Bullough

Question 1

differences between internal lipid anchors

Answer 1

prenylation: thioester link, C-terminal cytosine, polymer of isoprene, post-translational
acetylation: amide bond, N-terminal glycine, carboxylic acid, co-translational

Question 2

carrier (membrane protein)

Answer 2

no channel all the way through, only open one side at a time
shows Michalis-Menton kinetics as it as a saturable binding site
eg. Glut1 as glucose it to be transported through a channel, ion gradient would dissipate

Question 3

what is the selective part of KcsA

Answer 3

the selectivity filter on the pore helix, carbonyls

Question 4

what is KcsA

Answer 4

a potassium channel

Question 5

what are the ionic radii of Na+ and K+

Answer 5

Na+ = 0.95Å
K+ = 1.33Å

Question 6

what are energies of hydration on Na+ and K+

Answer 6

Na+ = 301 kJ mol-1
K+ = 230 kJ mol-1

Question 7

what is KvaP

Answer 7

a voltage gated potassium channel

Question 8

what is the lever helix of KvaP

Answer 8

helix 4 which moves the gate into open or closed
contains positively 4 charged arginine residues
decrease in voltage closes the gate

Question 9

what happens when light hits the retinal of bacteriorhodopsin

Answer 9

all trans –> 13-cis

Question 10

which residues in bacteriorhodopsin are responsible for the movement of protons

Answer 10

D = aspartate
D85 - counter ion (negative) to retinal (Schiff base)
D96 - close to cytoplasmic entrance

Question 11

what is the structure of retinal

Answer 11

ring - (in a tight space)
polyene chain
link to a lysine (forming a Schiff base)

Question 12

what is the pathway of a proton through bacteriorhodopsin

Answer 12

1. starts as part of a Schiff base on retinal goes to D85
2. then outside the cell
3. a new proton enters the cell binding to D96
4. this proton then reprotonates retinal
   the deprotonation of D96 is allowed because it changes pKa when the strain moves helix F - opening up the vestibule and making it more aqueous

Question 13

what happens when light hits retinal in rhodopsin

Answer 13

11-cis –> all trans

Question 14

what is the G protein complex called in rhodopsin

Answer 14

transducin

Question 15

how does signalling rhodopsin differ from a normal GPCR

Answer 15

when G-alpha is activated (GDP–>GTP) it activates phosphodiesterase which causes an decrease of cGMP
therefore cGMP gated ion channel closes and the membrane becomes hyperpolarised

Question 16

what is the CMC

Answer 16

critical micellar concentration - when detergents form micelles

Question 17

what are detergents

Answer 17

amphipathic molecules
polar/ionic (harsher) headgroup
hydrophobic tail

Question 18

what do you need to determine the structure of a protein from x-ray crystallography

Answer 18

Fournier transformation
amplitude = intensity of scatter pattern
phase = spacial info cannot be measured needs heavy ions

Question 19

what is the set up of cryo-EM

Answer 19

film of protein, frozen using liquid ethane so the ice does not crystallise
proteins can be in different directions and different conformations
EM to take pictures from differnet angles –> software to make it 3D

Question 20

size restriction in aquaporin

Answer 20

histidine bulky residue - ring

Question 21

electrostatic repulsion in aquaporin

Answer 21

R - repels H+

Question 22

dipole reorientation in AP

Answer 22

D

Question 23

what is recovery (GLUT1)

Answer 23

resetting