1. ATP is the cell’s “energy” BUT –Cells also have….REDUCING POWER! Processes (such as photosynthesis) require NADPH as well as ATP NADH and NADPH are NOT interchangable Pentose Phosphate Pathway Hexose monophosphate (HMP) shunt / Phosphogluconate pathway.

2. NADH and NADPH are NOT interchangable NAD + participates in synthesis of ATP glycoloysis, oxidative phosphorylation NADPH is a reducing agent produced in light reactions and consumed in Calvin cycle of photosynthesis NADP + + 2H ---> NADPH + H + In the cell… [NAD+] ~ 1000 [NADP+] ~ 0.01 [NADH] [NADPH]

3. 1C5 to 1C5 2C5 to 2C5 2C5 to 1C7 + 1C3 3C6 3C5 3C1 1C7 + 1C3 to 1C6 + 1C4 1C4 + 1C5 to 1C6 + 1C3

7. Summary of carbon skeleton rearrangements in the pentose phosphate pathway. 3C 6 ---> 3C 5 + 3C 1 2 3 2

8. 3 ribulose-5-P ---> 2 xylulose-5-P + 1 ribose-5-P

10. Transketolase: catalyzes the transfer of C2 units

11. C3C3 C7C7 CH 3

12. Transaldolase: catalyzes the transfer of C3 units

13. C7C7 C4C4 C6C6 C3C3

14. C5C5 C3C3 C4C4 C6C6

15. Summary of the pentose phosphate pathway 3G6P + 6NADP + + 3H 2 O 6NADPH + 6H + + 3CO 2 + 2F6P + GAP Important intermediates Ribose-5-phosphate (nucleic acids, histidine) Erythrose-4-phosphate (aromatic amino acids)

16. What is the purpose of the pentose phosphate pathway? 1)Biosynthetic precursors 2)NADPH for biosynthesis 3)NADPH to keep cell reduced

17. O 2 + 2e - + 2H + ----> H 2 O 2 H 2 O 2 + 2e - + 2H + ----> 2H 2 O O 2 + 4H + + 4e - ----> 2H 2 O Eº (V) vs. NHE +0.28 +1.35 +0.82 Oxygen Biochemistry Reduction of O 2 or H 2 O 2 can be used as a thermodynamic driving force to drive oxidation of various molecules

18. O 2 + 2e - + 2H + ----> H 2 O 2 S ----> S 2+ + 2e - O 2 + 4e - + 2H + ----> 2H 2 O 2S ----> 2S 2+ + 4e - H 2 O 2 + 2e - + 2H + ----> 2H 2 O S ----> S 2+ + 2e - Oxidative Damage

19. Peptide and phosphodiester cleavage Iron-sulfur cluster disassembly

20. Oxygen Diradical OO 1s 2s 2p x 2p y 2p z 1s 2s 2p x 2p y 2p z  2s  2s*  1s  1s*  2p x  2p x *

21. 3 O 2 (up/up) + 1 X (paired) ---> 1 XO 2 (paired) 1 O 2 (paired) + 1 X (paired) ---> 1 XO 2 (paired) 3 O 2 (up/up) + 3 X (up/up) ---> 1 XO 2 (paired) Need to alleviate spin restriction

22. O 2 + e - ----> O 2 - O 2 - + e - + 2H + ----> H 2 O 2 H 2 O 2 + e - + H + ----> H 2 O + OH OH + e - + H + ----> H 2 O O 2 + 2e - + 2H + ----> H 2 O 2 H 2 O 2 + 2e - + 2H + ----> 2H 2 O O 2 + 4H + + 4e - ----> 2H 2 O Eº (V) vs. NHE -0.33 +0.89 +0.38 +2.31 +0.28 +1.35 +0.82

23. Homolytic peroxide cleavage

24. Heterolytic peroxide cleavage: The Fenton Reaction Eº = +0.38 V Catalyzed by metals like iron and copper

25. OH + RH ----> H 2 O + R R + O 2 ----> ROO RH + ROO ----> R + ROOH

26. Antioxidants

29. Initiation X 2 ----> 2X X + RH ----> XH + R Propagation R + O 2 ----> ROO ROO + RH ----> ROOH + R Termination R + ROO ----> ROOR R + R ----> R 2 ROO + ROO ----> ROOOOR ----> O 2 + ROOR Free Radical Chain Reactions X = OH, O 2 -, O 2

30. If R = lipid The E/C couple Termination R + EH ----> RH + E ROO + EH ----> ROOH + E Recovery AH - + E ----> A - + EH A - + E ----> A + EH A + NADPH ----> AH - + NADP + 1/6Glucose + NADP + ----> 1/3CO 2 + NADPH DHAR DHAR = dehydroascorbate reductase PPP = pentose phosphate pathway PPP or Photosynthesis

31. If R = soluble, C or GSH Termination R + AH - ----> RH + A - ROO + AH - ----> ROOH + A - 2A - + H + ----> AH - + A Recovery A + NADPH ----> AH - + NADP + 1/6Glucose + NADP + ----> 1/3CO 2 + NADPH Termination R + GSH ----> RH + GS ROO + GSH ----> ROOH + GS 2GS ----> GSSG Recovery GSSG + NADPH + H + ----> 2GSH + NADP + 1/6Glucose + NADP + ----> 1/3CO 2 + NADPH

32. Peroxide reduction Eº = +1.35 V Can be used to extract hydrides from substrates

33. Oxygen reduction Eº = +0.82 V Can be used to extract hydrides from substrates

34. Acetyl-CoA Some Bacteria/Plants CO 2 fixation Fungi/plants

35. Extant ways of fixing CO 2 Reductive TCA cycle Calvin Cycle Acetyl-CoA Synthase

36. Reversing the TCA Cycle Pyruvate ∆G ~ 0 ∆G <<< 0

37. How do you reverse KGDH? Ketoglutarate synthase 2-oxoglutarate:ferredoxin oxidoreductase Photosynthetic bacteria Anaerobic bacteria

38. What about isocitrate dehydrogenase? This step can be made reversible if you use a different source of electrons. Use NADPH instead of NADH.

39. Citrate lyase

40. Pyruvate synthase Acetyl-CoA + CO 2 ---> pyruvate Pyruvate:ferredoxin oxidoreductase Photosynthetic bacteria Anaerobic bacteria

41. Furdui, C. et al. J. Biol. Chem. 2000;275:28494-28499 Other bacteria

42. The Calvin cycle. 3CO 2 -----> GAP 9 ATP and 6 NADPH

44. 3C5 3C1 6C3 1C3 C6 C3+C3 C3+C4 C6+C3 C5 C4 C7+C3 C7 C5

45. Most important enzyme is Ribulose-5- phosphate carboxylase (Rubisco)

47. Transketolase: catalyzes the transfer of C2 units Aldolase: catalyzes the condensation of C3 ketoses with aldoses

48. C3 + C3 ---> C6 C3 + C6 ---> C4 + C5 C3 + C4 ---> C7 C3 + C7 ---> C5 + C5 Overal reaction = 5C3 ---> 3C5 1 GAP molecule is made from 3CO 2 3CO 2 + 9ATP + 6NADPH ---> GAP + 9ADP + 8P i + 6NADP + GAP is converted to glucose by gluconeogenesis

49. C3 + C3 = C6 Aldolase Reverse of the step in glycolysis

50. C3 + C6 = C4 + C5 Transketolase

51. Acetyl-CoA synthase The Wood-Ljungdahl Pathway 2 CO 2 ----> Acetyl-CoA

52. Western Branch Eastern Branch

53. CH 3, CH 2 OH, and CHO transfer

54. Corrinoid CH 3 transfer

55. Formate dehydrogenase Can also use Mo H- from NADPH

57. CODH: carbon monoxide dehydrogenase

58. Acetyl-CoA synthase

59. Assimilating Acetyl-CoA:The glyoxalate cycle

60. Acetyl CoA Citrate Synthase Oxaloacetate Claisen condensation Ligase

61. Aconitase: lyase

62. Isocitrate lyase

63. Malate synthase

64. Malate Dehydrogenase

66. Acetyl-CoA Some Bacteria/Plants CO 2 fixation Fungi/plants

67. Pyruvate AA’s AA’s, Acetyl-CoA AA’s FA’s, AA’s

68. Malate Pyruvate Malate dehydrogenase/cytosolic Oxaloacetate Glycolytic intermediates Pyruvate carboxylase PEP Carboxykinase

69. ∆G ~ 0 ∆G <<< 0 ∆G ~ 0 ∆G <<< 0

70. Pyruvate Carboxylase

72. Fructose-1,6-bisphosphate + H 2 O ---> fructose-6-phosphate + P i ∆G’º = -16.3 kJ/mol Glucose-6-phosphate + H 2 O ---> glucose + P i ∆G’º = -13.8 kJ/mol