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138 Cards in this Set
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Alternative names for NADH-Q oxidoreductase, Q-cytochrome c oxidase, cytochrome c oxidase, and succinate-Q reductase
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complex I, complex III, complex IV, complex II (does not pump protons)
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What is the supramolecular complex?
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respirasome
-large protein complexes |
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What is the purpose of the supramolecular complex?
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To facilitate rapid transfer of substrate
To prevent release of reaction intermediates |
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Name the 4 large protein complexes in ETC
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NADH-Q oxidoreductase
succinate-Q reductase Q-cytochrome c oxidase cytochrome c oxidase |
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Name the 2 electron carriers in ETC
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coenzyme Q / ubiquinone
cytochrome c |
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coenzyme Q
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Q/ubiquinone
-hydrophobic quinone -diffuses rapidly within inner mito membrane -carries e- from complex I to III |
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Which carrier shuttles e- from complex I to III?
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coenzyme Q
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What is coenzyme Q?
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quinone derivative with long tail of 5-C isoprene units
-most common is 10 isoprene (Q10) |
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How many oxidation states does quinone have?
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3
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Describe coupling with Q
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e- transfer coupled to proton binding and release
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What is the Q pool?
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ubiquinone is soluble in membrane, so a pool of Q and QH2 is thought to exist within the inner mito membrane
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What is cytochrome c?
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A small soluble protein that shuttles e- from complex II to VI
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Which carrier shuttles e- from complex II to VI?
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cytochrome c
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complex I
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NADH-Q oxidoreductase
NADH dehydrogenase |
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complex II
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succinate dehydrogenase
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complex III
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cytochrome c reductase
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complex IV
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cytochrome c oxidase
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Which protein does not pump protons?
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succinate dehydrogenase
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How is coupling of proton binding and release to e- transfer accomplished with Q?
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QH2 (fully reduced) holds onto protons more tightly
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Where are the genes that encode for 3 proteins in respirasome?
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mitochondria and nucleus
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Shape of NADH-Q oxidoreductase
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L
arm projects to matrix |
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Reaction catalyzed by NADH-Q oxidoreductase
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NADH + Q + 5H(matrix) --> NAD+ + QH2 + 4H(cyto)
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1st prosthetic group of complex I
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flavin mononucleotide
FMN -> FMNH2 |
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e- acceptor of FMN
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isoalloxazine ring
identical with that of FAD |
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2nd prosthetic group of complex I
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series of iron-sulfur clusters (non-heme proteins)
complex I contains 2Fe-2S and 4Fe-4S |
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two states of Fe-S
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Fe2+(reduced) and Fe3+(oxidized)
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Which prosthetic groups bind/release protons in redox?
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quinones and flavins (not Fe-S clusters)
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Where do the redox reactions take place in complex I?
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extramembranous part
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When 2e- flow from NADH to coenzyme Q...
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4H+ pumped out of matrix into intermembrane space
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Q accepts 2 - from - and 2 - from - to be reduced to QH2. QH2 leaves - to -.
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Q accepts 2 e- from complex I and 2 H+ from matrix to be reduced to QH2. QH2 leaves enzyme to hydrophobic interior of membrane.
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What are the sources of NADH for ETC?
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-citric acid cycle
-fatty acid degradation -cytoplasmic |
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Where is FADH2 generated?
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CAC in oxidation of succinate to fumarate by succinate deHase which is part of complex II
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flow of e- in complex I
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(NAD+ -> NADH) -> (FMN -> FMNH2) -> n(Fe3+S -> Fe2+S)
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flow of e- in complex II (Q-cytochrome c oxidoreductase)
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(FADH2 -> FAD) -> n(Fe3+S -> Fe2+S) -> (Q -> QH2)
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Which oxidation produces less ATP
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oxidation of FADH2 b/c it doesn't pump protons
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What other enzymes are electron carriers for FADH2 to O2?
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glycerol phosphate deHase, fatty acyl CoA deHase
these don't pump protons (like Fe-S in complex II) |
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What is the fate of QH2 (ubiquinol) generated from complex I and II?
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passed to complex III to cytochrome c
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What is the role of Q-cytochrome oxidoreductase?
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Catalyze transfer of e- from QH2 to oxidized cytochrome c (water soluble), and pump protons out of the matrix
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How many H+ does complex III pump out?
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2
less than complex I between of smaller thermodynamic force |
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eq of QH2 and Cyt c e- transfer
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QH2 + 2Cytc(ox) + 2H+(matrix) -> Q + 2Cytc(red) + 4H+(cyto)
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Definition of cytochrome
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e- transferring protein that contains heme prosthetic group
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How many total hemes are in Q-cytochrome oxidoreductase (cytochrome bc1)? what type are they?
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3 hemes total
-2 within cytochrome b (bL and bH) -1 within cytochrome c1 iron-protoporphyrin IX type hemes |
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How many subunits are in Q-cytochrome oxidoreductase?
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2
b and c1 |
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What type of heme is present in both cytochrome bc1 and myo/hemoglobin?
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iron-protoporphyrin IX
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Describe the Rieske center
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2Fe-2S center in cytochrome bc1 (Q-cytochrome c oxidoreductase)
-1 Fe coordinated with his, not cys |
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Strategy of Fe-S coordination
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stabilizes Fe center in reduced form, raising reduction potential so it can readily accept electrons
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Q cycle
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mechanism of coupling of e- transfer (Q -> cytochrome c) to transmembrane proton transport
1. 2 QH2 bind to complex consecutively, each giving up 2e- and 2H+ (protons released to cyto) |
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Can cytochrome c accept both 2e- from QH2?
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no, 1 at a time - Q cycle
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Q cycle sum
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4H+ released to cyto, 2H+ removed from matrix
2QH2 + Q + 2Cytc(ox) + 2H+(matrix) -> 2Q +QH2 + 2Cytc(red) + 4H+(cyto) |
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How to solve problem of efficiently funneling e- from 2e- carrier to 1e- carrier?
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Q cycle
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Component of cytochrome that does Q cycle
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cytochrome b
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Role of cytochrome c oxidase (complex IV)
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catalyzes transfer of e- from reduced form of cytochrome c to molecular oxygen
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eq of cytochrome c oxidase
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4Cytc(red) + 8H+(matrix) -> 4Cytc(ox) +2H2O + 4H+(cyto)
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Prosthetic groups of cytochrome c oxidase
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2 heme A groups, 3 Cu ions arranged as 2 Cu centers (A, B)
CuA center: (CuA/CuA) linked by 2 cys residues CuB center: 3 his residues |
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^Go' of cytochrom c oxidase reaction
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-231.8 kJ/mol (highly favorable)
energy captured as a proton gradient |
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e- flow in cytochrome c oxidase
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cytochrome c -> CuA/CuA -> heme a -> heme a3 -> CuB -> O2
-heme a3 and CuB directly adjacent -> formed active center |
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Which prosthetic groups form active center at which O2 reduced to H2O?
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heme a3 and CuB
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How many cytochrome c bind to cytochrome c oxidase to reduce one O2?
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4 bind consecutively
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Steps of cytochrome c e- transfer to O2
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1. 2 molecules of cytochrome c sequentially transfer e- to reduce CuB and heme a3 --> ready to bind O2
2. reduced CuB and Fe (heme a3) bind O2, which forms peroxide bridge (O22-) 3. addition of 2 more e- and 2 more H+ from 2 cytochrome c, which travel to active center and cleave peroxide bridge 4. addition of 2 more H+ leads to release of H2O from heme and Cu. cytochrome c oxidase regenerated *4H+ come from matrix -> contribute to H+ gradient |
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How much energy does each proton contribute to gradient?
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21.8 kJ/mol
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Where does free energy from reduction of water go to?
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-pump 4H+ into matrix
-pump 4 additional H+ into matrix |
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eq of Cyt c
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4Cytc(red) + 4H+(matrix) + O2 -> 4Cytc(ox) + 2H2O
overall: 4Cytc(red) + 8H+(matrix) + O2 -> 4Cytc(ox) + 2H2O 4H+(cyto) |
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What are the effects that contribute to mechanism of how protons transport through cytochrome c oxidase
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1. charge neutrality maintained in interior of proteins
-addition of e- to site favors binding of H+ to nearby site 2. conformation changes take place (heme a3-CuB center) -in one conformation, protons may enter exclusively from matrix side, or exit exclusively to cytoplasm in another |
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transfer of single e- to O2 yields:
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superoxide anion
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transfer of 2e- to O2 yields:
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peroxide
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Why does O2 get reduced?
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-ideal terminal e- acceptor
-high affinity for e- provides large thermdynamic driving force |
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Strategy to reduce O2 safely
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catalyst does not release partly reduced intermediate
-cytochrome c oxidase holds O2 tighly between Fe and Cu |
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Name some reactive oxygen species
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superoxide, hydrogen peroxide, OHdot
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Defense strategies against oxidative damage by ROS
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-superoxide dismutase in mito(Mn) and cyto(Cu):
O2-dot + 2H+ <-> O2 + H2O2 -catalase: heme 2H2O2 <-> O2 + H2O -glutathione peroxidase -antioxidant vitamins E and C -aerobic exercise |
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What can ROSs be helpful for?
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signal transduction pathways
-growth factors increase ROS levels -ROS regulate channels and transcription factors |
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What is the average separation between e- carrying groups?
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15 angstroms
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Why are proteins more efficient in e- transfer?
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In vacuum, e- transfer rate decreases by a factor of 10 for every 0.8 A.
Through proteins, the rate decreases by 10 for every 1.7 A, making it efficient. |
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Which protein in ETC has been conserved?
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cytochrome c
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What proves that cytochrome c is preserved?
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Cytochrome c of any eukaryotic species reacts in vitro with cytochrome c oxidase of any other species
-wheat germ cyto c and human cyto c oxidase 21/104 residues have been invariant for over 1.5 billion years |
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eq for flow of e- from NADH to O2
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NADH + .5O2 + H+ <-> H2O + NAD+
^Go' = -220.1 kJ/mol exergonic |
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eq for ATP synthesis coupled with proton flow
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ADP + Pi + H+ <-> ATP + H2O
^Go' = +30.5 kJ/mol endergonic |
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Name of enzyme that synthesizes ATP
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ATP synthase or Complex V
(discovered as mitochondrial ATPase or F1F0ATPase) |
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Chemiosmotic hypothesis
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e- transport and ATP synthesis are coupled by proton gradient across inner mito membrane
-flow of protons back into matrix drives ATP synthase |
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What is the proton-motive force?
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energy-rich unequal distribution of protons
-chemical (pH) and charge (psi) gradients both power synthesis of ATP -pH outside is 1.4 units higher -membrane potential is 0.14 V (outside +) |
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Describe the structure of ATP
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'ball and stick'
stick - F0 subunit in the inner mito membrane ball - F1 subunit in the mito matrix (85 D diameter) |
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Which subunit of ATP synthase contains catalytic activity?
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F1 subunit
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Structure of the F1 subunit
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5 types of polypeptide chains (a3, B3, y, del, e)
-a and B arranged in hexameric ring (a3B3), members of P-loop NTPase family. both bind nucleotides but only B units participate directly in catalysis -y subunit is a long helical coiled coil in the center of hexamer, breaks symmetry of hexamer |
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How are the 3 beta subunits in F1 distinguished?
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by the direction of the y subunit
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Which subunit contains the proton channel of ATP synthase?
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F0
ring with 10-14 c subunits embedded in membrane a single a (NOT alpha) subunit binds to outside of ring |
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How are F1 and F0 subunits connected?
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by central y-e stalk, and by an exterior colummn (a, b, del subunits)
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Formation of ATP from ADP and orthophosphate
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ADP3- + HPO42- + H+ <-> ATP4- + H2O
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What kind of intermediate is formed in ATP synthesis?
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pentacovalent intermediate on the terminal phosphate
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What is the very main role of the proton gradient in ATP synthesis?
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to release ATP from the synthase
(isotopic exchange experiments, 18O labeled Pi) |
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Which part of the ATP synthase is the roto?
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c ring and ye stalk
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Which part of the ATP synthase is the stator (stationary unit)
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hexamer
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binding change mechanism of ATP synthesis
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1. ADP and Pi binding (L conformation)
2. ATP synthesis (T conformation) 3. ATP release (O conformation) |
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What are the conformations and sequence of the hexamer?
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L (loose) -> T (tight) -> O (open) -> L -> T -> O ->.....
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What drives the interconversion of the 3 forms of the ATP binding sites?
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rotation of the y subunit
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What direction does the y subunit rorate in?
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counterclockwise
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How does proton flow through F0 drive the rotation of the y subunit?
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2 half channels in the a subunit does not span the membrane - each half channel directly interacts with one c subunit
-the c subunit with a proton attached it its asp residue will rotate until it is in a proton-poor environment |
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What powers the rotation of the c ring?
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movement of protons through the half-channels from the high proton concentration of the cytoplasm to the low proton concentration of the matrix
-ability of neutralized asp residue to occupy hydrophobic membrane |
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How does c ring rotation lead to synthesis of ATP?
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the c ring is tightly bound to y and e subunits - as the c ring turns, the y and e subunits are turned inside the hexamer unit of F1 and cause binding changes
-2 b chains and del subunits on the exterior prevent the hexamer from rotating |
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About how many protons are required to generate 1 ATP?
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10 / 3 ~ 3.33 protons
e- from NADH pump enough protons for 2.5 ATP e- from FADH2 yield 1.5 ATP |
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How is ATP synthase analogous to G proteins?
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they are both P-loop NTPases
G proteins don't bind unless they interact with other proteins -analogous to the binding-change mechanism -the P-loop regions of B subunits will bind either ADP or ATP (or release) depending of y subunit direction |
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Is the inner mito membrane permeable to NADH and NAD+?
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no!
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How is the respiratory chain important for glycolysis?
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it regenerates NAD+
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How is cytoplasmic NADH reoxidized to NAD+ under aerobic conditions?
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e- from NADH are passed across mito membrane
-glycerol 3-phosphate shuttle (muscle) -malate-aspartate shuttle (heart, liver) |
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glycerol 3-phosphate shuttle
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1. Transfer e- from NADH to dihydroxyacetone phosphate to form glycerol 3-phosphate (catalyzed by glycerol 3-phosphate dehydrogenase in cytoplasm)
2. Glycerol 3-phosphate is reoxidized to dihydroxyacetone phosphate on the outer surface of the inner mito membrane by a membrane-bound isozyme of glycerol 3-phosphate deHase 3. An e-pair from glycerol 3-P is transferred to FAD in the enzyme to form FADH2, also regenerating dihydroxyacetone phosphate 4. The reduced flavin transfers e- to Q, which enters respiratory chain as QH2 **1.5, not 2.5 ATP formed because FAD, not NAD+ is e- acceptor ***use of FAD enables e- from cytoplasmic NADH to be transported into mito against an [NADH] gradient ****price = 1 ATP per 2e- |
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Where is the glycerol 3-P shuttle prominent?
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in muscle
-enables it to sustain a very high rate of oxidative phosphorylation |
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If insects lack lactate dehydrogenase, how do they regenerate cytoplasmic NAD+?
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They use the glycerol 3-P shuttle
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malate-asparate shuttle
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Mediated by 2 membrane carriers and 4 enzymes
1. e-'s are transferred from cytoplasmic NADH to oxaloacetate, forming malate, which passes inner mito membrane in exchange for alpha-kg 2. Malate is reoxidized by NAD+ to form oxaloacetate and NADH in the matrix by malate deHase from the citric acid cycle 3. Oxaloacetate undergoes transamination reaction to form aspartate which can be transported to the cyto in exchange for glutamate 4. Glutamate donates an amino group to oxaloacetate to form aspartate and a-kg 5. In the cytoplasm, asparate is deaminated to form oxaloacetate |
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How are ATP and ADP transported across the inner mitochondrial membrane?
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via ATP-ADP translocase
*the flows of ATP and ADP are coupled ADP3- transported into matrix, ATP4- transported to cytoplasm |
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What type of transport protein is ATP translocase? How abundant is it?
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-antiporter
-constitutes about 15% of proteins in the inner mito membrane |
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Describe the ATP-ADP exchange
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ATP and ADP bind to the translocase (not Mg2+)
-in an actively respiring mito with positive membrane potential, ATP4- transport out of mito matrix and ADP3- transport into the matrix are favored -this is energetically expensive: 1/4 energy yield from e- transfer is consumed to REGENERATE the membrane potential tapped by the exchange process -inhibition of this process leads to inhibition of respiration |
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Describe the common tripartite structure of mitochondrial transporters
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-tripartite structure: 3 tandem repeats of 100 aa module, each with 2 transmembrane segments
-the transmembrane helices form a tepeelike structure with the nucleotide binding site in the center |
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What other molecules do the various mitochondrial transporters transport?
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(matrix/cytoplasm)
ADP/ATP - translocase phosphate/malate - dicarboxylate carrier malate/citrate + H+ - tricarboxylate carrier pyruvate/OH- - pyruate carrier phosphate/OH- - phosphate carrier |
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Which carrier works in concert with ATP-ADP translocase?
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The phosphate carrier
-mediates exchange of H2PO4- for OH- -this leads to the exchange of cytoplasmic ADP and Pi for matrix ATP at the cost of influx of H+ (as said before, OH- outflux) |
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What comprises the ATP synthasome?
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ATP-ADP translocase and the phosphate carrier
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Other homologous carriers in the inner mito membrane
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-dicarboxylate carrier enables malate, succinate, fumarate export in exchange for Pi
-tricarboxylate carrier exchanges citrate and H+ for malate |
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How many molecules does the complete oxidation of glucose yield?
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30 molecules of ATP
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Can you know the number of ATP (or GTP) formed in glycolysis and the citric acid cycle for certain? How about ETC?
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Yes, because it is determined by the stoichiometries of chemical reactions.
Not in ETC because ATP yield because the stoichiometries of proton pumping, ATP synthesis, and metabolite-transport processes are not integers or fixed values |
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What is the estimate for number of H+ pumped out of the matrix per e- pair by NADH-Q oxidoreductase, Q-cytochrome c oxidoreductase, and cytochrome c oxidase?
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4, 2, 4
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How many protons are consumed in transporting ATP out of the matrix?
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1 proton influx
from coupling with the phosphate carrier which outfluxes 1 OH- |
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How many molecules of cytoplasmic ATP generated from the flow of e- pair from NADH to O2?
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2.5 molecules of ATP
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How many molecules of cytoplasmic ATP generated from the flow of e- pair from complex II (succinate oxidation or cytoplasmic NADH) to O2?
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1.5 molecules of ATP
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Describe respiratory control or acceptor control
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Regulation of the rate of oxidative phosphorylation by ADP level
-rate of O2 consumption by mito increases markedly when ADP is added, returns to normal when ADP converted to ATP |
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How is the citric acid cycle affected by the level of ADP?
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At low [ADP], NADH and FADH2 are not consumed by the ETC. The citric acid slows because there is less NAD+ and FAD to feed the cycle. As [ADP] rises and ETC speeds up, NADH and FADH2 are oxidized and the citric acid cycle speeds up.
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Describe the regulatory significance of energy change in ETC
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e- do not flow from fuel molecules to O2 unless ATP needs to be synthesized
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How can you generate heat from oxidative phosphorylation?
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Uncouple ETC from ATP synthesis.
-in humans, coupling is in brown adipose tissue for nonshivering thermogenesis |
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What is brown fat?
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-specialized tissue for nonshivering thermogenesis
-very rich in mitochondria -brown from greenish cytochromes in many mitochondria and red hemoglobin in extensive blood supply that carries heat |
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Uncoupling protein (UCP-1)
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also known as thermogenin (resembles translocase)
-Forms a pathway for flow of protons from cytoplasm to matrix -short-circuits the mito proton battery -activated when core body temp falls -> released hormones release fatty acids that activate thermogenin -others include UCP-2 and UCP-3 in other tissues |
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Where can oxidative phosphorylation be inhibited?
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1. inhibition of ETC
2. Inhibition of ATP synthase 3. Uncoupling from ATP synthesis 4. Inhibition of ATP export |
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rotenon and amytal
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block e- transfer in complex I and prevent use of NADH as a substrate
However, e- can flow from oxidized succinate because they enter through QH2, not through complex I |
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antimycin A
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interferes with e- flow from cytochrome bH in complex III
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cyanide (CN-) and azide (N3-) and carbon monoxide (CO)
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interferes with complex IV
-cyanide and azide react with ferric heme a3 -CO inhibits ferrous heme a3 |
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oligomycin and dicyclohexylcarbodiimide (DCC)
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prevent the influx of protons through ATP synthase
-oligomycin an antifungal agent |
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2,4-dinitrophenol (DNP) and some acidic aromatic compounds
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uncouples the tight coupling of ETC and phosphorylation
-carry H+ across inner mito membrane along [gradient] -ATP not synthesized because the proton-motive force is dissipated -O2 and NADH consumed -energy not captured as ATP, but released as heat |
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atractyloside and bongkrekic acid
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-atractyloside binds to translocase when it faces the cytoplasm
-bongkrekic acid binds toe translocase when it faces the mito matrix -oxidative phosphorylation stops soon after - translocase is essntial for maintaining ADP to accept proton-motive force energy |
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Name the uses for the energy produced by the proton gradient
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active transport
electron potential heat production NADPH synthesis ATP flagellar motion |
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apoptosis
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programmed cell death regulated by mitochondria
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mitochondrial outer membrane permeabilization (MOMP)
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Process by which the outer membrane of damaged mitochondria becomes highly permeable
-initiated by Bcl family proteins 1. cytochrome c exits the mitochondira and interacts with apoptotic pertidase-activating factor 1 (APAF-1), which leads to formation of the apoptosome 2. apoptosome activates proteolytic enzyme called caspase 9 that activates a cascade of other caspases also destroys the inhibitor of caspase-activated DNAase or CAD |
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What are the e- carriers in the respirasome?
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quinones, flavins, iron-sulfur complexes, heme groups of cytochromes, copper ions
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Sequence of ETC
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1. Electrons from NADH are transferred to the FMN prosthetic group of NADH-Q oxidoreductase (Complex I), the first of four complexes. This oxidoreductase also contains Fe-S centers.
2. The electrons emerge in QH2, the reduced form of ubiquinone (Q). The citric acid cycle enzyme succinate dehydrogenase is a component of the succinate-Q reductase complex (Complex II), which donates electrons from FADH2 to Q to form QH2. 3. This highly mobile hydrophobic carrier transfers its electrons to Q-cytochrome c oxidoreductase (Complex III), a complex that contains cytochromes b and c1 and an Fe-S center. This complex reduces cytochrome c, a water-soluble peripheral membrane protein. 4. Cytochrome c, like Q, is a mobile carrier of electrons, which it then transfers to cytochrome c oxidase (Complex IV). This complex contains cytochromes a and a3 and three copper ions. 5. A heme iron ion and a copper ion in this oxidase transfer electrons to O2, the ultimate acceptor, to form H2O. |