L1+L2

Question 1

How may the pI of an amino acid be determined?

Answer 1

½(pk1 + pK2)

Question 2

How do you find the Pk?

Answer 2

Flattest part of the curve (buffered by equilibrium)

Question 3

how do ionisable side groups affect the pI?

Answer 3

Acidic groups have lower pI, alkaline have higher pI

Question 4

Draw the structure of Arginine

Answer 4

(see)

Question 5

Draw the structure of lysine

Answer 5

(see)

Question 6

What is chymotrypsin specific to? Trypsin?

Answer 6

Aromatic amino acids, positively charged (Lys arg)

Question 7

Draw asparagine and glutamine

Answer 7

(see)

Question 8

Draw methionine

Answer 8

(see)

Question 9

Draw histidine

Answer 9

(see)

Question 10

What are the stats of an alpha helix?

Answer 10

3.6aa
5.4A
n and n+4
right handed

Question 11

What is an ampholyte?

Answer 11

Can act as acid and base

Question 12

what is a psi angle? What is a thi angle? draw a ramachandran plot

Answer 12

psi - carbon alpha carbon
thi - carbon nitrogen
thi in x, psi in y

Question 13

What are the angles of Beta sheets and aloha helices?

Answer 13

50-60 degree turn for alpha helices, 180 for beta sheets

Question 14

what forces stabilise alpha helices?

Answer 14

hydrophobic effect, intrahelical hydrogen bonding

Question 15

what forces stabilise beta sheets?

Answer 15

interstrand hydrogen bonds, van der waals between stacked sheets

Question 16

Define the van der waals contact distance and minimum distance allowed with a graph

Answer 16

See notes

Question 17

what is a helix-loop helix?

Answer 17

protein domain - helix loop helix, fits in major groove of DNA

Question 18

Give an example of a helix loop helix motif

Answer 18

EF hand motif, Central loop binds and coordinates calcium ion

Question 19

What is a beta alpha beta helix?

Answer 19

joined by alpha helix, more energetically favourable to form an alpha helix than long unstructured region

Question 20

give an example of a beta alpha beta

Answer 20

Central subunit of pyruvate kinase formed from beta alpha barrel, and leucine rich repeat alpha beta alpha forms horseshoe fold

Question 21

What does rcsb stand for and what is it used for?

Answer 21

research collabaratory for structural bioinformatics

grab pdb files of crystal structures