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Biochemistry Lectures > Bioc lec 6 > Flashcards

Bioc lec 6 Flashcards

1
Q

Why must NADH formed in glycolysis be oxidized back to NAD+?

A

Cells have limited NAD+, so NADH must be oxidized back to NAD+ to ensure glycolysis continues as an ongoing process.

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2
Q

What determines the metabolic fate of pyruvate?

A

The metabolic fate of pyruvate depends on the available route to oxidize NADH formed in glycolysis.

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3
Q

How does glycolysis function under both aerobic and anaerobic conditions?

A

By ensuring NADH formed in glycolysis is oxidized back to NAD+ through different pathways depending on the physiological condition.

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4
Q

What happens to pyruvate under aerobic conditions?

A

It is oxidized to acetyl-CoA by pyruvate dehydrogenase (PDH).

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5
Q

How is pyruvate transported into the mitochondria?

A

Through a specific transporter.

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6
Q

Where does pyruvate dehydrogenase (PDH) function?

A

In the mitochondrial matrix.

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7
Q

What type of reaction does pyruvate dehydrogenase catalyze?

A

An irreversible oxidative decarboxylation.

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8
Q

Why is pyruvate dehydrogenase considered a key enzyme in metabolism?

A

It links glycolysis to the citric acid cycle.

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9
Q

Which enzyme in the TCA cycle is closely related to pyruvate dehydrogenase

A

Alpha-ketoglutarate dehydrogenase, which catalyzes an analogous reaction.

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10
Q

How many coenzymes does the Pyruvate Dehydrogenase Complex require?

A

Five coenzymes.

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11
Q

What are the five coenzymes required by the Pyruvate Dehydrogenase Complex?

A

NAD+, FAD, CoA, TPP (Thiamine pyrophosphate), and lipoate.

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12
Q

Which vitamins are the coenzymes of the Pyruvate Dehydrogenase Complex derived from?

A

B vitamins.

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13
Q

What is the next step for acetyl CoA once it is formed?

A

It enters the TCA Cycle.

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14
Q

How is NADH oxidized under aerobic conditions?

A

By the Electron Transport Chain (ETC) with O₂ as the ultimate oxidant.

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15
Q

What is the purpose of transferring electrons to the Electron Transport Chain (ETC)?

A

ATP generation via oxidative phosphorylation

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16
Q

Where does glycolysis occur, and where must NADH be transferred for the ETC?

A

Glycolysis occurs in the cytosol, and NADH must be transferred to the mitochondria.

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17
Q

Why are special shuttle systems required to transport cytosolic NADH to mitochondria?

A

The inner mitochondrial membrane (IMM) is impermeable to NADH.

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18
Q

What is the malate-aspartate shuttle?

A

A system used in the liver, kidney, and heart to transfer reducing equivalents from cytosolic NADH to the mitochondria.

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19
Q

What are reducing equivalents?

A

Electrons, possibly accompanied by protons, in the form of electrons alone (e⁻), H atoms (e⁻ + H⁺), or hydride ions (H⁻).

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20
Q

What is the glycerol 3-phosphate shuttle?

A

A system used in skeletal muscle and brain to transfer reducing equivalents from cytosolic NADH to mitochondrial FADH₂.

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21
Q

What happens to the reducing equivalents in the glycerol 3-phosphate shuttle?

A

They are passed onto FADH₂ and directly delivered to coenzyme Q in the electron transport chain, bypassing complex I.

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22
Q

What does bypassing complex I in the ETC imply?

A

It has consequences for the efficiency of ATP production (less ATP generated per NADH).

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23
Q

What happens to pyruvate under anaerobic conditions in animals?

A

Pyruvate is reduced to lactate by lactate dehydrogenase, regenerating NAD⁺.

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24
Q

Why is the reduction of pyruvate to lactate important?

A

It regenerates NAD⁺, allowing glycolysis to continue under anaerobic conditions.

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25
Q

Where does the reduction of pyruvate to lactate occur?

A

In the cytosol.

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26
Q

Why is the reduction of pyruvate to lactate important?

A

It allows regeneration of NAD⁺ and redox balance, enabling glycolysis to continue under anaerobic conditions.

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27
Q

What are the consequences of a deficiency in pyruvate reduction to lactate in muscles?

A

Muscle fatigue and reduced ATP production during intense exercise.

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28
Q

How does glucose oxidation differ from fat oxidation due to this reaction?

A

Glucose oxidation can proceed anaerobically through lactate formation, while fat oxidation requires oxygen.

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29
Q

What happens to NADH under anaerobic conditions?

A

NADH cannot be oxidized via the ETC and must be reoxidized by an alternative pathway.

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30
Q

How is NAD⁺ regenerated in anaerobic conditions?

A

Pyruvate is reduced to lactate by lactate dehydrogenase, regenerating NAD⁺.

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31
Q

Where does the reduction of pyruvate to lactate occur?

A

In the cytosol.

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32
Q

Why is the reduction of pyruvate to lactate critical under anaerobic conditions?

A

It ensures the continuation of glycolysis by maintaining a supply of NAD⁺.

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33
Q

what enzyme does pyruvate to lactate?

A

lactate dehydrogenase

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34
Q

What is the Cori cycle?

A

The metabolic exchange where lactate from muscles is transported to the liver, converted back to glucose via gluconeogenesis, and returned to the muscles to replenish glycogen stores.

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35
Q

Why is lactate transported to the liver after strenuous exercise?

A

To be converted back to glucose, which can replenish muscle glycogen.

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36
Q

What is the main purpose of converting pyruvate to lactate in muscles under anaerobic conditions?

A

To regenerate NAD⁺, ensuring glycolysis can continue.

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37
Q

What do yeast and other microorganisms convert pyruvate into under anaerobic conditions?

A

Ethanol and CO₂, in a process called alcoholic fermentation.

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38
Q

Why is alcoholic fermentation important for microorganisms under anaerobic conditions?

A

It regenerates NAD⁺, allowing glycolysis to continue.

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39
Q

What are the key enzymes involved in alcoholic fermentation, and their roles?

A
  1. Pyruvate decarboxylase: Converts pyruvate to acetaldehyde, releasing CO₂.
  2. Alcohol dehydrogenase: Reduces acetaldehyde to ethanol, regenerating NAD⁺.
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40
Q

Why can’t animals perform alcoholic fermentation?

A

Animals lack the enzyme pyruvate decarboxylase.

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41
Q

What is the function of alcohol dehydrogenase in humans?

A

It catalyzes the NAD⁺-dependent oxidation of ethanol to acetaldehyde, the reverse of its role in fermentation.

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42
Q

What is the role of the TCA cycle in metabolism?

A

The TCA cycle oxidizes acetate (from acetyl-CoA) to CO₂, conserving energy in the form of NADH and FADH₂.

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43
Q

What types of molecules can be catabolized through the TCA cycle?

A

Fats, carbohydrates, and certain amino acids, all converted to acetyl-CoA before entering the TCA cycle.

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44
Q

Why is the TCA cycle oxygen-dependent?

A

The TCA cycle requires NAD⁺ and FAD to be reoxidized back to NADH and FADH₂ through the electron transport chain, which is oxygen-dependent.

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45
Q

What are the main products of the TCA cycle?

A

CO₂, NADH, FADH₂, and GTP (or ATP).

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46
Q

What is the first step of the TCA cycle?

A

The condensation of acetyl-CoA with oxaloacetate to form citrate, catalyzed by citrate synthase.

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47
Q

What is the significance of the first step in the TCA cycle?

A

It is the only step in the TCA cycle that forms a carbon-carbon bond.

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48
Q

What is the second step of the TCA cycle?

A

Isomerization of citrate by aconitase to form isocitrate.

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49
Q

Why is citrate isomerized to isocitrate in the TCA cycle?

A

Citrate, being a tertiary alcohol, is a poor substrate for oxidation. The isomerization converts it to isocitrate, a secondary alcohol, which is a better substrate for oxidation.

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50
Q

What occurs during the isomerization of citrate?

A

The elimination of water from citrate forms cis-aconitate, which is then hydrated to form isocitrate.

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51
Q

what catalyzes citrate to its next form in TCA and what is this next form called?

A

aconitase catalyzes citrate to isocitrate

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52
Q

what does isocitrate become next in TCA and what does this? What coupled reaction occurs as well?

A

isocitrate dehydrogenase makes isocitrate into alpha-ketoglutarate.

NAD is reduced to NADH +H

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53
Q

What happens in Step 4 of the TCA cycle?

A

The oxidative decarboxylation of α-ketoglutarate, catalyzed by the α-ketoglutarate dehydrogenase complex, converts α-ketoglutarate to succinyl-CoA.

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54
Q

What is the product formed from α-ketoglutarate in Step 4?
What does the coupled reaction produce?

A

Succinyl-CoA, a high-energy thioester.

CoASH oxidized to CO2
and NAD reduced to NADH +H

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55
Q

What is the reaction mechanism of α-ketoglutarate dehydrogenase complex similar to?

A

It is identical to the pyruvate dehydrogenase complex, involving decarboxylation and the formation of a high-energy thioester bond.

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56
Q

What occurs in Step 5 of the TCA cycle?

A

The high-energy thioester bond of succinyl CoA is hydrolyzed in a reaction coupled to either GTP or ATP synthesis.

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57
Q

Which enzyme catalyzes Step 5 of the TCA cycle?

A

Succinyl CoA synthetase.

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58
Q

What type of intermediate is formed during Step 5 of the TCA cycle?

A

A phosphoenzyme intermediate is formed.

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59
Q

What happens first in the reaction mechanism of Succinyl CoA synthetase?

A

Inorganic phosphate displaces coenzyme A from succinyl CoA to form a high-energy acyl phosphate (succinyl phosphate).

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60
Q

What residue at the active site of Succinyl CoA synthetase is involved in the reaction mechanism?

A

A reactive histidine residue at the active site of the enzyme accepts the phosphate.

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61
Q

What is released when the histidine residue accepts the phosphate in the Succinyl CoA synthetase mechanism?

A

Succinate is released.

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62
Q

How is the phosphate transferred in the Succinyl CoA synthetase reaction mechanism?

A

The phosphate is transferred from the phosphoenzyme to ADP (or GDP), releasing the free enzyme.

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63
Q

What happens in Step 6 of the TCA cycle?

A

Succinate is oxidized to fumarate by succinate dehydrogenase.

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64
Q

What coenzyme does succinate dehydrogenase use in Step 6 of the TCA cycle?

A

Succinate dehydrogenase uses FAD to oxidize succinate

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65
Q

What type of bond is formed in the reaction between succinate and fumarate in Step 6 of the TCA cycle?

A

The reaction forms an alkene (double bond) between the two carbons of fumarate.

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66
Q

What is the reaction in Step 6 of the TCA cycle analogous to?

A

It is analogous to the acyl-CoA dehydrogenase reaction of β-oxidation.

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67
Q

what coenzyme is used in step 6 of TCA cycle where succinate becomes fumarate?

A

FAD is reduced to FADH2

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68
Q

What happens in Step 7 of the TCA cycle?

A

Fumarate is hydrated to form malate.

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69
Q

Which enzyme catalyzes the hydration of fumarate to malate in Step 7 of the TCA cycle?

A

Fumarase.

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70
Q

What is the hydration reaction in Step 7 of the TCA cycle analogous to?

A

It is analogous to the enoyl-CoA hydratase reaction of β-oxidation.

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71
Q

What happens in Step 8 of the TCA cycle?

A

Malate is oxidized to oxaloacetate by NAD+, completing the cycle

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72
Q

Which enzyme catalyzes the oxidation of malate to oxaloacetate in Step 8 of the TCA cycle?

A

Malate dehydrogenase.

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73
Q

What is the role of NAD+ in Step 8 of the TCA cycle?

A

NAD+ oxidizes malate to oxaloacetate. This means NAD is reduced to NADH + H

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74
Q

What is the oxidation reaction in Step 8 of the TCA cycle analogous to?

A

It is analogous to the hydroxyacyl-CoA dehydrogenase reaction of β-oxidation.

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75
Q

What is the net equation for the Citric Acid Cycle?

A

Acetyl-CoA + 3NAD+ + FAD + GDP + Pi + 2 H2O → 2CO2 + 3NADH + FADH2 + GTP + CoA + 3H+.

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76
Q

What happens to the two carbons of the acetyl group in the Citric Acid Cycle?

A

The two carbons of the acetyl group are oxidized to CO2.

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77
Q

How are electrons transferred in the Citric Acid Cycle?

A

Electrons from the oxidation of acetyl-CoA reduce 3 NAD+ and 1 FAD.

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78
Q

What is produced in terms of energy during the Citric Acid Cycle?

A

One GTP (or ATP) is formed per cycle.

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79
Q

Are intermediates in the Citric Acid Cycle depleted?

A

No, the intermediates in the cycle are not depleted.

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80
Q

What is the most important role of the TCA cycle in terms of bioenergetics?

A

The most important role is to generate high-energy electron carriers (NADH and FADH2) and GTP (or ATP) for further energy production in the electron transport chain.

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81
Q

In an experiment with pigeon breast muscle, the addition of fumarate stimulates the removal of acetyl-CoA in a 1:1 stoichiometric fashion. Which statement best explains this observation?

A

The cycle is inhibited between succinate and fumarate.

Explanation: The inhibition between succinate and fumarate prevents the normal conversion of succinate to fumarate. This causes fumarate to accumulate, and adding fumarate bypasses the block, stimulating the removal of acetyl-CoA in a 1:1 ratio.

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82
Q

What is Stage 3 of catabolism?

A

Stage 3 is Electron Transfer and Oxidative Phosphorylation.

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83
Q

What happens during oxidative phosphorylation?

A

The energy released from the oxidation of NADH and FADH2 is used to synthesize ATP.

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84
Q

Where does oxidative phosphorylation occur?

A

It occurs in the mitochondria.

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85
Q

What types of molecules undergo oxidation in Stage 3 of catabolism?

A

Carbohydrates, lipids, and amino acids.

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86
Q

What happens during the direct oxidation of NADH and FADH2 by O2?

A

The direct oxidation releases a large amount of energy, enough to synthesize several moles of ATP.

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87
Q

Q: What is the formula for calculating the change in Gibbs free energy (ΔG0’)?

A

ΔG0’ = -n F ΔE0’

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88
Q

What is the value of ΔE0’ for the oxidation of FADH2?

A

ΔE0’ = +1.04 V (calculated from 0.82 - (-0.22)).

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89
Q

What is the value of ΔG0’ for the oxidation of FADH2?

A

ΔG0’ = -200 kJ/mol for the reaction FADH2 + ½ O2 → FAD + H2O.

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90
Q

What is the value of ΔE0’ for the oxidation of NADH?

A

ΔE0’ = +1.14 V (calculated from 0.82 - (-0.32)).

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91
Q

What is the value of ΔG0’ for the oxidation of NADH?

A

ΔG0’ = -220 kJ/mol for the reaction NADH + H+ + ½ O2 → NAD+ + H2O.

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92
Q

Why is the direct oxidation of NADH and FADH2 by O2 energetically wasteful?

A

The direct reaction would be energetically wasteful because no covalent bond could contain more than a fraction of the energy released.

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93
Q

How are the reducing equivalents from NADH and FADH2 passed to oxygen in the electron transport chain?

A

The reducing equivalents are passed to oxygen indirectly along the electron transport chain.

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94
Q

What is the advantage of passing electrons through the electron transport chain rather than directly to oxygen?

A

The process breaks up the release of energy into several distinct steps with smaller free energy changes, preventing the release of all energy at once.

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95
Q

What is the electron transport chain composed of?

A

The electron transport chain comprises a special set of electron carriers, arranged in order of increasing reduction potentials.

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96
Q

What happens to the reducing equivalents in the electron transport chain?

A

The reducing equivalents are passed from molecule to molecule all the way up to oxygen, the “terminal electron acceptor.”

97
Q

How many unique enzymes catalyze the transfer of electrons in the mitochondrial electron transport chain?

A

Four unique enzymes (electron carrier complexes) catalyze the transfer of electrons from one carrier to another.

98
Q

What is Coenzyme Q (ubiquinone)?

A

Coenzyme Q is a lipid-soluble benzoquinone with a long isoprenoid tail (R).

99
Q

What happens when Coenzyme Q (ubiquinone) accepts one electron?

A

It forms a semiquinone radical (●QH) by accepting one electron and one proton.

100
Q

What happens when Coenzyme Q (ubiquinone) accepts two electrons?

A

It forms the alcohol ubiquinol (QH2) by accepting two electrons and two protons.

101
Q

Why is Coenzyme Q (ubiquinone) important in the electron transport chain?

A

It functions at junctions between two-electron donors and one-electron acceptors.

102
Q

What is the role of ubiquinol in the electron transport chain?

A

Ubiquinol can freely move in the membrane, carrying electrons from one electron transport chain complex to another.

103
Q

What are cytochromes?

A

Cytochromes are a family of proteins with iron-containing heme prosthetic groups

104
Q

Where is Cytochrome c located, and what is its role in the electron transport chain?

A

Cytochrome c is a soluble protein in the mitochondrial intermembrane space that shuttles electrons from complex III to complex IV of the electron transport chain.

105
Q

How does the iron atom in cytochrome c function?

A

The iron atom of the heme acts as the redox-active component, carrying one electron at a time.

106
Q

What is the redox reaction involving Cytochrome c?

A

Cytochrome c (Fe3+) + e⁻ → Cytochrome c (Fe2+).

107
Q

Which complexes in the electron transport chain transfer electrons to Coenzyme Q (Q)?

A

Complexes I and II transfer electrons to Q, reducing it to QH2.

108
Q

How does QH2 pass electrons to cytochrome c?

A

QH2 passes electrons to cytochrome c through complex III.

109
Q

What is the role of cytochrome c in the electron transport chain?

A

Cytochrome c is a mobile electron carrier that shuttles electrons from complex III to complex IV.

110
Q

What happens in Complex IV of the electron transport chain?

A

Complex IV transfers electrons from reduced cytochrome c to O2, forming water.

111
Q

What is the effect of electron flow through Complexes I, III, and IV?

A

Electron flow through these complexes is accompanied by proton flow from the mitochondrial matrix to the intermembrane space.

112
Q

What is the role of Coenzyme Q (CoQ) in the electron transport chain?

A

CoQ acts as a collector of reducing equivalents, transferring electrons from various sources to the electron transport chain.

113
Q

Which source provides reducing equivalents to CoQ via Complex I?

A

NADH provides reducing equivalents to CoQ via Complex I.

114
Q

How does succinate dehydrogenase (FADH2) contribute to the electron transport chain?

A

Succinate dehydrogenase (FADH2) transfers electrons to CoQ via Complex II.

115
Q

How does Acyl-CoA dehydrogenase (FADH2) contribute to the electron transport chain?

A

Acyl-CoA dehydrogenase (FADH2) transfers electrons to CoQ through a series of electron carriers.

116
Q

ow does the glycerol-3-phosphate dehydrogenase shuttle (FADH2) contribute to the electron transport chain?

A

The glycerol-3-phosphate dehydrogenase shuttle (FADH2) transfers electrons to CoQ.

117
Q

ow can the sequence of electron carriers in the electron transport chain be determined?

A

The sequence can be determined by using respiratory inhibitors that act at different points in the chain.

118
Q

What respiratory inhibitor acts at Complex I?

A

Rotenone and barbiturates act at Complex I.

119
Q

What respiratory inhibitor acts at Complex III?

A

Antimycin A acts at Complex III.

120
Q

What respiratory inhibitors act at Complex IV?

A

Cyanide (CN-) and carbon monoxide (CO) act at Complex IV.

121
Q

Which electron carriers are involved in the sequence?

A

NADH, Coenzyme Q (Q), cytochrome c (cyt. c), and O2 are involved in the electron transport chain sequence.

122
Q

What happens to the electron carriers in the electron transport chain in the presence of an electron donor and O2?

A

All the carriers occurring before the point of obstruction become reduced, and the carriers beyond the obstruction become oxidized.

123
Q

Why is it possible to identify the redox state of electron carriers in the chain?

A

Many of the carriers have distinctive optical chromophores with different optical spectra in their oxidized and reduced states.

124
Q

What allows for the identification of the redox state of electron carriers?

A

The different optical spectra of the carriers in their oxidized and reduced states allow their identification.

125
Q

How is the energy from the oxidation of NADH and FADH2 conserved?

A

The energy is conserved in the form of a proton gradient across the inner mitochondrial membrane.

126
Q

How many protons are pumped for each pair of electrons transferred from NADH to O2?

A

Four protons are pumped by Complex I, four by Complex III, and two by Complex IV, for a total of 10 protons.

127
Q

How many protons are pumped for each FADH2 oxidized?

A

A total of 6 protons are pumped for each FADH2 oxidized, since electrons from FADH2 bypass Complex I.

128
Q

What does the proton gradient across the inner mitochondrial membrane act as?

A

The proton gradient acts as a temporary reservoir of much of the energy of electron transfer.

129
Q

What is the energy stored in the proton gradient called?

A

The energy stored in the proton gradient is called the proton motive force.

130
Q

What are the two components of Proton Motive Force?

A
  1. Chemical potential energy (due to difference in concentration of H⁺)
  2. Electrical potential energy (due to the separation of charges).
131
Q

What does the chemical potential energy in Proton Motive Force result from?

A

The chemical potential energy results from the difference in concentration of H⁺ (protons) across the membrane.

132
Q

hat does the electrical potential energy in Proton Motive Force result from?

A

The electrical potential energy results from the separation of charges (protons are positively charged).

133
Q

what transports protons across membrane?

A

proton pump

134
Q

How much of the energy available from NADH oxidation is conserved in the proton gradient?

A

Approximately 200 kJ of the 220 kJ available from NADH oxidation is conserved in the proton gradient (10 H⁺ per NADH).

135
Q

How is the concentration of protons used to generate ATP?

A

The free energy from redox reactions is used by the electron transport chain (ETC) to pump protons from the matrix to the intermembrane space, creating an electrochemical gradient (proton motive force).

136
Q

What is the electrochemical gradient formed by protons?

A

The electrochemical gradient, also called the proton motive force, stores energy created by the movement of protons from the matrix to the intermembrane space.

137
Q

How do protons flow back into the matrix?

A

Protons flow back into the matrix passively down their concentration gradient through the proton pore of the ATP synthase enzyme.

138
Q

What happens to the energy from the electrochemical gradient?

A

The energy of the electrochemical gradient is released and used to generate ATP by the ATP synthase enzyme.

139
Q

How are electron transfer and ATP synthesis related?

A

Electron transfer and ATP synthesis are coupled to each other; neither reaction occurs without the other.

140
Q

What theory explains the obligatory coupling between electron transfer and ATP synthesis?

A

The chemiosmotic theory explains this obligatory coupling.

141
Q

What happens if electron transfer is inhibited?

A

Inhibition of electron transfer will inhibit both oxygen consumption and ATP synthesis.

142
Q

Why does inhibition of electron transfer inhibit ATP synthesis?

A

Since the energy for ATP synthesis is derived from the oxidation process, inhibition of electron transfer by various inhibitors will invariably inhibit ATP synthesis.

143
Q

What happens when ATP synthase is inhibited?

A

Inhibition of ATP synthase (by venturicidin or oligomycin) prevents protons from flowing back into the matrix, causing protons to accumulate in the intermembrane space.

144
Q

What is the effect of proton accumulation in the intermembrane space?

A

Proton accumulation in the intermembrane space builds up a high concentration, creating a proton gradient.

145
Q

Why does inhibition of ATP synthase block the electron transport chain?

A

The energy required to pump protons against the gradient exceeds the energy available from NADH oxidation, which prevents proton translocation. As proton translocation is an obligatory part of the catalytic cycle of the electron transport chain complexes, they can no longer perform electron transport.

146
Q

What happens if protons in the intermembrane space can cross back into the matrix without passing through ATP Synthase?

A

The proton gradient is eliminated, electron transport continues, but ATP synthesis stops. The system becomes “uncoupled.”

147
Q

What is a classic example of a chemical uncoupler?

A

Dinitrophenol (DNP) is a classic example of a chemical uncoupler.

148
Q

What happens when DNP is added to mitochondria?

A

When DNP is added to mitochondria, ATP production ceases, but electron transport continues.

149
Q

How does 2,4-DNP (dinitrophenol) work to uncouple oxidative phosphorylation?

A

The dinitrophenolate anion (DNP⁻) picks up a proton to form DNPH and transports it across the inner mitochondrial membrane (IMM), releasing the proton in the matrix to form DNP⁻.

150
Q

Why does DNP cross back to the intermembrane space after releasing the proton in the matrix?

A

DNP⁻ crosses back to the intermembrane space because its negative charge is delocalized over the aromatic ring, and the structure retains considerable hydrophobic character.

151
Q

What is the result of DNP’s action on the proton gradient?

A

The proton gradient is collapsed, and ATP synthesis stops.

152
Q

What happens to the energy of oxidation when DNP uncouples oxidative phosphorylation?

A

Since energy of oxidation is not conserved by ATP formation, it dissipates as heat

153
Q

What does rotenone block in tightly coupled mitochondria?

A

Rotenone blocks the transfer of electrons from NADH to ubiquinone.

154
Q

What happens if succinate is added to the mixture when rotenone blocks electron transfer from NADH to ubiquinone?

A

Electron transfer to O₂ will continue because succinate bypasses the NADH pathway, entering the electron transport chain at a later point.

155
Q

How is the proton gradient used to drive the synthesis of ATP?

A

The proton gradient drives the synthesis of ATP by enabling protons to flow through ATP synthase, which uses the energy from this flow to catalyze the synthesis of ATP.

156
Q

What are the two functional domains of ATP synthase?

A

The two functional domains of ATP synthase are F1 (peripheral membrane protein) and Fo (integral membrane protein).

157
Q

What is the function of the F1 domain of ATP synthase?

A

The F1 domain has ATP synthase/ATPase activity, responsible for catalyzing the synthesis and hydrolysis of ATP.

158
Q

What is the F1 domain of ATP synthase?

A

peripheral membrane protein

159
Q

What is the Fo domain of ATP synthase?

A

Integral membrane protein

160
Q

How many subunits does the F1 domain of ATP synthase consist of?

A

The F1 domain consists of 9 subunits: α₃β₃γδε.

161
Q

What is the role of the α and β subunits in F1?

A

The three α subunits are identical, and the three β subunits are identical. Each β subunit contains a catalytic site for ATP synthesis.

162
Q

What is the role of the γ subunit in ATP synthase?

A

The γ subunit forms a stalk in the center of the α₃β₃ complex and, through the ε subunit, attaches F1 to the membrane-embedded “C” ring of Fo.

163
Q

What is the composition of the Fo domain in ATP synthase?

A

The Fo domain has the composition ab₂C₈₋₁₇.

164
Q

What is the structure of the c subunits in Fo?

A

The c subunits are multiple hairpins of two hydrophobic α-helices that assemble to form the transmembrane C₁₀ ring.

165
Q

How does the number of c subunits vary?

A

The number of c subunits varies among different kingdoms of life.

166
Q

What is the significance of the conserved aspartic acid residue in the c subunits?

A

Each c subunit contains a conserved aspartic acid residue (Asp 61) in the middle of one of its helices, which plays a key role in proton translocation.

167
Q

What role do the b subunits play in the Fo domain?

A

The two b subunits, acting through δ, associate firmly with the α₃β₃ complex in F1.

168
Q

Where is the “a” subunit located, and what is its function?

A

The “a” subunit resides in the membrane, wraps partially around the c-10 ring, and contains two half-channels for proton movement.

169
Q

What did Paul Boyer discover about the equilibrium constant for the reaction ADP + Pi → ATP + H₂O?

A

Paul Boyer found that the equilibrium constant for this reaction is close to 1 when it occurs in the active site of ATP synthase, meaning the free energy change is about zero

170
Q

How does ATP formed in the ATP synthase active site behave?

A

The formed ATP remains very tightly bound to the active site.

171
Q

What provides the energy for the release of ATP from the ATP synthase active site?

A

The proton gradient provides the energy required for the release of ATP.

172
Q

How does the proton gradient affect ATP release from ATP synthase?

A

The proton gradient drives the release of ATP from the active site of ATP synthase.

173
Q

How does the energy barrier for ATP synthase differ from a typical enzyme-catalyzed reaction?

A

Unlike a typical enzyme-catalyzed reaction, the energy barrier for ATP synthase is not about reaching the transition state but about the release of formed ATP from the enzyme.

174
Q

???Why is it hard to release ATP from ATP synthase???

A

The release of ATP from the enzyme is difficult because the formed ATP is tightly bound to the active site, and the energy required for its release is provided by the proton gradient.

175
Q

How does ATP synthase overcome the large energy barrier for ATP release?

A

ATP synthase overcomes the energy barrier through rotational catalysis, where the active site cycles between a form that tightly binds ATP and a form that releases ATP.

176
Q

What is the process of rotational catalysis in ATP synthase?

A

In rotational catalysis, the active site of ATP synthase is formed, torn apart, and then re-formed in a cyclic fashion, allowing the continued synthesis of ATP.

177
Q

How many different conformations can each β subunit of F1 assume?

A

Each β subunit of F1 can assume 3 different conformations.

178
Q

How does the γ subunit interact with the α₃β₃ complex in ATP synthase?

A

The γ subunit interacts asymmetrically with the α₃β₃ complex, causing the three β subunits to adopt different conformations, each associated with differences in their ADP/ATP binding site.

179
Q

What are the three conformations that the β subunits cycle through?

A

The three conformations are: Loose (L), Tight (T), and Open (O).

180
Q

How do the β subunits change between their conformations?

A

Each β subunit is able to cycle between the Loose, Tight, and Open conformations.

181
Q

What happens during catalysis in ATP synthase?

A

During catalysis, the γ subunit rotates in the center of the α₃β₃ complex.

182
Q

How does the rotation of the γ subunit affect the β subunits?

A

With each 120° turn of the γ subunit, a different face comes into contact with each β subunit, rotating them between the three different conformations.

183
Q

What are the steps a given β subunit undergoes during rotational catalysis?

A

A given β subunit starts in the Loose conformation (binding ADP and Pi), moves to the Tight form (where ATP is formed), and finally to the Open form (where ATP is released).

184
Q

What happens to ATP when conformation is tight?

A

binding ADP +Pi

185
Q

What happens to ATP when conformation is tight?

A

ATP being synthesized

186
Q

What happens to ATP when conformation is loose?

A

ATP can be released

187
Q

What forms the stator arm of ATP synthase?

A

The a, b, and δ subunits form the stator arm, which remains fixed with respect to the inner membrane.

188
Q

Which part of ATP synthase remains stationary?

A

The α₃β₃ complex remains stationary, held in place by the δ subunit.

189
Q

How does the proton gradient power ATP synthase?

A

The ring of c subunits rotates with respect to the stator (a, b, and δ), powered by the proton gradient.

190
Q

Which subunits rotate along with the c-ring in ATP synthase?

A

The ε and γ subunits rotate along with the c-ring.

191
Q

What is the net result of the rotation in ATP synthase?

A

The net result is that the γ subunit turns within the core of the α₃β₃ complex.

192
Q

What does the “a” subunit of ATP synthase provide?

A

The “a” subunit provides a passage for the movement of protons across the inner mitochondrial membrane (IMM) through two half-channels.

193
Q

What are the two half-channels in the “a” subunit?

A

One half-channel leads from the intermembrane space side of the membrane into the “a” subunit, and the other half-channel leads from inside the “a” subunit to the matrix.

194
Q

How do protons move between the half-channels in ATP synthase?

A

Protons must jump from the “a” subunit onto the adjacent “c” subunit, travel around the “c” subunit, and move out through the second half-channel.

195
Q

What does the passage of protons do in ATP synthase?

A

The passage of protons makes the c-ring rotate.

196
Q

What holds the C₁₀ ring in place in ATP synthase?

A

The C₁₀ ring is held in place by the ionic interaction between Asp 61 of “c” and a conserved arginine residue of “a”.

197
Q

What happens when a proton jumps from the intermembrane-space half-channel of “a” to “c”?

A

The proton protonates Asp 61 on the “c” subunit.

198
Q

What is the effect of protonating Asp 61 in ATP synthase?

A

The protonation of Asp 61 breaks the ionic interaction between Asp 61 and the conserved arginine residue on “a”, setting the C₁₀ ring free to rotate.

199
Q

What happens after the protonated “c” moves away from the “a” subunit in ATP synthase?

A

The “c” subunit moves into the hydrophobic membrane environment, and another “c” subunit is forced into contact with the matrix-facing half-channel of “a.”

200
Q

What happens when a “c” subunit comes into contact with the matrix-facing half-channel of “a”?

A

The proton carried by that “c” subunit is released into the mitochondrial matrix.

201
Q

What happens after the protonated “c” subunit moves away from the “a” subunit in ATP synthase?

A

The protonated “c” subunit moves into the hydrophobic region of the membrane, while another “c” subunit is brought into contact with the matrix-facing half-channel of “a.”

202
Q

What happens when another “c” subunit comes into contact with the matrix-facing half-channel of the “a” subunit in ATP synthase?

A

The proton carried by this “c” subunit is released into the matrix.

203
Q

How does the protonation process continue in ATP synthase after a proton is released into the matrix?

A

A new proton enters through the IMS half-channel to protonate Asp 61 on the next “c” subunit, continuing the cycle.

204
Q

What occurs after each protonation/deprotonation event in ATP synthase?

A

The C₁₀ ring rotates, bringing a new protonated “c” subunit into contact with the matrix half-channel, where the proton is released and a new proton enters the ring

205
Q

How many protonation/deprotonation events are needed for the C₁₀ ring to complete a full revolution?

A

After 10 protonation/deprotonation events, the C₁₀ ring performs one complete revolution.

206
Q

What is the result of the rotation of the C₁₀ ring in ATP synthase?

A

The rotation of the C₁₀ ring leads to the rotation of the γ subunit within the α₃β₃ complex, causing each β subunit to cycle through all three conformations (loose, tight, open).

207
Q

How does the rotation of the γ subunit in ATP synthase lead to ATP synthesis?

A

The rotation of the γ subunit drives the synthesis and release of three ATP molecules, one from each β subunit during the cycling process.

208
Q

What does the equation for oxidative phosphorylation describe?

A

The equation for oxidative phosphorylation describes the process:
x (ADP+Pi) + NADH + H^+ + 1/2O2 –> x ATP + NAD+ + H2O

209
Q

What is the P/O ratio in oxidative phosphorylation?

A

The P/O ratio represents the number of moles of ATP synthesized per mole of NADH or FADH₂ oxidized (or per 2 electrons passed along the electron transport chain).

210
Q

What is the P/O ratio for NADH in oxidative phosphorylation?

A

The P/O ratio for NADH is approximately 2.5, meaning 2.5 ATP molecules are produced per NADH molecule oxidized.

211
Q

What is the P/O ratio for FADH₂ in oxidative phosphorylation?

A

The P/O ratio for FADH₂ is approximately 1.5, meaning 1.5 ATP molecules are produced per FADH₂ molecule oxidized.

212
Q

Why do non-integral P/O ratios occur in oxidative phosphorylation?

A

Non-integral P/O ratios occur due to chemiosmotic coupling, which depends on the detailed mechanism by which the proton gradient is used to drive ATP synthesis.

213
Q

How many protons are pumped during the oxidation of one mole of NADH?

A

The oxidation of one mole of NADH pumps 10 protons across the inner mitochondrial membrane.

214
Q

How many protons are needed to complete one full revolution of the ATP synthase C10 ring?

A

10 protons are needed to turn the ATP synthase C10 ring through one full revolution.

215
Q

How many ATP molecules are formed after one revolution of the ATP synthase C10 ring?

A

3 moles of ATP are formed after one revolution of the ATP synthase C10 ring.

216
Q

What is the theoretical P/O ratio for NADH in oxidative phosphorylation?

A

3 ATP per 10 protons

217
Q

Why is the P/O ratio for NADH less than 3?

A

Some of the proton gradient energy is used for purposes other than ATP synthesis, such as powering the transport of solutes across the inner mitochondrial membrane.

218
Q

What is one example of energy from the proton gradient being used for something other than ATP synthesis?

A

One proton per ATP synthesized is used to pump inorganic phosphate (Pi) into the matrix via the phosphate translocase symporter.

219
Q

What is the role of the phosphate translocase symporter in the proton gradient?

A

It uses one proton per ATP synthesized to pump inorganic phosphate (Pi) into the matrix, which reduces the energy available for ATP production.

220
Q

How does the transport of solutes across the inner mitochondrial membrane impact the P/O ratio?

A

It uses some of the proton gradient energy, meaning fewer protons are available for ATP synthesis, leading to a P/O ratio less than 3 for NADH.

221
Q
A
222
Q

How many protons would be required to turn a c-ring one full circle if
the C ring is made of 14 subunits?

A

14

223
Q

What are the end products of fatty acid oxidation?

A

Fatty acid oxidation produces CO2 and H2O.

224
Q

What are the end products of glucose oxidation?

A

Glucose oxidation produces CO2 and H2O.

225
Q

How many rounds of beta oxidation are required to remove all carbon atoms of palmitate (a fatty acid) as acetyl CoA?

A

7 rounds of beta oxidation are required.

226
Q

How many moles of acetyl CoA would be produced through beta oxidation of palmitate?

A

8 moles of acetyl CoA would be produced.

227
Q

What is the ATP cost for the activation of palmitate to palmitoyl-CoA?

A

The activation of palmitate costs 2 ATP (hydrolysis of ATP to AMP + 2Pi).

228
Q

What is the net gain of ATP from the oxidation of one molecule of palmitate?

A

The net gain of ATP per molecule of palmitate is 106 ATP (108 ATP from oxidation - 2 ATP cost for activation).

229
Q

hat is the total ATP yield from the complete oxidation of one mole of glucose to CO2 and H2O?

A

The total ATP yield from the complete oxidation of one mole of glucose is 30 or 32 ATP, depending on the shuttle system used for NADH transport into the mitochondria.

230
Q

What is the ATP yield from the complete oxidation of one mole of glucose to CO2 and H2O?

A

The total ATP yield from the complete oxidation of one mole of glucose is 30 or 32 ATP, depending on the shuttle system used.

231
Q

How does the shuttle system affect the ATP yield from glucose oxidation?

A

The ATP yield depends on the shuttle system that transfers cytosolic reducing equivalents into the mitochondrion:

Malate-Aspartate shuttle: Each cytosolic NADH gives rise to 2.5 moles of ATP.
Glycerol-3-phosphate (G-3-P) shuttle: Each cytosolic NADH gives rise to 1.5 moles of ATP.

232
Q

What is the ATP yield from the oxidation of one mole of glucose under anaerobic conditions?

A

The total ATP yield from the oxidation of one mole of glucose under anaerobic conditions is 2 ATP.

233
Q

What is the ΔG0′ for the oxidation of palmitate to CO2 and H2O?

A

The ΔG0′ for the oxidation of palmitate to CO2 and H2O is about 9800 kJ/mol.

234
Q

How much energy is recovered as the phosphate bond energy of ATP during the oxidation of palmitate?

A

The energy recovered as the phosphate bond energy of ATP is 3230 kJ/mol (106 ATP x 30.5 kJ/mol).

235
Q

What is the thermodynamic efficiency of palmitate oxidation under standard conditions?

A

The thermodynamic efficiency of palmitate oxidation under standard conditions is about 33% of the theoretical maximum.

236
Q

How efficient is energy recovery from palmitate oxidation under intracellular conditions?

A

Under intracellular conditions, the free energy recovery from palmitate oxidation is more than 60%.

237
Q

What is the thermodynamic efficiency of glucose oxidation?

A

The thermodynamic efficiency of glucose oxidation is around 50-60%.

238
Q

How does the thermodynamic efficiency of glucose oxidation compare to that of a modern combustion engine?

A

The thermodynamic efficiency of glucose oxidation is almost twice as efficient as a modern combustion engine, which operates at 35% efficiency.

239
Q
A

Biochemistry Lectures (4 decks)

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