biochem lectures 6 & 7 pt 1 Flashcards
(198 cards)
1
Q
describe mitochondria structure
A
double membrane organelle; has 2 membranes
2
Q
describe origins of mitochondria
A
endosymbiotic
3
Q
what does two membranes in mitochondria allow for
A
creates microcompartments
4
Q
what is double membrane structure of mitochondria important for
A
important for how ox phos takes place
5
Q
what 2 membranes in mitochondria
A
outer and inner mitochondrial membrane
6
Q
describe inner membrane of mitochondria
A
involuted, creates more surface area, more space
7
Q
what does more space in inner membrane allow for
A
more space for localization of ETC and ATP synthase components
8
Q
where else do we see double membrane organelle
A
chloroplast
9
Q
what does electron transport lead to
A
leads to proton pumping across inner mitochondrial membrane
10
Q
what are cristae
A
involuted membrane based structure, provides increase in SA that allows for more spacew
11
Q
what does more space mean
A
more copies of ETC, ATP synthase complexes; more efficient, more functionality
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)
13
Q
how do we establish proton gradient
A
establish a concentration differential of H+ ions / protons
14
Q
what is proton-motive force
A
describes [ ] differential across inner mitochondrial membrane (high [ ] of protons in intermembrane space)
15
Q
where is higher concentration of protons
A
in intermembrane space
16
Q
what does high [ ] of protons create in intermembrane space
A
low pH / acidic pH relative to mitochondrial matrix
17
Q
proton motive force is a combo of
A
chemical potential and electric potential
18
Q
chemical potential
A
concentration diff of protons across inner mitochondrial membrane
19
Q
electrical potential
A
charge diff that arises b/c you have abundance of protons in intermembrane space relative to mitochondrial matrix
20
Q
what does membrane potential describe
A
just describes a charge diff across membrane, one side vs. other
21
Q
what aspects of proton motive force are important
A
both chemical potential (pH gradient / H+ ion concentration) and electrical potential
22
Q
what are chemical and electrical potential important for
A
facilitated diffusion of protons thru F0 component
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
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
25
how many complexes in ETC
4; complex I, II, III, IV
26
how is NADH oxidized in ETC
oxidized by donating its electrons and protons to complex I of ETC
27
where do we generate most of reducing power in cell respiration
TCA cycle
28
what do we generate from TCA, and how
NADHs, FADH2s from oxidation of glucose
29
what do these reduced electron carriers (NADH, FADH2) do
dump electrons off to ETC & flow of electrons
30
what happens as you go from complex 1, 3, 4 and 2 ,3 ,4
increased affinity for electrons
31
what are two ports of entry for electrons in ETC
one for NADH dumping electrons off to complex 1, second is succinate dehydrogenase in complex 2
32
describe the first port of entry (NADH in complex 1)
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)
33
what is coenzyme q
a lipophilic electron shuttler
34
what happens after NADH dumps electrons to complex I
electrons are fed into Q pool, coenzyme q
34
what happens after electrons go into coenzyme Q
dumped off to complex III
35
what happens after electrons go through complex III
transferred to complex 4 via cytochrome C
36
what transfers electrons from complex 3 to 4
cytochrome C
37
what happens after electrons go thru complex 4
electrons are donated/transferred to oxygen, results in reduction of O2 to H2O
38
describe second means of entry
succinate dehydrogenase (TCA cycle)
39
what does succinate dehydrogenase do
catalyzes a step in TCA cycle; oxidizes succinate to fumarate AND reduces FAD to FADH2
40
what happens to FADH2 produced by succinate dehydrogenase
electrons dumped off into q pool (cytochrome q), transferred down to complex 3, 4, and oxygen as final electron acceptor
41
what is final electron acceptor
oxygen
42
what is the importance of electron flow thru ETC?
represents release of energy
43
what are thermodynamics of electron flow thru ETC
exergonic process
44
what is direction of flow of electrons thru ETC favored by
increasing affinity for those electrons
45
describe increasing affinity for electrons
increasing affinities as you move from complex 1 to 3, 4, ; and complex 2, 3, 4
46
what does the increasing affinities create
thermodynamic waterfall; downhill flow of electrons
47
what happens as electrons drop into that waterfall
release of small amounts of free E
48
what happens to small amounts of E released in ETC
some released as heat, some will help pump protons
49
what is important besides electrons
protons (from H)
50
what happens to protons
pumped across inner mitochondrial membrane through parts of complexes 1, 3, 4
51
what complexes pump protons in ETC
complexes. 1, 3, 4
52
where does the E needed to pump protons across this membrane come from
flow of electrons down ETC
53
does it take E to pump protons into intermembrane space
yes
54
why does it take E to pump protons
cuz as you pump more protons, [ ] of protons in intermembrane space increases, making it harder
55
what happens to protons in intermembrane space as more gets pumped
accumulation of protons
56
what happens as those protons accumulate
we are pumping more, and working against concentration gradient at that point
57
so how do we pump protons against [ ] gradient
couple it to free E release achieved from transfer of electrons thru ETC
58
what are we coupling w/ ETC
we're coupling the free E release from flow of electrons thru ETC w/ pumping of protons across inner mitochondrial membrane into intermembrane space
59
what happens to protons when we establish proton motive force
protons can diffuse back thru ATP synthase through F0
60
what part of ATP synthase can protons diffuse back through
F0 subunit
61
what are thermodynamics of flow of protons thru F0
exergonic
62
what does facilitated diffusion of protons thru F0 do
drives F1 subunit (catalytic component of ATP synthase)
63
what catalyzes formation of ATP from ADP and Pi
F1 subunit
64
describe thermodynamics of ATP formation from F1
endergonic (cuz we're sticking a negative phosphate group onto negative ADP)
65
what does ATP formation require
input of energy
66
where does E needed for ATP come from
facilitated diffusion of protons thru F0
67
what does facilitated diffusion of protons thru F0 component do
drives conformational changes in F1 necessary to synthesize ATP
68
basically how do we get ATP production
couple electron flow to establishment of proton-motive force which leads to synthesis of ATP
69
what do electron transport and oxidative phosphorylation do
capture E in reduction potential of NADH and FADH2
70
what happens to energy as electrons travel thru ETC
energy is lost in small amounts
71
what is energy captured from reduced electron carriers used for
ATP production
72
what things does coupling depend on
1) sequential redox rxns that pass electrons from NADH to O2, 2) compartmentalization of these rxns in mitochondria, 3) generation of proton gradient
73
what 2 ways to synthesize ATP
substrate level phosphorylation, oxidative phosphorylation
74
what do you need whenever you make ATP
need an exergonic component to drive endergonic process of making ATP from ADP and Pi
75
where does free E to drive ATP synthesis come from in substrate level phosphorylation
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
76
where does free E to drive ATP synthesis come from in oxidative phosphorylation
coupling establishment of PMF via electron flow; electrochemical gradient across membrane helps drive ATP synthesis via ATP synthase enzyme complex
77
what happens in the sequential redox reactions
electrons are being passed on to other complexes within ETC
78
what is directional transfer of electrons reflective of
increasing affinity that the different complexes have for those electrons
79
what defines direction of transfer of electrons
increasing affinity
80
what is importance of compartmentalization
having micro-compartments due to double membrane structure (intermembrane space, matrix side, etc.) is important for proton motive force
81
what is important for proton motive force
compartmentalization in mitochondria
82
what does intermembrane space allow for
protons to accumulate and diffuse back through ATP synthase into matrix to drive ATP synthesis
83
describe ETC
set of complexes thru which electrons pass in set of sequential redox reactions;
84
what does electrons being donated to each complex do
reduces it
85
what is energy from glucose used for
to produce ATP from ADP and Pi
86
where do electrons go
carried by reduced coenzymes, passed through chain of proteins and coenzymes
87
what are electrons carried by
reduced coenzymes
88
what does ETC drive
generation of proton gradient across inner mitochondrial membrane
89
what happens when electrons get transferred to the next complex
reduce it, leaving previous complex oxidized (???)
90
what is final destination / final electron acceptor
oxoygen
91
why is O2 an effective electron sink
very EN atom, has highest affinity for electrons
92
what happens as electrons flow thru "waterfall"
loses a bit of E
93
what happens to E by the time electrons are donated to oxygen, and reduce O2 to H2O
some E released in form of heat, some E goes to pumping of protons
94
describes O2s role in ETC
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
where does majority reducing power come from
TCA cycle
96
what do those reduced electron carriers do
deposit electrons into ETC, gonna be used in ox phos (where ATP is synthesized)
97
what does movement of electrons involve
series of redox reaction
98
what does the directional movement of those electrons depend on
increase in affinities for electrons as you move down ETC
99
describe affinity of each of subsequent acceptors relative to previous
increased affinity
100
what defines something's relative affinity for electrons
standard reduction potential
101
what is standard reduction potential
a measure of how easily something can be reduced
102
what does a more positive standard reduction potential mean
the more the compound 'wants' electrons
103
where do electrons pass from
electron donors to electron acceptors
104
basically what does "how easily a compound can be reduced" mean
what affinity that compound has for electrons
105
what does more positive standard reduction potential value mean
greater affinity for electrons, so compound wants electrons more
106
what is standard reduction potential measured in
volts
107
in electron transport chain, what is carrier function in order
in order of increasing reduction potential
108
how do electrons move
spontaneously, from carriers of low E*' (reduction potential ) to carriers of high E*'
109
how do electrons move in terms of affinity
electrons move from things of low affinity to things of higher affinity
110
what is bottom of affinity chain (so highest)
oxygen
111
who has highest, most positive E value
oxygen (that's why its final E acceptor)
112
describe the process of movement of electrons down affinity change
spontaneous/favorable/exergonic
113
why is electrons moving down affinity change exergonic
because we can couple it to pumping of protons against their [ ] gradient to establish PMF
114
where is high end [ ] of protons
intermembrane space
115
where do electrons flow between
through a series of membrane bound carriers
116
what are 2 main portals of entry
complex I and complex II
117
describe complex I portal of entry
oxidation of NADH
118
describe complex II portal of entry
succinate dehydrogenase, where FAD is reduced to FADH2
119
where do these 2 pathways/complexes/portals of entry converge
at level of coenzyme q (which donates e- to complex III)
120
what does coenzyme q do
donates electrons to complex 3
121
what does complex 3 have
various cytochromes
122
what cytochromes in complex 3
cytochrome B, cytochrome C1, iron-sulfur proteins
123
what does cytochrome c do
accepts electrons from complex III, donates to cpmplex IV
124
what does complex IV have
its own set of cytochromes
125
what happens after complex IV
those electrons donated to oxygen, reducing the oxygen to water
126
what does specific positioning of these complexes allow
for efficient and sequential directional flow of electrons
127
what does establishment of PMF and having mitochondrial membrane mean
you can set up a [ ] gradient, crucial for synthesis of ATP
128
what is ETC made up of
4 large complexes
129
complex I
NADH dehydrogenase
130
complex II
succinate dehydrogenase
131
complex III
ubiquinone cytochrome c oxidoreductase
132
complex IV
cytochrome oxidases
133
what else do these subunits have
diff prosthetic groups
134
examples of prosthetic groups
FAD, FMN, iron-sulfur centers for protein hemes (part of cytochrome structure)
135
what are 2 intermediaries/shufflers of electrons
coenzyme q / ubiquinone and cytochrome C
136
another name for coenzyme Q
ubiquinone
137
what is coenzyme Q / ubiquinone
lipid soluble / lipophilic carrier molecule
138
what does coenzyme q do
shuttles electron b/w complexes I and III,
complexes II and III
139
what is crucial role of coenzyme q
its role as a lipophilic
140
where is coenzyme Q located
mitochondria membrane
141
what does coenzyme q do
accept electrons from complexes I and II, donate to complex III
142
what leads to establishment of coenzyme q cycle or q pool
moves back and forth b/w cycles of oxidation and reduction
143
what helps keep electrons moving thru ETC
repetitive reduction and oxidation of coenzyme Q
144
how does ubiquinone work
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
what is isoprenoid side chain
hydrophobic anchor
146
what does complete reduction of coenzyme q require
2 electrons and 2 protons
147
what to know about ubiquinone
**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
what does isoprenoid mark it as
lipophilic or hydrophobic molecule
149
what do we find embedded in ETC complex proteins
flavins (FAD and FMN), iron-sulfur groups
150
what does it mean when we see something w/ a metal atom
suitable for carrying out redox rxns, transfer of electrons
151
main idea of ETC
coupling free E released from flow of electrons thru ETC w/ pumping of protons across inner mitochondrial membrane into intermembrane space
152
crucial nature of eTC
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
where does TCA cycle and ETC converge
complex 2
154
describe electron flow in complex 2
succinate --> ubiquinone
155
what is unique about complex II
only complex where you don't have shuttling/movement of protons across inner mitochondrial membrane
156
why does complex II not have proton movement
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
do complexes I, III, IV have proton movement
yup
158
so what do we do in complex II instead of pumping protons
electrons enter coenzyme q pool or Q cycle
159
what happens to electrons that enter coenzyme q pool/cycle
some get transferred complex 3, some recycle where CoQ can pick up more electrons from complexes I and II
160
does complex III have enough E
yup, enough free E to pump protons across complex III
161
where do the electrons go after complex III
cytochrome C
162
describe CoQ
lipophilic electron shuttler
163
describe cytochrome C
not lipophilic
164
where does cytochrome C reside
on outer leaflet of inner mitochondrial membrane; so within intermembrane space
165
what does cytochrome c do
picks up electrons from complex III, transfers to IV
166
what does complex IV use
energy of reduction of O2 to pump one H+ into intermembrane space for each electron passes thru
167
what is job of complex IV
job of transferring electrons to final electron acceptor, oxygen
168
which complexes do proton pumping
I, III, IV
169
what happens in the final redox step
O2 reduced to water
170
what is crucial for establishing electrochemical proton gradient or proton motive force
complexes pumping protons across inner mitochondrial membrane into intermembrane space
171
net NADH gain for ETC
3 ATP (technically 2.5)
172
net FADH2 gain for ETC
2 ATP (2.5)
173
how many protons to make 1 ATP molecule
3 protons
174
how many H+ must be transported to make 1 ATP
3 H+
175
how many protons pumped derived from NADH
10 protons pumped
176
how many protons pumped derived from FADH2
6 protons
177
how did we figure out order of electron flow thru ETC
experiments; pharmacologic inhibitors
178
rotenone
ETC inhibitor, blocks transfer of electrons from NADH to complex 1, and complex I to coenzyme q
179
what happens if you block transfer of e- from NADH to complex I
everything upstream of that inhibitor will remain reduced, cuz no place for electrons
180
what happens to NADH under rotenone
NADH remains reduced, doesn't undergo process of reoxidation when it dumps electrons to complex I
181
amytal
inhibitor, same site as rotenone
182
describe how these inhibitors work
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
why is everything downstream of inhibitor gonna be oxidized
cuz no longer gonna be receiving electrons, so can't be reduced
184
antimycin A
inhibitor of complex III
185
what does antimycin do
prevents electrons that are donated to complex III from being donated to cytochrome c, etc. down the line
186
what does antmycin cause
accumulation/back up of reduced substrates NADH, coenzyme Q, cytochrome B (one of the cytochromes within complex 3)
187
what is cytochrome B
one of the cytochromes within complex III
188
where does antimycin A work
b/w where those electrons would be dumped off from cytochrome C to cytochrome C1
189
describe what happens upstream/downstream of this block
everything downstream of that remains oxidized, everything upstream accumulates and builds up as reduced substrate
190
azide, cyanide, carbon monoxide
block at complex IV
191
what does azide do
reduction of everything, but we don't get final step (reduction of O2 to water)
192
how can we determine sequence of electron transport
by using these inhibitors in clever ways
193
who came up w/ idea of coupling facilitated diffusion of protons w/ ATP synthesis
peter mitchell
194
what else did peter mitchell come up w/
chemiosmotic theory
195
what is chemiosmotic theory
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
where do protons go
move passively back into matrix thru a special transmembrane protein, ATP synthase
197
what is used to make ATp
energy stored in this electrochemical gradient
