modular structure of proteins

Question 1

what’s evolutionarily significant about motifs and domains

Answer 1

commonly found and conserved across functionally related proteins

Question 2

what is a motif

Answer 2

minimum arrangement of independently forming secondary structures combining recognisable folds/arrangements across many different proteins

Question 3

what’s a domain

Answer 3

more complex structure, at the 3* or 4* level, often involving interaction between distant motifs on separate chains

Question 4

what does an EF hand motif do

Answer 4

Ca2+ binding e.g. calmodulin and troponin C

Question 5

what does a DNA binding motif do

Answer 5

helices can be inserted into the major groove of DNA in a sequence specific manner

Question 6

where can a helix loop helix motif be found

Answer 6

Max, Mad, Ca2+ binding

Question 7

where can a helix turn helix be found

Answer 7

Cro, trypt, lac repressors

Question 8

where can you find a leucine zipper

Answer 8

GCN4

Question 9

where are there zinc fingers

Answer 9

hormone receptors

Question 10

what shape is a greek motif

Answer 10

antiparallel beta strands - so common that it’s not associated with a specific function

Question 11

the domain represented in membrane bound receptors is the most easily understood functional domain - give an example

Answer 11

7 transmembrane arrangement of alpha helices in a G protein coupled receptor

Question 12

where can you find a 7 TM arrangement of alpha helices

Answer 12

rhodopsin, TSHr, many pharmacological receptors, and also receptors for some polypeptide hormones

Question 13

how many domains in PLC

Answer 13

4 - each found individually in other proteins eg troponin C, bacterial PLC, recoverin, synaptotagmin

Question 14

Hb and myoglobin chains have a similar 3* structure - what does that suggest?

Answer 14

common ancestral O2 - binding polypeptide

Question 15

why are alpha helices important in DNA binding

Answer 15

can fit within DNA major groove - AA sequence of a DNA binding motif provides specificity

Question 16

what’s important about how the helix loop helix motif binds DNA

Answer 16

only binds DNA in the dimeric form, but can be hetero or homodimers

Question 17

describe the structure of a helix loop helix motif

Answer 17

central portion formed from overlapping helices forms structure that enables dimerisation
the terminal part of the lower opposing helices contain basic AAs that interact w/ the major DNA groove, giving rise to a b/HLH domain

Question 18

what is a leucine zipper motif formed from

Answer 18

2 contiguous alpha helices - it’a a dimeric protein formed from 2 pp chains

Question 19

how do the dimers that make up a leucine zipper polymerise

Answer 19

dimers zip together in the top ‘stalk’ to form a short coiled coil

Question 20

what holds together the coil in a leucine zipper

Answer 20

hydrophobic interactions down opposing sides of the helix

Question 21

how is the regulatory potential of leucine zippers increased

Answer 21

heterdimerisation

Question 22

how is a helix turn helix motif structured

Answer 22

consists of 2 short helices orientated at right angles to each other and connected by a turn

Question 23

where is ‘helix turn helix’ found

Answer 23

pro and eu DNA binding proteins eg CRO repressor and homeobox proteins

Question 24

what does the CRO protein do

Answer 24

homodimer that recognises palindromic sequences and represses transcription by binding DNA.

Question 25

how does the helix turn helix work

Answer 25

interacts with the nucleotide sequence itself and locates within the major groove

Question 26

structure of the zinc finger motif

Answer 26

alpha helix and beta sheet, held together by noncovalent interactions with zinc

Question 27

how does the zinc finger motif work

Answer 27

alpha helix of each motif interacts with the major groove and recognises a specific DNA sequence

Question 28

where are zinc fingers found

Answer 28

hormone receptors eg glucocorticoids, mineralcorticoids, oestrogen, progesterone, vit D receptors.