Honours lectures (chose no 3)

Question 1

what are the methods to determine protein structures?

Answer 1

x ray crystallography
NMR
molecular modelling

Question 2

describe x ray crystallography

Answer 2

shine x rays through a crystal of a molecule.
crystal refract x rays, can analyse the pattern.

hard to get the crystals in the first place for proteins. proteins dissolved in lipids, need to place it in water.

membrane proteins don’t like being in solution.

Question 3

what is a template?

Answer 3

homology modelling

a protein who’s structure we can solve, that can be used as a starting point for other proteins.

line up primary sequence so TMD are next to each other, use a computer model to fill in the bits in-between.

Question 4

what is halobacterium halobium?

Answer 4

archae bacteria kingdom, live in extreme environments.
very high salt conditions.
Gets it’s energy from bacteriorhodopsin, photopigment.
grows in large quantities.

has a 7 transmembrane structure when crystallised. similar to GPCR. used as a template.

Water in which H. halobium grows can take on a purple colour idue to the presence of bacteriorhodopsin – this forms very high density crystal like arrays in the membrane of H. halobium

Question 5

how do protein super families evolve?

Answer 5

duplication of a protein, a mutation on the copy doesn’t affect the function of the original.

Question 6

what are the families of GPCR?

Answer 6

A B C D.
A rhodopsin (eye pigment)
B secretin
C metabotropic glutamate
D others

Question 7

Describe family A.

Answer 7

rhodopsin (activated by light)
acetylcholine
noradrenaline
histamine
dopamine
cannabinoids

19 subgroups. A1-A19
most monomers

Question 8

describe the structure of family A

Answer 8

Note the ligand binding domains are buried in the membrane.

7TMD

Question 9

Describe family C

Answer 9

GABAb
metabotropic glutamate
calcium sensing receptors

form dimers, not all monomers.

Question 10

describe the structure of family C

Answer 10

much larger extracellular domain, has a venus fly trap domain with an agonist binding site.
7TMD

allosteric ligand site, drugs can bind even though agonist like glutamate and GABA don’t.

Question 11

Describe the GABAb receptor.

Answer 11

family C

GABAB1 and GABAB2
B1 binds to the agonist, B2 interacts with the G protein.