Modular structure of proteins

Question 1

What is a structural motif

Answer 1

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

Question 2

How does a motif and domain differ

Answer 2

A domain more clearly defines a functional unit

Question 3

How are motifs and domains similar

Answer 3

both are modular in nature and both are evolutionarily conserved

Question 4

What is a domain

Answer 4

A complex structure at the tertiary or quaternary level, often involving interaction between distant parts of a protein or motifs

Question 5

EF hand motif

Answer 5

Calcium binding motif
Resembles a helix turn helix with a metal ion such as calcium that stabilises the overall structure
Calmodulin has 4 EF hand motifs

Question 6

Greek key motif

Answer 6

Consists of antiparallel beta strands that generally isnt associated with a specific function

Question 7

Beta barrel motif

Answer 7

Beta strands forming beta sheets which are wrapped around to form a circular tunnel

Question 8

Beta-alpha-beta motif

Answer 8

Two parallel strands of a beta sheet interlinked with an alpha helix

Question 9

What are DNA binding motifs

Answer 9

They are helices which can be inserted into the major groove of DNA, often dimerise creating a a larger and more complex DNA binding domain

Question 10

What is a membrane bound receptor domain

Answer 10

Bundles of alpha helices or beta sheets

Question 11

What is the extracellular region

Answer 11

ligand binding domain

Question 12

What is the transmembrane region

Answer 12

Domain that anchors the protein to the membrane and embeds it into the lipid bilayer

Question 13

What is the intracellular region

Answer 13

Domain that interacts with the interior of the cell or organelle relaying the signal

Question 14

What does domain shuffling achieve

Answer 14

Results in modular units of function being evolutionarily conserved

Question 15

Helix-loop-helix motif structure and function

Answer 15

• DNA binding motif in the dimeric form
• Central portion formed from overlapping helices that allow for dimerisation
• Terminal parts contain basic amino acids that interact with the positively charged major groove of DNA

Question 16

What is the advantage of helix-loop-helix motifs being able to form heterodimers

Answer 16

Extends the functionality of individual proteins as different monomers can join together allowing the regulation of different genes in different ways in response to different stimuli

Question 17

Leucine zipper motif structure

Answer 17

Formed from 2 contiguous alpha helices, the dimers zip together forming a coil a the top
The coil is held together by hydrophobic interactions down opposing sides of the helix
The basic amino acids are also on the lower part of the helix

Question 18

Helix-turn-helix structure

Answer 18

Consists of two short helices oriented at right angles to each others and connected by a ‘turn’

Question 19

Where are H-T-H found

Answer 19

In eukaryotic and prokaryotic DNA binding poteins e.g. CRO repressor and homebox proteins

Question 20

What does the CRO repressor do

Answer 20

Recognises palindromic sequences and binding to the DNA it represses transcription

Question 21

Zinc finger motif

Answer 21

It is an alpha helix and a beta sheet held together by non-covalent interactions with zinc

Question 22

Where do you find zinc finger motive

Answer 22

In manu ornate receptors e.g. glucocorticoid, mineralocorticoid, oestrogen, progesterone and vit D receptors