Protein stuff

Question 1

Pitch of alpha helix

Answer 1

5.6 A

Question 2

n of alpha helix

Answer 2

3.6 residues per turn

Question 3

d of alpha helix

Answer 3

1.5 A

Question 4

What is meant by notation n (subscript m)

Answer 4

n = number of residues per turn (subscript number of atoms enclosed by H bond)

Question 5

What is pi helix

Answer 5

A wider version of the alpha helix

Question 6

What is the n and p of a 3 (subscript ten) helix

Answer 6

n = 3
p = 6

Question 7

What is the n and p of a pi helix

Answer 7

n = 4.4
p = 5.2 A

Question 8

What is the n and p of the polyproline 2 helix

Answer 8

n = 3
p = 9.4

Question 9

secondary structure of insulin

Answer 9

1 alpha helix
2 beta bridges
1 3-10 helix
1 bend

Question 10

structure of B-amyloid

Answer 10

mostly loops and 3 B-sheets

Question 11

structure of HIV protease

Answer 11

no secondary structure

Question 12

Phi and psi angles of alpha helix

Answer 12

-57 and -47

Question 13

What is the difference between Type 1 B bend and type 2 B bend?

Answer 13

The amide group (joined to hydroxyl between 2nd and 3rd polypeptides) is flipped out on the Type 2, give it a stronger linear H bond

Question 14

What is the function of omega loops?

Answer 14

Used for recognition and connection, they are the structures which are not alpha helixes or beta sheets/turns

Question 15

Which is more favoured: right handed or left handed parrallel B-sheets

Answer 15

Right handed

Question 16

What is meant by the 2.2 (subscript 7) ribbon?

Answer 16

2.2 residues per turn, 7 atoms enclosed by hydrogen bond.

Question 17

How many atoms are enclosed by hydrogen bond in alpha helix? pi helix?

Answer 17

13, 16

Question 18

Which is the more common-handed alpha helix?

Answer 18

Right handed

Question 19

what is collagen rich in?

Answer 19

Proline and glycine