1. Chapter 12 (part 1) Citric Acid Cycle

2. Gylcolysis Electron Transport and Oxidative phosphorylation TCA Cycle

3. The TCA Cycle • (aka Citric Acid Cycle, Krebs Cycle) • Pyruvate (actually acetate) from glycolysis is degraded to CO2 • Some ATP is produced • More NADH is made • NADH goes on to make more ATP in electron transport and oxidative phosphorylation

5. Entry into the TCA Cycle • Pyruvate is translocated from the cytosol to the mitochondria • Pyruvate is oxidatively decarboxylated to form acetyl-CoA • Pyruvate dehydrogenase uses TPP, CoASH, lipoic acid, FAD and NAD+ • Acetyl-CoA then enters TCA cycle thru citrate synthase

6. Pyruvate Dehydrogenase Complex Composed of three enzymes: • pyruvate dehydrogenase (E1) (cofactor = TPP) • Dihydrolipoamide acetyltransferase (E2) (cofactor = Lipoamide, CoA) • Dihydrolipoamide dehydrogenase (E3) (cofactor = FAD, NAD+)

7. Pyruvate Dehydrogenase

9. Citrate Synthase • Only step in TCA cycle that involves the formation of a C-C bond

11. Aconitase • Isomerization of Citrate to Isocitrate • Citrate is a poor substrate for oxidation • So aconitase isomerizes citrate to yield isocitrate which has a secondary-OH, which can be oxidized • Aconitase uses an iron-sulfur cluster to position citrate (binds –OH and carboxyl of central carbon)

13. Isocitrate Dehydrogenase • Oxidative decarboxylation of isocitrate to yield  -ketoglutarate • Classic NAD+ chemistry (hydride removal) followed by a decarboxylation • Isocitrate dehydrogenase is a link to the electron transport pathway because it makes NADH • Rxn is metabolically irreversible

15.  -Ketoglutarate Dehydrogenase • A second oxidative decarboxylation • This enzyme is nearly identical to pyruvate dehydrogenase - structurally and mechanistically • Five coenzymes used - TPP, CoASH, Lipoic acid, NAD+, FAD

17. Succinyl-CoA Synthetase • A substrate-level phosphorylation • A nucleoside triphosphate is made (ATP in plants/bacteria and GTP in animals) • Its synthesis is driven by hydrolysis of a CoA ester

19. Succinate Dehydrogenase • An oxidation involving FAD • Mechanism involves hydride removal by FAD and a deprotonation • This enzyme is actually part of the electron transport pathway in the inner mitochondrial membrane • The electrons transferred from succinate to FAD (to form FADH2) are passed directly to ubiquinone (UQ) in the electron transport pathway • Enzyme inhibited by malonate

21. Fumarase • Hydration across the double bond • trans-addition of the elements of water across the double bond • Stereospecific reaction

23. Malate Dehydrogenase • An NAD+-dependent oxidation • The carbon that gets oxidized is the one that received the-OH in the previous reaction • This reaction is energetically expensive • Go' = +30 kJ/mol

25. Reduced Coenzymes Fuel ATP Production • Acetyl-CoA + 3 NAD+ + Q + GDP + Pi +2 H20  HS-CoA + 3NADH + QH2 + GTP + 2 CO2 + 2 H+ • Isocitrate Dehydrogenase 1 NADH=2.5 ATP • a-ketoglutarate dehydrogenase 1 NADH=2.5 ATP • Succinyl-CoA synthetase 1 GTP=1 ATP • Sunccinate dehydrogenase 1 QH2=1.5 ATP • Malate Dehydrogenase 1 NADH=2.5 ATP • Total of 10 ATPs gained from oxidation of 1 Acetyl-CoA

27. Regulation of TCA Cycle

29. Protein/amino acid Catabolites feed Into the TCA Cycle

30. Fats breakdown and feed into the TCA Cycle

31. TCA Cycle provides intermediates for many biosynthetic processes

32. The Anaplerotic Reactions • The "filling up" reactions • PEP carboxylase - converts PEP to oxaloacetate • Pyruvate carboxylase - converts pyruvate to oxaloacetate • Malic enzyme converts pyruvate into malate

33. Following the carbons through the TCA cycle

34. The Glyoxylate Cycle • A variant of TCA for plants and bacteria • Acetate-based growth - net synthesis of carbohydrates and other intermediates from acetate - is not possible with TCA • Glyoxylate cycle offers a solution for plants and some bacteria and algae • The CO2-evolving steps are bypassed and an extra acetate is utilized • Isocitrate lyase and malate synthase are the short-circuiting enzymes

36. Glyoxylate Cycle • Rxns occur in specialized organelles (glycoxysomes) • Plants store carbon in seeds as oil • The glyoxylate cycle allows plants to use acetyl-CoA derived from B-oxidation of fatty acids for carbohydrate synthesis • Animals can not do this! Acetyl-CoA is totally oxidized to CO2 • Malate used in gluconeogenesis