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BM 210: Introduction to Biochemistry > Block D Part 3: The Tricarboxylic Acid Cycle > Flashcards

Block D Part 3: The Tricarboxylic Acid Cycle Flashcards

1
Q

What is the matrix of the mitochondria?

A

An internal space containing enzymes of the TCA cycle and oxidative decarboxylation of pyruvate
(Lecture 3, Slide 4)

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2
Q

What is the inner membrane of the mitochondria?

A

A large surface created by invaginations (cristae) ,proteins of the electron transport chain, ATP synthase, transport proteins and the electrochemical gradient of H+
(Lecture 3, Slide 4)

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3
Q

What is the outer membrane of the mitochondria made of?

A

It’s made up of channel proteins called porin
(Lecture 3, Slide 4)

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4
Q

What is the highest molecular weight that can enter the intermembrane space of the mitochondria?

A

5kDa
(Lecture 3, Slide 4)

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5
Q

What is the irreversible link from glycolysis to the TCA cycle?

A

Pyruvate Dehydrogenase
(Lecture 3, Slide 5)

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6
Q

What type of reaction is the conversion from Pyruvate to Acetyl CoA?

A

It’s a redox reaction, called an oxidative decarboxylation
(Lecture 3, Slide 5)

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7
Q

How is the acetate unit within pyruvate activated?

A

By linking it to Coenzyme A
(Lecture 3, Slide 5)

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8
Q

Why is pyruvate linked to Coenzyme A?

A

So it can undergo further reaction
(Lecture 3, Slide 5)

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9
Q

What is pyruvate dehydrogenase complex?

A

A multi enzyme complex which catalyses the conversion of pyruvate to Acetyl CoA
(Lecture 3, Slide 6)

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10
Q

What are the 3 enzymes in pyruvate dehydrogenase complex?

A

Pyruvate dehydrogenase
Dihydrolipoamide acetyltransferase
Dihydrolipoamide dehydrogenase
(Lecture 3, Slide 6)

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11
Q

What is the energy output per acetyl CoA in the TCA cycle?

A

3 NADH
1 FADH2
1 GTP
(Lecture 3, Slide 8)

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12
Q

What is reformed and what is released in the TCA cycle?

A

Oxaloacetate is reformed and 2 CO2 are released
(Lecture 3, Slide 8)

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13
Q

What 3 enzymes is the TCA cycle regulated by in humans?

A

Pyruvate dehydrogenase
Isocitrate dehydrogenase
α-Ketoglutarate dehydrogenase
(Lecture 3, Slide 9)

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14
Q

What is an additional 4th enzyme which regulates the TCA cycle in bacteria?

A

Citrate synthease

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15
Q

What 2 things is pyruvate dehydrogenase activated by?

A

ADP and pyruvate
(Lecture 3, Slide 9)

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16
Q

What 3 things is pyruvate dehydrogenase inhibited by?

A

ATP, Acetyl CoA and NADH
(Lecture 3, Slide 9)

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17
Q

What allosterically activates isocitrate dehydrogenase?

A

ADP
(Lecture 3, Slide 9)

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18
Q

What 2 things inhibit isocitrate dehydrogenase?

A

ATP and NADH
(Lecture 3, Slide 9)

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19
Q

What happens when isocitrate dehydrogenase is inhibited?

A

Citrate accumulates and then moves to the cytoplasm and inhibits phosphofructokinase, which halts glycolysis
(Lecture 3, Slide 9)

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20
Q

What 3 things inhibit α-Ketoglutarate dehydrogenase and how?

A

Feedback inhibition by succinyl CoA and NADH and is also inhibited by high levels of ATP
(Lecture 3, Slide 9)

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21
Q

What inhibits citrate synthease?

A

ATP
(Lecture 3, Slide 9)

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22
Q

What is the order of reactions in the TCA cycle?

A

Pyruvate
Acetyl CoA + Oxaloacetate
Citrate
Isocitrate
α-Ketoglutarate
Succinyl CoA
Succinate
Fumarate
Malate
Oxaloacetate
(Lecture 3, Slide 9)

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23
Q

Roughly how much ATP can the body possess at a time?

A

~250g
(Lecture 3, Slide 12)

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24
Q

Approximately how many times does ADP needs to be recycled to ATP a day?

A

~300
(Lecture 3, Slide 12)

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25
Q

What is oxidative phosphorylation?

A

The last stage of aerobic energy production from all fuels
(Lecture 3, Slide 15)

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26
Q

Is oxidative phosphorylation the same as the electron transport chain?

A

No, the electron transport chain is the first of 2 parts of oxidative phosphorylation
(Lecture 3, Slide 15)

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27
Q

How are electrons from the TCA cycle’s reducing equivalents (NADH, FADH2) transferred to oxygen and what is released during this?

A

By a series of electron carriers, releasing energy to form ATP
(Lecture 3, Slide 15)

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28
Q

What is the location of oxidative phosphorylation in eukaryotes?

A

The inner membrane of the mitochondria
(Lecture 3, Slide 16)

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29
Q

What is the location of oxidative phosphorylation in prokaryotes (bacteria)?

A

The plasma membrane
(Lecture 3, Slide 16)

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30
Q

What is the first step of oxidative phosphorylation?

A

Electrons from NADH and FADH2 flow through complexes in the inner mitochondrial membrane
(Lecture 3, Slide 17)

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31
Q

What does electrons from NADH and FADH2 flowing through complexes in the inner mitochondrial membrane drive and what does this result in?

A

The export of protons (H+) to the intermembrane space of the mitochondria, resulting in a proton gradient
(Lecture 3, Slide 17)

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32
Q

How is the proton gradient used by ATP synthase?

A

It makes ATP by phosphorylating ADP
(Lecture 3, Slide 17)

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33
Q

What is the concept of oxidative phosphorylation called?

A

Chemiosmotic theory
(Lecture 3, Slide 17)

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34
Q

How many complexes are there in the electron transport chain?

A

4
(Lecture 3, Slide 20)

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35
Q

How do electrons pass through the electron transport chain?

A

By cycles of redox reactions
(Lecture 3, Slide 22)

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36
Q

Where does NADH pass electrons to?

A

Complex I
(Lecture 3, Slide 22)

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37
Q

Where does FADH2 pass electrons to?

A

Complex II
(Lecture 3, Slide 22)

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38
Q

What does complex I catalyse?

A

The transfer of 2H+ (one from NADH + another H+) to CoQ via several redox centres
(Lecture 3, Slide 23)

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39
Q

How many protons (H+) are pumped from the mitochondrial matrix to the intermembrane space by complex I?

A

4
(Lecture 3, Slide 23)

40
Q

What is the full equation of the reaction that complex I catalyses?

A

NADH + H+ + CoQ + 4H+ (matrix) —> NAD+ + CoQH2 + 4H+ (intermembrane space)
(Lecture 3, Slide 23)

41
Q

What is complex I inhibited by?

A

Rotenone
(Lecture 3, Slide 23)

42
Q

What is complex II also known as?

A

Succinate dehydrogenase
(Lecture 3, Slide 24)

43
Q

What does complex II catalyse?

A

The transfer of 2H from Succinate via FADH2 to CoQ
(Lecture 3, Slide 24)

44
Q

What is the full equation of the reaction that complex II catalyses?

A

Succinate + CoQ —> Fumarate + CoQH2
(Lecture 3, Slide 24)

45
Q

What is Coenzyme Q also known as?

A

Ubiquinone
(Lecture 3, Slide 25)

46
Q

What is Coenzyme Q?

A

A small lipid soluble electron carrier
(Lecture 3, Slide 25)

47
Q

What does Coenzyme Q do?

A

It accepts electrons from complexes I and II and diffuses through the membrane to deliver them to complex III
(Lecture 3, Slide 25)

48
Q

What does complex III catalyse and how?

A

the transfer of electrons from Coenzyme Q to cytochrome c by accepting electrons from CoQH2 and channelling them to cytochrome c via cytochrome b and FeS-clusters
(Lecture 3, Slide 27)

49
Q

What cycle occurs when complex III is accepting electrons from CoQH2?

A

A “Q-cycle”
(Lecture 3, Slide 27)

50
Q

What does the “Q-cycle” result in?

A

2 extra protons (H+) being transported
(Lecture 3, Slide 27)

51
Q

How many protons (H+) are pumped from the mitochondrial matrix to the intermembrane space by complex III?

A

4
(Lecture 3, Slide 27)

52
Q

What is the full equation of the reaction which complex III catalyses?

A

CoQH2 + Cyt c(oxidated) + 4H+ (matrix) —> CoQ + Cyt c(reduced) + 4H+ (intermembrane space)
(Lecture 3, Slide 27)

53
Q

What is complex III inhibited by?

A

Antimycin A
(Lecture 3, Slide 27)

54
Q

What is cytochrome c?

A

A small water-soluble heme-containing protein
(Lecture 3, Slide 28)

55
Q

What does cytochrome c do?

A

It diffuses in the intermembrane space between complex III and complex IV
(Lecture 3, Slide 28)

56
Q

How many electrons can the heme group iron contained in cytochrome c carry at a time?

A

1
(Lecture 3, Slide 28)

57
Q

What reaction does complex IV catalyse and how?

A

The transfer of 4 electrons from 4 cytochrome C to oxygen by collecting the electrons from cytochrome Cs redox centres and passing them to oxygen
(Lecture 3, Slide 29)

58
Q

How many protons (H+) are pumped from the mitochondrial matrix to the intermembrane space per 2e-?

A

2 (4 per O2)
(Lecture 3, Slide 29)

59
Q

What 3 things is complex IV inhibited by?

A

Cyanide (CN-), azide (N3-) and carbon monoxide (CO)
(Lecture 3, Slide 29)

60
Q

What is the full equation of the reaction complex IV catalyses?

A

4 Cyt c (reduced) + O2 + 8H+ (matrix) —> 4 Cyt c (oxidised) + 2H2O + 4H+ (intermembrane space)
(Lecture 3, Slide 29)

61
Q

What is ATP synthase also known as?

A

Complex V
(Lecture 3, Slide 34)

62
Q

What is ATP synthase?

A

A protein complex that uses the proton (H+) gradient to synthesise ATP
(Lecture 3, Slide 34)

63
Q

How does ATP synthase have a “knob-and-stalk” structure?

A

F1 (knob) contains the catalytic subunits for ATP formation
F0 (stalk) has a protein channel with spans the membrane
(Lecture 3, Slide 34)

64
Q

What is the function of the 3 α subunits contained in the F1 component of ATP synthase?

A

Regulatory & structural component to provide rigidity for beta-subunit conformational changes.
(Lecture 3, Slide 36)

65
Q

What is the function of the 3 ß subunits contained in the F1 component of ATP synthase?

A

It is the catalytic site for ATP synthesis
(Lecture 3, Slide 36)

66
Q

What is the function of the γ subunit contained in the F1 component of ATP synthase?

A

It transmits conformational change between F0 & F1 by rotation
(Lecture 3, Slide 36)

67
Q

What is the function of the δ subunit contained in the F1 component of ATP synthase?

A

It prevents F1 from rotation
(Lecture 3, Slide 36)

68
Q

What is the function of the ε subunit contained in the F1 component of ATP synthase?

A

Correct binding to F0 (assembly and orientation)
(Lecture 3, Slide 36)

69
Q

What is the a subunit contained in the component F0 of ATP synthase?

A

2 proton half channels connected to a c-ring
(Lecture 3, Slide 36)

70
Q

What is the function of the 2 b subunits contained in the F0 component of ATP synthase?

A

Has an F1 binding stalk interaction and prevents F1 rotation
(Lecture 3, Slide 36)

71
Q

What is the function of the 10 - 14 C subunits contained in the F0 component of ATP synthase?

A

Rotating proton motor with proton binding sites on the COO- group of aspartate
(Lecture 3, Slide 36)

72
Q

What drives proton (H+) passage through the F0 component of ATP synthase?

A

The proton gradient
(Lecture 3, Slide 38)

73
Q

What does H+ passage through the F0 component of ATP synthase cause?

A

The c-ring to rotate in the membrane
(Lecture 3, Slide 38)

74
Q

What does the c-ring of ATP synthase rotating in the membrane drive?

A

Rotation of the γ-spindle that connects F0 to F1
(Lecture 3, Slide 38)

75
Q

What does rotation of the y-spindle in ATP synthase cause?

A

Conformational changes in the αß-hexamer
(Lecture 3, Slide 38)

76
Q

What is a hexamer?

A

A complex or structure composed of 6 subunits or units.
E.g in ATP synthase, the α3ß3 indicates a structure of α and ß subunits arranged alternatively in a hexagonal structure
(Lecture 3, Slide 38)

77
Q

What does conformational changes in the αß-hexamer in ATP synthase result in?

A

ADP + Pi —> ATP + H20 reaction and ATP release
(Lecture 3, Slide 38)

78
Q

What 2 things hold the αß-hexamer in ATP synthase in place, making it static?

A

The b and δ subunits
(Lecture 3, Slide 38)

79
Q

What is the ß-subunit catalytic cycle?

A

ß subunits go from loose (L) —> tight (T) —> open (O) —> loose (L) etc conformation
(Lecture 3, Slide 39)

80
Q

What occurs during the loose conformation of the ß-subunit catalytic cycle?

A

The site closes - trapping ADP and pi inside, this is also the conformation when ATP synthesis occurs
(Lecture 3, Slide 39)

81
Q

What occurs during the tight conformation of the ß-subunit catalytic cycle?

A

ATP is formed and released from the site
(Lecture 3, Slide 39)

82
Q

What occurs during the open conformation of the ß-subunit catalytic cycle?

A

The site is open allowing ADP and inorganic phosphate (Pi) to enter
(Lecture 3, Slide 39)

83
Q

Why is the energy yield for oxidative phosphorylation less than expected?

A

As the transport processes dissipates (disperses or spreads out) some of the proton (H+) gradient
(Lecture 3, Slide 42)

84
Q

What does oxidative phosphorylation dissipating some of the proton (H+) gradient affect?

A

The ratio of ATP formed per 1/2 O2
(Lecture 3, Slide 42)

85
Q

How many electrons are required for each 1/2 O2 reduced H2O?

A

2
(Lecture 3, Slide 42)

86
Q

How many protons are translocated per each ATP synthesised?

A

3
(Lecture 3, Slide 42)

87
Q

How many protons are exported per each NADH(2e-) and therefore how much ATP is synthesised?

A

10H+ exported = 2.5 ATP
(Lecture 3, Slide 42)

88
Q

How many protons are exported per each FADH2(2e-) and therefore how much ATP is synthesised?

A

6H+ exported = 1.5 ATP
(Lecture 3, Slide 42)

89
Q

How many NADH molecules are produced during glycolysis?

A

2
(Lecture 3, Slide 43)

90
Q

Can NADH be using during anaerobic conditions?

A

No
(Lecture 3, Slide 43)

91
Q

What happens to NADH during anaerobic conditions?

A

It is recycled by lactate dehydrogenase (LDH)
(Lecture 3, Slide 43)

92
Q

What is the ATP yield of glycolysis per glucose and therefore the ATP yield anaerobic conditions?

A

2
(Lecture 3, Slide 43)

93
Q

What is the ATP yield per glucose during aerobic conditions?

A

30
(Lecture 3, Slide 44)

94
Q

How is 30 ATP generated per glucose in aerobic conditions?

A

2 ATP from glycolysis +
2 GTP from TCA cycle +
3 - (21.5) for 2 NADH produced during glycolysis (some energy lost on transport to mitochondria) +
5 - (22.5) for 2 NADH produced from pyruvate dehydrogenase +
15 - (62.5) for 6 NADH produced from TCA cycle
3 - (21.5) for 2 FADH2 produced from TCA cycle
(Lecture 3, Slide 44)

95
Q

How many molecules of NADH + H+ are generated in one cycle of the TCA cycle?

A

3

BM 210: Introduction to Biochemistry (12 decks)

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