biochem lectures 6 & 7 pt 1 Flashcards

1
Q

describe mitochondria structure

A

double membrane organelle; has 2 membranes

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2
Q

describe origins of mitochondria

A

endosymbiotic

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3
Q

what does two membranes in mitochondria allow for

A

creates microcompartments

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4
Q

what is double membrane structure of mitochondria important for

A

important for how ox phos takes place

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5
Q

what 2 membranes in mitochondria

A

outer and inner mitochondrial membrane

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6
Q

describe inner membrane of mitochondria

A

involuted, creates more surface area, more space

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7
Q

what does more space in inner membrane allow for

A

more space for localization of ETC and ATP synthase components

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8
Q

where else do we see double membrane organelle

A

chloroplast

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9
Q

what does electron transport lead to

A

leads to proton pumping across inner mitochondrial membrane

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10
Q

what are cristae

A

involuted membrane based structure, provides increase in SA that allows for more spacew

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11
Q

what does more space mean

A

more copies of ETC, ATP synthase complexes; more efficient, more functionality

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12
Q

what is proton gradient

A

means by which ATP synthase generates ATP by coupling endergonic process of making ATP w/ exergonic process of facilitated diffusion of protons thru F0 (part of ATP synthase)

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13
Q

how do we establish proton gradient

A

establish a concentration differential of H+ ions / protons

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14
Q

what is proton-motive force

A

describes [ ] differential across inner mitochondrial membrane (high [ ] of protons in intermembrane space)

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15
Q

where is higher concentration of protons

A

in intermembrane space

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16
Q

what does high [ ] of protons create in intermembrane space

A

low pH / acidic pH relative to mitochondrial matrix

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17
Q

proton motive force is a combo of

A

chemical potential and electric potential

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18
Q

chemical potential

A

concentration diff of protons across inner mitochondrial membrane

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19
Q

electrical potential

A

charge diff that arises b/c you have abundance of protons in intermembrane space relative to mitochondrial matrix

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20
Q

what does membrane potential describe

A

just describes a charge diff across membrane, one side vs. other

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21
Q

what aspects of proton motive force are important

A

both chemical potential (pH gradient / H+ ion concentration) and electrical potential

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22
Q

what are chemical and electrical potential important for

A

facilitated diffusion of protons thru F0 component

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23
Q

what is the charge difference gonna do to protons

A

will draw positive ions thru F0 component to the negatively charged side here

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24
Q

what is the concentration difference gonna do

A

via facilitated diffusion, things are gonna pas from high end of [ ] to lower end of [ ] gradient

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25
Q

how many complexes in ETC

A

4; complex I, II, III, IV

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26
Q

how is NADH oxidized in ETC

A

oxidized by donating its electrons and protons to complex I of ETC

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27
Q

where do we generate most of reducing power in cell respiration

A

TCA cycle

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28
Q

what do we generate from TCA, and how

A

NADHs, FADH2s from oxidation of glucose

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29
Q

what do these reduced electron carriers (NADH, FADH2) do

A

dump electrons off to ETC & flow of electrons

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30
Q

what happens as you go from complex 1, 3, 4 and 2 ,3 ,4

A

increased affinity for electrons

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31
Q

what are two ports of entry for electrons in ETC

A

one for NADH dumping electrons off to complex 1, second is succinate dehydrogenase in complex 2

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32
Q

describe the first port of entry (NADH in complex 1)

A

NADH dumps electrons to complex 1, electrons are fed into coenzyme Q pool, dumped off to complex III, transferred via cytochrome C to complex 4, and then to oxygen (reduce oxygen and form water)

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33
Q

what is coenzyme q

A

a lipophilic electron shuttler

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34
Q

what happens after NADH dumps electrons to complex I

A

electrons are fed into Q pool, coenzyme q

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34
Q

what happens after electrons go into coenzyme Q

A

dumped off to complex III

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35
Q

what happens after electrons go through complex III

A

transferred to complex 4 via cytochrome C

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36
Q

what transfers electrons from complex 3 to 4

A

cytochrome C

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37
Q

what happens after electrons go thru complex 4

A

electrons are donated/transferred to oxygen, results in reduction of O2 to H2O

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38
Q

describe second means of entry

A

succinate dehydrogenase (TCA cycle)

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39
Q

what does succinate dehydrogenase do

A

catalyzes a step in TCA cycle; oxidizes succinate to fumarate AND reduces FAD to FADH2

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40
Q

what happens to FADH2 produced by succinate dehydrogenase

A

electrons dumped off into q pool (cytochrome q), transferred down to complex 3, 4, and oxygen as final electron acceptor

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41
Q

what is final electron acceptor

A

oxygen

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42
Q

what is the importance of electron flow thru ETC?

A

represents release of energy

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43
Q

what are thermodynamics of electron flow thru ETC

A

exergonic process

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44
Q

what is direction of flow of electrons thru ETC favored by

A

increasing affinity for those electrons

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45
Q

describe increasing affinity for electrons

A

increasing affinities as you move from complex 1 to 3, 4, ; and complex 2, 3, 4

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46
Q

what does the increasing affinities create

A

thermodynamic waterfall; downhill flow of electrons

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47
Q

what happens as electrons drop into that waterfall

A

release of small amounts of free E

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48
Q

what happens to small amounts of E released in ETC

A

some released as heat, some will help pump protons

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49
Q

what is important besides electrons

A

protons (from H)

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50
Q

what happens to protons

A

pumped across inner mitochondrial membrane through parts of complexes 1, 3, 4

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51
Q

what complexes pump protons in ETC

A

complexes. 1, 3, 4

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52
Q

where does the E needed to pump protons across this membrane come from

A

flow of electrons down ETC

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53
Q

does it take E to pump protons into intermembrane space

A

yes

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54
Q

why does it take E to pump protons

A

cuz as you pump more protons, [ ] of protons in intermembrane space increases, making it harder

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55
Q

what happens to protons in intermembrane space as more gets pumped

A

accumulation of protons

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56
Q

what happens as those protons accumulate

A

we are pumping more, and working against concentration gradient at that point

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57
Q

so how do we pump protons against [ ] gradient

A

couple it to free E release achieved from transfer of electrons thru ETC

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58
Q

what are we coupling w/ ETC

A

we’re coupling the free E release from flow of electrons thru ETC w/ pumping of protons across inner mitochondrial membrane into intermembrane space

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59
Q

what happens to protons when we establish proton motive force

A

protons can diffuse back thru ATP synthase through F0

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60
Q

what part of ATP synthase can protons diffuse back through

A

F0 subunit

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61
Q

what are thermodynamics of flow of protons thru F0

A

exergonic

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62
Q

what does facilitated diffusion of protons thru F0 do

A

drives F1 subunit (catalytic component of ATP synthase)

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63
Q

what catalyzes formation of ATP from ADP and Pi

A

F1 subunit

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64
Q

describe thermodynamics of ATP formation from F1

A

endergonic (cuz we’re sticking a negative phosphate group onto negative ADP)

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65
Q

what does ATP formation require

A

input of energy

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66
Q

where does E needed for ATP come from

A

facilitated diffusion of protons thru F0

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67
Q

what does facilitated diffusion of protons thru F0 component do

A

drives conformational changes in F1 necessary to synthesize ATP

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68
Q

basically how do we get ATP production

A

couple electron flow to establishment of proton-motive force which leads to synthesis of ATP

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69
Q

what do electron transport and oxidative phosphorylation do

A

capture E in reduction potential of NADH and FADH2

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70
Q

what happens to energy as electrons travel thru ETC

A

energy is lost in small amounts

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71
Q

what is energy captured from reduced electron carriers used for

A

ATP production

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72
Q

what things does coupling depend on

A

1) sequential redox rxns that pass electrons from NADH to O2, 2) compartmentalization of these rxns in mitochondria, 3) generation of proton gradient

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73
Q

what 2 ways to synthesize ATP

A

substrate level phosphorylation, oxidative phosphorylation

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74
Q

what do you need whenever you make ATP

A

need an exergonic component to drive endergonic process of making ATP from ADP and Pi

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75
Q

where does free E to drive ATP synthesis come from in substrate level phosphorylation

A

high E intermediates; phosphorylate them, break that phosphate bond, phosphoryl group transfer potential of high E intermediate, releases E which helps facilitate transfer of phosphate group from high E intermediate to molecule of ATP

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76
Q

where does free E to drive ATP synthesis come from in oxidative phosphorylation

A

coupling establishment of PMF via electron flow; electrochemical gradient across membrane helps drive ATP synthesis via ATP synthase enzyme complex

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77
Q

what happens in the sequential redox reactions

A

electrons are being passed on to other complexes within ETC

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78
Q

what is directional transfer of electrons reflective of

A

increasing affinity that the different complexes have for those electrons

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79
Q

what defines direction of transfer of electrons

A

increasing affinity

80
Q

what is importance of compartmentalization

A

having micro-compartments due to double membrane structure (intermembrane space, matrix side, etc.) is important for proton motive force

81
Q

what is important for proton motive force

A

compartmentalization in mitochondria

82
Q

what does intermembrane space allow for

A

protons to accumulate and diffuse back through ATP synthase into matrix to drive ATP synthesis

83
Q

describe ETC

A

set of complexes thru which electrons pass in set of sequential redox reactions;

84
Q

what does electrons being donated to each complex do

A

reduces it

85
Q

what is energy from glucose used for

A

to produce ATP from ADP and Pi

86
Q

where do electrons go

A

carried by reduced coenzymes, passed through chain of proteins and coenzymes

87
Q

what are electrons carried by

A

reduced coenzymes

88
Q

what does ETC drive

A

generation of proton gradient across inner mitochondrial membrane

89
Q

what happens when electrons get transferred to the next complex

A

reduce it, leaving previous complex oxidized (???)

90
Q

what is final destination / final electron acceptor

A

oxoygen

91
Q

why is O2 an effective electron sink

A

very EN atom, has highest affinity for electrons

92
Q

what happens as electrons flow thru “waterfall”

A

loses a bit of E

93
Q

what happens to E by the time electrons are donated to oxygen, and reduce O2 to H2O

A

some E released in form of heat, some E goes to pumping of protons

94
Q

describes O2s role in ETC

A

final electron acceptor (cuz of its high electron affinity), performs function of an electron sink (sitting at bottom of waterfall that attracts those electrons, down that electrochemical gradient til it reaches oxygen)

95
Q

where does majority reducing power come from

A

TCA cycle

96
Q

what do those reduced electron carriers do

A

deposit electrons into ETC, gonna be used in ox phos (where ATP is synthesized)

97
Q

what does movement of electrons involve

A

series of redox reaction

98
Q

what does the directional movement of those electrons depend on

A

increase in affinities for electrons as you move down ETC

99
Q

describe affinity of each of subsequent acceptors relative to previous

A

increased affinity

100
Q

what defines something’s relative affinity for electrons

A

standard reduction potential

101
Q

what is standard reduction potential

A

a measure of how easily something can be reduced

102
Q

what does a more positive standard reduction potential mean

A

the more the compound ‘wants’ electrons

103
Q

where do electrons pass from

A

electron donors to electron acceptors

104
Q

basically what does “how easily a compound can be reduced” mean

A

what affinity that compound has for electrons

105
Q

what does more positive standard reduction potential value mean

A

greater affinity for electrons, so compound wants electrons more

106
Q

what is standard reduction potential measured in

A

volts

107
Q

in electron transport chain, what is carrier function in order

A

in order of increasing reduction potential

108
Q

how do electrons move

A

spontaneously, from carriers of low E’ (reduction potential ) to carriers of high E

109
Q

how do electrons move in terms of affinity

A

electrons move from things of low affinity to things of higher affinity

110
Q

what is bottom of affinity chain (so highest)

A

oxygen

111
Q

who has highest, most positive E value

A

oxygen (that’s why its final E acceptor)

112
Q

describe the process of movement of electrons down affinity change

A

spontaneous/favorable/exergonic

113
Q

why is electrons moving down affinity change exergonic

A

because we can couple it to pumping of protons against their [ ] gradient to establish PMF

114
Q

where is high end [ ] of protons

A

intermembrane space

115
Q

where do electrons flow between

A

through a series of membrane bound carriers

116
Q

what are 2 main portals of entry

A

complex I and complex II

117
Q

describe complex I portal of entry

A

oxidation of NADH

118
Q

describe complex II portal of entry

A

succinate dehydrogenase, where FAD is reduced to FADH2

119
Q

where do these 2 pathways/complexes/portals of entry converge

A

at level of coenzyme q (which donates e- to complex III)

120
Q

what does coenzyme q do

A

donates electrons to complex 3

121
Q

what does complex 3 have

A

various cytochromes

122
Q

what cytochromes in complex 3

A

cytochrome B, cytochrome C1, iron-sulfur proteins

123
Q

what does cytochrome c do

A

accepts electrons from complex III, donates to cpmplex IV

124
Q

what does complex IV have

A

its own set of cytochromes

125
Q

what happens after complex IV

A

those electrons donated to oxygen, reducing the oxygen to water

126
Q

what does specific positioning of these complexes allow

A

for efficient and sequential directional flow of electrons

127
Q

what does establishment of PMF and having mitochondrial membrane mean

A

you can set up a [ ] gradient, crucial for synthesis of ATP

128
Q

what is ETC made up of

A

4 large complexes

129
Q

complex I

A

NADH dehydrogenase

130
Q

complex II

A

succinate dehydrogenase

131
Q

complex III

A

ubiquinone cytochrome c oxidoreductase

132
Q

complex IV

A

cytochrome oxidases

133
Q

what else do these subunits have

A

diff prosthetic groups

134
Q

examples of prosthetic groups

A

FAD, FMN, iron-sulfur centers for protein hemes (part of cytochrome structure)

135
Q

what are 2 intermediaries/shufflers of electrons

A

coenzyme q / ubiquinone and cytochrome C

136
Q

another name for coenzyme Q

A

ubiquinone

137
Q

what is coenzyme Q / ubiquinone

A

lipid soluble / lipophilic carrier molecule

138
Q

what does coenzyme q do

A

shuttles electron b/w complexes I and III,
complexes II and III

139
Q

what is crucial role of coenzyme q

A

its role as a lipophilic

140
Q

where is coenzyme Q located

A

mitochondria membrane

141
Q

what does coenzyme q do

A

accept electrons from complexes I and II, donate to complex III

142
Q

what leads to establishment of coenzyme q cycle or q pool

A

moves back and forth b/w cycles of oxidation and reduction

143
Q

what helps keep electrons moving thru ETC

A

repetitive reduction and oxidation of coenzyme Q

144
Q

how does ubiquinone work

A

as soon as it picks up e- from complex I or II, dumps them off to complex III, comes back and picks up more

145
Q

what is isoprenoid side chain

A

hydrophobic anchor

146
Q

what does complete reduction of coenzyme q require

A

2 electrons and 2 protons

147
Q

what to know about ubiquinone

A

**lipophilic structure, characterized by hydrophobic aromatic ring structure, units of isoprenoid side chains, marks it as lipophilic/hydrophobic molecule; important for movement of electrons b/w complexes I and III, II and III

148
Q

what does isoprenoid mark it as

A

lipophilic or hydrophobic molecule

149
Q

what do we find embedded in ETC complex proteins

A

flavins (FAD and FMN), iron-sulfur groups

150
Q

what does it mean when we see something w/ a metal atom

A

suitable for carrying out redox rxns, transfer of electrons

151
Q

main idea of ETC

A

coupling free E released from flow of electrons thru ETC w/ pumping of protons across inner mitochondrial membrane into intermembrane space

152
Q

crucial nature of eTC

A

Crucial nature of this is that as you pump these protons into intermembrane space, it gets progressively harder and harder to do this because you have a greater and greater concentration difference, were you have higher[ ] of protons within this inter membrane space relative to the mitochondrial matrix side of that inner membrane

153
Q

where does TCA cycle and ETC converge

A

complex 2

154
Q

describe electron flow in complex 2

A

succinate –> ubiquinone

155
Q

what is unique about complex II

A

only complex where you don’t have shuttling/movement of protons across inner mitochondrial membrane

156
Q

why does complex II not have proton movement

A

cuz the free e made from oxidation of succinate –> fumarate, reduction of FAD –> FADH, is not enough free E to allow movement of protons

157
Q

do complexes I, III, IV have proton movement

A

yup

158
Q

so what do we do in complex II instead of pumping protons

A

electrons enter coenzyme q pool or Q cycle

159
Q

what happens to electrons that enter coenzyme q pool/cycle

A

some get transferred complex 3, some recycle where CoQ can pick up more electrons from complexes I and II

160
Q

does complex III have enough E

A

yup, enough free E to pump protons across complex III

161
Q

where do the electrons go after complex III

A

cytochrome C

162
Q

describe CoQ

A

lipophilic electron shuttler

163
Q

describe cytochrome C

A

not lipophilic

164
Q

where does cytochrome C reside

A

on outer leaflet of inner mitochondrial membrane; so within intermembrane space

165
Q

what does cytochrome c do

A

picks up electrons from complex III, transfers to IV

166
Q

what does complex IV use

A

energy of reduction of O2 to pump one H+ into intermembrane space for each electron passes thru

167
Q

what is job of complex IV

A

job of transferring electrons to final electron acceptor, oxygen

168
Q

which complexes do proton pumping

A

I, III, IV

169
Q

what happens in the final redox step

A

O2 reduced to water

170
Q

what is crucial for establishing electrochemical proton gradient or proton motive force

A

complexes pumping protons across inner mitochondrial membrane into intermembrane space

171
Q

net NADH gain for ETC

A

3 ATP (technically 2.5)

172
Q

net FADH2 gain for ETC

A

2 ATP (2.5)

173
Q

how many protons to make 1 ATP molecule

A

3 protons

174
Q

how many H+ must be transported to make 1 ATP

A

3 H+

175
Q

how many protons pumped derived from NADH

A

10 protons pumped

176
Q

how many protons pumped derived from FADH2

A

6 protons

177
Q

how did we figure out order of electron flow thru ETC

A

experiments; pharmacologic inhibitors

178
Q

rotenone

A

ETC inhibitor, blocks transfer of electrons from NADH to complex 1, and complex I to coenzyme q

179
Q

what happens if you block transfer of e- from NADH to complex I

A

everything upstream of that inhibitor will remain reduced, cuz no place for electrons

180
Q

what happens to NADH under rotenone

A

NADH remains reduced, doesn’t undergo process of reoxidation when it dumps electrons to complex I

181
Q

amytal

A

inhibitor, same site as rotenone

182
Q

describe how these inhibitors work

A

its like putting a dam on the river; everything upstream of that, the water backs up (accumulation of reduced substrates), everything downstream is gonna be oxidized

183
Q

why is everything downstream of inhibitor gonna be oxidized

A

cuz no longer gonna be receiving electrons, so can’t be reduced

184
Q

antimycin A

A

inhibitor of complex III

185
Q

what does antimycin do

A

prevents electrons that are donated to complex III from being donated to cytochrome c, etc. down the line

186
Q

what does antmycin cause

A

accumulation/back up of reduced substrates NADH, coenzyme Q, cytochrome B (one of the cytochromes within complex 3)

187
Q

what is cytochrome B

A

one of the cytochromes within complex III

188
Q

where does antimycin A work

A

b/w where those electrons would be dumped off from cytochrome C to cytochrome C1

189
Q

describe what happens upstream/downstream of this block

A

everything downstream of that remains oxidized, everything upstream accumulates and builds up as reduced substrate

190
Q

azide, cyanide, carbon monoxide

A

block at complex IV

191
Q

what does azide do

A

reduction of everything, but we don’t get final step (reduction of O2 to water)

192
Q

how can we determine sequence of electron transport

A

by using these inhibitors in clever ways

193
Q

who came up w/ idea of coupling facilitated diffusion of protons w/ ATP synthesis

A

peter mitchell

194
Q

what else did peter mitchell come up w/

A

chemiosmotic theory

195
Q

what is chemiosmotic theory

A

diffusion/movement of protons across inner mitochondrial membrane is somehow linked/coupled to ATP synthesis; basically proton motive force is coupled to functioning of ATP synthase complex

196
Q

where do protons go

A

move passively back into matrix thru a special transmembrane protein, ATP synthase

197
Q

what is used to make ATp

A

energy stored in this electrochemical gradient