Lecture 5 - elements of protein structure

Question 1

what is the primary structure of a protein

Answer 1

the linear sequence of amino acids that make up the polypeptide

Question 2

what the secondary structure of a protein

Answer 2

the three dimensional arrangement of a protein chain over a short stretch of adjacent amino acid residues (includes a-helices and b-sheets

Question 3

what is the tertiary structure of a protein

Answer 3

the three dimensional structure of a complete protein chain

Question 4

what is the quaternary structure of a protein

Answer 4

• only some have this
  interchain packing and structure for a protein that contains multiple polypeptide chains (e.g haemoglobin)

Question 5

what are Phi bond angles

Answer 5

between the N and alpha carbon

Question 6

what are Psi bond angles

Answer 6

between the alpha carbon and the C

Question 7

what are omega chain angles

Answer 7

between the C and N, usually or very close to 180 or 0 degs

Question 8

why do Phi and Psi angles have restrictions in their values

Answer 8

because of steric hinderance

Question 9

what is the shape of an a-helix

Answer 9

main chain spirals around the central axis like a staircase

Question 10

what is the non covalent interaction (hydrogen bond) between in an a-helix

Answer 10

between the carbonyl of N and N-H of residue N+4

Question 11

what is the role of hydrogen bonds in the alpha helix structure

Answer 11

to provide stability

Question 12

What is the range of values for phi and psi?

Answer 12

0 +/- 180 degrees

Question 13

Can phi bonds twist?

Answer 13

yes

Question 14

Can psi bonds twist?

Answer 14

yes

Question 15

Can omega bonds twist?

Answer 15

no

Question 16

Where are the side chains in alpha helices?

Answer 16

They point outwards to help stabilise the alpha helix

Question 17

Which amino acid residues break the alpha helix pattern?

Answer 17

Glycine and proline

Question 18

What exists in the aloha helix?

Answer 18

A dipole, positive at the N terminus

Question 19

What is the beta structure comprised of?

Answer 19

Peptide chains with a more extended structure than the alpha helix. Each is called a beta strand (not stable on own)

Question 20

What occurs between adjacent beta strands?

Answer 20

hydrogen bonding

Question 21

how many strands are there per beta sheet

Answer 21

2-10

Question 22

what are the two types of hydrogen bonding interactions in a B sheet

Answer 22

anti parallel and parallel

Question 23

describe the parallel structure

Answer 23

The two strands run in the same direction but the hydrogen bonds aren’t parallel

Question 24

describe the anti parallel structure

Answer 24

The two strands run in the opposite direction and the hydrogen bonds are parallel

Question 25

Where are the side chains in beta sheets?

Answer 25

above and below

Question 26

What are turns needed for?

Answer 26

to form globular proteins

Question 27

what are turns often like

Answer 27

Short, hairpin like, involving 3 or 4 residues

Question 28

What amino acids are in high amounts in turns?

Answer 28

Gly (flexibility) and Pro (rigidity)