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Flashcards in TCA Cycle Deck (19)
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1

How do bacteria regenerate needed NAD+?

Two step reaction:
1. Pyruvate-->CO2+acetaldehyde via pyruvate decarboxylase.
2. Acetaldehyde+NADH-->ethanol+NAD+ via alcohol dehydrogenase

2

Where does CoA come from?

It is derived from ATP and vitamin B5 (pantothenic acid). It contains a thiol S-H that reacts with acetyl group to form an -S- bridge connecting it to CoA.

3

Describe how CoA is formed from pyruvate, generally.

Pyruvate is moved into the mitochondria via mitochondrial pyruvate carrier, and then via pyruvate dehydrogenase complex action it becomes acetyl-CoA, releasing 33.4 kJ/mol of energy.

4

Describe the subunits of pyruvate dehydrogenase complex, and their stoich in one PHD complex.

E1: Pyruvate dehydrogenase, 30.
E2: Dihydrolipoyl transacetylase, 60.
E3: Dihydrolipoyl dehydrogenase, 12.

5

Describe the overall reaction scheme of the pyruvate to acetyl CoA reaction.

1. Pyruvate is decarboxylated and bound to the TPP coenzyme prosthetic group of E1.
2. Hydroxyethyl derivative bound to E1 is oxidized and transferred from the TPP if E1 to the lipoic acid of E2 (links to it via a sulfur bridge of lipoic acid's sulfur).
3. Acetyl group bound to lipoic acid is transferred to CoA, forming acetyl CoA.
4. E3 regenerates oxidized lipoic acid on E2 so it can function again. This involves FAD alteration to FADH2, which is then regranted to FAD via NAD+ to NADH+H transfer.

6

What is notable of the structure of E2?

It contains a long lysine side chain that accepts the acetyl group from E1 and transfers it to E3, ensuring that no intermediates diffuse away (this is an example of substrate channeling, where intermediates are contained within one complex).

7

What can lead to dysfunction of the PDH complex?

1. Niacin or thiamine deficiency, precursors to NAD+ and TPP, respectively, are not present and thus block the activity of PDH, eventually stopping all ATP synthesis. This is most damaging to the CNS.
2. Trivalent arsenite forms a stable complex with lipoic acid of E2, and it no longer functions as a PDH coenzyme.
Either of above cause pyruvate and NADH to be transferred to the lactate dehydrogenase pathway, resulting in lactic acid increase and metabolic acidosis.

8

How is the PDH complex regulated?

1. Feedback inhibition by acetyl-CoA and NADH.
2. PDH kinase phosphorylates and inactivates E1, PDH phosphatase does the opposite. Note high energy signals of ATP, acetyl-CoA, and NADH increase PDH kinase activity. Pyruvate decreases PDH kinase activity, and Ca2+ increases PDH phosphatase activity (this calcium method is of most importance in the skeletal muscle as Ca2+ release during contraction leads to more ATP production for more contraction through this pathway).

9

What is the overall reaction of the TCA?

Acetyl-CoA+(3NAD+)+FAD-->(2CO2)+3NADH+FADH2.

10

What is the first reaction of the TCA?

Acetyl-CoA and OAA are converted to citrate via citrate synthase.
Is irreversible due to hydrolysis of thioester bond within acetyl-CoA (goes back to PDH)

11

What is the second step of the TCA?

Citrate is isomerized to isocitrate via aconitase function.
This reaction is energetically favorable in the reverse, but fast consumption of isocitrate pulls it forward.

12

What is the third step of the TCA?

Isocitrate is decarboxylated to alpha-ketoglutarate via isocitrate dehydrogenase.
Is irreversible as a CO2 is released and an NADH is produced.

13

What is the fourth step of the TCA?

Alpha-ketoglutarate is oxidated to succinyl-CoA.
Reaction is irreversible due to CO2 and NADH production as byproducts.

14

What is the fifth step of the TCA?

Succinyl-CoA is converted to succinate via succinyl-CoA synthetase, which also produces a GTP (from a GDP and Pi, due to energy released from cleavage of thioester bond in reactant).
GTP can then interact with ADP and nucleoside diphosphyl kinase to form ATP and GDP.

15

What is the sixth step of the TCA?

Succinate is oxidized to fumarate via succinate dehydrogenase (this enzyme is not in the matrix like the others, but rather the inner membrane).
This also converts FAD to FADH2.

16

What is the seventh and eighth steps of the TCA?

7th: Fumarate is converted to malate via fumarase.
8th: Malate is converted to OAA via malate dehydrogenase, which also converts NAD+ and NADH and H. This reaction is strongly favorable in the reverse, but continuous removal of OAA via citrate synthase pulls it forward.

17

What are the main ways in which the TCA cycle is regulated?

1. Citrate synthase via feedback inhibition from citrate.
2. Isocitrate dehydrogenase inhibited by ATP and NADH, and stimulated by ADP and Ca2+.
3. Alpha-ketoglutarate dehydrogenase inhibited by succinyl-COA and NADH, and activated by Ca2+.

18

What can feed into the TCA cycle?

Amino acid metabolism mainly.
1. Amino acids can form pyruvate, which enters the cycle at step 1.
2. Glutamate can form alpha-ketoglutarate.
3. Valine and isoleucine can form propionyl CoA, which can form succinyl-CoA.
4. Some amino acids can form fumarate.
5. Aspartate can form OAA.

19

What cycles can TCA intermediates transfer to?

1. CItrate can function in fatty acid synthesis.
2. Alpha-ketoglutarate can function in amino acid synthesis.
3. Succinyl-CoA can function in heme synthesis.
4. Malate can function in gluconeogenesis.
5. OAA can function in amino acid synthesis.