3 - Citric Acid Cycle

• The Krebs Cycle was first discovered by Hans Krebs in 1937
• The acetyl unit contains 2 carbon atoms
• 4C oxaloacetate becomes 6C citrate via a condensation reaction with the 2C acetyl unit forming citryl CoA, then a hydrolysis reaction to form citrate
• 6C citrate is isomerised into 6C isocitrate
• 6C isocitrate is decarboxylated into 5C a-ketoglutarate
• 5C a-ketoglutarate is decarboxylated into 4C succinyl-CoA
• The citric acid is made up of purely catabolic reactions
• The intermediates in the citric acid cycle go from a more reduced state to a more oxidised state (loss of electrons, carried away by electron carriers- NAD+ and FADH)

  
• Citrate formation from oxaloacetate is catalysed by citrate synthase

  
• The intermediate between oxaloacetate and citrate is citryl CoA, which is relatively unstable. The thioester bond is broken via hydrolysis to release coenzyme A
• The energy released from the hydrolysis of the energy-rich thioester bond in citryl CoA drives the condensation reaction between oxaloacetate and acetyl CoA
• Mammalian citrate synthase is made of 2 identical subunits of 49 kDa
• Citrate synthase undergoes a conformational change when oxaloacetate binds, creating a binding site for acetyl CoA which forces sequential binding and prevents wasteful enzyme activity in the absence of oxaloacetate
• The open form of citrate synthase binds to oxaloacetate, then after a major conformational change of the 2 identical subunits, the closed form binds to acetyl CoA
• If there was no sequential binding of citrate synthase, then it would hydrolyse the thioester bond of acetyl CoA as a wasteful side reaction
• Citrate undergoes dehydration and rehydration to change the position of a H atom and OH group to form isocitrate, with cis-actonitate as an intermediate

  
• The isomerisation of citrate into isocitrate is catalysed by aconitase
• The first oxidative decarboxylation of the citric acid cycle happens to isocitrate
• Isocitrate is oxidised to oxalosuccinate (losing 2 electrons to NAD+) which is then decarboxylated into a-ketoglutarate

  
• a-ketoglutarate formation is catalysed by isocitrate dehydrogenase
• Oxalosuccinate (intermediate between isocitrate and a-ketoglutarate) is unstable and remains bound to isocitrate dehydrogenase enzyme
• a-ketoglutarate is combined with NAD+ and coenzyme A to form succinyl CoA, CO2 and NADH in an oxidative decarboxylation reaction catalysed by a-ketoglutarate dehydrogenase
• a-ketoglutarate dehydrogenase has a very similar structure to PDH, with the same 5 cofactors (NAD, coenzyme A, FAD, lipoamide, thiamine pyrophosphate)
• a-ketoglutarate dehydrogenase subunit functions:

  • E1 = decarboxylation
  • E2 = formation of succinyl CoA
  • E3 = sequential reduction of FAD and NAD+
• Thiamine deficiency can induce low activities of a-ketoglutarate dehydrogenase as well as PDH, causing Beriberi but also associated with amnesia and nystagmus (uncontrollable eye movements)
• Energy is transferred from succinyl CoA to succinate using succinyl CoA synthetase

  
• Succinyl CoA + Pi + GDP --> Succinate + Coenzyme A + GTP
• The energy from the thioester bond on succinyl CoA is transfered to a phosphoanhydride bond on GTP
• Succinyl CoA synthetase facilitates energy transfer due to the imidazole rings on its conserved Histidine residue which contain Nitrogen atoms that are able to change oxidation states and act as an electron sink
• The intermediate between succinyl CoA and succinate is the phosphorylated succinyl phosphate
• Succinate is oxidised to fumarate using FAD (which gains 2 electrons to form FADH2)
• Succinate is oxidised to fumarate using FAD (which gains 2 electrons to form FADH2) via succinate dehydrogenase
• Succinate dehydrogenase is the only enzyme of the citric acid cycle that is bound to the inner membrane of the mitochondria
• Succinate dehydrogenase has 2 subunits in a dimer, 70 and 27 kDa each
• FAD is bound to succinate dehydrogenase and FADH2 transfers electrons to the Fe-S clusters of the enzyme
• Succinate dehydrogenase has 2 different types of Fe-S cluster:

  • 2Fe-2S
  • 3Fe-4S
  • 4Fe-4S
• Electrons are passed through the Fe-S centres of succinate dehydrogenase before the ETC because of iron's capability to transition from oxidised to reduced forms
• Fumarate is hydrated to malate via fumarase

  
• The two possible mechanisms of fumarate hydration:

  • Via an electron-rich carbocanion state (binds to OH group first, then H+)
  • Via a carbocation transition state (binds to H+ first, then OH group)
• Malate is oxidised to oxaloacetate using NAD+ via malate dehydrogenase