MolBio1 - 32

Question 1

List 9 common protein modifications

Answer 1

Glycosylation, lipid addition, phosphorylation, hydroxylation, methylation, acetylation, ubiquitination, SUMOylation, oxidation

Question 2

Describe the effects of protein phosphorylation

Answer 2

Addition of PO4-, adding mass, charge and altering conformation

Question 3

How does protein phosphorylation commonly act?

Answer 3

To alter protein function is a positive way

Question 4

What two kinds of ubiquitination are common, and what is their signal?

Answer 4

Poly = degradation; mono = recycling

Question 5

What is SUMOylation?

Answer 5

Small Ubiquitin-related Modifier (12kDa protein) added

Question 6

What is the function of SUMOylation?

Answer 6

Protein stabilisation and targetting to nucleus

Question 7

What are protein domains?

Answer 7

Segments of proteins conserved through evolution that have functionally similar structures

Question 8

List 6 commonly occuring domains

Answer 8

SH2, SH3, pleckstrin homology domain, zinc finger, EF hand and leucine zipper

Question 9

What does SH stand for in SH2 and SH3?

Answer 9

Src Homology

Question 10

What does SH2 do?

Answer 10

Binds phosphorylation tyrosine

Question 11

What does SH3 do?

Answer 11

Binds proline rich motifs

Question 12

What does pleckstrin homology domain do?

Answer 12

Binds phospholipids

Question 13

What does the zinc finger domain do?

Answer 13

Binds zinc

Question 14

What does the EF hand do?

Answer 14

Binds calcium/magnesium

Question 15

What does the leucine zipper domain deal with?

Answer 15

Protein-protein or protein-DNA interactions

Question 16

What is SH2 usually involved in?

Answer 16

Signalling mechanisms

Question 17

What characterises SH2 binding site?

Answer 17

Particular positive area that attracts negatively charged p-Tyr

Question 18

What dictates SH2 interaction?

Answer 18

Ionic specificity between negative phosphate group and positive a/a’s

Question 19

How does SH3 usually act?

Answer 19

As an adaptor to link proteins

Question 20

What is the minimum consensus sequence for SH3 binding?

Answer 20

PxxP

Question 21

Describe aromatic stacking.

Answer 21

SH3 has several aromatic residues - these interdigitate between prolines and stabilise the PxxP motif

Question 22

What roles does pleckstrin homology domain take?

Answer 22

Signalling and anchoring proteins to membranes

Question 23

What typical metal ion binds for structural roles?

Answer 23

Zinc

Question 24

What typical metal ion binds for regulatory roles?

Answer 24

Calcium

Question 25

What typical metal ions bind for catalytic roles?

Answer 25

Iron or copper

Question 26

How are zinc fingers co-ordinated?

Answer 26

Tetrahedrally by cysteine or histidine residues always separated by at least 2 residues, i.e. CxxHxxC

Question 27

What are the two main roles of EF hands?

Answer 27

Regulatory or structural

Question 28

Describe the EF hand structure

Answer 28

Octadentate - 7 co-ordinating oxygens and one water when in solution

Question 29

Describe DNA binding domains

Answer 29

Many and varied, same overall basic charge to mediate DNA interaction through major groove

Question 30

List 4 classes of DNA binding domains

Answer 30

Helix-loop-helix, zinc finger, beta-sheet, leucine zipper motifs

Question 31

What analogy describe leucine zipper-DNA interaction?

Answer 31

Peg (leucine zipper) on washing line (DNA)

Question 32

What is the zipper in the leucine zipper?

Answer 32

An area away from DNA that keeps it as a dimer