membrane proteins

Question 1

four major classes of lipids

Answer 1

phospholipids- ester bonds
sterols- cholesterol
sphingolipids - major in neuronal membrane
primary found in plasma membrane
glycolipids- found on the outside of cell
synthesised in ER/golgi

Question 2

what causes the classic bilayer

Answer 2

POPC

Question 3

conical

Answer 3

hexagonal phase
maximises hydrophobic out and
hydrophilic in
vesicles support conical bilayer

Question 4

micelle shape

Answer 4

hydrophobic roots are on the inside

Question 5

overall shape of lipid effects what

Answer 5

phase adapted

Question 6

bilayer structure

x-ray/ neutron diffraction facts

Answer 6

doesnt need to be a crystal
can use on any repeated pattern
scatter tells us the spacing between repeated structures

Question 7

waves get scattered when it hits the bilayer

what law do they follow

Answer 7

Braggs law:
n(lambda)=2dsin (thita)
d is spacing

Question 8

influence of bilayer on protein structure

4 points

Answer 8

protein must interact with hydrophobic bilayer core
must cope with changes in environment at bilayer surface
bilayer highly dynamic, but solid interface required from both protein and bilayer integrity
must provide architecture to carry out its function

Question 9

membrane protein structure

what do you consider

Answer 9

thermodynamics

maximise h-bonds to get the lowest free energy

Question 10

what happens when inserting protein sidechains into the bilayer?

Answer 10

-ch3 and -ch2

will cause vdm giving us hydrophobic port

Question 11

key points for membrane protein

Answer 11

maximise the number of hydrogen bonds

choose your aa sequence carefully

Question 12

secondary structure of membrane proteins

what do they achieve

Answer 12

no N-h or carbonyl groups that are unpaired

maximising the number of H-bonds

Question 13

alpha helical transmembrane domains

what do the side chains provide

Answer 13

all side chains are pointing away from core of the helix

interacts with bilayer

Question 14

length of alpha helical TM domains

Answer 14

each AA gives a rise of 1.5A
bilayer about 36A long
so at least 24 residues to cross the bilayer
acyl chains that are shorter make the bilayer thinner

Question 15

hydrophobic aa are located in the hydrophobic core on the membrane what are they

Answer 15

ala
val
leucine
isoleucine

Question 16

aromatic residues what do they provide

Answer 16

around head group

because they are amphipathic they can change switch from hydrophobic to phillic

Question 17

what aromatic residues are they

Answer 17

phenylalanine
tysosine
tryptophan

Question 18

positive inside rule

Answer 18

arg and lys

found on the inside

Question 19

helix packing

what are the crossing angles

Answer 19

-37
+83
+22

Question 20

TM helical packing normally occurs between

Answer 20

+5 and +25

antiparallel packing preferred

Question 21

helix interactions promoted by

small sidechain:

Answer 21

spacially Gs are 1 above each other

• maximises interactions between species
• this causes a gap

Question 22

helix interactions promoted by

polar residues:

Answer 22

generates stable interactions between 2 TM domains

Question 23

identification between membrane proteins

Answer 23

kyte-doolittle plots

based on hydrophobicity of aa

Question 24

what does the 7 regions of hydrophobicity give us

Answer 24

they give us 7 regions of TM domains

Question 25

orientation depends on what

Answer 25

on length of TM domain and bilayer thickness

Question 26

what are involved in helical packing

Answer 26

charged groups

Question 27

beta barrel proteins | facts

Answer 27

``` 7 residues needed to cross membrane typical strands 9 - 11 slanted by 45 degrees 10 aa that hydrogen bond per strand size of pore determined by number of strands ```

Question 28

connection between beta strands

Answer 28

connections between extracellular loops tend to be long and have high sequence variability periplasmic loops are typically small formed by tight loop turns

Question 29

short loops formed by beta turns what are the types

Answer 29

type 1 beta turn | type 2 beta turn

Question 30

distribution of residues in a beta barrel

Answer 30

internal cavity - depends on its function even distribution of aa aa can flip from 1 side to another

Question 31

lots of sugar residues interact with

Answer 31

tyr phe trp

Question 32

what buffers between lipids and water

Answer 32

aromatic aa

Question 33

roll of extracellular loops

Answer 33

loops cause constriction in pores residues on loops can contribute to selectivity long loops which fold over carry out a lot of these functions