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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
What is the entry point to the TCA cycle?
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
26
TCA I Reactant
TCA I Reactant: Acteyl-Coenzyme A (AcCoA) + Oxaloacetate (OxAc)
27
TCA I Product
TCA I Product: Citrate (Cit)
28
TCA I Reactant Product
TCA I Reactant: Acteyl-Coenzyme A (AcCoA) + Oxaloacetate (OxAc) Product: Citrate (Cit)
29
TCA I Type of Reaction Enzyme Cofactor
TCA I Type of Reaction: Condensation Enzyme: Citrate synthase Cofactor: none (remember water is required because this is a condensation reaction)
30
TCA I Enzyme
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.”
31
TCA I Cofactor
TCA I Cofactor: none (remember water is required because this is a condensation reaction)
32
TCA I Reactant Product Type of Reaction Enzyme Cofactor
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)
33
citrate synthase reaction mechanism
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
34
Citrate (Cit)
35
Isocitrate
36
Structure of citrate
37
Structure of isocitrate
38
Structure of pyruvate
39
40
Where is pyruvate decarboxylated?
While bound to thiamine pyrophosphate (TPP) on the E1 complex of pyruvate dehydrogenase complex.
41
Subunits of Coenzyme A
3'-AMP pantothenic acid β-mercaptoethylamine
42
Acetyl Coenzyme A structure
43
FAD name and structure
Flavin Adenine Dinucleotide
44
Where is FAD reduced?
45
46
What structural modification does pyruvate dehydrogenase complex perform?
Removes CO2 from pyruvate, generates NADH + H+
47
TCA II Reactant
TCA II Reactant: Citrate
48
TCA II Product
TCA II Product: Isocitrate
49
TCA II Reactant Product
TCA II Reactant: Citrate Product: Isocitrate
50
TCA II Type of Reaction Enzyme Cofactor
TCA II Type of Reaction: Isomerisation
51
TCA II Enzyme
TCA II Enzyme: Aconitase
52
TCA II Cofactor
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
TCA II Reactant Product Type of Reaction Enzyme Cofactor
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
Why is citrate prochiral?
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
TCA III Reactant
TCA III Reactant: Isocitrate
56
TCA III Product
TCA III Product: α-Ketoglutarate, NADH + H+, CO2
57
TCA III Reactant Product
TCA III Reactant: Isocitrate Product: α-Ketoglutarate, NADH + H+, CO2
58
TCA III Type of Reaction
TCA III Type of Reaction: Decarboxylation
59
TCA III Enzyme
TCA III Enzyme: Isocitrate dehydrogenase
60
TCA III Cofactor
TCA III Cofactors: NAD+, then H+
61
TCA III Reactant Product Type of Reaction Enzyme Cofactor
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
TCA IV Reactant
TCA IV: Reactant: α-Ketogluterate
63
TCA IV Product
TCA IV: Product: Succinyl-coenzyme A (Suc-CoA), NADH + H+, CO2
64
TCA IV Reactant Product
TCA IV: Reactant: α-Ketogluterate Product: Succinyl-coenzyme A (Suc-CoA), NADH + H+, CO2
65
TCA IV Type of Reaction
TCA IV: Type of Reaction: β-cleavage of carboxy group
66
TCA IV Enzyme
TCA IV: Enzyme: α-Ketogluterate dehydrogenase complex
67
TCA IV Cofactor
TCA IV: ## Footnote **Cofactors: TPP, Lipoic Acid, CoA, FAD, NAD+**
68
TCA IV Reactant Product Type of Reaction Enzyme Cofactor
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
Succinyl-CoA structure
70
Succinyl-CoA
71
TCA V Reactant
TCA V Reactant: Succinyl-CoA
72
TCA V Product
TCA V Product: Succinate + GTP (in mammals, else ATP) + CoA-SH
73
TCA V Reactant Product
TCA V Reactant: Succinyl-CoA Product: Succinate + GTP (in mammals, else ATP) + CoA-SH
74
TCA V Type of Reaction
TCA V Type of Reaction: Hydrolysis
75
TCA V Enzyme Cofactor
TCA V Enzyme: Succinyl CoA synthetase Cofactor: GDP + Pi (in mammals, else ATP + Pi) ∆G°' = -2.9kJ/mol
76
TCA V Cofactor
TCA V Cofactor: GDP + Pi (in mammals, else ATP + Pi)
77
TCA V Reactant Product Type of Reaction Enzyme Cofactor
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
TCA VI Reactant
TCA VI Reactant: Succinate (Suc)
79
TCA VI Product
TCA VI Product: Fumarate (Fum) + FADH2
80
TCA VI Type of Reaction
TCA VI Type of Reaction: Dehydrogenation
81
TCA VI Enzyme
TCA VI Enzyme: Succinate dehydrogenase
82
TCA VI Reactant Product
TCA VI Reactant: Succinate (Suc) Product: Fumarate (Fum) + FADH2
83
TCA VI Cofactor
TCA VI Cofactor: FAD
84
TCA VI Reactant Product Type of Reaction Enzyme Cofactor
TCA VI Reactant: Succinate (Suc) Product: Fumarate (Fum) + FADH2 Type of Reaction: Dehydrogenation Enzyme: Succinate dehydrogenase Cofactor: FAD ∆G°' = 0 kJ/mol
85
TCA VII Reactant
TCA VII Reactant: Fumarate
86
TCA VII Product
TCA VII Product: L-Malate (Mal)
87
TCA VII Reactant Product
TCA VII Reactant: Fumarate Product: L-Malate (Mal)
88
TCA VII Type of Reaction
TCA VII Type of Reaction: Hydration of alkene
89
TCA VII Enzyme
TCA VII Enzyme: Fumarase
90
TCA VII Cofactor
TCA VII Cofactor: none (water required for hydration)
91
TCA VII Reactant Product Type of Reaction Enzyme Cofactor
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
TCA VIII Reactant
TCA VIII Reactant: L-Malate
93
TCA VIII Product
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
TCA VIII Reactant Product
TCA VIII Reactant: L-Malate Product: Oxaloacetate, NADH + H+
95
TCA VIII Type of Reaction
TCA VIII Type of Reaction: Dehydrogenation
96
TCA VIII Enzyme
TCA VIII Enzyme: L-Malate dehydrogenase
97
TCA VIII Cofactor
TCA VIII Cofactor: NAD+
98
TCA VIII Reactant Product Type of Reaction Enzyme Cofactor
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
Summize the TCA cycle
* 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
Describe β cleavage
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.
101
102
How many ATP per NADH reduced are formed from glycolysis to PDC through TCA and Oxidative phosphorylation? Per FADH2 reduced?
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
103
104
What are the rate-limiting enzymes of the TCA cycle?
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
What do the rate-limiting enzymes of the TCA cycle have in common?
They all reduce NADH, and are the only ones in the TCA cycle that do ## Footnote *"product inhibition"*
106
What inhibits the TCA cycle?
High ATP/NADH | (High energy levels)
107
What activates the TCA cycle?
Low ATP or high AMP | (Low energy levels)
108
α-Ketoglutarate
109
α-Ketoglutarate structure
110
Oxyacetate (OxAc)
111
Oxyacetate structure
(OxAc)
112
Fumarate (Fum)
113
Fumarate structure
(Fum)

BIOC 4331 (19 decks)

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