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SMP - MNE Exam 1 > Lecture 16: Pyruvate Dehydrogenase & the TCA Cycle > Flashcards

Lecture 16: 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 dehydrogenase
E2: 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 + CO2
  2. E2: lipoic acid accepts 2Cs from TPP = LA acetylated form = acyl lipollysine
  3. E2: CoA accepts 2Cs from LA = Acetyl CoA + reduced LA
  4. 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 CoA
  2. NADH
  3. CO2
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10
Q

What are the 2 regulation mechanisms of the PDC?

A
  1. Product inhibition

2. 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 it
Stimulation: 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 PEPCK
  2. Pyruvate conversion to oxaloacetate by pyruvate carboxylase using ATP
  3. Pyruvate conversion to malate by malic enzyme
  4. 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

Thioester

Very 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. ADP
  2. 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

SMP - MNE Exam 1 (25 decks)

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