Oxidative Phosphorylation

Question 1

Chemiosmosis

Answer 1

electron transfer and ATP synthesis coupled by a proton gradient across the IMM
- matrix more negative and has a lower pH

Question 2

Electron Transport Chain

Answer 2

Electrons from reduced electron carriers pass to molecular oxygen through a chain of 3 protein complexes

• 2 mobile electron carriers (ubiquinone and cyt. c)
• electron flow between carriers directed by differences in reduction potential

Question 3

Proton Motive Force

Answer 3

chemical gradient + charge gradient

• drives ATP synthesis
• proton flow back into the matrix through ATP synthase. = ATP synthesized

Question 4

Reduction Potential

Answer 4

• tendency to acquire electrons and be reduced
• electrons are passed to carriers with more positive reduction potentials so a higher affinity for electrons
• electrons flow down energy gradient
• free energy released is used to generate the proton gradient (forms pmf)

Question 5

ETC Flow

Answer 5

NADH - complex I - CoQ - complex III - complex IV

FADH2 gives electrons to complex II which feeds into CoQ

Question 6

Complex I

Answer 6

NADH-Q oxidoreductase

• NADH electrons pass to FMN
• electrons go through Fe-S centers passed one at a time (reduction of one iron atom)
• 4 protons pumped into the IMS
• 2 electrons passed to coenzyme Q

NADH + Q + 5H = NAD + QH2 + 4H

Question 7

Flavin Mononucleotide

Answer 7

FMN reduced by 2 electrons and 2 protons from the matrix

Question 8

Coenzyme Q

Answer 8

• mobile electron carrier
• electron transfer coupled to proton binding/release
• very hydrophobic and membrane soluble
• oxidised ubiquinol with two ketone groups
• addition of electron/proton forms semiquinone intermediate
• able to lose one proton to form semiquinone radical ion
• semiquinone intermediate accepts another electron/proton to reduced ubiquinol (hydroxyl groups instead of ketones)

Question 9

Complex III

Answer 9

• ubiquinone cytochrome c oxidoreductase
• accepts electrons from QH2 passes them to cyt. c
• contains 3 heme groups (c1, bL, bH)
• 2 iron sulfur centers

QH2 + 2 oxidised cyt. c + 2H (from matrix) = Q + 2 reduced cyt. c + 4H (to IMS)

Question 10

Use of Q Cycle

Answer 10

• solves the problem of cyt. c only carrying one electron but coenzyme Q donates 2 electrons
• 2QH2 bind consecutively to each pass 2e/2H
• 2 protons are released into the IMS
• in one cycle, 2QH2 oxidised to 2Q and 1Q reduced to QH2
• 2 binding sites: Q1/Q0

Question 11

Q Cycle

Answer 11

1. first QH2 binds to Q0 site
   - one electron goes to FeS center - heme c1 - reduces cytochrome c that diffuses away
   - one electron goes to heme bL - heme bH - oxidises Q bound to Q1 binding site - semiquinone radical anion formed
2. second QH2 binds to Q0 site
   - one electron goes to FeS center - heme c1 - reduces cytochrome c that diffuses away
   - one electron goes to heme bL - heme bH - oxidises Q bound to Q1 binding site - fully reduces semiquinone radical anion to ubiquinol

Question 12

Cytochrome C

Answer 12

• mobile electron carrier
• small soluble protein that diffuses in IMS
• heme group that accepts 1 electron
• binding site on complex III where it is reduced and diffuses to complex IV to be reoxidised

Question 13

Complex IV

Answer 13

• cytochrome c oxidase
• catalyses reduction of O2 to water requiring 4e
• 4 x cyt. c oxidised to give 4e
• electrons pass to copper center A, then heme A, heme A3, and copper center B
• four protons combine with oxygen and electrons to give two water moleucles
• 4 protons pumped into IMS and 4 chemical protons form water

4 reduced cyt. c + 8H (matrix) + O2 = 4 oxidised cyt. c + 2H2O + 4H (IMS)

Question 14

Complex II

Answer 14

• succinate dehydrogenase
• no proton pumping
• accepts 2 electrons from FADH2
• Q - QH2
• electrons passed to Fe-S to Q

Question 15

Proton Transfer to IMS

Answer 15

2e from NADH

• complex I: 4H
• complex III: 4H
• complex IV: 2H

2e from FADH2 (less ATP than NADH)

• complex III: 4H
• complex IV: 2H

Question 16

Uncouplers

Answer 16

• compounds carrying protons through IMM to matrix
• uncouple electron transfer from ATP synthesis
• destroys proton gradient so no ATP synthesis but electrons still flow through the ETC
• energy of proton gradient released as heat (wasted)
• eg. dinitrophenol (DNP) is a chemical uncoupler
• physiologically found in brown adipose tissue (hibernation and in babies)

Question 17

ATP Synthase

Answer 17

• enzyme catalyses ATP synthesis using proton motive force for energy
• hydrophobic section in IMM responsible for ATP synthesis and a section that sticks out into the matrix
• whole molecule is a rotary motor: rotation drives ATP synthesis

Question 18

F1 structure

Answer 18

• 3 alpha units and 3 beta units arranged alternately
• 1 delta, gamma, epsilon unit
• gamma unit is a long helix going through the ring middle
• B units are catalytic and aB bind nucleotides
• 3 B units have different conformations and identical sequences (because of gamma unit interactions)

Question 19

F0 structure

Answer 19

• ring of identical c subunits (8 in mammals)
• 3 subunits connect F0 to F1 : stator (aB2)
• a is hydrophobic and next to the c ring in IMM
• aB2 stator connected to F0 + delta subunit of F1

Question 20

Binding Mechanism

Answer 20

3 conformational (active site) states of the B subunits

1. loose L binds ADP and Pi
2. tight T binds ATP tightly (allows ADP to ATP conversion)
3. open O has open conformation and releases ATP

Question 21

B subunit rotation

Answer 21

• rotates through 3 different conformations due to rotation of subunit (Which unit??) and c ring
• interaction of B unit with top of delta unit in middle of ring
• each subunit goes from T to O to L and each unit is in a different form to the others
• 120 degree rotation between conformation

Question 22

B subunit cycles

Answer 22

1. T rotates to give O form with bound ATP
2. L form rotates to T form to produce ATP
3. ATP in O form leaves and is replaced by ADP + Pi
4. rotation to convert to T form

Question 23

C ring

Answer 23

• proton flow around c ring powers rotation and ATP synthesis
• proton binding to carboxyl residue in C ring causes conformational change
• each c unit has 2 alpha helices which span the membrane (each helix with a glutamate/aspartate residue)
• proton from proton rich IMS enter half-channel on c subunit
• rotation of bound proton channel into the membrane bringing the deprotonated unit into place
• proton is released from half channel closest to matrix where concentration is low
• full rotation of c ring 1 proton is needed per c-unit )8 c rings in mammals)
• 3 ATP made per rotation

Question 24

IMM Transporters

Answer 24

1. ADP/ATP translocator couples ATP exit with ADP entry

2. phosphate carrier brings Pi in using proton exit

Question 25

Glycerol 3 Phosphate Shuttle

Answer 25

1. glycerol 3 phosphate shuttle - regenerates NAD from NADH - In this shuttle, cytoplasmic glycerol-3-phosphate dehydrogenase 1 (GPDH-C) converts dihydroxyacetone phosphate (2) to glycerol 3-phosphate (1) by oxidizing one molecule of NADH to NAD+ - Glycerol-3-phosphate gets converted back to dihydroxyacetone phosphate by an inner membrane-bound mitochondrial glycerol-3-phosphate dehydrogenase 2 (GPDH-M), this time reducing one molecule of enzyme-bound flavin adenine dinucleotide (FAD) to FADH2. FADH2 then reduces coenzyme Q (ubiquinone to ubiquinol) which enters into oxidative phosphorylation. This reaction is irreversible. The glycerol-3-phosphate shuttle allows the NADH synthesized in the cytosol by glycolysis to contribute to the oxidative phosphorylation pathway in the mitochondria to generate ATP.

Question 26

ATP Yield from ETC

Answer 26

glycolysis: 5/7 ATP and 2NADH PDH: 2NADH TCA Cycle: 2 ATP, 6 NADH, 2 FADH2 ETC: 15 ATP from NADH and 3 ATP from FADH2 - Total 30-32 ATP from complete oxidation of one glucose

Question 27

ATP synthesis from reduced electron carriers

Answer 27

- animal mitochondria had 8 c subunits, 8 protons needed for full rotation - 3 ATP made - need 1 proton to transport Pi into the matrix (11 proton in total: 3 more need to be brought in) - 3.7 H per ATP - NADH electrons pumps 10 protons / 3.7 = 2.7 moles of ATP per electron pair - FADH2 electrons pumps 6 protons / 3.7 = 1.6 moles of ATP per electron pair

Question 28

Malate Aspartate Shuttle

Answer 28

translocating electrons produced during glycolysis across the semipermeable inner membrane of the mitochondrion for oxidative phosphorylation. - These electrons enter the electron transport chain of the mitochondria via reduction equivalents to generate ATP. The shuttle system is required because the mitochondrial inner membrane is impermeable to NADH, the primary reducing equivalent of the electron transport chain. To circumvent this, malate carries the reducing equivalents across the membrane. * need mechanism details?*