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Y2 Biostructures > Content I missed > Flashcards

Content I missed Flashcards

1
Q

How is light absorption maximised in chloroplasts?

A

Antenna proteins are non-covalently bound to proteins and provide a large spatial cross section for absorption

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2
Q

What happens in cyt b6f?

A

Bifurated electron transfer:
When a PQH2 molecule is oxidised, two protons move into the lumen, creating a proton gradient. One electron is stored on haem C and another electron reduces Pc.

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3
Q

What is the redox potential across PSI?

A

P700+/P700 redox couple is +480mV
This can reduce free floating 4Fe-4S clusters which reduce 2Fe-2S clusters on feerodoxin (-420mV). Pc oxidation is +370mV

-790mV

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4
Q

What is the energy budget of linear electron transfer compared to cyclic electron transfer?

A

Linear- 1.28ATP per NADPH
Cyclic- 1.5ATP per NADPH

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5
Q

What is the speed of internal conversion between S2 and S1 compared to S1 and S0?

A

S2 –> S1 10^-12S
S1 –> S0 10^-9S

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6
Q

How are C type haems linked to cyt b6f?

A

Covalent bonds

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7
Q

How are B type haems linked to cyt b6f?

A

Coordination bond with Fe ions

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8
Q

What do α subunits in ATP synthase do?

A

Play a structural role

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9
Q

What do β subunits in ATP synthase do?

A

Catalyse ATP production and releasing it

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10
Q

What does thioredoxin detect?

A

Changes in redox state of the stroma due to reduction of Fd and NADP+.

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11
Q

What does thioredoxin regulate?

A

Calvin cycle enzymes

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12
Q

How does CO2 react with RuBP?

A

CO2 reacts with the lysine residue in rubisco which forms a carbonate ion. This is attracted to Mg2+ which activates RuBP.

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13
Q

Why are thioester bonds favourable in group carriers?

A

They are less stable than ester bonds so are ideal for donating groups. E.g in Coenzyme A

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14
Q

Which isozyme subunit of lactate dehydrogenase is inhibited by pyruvate?

A

H form as the M form is more favourable under aerobic conditions

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15
Q

Outline the alanine transaminase reaction?

A

Glutamate + Pyruvate <-> Alanine + α-ketoglutarate

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16
Q

What stimulates the pentose phosphate pathway?

A

Low NADPH and low ribulose

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17
Q

What cofactors do the link reaction have?

A

pyrophosphate, thiamine, lipoic acid, FAD, CoA, NAD

18
Q

Outline pyrimidine synthesis

A

Bases are assembled by adding amino acids to ribulose from PPP. Ribose is then attached

19
Q

Outline purine synthesis

A

Rings assembled onto ribose and groups added bit by bit
Ribose activation is very intense: 2 ATP to activate bicarbonate and add it onto ribose

20
Q

How is phophatetidylethanolamine structured and where does it usually sit in cell membranes?

A

Small phosphate head, allowing curvature and it is usually in the inner monolayer

21
Q

How is phosphatidylserine moved in plasma membranes in response to apoptosis?

A

PS moves to the surface of plasma membranes signals to macrophages to phagocytose and digest the dead cell.
1. Phospholipid translocators transport PS to the inner monolayer. These are deactivated
2. Scramblase is activated, allowing phospholipids to transfer to both sides of the membrane non-specifically

22
Q

Outline a Gq protein coupled response

A
  1. A Gαq subunit stimulates phospholipase C
  2. Phospholipase C cleaves phosphatidylinositol phospholipid (PIP2) in the cytoplasmic monolayer of the plasma membrane
  3. This splits into protein kinase C and IP3. PKC remains in the membrane and IP3 stimulates Ca2+ release from the endoplasmic reticulum
23
Q

What increases plasma membrane fluidity?

A

Cis fatty acids
Phospholipids
Cholesterol squashing against fatty acids
Shorter fatty acids

24
Q

What are the 5 main ways of changing membrane curvature?

A

Changing lipid composition
Amphipathic helix insertion
Indirect scaffolding
Actin cytoskeleton pushing the membrane out
Microtubule motors

25
Q

Which phospholipids facilitate positive membrane curvature?

A

PI and PC

26
Q

Which phospholipids facilitate negative membrane curvature?

A

PE

27
Q

Give 4 functions of membrane rafts

A

Concentrate proteins for signal transduction
Organising the start of endocytosis
T cell activation
Bridging gaps between differently sized membranes

28
Q

How do voltage gated Na+ channels open and close?

A

They have a plug which has voltage-sensing α-helices which move up or down depending on the side they are attracted to

29
Q

How is a G protein switch turned off?

A

GAP hydrolyses GTP to GDP which is bound to a phosphate.
This binds Thr35 and Gly60 to closes switches 1 and 2 respectively

30
Q

What is a similarity between rhodopsin and β-adrenergic receptor

A

Locations of 11-cis retinal

31
Q

Which residues flip water dipoles in aquaporins?

A

Asn76 and Asn192

32
Q

What does the NPA motif do in aquaporins?

A

Prevents ions moving through the middle of the channel

33
Q

What does histidine do in aquaporins?

A

Makes a size restriction to prevent water moving through

34
Q

What does arginine do in aquaporins?

A

Keeps protons out of the aquaporin with electrostatic respulsions

35
Q

Which residues carry the proton in bacteriorhodopsin?

A

Asp96
Retinol- Lys216 schiff base
Asp85

36
Q

How does rhodopsin wave absorption compare to that of transient receptor potentials (TRPs)?

A

The extinction coefficient is 100 times greater

37
Q

How is the positive charge of the protonated schiff base on retinal in rhodopsin compensated for?

A

Glutamate counterion on helix 2

38
Q

Outline the order of the rhodopsin cycle

A

Retinal (11-cis retinal, red)
Bathorhodopsin (all-trans retinal)
Lumirhodopsin
Metarhodopsin I
Metarhodopsin II
Free-all trans retinal (white)

39
Q

Name some properties of detergents

A

Amphiphilic- crucial for ejecting proteins
More water soluble than lipids
Alter surface tension

40
Q

What are the main limitations of cryo-em?

A

Limited to large particles (>500kDa)
Resolution limited to 10Å, unless the molecule has high symmetry

Y2 Biostructures (5 decks)

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