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ETC + ATP Flashcards

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Organic Chemistry 101 flashcards
1
Q

why are metal centres used in the ETC?

A

organic chemistry isn’t good at e- transfer

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2
Q

what is the ETC?

A

series of 5 electron-carrying protein complexes + cofactors located in IMM of eukaryotic cells

involved in generation of proton gradient across the membrane

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3
Q

what is a respirasome?

A

a super complex able to fulfill the respiration activity

combo of complex I, III and IV

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4
Q

what is the gradient produced by the ETC used for?

A

allows ATP synthase (complex V) to produce ATP for use by the cell

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5
Q

what allows the complexes to transfer electrons sequentially?

A

having a unique set of redox potentials

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6
Q

where do complexes I through IV receive their electrons from? where are these produced?

A

NADH and FADH2

NADH: glycolysis, krebs cycle, fatty acid oxidation
FADH2: krebs cycle

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7
Q

how does the ETC ensure electrons don’t flow backwards?

A

electrons passed through a series of redox reactions with increasing redox potential so it’s not energetically favourable to flow backwards

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8
Q

what are the 3 ion complexes used in the ETC?

A

iron-sulphur clusters
heme in cytochromes
copper

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9
Q

what happens to iron in iron sulphur clusters?

A

Fe2+ reduced to Fe3+

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10
Q

what happens to the iron in iron-sulphur clusters?

A

Fe2+ reduced to Fe3+

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11
Q

what complexes is iron as heme in cytochromes present in?

A

III and IV

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12
Q

what happens to copper in the ETC complexes? and which complex?

A

shifts between Cu2+ and Cu3+
complex IV

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13
Q

what happens to electrons at complex I?

A

NADH donates 2 e- which reduce Flavin Mononucleotide (FMN) to FMNH2

they then pass iron sulphur clusters which pass e- onto ubiquinone, combining them with 2 H+s from the matrix

pumps 4 H+ across IMM into IMS

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14
Q

what is the structure of complex I?

A

NADH dehydrogenase
44 amino acid ppc
spans IMM

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15
Q

what is ubiquinone and what does it do?

A

mobile electron carrier
highly hydrophobic due to long carbon tail so residues in IMM

can shift between donating and accepting e-, existing in electron bound QH2 state

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16
Q

what does complex II serve as in terms of metabolic coupling?

A

the point of physical coupling of the ETC to the citrate cycle

physically linked to succinate dehydrogenase, tethering the citric cycle mechanism to the inner side of the IMM

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17
Q

what does FADH2 act as to succinate dehydrogenase?

A

prosthetic group

cannot freely diffuse around cytoplasm

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18
Q

why can’t complex II pump protons? what does this mean about FADH2?

A

complex does not span entire membrane

less efficient electron acceptor for oxidative phosphorylation, as contributes to pumping of fewer protons across IMM

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19
Q

how does complex II work?

A

2 e- passed from FADH2 to series of iron-sulphur clusters

e- passed to Q, combing with 2 H+ from matrix to form QH2

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20
Q

how was it discovered that complex I and II are independent?

A

if you block complex I (how?) and add FADH2, aerobic resp can still occur, demonstrating there are 2 entry points to ETC that don’t converge until complex III

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21
Q

how does complex III work?

A

accepts e- from ubiquinol 2 at a time, but can only actively process 1

if III were to leave the 2nd electron loose while it reacted with the other, a large number of single e- would exist in the cell, which damages DNA, proteins, lipids and the cell

unloads both e- to complex III at once

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22
Q

how does ubiquinol unload electrons to complex III?

A

both at once

cytochrome b binds ubiquinol + ubiquinone
iron-sulphur cluster + hemeBL pull e- each off ubiquinol, releasing 2 H+ into IMS

1 e- transferred to cytochrome c1 from iron-sulphur cluster (Rieske), other transferred from hemeBL to hemeBH

cytochrome c1 reduces cytochrome c by transferring e- and hemeBH transfers e- to ubiquinone = semiquinone

first ubiquinol released, semiquinone stays bound

1 through 3 happens again, then semiquinone picks up 2nd e- from hemeBH, and 2 H+ from matrix (oxidises to ubiquinone)

ubiquinols released

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23
Q

what is the other name for complex III?

A

cytochrome c oxidoreductase

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24
Q

what are the inhibitors of complex III?

A

antimycin A (binds to Qi site and inhibits e- transfer from hemeBH to Q)

myxothiazol (binds Qo site and inhibits e- transfer from QH2 to Rieske)

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25
Q

what is the structure of Rieske?

A

iron-sulphur cluster coordinated by 2 histidine residues

26
Q

what is the purpose of the Q cycle?

A

‘juggling’ of e- to prevent them leaking out of the mitochondria and damaging cell

makes effficne tuse of fact we have 2e- available w each ubiquinol

generates enough energy to pump 4 H+ from matrix to IMM

27
Q

what is complex IV composed of?

A

cytochrome C oxidase

heme a and haem a1, which possess different redox potentials due to dif environments in the protein

also 3 Cu ions, 2 clusters: CuA/CuB (2 copper ions bridging 2 cysteine resiudes) and CuB (bonded to 3 histidine residues, 1 covalently linked to tyrosine)
alternate between Cu+ form and oxidised Cu2+ to accept/donate e-

28
Q

how do haem a and haem a3 differ from haem?

A

formyl group replaces methyl group

C17 hydrocarbon chain replaces vinyl group

haem is not attached to protein

29
Q

what binds to complex IV? what does this allow?

A

4 molecules of cytochrome C, each transferring 1 e-

allows complex to reduce 1 molecule of O2 to water

30
Q

what happens once the CuB centre and haemA3 have been reduced?

A

can together bind an O2 molecule, abstracting 2 e- from enzyme’s active centre to form peroxide bridge between the ions

2 more cytochrome Cs donate e-, another O2 is bond and H+ are added to each O2 atom to produce 2 ion-oxygen groups:
CuB2+ –OH
Fe3+–OH

31
Q

when happens when the ion-oxygen groups react with more protons

A

2 more protons = 2 more H2O mols released

fully oxidises whole complex and removes 4 H+ from the matrix total, the energy from which is used to pump 4 H+ into the IMS

32
Q

what is an inhibitor of complex IV?

A

cyanide

no consumption of O2 when it is added to respiring mitochondria preparation as there is no way to bypass its inhibition

33
Q

what do mutations or defects in ETC proteins lead to?

A

diseases e.g. mitochondrial encephalomyopathies
from impaired oxidative phosphorylation and ATP production

34
Q

how is the ETC coupled to the phosphorylation apparatus?

A

the utilisation of the H+ gradient across the IMM by ATP synthase

35
Q

which molecules use the proton gradient across the IMM?

A

ATP synthase
Adenine Nucleotide Translocase
phosphate carriers (ANT + PC bring stuff into the mitochondria)

36
Q

what is the importance of ANT and phosphate carriers?

A

synthesis could not occur without the accessory proteins maintaining the supply of substrates

37
Q

what is the structure of ATP synthase?

A

2 large subunits: F0 and F1 head

F1 (water soluble) protrudes from IMM into matrix and is free to rotate
composed of alternating alpha and beta subunits to make hexameric ring containing ATP-hydrolysing/producing core

Fo (in the IMM): receives H+ from IMS

38
Q

what is the role of the alpha subunits of ATP synthase?

A

regulatory

39
Q

what is the role of the 3 beta subunits of ATP synthase? what are the 3 states?

A

can catalyse ATP synthesis

exist in 3 conformationally different states at any moment, 1 in each of the 3 states: open, loose, tight

40
Q

what is the open conformation of beta?

A

ADP + Pi can enter the molecule and synthesised ATP can leave

41
Q

what is the loose conformation of beta?

A

when ADP + Pi are held in place

42
Q

what is the tight conformation of beta?

A

when ATP is synthesised

43
Q

what is the order of the subunit movement in ATP synthase?

A

Fo causes rotation of F1

44
Q

what are the inhibitors of ATP synthase?

A

oligomycin and DCCD

45
Q

how can ATP synthase run in reverse? what does this result in?

A

large enough quantities of ATP present can cause creation of transmembrane proton gradient, hydrolysing ATP

mostly used in fermenting bacteria to drive flagella and transport of nutrients

46
Q

describe the structure of the Fo

A

proton pore: 8 subunits, transmembrane ring (h-l-h protein that goes through conformational changes when protonated vs deprotonated)

pushes neighbouring subunits to rotate, affecting conformation of F1: alpha and beta units switch states

47
Q

what are the subunits of Fo?

A

a: connects b to the c ring
b: a stalk that connects Fo to F1 and prevents alpha-beta hexamer from rotating
c: 8-14 subunits make up the rotor ring

48
Q

what is the purpose of Fo?

A

couples H+ translocation to the rotation that causes ATP synthesis in the F1 region

49
Q

describe the structure of the F1

A

hydrophilic
alpha and beta make a hexamer with 6 binding sites
alpha = catalytically inactive, bind ADP
beta = catalyse ATP synthesis
gamma = allows beta to go through conform changes: rotates and sits in middle of hexamer
delta = joins b of Fo to alpha
epsilon = part of rotational motor mechanism

50
Q

what is the actual role of the proton gradient in making ATP?

A

the release of the ATP from the synthase active site

51
Q

what was the experiment that allowed us to discover the structure of the F1?

A

Boyer and Walker

crystallized the F1 catalytic domain: demonstrated rotary-catalysis model correct

52
Q

how does ATP synthase generate ATP?

A
  1. transmembrane proton gradient from ETC drives H+ through a subunit of Fo region of ATP synthase

1a) a subunit contains 2 hydrophilic half channels so H+ can enter membrane but not completely cross it

1b) H+ binds to aspartate residues in c, neutralising polar amino acids glutamate + aspartate, encouraging rotation of once-polar subunit into the membrane, moves the H+ out of the hemichannel facing the IMS and into the one facing the matrix

  1. the ring of c subunits rotates as H+ pass through the membrane
  2. c ring is attached to asymm central stalk (gamma), causing it to rotate within the hexamer
  3. hexamer cannot rotate due to peripheral stalk (b + delta)
  4. causes catalytic nucleotide binding beta sites to conform change (open, loose, tight), leading to ATP synthesis
  5. once this has been repeated7-13 more times, the H+ in the hemichannel returns to where it started but can only leave ‘upwards’ i.e. into the matrix
  6. each H+ is expelled from IMS after use
53
Q

what other experiment did Boyer and Walker do to demonstrate the mechanism of ATP synthesis?

A

tethered F1 subunit of ATP synthase to a coverslip by beta subunits engineered to have tags which have high affinity for Ni.

alphabeta assembly immobilised on glass surface coated w Ni

gamma linked to fluoro labelled actin filament to provide long segment to be observed under microscope

addition of ATP caused filament to rotate as gamma rotates driven by hydrolysis of ATP (since enzyme can run backwards)

enzyme operates at near 100% efficiency and almost all energy released by hydrolysis converted to rotational motion

54
Q

how many H+ produce 1 mol of ATP

A

2

55
Q

how did experiments show that ADP, not the substrate (glucose), is the driving factor for ATP production?

A

If you put mitochondria in a sealed unit with a set amount of oxygen, oxygen levels deplete in the right environment. The addition of ADP is directly correlated with oxygen consumption, and when [ADP] drops to zero, oxygen consumption stops.

56
Q

how does NADH cross the IMM to enter the ETC?

A

malate/aspartate shuttle

[malate > oxaloacetate > aspartate] in matrix
and back again in cytoplasm

57
Q

how many H+ are extruded into the IMS for each NADH oxidised?

A

10H+

58
Q

how many H+ are extruded into the IMS for each NADH oxidised?

A

6H+

59
Q

what is the evidence for the chemiosmotic theory?

A

” proton pumping of the ETC complexes leads to generation of the PMF”

agents that collapse the PMF inhibit ATP formation

60
Q

why must ATP production match usage?

A

ATP cannot be stored and ATP molecules have a half-life in the order of seconds

61
Q

how do half channels work?

A

a subunit has 2
each interacts with 1 c subunit

has glutamate in middle, if is unprotonated, will not move into membrane, in H+ rich environment, H+ enters channel + binds glutamate, while glutamate in proton-poor environment of the other half channel releases H+

powers rotation of c ring, subunits moving into membrane due to movement of H+ from high [H+] IMS to low [H+] matrix

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