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Block 4 Nelson Questions Flashcards

1
Q

How many protein coding genes in mitochondria?

A

13

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2
Q

How many proteins in mitochondria?

A

About 683

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3
Q

Permeability of Outer Mitochondrial Membrane

A

Porous to molecules smaller than 5 kDa

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4
Q

Permeability of Inner Mitochondrial Membrane

A

Impermeable to ions, including protons

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5
Q

Location of Cytochrome C

A

Intermembrane space

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6
Q

State 3 Respiration

A

Active state when ADP added; Significant oxygen consumption

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7
Q

State 4 Respiration

A

Resting State when ADP runs out; Low rate of oxygen consumption

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8
Q

Mitochondrial morphology during resting state

A

Matrix space large; Intermembrane space small

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9
Q

Mitochondrial morphology during active respiration state

A

Matrix space small; Intermembrane space large (pumped full of protons, water follows)

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10
Q

Purpose of condensed cristae during Active (State 3) Respiration

A

Fusion may mediate rapid exchange of metabolites with cytosol

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11
Q

Protein linked to Cristae morphology

A

Mitofilin (MINOS complex)

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12
Q

Mitofilin

A

Linked to cristae morphology; Tubular junctions eliminated in knockdown, can’t export anything to cytosol

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13
Q

What releases Cytochrome C

A

Signal from Bid, Bad, and/or Bax opens pores in outer membrane, releasing cytochrome C

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14
Q

Action of Cytochrome C once released

A

Cytochrome C and Apaf1 recruit Caspase 9, forming Apoptosome

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15
Q

Effect of apoptotic signal on morphology

A

Extensive fusion of cristae preceding Cytochrome C release

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16
Q

Porin protein

A

Beta barrel protein that forms trimers in outer membrane of mito; allows small molecules (not proteins) to pass freely

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17
Q

Protein:Lipid Ratio in Inner vs Outer Mitochondrial Membrane

A

3:1 inner, 1:1 outer

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18
Q

Cardiolipin

A

Associated with many membrane complexes on inner mito membrane, essential for their proper function; 4 FA chains linked by Glycerol

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19
Q

Barth Syndrome

A

Mutation in Cardiolipin synthesis gene; Results in defective mito, cardiomyopathy, muscle weakness

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20
Q

Goal of Respiration

A

Reduce Oxygen to H20; Capture energy of electrons removed from Pyruvate

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21
Q

Function of Superoxide Dismutase

A

Eliminates Superoxide (O2-) by converting it to H202; Deficient in Lou Gehrig’s

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22
Q

What converts Superoxide to H2O2

A

Superoxide Dismutase

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23
Q

Function of Catalase

A

Convert H2O2 to oxygen and water; Found in mitochondria; Also found in RBCs

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24
Q

What converts H2O2 to oxygen and water

A

Catalase

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25
Q

What happens to H2O2 when Fe2+ is present?

A

Can react to form Hydroxyl Radical

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26
Q

What forms Hydroxyl Radical?

A

H2O2 reacting with Fe2+

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27
Q

What protects against Hydroxyl radicals

A

Vit C and E

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28
Q

Vit C and E

A

Protect against Hydroxyl Radicals

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29
Q

2 Functions of CAC

A

Electrons to ETC; Precursors for Biosynthesis

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30
Q

2 moeities on cytosolic side of Complex 3

A

Rieske Iron-Sulfur protein, Cytochrome C1

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31
Q

2 Regulatory components of PDH Complex

A

PDH Kinase and Phosphatase

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32
Q

3 Main Enzymes of PDH Complex

A

Pyruvate Decarboxylase E1, Dihdrolipoyl Transacetylase E2, Dihydrolipoyl Dehydrogenase E3

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33
Q

3 Postulates of Binding Change Mechanism

A

(1) Energy from H+ gradient used to release ATP; (2) 3 catalytic sites are each in unique conformation, conf’s are interconvertible, rep the 3 stages of catalytic cycle (L -> T -> O); (3) Conf changes at 3 sties are driven by rotation of gamma sub relative to F1 ball

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34
Q

4 Steps that produce NADH in CAC

A

Pyruvate DH, Isocitrate DH, A-KG DH, Malate DH

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35
Q

5 Cofactors for PDH Complex

A

TPP, FAD, NAD, CoA, Lipoic Acid

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36
Q

5 Sources of Acetyl CoA

A

Pyruvate (Glycolysis); AA Degradation; FA B-oxidation; KBs; Ethanol Metabolism

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37
Q

Alpha and Beta Subunits of ATP Synthase

A

Form the “Ball” of F1; Only beta has catalytic activity

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38
Q

Antimycin

A

Binds to N center on matrix side of Complex 3 (prevents e’s from reaching b hemes)

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39
Q

Aspartate/Malate Shuttle vs Glycerophosphate shuttle

A

NADH vs Ubiquinone Level

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40
Q

Branchpoint of Citrate in Mitochondria

A

(1) Can enter TCA Cycle; (2) exit through Citrate Shuttle to Export AcetylCoA for FA Synthesis; (3) Make alpha ketogluterate

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41
Q

CAC when Acetyl CoA high

A

Need for OAA; Pyruvate Decarboxylase stimulated (Pyruvate to OAA) and PDH inhibited; Shift from from oxidative to biosynthetic mode

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42
Q

Chemiosmotic Hypothesis

A

Inner membrane impermeable to H+, allowing gradient to be used for ATPase

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43
Q

Cofactor necessary for E1 Complex

A

Thiamin Pyrophosphate TPP (stabilize carbanion)

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44
Q

Cofactor necessary for E2 Complex

A

Lipoic Acid, Reacts w/ Carbanion intermediate from E1

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45
Q

Cofactor necessary for E3 Complex

A

?

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46
Q

Complex 2

A

Succinate DH; Tetramer; FAD and 3 Iron-Sulfur Clusters; Doesn’t pump protons

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47
Q

Complex 4

A

Cytochrome C oxidase; reduces O2 to H20; Proton pump; Redox centers

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48
Q

Complex I

A

NADH DH; 7 subunits in mito genome; Membrane and Peripheral Arm

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49
Q

Defect in Mitofilin

A

No contacts b/t Cristae and bounding Inner Membrane; Can’t export to Cytosol

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50
Q

Does FADH2 or NADH carry more energy?

A

NADH

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51
Q

E1 Reaction of PDH Complex

A

Decarboxylation of Pyruvate by E1; Produces unstable carbanion; Needs TPP

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52
Q

E2 Reaction of PDH Complex

A

Picks up Acetyl Group from TPP; Forms AcetylCoA

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53
Q

Elevator Model

A

Mutation of just 1 of 10-12 c subunits halts transport; Suggests subunit c rotates relative to a to form complete proton pathway

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54
Q

Energy made directly during TCA Cycle

A

1 GTP (Substrate-Level Phosphorylation)

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55
Q

Estimate for protons consumed per ATP synthesized

A

4

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56
Q

Fate of Pyruvate in TCA Cycle

A

Oxidized to 3 CO2 molecules

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57
Q

Findings of Noji experiment

A

Gamma subunit rotates

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58
Q

First place electrons go upon leaving cyt c

A

Copper A redox site of complex 4

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59
Q

First Ubiquinone binding site on Complex 3

60
Q

Flavoproteins

A

Flavin gets electrons to pass to iron sulfur centers

61
Q

Flow of electrons in Complex 2

A

Succinate -> FAD -> Iron-Sulfur Clusters -> Ubiquinone

62
Q

FMN + AMP =

63
Q

FMN in ETC

A

Cofactor bound to peripheral arm of Complex 1; Flavoprotein

64
Q

How do electrons get to Complex 4

A

Cytochrome C carrier (one at a time)

65
Q

How do oxygens reach active site of Complex 4?

A

Through lipid bilayer, not aqueous phase

66
Q

How does Complex 4 compensate for adding electron to protein interior?

A

Take up a proton

67
Q

How does structure change in Apoptotic Pathway

A

Extensive fusion of the Cristae precedes Cyt C release

68
Q

How does the matrix appear in actively respirating mitochondria?

69
Q

How is NADH re-oxidized in aerobic conditions?

A

Passes electrons to ETC

70
Q

How is NADH re-oxidized in anaerobic conditions?

A

Pyruvate is reduced to Lactate

71
Q

How is Pyruvate imported into Mito Matrix?

A

Portin in Outer, Pyruvate Transport in Inner

72
Q

How is the Intermembrane Space enlarged during Active Respiration?

A

Protons pumped in, and water follows

73
Q

How many ATPs are made per complete revolute of gamma subunit relative to F1

74
Q

How many e’s are needed to reduce oxygen?

75
Q

How many protons are pumped at each complex?

A

4 at Complex 1; 4 at Complex 3; 2 at Complex 4 (per pair of e’s)

76
Q

How many protons pumped per turn of Q cycle?

77
Q

How many turns of Q cycle to fully reduce Ubiquinone?

78
Q

How many turns of Q cycle to get 2 to Cytochrome C?

A

2, 1 per turn

79
Q

How to Uncouple

A

Destroy proton gradient necessary for ox phosph (eg DNP)

80
Q

Inhibitors of Isocitrate DH

81
Q

Inhibitors of PDH Complex

A

Acetyl CoA, NADH, ATP (inhibitory phosphorylation)

82
Q

Initial Reaction of PDH Complex

A

Decarboxylation of Pyruvate by E1; Produces unstable carbanion

83
Q

Intermediate b/t NADH and Iron-Sulfur Center

A

Flavoprotein

84
Q

Iron-Sulfer Clusters

A

Redox active centers that can accept and donate electrons; Conduit from FMN to Ubiquinone

85
Q

Isocitrate Lyase

A

Cleaves isocitrate into Succinate and Glycoxylate

86
Q

Main source of captured energy in TCA Cycle

A

NADH and FADH2

87
Q

Malate Synthase

A

Adds Acetyl CoA to Glycoxylate to make Malate

88
Q

Mito sn-Glycerophosphate DH

A

Part of Glycerophosphate shuttle for moving e’s from Cytosolic NADH into ETC

89
Q

Most important anapleurotic rxn of CAC?

A

Pyruvate Carboxylase: Pyruvate -> OAA

90
Q

Only ETC Complex that doesn’t pump protons

A

2, Succinate DH

91
Q

Only membrane-bound enzyme in TCA cycle

A

Succinate Dehydrogenase

92
Q

P/O Ratio

A

ATP Molecules produced per oxygen consumed, aka ATP produced/atom of oxygen

93
Q

PEPCK

A

When OAA too high, coverts to PEP; uses one GTP

94
Q

Problem with acetyl coA being precursor for FA biosynthesis

A

AcCoA made by PDH complex in mito, but FA synthesis occurs in cytosol

95
Q

Purpose of E3 of PDH Complex

A

Removes electrons of sulfhydryls from Lipoic Acid; Forms NADH

96
Q

Pyruvate Carboxylase

A

Pyruvate -> OAA; Can be used when not enough OAA for AcCoA

97
Q

Pyruvate Dehydrogenase Action

A

Pyruvate to Acetyl CoA (irreversible)

98
Q

Q Cycle

A

Ubiquinones at center P, one e to Rieske iron-sulfur and one to first b heme; e from Rieske to cytochrome c and e from heme to ubuiquinone at N center

99
Q

Reaction mediated by Citrate Synthase

A

AcCoA + OAA -> Citrate (6C)

100
Q

Redox centers of Complex 3

A

Two b type hemes in membrane subunit

101
Q

Redox centers on Complex 4

A

2 Copper, 2 Hemes, Mg and Zn

102
Q

Reduction Potentation of NADH/FADH2

A

Very high negative, tendency to move toward positive and release free energy

103
Q

Role of Anconitase

A

Permits formation of A-KG

104
Q

Rotenone Inhibitor

A

Binds to Complex 1 and Competes at Ubiquinone binding site (Electron transfer blocked)

105
Q

Step that produces FADH2 in CAC

A

Succinate DH

106
Q

Stigmatelin

A

Binds at P cener, the interface b/t iron-sulfur and cyt b (stops electron flow)

107
Q

Stoichiometry of protons to electrons in ETC

A

4 protons/2 electonrs

108
Q

T/F: The gamma subunit of ATP Synthase is symmetrical

A

False, different interactions with beta subunits around it

109
Q

The addition of which enzyme joins the 2 halves of the CAC

A

A-KG Dehydrogenase

110
Q

Two extra enzymes in Glycoxylate Cycle

A

Isocitrate Lyase and Malate Synthase

111
Q

Ubiquinone

A

Lipid soluble e- carrier; Carries e’s b/t complexes in ETC; Can accept one at a time, but can carry 2

112
Q

Ubiquinone Binding Sites at Complex 1

A

1 Tightly Bound, 1 Loose (transfer from Complex 1 to 3)

113
Q

UCP2 protein

A

Exist in adult human tissue, could be turned on to uncouple and waste energy

114
Q

Uncoupling

A

ETC and Oxygen reduction work, but not ox phosph (removal of F1)

115
Q

What are the 2 reactions that make the TCA Cycle

A

AcetylCoA + OAA -> A-KG (forward); OAA -> SuccinylCoA (reverse, heme)

116
Q

What can block the transfer of electrons from Complex 1 to 3

117
Q

What converts Pyruvate to Acetyl CoA

A

Pyruvate Dehydrogenase

118
Q

What did famous reconstitution experiment show?

A

No intermediate, just protone gradient could power ATP synthesis

119
Q

What do flavoproteins carry e’s between?

A

Flavoproteins and Complex 3

120
Q

What does Glycoxylation cycle bypass?

A

Decarboxylation steps of CAC

121
Q

What does the Isocitrate Dehydrogenase enzyme produce?

A

Alpha-KG, CO2, NADH

122
Q

What happens in too much OAA in CAC?

A

PEPCK converts it to PEP (costs one GTP)

123
Q

What molecule from Glycolysis has to be imported into Mito Matrix for TCA?

124
Q

What parts still work when F1 part removed?

A

ETC and Oxygen reduction, but oxidative phosphorylation cannot

125
Q

What prevents making sugar form fat in CAC?

A

Two decarboxylation steps; Acetyl CoA that enters is lost as CO2

126
Q

What substrate in CAC is used for AA synthesis?

127
Q

What substrate in CAC is used for heme synthesis?

A

Succinyl CoA

128
Q

Where does TCA cycle occur?

A

Mito Matrix

129
Q

Which arm of Complex 1 contains all the redox active centers?

A

Peripheral

130
Q

Which arm of Complex 1 contains the mito encoded subunits?

131
Q

Which Complex has channel for oxygen to reach active site?

A

Cytocrhome C Oxidase = Complex 4

132
Q

Which complex has most mito coded subunits?

133
Q

Which Complex hosts Q cycle

134
Q

Which Complex of ETC contains Rieske Iron-Sulfur protein

135
Q

Which complex reduces oxygen to water?

A

Complex 4 (cytochrome c oxidase)

136
Q

Which E of PDH forms Acetyl CoA

137
Q

Which F is membrane part?

138
Q

Which subunit forms the “axel” of F1

139
Q

Which subunit is identical b/t PDH and A-ketogluterate

140
Q

Which subunits form the rotor?

A

Subunit c, Epsilon, and Gamma

141
Q

Which subunits form the stator?

A

a, b, alpha, beta, delta

142
Q

Why do ETC complex proteins accept electons?

A

More positive reduction potential

143
Q

Why is Succinate Dehydrogenase unusual in CAC?

A

Membrane bound and part of Complex 2

144
Q

Why would A-KG leave the CAC?

A

AA synthesis, Glutamate

145
Q

Why would OAA leave the CAC?

146
Q

Why would we need to uncouple?

A

Allow electrons to flow in presence of high gradient

147
Q

Yield from PDH Complex

A

1 Acetyl CoA and 1 NADH

Molecular Block 4 (2 decks)

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