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Metabolism > Bioenergetics, Krebs cycle, and oxidative phosphorylation > Flashcards

Bioenergetics, Krebs cycle, and oxidative phosphorylation Flashcards

1
Q

What is the value of the gas constant (R)?

in cal K–1 mol–1

A

1.987

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2
Q

What is the equation for calculating the Gibbs free energy change (∆G) from an equilibrium constant?

A

∆G = ∆Gº + RTln([products]/[substrates])

If the reaction is at equilibrium, ∆G = 0
∴ ∆Gº = –RTln([products]/[substrates])

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3
Q

Under which conditions may a reaction with ∆Gº > 0 proceed in the forward direction?

A

If [substrates] is much larger than [products]

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4
Q

In metabolism, what are stage I reactions?

A

Degradation of large molecules into small monomers

  • E.g. proteins to amino acids, fats to fatty acids/glycerol, polysaccharides to monosaccharides
  • Enzymes involved: amylase, lipases, proteases
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5
Q

In metabolism, what are stage II reactions?

A

Degradation of monomers to energetically useful products (most acetyl CoA), often accompanied by a small release of ATP

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6
Q

In metabolism, what are stage III reactions?

A

Production of large amounts of ATP from acetyl CoA by the TCA cycle and oxidative phosphorylation

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7
Q

What is the standard free energy change (∆Gº) for the hydrolysis of ATP?

in kcal mol–1

A

–7.3

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8
Q

How are energy barriers for endergonic reactions overcome?

A
  • Reaction coupling: coupling an endergonic reaction to a favorable, exergonic one (e.g. ATP hydrolysis)
  • Common intermediates: for A ⇌ B, if B is consumed by another reaction and kept at low concentration, the equilibrium will shift in favor of the production of B
  • Active intermediates: phosphorylation of a substrate using UDP, GTP, or creatine phosphate may make it more reactive
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9
Q

How is creatine phosphate (CP) synthesized in the cell?

A

ATP + creatine → ADP + CP (∆Gº = +2.5 kcal mol–1)

  • If the energy charge of the cell is low, eqm shifts in favor of ATP production
  • If the energy charge of the cell is high, eqm shifts in favor of CP production
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10
Q

How can ∆Gº be calculated from a redox potential?

A

∆Gº = –nFEº

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11
Q

What is the value of Faraday’s constant (F)?

kcal equivalent

A

23.060

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12
Q

What is the Nernst equation?

A

E = Eº + 2.303(RT/nF)∙log([ox]/[red])

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13
Q

Pyruvate is an important metabolite and the end-product of glycolysis. What are the metabolic fates of pyruvate?

A
  1. Reduction to lactate (lactate dehydrogenase)
  2. Decarboxylation to acetate (pyruvate dehydrogenase complex)
  3. Synthesis of fatty acids (via acetyl CoA)
  4. Synthesis of ketone bodies (via acetyl CoA)
  5. Carboxylation to oxaloacetate (pyruvate carboxylase)
  6. Transamination reactions to form alanine
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14
Q

What are the components of the pyruvate dehydrogenase complex?

A
  • E1: pyruvate decarboxylase/dehydrogenase
  • E2: dihydrolipoyl transacetylase
  • E3: dihydrolipoyl dehydrogenase
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15
Q

What are the coenzymes in the conversion of pyruvate to acetyl CoA?

A
  • E1: thiamine pyrophosphate (TPP)
  • E2: CoA-SH, lipoic acid
  • E3: NAD+, FAD
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16
Q

Is the conversion of pyruvate to acetyl CoA reversible or irreversible?

A

Irreversible

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17
Q

What is the overall reaction of the conversion of pyruvate to acetyl CoA?

A

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

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18
Q

What is the function of E1 in the pyruvate dehydrogenase complex?

A

Decarboxylates pyruvate and binds the product to TPP, the coenzyme

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19
Q

What is the function of E2 in the pyruvate dehydrogenase complex?

A
  1. Oxidizes the product of E1 (liberating it from TPP) to acetyl by transferring it to disulfide lipoic acid, which is reduced
  2. Acetyl is transferred to CoA. Reduced lipoic acid is released
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20
Q

What is the function of E3 in the pyruvate dehydrogenase complex?

A
  1. Reduced lipoic acid is re-oxidized by FAD
  2. FAD is regenerated by reducing NAD+
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21
Q

How is the pyruvate dehydrogenase complex allosterically regulated?

A

Inhibited by the end products, NADH and acetyl CoA

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22
Q

How is the pyruvate dehydrogenase complex covalently regulated?

A
  • E1 is phosphorylated by a kinase—INACTIVE
  • E1 is dephosphorylated by a phosphatase—ACTIVE
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23
Q

What are the regulators of the kinase of pyruvate dehydrogenase E1?

A

Activators

  • NADH
  • ATP (high energy charge)
  • Acetyl CoA

Inhibitors

  • CoA-SH
  • ADP/AMP (low energy charge)
  • NAD+
  • Pyruvate
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24
Q

What are the regulators of the phosphatse of pyruvate dehydrogenase E1?

A

Activators

  • Mg2+
  • Ca2+
  • Insulin, in adipocytes
  • Catecholamines (Epi, NE), in cardiac cells
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25
Q

Where are the enzymes of the Krebs cycle located?

A

All in the mitochondrial matrix, except succinate dehydrogenase, which is embedded in the inner mitochondrial membrane

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26
Q

How many steps are there in the Krebs cycle (excluding the conversion of pyruvate to acetyl CoA)?

A

8

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27
Q

In what form does NAD+ accept electrons?

A

2 hydride (H–) ions

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28
Q

In what form does FAD accept electrons?

A

2 hydrogen atoms (H), one at a time

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29
Q

What is the net change in number of carbons in the Krebs cycle?

A

0

For each turn of the cycle, 2C atoms are taken up from acetyl CoA, and 2 are lost as CO2—but these are not the same 2 carbons

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30
Q

What are the net products of 1 turn of the Krebs cycle (i.e. per 1 molecule of acetyl CoA)?

A

3NADH + 3H+ + FADH2 + 2CO2 + GTP

(In some tissues, GTP may be converted to ATP)

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31
Q

What type of cycle is the Krebs cycle?

A

Amphibolic

  • It is catabolic as it is involved in the breakdown of many molecules, e.g. monosaccharides, fatty acids
  • It is anabolic as its intermediates are involved in the biosynthesis of many molecules, e.g. α-ketoglutarate is transaminated with Ala to produce Glu
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32
Q

What is the most exergonic step of the Krebs cycle?

A

Step 1 (∆G° = –9 kcal mol–1)

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33
Q

What is the most endergonic step of the Krebs cycle?

A

Step 8 (∆G° = +7.1 kcal mol–1)

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34
Q

In which steps of the Krebs cycle is NADH produced?

A

Steps 3, 4, and 8

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35
Q

In which steps of the Krebs cycle is CO2 produced?

A

Steps 3 and 4

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36
Q

In which step of the Krebs cycle is GTP produced?

A

Step 5

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37
Q

What is step 1 of the Krebs cycle?

A

oxaloacetate + acetyl CoA → citrate + CoA-SH
Catalyzed by citrate synthase

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38
Q

What is step 2 of the Krebs cycle?

A

citrate → isocitrase
(by dehydration to aconitate and rehydration; OH moves from C3 to C2)
Catalyzed by aconitase

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39
Q

How is citrate isomerized to isocitrate?

A

Aconitase dehydrates and rehydrates citrate, moving the hydroxyl from C3 to C2

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40
Q

What is step 3 of the Krebs cycle?

A

isocitrate → α-ketoglutarate + CO2 + NADH
Catalyzed by isocitrate dehydrogenase

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41
Q

What is the first step of the Krebs cycle in which CO2 is released?

A

Step 3

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42
Q

What is the first step of the Krebs cycle in which NADH is produced?

A

Step 3

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43
Q

What is step 4 of the Krebs cycle?

A

α-ketoglutarate → succinyl CoA + CO2 + NADH
Catalyzed by α-ketoglutarate dehydrogenase complex

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44
Q

What is step 5 of the Krebs cycle?

A

succinyl CoA → succinate + GTP + CoA-SH
Catalyzed by succinate thiokinase

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45
Q

What is the enzyme of the Krebs cycle that resembles the pyruvate dehydrogenase complex?

A

α-ketoglutarate dehydrogenase complex

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46
Q

The α-ketoglutarate dehydrogenase complex resembles the pyruvate dehydrogenase complex. What are the component enzymes of the α-ketoglutarate dehydrogenase complex?

A
  • E1: α-ketoglutarate dehydrogenase/decarboxylase
  • E2: dihydrolipoyl transsuccinylase
  • E3: dihydrolipoyl dehydrogenase
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47
Q

What is step 6 of the Krebs cycle?

A

succinate → fumarate + FADH2
Catalyzed by succinate dehydrogenase

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48
Q

What is step 7 of the Krebs cycle?

A

fumarate + H2O → malate
Catalyzed by fumarase

49
Q

What is step 8 of the Krebs cycle?

A

malate → oxaloacetate + NADH
Catalyzed by malate dehydrogenase

50
Q

What are the enzymes of the Krebs cycle?

A
  • Citrate synthase
  • Aconitase
  • Isocitrate dehydrogenase
  • α-ketoglutarate dehydrogenase complex
  • Succinate thiokinase
  • Succinate dehydrogenase
  • Fumarase
  • Malate dehydrogenase
51
Q

The final step of the Krebs cycle, which regenerates oxaloacetate, is highly endergonic. How is it driven in the forward direction without the investment of energy?

A

The concentration of oxaloacetate is kept very low by consumption in the highly exergonic reaction of citrate synthase. This shifts the equilibrium to the right.

52
Q

How is the Krebs cycle regulated?

A

Step 1

  • Activators: ADP
  • Inhibitors: NADH, ATP, citrate, succinyl CoA

Step 3

  • Activators: Ca2+, ADP/AMP (activate by lowering Km)
  • Inhibitors: ATP, NADH

Step 4

  • Activators: Ca2+, AMP
  • Inhibitors: succinyl CoA, NADH, ATP, GTP

Step 5

  • Activator: AMP
  • Inhibitor: ATP
53
Q

What is the common characteristic of the regulated steps of the Krebs cycle?

A

They are all exergonic

54
Q

What are the irreversible steps of the Krebs cycle?

A
  • Step 1
  • Step 3
  • Step 4
55
Q

How do the inner and outer mitochondrial membranes differ in permeability?

A
  • Outer: special pores make it freely permeable to most ions and small molecules (MW < 10 kDa)
  • Inner: impermeable to most small ions (including H+, Na+, K+), small molecules (including ATP, ADP, pyruvate), and other metabolites important to the mitochondria. Special carriers and transport systems are required to move these particles
56
Q

What are the mechanisms by which the electrons stored in NADH from glycolysis are transported into the mitochondria?

A
  • Malate–aspartate shuttle
  • Glycerol-3-phosphate shuttle
57
Q

Where in the body is the malate–aspartate shuttle predominant?

A
  • Liver
  • Heart
58
Q

Where in the body is the glycerol-3-phosphate shuttle predominant?

A
  • Most body tissues, including muscle
59
Q

Which of the two electron shuttles to the mitochondria is more efficient?

A

The malate–aspartate shuttle, as it preserves the electrons in NADH (which produces 2.5ATP), rather than transferring them to FADH2 (which produces 1.5ATP)

60
Q

What is the mechanism of the malate–aspartate shuttle?

A
  • NADHcyt is used to reduce cytosolic oxaloacetate to malate
  • Cytosolic malate is transported across the inner mitochondrial membrane using a specific translocase
  • In the matrix, malate is oxidized to oxaloacetate, reducing NAD+mit to NADHmit
  • Oxaloacetate cannot pass back to the cytosol, so it is returned using transaminases and antiporters

Summary: NADHcyt + NAD+mit → NAD+cyt + NADHmit

61
Q

What is the mechanism of the glycerol-3-phosphate shuttle

A
  • NADHcyt is used to reduce DHAP to glycerol-3-phosphate (via the cytosolic enzyme glycerol-3-phosphate dehydrogenase)
  • Glycerol-3-phosphate diffuses through the outer mitochondrial membrane
  • At the inner mitochondrial membrane, G3P donates electrons to the membrane-bound FAD-containing glycerol-3-phosphate dehydrogenase, which reduces FADmit

Summary: NADHcyt + FADmit → NAD+cyt + FADH2 mit

62
Q

What are the 4 classes of electron carriers in the electron transport chain?

A
  • Coenzyme Q (ubiquinone)
  • Cytochromes
  • Fe∙S centers
  • Copper-containing proteins
63
Q

What are the structural features of Q?

A
  • Only non-protein bound electron carrier
  • Has a long hydrophobic isoprenoid tail which helps it diffuse quickly through the hydrocarbon tails of the phospholipids in the inner mitochondrial membrane
64
Q

How does Q accept electrons?

A
  • Q + e–→ Q∙–
  • Q∙– + e– + 2H+ → QH2

Ubiquinone → semiquinone → ubiquinol

65
Q

What is the structure of the cytochromes?

A
  • Heme-containing proteins
  • Each cytochromes differs in protein structure, in the conjugation pattern of the heme groups, and the side chains of the pyrrole ring, leading to different reduction potentials (E°red)
66
Q

How do cytochromes accept electrons?

A
  • Each cytochrome accepts only one electron
  • The central Fe3+ is reduced to Fe2+
67
Q

What is the oxidation state of iron in cytochromes that have not accepted an electron?

A

+3

68
Q

What is the structure of Fe∙S centers?

A
  • A core of either Fe2S2 or Fe4S4
  • Iron is also bound to the S of Cys side chains
69
Q

What is the role of copper-containing proteins in the ETC?

A
  • Cytochromes also have copper to help reduce oxygen
  • Copper is reduced from Cu2+ to Cu+
70
Q

Where in the ETC are protons pumped into the intermembrane space?

A

Complexes I, III, and IV

71
Q

How many protons are pumped at each complex of the ETC?

A
  • Complex I: 4H+
  • Complex II: 0H+
  • Complex III: 4H+
  • Complex IV: 2H+
72
Q

What is the name of complex I of the ETC?

A

NADH:Q oxidoreductase (or, NADH reductase)

73
Q

What are the structure features of complex I?

A
  • A large, transmembrane flavoprotein
  • Contains more than 25 polypeptide chains
  • Contains tightly bound FMN
  • Seven of Fe∙S centers of at least two types
74
Q

What is the sequence of electron transfer reactions in complex I?

A

NADH + H+ (from Krebs, etc.) → FMN → Q, forming QH2

75
Q

What happens to coenzyme Q at the end of the complex I transfer reactions?

A

Ubiquinol (QH2) dissociates from the complex

76
Q

How many electrons are fed through complex I?

A

2e–

77
Q

What is the source of the electrons passed through complex I?

A

NADH + H+ from the Krebs cycle, glycolysis, etc.

78
Q

What is the decreasing order of the reduction potentials (Eºred) for the complexes of the ETC?

A

complex IV > complex III > complex II > complex I

(Not actually sure if II is > I tbh)

79
Q

What is the name of complex II of the ETC?

A

Succinate dehydrogenase

80
Q

What are the three enzyme systems comprising complex II of the ETC?

A
  • Succinate dehydrogenase
  • Glycerol-3-phosphate dehydrogenase
  • Fatty-acyl CoA dehydrogenase
81
Q

What is the sequence of electron transfer reactions in the succinate dehydrogenase system of complex II?

A

succinate → fumarate + FADH2 (in the Krebs cycle)
FADH2 → Fe∙S → Q, forming QH2

82
Q

What is the sequence of electron transfer reactions in the glycerol-3-phosphate dehydrogenase system of complex II?

A

glycerol-3-phosphate → FADH2 → Q, forming QH2

(This is the reaction of glycerol-3-phosphate shuttle)

83
Q

What is the sequence of electron transfer reactions in the fatty-acyl CoA dehydrogenase system of complex II?

A

fatty-acyl CoA → FADH2 (in β-oxidation)
FADH2 → Q, forming QH2

84
Q

Why are no protons pumped at complex II?

A

The Eº (and thereby ∆Gº) are insufficient for proton pumping

85
Q

What is the name of complex III of the ETC?

A

Cytochrome bc1 (or, Q:cytochrome c oxidoreductase)

86
Q

What is source of electrons passed through complex II of the ETC?

A

FADH2 (generated from various sources)

87
Q

What are the structural features of complex III of the ETC?

A
  • Contains 11 subunits
  • Contains 2 cytochromes: cyt b, cyt c1
  • Contains 1 Fe∙S center
  • Contains 3 heme groups: one two in cyt b, one in cyt c1
  • Contains 2 Q binding sites
88
Q

How many subunits are there in complex III of the ETC?

A

11

89
Q

How many cytochromes are there in complex III of the ETC?

A

2: cyt b, cyt c1

90
Q

How many heme groups are there in complex III of the ETC? How are they distributed?

A

3 heme groups

  • cyt b: 2 heme group
  • cyt c1: 1 heme groups
91
Q

How many electrons are fed through complex III of the ETC?

A

2e–

(Technically 4e–. 2e– continue through the ETC to cyt c and complex IV, the other 2e– are used to regenerate QH2)

92
Q

What is source of electrons passed through complex III of the ETC?

A

2QH2; from either complex I or complex II

93
Q

What is the sequence of electron transfer reactions in complex III?

(The main chain, not the Q cycle steps)

A

QH2 → Fe∙S → cyt c1 → cyt c

  • This repeats twice: each QH2 donates only one e– to this chain, the other goes to Q cycle
  • cyt c is not part of complex III: it freely shuttles between complexes III and IV
94
Q

What is the name of complex IV of the ETC?

A

Cytochrome c oxidase

95
Q

What are the structural features of complex IV of the ETC?

A
  • Contains two cytochromes: cyt a and cyt a3
  • Contains two copper sites
  • Contains oxygen binding sites
96
Q

How is O2 reduced to H2O?

A

cyt cred + 0.5O2 + 2H+ → cyt cox + H2O

Superoxide (O2∙–) is formed as an intermediate, but remains tightly bound to CuB until it is reduced to water

97
Q

What is the sequence of electron transfer reaction in complex IV?

A

cyt c → CuA → cyt a → CuB → cyt a3 → O2

98
Q

What is the source of electrons passed through complex IV of the ETC?

A

cyt c, which carries one e– from complex III

4e– are required to reduce oxygen to water, and thus 4 molecules of reduced cyt c

99
Q

What are the inhibitors of complex I of the ETC?

A
  • Rotenone: an insecticide
  • Amytal: a sedative
100
Q

What are inhibitors of complex III of the ETC?

A
  • Antimycin A: inhibits transfer of e– from cyt b to cyt c1. Complex III cannot be reoxidized
101
Q

What are the inhibitors of complex IV of the ETC?

A
  • CO
  • Sodium azide
  • Cyanides
102
Q

What are the inhibitors of ATP synthase?

A
  • Oligomycin: interferes with the utilization of the proton gradient by targeting the stalk of ATP synthase
103
Q

What is the proton motive force—the force that drives protons to diffuse back through the inner mitochondrial membrane?

A

An electrochemical gradient:

  • A pH gradient (∆pH): concentration gradient of H+
  • A membrane potential (∆ψ)
104
Q

What is a P/O ratio?

A

The ratio of phosphate incorporated into ATP to atoms of O2 utilized

It is a measure of the number of ATP molecules formed during the transfer of two electrons through all or part of the ETC

105
Q

What is the P/O ratio of NADH?

A

2.5

106
Q

What is the P/O ratio of FADH2?

A

1.5

107
Q

What is the evidence for the chemiosmotic hypothesis?

A
  • During the ETC, a pH gradient of 1.4 and a ∆ψ of +1.4 V are generated
  • ATP synthesis occurs in the presence of an externally applied pH gradient, without the ETC
  • A closed vesicle is required for ATP synthesis; membrane fragments do not suffice
  • Decoupling proteins halt ATP synthesis
108
Q

What is chemiosmosis?

A

The coupling of ATP synthesis to the diffusion of protons down an electrochemical gradient

109
Q

What is an uncoupling protein (UCP)?

A

Carrier protons that create a “proton leak”—they allow proteins to re-enter the mitochondrial matrix without energy capture to form ATP. The energy is released as heat—thermogenesis

110
Q

What are the types and distributions of natural, endogenous UCPs?

A
  • UCP1: found in brown adipose (head, neck, chest, around the kidneys in infants)
  • UCP2: found in most cells
  • UCP3: found in skeletal muscle
  • UCP4/5: found in the brain
111
Q

What is the structure of ATP synthase?

A

F1: a headpiece in the matrix

  • α-subunits (1–3): structural
  • β-subunits (1–3): catalytic and binding site
  • γ-subunit: rotating stalk

FO: a transmembrane pore

  • a-subunit: channel for proton passage. Consists of two half passages
  • c-subunits (1–12): rotate to spin the stalk. Each consists of 2 transmembrane α-helices with an Asp residue midway
112
Q

How do protons spin through the F0 portion?

A
  • A proton passes through the first a-subunit half-passage
  • The proton binds to the Asp of c1 (protonating the carboxyl group)
  • The proton cycles through c1–9, allowing F0 to rotate
  • c9 interfaces with the a-subunit’s second half-passage, allowing the proton to exit into the matrix
113
Q

How is ATP synthesized by ATP synthase?

A
  • The membrane portion (F0) has a channel that allows for proton passage
  • Diffusion of protons spins the C subunits of F0, which causes the rod to spin
  • The rod spinning activates the matrix portion (F1), allowing for catalysis

4 protons are needed for synthesis of 1 ATP molecule

114
Q

What is conformational coupling?

A

The proton gradient leads to conformational changes in ATP synthase

115
Q

What are the types of conformational states of ATP synthase?

A
  • Open (O): low affinity for substrate
  • Loose binding (L): not catalytically active
  • Tight binding (T): catalytically active
116
Q

How many substrate sites are there on one ATP synthase enzyme?

A

3

117
Q

How does the protein gradient contribute to conformational coupling?

A

Provides the energy for:

  • O→L
  • L→T
  • T→O
118
Q

What is an example of a synthetic uncoupler?

A

2,4-dinitriphenol

119
Q

What is acceptor (receptor) control?

A
  • Electron transport is coupled with ATP synthesis, so the ETC does not run unless ADP is phosphorylated
  • Addition of uncouplers (synthetic or endogenous) allows the ETC to run at maximum speed without ATP production
  • Oligomycin inhibits ATP synthase, so its addition also stops the ETC

Metabolism (6 decks)

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