an amide bond to the e-amino group of a Lys residue

9. Oxidative decarboxylation of pyruvate to acetyl-CoA by the PDH complex In substrate channeling, intermediates never leave the enzyme surface (and the local concentration of the substrate of E2 is kept very high)

10. Reactions of the citric acid cycle Claisen condensation thioester + ketone The citric acid cycle has eight steps

11. 1. Formation of citrate

12. The citrate synthase reaction The citrate synthase reaction Structure of citrate synthase

13. 2. Formation of isocitrate via cis-aconitate Iron-sulfur center in aconitase

14. 3. Oxidation of isocitrate to a-ketoglutarate and CO2 The NADH produced here is the first link between the TCA cycle and electron transport and oxidative phosphorylation.

15. 4. Oxidation of a-ketoglutarate to Succinyl-CoA and CO2 E1a-ketoglutarate dehydrogenase E2 dihydrolipoyl transsuccinylase E3 dihydrolipoyl dehydrogenase

16. 5. Conversion of succinyl-CoA to succinate

17. The succinyl-CoA reaction

18. 6. Oxidation of succinate to fumarate Malonate is a strong competitive inhibitor of succinate dehydrogenase

19. 7. Hydration of fumarate to malate

20. 8. Oxidation of malate to oxaloacetate

21. Products of one turn of the citric acid cycle

23. Role of the citric acid cycle in anabolism

25. The two phases of glycolysis

26. Opposing pathways of glycolysis and gluconeogenesis in rat liver

28. Synthesis of phosphoenolpyruvate from pyruvate

30. Feeder pathways for glycolysis (preparatory phase)

31. General scheme of the pentose phosphate pathway of glucose oxidation