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Tissues > T05 - TCA and OxPhos > Flashcards

T05 - TCA and OxPhos Flashcards

1
Q

Pyruvate dehydrogenase catalyzes what reaction?

A

catalyzes the following irreversible reaction:

pyruvate + CoA + NAD+ → acetyl-CoA + CO2 + NADH

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2
Q

Which reaction/enzyme serves as the key control point for entry of carbon into the TCA cycle?

A

pyruvate dehydrogenase reaction (which converts pyruvate to acetyl-CoA)

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3
Q

The pyruvate dehydrogenase enzyme is a critical control point for which processes? (3)

A

entry of carbon into TCA cycle

activation of gluconeogenesis

glucose → fat conversion

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4
Q

Where in the cell is the pyruvate dehydrogenase complex located?

A

mitochondria

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5
Q

Differentiate between fatty acid synthesis and oxidation in terms of where these processes occur.

A

fatty acid synthesis = cytosol

fatty acid oxidation = mitochondria

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6
Q

The pyruvate dehydrogenase conversion of pyruvate to acetyl-CoA can be broken down into how many steps?

A

3

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7
Q

What happens in the first reaction of the pyruvate dehydrogenase complex?

A

E1 oxidizes hydroxyethyl group of thiamine pyrophosphate (coenzyme form of vit B1) and transfers group to lipoamide

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8
Q

What happens in the second reaction of the pyruvate dehydrogenase complex?

A

E2 transfers acetyl group from lipoamide to acetyl-CoA

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9
Q

What happens in the third reaction of the pyruvate dehydrogenase complex?

A

E3 regenerates oxidized lipoamide, using FADH2 and NADH as cofactors

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10
Q

The pyruvate dehydrogenase complex requires what five cofactors?

A

thiamine pyrophosphate (TPP, a form of vit B1)

FAD (vit B2/riboflavin)

NAD (vit B3/niacin)

lipoamide

CoA

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11
Q

Describe how the pyruvate dehydrogenase complex is regulated.

A

PDH kinase → phosphorylates E1 → inhibits/reduces activity of PDH

PDH phosphatase → dephosphorylates E1 → restores PDH activity

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12
Q

What stimulates and inhibits PDH kinase?

A

stimulates — high ATP:AMP/ADP ratio, high NADH:NAD+ ratio, high acetyl-CoA:CoASH ratio [these ultimately inhibit PDH activity]

inhibits — ADP, NAD+

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13
Q

What stimulates and inhibits PDH phosphatase?

A

stimulates — insulin, Ca2+

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14
Q

How is the outer membrane of the mitochondria unusual?

A

small molecules (i.e. metabolites) can readily cross the bilayer, but larger molecules such as proteins can’t cross

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15
Q

Describe the permeability of the inner membrane of the mitochondria.

A

semipermeable such that charged molecules cannot cross the inner membrane except via transporter proteins

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16
Q

What does the TCA cycle ultimately do to the acetyl-CoA that is fed in?

A

acetyl-CoA is oxidized into CO2 + H2O

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17
Q

Where are the enzymes of the TCA cycle located?

A

in the mitochondrial matrix

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18
Q

Draw out the TCA cycle.

A
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19
Q

Describe the features of the citrate synthase reaction of the TCA cycle. (2)

A

irreversible (because of very negative ΔG value)

important regulatory control point

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20
Q

What inhibits the citrate synthase reaction of the TCA cycle?

A

high ATP:ADP

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21
Q

What is the limiting reagenet in the citrate synthase reaction of the TCA cycle?

A

oxaloacetate — concentration is extremely low and is tightly controlled by several factors

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22
Q

What are the activators and inhibitors of isocitrate dehydrogenase?

A

activators = ADP

inhibitors = NADH, ATP

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23
Q

How does an increasing NADH/NAD+ ratio affect the malate dehydrogenase reaction?

A

increasing NADH/NAD+ shifts equilibrium to favor malate over oxaloacetate, which decreases [oxaloacetate] and therefore slows down citrate synthase

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24
Q

Citrate, as a TCA intermediate, can be shunted to produce which biosynthetic molecules? (2)

A

fatty acids

sterols

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25
Q

Alpha-ketoglutarate, as a TCA intermediate, can be shunted to produce which biosynthetic molecules? (3)

A

glutamate

AAs

purines

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26
Q

Succinyl-CoA, as a TCA intermediate, can be shunted to produce which biosynthetic molecules? (2)

A

porphyrins

heme

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27
Q

Oxaloacetate, as a TCA intermediate, can be shunted to produce which biosynthetic molecules? (4)

A

aspartate

AAs

purines

pyrimidines

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28
Q

Differentiate between cataplerotic and anaplerotic reactions.

A

cataplerotic = draining TCA intermediates toward biosynthetic pathways

anaplerotic = repleneshing TCA intermediates from other nutrients/metabolites

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29
Q

Is the reduction of O2 to H2O exergonic or endergonic?

A

extremely exergonic

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30
Q

Where does oxidative phosphorylation take place?

A

in inner mitochondrial membrane

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31
Q

Describe the structure of quinones.

A

variable number of isoprene units

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32
Q

Where in the body are quinones found?

A

found in all tissues

33
Q

Describe how quinones are reduced.

A

reduced by one electron to both semiquinone and hydroquinone → act as both electron and proton carriers

reduced by two electrons (hydride ion)

34
Q

Are quinone reductions reversible?

A

Yes, both reduction by one electron and two electrons is reversible.

35
Q

Flavoproteins are derivatives of

A

riboflavin (vitamin B2)

36
Q

What are the two predominant forms of flavoproteins?

A

FMN

FAD

37
Q

What is the function of flavoproteins in the context of oxidative phosphorylation?

A

funnel electrons removed from a variety of sources into the respiratory chain

38
Q

Describe the composition of iron-sulfur proteins.

A

contain Fe (not part of heme) in association w/ S atoms in the form of sulfides and cysteines

39
Q

How do iron-sulfur proteins function as electron carriers?

A

oscillate between Fe2+ and Fe3+ states

40
Q

What are cytochromes?

A

hemeproteins found in close association with both inner mitochondrial membrane and cytoplasmic face of ER

41
Q

Describe how the heme in cytochromes differ from the heme in hemoglobins.

A

heme in cytochromes = electron carrier (alternating between Fe2+ and Fe3+)

heme in hemoglobin = oxygen carrier

42
Q

Name the following complexes in the mitochondrial respiratory chain:

Complex I

Complex II

Complex III

Complex IV

A

Complex I = NADH-Q oxidoreductase

Complex II = succinate-Q-reductase

Complex III = Q-cytochrome c oxidoreductase

Complex IV = cytochrome c oxidase

43
Q

What is the significance of Complex II in the mitochondrial respiratory chain?

A

Complex II (a.k.a. succinate-Q-reductase) is part of the TCA cycle

it is the only complex that doesn’t transport H+ across the inner membrane

44
Q

What is the ratio of NADH oxidized to ATP produced?

A

for every 1 NADH oxidized (i.e. 2 electrons transferred to O2), 3 ATP produced

[results from highly exergonic oxidation of NADH coupled to slightly endergonic synthesis of ATP]

45
Q

Describe the stoichiometry and mechanism of protons crossing the mitochondrial respiratory chain complexes.

A

4 H+ extruded into intermembrane space as electrons pass through Complexes I and IV

2 H+ extruded into intermembrane space as electrons pass through Complex III

46
Q

Describe the composition of Complex I/NADH-Q oxidoreductase.

A

FMN-bound NADH dehydrogenase

Fe-S proteins

47
Q

Write out the mechanism of the Complex I/NADH-Q oxidoreductase reaction. (6)

A

transfers NADH 2e- → FMN → series of Fe-S clusters → CoQ → QH2 → QH2 leaves and diffuses through membrane

48
Q

CoQ in Complex I/NADH-Q oxidoreductase can exist in what three forms?

A

fully oxidized state (Q)

semiquinone (QH•)

ubiquinol (QH2)

49
Q

(T/F) Electron flow through Complex I/NADH-Q oxidoreductase alone is capable of driving ATP synthesis.

A

True.

50
Q

Describe what occurs in Complex II/succinate-Q reductase of the mitochondrial respiratory chain.

A

e- from TCA cycle shuttled from protein-found FADH2 → Fe-S clusters → CoQ

51
Q

Complex II/succinate-Q reductase shuttles electrons from the TCA from FADH2 to CoQ without extrusion of protons. What two other enzymes are also capable of accomplishing this?

A

glycerol phosphate dehydrogenase

fatty acyl CoA dehydrogenase

52
Q

Broadly speaking, what is the function of Complex III/Q-cytochrome c oxidoreductase?

A

to relocate electrons from QH2 to oxidized cytochrome c

53
Q

Describe the composition of complex III/Q-cytochrome c oxidoreductase.

A

contains multiple cytochrome proteins, each with different electron affinities

54
Q

Is cytochrome c a one-electron or two-electron carrier?

A

cytochrome c is a one-electron carrier (electrons to it are handed off by a two-electron carrier)

55
Q

What is the function of Complex IV/cytochrome c oxidase?

A

transfer cytochrome c electrons to O2

56
Q

Describe the composition of Complex IV/cytochrome c oxidase. (2)

A

contains:

multiple heme-containing cytochromes

Cu+ → Cu2+ oscillating copper-bound proteins

57
Q

Describe the stoichiometry of the Complex IV/cytochrome c oxidase reaction.

A

4 H+ taken up from matrix to reduce 1 equivalent of O2, generating 2 H2O

58
Q

What were the three underlying observations of the chemiosmotic hypothesis postulated by Peter Mitchell?

A

(1) there are 3 sites of energy conservation
(2) ATP synthase requires intact inner mitochondrial membrane
(3) uncouplers of oxidation from phosphorylation were small molecules that could equilibrate a proton gradient across a membrane

59
Q

Three complexes of the mitochondrial respiratory chain pump protons across the inner membrane, creating an energized proton gradient. How is the energy contained in this gradient conserved? (2)

A

conserved through ADP + Pi → ATP synthesis, mediated by ATP synthase enzyme

[H+] is equilibrated across the membrane in the process

60
Q

In the context of chemiosmosis, what are uncouplers? Give three examples.

A

compounds that disrupt the proton gradient by increasing permeability of membrane to protons

examples of uncouplers: dinitrophenol, FCCP, valinomycin

61
Q

What is another name for the ATP synthase enzyme?

A

F1-ATP synthase

62
Q

Describe the conformational change that leads to ATP synthesis in F1-ATP synthase.

A

H+ flow down gradient → rotation of dimers w/ respect to stalk → conformational change from open (release ATP) → loose (ADP + Pi) → tight (dissociation and formation of ATP)

63
Q

Respiration and phosphorylation are well coupled in most mitochondria. What is an exception to this trend?

A

not well coupled in mitochondria of brown adipose tissue

64
Q

How is respiratory control measured?

A

ratio of rate of oxygen consumption in presence of ADP to rate of oxygen consumption in absence of ADP

the higher the ratio with a specified substrate, the more tightly coupled the mitochondria

65
Q

Uncoupling proteins cause a short-circuit in the proton gradient necessary to drive ATP synthesis, but are still clinically important. Why?

A

in short-circuiting the proton gradient, uncoupling proteins such as thermogenin generate heat → method for generating heat to maintain body temperature

66
Q

In a healthy cell, how do ATP and ADP levels compare?

A

ATP levels exceed that of ADP by factor of 4-10

67
Q

(T/F) NADH/NAD+ are transported into the mitochondrial matrix using a specific carrier.

A

False. There is no means to transport NAD+ or NADH across the mitochondrial inner membrane.

68
Q

What is the purpose of the malate-aspartate shuttle?

A

to get NADH from the cytosol into the mitochondrial matrix

69
Q

Write out the pathway of the malate-aspartate shuttle.

A

OAA reduced to malate in cytosol using NADH → malate exchanged for a-KG → travels to mitochondrial matrix → mitochondrial malate dehyrogenase oxidizes malate back into OAA, producing NADH

70
Q

Describe what happens in ethanol metabolism. (8)

A

ethanol oxidation → buildup of NADH → cells reduce pyruvate to lactate → less pyruvate for gluconeogenesis → acetate from ethanol oxidation converted to acetyl-CoA → can’t be oxidized via TCA because not enough NAD+ → converted to fat → fatty liver

71
Q

Isocitrate dehydrogenase and cancer: location, mutation, and disease

A

location = mitochondria/cytoplasm

mutation = dominant

disease = glioma, acute myeloid leukemia

72
Q

Succinate dehydrogenase and cancer: location, mutation, and disease

A

location = mitochondria

mutation = dominant

disease = several

73
Q

Fumarase and cancer: location, mutation, and disease

A

location = mitochondria

mutation = dominant

disease = renal cell cancer

74
Q

What are the allosteric inhibitors of pyruvate dehydrogenase?

A

ATP

Acetyl-CoA

NADH

75
Q

What are the allosteric activators of pyruvate dehydrogenase?

A

AMP

CoA

NAD+

76
Q

What are the covalent activators of pyruvate dehydrogenase?

A

activation by dephosphorylation

77
Q

What are the covalent inhibitors of pyruvate dehydrogenase?

A

phosphorylation of E1 (pyruvate dehydrogenase)

78
Q

Write out the equation for complete oxidation (i.e. via TCA/OxPhos) of one glucose molecule.

A

glucose + 32 Pi + 32 ADP + 32 H+ + 6 O2 → 6 H2O + 32 ATP + 6 CO2

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