Chapter 13 - The Citric Acid Cycle

1. Chapter 13 - The Citric Acid Cycle • The citric acid cycle is involved in the aerobiccatabolism of carbohydrates, lipids and amino acids • Intermediates of the cycle are starting points for many biosynthetic reactions • Enzymes of the cycle are in the mitochondria of eukaryotes • Energy of the oxidation reactions is largely conserved as reducingpower (stored electrons) • Coenzymes reduced: • NAD+ NADH • FAD FADH2 • Ubiquinone (Q) Reduced Ubiquinone (QH2) Chapter 12

2. Transport of Pyruvate from the cytosol into the Mitochondria • Pyruvate translocase transports pyruvate into the mitochondria in symport with H+ Pyruvate dehydrogenase complex Chapter 12

3. Conversion of Pyruvate to Acetyl CoA • Pyruvate dehydrogenase complex is a multienzyme complex containing: • 3 enzymes + 5 coenzymes + other proteins • E1 = pyruvate dehydrogenase • E2 = dihydrolipoamide acetyltransferase • E3 = dihydrolipoamide dehydrogenase Chapter 12

4. Components of the PDH Complex in mammals and E. coli Chapter 12

5. Fig 13.1 Reactions of the PDH complex Chapter 12

6. Fig 13.1 Reactions of the PDH complex Chapter 12

7. Fig 13.1 Reactions of the PDH complex Acetylated lipoamide Chapter 12

8. Fig 13.1 Reactions of the PDH complex TCA cycle Reduced lipoamide Chapter 12

9. Fig 13.1 Reactions of the PDH complex Oxidized lipoamide Chapter 12

10. Fig 13.1 Reactions of the PDH complex Oxidized lipoamide Chapter 12

11. Fig 13.1 Reactions of the PDH complex Acetylated lipoamide Chapter 12

12. Fig 13.1 Reactions of the PDH complex TCA cycle Reduced lipoamide Chapter 12

13. Fig 13.1 Reactions of the PDH complex Oxidized lipoamide Chapter 12

14. The Citric Acid Cycle Oxidizes AcetylCoA • Table 13.1 Chapter 12

15. Summary of the citric acid cycle • For each acetyl CoA which enters the cycle: • (1) Two molecules of CO2 are released • (2) Coenzymes NAD+ and Q are reduced • to NADH and QH2 • (3) One GDP (or ADP) is phosphorylated • (4) The initial acceptor molecule (oxaloacetate) is reformed Chapter 12

16. Fig 13.3 • Citric acid cycle Chapter 12

17. Fig 13.3 Chapter 12

18. Fig 13.3 Chapter 12

19. 6. The Succinate Dehydrogenase (SDH) Complex • Located on the inner mitochondrial membrane, in contrast to other enzymes of the TCA cycle which are dissolved in the mitochondrial matrix • Complex of polypeptides, FAD and iron-sulfur clusters • Electrons are transferred from succinate to FAD, forming FADH2, then to ubiquinone (Q), a lipid-soluble mobile carrier of electrons • Reduced ubiquinone (QH2) is released as a mobile product Chapter 12

20. Fig 12.4 Chapter 12

21. Fates of carbon atoms in the cycle • 6C5C4C Chapter 12

22. Energy conservation by the cycle • Energy is conserved in the reduced coenzymes NADH, QH2 and one GTP • NADH, QH2 can be oxidized to produce ATP by oxidative phosphorylation Chapter 12

23. Reduced Coenzymes Fuel the Production of ATP • Each acetyl CoA entering the cycle nets: • (1)3 NADH • (2) 1 QH2 • (3) 1 GTP (or 1 ATP) • Oxidation of each NADH yields 2.5 ATP • Oxidation of each QH2 yields 1.5 ATP • Completeoxidation of 1 acetyl CoA = 10 ATP Chapter 12

24. Fig 13.10 Glucose degradation via glycolysis, citric acid cycle, and oxidative phosphorylation Chapter 12

25. Regulation of the Citric Acid Cycle • The citric acid cycle is controlled by: • (1) Allosteric modulators • (2) Covalent modification of cycle enzymes • (3) Supply of acetyl CoA • (4) Regulation of pyruvate dehydrogenase complex controls acetyl CoA supply Chapter 12

26. Fig 13.11Regulation of the pyruvate dehydrogenase complex • Increased levels of acetyl CoA and NADH inhibit E2, E3 • Increased levels of CoA and NAD+ activate E2, E3 Chapter 12

27. Fig 13.12 Regulation of mammalian PDH complex by covalentmodification • Phosphorylation/dephosphorylation of E1 Chapter 12

28. Regulation of isocitrate dehydrogenase • MammalianICDH • Activated by calcium (Ca2+) and ADP • Inhibited by NADH (-) + + NAD+ NADH Chapter 12

29. Regulation of thecitric acid cycle Chapter 12

30. Entry and Exit of Metabolites • Intermediates of the citric acid cycle are precursors for carbohydrates, lipids, amino acids, nucleotides and porphyrins • Reactions feeding into the cycle replenish the pool of cycle intermediates Chapter 12

31. Fig 13.13 Chapter 12

32. 1. Citrate Synthase • Citrate formed from acetyl CoA and oxaloacetate • Only cycle reaction with C-C bond formation Chapter 12

33. 2. Aconitase • Elimination of H2O from citrate to form C=C bond of cis-aconitate • Stereospecific addition of H2O to cis-aconitate to form 2R,3S-Isocitrate Chapter 12

34. 3. Isocitrate Dehydrogenase • Oxidative decarboxylation of isocitrate toa-ketoglutarate (a metabolically irreversible reaction) • One of four oxidation-reduction reactions of the cycle • Hydride ion from the C-2 of isocitrate is transferred to NAD+ to form NADH Chapter 12

35. 4. The a-Ketoglutarate Dehydrogenase Complex • Similar to pyruvate dehydrogenase complex • E1 - a-ketoglutarate dehydrogenase (with TPP) • E2 - succinyltransferase (with flexible lipoamide prosthetic group) • E3 - dihydrolipoamide dehydrogenase (with FAD) Chapter 12

36. 5. Succinyl-CoA Synthetase • Free energy in thioester bond of succinyl CoA is conserved as GTP (or ATP in plants and some bacteria) Chapter 12

37. 6. The Succinate Dehydrogenase (SDH) Complex • Located on the inner mitochondrial membrane, in contrast to other enzymes of the TCA cycle which are dissolved in the mitochondrial matrix • Complex of polypeptides, FAD and iron-sulfur clusters • Electrons are transferred from succinate to FADH2, then to ubiquinone (Q), a lipid-soluble mobile carrier of electrons • Reduced ubiquinone (QH2) is released as a mobile product Chapter 12

38. 7. Fumarase • Addition of water to the double bond of fumarate to form malate Chapter 12

39. 8. Malate Dehydrogenase • Oxidation of malate to oxaloacetate, with transfer of electrons to NAD+ to form NADH Chapter 12

40. The Glyoxylate Cycle • Pathway for the formation of glucose from noncarbohydrate precursors in plants, bacteria and yeast (not animals) • Glyoxylate cycle leads from 2-carbon compounds to glucose • In animals, acetyl CoA is not a carbon source for the net formation of glucose (2 carbons of acetyl CoA enter cycle, 2 are released as 2 CO2) • Allows for the formation of glucose from acetyl CoA • Ethanol or acetate can be metabolized to acetyl CoA and then to glucose via the glyoxylate cycle • Stored seed oils in plants are converted to carbohydrates during germination Chapter 12

41. Fig 13.14 The Glyoxylate Cycle bypasses the twodecarboxylation stepsof the citric acid cycle,conserving the carbon atoms as glyoxylate for synthesis of glucose. Germinating seeds use this pathway to synthesize sugar (glucose) from oil (triacylglycerols). Chapter 12

42. Glyoxylate cycle in germinating castor beans • Conversion of acetyl CoA to glucose requires the transfer of metabolites among three metabolic compartments(1) The glyoxysome (2) The cytosol (3) The mitochondria Chapter 12

43. Fig 13.14 Isocitrate lyase: first bypass enzyme of glyoxylate cycle Chapter 12

44. Malate synthase: second bypass enzyme of glyoxylate cycle Chapter 12

45. Bypass reactions of glyoxylate cycle Citric Acid Cycle Chapter 12