Secondary structure

Question 1

What is secondary structure?

Answer 1

The regular conformation and H bonding arrangement in a local part of the polypeptide peptide (close in sequence)

Question 2

What are the 2 regular secondary structures?

Answer 2

Alpha helix and beta sheet

Question 3

What are the 2 irregular secondary structures?

Answer 3

Beta turns and loops

Question 4

What is the handedness of the turn in an alpha helix?

Answer 4

Right handed

Question 5

What is the H bonding pattern in an alpha helix?

Answer 5

i to i+4 (C=O at position 1 to NH at position 5)

Question 6

Which direction do the side chains project in an alpha helix?

Answer 6

Away from the core

Question 7

How many amino acids per turn are there in an alpha helix?

Answer 7

3.6

Question 8

How many angstroms per turn are there in an alpha helix?

Answer 8

5.4

Question 9

What does a lower helical propensity number indicate?

Answer 9

It is more favourable for an amino acid to be in an alpha helix

Question 10

What is the most favourable amino acid to be in an alpha helix?

Answer 10

Alanine

Question 11

What are the least favourable amino acids to be in an alpha helix?

Answer 11

Proline and glycine

Question 12

Why is it unfavourable for proline to be in an alpha helix?

Answer 12

The backbone NH can’t H bond because of the proline side chain, so the gets disrupted and destabilized

Question 13

Why is it unfavourable for glycine to be in an alpha helix?

Answer 13

It has so much conformational flexibility that it is unfavourable to have it stuck in one conformation

Question 14

Which side chains will interact in an alpha helix?

Answer 14

i, i+3 and i+4

Question 15

What is the helix dipole?

Answer 15

The cumulative effect of all the peptide bond dipoles so the N terminus end of the helix is partially positive and the C terminus is partially negative

Question 16

How does the helix dipole affect which amino acids make up the helix?

Answer 16

More favourable for positive amino acids to be near the C terminus and negative amino acids to be near the N terminus

Question 17

What are the 2 types of beta sheets?

Answer 17

Parallel and antiparallel

Question 18

What is a parallel beta sheet?

Answer 18

Adjacent strands run in the same direction

Question 19

What is an antiparallel beta sheet?

Answer 19

Adjacent strands run in opposite strands

Question 20

Where are the side chains in a beta sheet?

Answer 20

Above and below the backbone

Question 21

Which side chains in a beta sheet will interact?

Answer 21

i and i+2

Question 22

What sort of connecting structures will connect polypeptide chains parallel beta sheets?

Answer 22

An alpha helix

Question 23

What sort of connecting structures will connect polypeptide chains antiparallel beta sheets?

Answer 23

Loops and turns

Question 24

What is the handedness of the turn when a beta sheet is twisted into a beta barrel?

Answer 24

Right

Question 25

Which amino acids are often found in beta turns?

Answer 25

Glycine and proline

Question 26

Why is proline so good to have in a beta turn?

Answer 26

It can form a cis peptide bond that allows for a really tight turn (cis peptide bonds are still pretty rare)

Question 27

Where in a protein are beta turns usually found?

Answer 27

On the outside, so the backbone can hydrogen bond with the water

Question 28

Which enzyme catalyzes the formation of a cis peptide bond?

Answer 28

PPI (peptidyl prolyl cis-trans isomerase)