biochem lectures 6 & 7 pt 1 Flashcards
describe mitochondria structure
double membrane organelle; has 2 membranes
describe origins of mitochondria
endosymbiotic
what does two membranes in mitochondria allow for
creates microcompartments
what is double membrane structure of mitochondria important for
important for how ox phos takes place
what 2 membranes in mitochondria
outer and inner mitochondrial membrane
describe inner membrane of mitochondria
involuted, creates more surface area, more space
what does more space in inner membrane allow for
more space for localization of ETC and ATP synthase components
where else do we see double membrane organelle
chloroplast
what does electron transport lead to
leads to proton pumping across inner mitochondrial membrane
what are cristae
involuted membrane based structure, provides increase in SA that allows for more spacew
what does more space mean
more copies of ETC, ATP synthase complexes; more efficient, more functionality
what is proton gradient
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)
how do we establish proton gradient
establish a concentration differential of H+ ions / protons
what is proton-motive force
describes [ ] differential across inner mitochondrial membrane (high [ ] of protons in intermembrane space)
where is higher concentration of protons
in intermembrane space
what does high [ ] of protons create in intermembrane space
low pH / acidic pH relative to mitochondrial matrix
proton motive force is a combo of
chemical potential and electric potential
chemical potential
concentration diff of protons across inner mitochondrial membrane
electrical potential
charge diff that arises b/c you have abundance of protons in intermembrane space relative to mitochondrial matrix
what does membrane potential describe
just describes a charge diff across membrane, one side vs. other
what aspects of proton motive force are important
both chemical potential (pH gradient / H+ ion concentration) and electrical potential
what are chemical and electrical potential important for
facilitated diffusion of protons thru F0 component
what is the charge difference gonna do to protons
will draw positive ions thru F0 component to the negatively charged side here
what is the concentration difference gonna do
via facilitated diffusion, things are gonna pas from high end of [ ] to lower end of [ ] gradient
how many complexes in ETC
4; complex I, II, III, IV
how is NADH oxidized in ETC
oxidized by donating its electrons and protons to complex I of ETC
where do we generate most of reducing power in cell respiration
TCA cycle
what do we generate from TCA, and how
NADHs, FADH2s from oxidation of glucose
what do these reduced electron carriers (NADH, FADH2) do
dump electrons off to ETC & flow of electrons
what happens as you go from complex 1, 3, 4 and 2 ,3 ,4
increased affinity for electrons
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
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)
what is coenzyme q
a lipophilic electron shuttler
what happens after NADH dumps electrons to complex I
electrons are fed into Q pool, coenzyme q
what happens after electrons go into coenzyme Q
dumped off to complex III
what happens after electrons go through complex III
transferred to complex 4 via cytochrome C
what transfers electrons from complex 3 to 4
cytochrome C
what happens after electrons go thru complex 4
electrons are donated/transferred to oxygen, results in reduction of O2 to H2O
describe second means of entry
succinate dehydrogenase (TCA cycle)
what does succinate dehydrogenase do
catalyzes a step in TCA cycle; oxidizes succinate to fumarate AND reduces FAD to FADH2
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
what is final electron acceptor
oxygen
what is the importance of electron flow thru ETC?
represents release of energy
what are thermodynamics of electron flow thru ETC
exergonic process
what is direction of flow of electrons thru ETC favored by
increasing affinity for those electrons
describe increasing affinity for electrons
increasing affinities as you move from complex 1 to 3, 4, ; and complex 2, 3, 4
what does the increasing affinities create
thermodynamic waterfall; downhill flow of electrons
what happens as electrons drop into that waterfall
release of small amounts of free E
what happens to small amounts of E released in ETC
some released as heat, some will help pump protons
what is important besides electrons
protons (from H)
what happens to protons
pumped across inner mitochondrial membrane through parts of complexes 1, 3, 4
what complexes pump protons in ETC
complexes. 1, 3, 4
where does the E needed to pump protons across this membrane come from
flow of electrons down ETC
does it take E to pump protons into intermembrane space
yes
why does it take E to pump protons
cuz as you pump more protons, [ ] of protons in intermembrane space increases, making it harder
what happens to protons in intermembrane space as more gets pumped
accumulation of protons
what happens as those protons accumulate
we are pumping more, and working against concentration gradient at that point
so how do we pump protons against [ ] gradient
couple it to free E release achieved from transfer of electrons thru ETC
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
what happens to protons when we establish proton motive force
protons can diffuse back thru ATP synthase through F0
what part of ATP synthase can protons diffuse back through
F0 subunit
what are thermodynamics of flow of protons thru F0
exergonic
what does facilitated diffusion of protons thru F0 do
drives F1 subunit (catalytic component of ATP synthase)
what catalyzes formation of ATP from ADP and Pi
F1 subunit
describe thermodynamics of ATP formation from F1
endergonic (cuz we’re sticking a negative phosphate group onto negative ADP)
what does ATP formation require
input of energy
where does E needed for ATP come from
facilitated diffusion of protons thru F0
what does facilitated diffusion of protons thru F0 component do
drives conformational changes in F1 necessary to synthesize ATP
basically how do we get ATP production
couple electron flow to establishment of proton-motive force which leads to synthesis of ATP
what do electron transport and oxidative phosphorylation do
capture E in reduction potential of NADH and FADH2
what happens to energy as electrons travel thru ETC
energy is lost in small amounts
what is energy captured from reduced electron carriers used for
ATP production
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
what 2 ways to synthesize ATP
substrate level phosphorylation, oxidative phosphorylation
what do you need whenever you make ATP
need an exergonic component to drive endergonic process of making ATP from ADP and Pi
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
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
what happens in the sequential redox reactions
electrons are being passed on to other complexes within ETC
what is directional transfer of electrons reflective of
increasing affinity that the different complexes have for those electrons
what defines direction of transfer of electrons
increasing affinity
what is importance of compartmentalization
having micro-compartments due to double membrane structure (intermembrane space, matrix side, etc.) is important for proton motive force
what is important for proton motive force
compartmentalization in mitochondria
what does intermembrane space allow for
protons to accumulate and diffuse back through ATP synthase into matrix to drive ATP synthesis
describe ETC
set of complexes thru which electrons pass in set of sequential redox reactions;
what does electrons being donated to each complex do
reduces it
what is energy from glucose used for
to produce ATP from ADP and Pi
where do electrons go
carried by reduced coenzymes, passed through chain of proteins and coenzymes
what are electrons carried by
reduced coenzymes
what does ETC drive
generation of proton gradient across inner mitochondrial membrane
what happens when electrons get transferred to the next complex
reduce it, leaving previous complex oxidized (???)
what is final destination / final electron acceptor
oxoygen
why is O2 an effective electron sink
very EN atom, has highest affinity for electrons
what happens as electrons flow thru “waterfall”
loses a bit of E
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
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)
where does majority reducing power come from
TCA cycle
what do those reduced electron carriers do
deposit electrons into ETC, gonna be used in ox phos (where ATP is synthesized)
what does movement of electrons involve
series of redox reaction
what does the directional movement of those electrons depend on
increase in affinities for electrons as you move down ETC
describe affinity of each of subsequent acceptors relative to previous
increased affinity
what defines something’s relative affinity for electrons
standard reduction potential
what is standard reduction potential
a measure of how easily something can be reduced
what does a more positive standard reduction potential mean
the more the compound ‘wants’ electrons
where do electrons pass from
electron donors to electron acceptors
basically what does “how easily a compound can be reduced” mean
what affinity that compound has for electrons
what does more positive standard reduction potential value mean
greater affinity for electrons, so compound wants electrons more
what is standard reduction potential measured in
volts
in electron transport chain, what is carrier function in order
in order of increasing reduction potential
how do electrons move
spontaneously, from carriers of low E’ (reduction potential ) to carriers of high E’
how do electrons move in terms of affinity
electrons move from things of low affinity to things of higher affinity
what is bottom of affinity chain (so highest)
oxygen
who has highest, most positive E value
oxygen (that’s why its final E acceptor)
describe the process of movement of electrons down affinity change
spontaneous/favorable/exergonic
why is electrons moving down affinity change exergonic
because we can couple it to pumping of protons against their [ ] gradient to establish PMF
where is high end [ ] of protons
intermembrane space
where do electrons flow between
through a series of membrane bound carriers
what are 2 main portals of entry
complex I and complex II
describe complex I portal of entry
oxidation of NADH
describe complex II portal of entry
succinate dehydrogenase, where FAD is reduced to FADH2
where do these 2 pathways/complexes/portals of entry converge
at level of coenzyme q (which donates e- to complex III)
what does coenzyme q do
donates electrons to complex 3
what does complex 3 have
various cytochromes
what cytochromes in complex 3
cytochrome B, cytochrome C1, iron-sulfur proteins
what does cytochrome c do
accepts electrons from complex III, donates to cpmplex IV
what does complex IV have
its own set of cytochromes
what happens after complex IV
those electrons donated to oxygen, reducing the oxygen to water
what does specific positioning of these complexes allow
for efficient and sequential directional flow of electrons
what does establishment of PMF and having mitochondrial membrane mean
you can set up a [ ] gradient, crucial for synthesis of ATP
what is ETC made up of
4 large complexes
complex I
NADH dehydrogenase
complex II
succinate dehydrogenase
complex III
ubiquinone cytochrome c oxidoreductase
complex IV
cytochrome oxidases
what else do these subunits have
diff prosthetic groups
examples of prosthetic groups
FAD, FMN, iron-sulfur centers for protein hemes (part of cytochrome structure)
what are 2 intermediaries/shufflers of electrons
coenzyme q / ubiquinone and cytochrome C
another name for coenzyme Q
ubiquinone
what is coenzyme Q / ubiquinone
lipid soluble / lipophilic carrier molecule
what does coenzyme q do
shuttles electron b/w complexes I and III,
complexes II and III
what is crucial role of coenzyme q
its role as a lipophilic
where is coenzyme Q located
mitochondria membrane
what does coenzyme q do
accept electrons from complexes I and II, donate to complex III
what leads to establishment of coenzyme q cycle or q pool
moves back and forth b/w cycles of oxidation and reduction
what helps keep electrons moving thru ETC
repetitive reduction and oxidation of coenzyme Q
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
what is isoprenoid side chain
hydrophobic anchor
what does complete reduction of coenzyme q require
2 electrons and 2 protons
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
what does isoprenoid mark it as
lipophilic or hydrophobic molecule
what do we find embedded in ETC complex proteins
flavins (FAD and FMN), iron-sulfur groups
what does it mean when we see something w/ a metal atom
suitable for carrying out redox rxns, transfer of electrons
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
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
where does TCA cycle and ETC converge
complex 2
describe electron flow in complex 2
succinate –> ubiquinone
what is unique about complex II
only complex where you don’t have shuttling/movement of protons across inner mitochondrial membrane
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
do complexes I, III, IV have proton movement
yup
so what do we do in complex II instead of pumping protons
electrons enter coenzyme q pool or Q cycle
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
does complex III have enough E
yup, enough free E to pump protons across complex III
where do the electrons go after complex III
cytochrome C
describe CoQ
lipophilic electron shuttler
describe cytochrome C
not lipophilic
where does cytochrome C reside
on outer leaflet of inner mitochondrial membrane; so within intermembrane space
what does cytochrome c do
picks up electrons from complex III, transfers to IV
what does complex IV use
energy of reduction of O2 to pump one H+ into intermembrane space for each electron passes thru
what is job of complex IV
job of transferring electrons to final electron acceptor, oxygen
which complexes do proton pumping
I, III, IV
what happens in the final redox step
O2 reduced to water
what is crucial for establishing electrochemical proton gradient or proton motive force
complexes pumping protons across inner mitochondrial membrane into intermembrane space
net NADH gain for ETC
3 ATP (technically 2.5)
net FADH2 gain for ETC
2 ATP (2.5)
how many protons to make 1 ATP molecule
3 protons
how many H+ must be transported to make 1 ATP
3 H+
how many protons pumped derived from NADH
10 protons pumped
how many protons pumped derived from FADH2
6 protons
how did we figure out order of electron flow thru ETC
experiments; pharmacologic inhibitors
rotenone
ETC inhibitor, blocks transfer of electrons from NADH to complex 1, and complex I to coenzyme q
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
what happens to NADH under rotenone
NADH remains reduced, doesn’t undergo process of reoxidation when it dumps electrons to complex I
amytal
inhibitor, same site as rotenone
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
why is everything downstream of inhibitor gonna be oxidized
cuz no longer gonna be receiving electrons, so can’t be reduced
antimycin A
inhibitor of complex III
what does antimycin do
prevents electrons that are donated to complex III from being donated to cytochrome c, etc. down the line
what does antmycin cause
accumulation/back up of reduced substrates NADH, coenzyme Q, cytochrome B (one of the cytochromes within complex 3)
what is cytochrome B
one of the cytochromes within complex III
where does antimycin A work
b/w where those electrons would be dumped off from cytochrome C to cytochrome C1
describe what happens upstream/downstream of this block
everything downstream of that remains oxidized, everything upstream accumulates and builds up as reduced substrate
azide, cyanide, carbon monoxide
block at complex IV
what does azide do
reduction of everything, but we don’t get final step (reduction of O2 to water)
how can we determine sequence of electron transport
by using these inhibitors in clever ways
who came up w/ idea of coupling facilitated diffusion of protons w/ ATP synthesis
peter mitchell
what else did peter mitchell come up w/
chemiosmotic theory
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
where do protons go
move passively back into matrix thru a special transmembrane protein, ATP synthase
what is used to make ATp
energy stored in this electrochemical gradient
