Biochemistry - Electron Transport And Oxidative Phosphorylation. Chapter 17

Front 1

1. Rank the following redox-active coenzymes and prosthetic groups of the electron-transport chain in order of increasing electron affinity: cytochrome a, CoQ, FAD, cytochrome c, NAD, FeS, Cu, cytochrome c1.

Back 1

1. Cytochrome a @ Cu > cytochrome c1 @ cytochrome c > CoQ > FAD > NAD. Where are the FeS cluster(s) ranked? They are in the NADH-Q reductase, succinate Q and cytochrome reductases. They will assume an E˚’ close to what complex they are in. Their electron affinity or E˚’ is thus variable.

Front 2

2. Why is the oxidation of succinate to fumarate only associated with the production of two ATPs during oxidative phosphorylation while the oxidation of malate to oxaloacetate is associated with the production of 3 ATPs?

Back 2

The oxidation of succinate to fumarate catalyzed by succinate dehydrogenase reduces FAD to FADH2 . The FADH2 electrons enter the electron transport chain at CoQ bypassing the first oxidative phosphorylation (ATP forming) step, NADH -> CoQH2.Thus only 2 ATP forming steps in the electron chain from CoQ to O2 are utilized. In contrast the reaction malate to OAA produces NADH and therefore the electrons from NADH goes through the three ATP forming complexes in the electron transport chain.

Front 3

3. What is the thermodynamic efficiency of oxidizing FADH2 so as to synthesize two ATPs under standard biochemical conditions?

E' of 1/2O2 + 2H+ 2e- ---> H2O = +0.816 V and
E' of FAD + 2 H+ + 2 e- ---> FADH2 = 0.0 V

Back 3

∆E˚’ = +0.815V - (-0.0) = 0.815 V
∆G˚’ = -nF ∆E˚’ = -2 x 96.494 x 0.815 = - 157.3 kJ•mol-1
2Pi + 2ADP <===> 2ATP + 2 H2O
∆G˚’ = 2 x 30.5= +61 kcal •mol-1
Therefore, 61 / 157.3 = 0.388 or 38.8% efficiency.

Front 4

4. Match the compound with it’s behavior: (1) rotenone, (2) dinitrophenol and (3) antimycin A.

(a) Inhibits oxidative phosphorylation when the substrate is pyruvate but not when the substrate is succinate.

(b) Inhibits oxidative phosphorylation when the substrate is either pyruvate or succinate.

(c) Allows pyruvate to be oxidized by mitochondria even in the absence of ADP.

Back 4

1. answer is a. rotenone; rotenone inhibits complex I (pyruvate to Q) and not II (succinate to Q)

2. answer is c. dinitrophenol; uncouples oxidative phosphorylation from respiration. Thus pyruvate respiration goes on without ATP formation.

3. Answer is b. antimycin A; Antimycin A inhibits complex III, cytochrome c reductase.

Front 5

5. How does atractyloside affect mitochondrial respiration?

Back 5

Atractyloside inhibits the transport of ATP and ADP in the mitochondria by inhibiting the ATP/ADP translocase. Thus, it inhibits oxidative phosphorylation by decreasing the amount of ADP available for phosphorylation.

Front 6

6. What change will occur when each of the following substances is added to mitochondria carrying out oxidative phosphorylation? (a ), antimycin a, (b), amytal, (c), 2,4-dinitrophenol, (d), succinate.

Back 6

(a) antimycin a; inhibits complex III electron flow (CoQ -> Cyt c). Therefore NADH and FADH2 will accumulate while Cyt c and Cyt a3 oxidized forms will accumulate.

(b) amytal; inhibits complex I. Thus, NADH cannot be oxidized by CoQ and will accumulate.

(c) 2,4 Dinitrophenol; uncouples oxidative phosphorylation by dissipating the proton gradient across the inner mitochondrial membrane. O2 respiration increases without the production of ATP.

(d) succinate; it forms FADH2 which is oxidized by CoQ to form CoqH which is then oxidized by Cyt c which in turn is oxidized by O2. Two ATPs are formed per atom of Oxygen consumed.

Front 7

7. What are the functions of the following components of the ATP synthase? F1, F0 and stalk proteins.

Back 7

F1 is composed of 5 peptides, alpha3beta3,gamma,delta and epsilon.The alpha-beta subunits contain the ATP synthase active site. The gamma, epsilon peptides forms the gate coupling the stalk with F1 (see fig. 19-23f on page 711 in Lehninger or Fig. 11-39 in course pack (page 103) or in Lehninger, page 401). The Fo is composed of 4-5 peptides, is transmembrane and forms the proton channel. The stalk proteins,gamma and epsilon, interconnect F1 with F0. One protein binds oligomycin which blocks ATP synthesis by interfering with the utilization of the proton gradient.

Front 8

9. Can ATP be produced by oxidative phosphorylation in the presence of antimycin? If so, what is the P:O ratio for the reduction of two-electron donors?

Back 8

Yes. However you must use a reducing agent that will reduce cyt c (eg., ascorbate + TMPD). You will be able to use complex IV as the electron transport system and thus you will be able to synthesize one ATP per atom of O. thus P:O = 1.

Front 9

10. Functional electron-transport systems can be reconstituted from purified respiratory electron transport chain components and membrane vesicles. For each of the following sets of components, determine the final electron acceptor. Assume O2 is present.
(a) NADH,Q, complexes I, III & IV
(b) NADH, Q, cytochrome c, Complexes II & III
(c) Succinate, Q, cytochrome c, Complexes II, III
& IV
(d) Succinate, Q, cytochrome c, Complexes II & III
(e) Succinate, Q, cytochrome c, Complexes I & III

Back 9

10.
a) complex III. Cyt c is missing.

b) No reaction. Complex I is missing.

c) O2. System is complete.

d) Cyt c. Complex IV is missing.

e) No reaction. Complex II is missing.

Front 10

Outline the mechanism for the reduction of O2 to H2O via cytochrome C oxidase. Describe the path of the electrons from the heme a-CuA cluster to the heme a3-CuB cluster and note the changes in the oxidation states of Fe and O. Note the formation of the superoxyl anion intermediate.

Back 10

This answer is on page 702 (Fig. 19-14,also on page 99 in course pack). Reduced cytochrome c (ferrocytochrome c) transfers its electrons to the heme a- CuA cluster. The first electron goes to Cu++ then the next to Fe+++. Then the electrons from the heme a- CuA cluster are transferred to heme a3- CuB cluster. After reduction to the Cu+, Fe++ form in the heme a3- CuB cluster, O2 adds to Fe++ and the O2 of the complex then takes electrons from Cu and from Fe to form a Fe+++O2- -, Cu++ complex.This is known as a peroxy intermediate. Two protons and an electron are added and one oxygen atom is tranferred from the Fe to Cu. The electrons and protons combine with an Oxygen atom transferred to the Cu to give a Cu++-O-H2, Fe++++-O- - complex. An electron is added to the complex to form water with the oxygen associated with the the Cu which is oxidized to Cu++. Both waters are then released from the Fe and Cu with addition of another electron and two protons. The reduction of O2 is done this way by binding the partially oxidized intermediates tightly to both Fe and Cu in the heme a3- CuB cluster. Thus, no toxic partially reduced oxygen intermediates are released.

Front 11

13. Calculate the Delta Go’ for the reaction, Succinate + FAD -------> fumarate + FADH2
Fumarate:succinate Eo’ =0.03
FAD:FADH2 Eo’ = 0.0

F = 96.494 kcal/V ; 1V = 1 Joule/Kcal

Back 11

Delta Eo’ = E˚’ electron acceptor - E˚’ electron donor = 0 - (0.03) = - 0.03V

Therefore Delta Go’ = -nF Delta Eo’ = -2 x 96.494 kJ/V mol x (-0.03) = +5.79 kJ/mol.

The reaction is endergonic.

Front 12

What is the standard Potential Electrode of the hydrogen redox pair at at pH 7.0 the emf of the electrode ?

Back 12

the E’ 0 is -0.414 V.

Front 13

The salt bridge in test cell, usually saturated
KCl, is the path for?

Back 13

counter-ions.

Front 14

The salt bridge in test cell is usually saturated?

Back 14

KCl,

Front 15

What is a standard of
reference that is assigned a standard reduction potential of 0.00 V.

Back 15

H+ + e- ===> 1/2 H2

Front 16

Reduction potential of a reaction also depends on?

Back 16

the concentration of the reductant and
oxidant forms.

Thus the reaction of two reactants is,
An+ + B reduced <======> A reduced + B n+


Delta G = Delta G0’ = RT ln [A reduced ] [ Bn+ ] /[B reduced ] [ An+ ]


Now Delta G = -n F Delta E



Substitute Delta E for Delta G/- n ℑthen we have the Nernst Equation.

Delta E=

Delta E0’ – (RT/n F) ln ([A reduced ][ Bn+ ]/[B reduced ] [ An+ ])

Front 17

The half reactions are written in this manner
A (n+) + n e- <==> A (red)

E = E0’ – (RT/n F) ln [A red]/[An+]

B (n+) + n e- <==> B (red)

E = E0’ – (RT/n F) ln [B (red)]/[B(n+)]In the reaction where A is the electron acceptor and B is the donor we have what rxn and what equation:

Back 17

A (n+) + B (red) <==> A (red)+ B (n+)

and

Delta E0’ = E0’ (e- acceptor A) - E0’ (e- donor B)

If Delta E is positive then Delta G is negative and we have an _______ reaction.

Exergonic

Front 18

Cellular oxidation of glucose to CO2 requires specialized electron carriers known as
Coenzymes.

Four examples are?

Back 18

Pyridine nucleotides; Nicotinamide adenine dinucleotide (NAD+) and Nicotinamide
adenine dinucleotide 2’-phosphate (NADP)

Please note that reduction of NAD+ to NADH or NADP+ we have a two electron transfer
.
NAD(P)+ + 2 e- + 2 H+ ====>NAD(P)H + H+

NAD + NADH concentration is ~ 10-5 M and

cellular NAD/NADH ratio is >50 and

cellular NADPH/NADP ratio is > 50.

Front 19

What redox carriers are tightly bound to proteins?

Back 19

Flavin nucleotides

Front 20

There are two flavins. They are?

Back 20

FAD and FMN.

Front 21

FAD and FMN are what type of electron carriers?

Back 21

can be two electron carriers or one electron carriers as seen in their semi-quinone structure.

Front 22

What is the Delta G0’ of the oxidation of NADH by O2 ?

Back 22

NAD+ + H+ + 2 e- <=====> NADH E0’ = - 0.320 V

1/2 O2 + 2H+ + 2 e- <=====> H2O E0’ = + 0.816

Therefore the reaction is,

1/2 O2 + H+ + NADH <=====> H2O + NAD+
and Delta E0’ = 0.816 - (- 0.320) = 1.136 V

Delta G0’ = - nF Delta E0’ Thus, Delta G0’ = - 2 (96840) ( 1.136) = 220,020.48 J
Or 220.0 kJ.

For synthesis of ATP from ADP + Pi you need 30.5 kJ.

Therefore you could synthesize 220/30.5 or 7 ATPs from the oxidation of NADH by oxygen.

only 2.5 ATPs are synthesized when NADH is oxidized in the mitochondria by the electron transport chain with oxygen as the ultimate electron acceptor.

Front 23

What is the sub-cellular organelle where the
electron transfer system that transports electrons and hydrogen from the NADH and FADH2 produced in the TCA cycle to O2 to form H2O.

Back 23

The Mitochondria

Front 24

What is in the mitochondrion?

Back 24

The electron transfer (transport) system

The TCA cycle

Front 25

The electron transfer (transport) system is a series of oxidative reactions through respiratory carriers in 4
different enzyme complexes known as?

Back 25

complexes I-IV.

Front 26

The electron transfer (transport) system is?

Back 26

a series of oxidative reactions through respiratory carriers in 4 different enzyme complexes known as complexes I-IV.

Front 27

3 parts of the anatomy of
Mitochondrion

Back 27

Outer membrane:

Inner membrane:

Matrix

Front 28

What is the Outer membrane of Mitochondrion permeability?

Back 28

Freely permeable to small molecules and ions

Front 29

What is the inner membrane of Mitochondrion permeability?

Back 29

Impermeable to most small molecules and ions, including H+

Front 30

What is needed to penetrate inner membrane of Mitochondrion?

Back 30

Needs transporter

Front 31

What does the inner membrane of Mitochondrion Contain?

Back 31

Resp. electron carriers (complexes I-IV.)

ADP-ATP translocase

ATP Synthase (F0, F1)

Other membrane transporters

Front 32

What does the Matrix of Mitochondrion Contain?

Back 32

Pyruvate dehydrogenase complex

TCA enzymes

Fatty acid beta-oxidation enzymes

A.A oxidation enzymes

DNA, ribosomes

ATP, ADP, Pi, Mg2+, Ca2+. K+

Many soluble metabolic intermediates andother enzymes

The cristae are extensions of
the inner membrane.

Front 33

The mitochondria has its own?

Back 33

DNA
RNA
and can make proteins

Front 34

The proteins made in the mitochondria (G/S/L) than
proteins made in the cytosol

Back 34

Less than

Front 35

What are the other electron acceptors in the electron transport chain?

Back 35

FAD and FMN

Front 36

FAD and FMN accept electrons and hydrogen from?

Back 36

NADH as well as from succinate.

Front 37

What electron acceptors in the electron transport chain are tightly bound to proteins and sometimes they may be covalently linked to the
Protein?

Back 37

FAD and FMN

Front 38

FAD and FMN in the electron transport chain are tightly bound to proteins and sometimes they may be covalently linked to?

Back 38

The Protein

Front 39

FAD and FMN in the electron transport chain are tightly bound to proteins and sometimes they may be covalently linked to the Protein. What happens then?

Back 39

FADH2 then transfers its electrons to Ubiquinone or Coenzyme Q.

Front 40

Unlike NAD+ reduction which is a two electron transfer, ubiquinone can

Back 40

also undergo a one electron transfer where a semiquinone intermediate is formed.

Front 41

Heme A with its isoprenoid tail is found in?

Back 41

a-type cytochromes.

Front 42

being mobile and freely diffusible in the lipid bilayer of the inner mitochondrial membrane, Ubiquinone can do what?

Back 42

therefore transfer electrons from the soluble electron carriers to less mobile electron carriers in the membrane.

Front 43

NAD+ reduction involves what type of transfer?

Back 43

a two electron transfer

Front 44

Ubiquinone involves what type of transfer?

Back 44

undergo a one electron transfer where a semiquinone intermediate is formed or a two electron transfer

Front 45

What is Ubiquinone?

Back 45

a small molecule and is hydrophobic, being mobile and freely diffusible in the lipid bilayer of the inner mitochondrial membrane.

transfer electrons from the soluble electron carriers to less mobile electron carriers in the membrane.

Front 46

Ubiquenone is involved in ______ and are reduced to _______?

Back 46

in FAD and FMN electron acceptors

Ubiquinol

Front 47

The 4 five-membered nitrogen Containing rings in cyclic structure are named?

Back 47

porphyrins.

Front 48

In porphyrins, the 4 nitrogen atoms are coordinated with a?

Back 48

central Fe ion, either Fe2+ or Fe3+.

Front 49

Iron Protoporphyrin IX is found in

Back 49

b-type cytochromes
and in hemoglobin and Myoglobin.

Front 50

What is found in b-type cytochromes and in hemoglobin and Myoglobin?

Back 50

Iron Protoporphyrin IX

Front 51

Heme C is covalently bound to cytochrome C protein through?

Back 51

thioether bonds from Cys residues in the protein.

Front 52

What is covalently bound to cytochrome C protein through thioether bonds from Cys residues in the protein?

Back 52

Heme C

Front 53

Heme A with its ________ is found in a-type cytochromes.

Back 53

isoprenoid tail

Front 54

What are the 3 types of cytochrome structures?

Back 54

Heme A - isoprenoid
Heme B - hyrin
Heme C - Cys

Front 55

Cytochromes are proteins with strong absorption of visible light because?

Back 55

of their Fe-containing heme prosthetic groups.

Front 56

All cytochromes have in common?

Back 56

Same base structure
distinctive absorption spectra.

Front 57

What cytochromes are tightly bound?

Back 57

a and b cytochromes

Front 58

What cytochromes are tight, covalently bound?

Back 58

Heme C

Front 59

Cytochrome a and b are integral proteins of?

Back 59

the inner mitochondrial membrane

Front 60

What cytochrome is soluble and associates with the membrane through electrostatic interactions with the outer surface of the inner membrane and why?

Back 60

Mitochondrial Cytochrome c

Cause it’s has a tight, covalently bond

Front 61

Mitochondrial Cytochrome C Facts

Back 61

soluble

Cys side chain

associates w/ the membrane through electrostatic interactions with the outer surface of the inner membrane


Iron sulfur proteins. They are proteins in which one Fe atom is coordinated with inorganic sulfur atoms or with the sulfur atoms of Cys residues.

Front 62

What are the three iron sulfur centers?

Back 62

(a) a single Fe ion surrounded by S atoms of 4 Cys centers.

(b) as in (a) but two inorganic sulfur atoms are
between the Fe ions. This is known as a 2Fe-2S cluster or center.

(c) The middle is known as a 4Fe-4S center or cluster.

Front 63

What is known as a 2Fe-2S cluster or center?

Back 63

two inorganic sulfur atoms are between the Fe ions

Front 64

Electrons pahway from NADH to O2?

Back 64

from NADH or succinate through flavoproteins, ubiquinone, iron sulfur proteins,cytochromes and then to O2

Front 65

Electrons move from NADH or succinate through flavoproteins, ubiquinone, iron sulfur proteins,
cytochromes and then to O2

How was this sequence determined?

Back 65

Standard Reduction potential

Neg to positive

Front 66

What are the 3 method used to determine the sequence of electron carriers?


standard reduction potentials of the individual electron carriers that have been determined

having the whole electron transport chain being reduced and oxidized

the use of inhibitors of the electron tranport chain.




First the standard reduction potentials of the individual electron carriers have been determined experimentally. It is expected that the carriers to function in order of

Back 66

increasing reduction potential, from carriers of lower E’0 to carriers of higher E’0.

Front 67

The order of 8 carriers based on increasing reduction potentials is:

Back 67

NADH => Q => cytochrome b => cytochrome c1 => cytochrome c => cytochrome a => cytochrome a3 => O2.

Front 68

What is the second method used to determine the sequence of electron carriers?

Back 68

having the whole electron transport chain being reduced in the absence of
O2. Then introduce O2 in the system and see the sequence of oxidation of the
electron carriers (done spectrophotometrically).

Front 69

How is the carrier getting oxidized first in the second method determining the sequence of electron carriers?

Back 69

The carrier closest to O2 becomes oxidized first, the second closest oxidized next and so forth.

Front 70

Explain the second method used to determine the sequence of electron carriers?

Back 70

having the whole electron transport chain being reduced in the absence of
O2.

Then introduce O2 in the system and see the sequence of oxidation of the
electron carriers (done spectrophotometrically).

Front 71

What is the Third method used to determine the sequence of electron carriers?

Back 71

using inhibitors of the electron tranport chain.

Front 72

Explain the third method used to determine the sequence of electron carriers?

Back 72

In the presence of O2 electron donor carriers in the chain that function before the inhibited step becomes fully reduced. Those that function afterwards would remain oxidized.

Front 73

In the Inhibitor method for determining sequence of electron carriers, what is oxidized and what is reduced?

Back 73

Those before inhibition step is reduced and those after the
inhibition step remains

Front 74

The electron carriers are in multienzyme complexes that are?

Back 74

membrane-bound that can be physically separated.

Front 75

The electron carriers are in?

Back 75

multienzyme complexes

Front 76

What are the multienzyme complexes that the electron carriers?

Back 76

Complex I carries electrons from NADH to ubiquinone.

Complex II carries electrons from succinate to ubiquinone.

Complex III carries electrons from reduced ubiquinone to cytochrome c complex IV transfer electrons from cytochrome c to O2.

Front 77

What does Complex II do?

Back 77

Complex II carries electrons from succinate to ubiquinone.

Front 78

What does Complex III do?

Back 78

Complex III carries electrons from reduced ubiquinone to cytochrome c

Front 79

What does Complex IV do?

Back 79

complex IV transfer electrons from cytochrome c to O2.

Front 80

What does the Complex I proton pump do?

Back 80

transfers 4 protons in one direction, from the matrix to the inter- membrane space.

Front 81

What happens when the Complex I proton pump transferring 4 protons in one direction, from the matrix to the inter- membrane space.?

Back 81

The matrix becomes negative and the intermembrane space, positive.

Front 82

Other than carrying electrons from NADH to ubiquinone, Complex I also acts as?

Back 82

a proton pump

Front 83

The rxn that takes place in Complex I?

Back 83

NADH <~~~> ubiquinone oxidoreductase.

Front 84

In complex I, Why does 4 protons from the matrix transfer in a vectorial manner to the intermembrane space?

Back 84

due to electron transfer from NADH to Q to form QH2.

Front 85

What happens in the complex I do during electron transfer from NADH to Q to form QH2?

Back 85

4 protons from the matrix are transferred in a
vectorial manner to the intermembrane space

Front 86

What is the site where is the site where 4
protons from the matrix are transferred in a
vectorial manner to the intermembrane
space due to electron transfer from NADH
to Q to form QH2?

Back 86

matrix arm portion

Front 87

What causes formation of a proton gradient in Complex I?

Back 87

4 protons from the matrix are transferred in a vectorial manner to the intermembrane space

Front 88

What is the Complex rxn?

Back 88

NADH + H+ + Q →NAD+ + QH2 or

NADH + 5H+ N + Q →NAD+ + QH2 +4H+ P

Front 89

The rxn that takes place in Complex II?

Back 89

Succinate Dehydrogenase (SDH)

Front 90

Succinate Dehydrogenase is the only TCA cycle enzyme that is?

Back 90

membrane-bound, having 5 prosthetic groups and 4 different subunits.

Front 91

In the structure of complex II, succinate dehydrogenase, Two subunits of SDH are located __________ while the 2 other subunits are?

Back 91

the matrix of the mitochondria

membrane proteins.

Front 92

What is contained in the complex II, succinate dehydrogenase?

Back 92

The matrix proteins contain 3 2Fe-2S centers, FAD and a binding site for succinate.


The ultimate e- acceptor, ubiquinone, is bound to the membrane subunits.

A heme b molecule is present in the membrane subunits but is non-functional in the electron path.

Front 93

The matrix proteins in the complex II,Contain?

Back 93

3 ~~ 2Fe-2S centers, FAD and a binding site for succinate.

Front 94

What is the ultimate e- acceptor, contained in the complex II and what is bound to?

Back 94

ubiquinone, is bound to the membrane subunits.

Front 95

A ____ molecule is present in the complex II
membrane subunits but is non-functional in the electron path.

Back 95

heme b

Front 96

The rxn that takes place in Complex III?

Back 96

Ubiquinone:Cytochrome Oxidoreductase (also called cytochrome (bc1)Complex.

Front 97

In Complex III, The reduced ubiquinone also known as ________ in this complex, transfers its electrons eventually to cytochrome c

Back 97

Ubiquinol

Front 98

In Complex III, The reduced ubiquinone also known as ubiquinol in this complex What does what to electrons?

Back 98

transfers its electrons eventually to cytochrome c

Front 99

How many structure does the complex III have?

Back 99

(a) monomer structure
(b) dimeric unit

Front 100

Electron transport in complex III is
known as?

Back 100

the Q cycle.

Front 101

Electron transport in complex III is known as the Q cycle and the equation
is?

Back 101

QH2 + 2 Cyt c1 (ox.) + 2H+ N →Q + 2 Cyt c1 (red.) + 4H+P

Front 102

What is Q cycle?

Back 102

a process in the complex where a two e- carrier
becomes a single e- donor to cytochromes b562, b566, c1, and c.

Front 103

What is the net result of the Q cycle?

Back 103

one molecule of Ubiquinol is oxidized and 2 molecules of Cyt c are reduced and the reduced Cyt c moves to complex IV.