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Flashcards in Lecture 2 Deck (34)
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1

Explain how zinc finger domains interact with DNA

Zinc fingers consist of an ? helix and a ? sheet region linked together. The ? helical region rests in the major groove of the DNA with amino acid side chains that interact directly with DNA bases via hydrogen bonds. The identity of these interacting side chain amino acids in the helical region of the domain determines which bases it interacts with.

2

Give some examples of aromatic amino acids

Tyrosine, proline

3

Which metal ions bind to their binding domain and have a structural role, give some examples of protein that contain these domains

Zn2+ ions bind to zinc domains. Examples of proteins with these domains include botulinum toxin, zinc fingers and DNA binding proteins

4

Give an example of protein that contains EF-hand domains and describes its role

Calmodulin kinase – requires Ca2+ binding for its structure and regulation. Calmodulin is formed of a single polypeptide chain and contains N and C-terminal globular domains separated by an extended central helix. Each globular domain contains two high-affinity Ca2+ binding sites. Binding of four Ca2+ ions induces major allosteric changes in calmodulin. The two globular heads rotate relative to eachother enabling calmodulin to bind to target proteins and regulate their activity

5

Which metal ion binding domains have a regulatory role and give some examples of proteins that contain these domains

Ca2+ binding domains have a regulatory role. These include calmodulin and synaptogenin

6

Binding of SH2 domains to their phosphotyrosine ligands is involved in the formation of signalling complexes, T or F

T

7

Leucine zipper domains are protein-protein binding or protein-DNA binding domains, T or F

T

8

How does SH3 bind its ligand

Via aromatic amino acid stacking

9

What is the role of SH3 domains

SH3 domains bind to proline-rich motifs (poly-proline regions) and acts as an adaptor domain to link proteins together

10

Which metal ion(s) bind to catalytic metal ion domains

Fe2+ or Cu2+

11

Describe the role of zinc finger domains

Zinc finger domains are found in the most frequency classes of transcription factors and are DNA binding domains that recognise 3-base pairs of double-stranded DNA

12

Phosphatases and kinases used PH domains and have a direct role in lipid signalling, T or F

F – kinases and phospholipases contain PH domains involved in lipid signalling

13

What does SH3 stand for

Src homology 3 domain

14

Describe the basic structure of an EF-Hand domain

Consists of two ? helices linked by a short loop region of around 12 amino acids that bind to Ca2+

15

What are EF Hand domains

Ca2+ binding domains that have a regulatory or structural function

16

What do SH2 domains bind to

Phosphorylated tyrosine residues

17

EF-Hand motifs bind cations via 5 oxygen containing amino acid side chains, T or F

T

18

What do SH3 domains bind to

Proline-rich motifs

19

What do PH domains bind to

Phosphoinositide lipids

20

What does SH2 stand for

Src homology 2 domain

21

What is the role of SH2

Acts as an important phosphotyrosine binding domain that is often involved in signalling mechanisms

22

What is meant by PH domains and what is their function

Pleckstrin homology (PH) domains are involved in membrane binding with functions in signalling and the anchoring of proteins into the membrane

23

Explain the different functions of zinc finger domains in different proteins

Zinc fingers perform a structural function in protein-DNA interactions or a catalytic function in proteins such as botulinum toxin

24

What aspect of the SH2 domain provides specificity

Specificity comes from the interaction between the phosphate of the phosphotyrosine and consists of mainly ionic interactions between the negatively charged PO42- and positively charged amino acids. Some hydrogen bonding also contributes

25

What is the significance of tandem zinc finger repeats usually found in proteins

Tandem zinc finger repeat domains occur as part of larger DNA binding regions. Proteins with more zinc fingers can recognise longer sequences

26

How do aromatic amino acids interact with water

They don’t, aromatic amino acids are hydrophobic

27

What is meant by the minimum consensus sequence for SH3

The smallest region which SH3 will bind to. This is the P-x-x-P motif consisting of a 4 residue sequence with first and last residues being prolines

28

To which domain does Zn2+ bind in a structural mode

Zinc finger domains

29

Different sizes and valencies of metal ions are liganded by different numbers of amino acids and have different structural requisites, T or F

T

30

SH3 recognises proline-rich motifs, how does aromatic stacking account for the interdigitating of tyrosine residues with the target poly-proline domains

Aromatic stacking is the process by which the tyrosines contained within the SH3 domain interdigitate with proline residues within the binding proteins target domain. This is caused by an interaction between the aromatic side chains of tyrosine and proline residues with hydrogen atoms attached to the adjacent aromatic ring. This interaction is a dipole-dipole interaction due to the ?- aromatic rings and the ?+ hydrogen atoms. The aromatic residues (tyrosine) of the SH3 domain are positioned so that they can stack with aromatic (proline) residues contained in the proline-rich motifs