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Enzymes And Metabolism > Oxidative Phosphorylation > Flashcards

Oxidative Phosphorylation Flashcards

1
Q

What is oxidative phosphorylation

A

Mechanism of generating large amounts of ATP in a cell by chemiosmosis
Electron transfer and ATP synthesis is coupled to a proton gradient set up across IMM

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2
Q

Proton motive force

A

PMF = chemical gradient (change in pH) + charge gradient (membrane potential)
PMF drives ATP synthesis

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3
Q

What is the ETC

A

Present in IMM
Proteins free to move, dont have to be next to each other due to mobile electron carriers
E- from NADH and FADH2 passed down a series of protein complexes

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4
Q

Complex 1 overall reaction

A

NADH + Q + 5H+ —> NAD+ + QH2 + 4H+

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5
Q

Description of complex 1

A

NADH-Q Oxioreductase
FMN and FeS clusters
FMN covalently bound to protein
Accepts 2e- from NADH
Reduced to FMNH2
E- from FMNH2 passed one at a time through FeS clusters to reduce Q
Need many clusters as rate of e- movement through space very slow is carriers are more than 15A apart
When Q is reduced to QH2 it causes conformational change that opens water filled channels that allow 4H+ to pass from matrix to IMS

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6
Q

Ubiquinone (coenzyme Q)

A

Q (oxidised) —> semiquinone radical —> ubiquinol (QH2)
2 ketones reduced to 2 hydroxyl groups
Quinone ring can carry 2e-
Soluble in membrane as very hydrophobic so can move very fast
Acceptance and loss of e- is coupled to protein binding and release
Moves from complex 1 and 2 to 3

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7
Q

Cytochrome c

A

Small protein with haem group
Carries 1e-
No protons associated with its reduction

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8
Q

Complex 3 overall

A

Reduces cyt c and oxidises QH2
QH2 + 2CytCox + 2H+ —> Q + 2CytCred + 4H+

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9
Q

Complex 3 description

A

Ubiquinone-cytochrome c Oxioreductase
Whole complex is a dimer of complexes
Accepts 2e- from QH2 and passes them to cyt c
3 haem groups
Haem bH
Haem bL
Haem c1
Rieske 2Fe2S cluster with 2His and 2Cys
2 binding sites for Q
Q cycle takes place here

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10
Q

What is the Q cycle

A

Needed as QH2 carries 2e- but cyt c only accepts 1
QH2 binds to q0 site (near IMS)
1e- goes to FeS centre as it has higher reduction poteintial, then cyt c1, then to cyt c
2nd e- goes to haem bL as reduction of FeS cluster causes conformation change so it swings away from Q0, then to head bH, then to Q bound at Q1 site to form semiquinone
A new QH2 binds at Q0 site
E- go in same directions
Semiquinone fully reduced to QH2

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11
Q

Q cycle overall equation

A

2QH2 + Q + 2CtyCox + 2H+ —> 2Q + QH2 + 2CytCred + 4H+

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12
Q

Complex 4 overall equation

A

4cytCred + 8H+ + O2 —> 4CytCox + 2H2O + 4H+

For 2 e- coming from NADH or FADH2, 2 protons are pumped through complex 4 to IMS

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13
Q

Complex 4 description

A

Cytochrome c oxidase
2 haem groups
Haem A
Haem A3
2 copper centres
CUA (has 2Cu but only accepts 1 e- still)
CuB (has 1 Cu)
4 protons pumped per 4e-
Pumped through protein directly
Reduces O2 to H2O

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14
Q

Complex 2 info

A

Succinate dehydrogenase
Passes 2e- from FADH2 to QH2
FAD covalently bound to enzyme
When succinate is oxidised to fumarate FAD—>FADH2
E- pass through FeS cluster and haem to Q bound near membrane
Q picks up 2 proteins from matrix
No protons pumped or transferred

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15
Q

Number of H+ pumped or transferred by each complex

A

Complex 1 - 4H+
Complex 3 - 4H+
Complex 4 - 2H+ (per 2 e-)

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16
Q

What are uncouplers

A

Carry protons through IMM to matrix
Uncouple e- transfer from ATP synthesis
E- still pass to O2
No effect on e- transport
No ATP synthesised because protein gradient destroyed
Energy of proton gradient released as heat
E.g DNP (lipid soluble and can pick up protons in IMS)
Can be important in keeping babies and animals warm

17
Q

General ATP synthase structure

A

F1 sticks out into matrix
F0 is hydrophobic and is in the membrane
E- transport generates a PMF and ATP synthesis by ATP synthase is driven by the PMF

18
Q

F1 structure

A

3 alpha subunits
3 beta subunits
1 gamma, 1 delta, 1 epsilon
3 alpha and beta subunits arranged alternating in a ring
Gamma subunit is a long alpha helix that goes up through the middle of the ring
Alpha and beta subunits can both bind nucleotides but only beta subunits are catalytic
3 beta subunits have different conformations due to interaction with gamma subunit but have identical sequences

19
Q

F0 structure

A

Ring of identical c subunits
Number of c subunits depends on species but mammals have 8
3 subunits connect F1 to F0, collectively called the stator
Made up of hydrophobic a subunit next to c ring in IMM and 2 b subunits
Ab2 stator is connected to F0 and delta subunit of F1
Whole molecule is a rotary motor
Rotation drives atp synthesis
Stator keeps alpha beta ring stationary so gamma can rotate within it

20
Q

Binding change mechanism for ATP synthase

A

C ring rotates, causing gamma subunit to roatate, causes beta subunit to change through 3 different conformation states
1 active site in each beta subunit
Loose (L) binds ADP+Pi
Tight (T) binds ATP very tightly so ADP—> ATP
Open (O) has more open conformation so releases ATP
Rotates in steps of 120 degrees
Full 360 rotation produces 3 ATP
Each subunit changes T—>O—>L
At any given time only one subunit is in each conformation

21
Q

How does PMF drive rotation

A

Each c subunit has 2 alpha helices that span the membrane
In the middle of one of the alpha helices of each c subunit is Asp or Glu so they can pick up or release protons
A subunit has 2 half channels that dont span the membrane
H+ from IMS enter half channel on C subunit nearest half channel
On c subunit nearest matrix half channel H+ are lost
Protonated form more hydrophobic so pushes c subunits into membrane
Gain and loss of protons drives rotation of c ring
C ring rotation causes gamma subunit to rotate

22
Q

ATP/ADP translocase

A

Couples entry of ADP into matrix with exit of ATP
Pi and H+ brought into matrix
Therefore need one extra H+ for each ATP synthesised to bring in Pi

23
Q

2 methods of transport of cytoplasmic NADH from glycolysis into mitochondria

A

Glycerol-3-phosphate shuttle
Malate-aspartate shuttle

24
Q

Glycerol - 3 - phosphate shuttle

A

Dihydroxyacetone phosphate reduced to glycerol-3-p
Reoxidises NADH to NAD+
Glycerol-3-p can move to IMS
Oxidised back to dihydroxyacetone phosphate by mitochondrial glycerol-3-p dehydrogenase
Reduces FAD to FADH2
E- from FADH2 reduce Q to QH2
E- now from FADH2 so only 1.5 ATP

25
Q

Malate-aspartate shuttle

A

OAA can be converted to malate, oxidising NADH
Malate passes through IMM
Malate dehydrogenase reduces NAD+ to NADH and converts malate to OAA
OAA converted to aspartate and alpha keto glutarate that are transported back across IMM

26
Q

Difference between NAD and NADP

A

NADP has phosphate group on 2’ C of ribose
Phosphate group as no effect on e- carrying abilities
Phosphate tag allows enzymes to distinguish between them

27
Q

What is NAD for

A

Activated carrier of e- for fuel oxidation
Reduced in oxidation of fuel molecules

28
Q

What is NADP

A

E- donor in reductive biosynthesis reactions
Need high potential e- because precursors are more oxidised than products

29
Q

Why do we have different e- carriers in oxidative and reductive synthesis

A

Allows independent regulation
[NAD] can be high for catabolism and [NADPH] can be high for biosynthesis
Rato NAD/NADH kept high and ratio NADP/NADPH kept low
If using same carrier you can’t have both types of reaction occurring at same time

30
Q

Overall equation for oxidative phase of pentose phosphate pathway

A

Glucose-6-P + 2NADP + 2H2O —> 2NADPH + ribose-5-p + CO2 + 2H+
Ribose-5-P used to make nucleotides

31
Q

Allosteric regulation of oxidative phase of pentose phosphate pathway

A

NADP is an Allosteric activator of glucose-6-p dehydrogenase

32
Q

Non oxidative phase of pentose phosphate pathway

A

Just molecular rearrangements occurring
Coverts ribulose-5-p back to 2 molecules of fructose-6-p and one glyceraldehyde-3-p
Using transketolases and transaldolases
If nucleotides not needed, ribulose-5-p converted back to intermediates of glycolysis or gluconeogenesis

33
Q

What happens in oxidative phase of pentose phosphate pathway

A

Glucose-6-p —> 6-phosphogluconolactone produces 1 NADPH from NADP
6-phosphogluconolactone —> 6 phosphogluconate
6phosphogluconate —> ribulose-5-p produces 1 NADPH
Ribulose-5-p <—> ribose-5-p

34
Q

Uses of NADPH

A

Reductive biosynthesis in tissues that synthesise FAs or for cholesterol/steroid hormone synthesis
Used to prevent oxidative damage in all cells, particularly RBC

35
Q

What is GSH (reduced)

A

Tripeptide antioxidant in cytoplasm
Keeps cytoplasm as a reducing environment
Glutamate linked to cysteine by a gamma peptide bond
Gamma-Glu-cys-gly
Reduces ROS and keeps protein SH groups in reduced form

36
Q

What is GSSG

A

Glutathione (oxidised)
2 cys form disulphide bond

37
Q

Role of NADP in maintaining levels of GSH

A

Reduces GSSG to 2GSH
GSH can then reduce H2O2 to H2O
Important in RBC as they are directly exposed to oxygen

38
Q

Fates of G-6-P

A

Key intermediate in carbohydrate metabolism
Converted to G-1-p for UDP-glucose
Used in glycolysis to make pyruvate
Used in pentose phosphate for ribose-5-p and NADPH
Used in liver for glucose

Enzymes And Metabolism (4 decks)

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