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Metabolism > 5. Citric acid cycle > Flashcards

5. Citric acid cycle Flashcards

1
Q

Consumption of oxygen (respiration) depends on the rate of ________ and ________ reactions.

A

cytosol

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2
Q

A 1930 study of oxidation of glucose in muscle showed what?

A

Malonate inhibiting respiration

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3
Q

1935: Szent-Gyorgyi: demonstrated that little amounts (catalytic amounts) of succinate, fumerate, malate or oxaloacetate acelerated the rate of ___________.

A

respiration

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4
Q

He believed these must be acting as catalysts. But they aren’t enzymes. How can they act as catalysts?

A

participates but then comes back in tact after doing the reaction.

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5
Q

How many reactions in TCA cycle?

A

8

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6
Q

In order, name the reactions of TCA cycle by naming their enzymes. Add a * to the oxidation steps.

A
  1. Citrate synthase
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7
Q

and reaction:

A

CoA-SH, NAD, TPP, lipoate, FAD

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8
Q

Why is PDC exergonic?

A

exergonic because it is an oxidation reaction

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9
Q

Advantages of multienzyme complex:

A

1.Higher rate of reaction: Because product of one enzyme acts as a substrate of other, and is available for the active site of next enzyme without much diffusion.

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10
Q

Name the 3 enzymes part of the PDC multi-enzyme complex:

A

E-1 : Pyruvate dehydrogenase , uses Thiamine pyrophosphate as cofactor bound to E1

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11
Q

What are the three forms of lipoamide we see and what enzyme is it usually attached to?

A

Oxidized (disulfide bond)

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12
Q

What are the 5 co-factors found in PDC mechanism?

A

TPP, lipoamide, co-A, FAD, and NAD+

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13
Q

The first half of PDC mechanism is very similar to what?

A

First half is very similar to pyruvate decarboxylation reaction of alcohol fermentation

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14
Q

Provide the steps to the mechanism of PDC:

A
  1. TPP (with E1 bound to it) carbanion nucleophilicaly attacks carbonyl carbon of pyruvate, lose the double bonded O to form OH
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15
Q

Regulation of PDC by phosphorylation:

A

When PD kinase phosphorylates PDC to make it inactive

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16
Q

What activates and inhibits PD kinase?

A

PD kinase is activated by NADH and acetyl coa (makes sense because PDC forms NADH and acetyl coa)

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17
Q

What activates PD phosphatase?

A

PD phosphatase is activated by Mg2+ and Ca2+

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18
Q

How can hormones regulate PDC?

A

Insulin activates insulin-stim kinase which activates PP1, which activates PDC to form more acetylcoA

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19
Q

Why is insulin regulation of PDC somewhat contradictory?

A

Insulin is an anabolic hormone. However PDC catabolizes pyruvate, so it is a catabolic enzyme.

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20
Q

What is the cause of Beriberi?

A

If TPP is not there, PDC is not working. This results in issues with the brain, which depends on glucose. Brain cannot use anaerobic mechanism. (PDC is the entry-point for oxidative glucose catabolism. Brain has no fermentation to regenerate NAD+, so glycolysis cant just be used. U need OXIDATIVE catabolism.) So no TPP = no PDC = no oxidative glucose catabolism = no brain fuel = neurological symptoms

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21
Q

Why are arsenic compounds poisonous?

A

the sulfhydryl groups of dihydrolipoamide are covalently inactivated by arsenic compounds

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22
Q

Arsenic Compound poisoning: Inactivation of _______ of PDC, and other proteins

A

E2

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23
Q

Name and describe reaction 1 of CAC:

A

Citrate synthase: Formation of Citroyl CoA intermediate. Binding of Oxaloacetate to the enzyme results in conformational change which facilitates the binding of the next substrate, the acetyl Coenzyme A. There is a further conformational change which leads to formation of products.

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24
Q

Provide reaction 1 of CAC:

A

Acetyl-CoA + Oxaloacetate + H20 –> citrate (by citrate synthase)

25
Q

describe the free energy of reaction 1 of CAC and what the mechanism is:

A

VERY exergonic

26
Q

Describe structure of citrate:

A

Tricarboxylic acid with one of the carbons having an OH

27
Q

Name and describe reaction 2 of CAC:

A

Aconitase: This enzyme catalyses the isomerization reaction by removing and then adding back the water ( H and OH ) to cis-aconitate in at different positions. Isocitrate is consumed rapidly by the next step thus deriving the reaction in forward direction.

28
Q

Isocitrate is formed by removing water to form double bond and then adding water so there is addition of OH to C3 and H to C2 (switch places). True or false?

A

TRUE

29
Q

The formation of isocitrate is an _____________ attack on a symmetric structure. Why?

A

Asymmetric

30
Q

Name and describe reaction 3 of CAC:

A

Isocitrate dehydrogenase: converts isocitrate to a-ketoglutarate + CO2

31
Q

Name and describe reaction 4 of CAC:

A
  1. a-Ketoglutarate dehydrogenase complex: a-ketoglutarate to succinyl coA
32
Q

True or false?

A

TRUE

33
Q

So what are the co-factors of a-ketoglutarate dehydrogenase complex?

A

TPP, FAD, NAD+, lipoamide, CoA are the co-factors here too

34
Q

Name and describe reaction 5 of CAC:

A

Succinyl CoA synthetase: Succinyl-CoA is converted to Succinate, forming GTP in the process and releasing CoA

35
Q

Formation of GTP in Succinyl CoA synthetase reaction:

A

Succinyl co-A binds to succinyl co-A synthetase and Pi binds to the succinyl structure to replace coA

36
Q

Name and describe reaction 6 of CAC:

A

Succinate Dehydrogenase:

37
Q

How can succinate dehydrogenase be inhibited?

A

competitively by malonate (Similar structure to succinate)

38
Q

Get info from slide 27 question

A

okay

39
Q

Name and describe reaction 7 of CAC:

A

Fumarase: Hydration of Fumarate to L-malate: It is a highly stereospecific enzyme. Cis-Maleate (the cis form of fumarate) is not recognized by this enzyme.

40
Q

Name and describe reaction 8 of CAC:

A

L-Malate dehydrogenase: Oxidation of malate to oxaloacetate: It is an NAD+dependent enzyme. Reaction is pulled in forward direction by the next reaction (citrate synthase reaction) as the oxaloacetate is depleted at a very fast rate.

41
Q

So what are the standard and actual delta G signs of reaction 8?

A

Standard = +

42
Q

The two carbon acetyl group generated in PDC reaction enter the CAC, and two molecules of ________ are released in one cycle. Thus there is complete ________ of two carbons during one cycle. Although the two carbons which enter the cycle become the part of oxaloacetate, and are released as CO2 only in the ________ round of the cycle. The energy released due to this oxidation is conserved in the reduction of 3 ________ , 1 ________ molecule and synthesis of one ________ molecule which is converted to ________ .

A

CO2

43
Q

How many ATP per NADH and FADH2?

A

2.5, 1.5

44
Q

Indicate how much total ATP from glycolysis, PDC and CAC is received and detail where it comes from

A

From pyruvate in CAC, we get 4 NADH (1 pdc and 3 from cac), 1 FADH2, and 1 Atp from gtp. So PDC and CAC makes 12.5 ATP from one pyruvate. We get 2 pyruvates from glucose, so 25 ATP from one glucose from pyruvate onwards.

45
Q

Anaerobic bacteria use an incomplete form of the CAC. What is missing and why do they run this?

A

They do not have a-ketoglutarate dehydrogenase. They use this incomplete CAC for the production of biosynthetic products (AAs, nucleotides, heme, etc.)

46
Q

How did farmers take advantage of anaerobic bacteria ability to use the incomplete cycle?

A

Idea was to go to crops that were full of aluminum to chelate it with citrate produced by anaerobic bacteria to allow crops to grow by adding sugar.

47
Q

The citric acid cycle is considered to have a ____________ nature

A

amphibolic

48
Q

Explain the amphibolic nature of the CAC:

A

This pathway is utilized for the both catabolic reactions to generate energy as well as for anabolic reactions to generate metabolic intermediates for biosynthesis.

49
Q

read through amphibolic diagram on slide 33

A

okay

50
Q

What cycle is found in plants that has CAC intermediates?

A

Glyoxylate cycle

51
Q

Describe the glyoxylate cycle:

A

Start is same as CAC to form isocitrate, then you break it up by isocitrate lyase to form glyoxylate and 4C succinate is removed

52
Q

Why is the glyoxylate cycle very important to plants? Explain the importance to things like oil seeds:

A

Allows for the formation of biosynthetic products by forming succinate, while also not making any CO2.

53
Q

Ultimately, the glyoxysome allows for what to happen?

A

Convert FA to acetyl coa, then make carbs and proteins

54
Q

Rate controlling enzymes of PDC and CAC:

A
  • PDC
55
Q

Regulation of activity of CAC by: (3)

A
  • Substrate availability
56
Q

Read through slide 37 for what specifically inhibits and activates the 4 enzymes of PDC and CAC regulation.

A

okay

57
Q

Which reactions of glycolysis, PDC, and CAC produce CO2?

A

NONE during glycolysis.

58
Q

Carbons have been oxidized to CO2. Completely oxidized without oxygen. Where did the oxygen come from?

A

The water addition in GAPDH reaction in glycolysis, citrate synthase reaction, and fumarase reaction all contribute the oxygen for oxidation.

Metabolism (14 decks)

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