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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
What is oxidative phosphorylation?
The last stage of aerobic energy production from all fuels (Lecture 3, Slide 15)
26
Is oxidative phosphorylation the same as the electron transport chain?
No, the electron transport chain is the first of 2 parts of oxidative phosphorylation (Lecture 3, Slide 15)
27
How are electrons from the TCA cycle's reducing equivalents (NADH, FADH2) transferred to oxygen and what is released during this?
By a series of electron carriers, releasing energy to form ATP (Lecture 3, Slide 15)
28
What is the location of oxidative phosphorylation in eukaryotes?
The inner membrane of the mitochondria (Lecture 3, Slide 16)
29
What is the location of oxidative phosphorylation in prokaryotes (bacteria)?
The plasma membrane (Lecture 3, Slide 16)
30
What is the first step of oxidative phosphorylation?
Electrons from NADH and FADH2 flow through complexes in the inner mitochondrial membrane (Lecture 3, Slide 17)
31
What does electrons from NADH and FADH2 flowing through complexes in the inner mitochondrial membrane drive and what does this result in?
The export of protons (H+) to the intermembrane space of the mitochondria, resulting in a proton gradient (Lecture 3, Slide 17)
32
How is the proton gradient used by ATP synthase?
It makes ATP by phosphorylating ADP (Lecture 3, Slide 17)
33
What is the concept of oxidative phosphorylation called?
Chemiosmotic theory (Lecture 3, Slide 17)
34
How many complexes are there in the electron transport chain?
4 (Lecture 3, Slide 20)
35
How do electrons pass through the electron transport chain?
By cycles of redox reactions (Lecture 3, Slide 22)
36
Where does NADH pass electrons to?
Complex I (Lecture 3, Slide 22)
37
Where does FADH2 pass electrons to?
Complex II (Lecture 3, Slide 22)
38
What does complex I catalyse?
The transfer of 2H+ (one from NADH + another H+) to CoQ via several redox centres (Lecture 3, Slide 23)
39
How many protons (H+) are pumped from the mitochondrial matrix to the intermembrane space by complex I?
4 (Lecture 3, Slide 23)
40
What is the full equation of the reaction that complex I catalyses?
NADH + H+ + CoQ + 4H+ (matrix) ---> NAD+ + CoQH2 + 4H+ (intermembrane space) (Lecture 3, Slide 23)
41
What is complex I inhibited by?
Rotenone (Lecture 3, Slide 23)
42
What is complex II also known as?
Succinate dehydrogenase (Lecture 3, Slide 24)
43
What does complex II catalyse?
The transfer of 2H from Succinate via FADH2 to CoQ (Lecture 3, Slide 24)
44
What is the full equation of the reaction that complex II catalyses?
Succinate + CoQ ---> Fumarate + CoQH2 (Lecture 3, Slide 24)
45
What is Coenzyme Q also known as?
Ubiquinone (Lecture 3, Slide 25)
46
What is Coenzyme Q?
A small lipid soluble electron carrier (Lecture 3, Slide 25)
47
What does Coenzyme Q do?
It accepts electrons from complexes I and II and diffuses through the membrane to deliver them to complex III (Lecture 3, Slide 25)
48
What does complex III catalyse and how?
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
What cycle occurs when complex III is accepting electrons from CoQH2?
A "Q-cycle" (Lecture 3, Slide 27)
50
What does the "Q-cycle" result in?
2 extra protons (H+) being transported (Lecture 3, Slide 27)
51
How many protons (H+) are pumped from the mitochondrial matrix to the intermembrane space by complex III?
4 (Lecture 3, Slide 27)
52
What is the full equation of the reaction which complex III catalyses?
CoQH2 + Cyt c(oxidated) + 4H+ (matrix) ---> CoQ + Cyt c(reduced) + 4H+ (intermembrane space) (Lecture 3, Slide 27)
53
What is complex III inhibited by?
Antimycin A (Lecture 3, Slide 27)
54
What is cytochrome c?
A small water-soluble heme-containing protein (Lecture 3, Slide 28)
55
What does cytochrome c do?
It diffuses in the intermembrane space between complex III and complex IV (Lecture 3, Slide 28)
56
How many electrons can the heme group iron contained in cytochrome c carry at a time?
1 (Lecture 3, Slide 28)
57
What reaction does complex IV catalyse and how?
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
How many protons (H+) are pumped from the mitochondrial matrix to the intermembrane space per 2e-?
2 (4 per O2) (Lecture 3, Slide 29)
59
What 3 things is complex IV inhibited by?
Cyanide (CN-), azide (N3-) and carbon monoxide (CO) (Lecture 3, Slide 29)
60
What is the full equation of the reaction complex IV catalyses?
4 Cyt c (reduced) + O2 + 8H+ (matrix) ---> 4 Cyt c (oxidised) + 2H2O + 4H+ (intermembrane space) (Lecture 3, Slide 29)
61
What is ATP synthase also known as?
Complex V (Lecture 3, Slide 34)
62
What is ATP synthase?
A protein complex that uses the proton (H+) gradient to synthesise ATP (Lecture 3, Slide 34)
63
How does ATP synthase have a "knob-and-stalk" structure?
F1 (knob) contains the catalytic subunits for ATP formation F0 (stalk) has a protein channel with spans the membrane (Lecture 3, Slide 34)
64
What is the function of the 3 α subunits contained in the F1 component of ATP synthase?
Regulatory & structural component to provide rigidity for beta-subunit conformational changes. (Lecture 3, Slide 36)
65
What is the function of the 3 ß subunits contained in the F1 component of ATP synthase?
It is the catalytic site for ATP synthesis (Lecture 3, Slide 36)
66
What is the function of the γ subunit contained in the F1 component of ATP synthase?
It transmits conformational change between F0 & F1 by rotation (Lecture 3, Slide 36)
67
What is the function of the δ subunit contained in the F1 component of ATP synthase?
It prevents F1 from rotation (Lecture 3, Slide 36)
68
What is the function of the ε subunit contained in the F1 component of ATP synthase?
Correct binding to F0 (assembly and orientation) (Lecture 3, Slide 36)
69
What is the a subunit contained in the component F0 of ATP synthase?
2 proton half channels connected to a c-ring (Lecture 3, Slide 36)
70
What is the function of the 2 b subunits contained in the F0 component of ATP synthase?
Has an F1 binding stalk interaction and prevents F1 rotation (Lecture 3, Slide 36)
71
What is the function of the 10 - 14 C subunits contained in the F0 component of ATP synthase?
Rotating proton motor with proton binding sites on the COO- group of aspartate (Lecture 3, Slide 36)
72
What drives proton (H+) passage through the F0 component of ATP synthase?
The proton gradient (Lecture 3, Slide 38)
73
What does H+ passage through the F0 component of ATP synthase cause?
The c-ring to rotate in the membrane (Lecture 3, Slide 38)
74
What does the c-ring of ATP synthase rotating in the membrane drive?
Rotation of the γ-spindle that connects F0 to F1 (Lecture 3, Slide 38)
75
What does rotation of the y-spindle in ATP synthase cause?
Conformational changes in the αß-hexamer (Lecture 3, Slide 38)
76
What is a hexamer?
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
What does conformational changes in the αß-hexamer in ATP synthase result in?
ADP + Pi ---> ATP + H20 reaction and ATP release (Lecture 3, Slide 38)
78
What 2 things hold the αß-hexamer in ATP synthase in place, making it static?
The b and δ subunits (Lecture 3, Slide 38)
79
What is the ß-subunit catalytic cycle?
ß subunits go from loose (L) ---> tight (T) ---> open (O) ---> loose (L) etc conformation (Lecture 3, Slide 39)
80
What occurs during the loose conformation of the ß-subunit catalytic cycle?
The site closes - trapping ADP and pi inside, this is also the conformation when ATP synthesis occurs (Lecture 3, Slide 39)
81
What occurs during the tight conformation of the ß-subunit catalytic cycle?
ATP is formed and released from the site (Lecture 3, Slide 39)
82
What occurs during the open conformation of the ß-subunit catalytic cycle?
The site is open allowing ADP and inorganic phosphate (Pi) to enter (Lecture 3, Slide 39)
83
Why is the energy yield for oxidative phosphorylation less than expected?
As the transport processes dissipates (disperses or spreads out) some of the proton (H+) gradient (Lecture 3, Slide 42)
84
What does oxidative phosphorylation dissipating some of the proton (H+) gradient affect?
The ratio of ATP formed per 1/2 O2 (Lecture 3, Slide 42)
85
How many electrons are required for each 1/2 O2 reduced H2O?
2 (Lecture 3, Slide 42)
86
How many protons are translocated per each ATP synthesised?
3 (Lecture 3, Slide 42)
87
How many protons are exported per each NADH(2e-) and therefore how much ATP is synthesised?
10H+ exported = 2.5 ATP (Lecture 3, Slide 42)
88
How many protons are exported per each FADH2(2e-) and therefore how much ATP is synthesised?
6H+ exported = 1.5 ATP (Lecture 3, Slide 42)
89
How many NADH molecules are produced during glycolysis?
2 (Lecture 3, Slide 43)
90
Can NADH be using during anaerobic conditions?
No (Lecture 3, Slide 43)
91
What happens to NADH during anaerobic conditions?
It is recycled by lactate dehydrogenase (LDH) (Lecture 3, Slide 43)
92
What is the ATP yield of glycolysis per glucose and therefore the ATP yield anaerobic conditions?
2 (Lecture 3, Slide 43)
93
What is the ATP yield per glucose during aerobic conditions?
30 (Lecture 3, Slide 44)
94
How is 30 ATP generated per glucose in aerobic conditions?
2 ATP from glycolysis + 2 GTP from TCA cycle + 3 - (2*1.5) for 2 NADH produced during glycolysis (some energy lost on transport to mitochondria) + 5 - (2*2.5) for 2 NADH produced from pyruvate dehydrogenase + 15 - (6*2.5) for 6 NADH produced from TCA cycle 3 - (2*1.5) for 2 FADH2 produced from TCA cycle (Lecture 3, Slide 44)
95
How many molecules of NADH + H+ are generated in one cycle of the TCA cycle?
3

BM 210: Introduction to Biochemistry (12 decks)

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