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BIOCHEM 2 > Chapter 14 Pyruvate Dehydrogenase Complex and The Citric Acid Cycle > Flashcards

Chapter 14 Pyruvate Dehydrogenase Complex and The Citric Acid Cycle Flashcards

1
Q

What does the structure of the mitochondria consist of?

A

The structure of the mitochondria consists of the inner membrane, outer membrane, cristae, and matrix.

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2
Q

Which part of the mitochondria does the citric acid cycle take place?

A

The matrix

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3
Q

What are the three stages of cellular respiration in the presence of oxygen?

A

Glycolysis
Citric Acid Cycle
Oxidative Phosphorylation

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4
Q

What is the pyruvate dehydrogenase complex?

A

Pyruvate that is produced from glycolysis cannot directly enter the citric acid cycle; therefore, it goes through the pyruvate dehydrogenase complex where it is converted to acetyl coA. Acetyl coA is a substrate for the citric acid cycle.

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5
Q

What are the substrates and the products of the pyruvate dehydrogenase complex?

A

Substrates are pyruvate, products are acetyl coA, NADH, and CO2.

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6
Q

What are the four main steps for carbohydrate metabolism?

A

Pyruvate Dehydrogenase
Citric Acid Cycle
Electron Transport Chain
Oxidative Phosphorylation

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7
Q

What happens in the pyruvate dehydrogenase complex?

A

Pyruvate is converted to acetyl coA.

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8
Q

What happens in the citric acid cycle?

A

acetyl coA is converted to carbon dioxide.

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9
Q

What happens in the electron transport chain?

A

uses energy to create a proton gradient.

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10
Q

What happens in oxidative phosphorylation?

A

uses proton gradient to power synthesis of ATP.

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11
Q

How does pyruvate enter the mitochondrial matrix?

A

the mitochondrial pyruvate carrier spans the inner mitochondrial membrane and allows for the free diffusion of pyruvate into the matrix.

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12
Q

What two types of catalysis are used in the citric acid cycle?

A

catalyst that speeds up reaction

catalyst that behaves as a scaffold and is regenerated.

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13
Q

What are the two faces of pyruvate?

A

refer to doc

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14
Q

What is the first step of the pyruvate dehydrogenase complex?

A

refer to doc

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15
Q

What is the second step of the pyruvate dehydrogenase complex?

A

refer to doc

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16
Q

What is the last step of the pyruvate dehydrogenase complex?

A

refer to doc

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17
Q

Regulation of the pyruvate dehydrogenase complex

A

Pyruvate dehydrogenase complex is inhibited when ATP/ADP is high and when NADH/NAD+ is high.

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18
Q

What enzymes of the pyruvate dehydrogenase complex are regulated by allosteric modulators?

A

E2 and E3

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19
Q

What are the allosteric modulators of E2?

A

acetyl coA inhibits
coA activates

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20
Q

What are the allosteric modulators of E3?

A

NADH inhibits
pyruvate and NAD+ activates

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21
Q

What is the special regulation that only mammals use for the pyruvate dehydrogenase complex?

A

mammals use regulation by phosphorylation.

PDH kinase phosphorylates E1 —> inactivates E1.

PDH phosphatase dephosphorylates E1 —–> activates E1.

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22
Q

How does magnesium regulate the pyruvate dehydrogenase complex through E1?

A

Mg (II) stimulates the enzyme PDH phosphatase which dephosphorylates E1 making it active.

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23
Q

What is the magnesium sensor?

A

Mg binds to ATP more tightly than ADP. Amount of free magnesium is reflective of how much ATP there is in the cell.

Mg high, ATP low

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24
Q

What is special about arsenic?

A

Inhibits pyruvate dehydrogenase complex.

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25
Q

What is the biological function of the citric acid cycle?

A

it is a source of metabolic intermediates for biochemical pathways.

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26
Q

Why is the citric acid cycle chemically necessary?

A

oxidation of 2 carbon acetyl coA to recover energy rich electrons. 8 electrons per glucose.

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27
Q

What is the first step of the citric acid cycle?

A

oxaloacetate + acetyl coA forms citrate

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28
Q

Which enzyme catalyzes the first step of the citric acid cycle?

A

citrate synthase

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29
Q

How does citrate synthase use induced fit and an ordered, sequential model to avoid hydrolysis of a critical intermediate?

A

citrate synthase enzyme has two induced fit
1. oxaloacetate must bind first in order for the acetyl-coA to bind. There are no binding sites for acetyl-coA. Oxaloacetate will bind and do an induced fit to create acetyl-coA binding site.

  1. We don’t want hydrolysis of acetyl-coA, once citroyl-coA forms a second induced fit happens that causes the active site to come together and liberate coA from citroyl coA to form citrate.
30
Q

What type of reaction is the citrate synthase reaction?

A

Aldol condensation

31
Q

What is the second step of the citric acid cycle?

A

citrate to isocitrate catalyzed by the aconitase enzyme.

32
Q

What is the chemical necessity for the aconitase reaction?

A

citrate contains a tertiary alcohol which cannot be oxidized, the aconitase reaction converts the tertiary alcohol to a secondary alcohol that can be oxidized.

33
Q

What is the moonlighting function of aconitase?

A

absence of iron sulfur clusters binding to aconitase, aconitase can bind to RNA.

34
Q

What is the special feature of the aconitase reaction?

A

The three point attachment model

35
Q

What is the three point attachment model?

A

This model explains why one side of the molecule is reacting which is the side from the pre-existing oxaloacetate and not the acetyl-coA side because this is the only orientation in which the citrate can interact with the enzyme.

36
Q

Fluorocitrate is __________ of aconitase.

A

an inhibitor

37
Q

What is the isocitrate dehydrogenase step of the citric acid cycle?

A

Isocitrate to alpha ketoglutarate

38
Q

How is it possible to lose a carbon dioxide in the isocitrate dehydrogenase step in the absence of TPP or neighboring carbonyl group in the substrate?

A

The OH is oxidized to a carbonyl and that is where we put the electron onto.

39
Q

How does coupling contribute to the isocitrate dehydrogenase step?

A

coupling to the NAD+ —-> NADH reaction

40
Q

What is alpha ketoglutarate dehydrogenase step of the citric acid cycle?

A

alpha ketoglutarate to succinyl coA

41
Q

What is alpha ketoglutarate dehydrogenase step of the citric acid cycle similar to?

A

The Pyruvate Dehydrogenase complex

42
Q

Write the mechanism of the alpha ketoglutarate dehydrogenase step.

A

refer to slides

43
Q

What is the succinyl-coA synthetase reaction?

A

succinyl coA to succinate

44
Q

What type of reaction is the succinyl-coA synthetase reaction?

A

substrate level phosphorylation

45
Q

What happens in the succinyl-coA synthetase reaction?

A

an NTP is produced.

46
Q

Why is information lost in the succinyl-coA synthetase reaction?

A

the succinate is a symmetric molecule and we cannot tells which portion was derived from oxaloacetate vs. acetyl coA.

47
Q

What is the nucleophile of the succinyl-coA synthetase reaction?

A

a phosphoryl group

48
Q

What is the electrophile of the succinyl-coA synthetase reaction?

A

carbonyl carbon

49
Q

What is the leaving group of succinyl-coA synthetase reaction?

A

S-CoA

50
Q

Write the mechanism of succinyl-coA synthetase reaction

A

refer to slides

51
Q

What structural feature of the enzyme succinyl-coA synthetase is required for the chemical mechanism of this enzyme?

A

The power ranger helices, the power helices place the partial positive charges of the helix dipole near the phosphate group of P-His stabilizing the phosphohistidyl enzyme.

52
Q

What is the succinate dehydrogenase reaction?

A

succinate to fumarate.

53
Q

What are the two unique features of the succinate dehydrogenase reaction?

A
  1. FAD gets electron
  2. succinate dehydrogenase is a membrane protein and known as complex II.
54
Q

Why does the succinate dehydrogenase mechanism require an additional electron acceptor?

A

FAD can not leave the enzyme, there must be a sink to accept these electrons.

55
Q

Who is the additional electron acceptor in the succinate dehydrogenase mechanism?

A

quinone

56
Q

How many times must the citric acid cycle be completed before a molecule of glucose is fully oxidized?

A

2 times

57
Q

In which steps is NADH produced in the citric acid cycle?

A

isocitrate dehydrogenase, alpha ketoglutarate dehydrogenase, and malate dehydrogenase step

58
Q

In which step is FADH2 produced in the citric acid cycle?

A

succinate dehydrogenase

59
Q

Which steps in the citric acid cycle have large negative free energies?

A

citrate synthase, isocitrate dehydrogenase, and alpha-ketoglutarate dehydrogenase complex steps.

60
Q

What are the regulatory mechanisms used by the pyruvate dehydrogenase complex?

A

allosterically inhibited when [ATP]/[ADP], [acetyl coA]/[coA], and [NADH]/[NAD+] ratios are high

61
Q

What are the regulatory mechanisms used by the citric acid cycle?

A

citrate is an inhibitor of the citric acid cycle.

62
Q

What are anaplerotic reactions and why are they necessary?

A

allows the citric acid cycle to happen and not be diminished by other metabolic pathways happening at the same time.

63
Q

How does pyruvate carboxylase restore the citric acid cycle functionality?

A

by restoring oxaloacetate levels, enables the citric acid cycle to continue

64
Q

What are the three anaplerotic reactions?

A
  1. pyruvate to oxaloacetate (citric acid cycle)
  2. phosphoenolpyruvate to oxaloacetate (gluconeogenesis)
  3. pyruvate to malate (happens during lipid biosynthesis)
65
Q

What is the importance of transaminase enzymes?

A

generate citric acid cycle intermediates from amino acids. For example: glutamate to alpha ketoglutarate.

66
Q

Glucogenic

A

amino acids form glucose

67
Q

Ketogenic

A

amino acids form ketones

68
Q

What is the glyoxylate cycle?

A

variant of the citric acid cycle that occurs in bacteria, plants, and some algae.

69
Q

At what step in the citric acid cycle does the bypass occur?

A

decarboxylations of the citric acid cycle are bypassed. Allows for the net synthesis of glucose from acetyl coA.

isocitrate is converted to glyoxylate by isocitrate lyase.

70
Q

Why is the citric acid cycle a part of aerobic metabolism if no molecules of oxygen are consumed in the citric acid cycle?

A

Oxygen plays an essential role as the final acceptor in the electron transport chain which is coupled to the citric acid cycle.

71
Q

How many NADH are generated at the end of the citric acid cycle?

A

3 NADH molecules
6 NADH molecules per glucose

72
Q

How many FADH2 are generated at the end of the citric acid cycle?

A

1 FADH2
2 FADH2 molecules per glucose

BIOCHEM 2 (17 decks)

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