Oxidative Phosphorylation

Question 1

What is oxidative phosphorylation

Answer 1

1. The final step in the non-photosynthetic energy conversion pathways
2. Overall, the non-photosynthetic energy conversion pathways catabolize carbon-based fuels (carbohydrates and lipids) to reduce O2 and generate H2O and ATP

Question 2

What proportion of ATP is generated in the different parts of respiration

Answer 2

1. Glycolysis and citric acid cycle provide 1/8 of total that can be obtained from glucose oxidation
2. 7/8 of ATP that can be obtained from glucose oxidation available when NADH and FADH2 are oxidised by the electron transport

Question 3

Describe the structure of mitochondria

Answer 3

1. Mitochondria contain an inner membrane with a large surface area bounded by an outer membrane.
2. Complexes that make ATP are located in inner mitochondrial membrane- ATP synthase complexes
3. Cristae
4. Dark meat- high mitochondrial content
5. White meat- low mitochondrial content

Question 4

When and who invented the chemiosmotic theory

Answer 4

1. 1961

2. Peter Mitchell (and Bob Williams)

Question 5

What is the chemiosmotic theory

Answer 5

1. Describes energy conversion in essentially all organisms
2. H+ gradient across mitochondrial IM
3. Chemiosmosis: movement of H+ down the concentration gradient from high [H+] to low [H+]
4. ATP produced
5. Protons are pumped across the inner membrane- into intermembrane space as electrons flow through the respiratory chain
6. Producing a Proton gradient
7. When protons move back into matrix they drive ATP synthesis

Question 6

What are the two types of energy produced from chemiosmosis

Answer 6

1. Chemical potential energy- Difference in concentration of chemical species- pH difference
2. Electrical potential energy- difference in charge

Question 7

How is chemiosmosis similar to an electrical circuit

Answer 7

1. H+ flow – electric current
2. Battery – electron transport system
3. Capacitor – proton gradient
4. Resistor – ATP synthase

Question 8

What is uncoupling

Answer 8

1. Can be uncoupled so ATP synthesis no longer occurs
2. Uncoupling causes proton “leakage” and production of heat
3. Uncouplers, such as uncoupling proteins or 2,4-dinitrophenol, “short-circuit” the proton flow so that energy is converted to heat rather than to ATP synthesis.
4. Uncouplers- energy converted to heat rather than ATP synthesis

Question 9

What are blockers

Answer 9

1. Compounds that block the proton circuit (such as oligomycin) shut down energy conversion processes, leading to cell death.
2. Blockers- shut down H+ flow so delta pH and delta potential increase, causing cell death

Question 10

What are uses of uncoupling proteins

Answer 10

1. Hibernating animals rely on uncoupling proteins in brown adipose tissue to provide a mechanism that warms their tissues by using fatty acid degradation to convert chemical energy to thermal energy.
2. 2,4-Dinitrophenol has been used as a diet pill because it works in a similar way to stimulate fatty acid degradation in adipose cells.

Question 11

What were other theories suggested instead of chemiosmotic

Answer 11

1. Other theories in 1950-1960s
2. Conformational theory
3. Chemical theory

Question 12

Describe the experimental evidence for the chemiosmotic theory

Answer 12

1. Experimental evidence for chemiosmotic theory
2. Efraim Racker and Walter Stoeckenius, 1973
3. Light-activated ATP synthesis in reconstituted vesicles provided compelling evidence that Mitchell’s chemiosmotic hypothesis was correct.
4. The vesicles contained an artificial membrane, bacteriorhodopsin from Halobacterium halobium, and ATP synthase complexes from bovine heart mitochondria.
5. evidence that an electrochemical H+ gradient can link directly with an electron transport system and provide energy needed for oxidative phosphorylation (ATP synthesis)

Question 13

What are the proteins involved in the electron transport system

Answer 13

1. The four protein complexes of the electron transport system (I–IV), cytochrome c (Cyt c), and the ATP synthase complex (complex V) carry out the process of oxidative phosphorylation.
2. Porin proteins provide channels for small molecules to diffuse across the outer membrane of mitochondria.
3. Translocase proteins shuttle ATP, ADP, and Pi across the otherwise impermeable inner mitochondrial membrane.

Question 14

How many protons are moved when 2 electrons enter the electron transport system

Answer 14

1. When starting with electrons from NADH that enter through complex I, a total of 10 H+ are translocated by the electron transport system.
2. 2 electrons move 10 H+

Question 15

How many H+ reenter the matrix per ATP produced

Answer 15

1. Four H+ reenter the matrix for every ATP that is synthesized
2. 3 H+ through the ATP synthase complex
3. 1 H+ through the phosphate translocase

Question 16

What happens in the final step of the electron transport chain

Answer 16

1. Complex IV converts oxygen to water in final step

Question 17

How is ATP generated

Answer 17

1. Protons which have been moved to intermembrane space move back through ATP synthase- rotary motion which drives catalysis of ATP
2. Inner membrane is impermeable to protons unless uncoupler

Question 18

What happens to the redox potential of the proteins as you go along the chain

Answer 18

1. Redox potential increases as you go along the chain until you get to oxygen

Question 19

What is a measure of phosphoryl transfer potential

Answer 19

1. DG^o’ for hydrolysis of an activated phosphate compound.

Question 20

What does a biological electron transport involve

Answer 20

1. Biological electron transport: series of linked oxidation and reduction reactions (redox reactions).
2. Electron donor (the reductant) is oxidised while transferring electrons to an acceptor (the oxidant).

Question 21

What are the different ways electrons can be transferred from one molecule (donor) to another (acceptor)

Answer 21

1. Directly as electrons, e.g.:Fe2+ + Cu2+ Fe3+ + Cu+
2. As hydrogen atoms (a proton and a single electron): AH2A + 2e– + 2H+
   a) in which AH2 is the hydrogen/electron donor
   b) AH2 and A together constitute a redox couple (A/AH2), which can reduce another compound B (or redox couple B/BH2) by transfer of hydrogen atoms:
   c) AH2 + B A + BH2
3. As a hydride ion (:H–), which comprises a proton and two electrons
4. Direct combination with oxygen

Question 22

Which types of electron transfers are used in oxidative phosphorylation

Answer 22

1. Directly as electrons
2. As hydrogen atoms
3. As hydride ions

Question 23

What is the redox potential

Answer 23

1. Tendency of a redox couple to accept or donate electrons depends on the redox potential

Question 24

What is the standard redox potential based on

Answer 24

1. The standard redox potential of a couple, E^o’, is measured in an electrochemical cell relative to the standard hydrogen electrode (SHE)

Question 25

What does a standard hydrogen electrode look like

Answer 25

1. Hydrogen gas bubbled over a platinum electrode in 1 M acid solution. 2. The reaction 2H+ + 2e– H2 is given an Eo value of 0 volts (V) by convention

Question 26

What would you expect the redox potentials to be for strong reducing/ oxidising agents

Answer 26

1. A strong reducing agent (e.g. NADH) is poised to donate electrons and has a negative redox potential 2. A strong oxidising agent (e.g. O2 or Fe3+) is ready to accept electrons and has a positive redox potential

Question 27

What is the difference in standard redox potentials for biologically important reactions

Answer 27

1. Standard redox potentials for biologically important reactions are measured at pH 7 ([H+] = 10–7 M) instead of pH 0 ([H+] = 1 M). 2. Eo’ = potential of a redox couple in which reduced and oxidised species are present at 1 M concentration, 25 ºC, pH 7. 3. At pH 7, hydrogen electrode Eo’ = –0.42 V.

Question 28

What directions do electrons flow in a spontaneous reaction. e.g. NAD+/NADH

Answer 28

1. In a spontaneous reaction, electrons flow from redox couple of lower potential to redox couple of higher potential. 2. NAD+/NADH (Eo’ = –0.32 V) will lose electrons to SHE in 1 M acid (Eo = 0 V) 3. but will gain electrons from the hydrogen electrode at pH 7 (Eo’ = –0.42 V).

Question 29

How can you work out free energy changes for electrons moving over a potential difference

Answer 29

1. When an electron is moved in an electric field, work done = (electron charge x potential) 2. For electron(s) transferred over potential difference DEo’ , DGo’ = –nFDEo’ 3. n = number of electrons transferred- almost always 1 or 2 4. F = Faraday constant (96.5 kJ mol–1 V–1) 5. DEo’ = difference in standard reduction potentials between the two redox couples (V) 6. DGo’ is in kJ mol–1

Question 30

What should the signs be for a spontaneous reaction

Answer 30

1. For a spontaneous reaction (DGo’ negative), DEo’ must be positive

Question 31

What is free energy available from a redox reaction proportional to

Answer 31

1. Free energy available from a redox reaction is proportional to the difference in redox potentials between the acceptor and donor redox couples 2. DGo’ = –nFDEo’ 3. = –nF[Eo’(acceptor) – Eo’(donor)]

Question 32

Write the half equations for this: | pyruvate + NADH + H+ lactate + NAD+

Answer 32

1. pyruvate + 2H+ + 2e– lactate (Eo’ = –0.19 V) | 2. NAD+ + H+ + 2e– NADH (Eo’ = –0.32 V)

Question 33

How can the free energy be calculated for this half equation: pyruvate + 2H+ + 2e– lactate (Eo’ = –0.19 V)

Answer 33

1. n = 2: 2. DGo’ = –2 x 96.5 kJ mol–1 V–1 x –0.19 V 3. = + 36.67 kJ mol–1

Question 34

How can you calculate reduction potentials under non-standard conditions

Answer 34

1. Nernst equation 2. E’ = Eo’ + (2.303 RT / nF) log10 [e– acceptor] / [e– donor] 3. R = gas constant (8.314 J K–1 mol–1) 4. T = absolute temperature in kelvin 5. 2.303 = conversion factor from natural (base e) to common (base 10) logs

Question 35

What are the typical values for 1- and 2- electron transfers at 25 degrees

Answer 35

1. At 25 ºC, (2.303 RT / nF) = 0.059 for 1-electron transfer 2. At 25 ºC, (2.303 RT / nF) = 0.0295 for 2-electron transfer

Question 36

Describe the electron flow with electrons from NADH

Answer 36

1. Electrons from NADH enter the electron transport system at complex I, then flow to coenzyme Q, complex III, and complex IV. 3. A total of 10 H+ are concomitantly translocated.

Question 37

Describe the electron flow with electrons from FADH2

Answer 37

Electron pairs are derived from: 1. FADH2 oxidation at complex II (succinate dehydrogenase) 2. from ETF-Q oxidoreductase of the fatty acid oxidation pathway 3. or from mitochondrial glycerol-3-phosphate dehydrogenase, which is part of the glycerol-3-phosphate shuttle. 4. A total of 6 H+ are concomitantly translocated when electrons are derived from FADH2.

Question 38

What is the name of complex 1

Answer 38

NADH-Ubiquinone Oxidoreductase

Question 39

Describe what takes place in complex 1

Answer 39

1. Oxidation of NADH in the matrix releases 2 e− (in the form of a hydride ion), which are transferred to FMN in a coupled redox reaction. 2. Electrons move along at least 7 Fe-S centres carrying 1e- at a time – sulfur on cysteine side chains interact with iron inorganic cofactors 3. Electrons are then transferred from one carrier to another until they are donated in the last step to coenzyme Q (ubiquinone; Q) to form QH2 (ubiquinol). 4. In the process, 4 H+ from the matrix side of the membrane are translocated across the membrane by complex I, and 2 e− and 2 H+ are used to reduce coenzyme Q.

Question 40

Why are inorganic and organic cofactors used to help transfer electrons

Answer 40

1. Proteins are not good electrons conductors- inorganic and organic cofactors which help to transfer electrons

Question 41

Describe the structure of FMN

Answer 41

1. Like FAD, FMN can accept electrons one at a time 2. Reduction by one electron forms a semiquinone intermediate 3. Reduction by a second electron leads to the fully reduced species (FMNH2) 4. Contains an Isoalloxazine ring identical to that of FAD

Question 42

What are the Fe-S clusters structures in complex I

Answer 42

1. Complex I contains two types of Fe–S clusters, coordinated through cysteine residues in the protein subunits: 2. 2 Fe–2 S cluster 3. 4 Fe–4 S cluster

Question 43

What is the name of co-enzyme Q

Answer 43

Ubiquinone/Ubiquinol

Question 44

What is the net result of coupled redox reactions of complex 1

Answer 44

1. NADH oxidation + CoQ reduction

Question 45

Three key roles of CoQ

Answer 45

1. Mobile, lipid-soluble e- carrier - transports electrons in membrane from complex I to III 2. Entry point into electron transport system for e- pairs from citric acid cycle, fatty acid oxidation, and glycerol-3-phosphate dehydrogenase 3. Converts 2e- transport system in complexes I and II to 1e- system in complex III, which then passes electrons one at a time to cytochrome c

Question 46

What does coenzyme Q contain

Answer 46

1. Hydrocarbon tail of human coenzyme Q contains 10 isoprenoid units, hence CoQ10

Question 47

What is the name of complex II

Answer 47

1. Succinate dehydrogenase

Question 48

What happens in complex II

Answer 48

1. Direct physical link to citric acid cycle and electron transport chain 2. Doesn’t move protons across membrane-only complex that doesn't 3. Contribute to pool of reduced coenzyme Q 4. Oxidises succinate to fumarate, coupled to FAD/FADH2 5. Electron pair then used to reduce Q via Fe-S and a haem

Question 49

What is the name of complex III

Answer 49

1.Ubiquinone-cytochrome c Oxidoreductase

Question 50

What happens in complex III

Answer 50

1. Reduces cyt c (recipient of electrons), while translocating 4H+ for every 2 electrons 2. Dimeric complex: 2 x 11 subunits 3. CoQ uses Q cycle to convert 2e- process into two 1e- transfers 4. several prosthetic groups that function as electron carriers (Fe–S cluster and hemes bL, bH, and c1) 5. Does contribute to proton gradient

Question 51

Describe how different cytochromes are characterised

Answer 51

1. Types a, b, and c according to type of haem 2. e.g. Cyt c – c type haem group 3. Have characteristic absorption spectra

Question 52

Describe the different types of cytochrome

Answer 52

1. Cyt c- Haem group covalently linked to protein through thiol groups from Cys residues 2. Type a haem has a long hydrophobic tail 3. They all have inorganic cofactors

Question 53

What is the name of Complex IV

Answer 53

Cytochrome c oxidase

Question 54

What happens in complex IV

Answer 54

1. Cyt c oxidation 2. Where the electrons finish 3. Come from cytochrome c in intermembrane space 4. Copper centres 5. Then electron transport through one monomer of the homodimer, culminating in O2 reduction to form H2O

Question 55

How many H+ are involved in complex IV

Answer 55

1. Four H+ are involved in the complex IV reactions: 2. 2 H+ translocated into intermembrane space 3. 2 H+ used to form H2O

Question 56

What is the reaction in the final step in complex IV

Answer 56

1. O2 + 4e- + 4H+ --> H2O 2. Intermediates (reactive oxygen species) 3. Cellular defences 4. 2O2-(radicals) + 2H+ --> O2 + H2O2 5. SOD- superoxide dimutase- does above reaction 6. SOD- can be mutated in diseases- muscle wasting diseases 7. H2O2 can be converted into oxygen and water by catalase

Question 57

How many protons does each complex donate to the proton gradient

Answer 57

1. Complex 1- 4 H+ 2. Complex 2- no H+ 3. Complex 3- 4 H+ 4. Complex 4- 2 H+

Question 58

Describe the general structure of complexes I-IV

Answer 58

1. Complexes I-IV all have TM regions plus functional domains protruding into matrix 2. Complexes III and IV also have functional domains protruding into intermembrane space to interact with cyt c

Question 59

Describe the general process of electron transport chain

Answer 59

1. NADH oxidation starting with complex I results in translocation of 10 H+ 2. CoQ and FADH2 oxidation starting with complex II results in translocation of 6 H+ 3. CoQ and cyt c transport 1e- at a time, so must make two trips to transfer 2e- from NADH or FADH2 to ½ O2 to form H2O 4. Switch from 2 electron transport to 1 electron transport in complex 3