Modular Structure of Proteins

Question 1

what is a motif?

Answer 1

the minimum arrangement of independently forming 2° structures combining recognisable folds across many different proteins

Question 2

how are motifs organised?

Answer 2

organised into lager structural and functional domains

Question 3

what are domains?

Answer 3

more a more defined functional unit than a motif

Question 4

what is the function of domains?

Answer 4

usually they are responsible for a particular function or interaction, contributing to the overall role of a protein.

Question 5

how many structural motifs exist?

Answer 5

1400-1500

Question 6

what are some examples of motifs?

Answer 6

• EF hand

- Greek key

Question 7

what are the functions of DNA binding motifs?

Answer 7

arranged to recognise specific sequence of bases

Question 8

what are examples of DNA binding motifs?

Answer 8

• helix-loop-helix
• helix-turn-helix
• leucine zipper
• zinc finger

Question 9

what do all DNA binding motifs have in common?

Answer 9

all have α helices that are inserted into the major groove of the DNA sequence in a specific manner

Question 10

what are properties of the EF hand motif? and give an example

Answer 10

• resembles alpha helix-turn-helix
• but combines with a metal ion such as calcium

-(eg. Calmodulin, Troponin, etc. Calmodulin contains four EF hands, each binding to a single calcium ion)

Question 11

what are properties of a greek key motif?

Answer 11

• consist of antiparallel β strands

- motif that is so common that it isn’t generally associated with a specific function

Question 12

what is domain shuffling?

Answer 12

-domain shuffling is where gene segments coding for functional domains are shuffled between different genes during evolution

Question 13

what do transcription factors have in common across eukaryotes?

Answer 13

• there are many different transcription factors but they each contain a small number of conserved motifs which combine to form domains that interact with the DNA.
• these motifs are conserved across all phyla (ie huge variety of eukaryotes, ranging from fungi to plants and animals).
• these motifs form DNA binding domains that allow the regulatory function of their respective proteins.

Question 14

explain the importance of α helices

Answer 14

• can fit in major groove of DNA
• aa sequence of DNA binding motif provides specificity
• diff DNA binding domains and. motifs present binding helix using diff arrangements of structural motifs

Question 15

give some properties of the helix loop helix motif including what the central and terminal parts are made of and give examples

Answer 15

• binds to DNA in dimeric form
• exists as hetero- (different monomers) or homodimers (same monomer)
• central portion made of overlapping helices that form structure to enable dimerisation
• terminal part of opposing helices have basic aa that interact w major groove of DNA
  eg: mad, max, myc, myoD

Question 16

describe the leucine zipper motif

Answer 16

• resembles helix-loop-helix but formed from 2 contiguous α helices and dimeric protein formed form 2 polypeptides
• dimers ‘zip’ together in top ‘stalk’ to form short coiled coil
• basic aa dominate lower part of helix and interact w major groove
• heterodimerisation expands regulatory potential of leucine zippers
  eg: cFos, cJun

Question 17

describe the helix loop helix

Answer 17

• 2 short helices oriented at 90 ° and connected by ‘turn’
• found in prok. + euk. DNA binding proteins
• only recognition helix interacts w nucleotide sequence and locates within major groove
  eg: CRO, lambda repressors

Question 18

what does the CRO repressor do?

Answer 18

• is a homodimer

- recognises palindromic sequence by binding to DNA and repressing transcription

Question 19

describe the zinc finger motif

Answer 19

• α helix nad β sheet held together by non-covalent interactions w Zn
• α helix of each motif interacts w major groove and recognises specific DNA sequence
• other parts of dimer contributes to DNA binding domain in addition to each of the motifs
• other parts form diff functions domains
  eg: glucocorticoid, progesterone, vitamin D