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BIOC 4331 > TCA Cycle > Flashcards

TCA Cycle Flashcards

1
Q

Overall, what is the TCA cycle?

A

The overall process of glucose metabolism

Glucose is converted to CO2 and water in a reaction that is overall highly exergonic, with many intermediate steps.

Part of the released energy is captured as ATP

Part of the released energy is temporarily stored as NADH

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2
Q

Why does the TCA cycle exist?

A

Glycolysis can’t be the final step in catabolism

Need to regenerate NAD+ by oxidising NADH in order to metabilise more glucose

Most organisms oxidise pyruvate further, genrally using the TCA cycle

In order to regenerate NAD+, a final electron acceptor is needed to oxidise NADH

  • generally, this acceptor is O2
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3
Q

Where does the TCA cycle occur in prokaryotes?

A

In the cytoplasm

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4
Q

Where does the TCA cycle occur in eularyotes?

A

In the mitochondrion

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5
Q

What are the four generalised steps of the TCA cycle?

A
  1. Oxidation of pyruvate
  2. The production of isocitrate
  3. Two decarboxylations
  4. The regeneration of oxaloacetate
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6
Q

TCA 0:

Reactant

A

TCA 0:

Reactant: Pyruvate (Pyr)

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7
Q

TCA 0:

Product

A

TCA 0:

Product: Acetyl-coenzyme A (Ac-S-CoA or Acetyl CoA), NADH + H+, CO2

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8
Q

TCA 0:

Reactant

Product

A

TCA 0:

Reactant: Pyruvate (Pyr)

Product: Acetyl-coenzyme A (Ac-S-CoA or Acetyl CoA), NADH + H+, CO2

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9
Q

TCA 0:

Reaction type

A

TCA 0:

Reaction type: Pyruvate oxidation

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10
Q

TCA 0:

Enzyme

A

TCA 0:

Enzyme: Pyruvate dehydrogenase complex

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11
Q

TCA 0:

Cofactor

A

TCA 0:

Cofactors: 5 (below)

TPP: decarboxylates pyruvate, yeilds a hydroxyethyl-TPP anion

Lipoic Acid: accepts the hydroxyethyl anion from TPP as an acetyl group (the long arm of lipoamide swings the acetyl group between the active sites of the enzyme complex)

CoA: accepts the acetyl group from acetyl-dihydrolipoamide

FAD: reduced by dihydrolipoamide

NAD+ : reduced by FADH2

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12
Q

TCA 0:

Reactant

Product

Reaction type

Enzyme

Cofactor

A

TCA 0:

Reactant: Pyruvate (Pyr)

Product: Acetyl-coenzyme A (Ac-S-CoA or Acetyl CoA), NADH + H+, CO2

Reaction type: Pyruvate oxidation

Enzyme: Pyruvate dehydrogenase complex

Cofactors: 5 (below)

TPP: decarboxylates pyruvate, yeilds a hydroxyethyl-TPP anion

Lipoic Acid: accepts the hydroxyethyl anion from TPP as an acetyl group (the long arm of lipoamide swings the acetyl group between the active sites of the enzyme complex)

CoA: accepts the acetyl group from acetyl-dihydrolipoamide

FAD: reduced by dihydrolipoamide

NAD+ : reduced by FADH2

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13
Q

What is glucose converted to in the TCA cycle?

A

Glucose is oxidized as far as it can go, to CO2 and H2O

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14
Q

TPP

A

Thiamine pyrophosphate (TPP) a thiamine (vitamin B1) derivative which is a cofactor that is present in all living systems, in which it catalyzes several biochemical reactions. It is an essential nutrient (vitamin) in humans.

TPP works as a coenzyme in many enzymatic reactions, such as:

Pyruvate dehydrogenase complex:

  • decarboxylates pyruvate, yeilds a hydroxyethyl-TPP anion

Pyruvate decarboxylase in ethanol fermentation

Alpha-ketoglutarate dehydrogenase complex

Branched-chain amino acid dehydrogenase complex

2-hydroxyphytanoyl-CoA lyase

Transketolase

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15
Q

Lipoic Acid

A

Lipoic acid or lipoate

The lipoyllysyl moiety is the prosthetic group of dihydrolipoyl transacetylase (E2 of the PDH complex). The lipoyl group occurs in oxidised (disulfide) and reduced (dithiol) forms and acts as a carrier of both hydrogen and an acetyl (or other acyl) group.

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16
Q

CoA

A

Coenzyme A (CoA, CoASH, or HSCoA) is a coenzyme, notable for its role in the synthesis and oxidation of fatty acids, and the oxidation of pyruvate in the citric acid cycle.

In the pyruvate dehydrogenase complex, accepts the acetyl group from acetyl-dihydrolipoamide

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17
Q

PDC

A

The pyruvate dehydrogenase complex (PDC) serves as the enzymatic gatekeeper facilitating and regulating entry into the citric acid cycle for metabolites leaving glycolysis.

PDC is composed of multiple copies of three enzymes: pyruvate dehydrogenase (E1) (with its bound cofactor TPP); dihydrolipoyl transacetylase (E2) (with its covalently bound lipoyl group); and dihydrolipoyl dehydrogenase (E3) (with its cofactors FAD and NAD).

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18
Q

PDC E1

A

pyruvate dehydrogenase, E1 (with its bound cofactor TPP)

E1 catalyzes first the decarboxylation of pyruvate, producing hydroxyethyl-TPP, and then the oxidation of the hydroxyethyl group to an acetyl group. The electrons from this oxidation reduce the disulfide of lipoate bound to E2, and the acetyl group is transferred into thioester linkage with one — SH group of reduced lipoate.

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19
Q

PDC E2

A

dihydrolipoyl transacetylase, E2 (with its covalently bound cofactor lipoate)

E2 catalyzes the transfer of the acetyl group to coenzyme A, forming acetyl-CoA.

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20
Q

PDC E3

A

dihydrolipoyl dehydrogenase, E3 (with its cofactors FAD and NAD+)

E3 catalyzes the regeneration of the disulfide (oxidized) form of lipoate; electrons pass first to FAD, then to NAD+, forming NADH + H+

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21
Q

dihydrolipoyl dehydrogenase

A

dihydrolipoyl dehydrogenase, E3 (with its cofactors FAD and NAD+)

E3 catalyzes the regeneration of the disulfide (oxidized) form of lipoate; electrons pass first to FAD, then to NAD+, forming NADH + H+

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22
Q

pyruvate dehydrogenase

A

pyruvate dehydrogenase, E1 (with its bound cofactor TPP)

E1 catalyzes first the decarboxylation of pyruvate, producing hydroxyethyl-TPP, and then the oxidation of the hydroxyethyl group to an acetyl group. The electrons from this oxidation reduce the disulfide of lipoate bound to E2, and the acetyl group is transferred into thioester linkage with one — SH group of reduced lipoate.

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23
Q

dihydrolipoyl transacetylase

A

dihydrolipoyl transacetylase, E2 (with its covalently bound cofactor lipoate)

E2 catalyzes the transfer of the acetyl group to coenzyme A, forming acetyl-CoA.

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24
Q

How are intermediates shuffled through the pyruvate dehydrogenase complex?

A

The long lipoyllysyl (lipoic acid + lysine) arm swings from the active site of E1 to E2 to E3, tethering the intermediates to the enzyme complex to allow substrate channeling.

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25
Q

What is the entry point to the TCA cycle?

A

Acetyl-Coenzyme A

High-energy thioester bond:

DG°’ = -32.2 kJ/mol

Four electron pairs (in blue) of acetyl-CoA that are ultimately used to reduce NAD+ (3) and FAD (1) in the Citric Acid Cycle

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26
Q

TCA I

Reactant

A

TCA I

Reactant: Acteyl-Coenzyme A (AcCoA) + Oxaloacetate (OxAc)

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27
Q

TCA I

Product

A

TCA I

Product: Citrate (Cit)

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28
Q

TCA I

Reactant

Product

A

TCA I

Reactant: Acteyl-Coenzyme A (AcCoA) + Oxaloacetate (OxAc)

Product: Citrate (Cit)

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29
Q

TCA I

Type of Reaction

Enzyme

Cofactor

A

TCA I

Type of Reaction: Condensation

Enzyme: Citrate synthase

Cofactor: none (remember water is required because this is a condensation reaction)

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30
Q

TCA I

Enzyme

A

TCA I

Enzyme: Citrate synthase

(synthases: enzymes that catalyze condensation reactions but do not require ATP)

•This enzyme is a dimer that binds oxaloacetate first, then acetyl-CoA. Hence, an ordered bisubstrate reaction mechanism or “induced fit.”

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31
Q

TCA I

Cofactor

A

TCA I

Cofactor: none (remember water is required because this is a condensation reaction)

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32
Q

TCA I

Reactant

Product

Type of Reaction

Enzyme

Cofactor

A

TCA I

Reactant: Acteyl-Coenzyme A (AcCoA) + Oxaloacetate (OxAc)

Product: Citrate (Cit)

Type of Reaction: Condensation

Enzyme: Citrate synthase

Cofactor: none (remember water is required because this is a condensation reaction)

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33
Q

citrate synthase reaction mechanism

A

Citrate synthase is a dimer that binds oxaloacetate first, then acetyl-CoA. Hence, an ordered bisubstrate reaction mechanism or “induced fit.”

Found in TCA I

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34
Q
A

Citrate (Cit)

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35
Q
A

Isocitrate

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36
Q

Structure of citrate

A
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37
Q

Structure of isocitrate

A
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38
Q

Structure of pyruvate

A
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39
Q
A
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40
Q

Where is pyruvate decarboxylated?

A

While bound to thiamine pyrophosphate (TPP) on the E1 complex of pyruvate dehydrogenase complex.

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41
Q

Subunits of Coenzyme A

A

3’-AMP

pantothenic acid

β-mercaptoethylamine

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42
Q

Acetyl Coenzyme A structure

A
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43
Q

FAD name and structure

A

Flavin Adenine Dinucleotide

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44
Q

Where is FAD reduced?

A
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45
Q
A
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46
Q

What structural modification does pyruvate dehydrogenase complex perform?

A

Removes CO2 from pyruvate, generates NADH + H+

47
Q

TCA II

Reactant

A

TCA II

Reactant: Citrate

48
Q

TCA II

Product

A

TCA II

Product: Isocitrate

49
Q

TCA II

Reactant

Product

A

TCA II

Reactant: Citrate

Product: Isocitrate

50
Q

TCA II

Type of Reaction

Enzyme

Cofactor

A

TCA II

Type of Reaction: Isomerisation

51
Q

TCA II

Enzyme

A

TCA II

Enzyme: Aconitase

52
Q

TCA II

Cofactor

A

TCA II

Cofactor: none (acontiase dehydrates to form a double bond then hydrates the same double bond on the opposite carbon to isomerise the molecule)

53
Q

TCA II

Reactant

Product

Type of Reaction

Enzyme

Cofactor

A

TCA II

Reactant: Citrate

Product: Isocitrate

Type of Reaction: Isomerisation

Enzyme: Aconitase

Cofactor: none (acontiase dehydrates to form a double bond then hydrates the same double bond on the opposite carbon to isomerise the molecule)

54
Q

Why is citrate prochiral?

A

Because of the hydroxyl (-OH) group, only one CH2COO- is susceptable to attack due to the conformation of the active site. There is only one way in which the three specified groups of citrate can fit on the three points of the binding site.

55
Q

TCA III

Reactant

A

TCA III

Reactant: Isocitrate

56
Q

TCA III

Product

A

TCA III

Product: α-Ketoglutarate, NADH + H+, CO2

57
Q

TCA III

Reactant

Product

A

TCA III

Reactant: Isocitrate

Product: α-Ketoglutarate, NADH + H+, CO2

58
Q

TCA III

Type of Reaction

A

TCA III

Type of Reaction: Decarboxylation

59
Q

TCA III

Enzyme

A

TCA III

Enzyme: Isocitrate dehydrogenase

60
Q

TCA III

Cofactor

A

TCA III

Cofactors: NAD+, then H+

61
Q

TCA III

Reactant

Product

Type of Reaction

Enzyme

Cofactor

A

TCA III

Reactant: Isocitrate

Product: α-Ketoglutarate, NADH + H+, CO2

Type of Reaction: β-cleavage of carboxy group

Enzyme: Isocitrate dehydrogenase

Cofactors: NAD+, then H+

62
Q

TCA IV

Reactant

A

TCA IV:

Reactant: α-Ketogluterate

63
Q

TCA IV

Product

A

TCA IV:

Product: Succinyl-coenzyme A (Suc-CoA), NADH + H+, CO2

64
Q

TCA IV

Reactant

Product

A

TCA IV:

Reactant: α-Ketogluterate

Product: Succinyl-coenzyme A (Suc-CoA), NADH + H+, CO2

65
Q

TCA IV

Type of Reaction

A

TCA IV:

Type of Reaction: β-cleavage of carboxy group

66
Q

TCA IV

Enzyme

A

TCA IV:

Enzyme: α-Ketogluterate dehydrogenase complex

67
Q

TCA IV

Cofactor

A

TCA IV:

Cofactors: TPP, Lipoic Acid, CoA, FAD, NAD+

68
Q

TCA IV

Reactant

Product

Type of Reaction

Enzyme

Cofactor

A

TCA IV:

Reactant: α-Ketogluterate

Product: Succinyl-coenzyme A (Suc-CoA), NADH + H+, CO2

Reaction type: Decarboxylation

Enzyme: α-Ketogluterate dehydrogenase complex

Cofactors: TPP, Lipoic Acid, CoA, FAD, NAD+

∆G°’ = -33.4 kJ/mol

69
Q

Succinyl-CoA structure

70
Q
A

Succinyl-CoA

71
Q

TCA V

Reactant

A

TCA V

Reactant: Succinyl-CoA

72
Q

TCA V

Product

A

TCA V

Product: Succinate + GTP (in mammals, else ATP) + CoA-SH

73
Q

TCA V

Reactant

Product

A

TCA V

Reactant: Succinyl-CoA

Product: Succinate + GTP (in mammals, else ATP) + CoA-SH

74
Q

TCA V

Type of Reaction

A

TCA V

Type of Reaction: Hydrolysis

75
Q

TCA V

Enzyme

Cofactor

A

TCA V

Enzyme: Succinyl CoA synthetase

Cofactor: GDP + Pi (in mammals, else ATP + Pi)

∆G°’ = -2.9kJ/mol

76
Q

TCA V

Cofactor

A

TCA V

Cofactor: GDP + Pi (in mammals, else ATP + Pi)

77
Q

TCA V

Reactant

Product

Type of Reaction

Enzyme

Cofactor

A

TCA V

Reactant: Succinyl-CoA

Product: Succinate + GTP (in mammals, else ATP) + CoA-SH

Type of Reaction: Hydrolysis

Enzyme: Succinyl CoA synthetase

Cofactor: GDP + Pi (in mammals, else ATP + Pi)

∆G°’ = -2.9kJ/mol

78
Q

TCA VI

Reactant

A

TCA VI

Reactant: Succinate (Suc)

79
Q

TCA VI

Product

A

TCA VI

Product: Fumarate (Fum) + FADH2

80
Q

TCA VI

Type of Reaction

A

TCA VI

Type of Reaction: Dehydrogenation

81
Q

TCA VI

Enzyme

A

TCA VI

Enzyme: Succinate dehydrogenase

82
Q

TCA VI

Reactant

Product

A

TCA VI

Reactant: Succinate (Suc)

Product: Fumarate (Fum) + FADH2

83
Q

TCA VI

Cofactor

A

TCA VI

Cofactor: FAD

84
Q

TCA VI

Reactant

Product

Type of Reaction

Enzyme

Cofactor

A

TCA VI

Reactant: Succinate (Suc)

Product: Fumarate (Fum) + FADH2

Type of Reaction: Dehydrogenation

Enzyme: Succinate dehydrogenase

Cofactor: FAD

∆G°’ = 0 kJ/mol

85
Q

TCA VII

Reactant

A

TCA VII

Reactant: Fumarate

86
Q

TCA VII

Product

A

TCA VII

Product: L-Malate (Mal)

87
Q

TCA VII

Reactant

Product

A

TCA VII

Reactant: Fumarate

Product: L-Malate (Mal)

88
Q

TCA VII

Type of Reaction

A

TCA VII

Type of Reaction: Hydration of alkene

89
Q

TCA VII

Enzyme

A

TCA VII

Enzyme: Fumarase

90
Q

TCA VII

Cofactor

A

TCA VII

Cofactor: none (water required for hydration)

91
Q

TCA VII

Reactant

Product

Type of Reaction

Enzyme

Cofactor

A

TCA VII

Reactant: Fumarate

Product: L-Malate (Mal)

Type of Reaction: Hydration of alkene

Enzyme: Fumarase

Cofactor: none (water required for hydration)

∆G°’ = -3.8 kJ/mol

92
Q

TCA VIII

Reactant

A

TCA VIII

Reactant: L-Malate

93
Q

TCA VIII

Product

A

TCA VIII

Reactant: L-Malate

Product: Oxaloacetate, NADH + H+

Type of Reaction: Dehydrogenation

Enzyme: L-Malate dehydrogenase

Cofactor: NAD+

∆G°’ = +29.7 kJ/mol

94
Q

TCA VIII

Reactant

Product

A

TCA VIII

Reactant: L-Malate

Product: Oxaloacetate, NADH + H+

95
Q

TCA VIII

Type of Reaction

A

TCA VIII

Type of Reaction: Dehydrogenation

96
Q

TCA VIII

Enzyme

A

TCA VIII

Enzyme: L-Malate dehydrogenase

97
Q

TCA VIII

Cofactor

A

TCA VIII

Cofactor: NAD+

98
Q

TCA VIII

Reactant

Product

Type of Reaction

Enzyme

Cofactor

A

TCA VIII

Reactant: L-Malate

Product: Oxaloacetate, NADH + H+

Type of Reaction: Dehydrogenation

Enzyme: L-Malate dehydrogenase

Cofactor: NAD+

∆G°’ = +29.7 kJ/mol

99
Q

Summize the TCA cycle

A
  • Acetyl CoA from pyruvate condenses with oxaloacetate, a 4-C dicarboxylic acid to form citrate, a 6-C tricarboxylic acid
  • The citrate rearranges to form isocitrate
  • Isocitrate is oxidatively decarboxylated, yielding CO2 α-ketoglutarate (a 5-C dicarboxylic acid), and NADH
  • α-ketoglutarate is oxidatively decarboxylated to yield CO2, succinyl CoA (a derivative of a 4 carbon dicarboxylic acid) and NADH
  • Succinyl CoA is hydrolyzed to succinate and CoA, yielding one molecule of ATP
  • Succinate is converted in three steps to oxaloacetate

–The succinate is oxidized to yield fumarate, a 4-C dicarboxylic acid and FADH2.

–Water is added to fumarate to make malate

–Malate is oxidized to yield oxaloacetate and NADH.

100
Q

Describe β cleavage

A

Abstract proton from β-hydroxyl group, collapsing resulting C-O bond to a carbonyl, which leaves. Resonance stabilised carbanion is reprotonated to form methyl group.

102
Q

How many ATP per NADH reduced are formed from glycolysis to PDC through TCA and Oxidative phosphorylation? Per FADH2 reduced?

A

2.5 ATP/NADH and 1.5 ATP/FADH2

about 34% (32 x 30.5 kJ/mol = 976 kJ/mol) of the available energy (2,840 kJ/mol) in glucose is recovered

104
Q

What are the rate-limiting enzymes of the TCA cycle?

A

Citrate Synthase, Isocitrate Dehydrogenase and α-ketoglutarate Dehydrogenase

Unlike the rate limiting enzymes of glycolysis, which use elaborate systems of allosteric control and covalent modification as flux control mechanisms, the citric cycle rate-limiting enzymes are largely regulated by:

1) substrate availability
2) product inhibition
3) inhibition by other cycle intermediates.

Major regulators are: its substrates (acetyl CoA, oxaloacetate), its product (NADH).

105
Q

What do the rate-limiting enzymes of the TCA cycle have in common?

A

They all reduce NADH, and are the only ones in the TCA cycle that do

“product inhibition”

106
Q

What inhibits the TCA cycle?

A

High ATP/NADH

(High energy levels)

107
Q

What activates the TCA cycle?

A

Low ATP or high AMP

(Low energy levels)

108
Q
A

α-Ketoglutarate

109
Q

α-Ketoglutarate structure

110
Q
A

Oxyacetate (OxAc)

111
Q

Oxyacetate structure

112
Q
A

Fumarate (Fum)

113
Q

Fumarate structure

BIOC 4331 (19 decks)

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