Modular structure of proteins

Question 1

Name examples of the molecular interactions of a protein

Answer 1

Electrostatic - Carboxyl COO- and amine NH3+
Hydrogen bonding - Secondary amine NH, carbonyl C=O groups, hydroxyl OH
Non-polar/hydrophobic interactions -> Hydrocarbon
Covalent boding - Disulphide bonds

Question 2

What is a protein sequence motif?

Answer 2

A pattern of amino acids that are found in related genes or proteins

Question 3

Define a motif

Answer 3

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

Or

A combination of two or more secondary structures to form a recognisable localised folded arrangement of structure

Question 4

What is the difference between motif and domains

Answer 4

Domains more clearly define a functional unit than a motif but both are evolutionarily conserved and are modular in nature

Question 5

What is a definition of a domain

Answer 5

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

Question 6

Describe the EF hand

Answer 6

Calcium binding motif found in e.g. calmodulin and troponin-C. Combines with calcium, two hands at either end connected by an alpha helix

Question 7

Describe the Greek Key

Answer 7

Specific arrangement of beta strands forming antiparallel beta sheet

Question 8

Describe the beta barrel

Answer 8

Beta strands wrapped around to form circular tunnel

Question 9

Describe the alpha beta barrel

Answer 9

Parallel strands of a beta sheet interlinked with a alpha helix to form a beta-alpha-beta motif

Question 10

What happens as a result of domain shuffling in the genome

Answer 10

Modular units of function being conserved but shuffled between genes

E.g. mammalian phospholipase C contains 4 different recognisable domains. These can each be found individually in other proteins

Question 11

Describe myoglobin and haemoglobin’s relation

Answer 11

Haemoglobin chains have a similar tertiary structure to the single myoglobin chain, suggesting evolution from an ancestral oxygen binding polypeptide

Question 12

How are motifs used in DNA binding

Answer 12

The amino acid sequence of a DNA binding motif provides specificity

Different DNA binding domains and motifs present the binding helix using different arrangements of the structural motif

Question 13

Describe the helix-loop-helix motif

Answer 13

Binds DNA only in the dimeric form

Exists as hetero and homodimers

Central portion made from overlapping helices

Terminal part of lower opposing helices contain basic amino acids that interact with the major groove of the DNA - b/HLH functional domain

Question 14

Describe the leucine zipper motif

Answer 14

2 contiguous alpha helices and like the HLH, is a dimeric protein formed from two polypeptide chains

The dimers zip together in the top stalk to form a short coiled-coil

The coil is held together by hydrophobic interactions down opposing sides of the helix

As in the b/HLH basic amino acids dominate the lower part of the helix and interact with the DNA major groove

Heterodimerisation expands the regulatory potential of leucine zippers

Question 15

Describe the helix-turn-helix motif

Answer 15

Two short helices orientated at right angles to each other, connected by a turn

Motif found in both prokaryotic and eukaryotic DNA binding proteins

CRO protein is a homodimer

CRO recognises palindromic sequence and by binding DNA represses transcription

Only the recognition helix interacts with the nucleotide sequence itself and like other DNA binding motifs it locates within the major groove

Question 16

Describe the zinc finger motif

Answer 16

Alpha helix and a beta sheet held together by non-covalent interactions with zinc

Motif on polypeptide chain containing zinc atom stabilising the recognition helix and loop structure

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