Day 37

Question 1

Reaction 1 CAC: Citrate Synthase

Answer 1

• Catalyzes condenstaion of oxaloacetate and acetyl-CoA
• Dimer with open and closed conformations where open binds oxaloacetate and causes conformational change to allow acetyl Co-A binding site to open.
  1) removal of proton from methyl group of acetyl-CoA (base catalysis)
  2) formation of citryl-CoA by nucleophilic attack of enolate on oxaloacetate
  3) hydrolysis of citryl-CoA to citrate and CoA

Question 2

Reaction 2 CAC: Aconitase

Answer 2

• do not need to know
• citrate becomes isocitrate
• dehydration followed by rehydration gives right stereoisomer
• Some iron cluster thing

Question 3

Reaction 3 CAC: Isocitrate Dehydrogenase

Answer 3

• Decarboxylation of isocitrate to alpha-ketoglutarate which produces CO2 and NADH and the carbon on carbon dioxide comes from oxaloacetate not Acetyl CoA)
• requires NAD+ and either Mn2+ or Mg2+
• Isocitrate’s secondary alcohol is oxidized so that (NAD+) = NADH + (H+) and produces oxalosuccinate. This then does some interconversions and decarboxylation releases CO2. Add that H+ from earlier and you get alpha-ketoglutarate

Question 4

Reaction 4 CAC: alpha-ketoglutarate dehydrogenase

Answer 4

• similar to pyruvate dehydrogenase and has
  E1: ketoglutarate dehydrogenase
  E2: dihydrolipoyl transsuccinylase
  E3: dihydrolipoyl dehydrogenase (same as other one)
• decarboxylation of the alpha-keto group to produce Succinyl-CoA
  (CoASH) + (NAD+) —- (CO2) + (NADH + H+)
• carbons from oxaloacetate

Question 5

Reaction 5 CAC: Succinyl-CoA Synthetase

Answer 5

• don’t need to know
• couples cleavage of succinyl-CoA to sythesis of “high energy” nucleotide (GTP in animals ATP in plants but that nucleoside diphosphate kinase)
• succinyl CoA + Pi + GDP —– Succinate + CoA + GTP
• three step deal

Question 6

Reaction 6 CAC: Succinate Dehydrogenase

Answer 6

• dehydration of succinate to fumarate
• malonate looks like succinate and so acts like a strong competitive inhibitor for succinate dehydrogenase
• Catalyzes via covalently attached FAD
• FADH2 is reoxidized when electrons are transported through the electron transport chain
  succinate + E-FAD —- Fumarate + E-FADH2

Question 7

Reaction 7 CAC: Fumarase

Answer 7

• don’t need to know

- hydration of double bond in fumarate gets malate in two steps (carbanion transition state where OH- is added then H+)

Question 8

Reaction 8 CAC: Malate Dehydrogenase

Answer 8

• Regeneration of oxaloacetate though hydride transfer to NAD+
• Standard free energy is endergonic (+29.7kJ/mol) so very little malate is made into oxaloacetate
• When citrate is made, very very exergonic!
• Good so that this reaction will proceed even with the low oxaloacetate concentration

Question 9

The Citric Acid Cycle

Answer 9

1 glucose — 2 pyruvates — 2 acetyl CoA
2 CO2 released
2 NADH + H+ made

CAC (oxidation of acetyl group on acetyl-CoA to CO2 is a four elecron pair redox process with 3 to NAD+ and 1 to FAD+)
- acetyl CoA enters, adds acetyl group (C2) to oxaloacetate (C4) to make citrate (C6)
CO2 realeased twice
Oxidation/Reduction at 4 steps:
3 NADH + H+ made
1 FADH2
1 ATP generated directly 
2 turns per glucose.