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G2 2017-2018 > Biochemistry - Pyruvate Dehydrogenase & the TCA Cycle > Flashcards

Biochemistry - Pyruvate Dehydrogenase & the TCA Cycle Flashcards

1
Q

Where does conversion of pyruvate to acetyl-CoA happen?

A

Mitosol

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2
Q

Is the PDC reaction reversible or irreversible? Entirely?

A

Irreversible, but last 4 steps are reversible (first irreversible step makes the whole thing irreversible though)

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3
Q

What are the 3 enzymes of the PDC?

A

E1: pyruvate dehydrogenaseE2: dihydrolipoyl transcacetylase E3: dihydrolipoyl dehydrogenase

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4
Q

What is the cofactor in E1 of PDC? Vitamin precursor?

A

Thiamine pyrophosphate (TPP) = vitamin B1

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5
Q

What are the 2 cofactors in E2 of PDC? 2 names for 1st one? Vitamin precursor?

A
  1. Coenzyme A (panthothenic acid = B5)2. Lipoic acid
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6
Q

What are the 2 cofactors in E3 of PDC? Vitamin precursors?

A
  1. Flavin adenine dinucleotide (FAD) (riboflavin = B2)2. NAD (niacin = B3)
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7
Q

Of all of the cofactors used in PDC, which one is not considered a vitamin?

A

Lipoic acid

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8
Q

What are the 5 steps of pyruvate conversion to acetyl-CoA?

A
  1. E1: pyruvate decarboxylation: 2 Cs transfer to TPP (+ C=O reduced to C-OH) = hydroxyethyl TPP + CO22. E2: lipoic acid accepts 2Cs from TPP = LA acetylated form = acyl lipollysine3. E2: CoA accepts 2Cs from LA = Acetyl CoA + reduced LA4. E3: LA oxidized by FAD = oxidized LA (with disulfide bond) + FADH2 5. E3: FAHD2 oxidized by NAD+ + FAD + NADH
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9
Q

What are the 3 products of pyruvate conversion to acetyl CoA?

A
  1. Acetyl CoA2. NADH3. CO2
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10
Q

What are the 2 regulation mechanisms of the PDC?

A
  1. Product inhibition2. Covalent modification
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11
Q

Explain the product inhibition regulation of the PDC.

A

Acetyl CoA and NADH will drive the last 4 reactions of the PDC backward by competing with the binding sites on E2 and E3

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12
Q

Explain the covalent modification regulation of the PDC (inhibition and stimulation).

A

Inhibition: Build up of acetyl CoA and NADH will activate pyruvate dehydrogenase kinase, which will phosphorylate E1, inactivating itStimulation: Insulin will INDIRECTLY activate pyruvate dehydrogenase phosphatase which will dephosphorylate E1, activating it

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13
Q

What about CoA makes Acetyl CoA high in energy?

A

Very reactive thiol group (SH) in the beta-mercaptoethylamine end of CoA which binds the 2 carbons and contains a lot of energy

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14
Q

Can new TCA intermediates be made from acetyl-CoA?

A

NOPE

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15
Q

What are 4 ways to make TCA intermediates?

A
  1. Phosphoenolpyruvate conversion to oxaloacetate by PEPCK2. Pyruvate conversion to oxaloacetate by pyruvate carboxylase using ATP3. Pyruvate conversion to malate by malic enzyme2. Glutamate and aspartate conversion to alpha-ketoglutarate and oxaloacetate
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16
Q

What 5 steps of the TCA produces fuel (FADH2, NADH, ATP)?

A

3, 4, 5, 6, and 8

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17
Q

TCA step 1 enzyme?

A

Citrate synthase

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18
Q

TCA step 1 reactants/products?

A

Oxaloacetate + acetyl CoA + H2O = citrate + CoA-SH

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19
Q

How many Cs in citrate?

A

6

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20
Q

TCA step 1 ΔG°’? Why is this important?

A

Large negative ΔG°’ Important because oxaloacetate is present in very low concentrations in mitosol so it drives the reaction forward

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21
Q

TCA step 1: reversible or irreversible?

A

Irreversible

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22
Q

TCA step 2 enzyme?

A

Aconitase

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23
Q

TCA step 2 reactants/products?

A

Citrate –> cis-Aconitate + H2O–> Isocitrate

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24
Q

TCA step 2 ΔG°’?

A

Positive

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25
Q

TCA step 2: reversible or irreversible?

A

Reversible

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26
Q

TCA step 1: cofactor?

A

Water

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27
Q

TCA step 2: cofactor?

A

Water

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28
Q

TCA step 3 enzyme?

A

Isocitrate dehydrogenase

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29
Q

TCA step 3 reactants/products?

A

Isocitrate + NAD+ –> NADH + H+ + alpha-Ketoglutarate + CO2

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30
Q

TCA step 3 ΔG°’?

A

Large negative

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31
Q

TCA step 3: reversible or irreversible?

A

Irreversible

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32
Q

TCA step 3: cofactor?

A

NAD+

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33
Q

How many Cs in isocitrate?

A

6

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34
Q

How many Cs in alpha-ketoglutarate?

A

5

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35
Q

TCA step 4 enzyme?

A

Alpha-Ketoglutarate dehydrogenase complex

36
Q

TCA step 4 reactants/products?

A

alpha-Ketoglutarate + NAD+ + CoA –> Succinyl CoA + CO2 + NADH

37
Q

TCA step 4 ΔG°’?

A

Large negative

38
Q

TCA step 4: reversible or irreversible?

A

Irreversible

39
Q

TCA step 4: cofactor?

A

NAD+ and CoA-SH

40
Q

How many Cs in succinyl-CoA?

A

4

41
Q

What is notable about the alpha-Ketoglutarate dehydrogenase complex

A

Similar to PDC

42
Q

TCA step 5 enzyme?

A

Succinyl-CoA synthetase

43
Q

TCA step 5 reactants/products?

A

Succinyl CoA + Pi + GDP –> Succinate + CoA + GTP

44
Q

TCA step 5 ΔG°’?

A

Small negative

45
Q

TCA step 5: reversible or irreversible?

A

Reversible

46
Q

TCA step 5: cofactor?

A

GDP

47
Q

How many Cs in succinate?

A

4

48
Q

What 3 steps of the TCA are irreversible?

A

1, 3, and 4

49
Q

TCA step 6 enzyme?

A

Succinate dehydrogenase

50
Q

TCA step 6 reactants/products?

A

Succinate + FAD –> Fumarate + FADH2

51
Q

TCA step 6 ΔG°’?

A

0

52
Q

TCA step 6: reversible or irreversible?

A

Reversible

53
Q

TCA step 6: cofactor?

A

FAD

54
Q

How many Cs in fumarate?

A

4

55
Q

TCA step 7 enzyme?

A

Fumarase

56
Q

TCA step 7 reactants/products?

A

Fumarate + H2O –> L-malate

57
Q

TCA step 7 ΔG°’?

A

Small negative

58
Q

TCA step 7: reversible or irreversible?

A

Reversible

59
Q

TCA step 7: cofactor?

A

Water

60
Q

How many Cs in malate?

A

4

61
Q

TCA step 8 enzyme?

A

Malate dehydrogenase

62
Q

TCA step 8 reactants/products?

A

Malate + NAD+ –> oxaloacetate + NADH + H+

63
Q

TCA step 8 ΔG°’?

A

Large positive

64
Q

TCA step 8: reversible or irreversible?

A

Reversible

65
Q

TCA step 8: cofactor?

A

NAD+

66
Q

How many Cs in oxaloacetate?

A

4

67
Q

Where is the enzyme of the step 4 of the TCA (succinate dehydrogenase) located?

A

Inner membrane of mito: complex II

68
Q

How is the step 8 of the TCA driven forward?

A

Low concentrations of oxaloacetate

69
Q

Describe Wernick’s encephalopathy: 3 symptoms, 1 association, 1 cause?

A
  • Ocular abnormalities, ataxia, global confusion- Associated with chronic alcohol abuse- Cause: Thiamine/vitamin B1 deficiency
70
Q

Describe Pyruvate Dehydrogenase Complex Deficiency: type? onset? Symptoms type? 4 of them? Blood test? Cause?

A
  • X-linked genetic disorder - Manifested in infancy or later childhood - Neural symptoms: intermittent ataxia, poor muscle tone, abnormal eye movements, or seizure - Elevated blood lactate with a normal pyruvate/lactate ratio- Cause: defect in pyruvate dehydrogenase
71
Q

Describe Berberi. 5 symptoms and 1 cause?

A

Early manifestations include fatigue, irritability, sleep disturbance, abdominal pain, and anorexia.Cause: Thiamine=vitamin B1 deficiency

72
Q

What is the net rxn of the TCA?

A

AcetylCoA + 3NAD+ + FAD + GDP + Pi + 3H2O → 2CO2 + CoA + 3NADH + FADH2 + GTP + 2H+

73
Q

What 3 steps of the TCA require water as a cofactor?

A

1, 2, and 7

74
Q

What 2 steps of the TCA produce CO2?

A

3 and 4

75
Q

What kind of molecule is pyruvate?

A

Alpha-keto acid

76
Q

What happens to them when alpha keto acids are formed?

A

Taken up by mito

77
Q

What kind of molecule is acetyl-CoA? What is particular about these?

A

ThioesterVery unstable: high amount of energy

78
Q

Delta G of pyruvate conversion to acetyl-CoA?

A

Large (-)

79
Q

How is lipoic acid attached to E2?

A

Lys residue

80
Q

What does the rate of oxidation of acetyl-CoA depend on?

A

Concentration of oxaloacetate

81
Q

What’s aspartate’s role in biochemical reactions?

A

It can donate it’s nitrogen to become fumarate or oxaloacetate

82
Q

What happens to the acetyl-CoA when FA beta oxidation is high but gluconeogenesis using oxaloacetate is also high?

A

Too much acetyl CoA, can’t enter TCA => ketogenesis

83
Q

What do Wernicke encephalopathy, beriberi and pyruvate dehydrogenase complex deficiency have in common? Treatment for all three?

A

All have a deficient pyruvate dehydrogenase enzyme which causes neurological issues because the neurological cells do not have enough ATP. Treatment: ketogenic diet that tends to produce many ketone bodies for the brain

84
Q

What TCA intermediate is the most oxidized?

A

Oxaloacetate

85
Q

What are the 3 parts of CoA?

A
  1. ADP2. Pantothenic acid (VB5)3. Beta-mercaptoethylamine (with SH group)
86
Q

What does it mean for all of the cofactors used by the PDC to be essential nutrients?

A

We cannot synthesize them and obtain them from our diet

G2 2017-2018 (45 decks)

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