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9: The Respiratory Chain Flashcards

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1
Q

Respiratory chain overview

A

generate H+ gradient across membrane of mitochondria
> e+ transfer and H+ pump

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2
Q

Respiratory chain formed by

A

Complex 1-4
1: NADH dehydrogenase
2: Succinate dehydrogenase
3: Cytochrom-c Reduktase
4: Cytochrom-c Oxidase

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3
Q

1: NADH dehydrogenase summary

A

NADH is reduced and H+ is transferred to Coenzyme Q

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4
Q

2: Succinate dehydrogenase summary

A

FADH2 reduced and 2H+ transferred to Coenzyme Q

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5
Q

3: Cytochrom-c Reduktase

A

Uses Coenzyme Q to reduce Cytochrom-c to form electrons

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6
Q

4: Cytochrom-c Oxidase

A

Reduce O2 to oxygen to accept electrons from 3 to form H2O

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7
Q

ATP Synthesis + Respiratory chain aka

A

Oxidative phosphorylation

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8
Q

Overview of redox reaction

A

1NADH = Oxidation of 1/2O2 -> O
net transfer of 10 H+ and 2 e-
> 4 H+ at complex 1
> 4 H+ at complex 3
> 2 H+ at complex 4

Proton gradient enough to synthesise 2.5 ATP
> 35% energy efficiency

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9
Q

Redox reaction E- release

A

segmented across steps and used to pump protons across membrane

Coenzyme Q and Cytochrom C = Electron carriers

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10
Q

Respiratory chain co-factors overview

what do? where are they?

A

facilitate e- transfer

embedded in different parts of complex:
> some are associated to membrane while others are part of the integral membrane protein

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11
Q

Where does proton pumping happen in respiratory chain

A

always in transmembrane region

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12
Q

Respiratory chain proteins overview

A

very complex; many subunits with different membrane association all form an assembly
> allows co-factor specification

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13
Q

Biogenesis of Mitochondrial complex:
where proteins originate from?
2

A

Each protein can have 2 origins:

  1. Encoded in CELLULAR/NUCLEAR genome
    > tl and import to mitochondria
    > nDNA
  2. Encoded in MITOCHONDRIAL genome
    > mtDNA
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14
Q

Mitochondrial complexes (1-4) protein origin?

A

usually have both mtDNA and nDNA

Complex 2 ONLY has nDNA !!!

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15
Q

Mitochondrial complexes assembly?
2+1

A

usually in 2 steps

  1. Independent assembly (sub-complex)
  2. Association of whole complex from all the sub-complexes

> req. large number of assembly factors

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16
Q

Complex 1 Assembly: example Fe-S

A

Iron-sulfer co-factor subunit:

  1. Fe-S cluster assembly on main scaffold IscU
    > co-factor protein
  2. Fe-S cluster transfer to nascent Complex 1
    > from IscU (temporary just to assemble it) to final protein !
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17
Q

Co-factors!!

18
Q

Heme:

component in redox rxn
type of association
nu of e- transfered
reduction potential?

types?

Study These Flashcards
A

central Fe!! ion co-ordinated by 4 N atoms
= Redox rxn component

Prosthetic group association

Transfers 1e-

Reduction potential varies

B-type = precursor; complex 2, complex 3
C-type = cov. bound to protein; cytochrom c

19
Q

Iron sulfur clusters

component in redox rxn
type of association
nu of e- transfered
reduction potential?

Study These Flashcards
A

Component in redox = Fe ion

Prosthetic group function/association
> linked to protein via Cys or His residues

1e- transferred

Reduction potential varies

20
Q

Copper

component in redox rxn
type of association
nu of e- transfered
reduction potential?

Study These Flashcards
A

Copper ion = Component

Prosthetic group association

1e- transferred

[+0.2-0.35V] i wouldnt rmbr tbh

21
Q

Flavins

component in redox rxn
type of association
nu of e- transfered
reduction potential?

Study These Flashcards
A

Component: Isoalloxazine RING

Non-cov OR cov bound to protein: Prosthetic group association

1 or 2e- transferred

Redox potential varies

22
Q

Cofactors & protein env?

3

Study These Flashcards
A

biosynthesis of co-factors req. specialised proteins
> can be cov or non-cov linked

Protein localises and orientates cofactors

Redox potential correlated to protein environment
> stabilises IM states and shields radicals

23
Q

Cytochrom C

what does it do?
how? and which complex involved?

Study These Flashcards
A

e- carrier peripheral membrane protein
> positive charged surface allows docking on Complex 3 and 4 for optimal e- transfer!

Cytochrom c release from mitochondria = apoptosis
> compromised respiratory chain !

24
Q

Coenzyme Q/Ubiquinone/Uq10

what is it
component in redox rxn
type of association
nu of e- transfered
reduction potential?

Study These Flashcards
A

Integral membrane protein

component = benzoquinone RING

Coenzyme/Cosubstrate association

1 or 2 e- transferred

+0.10v for 2e-

25
What are the types of proton transport mechanisms?

Redox Loop Direct Proton Pump Conformational Pump
26
Redox loop def in relation to Coenzyme Q transport mechanism
Reduction and oxidation sites on opposite sites of membrane = e- transfer through quinone = proton transfer across membrane (its an integral m.p) e- taken in on one side h+ released on other side > inc gradient ! Implies fixed stereochemistry
27
Direct Proton pump transport mechanism
H+ from matrix to other side > no sterochem limits
28
Conformational pump transport mechanism
Redox carrier anchored in flexible protein undergoes redox induced pKa changes > directionality of proton transport via conf. changes > alternatively accessible from either side of memrbane
29
Electron transport: tunnelling factors that influence it? 3 + relation to biology
e- transferred over distances of up to 14-17 Angstom by tunnelling 3 factors that influence: > distance between Donor and Acceptor = protein in bio, however exact structure has little influence its just the distance that matters > Redox potential difference > Reoorganisation energy
30
Electron transport in proteins mediated by?
e- transfer over large distances in proteins is mediated by chains of redox centres with both uphill and downhill steps > uphill = low rate but still occur just distance is very important!
31
Electron transport and proton translocation Energy graph during respiratory chain
redox potential values for respiratory chain components = mostly iso-potential > almost identical redox potential > mostly for electron transfer efficiency, not energy harvesting. seperated by regions where redox potential is coupled to proton translocation > large drops in redox potential, like: Complex I (NADH → ubiquinone) Complex III (ubiquinol → cytochrome c) Complex IV (cytochrome c → O₂) > Drive conformational changes in the protein complexes > Pump H⁺ ions across the membrane > Only a few spots in the chain actually translocate protons (I, III, IV) = those are associated with sharp redox potential drops
32
Complexes in respiratory chain determination?
first with x-ray crystallography NOW cryoEM is used > good for larger complexes
33
Complex 1: role? eq? about it?
NADH-Ubiquinone/CoQ oxidoreductase > NADH+UQ+5H+=> NAD, UQH2 + 4H+ > 4 protons transported for 2 electrons in mammals very complex but in bacteria there exists simpler complex
34
Bacterial Complex 1 1+3
has core/essnetial functional components > 3 subunits in hydrophobic part = Na/H+ antiporters > C-terminal runs along the 3 antiporters > Redox cofactors in HYDROPHILLIC = conformational coupling to antiporter state = e- transfer indirectly coupled to H+ transfer
35
Mammalian Complex 1 units? and about them? 1+3
Core subunits = same as Bacterial e-/H+ transporters also has Supernumerary subunits > link to RIBOSOME > unique (not like sol. proteins or m.p) > large regions without defined structure
36
Mammalian Complex 1 summary of Proton transfer mechanism: 3
Proton transfer mechanism: - involves conformational coupling, long distance - builds on hydrophilic residues in kinked helices of antiporter like domains - natural conformational fluctuations can occur
37
unique discoveries in Mammalian Complex 1 2
ACP: acyl carrier protein > multi enzyme (used for second function) Lipids > Core components > e.g. Mito lipid
38
Complex 2 structure role? eq? about it? 3
Succinate: UQ Oxidoreductase Succinate + UQ -> Fumarate + UBH2 smallest complex > single UQ binding site > no net proton transfer > all 4 subunits nDNA encoded
39
Complex 3 structure role? eq? about it? struc specific ?
UQ- Cytochrom c oxidoreductase UQH2 + 2cyt c (3+) + 2H+ -> UQ + 2cyt c (2+) + 4H+ > net transport of 4 protons > homodimeric moleculeC
40
Complex 4 structure role? eq? about it? struc specific?
Cytochrom c Oxidase 4cyt c (2+) + O2 + 8H+ -> 4 cyt (3+) + 2H2O + 4H+ > Homodimer > Reduce O2 to 2H2O whilst 4 Cyt c get reduced
41
what does cryoEM show about the complexes?
it shows that complex 1, 3 and 4 associate with each other!
42
What is the significance of the protein environment for cofactors?
Modulates redox potential Localizes and orients cofactors Stabilizes intermediate states

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