Citric acid cycle Flashcards
What is Step 4 of the citric acid cycle
oxidative decarboxylation of a alpha ketoglutarate
(alpha-ketoglutaate dehydrogenase complex)
- reaction mechanism is identical to that of pyruvate dehydrogenase complex
- coverts alpha-ketoglutarate to the high energy thioester succinyl CoA
What is step 8 of the citric acid cycle
oxidation of Malate to Oxaloacetate
- malate is oxidized to oxaloacetate by NAD+ completing the cycle
- analogous to the hydroxyacyl CoA dehydrogenase rxn of beta oxidation
Starts with: Malate
enzyme: Malate dehydrogenase
cofactor: NAD+
Produces: Oxaloacetate
How does NADH + H+ get across membrane in liver kidney and heart
- special shuttle systems are required to carry reducing equivalents from cytosolic NADH to mitochondria as the IMM is impermeable to NADH
- malate-aspartate shuttle (liver, kidney,heart)
*malate is acting as the shuttle, going across membrane bringing electrons with it, once inside the matrix reverse of reaction happens
- malate is oxidized back to oxaloacetate and reduced NAD+ to NADH + H+
*NADH itself does not cross, they are present in both cytoplasm and inside mitochondria
-
What is the Cori Cycle
- during recovery from strenuous exercise, some lactate produced in muscles is exported to liver via blood
- liver converts lactate back to glucose through gluconeogenesis
- glucse is then returned to muscles to replenish muscle glycogen stores
- exchange of metabolities between rogans known as cori cycle
*why under anerobic conditions is pyruvate converted to lactate: cori cycle gets rid of lactate because want to oxidate cofactors
What is the Net effect of the citric acid cycle
= the two carbons of the acetyl group of acetyl-CoA are oxized to CO@
- electrons form the oxidation reduce #NAD+ and 1 FAD
- one GTP (or ATP) is formed per cycle
- intermediates in cycle are not deplated
Consider: what is the most important role of the TCA cycle in term of bioenergetics (ATP generation): biggest role is generation of the cofactors
What is step 1 of the Citric acid Cycle
Condensation of Acetyl CoA with oxaloacetate to form citrate (citrate synthase)
- this is only TCA step forming a C-C bond
Starts with: Acetyl CoA + Oxaloacetate
Enzyme: Citrate Synthase *synthase does not require ATP
cofactor: H2O -> CoASH
Produces: Citrate
*Methyl of acetyl CoA acts as the nucleophile once it has been deprotonated by the enzyme, which is odd, this happens because enzyme removes a proton and has a lone pair available
What is step 6 of the citric acid cycle
- oxidation of succinate to fumarate
(succinate dehydrogenase)
- succinate dehydrogenase uses FAD to oxidize succinate to the alkene fumarate
succinate needs to be converted back to oxaloacetate
*this reaction is analogous to the acyl CoA dehydrogenase reaction of Beta-oxidation
Starts with: succinate
Enzyme: succinate dehydrogenase
Cofactor: FAD -> FADH2
Produces: Fumarate
What is the outcome of pyruvate under aerobic conditions
*in aerobic, pyruvate was not needed to reoxidize NADH
- oxidized to Acetyl CoA by pyruvate dehydrogenase
- pyruvate is transported into mitochondria thorugh a transporter
- pyruvate dehydrogenase (PDH) occurs in mitochondiral matrix and catalyzes an irreversible oxidative decarboxylation
- PDH occupies a kew posiiton in metabolism: it is the link between glycolysis and the cirtic acid cycle
How does NADH pass membrane in skeletal muscle and the brain
* do not have malate shuttle
- reduce dihydroxyacetone phosphate to glycerol 3 phosphate
- reducing equivalents from cytosolic NADH are passed onto FADH2 and are directly delivered to coenzyme Q of ETC bypassing complex 1
*compare shuttle systems, other one molecule crosses membrane and when inside reoxidzied, here molecule does not cross membrane, here mitochondrial glycerol 3 phosphate dehydrogenase sits on membrane
How is pyruvate further metabolized
- purpose is to regenerate NAD+
- via one of three different routs depending on prevailing physiological condition
- cells have limited amounts of NAD+ (as well as FAD)
- Once NAD+ is converted to NADH in a reaction, it needs to be oxidized back to NAD+
- metabolism of pyruvaet depends on the route that is availble to oxidize the NADH that is formed in the G3PDH reaction of glycolysis
- ensures that glycolysis can function under both aerobic and anaerobic conditions
*need oxygen bc limited amount of cofactors, need oxygen to reoxidize
How is NAD+ regenerated under anaerobic conditions in animals
- reduce pyruvate to lactate regenerating the NAD+ used by G3P dehydrogenase
- tissues use pyruvate itself to reoxidize NADH, pyruvate is reduced to lactatic acid by lactate dehydrogenase, regenerating the NAD+ necessary to continue glycolysis *occurs in cytosol*
*red blood cells are completely dependent on glycolysis for energy, no mitochondria (location of beta oxidation, citric acid cycle and ETC,) presece of oxygen is not important because can’t send to ETC, needs this reaction
*only 2 ATP
***Look at questions on slide 2
What does isocitrate dehydrogenase do
Isocitrate into alpha keto glutarate +CO2
- uses NAD+ as cofactor
What is stpe 2 of the citric acid acycle
Isomerization of citrate by aconitase
Starts with: Citrate
Enzyme: aconitase
intermediate: Cis aconitate
produces: Isocitrate
- Cirtate ____ is a poor substrate for oxidation
- elimination of H2O from citrate gives a Cis C=C bond
- hydration of Cis-aconitatie gives the secondary alcohol isocitrate
What is Step 7 of the cirtic acid cycle
hydration of fumarate to malate
- the alkene, fumarate is hydrated to the alcohol malate
*analogous to the enoyl- CoA hydratase reaction of B oxidation
Starts with: Fumarate
Enzyme: fumarase
cofactor: none but H2O added
produces: malate
What is step 5 of the citric acid cycle
substrate level phosphorylation
*succinyl CoA synthetase
- high energy thioester bond of succinyl CoA is hydrolyzed in a reaction douples ot either DTP or ATP synthesis
- this step involes formation of a phosphoenzyme intermediate
- has thioester bond (high energy bond)
starts with: Succinyl CoA
enzyme: Succinyl CoA synthetase
cofactor: CoASH, GDP +Pi -> GTP
produces: Succinate
What is step 3 of the citric acid cycle
oxidative decarboxylation of isocitrate (isocitrate dehydrogenase)
- the isocitrate dehydrogenase reaction involves the oxidation of the alcohol to a ketone through transfer of a hydride from C-H of the alcohol to NAD+ followed by the loss of the -COO group as CO2 (oxidative decarboxylation)
Starts with: Isocitrate
Enzyme: Isocitrate dehydrogenase
Cofactor: NAD+ -> NADH + H+
Produces: Alpha Ketoglutarate + CO2
*note glutarte has simialr structure to glutamate
What s the reaction mechanism of Succinyl CoA Synthetase
- inorganic phosphate displaces coenzyme A from succinyl CoA to form high energy acyl phosphate (succinyl phosphate)
- high energy thioester bond is brocken createing phosphorylated intermediate
- Reactive histidine residue at the active site of enzyme accepts the phosphate, releasing succinate
- THe phosphate is transfered fromt he phosphoenzyme to the ADP (or GDP) releasing the free enzyme
*energy in thioester bond used to regenerate ATP/GTP
*do not need to reproduce but understand it and explain
Who is Alber Szent Gyorgyi
- hungarian biochemist
- studied oxidation of different organic acids
- measuring respiration rate of muscle tissue preparations he found that several organic acids aceted catalytically
- addition of succinic acid to tissue preparation stimulated a burst in O2 consumption, larger than could be explained by oxidation of added auccinic acid
*one mol of sucinate and hundredes of moles of oxygen used
What des Aconitase do
Citrate into isocitrate
What is the Pyruvate Dehydrogenase Complex
- once acetyl CoA is formed will enter into teh TCA cycle
Starts with: pyruvate + CaASH
Coenzymes: NAD+, FAD , CoA, TPP and lipoate
Produces: acetyl CoA + CO2
- CoA is derivaed from b vitamins and TPP from vitamin B1;thiamine), if there is a deficiency in these vitamins reactin cannot proceed
What is TCA cycle
- the citric acid cycle: stage 2 of oxidation
- takes the acetate moieties derived from catabolism of fatsm carbohydrates and certain amino acids (in form of acetyl CoA) and oxidizes them completely to carbon dioxide
-- the energy released though these oxidations is conserved in the form of reduced cofactors NADH and FADH2
*aerobic metabolism because requires oxidation of cofactors through ETC
-
How is NAD+ regenerated in yeast and other microorganisms (convert pyruvate)
- convert pyruvate to ethanol and CO2
- always under aneraobic
* this regenerates NAD+ to allow glycolysis to happen
- require a large amount of glucose because only 2 mol ATP per mol glucose
- NAD+ is regenerated thorugh these reactions allowing glycolysis to continue under anerobic conditions
Start with: pyruvate
Enzyme: pyruvate decarboxylase
Cofactors: Mg2+, TPP (CO2 comes off)
intermediate: acetaldehyde
Enzyme: alcohol dehydrogenase
Cofactors: NADH +H+ -> NAD+
Produces: Ethanol
*animals do not have pyruvate decorboxylase, do have alcohol dehydrogenase but makes reaction rpoceed in opposite direction (NAD+ depended from ethanol to acetaldehyde)
What are reducing equivalents
electrons, possibly accompanied by protons (could be in form of electrons alone, H atoms or hydride ions (H-)
NADH + H+-> NAD+ (involves gain/loss of hydride ion)
What deos fumarase do
fumarate into malate
H2O added
What deos alpha ketaglutarate dehydrogenase do
alpha ketoglutarate into succinyl CoA
- uses NAD+ as a cofactor
- CoASH added and CO2 comes off
What does Malate Dehydrogenase do
Malate into oxaloacetate
- NAD+ is cofactor
How is NADH oxidized under aerobic condiations
- with the ETC
- since glycolsys occurs in cytosol, NADH needs to be transferred to the mitochondria in order to enter the ETC
What does Citrate synthase do
- Oxaloacetate and acytyl CoA into citrate
Who is Hans Krebs
- discovered TCA
- realized that metabolism of all these organic acids was linked together in a cyclic rather than linear pathway (hence the catalyitc consumption of O2 that was observed)
- another finding that helped unravel the Kerbs cycle was inhibition of respiration by malonate( a competitive inhibitor of succinate dehydrogenase) as subsequent accumulation of sucinate
What does succinate dehydrogenase do
Succinate into fumarate
- FAD as cofactor
Who is Franz Knoop
- same scientist that discovered beta oxidation
- discovered a few reaction of the TCA cycle
What deos succinyl CoA synthetase do
Succinyl CoA into succinate
- this reaction produces GTP from GDP +Pi
- CoASH is removed
What steps in CTA use NAD+ as cofactor
step 3, 4, 8
