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Biochemistry I > Biochem Final Pyruvate Processing/TCA > Flashcards

Biochem Final Pyruvate Processing/TCA Flashcards

1
Q

where does each step of cell respiration take place?

A

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

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2
Q

which TCA enzyme is found outside the mitochondrial matrix?

A

succinate dehydrogenase is found in the inner mitochondrial membrane

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3
Q

through fermentation or anaerobic respiration pyruvate can form

A

fermentation: ethanol and CO2
anaerobic respiration: lactate

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4
Q

pyruvate conversion to acetyl coA

A

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

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5
Q

what catalyzes oxidative decarboxylation of pyruvate?
coenzymes and co-substrates
how is it regulated?

A

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

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6
Q

enzyme 1, 2 and 3 pyruvate dehydrogenase complex

A
  1. decarboxylation of pyruvate to form aldehyde
  2. oxidation of aldehyde to form carboxylic acid
    cofactor: TTP (binds aldehyde stage), lipoyl lysine is reduced
  3. formation of acetyl coA
    cofactor: lipoyl lysine binds carboxylic acid, coA-SH
  4. reoxidation of lipoamide cofactor
  5. regeneration of oxidixed FAD cofactor, and formation of NADH
    cofactor: FAD and NAD+
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7
Q

are coenzyme associated permanently with pyruvate dehydrogenase complex?

A

no, they associate, fill function and then disassociate

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8
Q

function of CoA

A

to accept and carry acetyl groups to the TCA

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9
Q

amphibolic

A

involving catabolism (breaking down) and anabolism (building)

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10
Q

TCA condensation of acetyl coA and oxaloacetate

A

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

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11
Q

TCA isomerization by dehydration/rehydration to form C=C bond

A

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

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12
Q

TCA oxidative decarboxylation #1

A

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

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13
Q

TCA oxidative decarboxylation #2

A

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

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14
Q

high energy molecules in TCA
thioester bonds

A

acetyl-CoA and succinyl-coA

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15
Q

TCA generation of GTP

A

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

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16
Q

TCA oxidation of alkane to alkene

A

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

17
Q

TCA hydration across double bond

A

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

18
Q

TCA oxidation of alcohol to ketone

A

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

19
Q

Net production of 1 turn of CAC

A

Consumed: 1 acetyl CoA, 3 NAD+, 1 FAD, 1 GDP, Pi, 2 H2O

Produced: CoA, 2 CO2, 3 NADH, 1 FADH2, 1 GTP, 3H+

20
Q

anaplerotic

A

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

21
Q

steps of TCA where NADH is produced

A

Step 3: isocitrate dehydrogenase
Step 4: a-ketoglutarate dehydrogenase complex
Step 8: L-malate dehydrogenase

22
Q

FADH2 is produced during which TCA

GTP is produced during which TCA step

A

Step 6: succinate dehydrogenase (forms fumarate)

Step 5: succinyl coA synthetase (forms succinate)

23
Q

CoA-SH is required or produced in which TCA steps

A

Step 1: citrate formation, CoA-SH produced
Step 4: succinyl coA formation, CoA-SH required
Step 5: succinate formation, CoA-SH produced

24
Q

irreversible TCA steps

A

steps 1, 3, 4

25
Q

every time there is a dehydrogenase

A

it is an oxidation reaction that produces NADH or FADH2

26
Q

3 enzymes of pyruvate oxidation

A

E1: pyruvate dehydrogenase
E2: dihydrolipoyl transacetylase
E3: dihydrolipoyl dehydrogenase

27
Q

lipoamide cofactor

A

cofactor for pyruvate dehydrogenase in pyruvate oxidation, reduced to transform aldehyde into carboxylic acid (E1)
reduced and then reoxidized by dihydrolipoyl dehydrogenase (E3)

28
Q

products of 1 pyruvate oxidation

A

1 acetyl coA and 1 NADH and 1 CO2

29
Q

flow of water molecules in TCA

A

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

30
Q

steps where CO2 is produced

A

Step 3: isocitrate dehydrogenase
Step 4: alpha ketoglutarate dehydrogenase complex

31
Q

H+ production steps

A

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+

32
Q

coenzyme A produced in CAC

A

1 net produced
Step 1: 1 released
Step 4: 1 used to make succinyl-coA
Step: 5: 1 released to make succinate

Biochemistry I (12 decks)

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