Biochem Final Pyruvate Processing/TCA Flashcards
where does each step of cell respiration take place?
glycolysis: cytosol in eukaryotes and prokaryotes
pyruvate processing and TCA: eukaryotes mitochondrial matrix, cytosol prokaryotes
ETC and oxidative phosphorylation: inner membrane mitochondria or plasma membrane of prokaryotes
which TCA enzyme is found outside the mitochondrial matrix?
succinate dehydrogenase is found in the inner mitochondrial membrane
through fermentation or anaerobic respiration pyruvate can form
fermentation: ethanol and CO2
anaerobic respiration: lactate
pyruvate conversion to acetyl coA
is oxidative decarboxylation of pyruvate
1. carboxyl is removed and CO2 is released
2. NAD+ is reduced
3. an acetyl group is transferred to coenzyme A forming acetyl coA
what catalyzes oxidative decarboxylation of pyruvate?
coenzymes and co-substrates
how is it regulated?
pyruvate dehydrogenase complex (3 enzymes)
coenzymes: TPP (thiamine pyrophosphate), lipoyl lysine, FAD, NAD+, CoA-SH
co-substrates: NAD+ and CoA-SH
regulated by feedback inhibition of products from glycolysis and pyruvate processing
enzyme 1, 2 and 3 pyruvate dehydrogenase complex
- decarboxylation of pyruvate to form aldehyde
- oxidation of aldehyde to form carboxylic acid
cofactor: TTP (binds aldehyde stage), lipoyl lysine is reduced - formation of acetyl coA
cofactor: lipoyl lysine binds carboxylic acid, coA-SH - reoxidation of lipoamide cofactor
- regeneration of oxidixed FAD cofactor, and formation of NADH
cofactor: FAD and NAD+
are coenzyme associated permanently with pyruvate dehydrogenase complex?
no, they associate, fill function and then disassociate
function of CoA
to accept and carry acetyl groups to the TCA
amphibolic
involving catabolism (breaking down) and anabolism (building)
TCA condensation of acetyl coA and oxaloacetate
Step 1: condensation of acetyl CoA and oxaloacetate into citrate
catalyzed by citrate synthase (carbon bonds formed)
1 H2O used, 1 CoA-SH released
rate limiting step
thermodynamically favorable/irreversible
regulated by substrate availability (oxaloacetate) and product inhibiion
TCA isomerization by dehydration/rehydration to form C=C bond
Step 2: condensation reaction of citrate to form cis-aconitate intermediate, then hydration reaction to form isocitrate
catalyzed both times by aconitase
creates better substrate for oxidation
thermodynamically unfavorable/reversible
TCA oxidative decarboxylation #1
Step 3: loss of 1 carbon from isocitrate by oxidative decarboxylation to form alpha-ketoglutarate + CO2 + NADH + H+
intermediate formed: oxalosuccinate
catalyzed by isocitrate dehydrogenase. NAD(P)+ and Mn2+
thermodynamically favorable/irreversible
regulated by ATP
TCA oxidative decarboxylation #2
Step 4: last oxidative decarboxylation of alpha-ketoglutarate to succinyl-coA + CO2 + NADH
catalyzed by alpha-ketoglutarate dehydrogenase complex: CoA-SH and NAD+
same enzymes as pyruvate dehydrogenase complex
thermodynamically favorable/irreversible
regulated by product inhibition
high energy molecules in TCA
thioester bonds
acetyl-CoA and succinyl-coA
TCA generation of GTP
Step 5: succinyl-coA (thioester) to succinate, forms phospho-enzyme intermediate
catalyzed by succinyl-CoA synthetase
GTP and CoA-SH released
slightly thermodynamically favorable/reversible
GTP can be converted to ATP
TCA oxidation of alkane to alkene
Step 6: oxidation of succinate to fumarate (alkene) + FADH2
catalyzed by succinate dehydrogenase and FAD (covalently bound)
bound by mitochondrial inner membrane (part of ETC)
near equilibrium/reversible
TCA hydration across double bond
Step 7: trans addition of H2O to fumarate to form L-malate (with carboanion transition state)
catalyzed by fumarase -OH then H+
slightly thermodynamically favorable/reversible
TCA oxidation of alcohol to ketone
Step 8: oxidation of L-malate to oxaloacetate (regeneration) and NADH + H+
catalyzed by L-malate dehydrogenase and NAD+
thermodynamically unfavorable/reversible
oxaloacetate concentration kept very low by citrate synthase
Net production of 1 turn of CAC
Consumed: 1 acetyl CoA, 3 NAD+, 1 FAD, 1 GDP, Pi, 2 H2O
Produced: CoA, 2 CO2, 3 NADH, 1 FADH2, 1 GTP, 3H+
anaplerotic
intermediates in CAC can be used in biosynthetic pathways
4 anaplerotic pathways to know:
1. pyruvate –> malate by malic enzyme
2. phosphoenolpyruvate –> oxaloacetate by PEP carboxylase or PEP carboxykinase
3. pyruvate –> oxaloacetate by pyruvate carboxylase
all involve 4C intermediates forming 3C intermediates
steps of TCA where NADH is produced
Step 3: isocitrate dehydrogenase
Step 4: a-ketoglutarate dehydrogenase complex
Step 8: L-malate dehydrogenase
FADH2 is produced during which TCA
GTP is produced during which TCA step
Step 6: succinate dehydrogenase (forms fumarate)
Step 5: succinyl coA synthetase (forms succinate)
CoA-SH is required or produced in which TCA steps
Step 1: citrate formation, CoA-SH produced
Step 4: succinyl coA formation, CoA-SH required
Step 5: succinate formation, CoA-SH produced
irreversible TCA steps
steps 1, 3, 4
every time there is a dehydrogenase
it is an oxidation reaction that produces NADH or FADH2
3 enzymes of pyruvate oxidation
E1: pyruvate dehydrogenase
E2: dihydrolipoyl transacetylase
E3: dihydrolipoyl dehydrogenase
lipoamide cofactor
cofactor for pyruvate dehydrogenase in pyruvate oxidation, reduced to transform aldehyde into carboxylic acid (E1)
reduced and then reoxidized by dihydrolipoyl dehydrogenase (E3)
products of 1 pyruvate oxidation
1 acetyl coA and 1 NADH and 1 CO2
flow of water molecules in TCA
step 1: H2O used in condensation rxn (loss 1 water)
Step 2: H2O is used and then remade in aconitase rxns
Step 7: fumarase adds -OH and H+ separately to form L-malate
net loss of 2 water molecules
steps where CO2 is produced
Step 3: isocitrate dehydrogenase
Step 4: alpha ketoglutarate dehydrogenase complex
H+ production steps
step 3: isocitrate dehydrogenase to a-ketoglutarate: NADH H+
Step 4: a-ketoglutarate dehydrogenase complex to succinyl coA: NADH H+
step 8: L-malate dehydrogenase to oxaloacetate: NADH H+
coenzyme A produced in CAC
1 net produced
Step 1: 1 released
Step 4: 1 used to make succinyl-coA
Step: 5: 1 released to make succinate
