Lecture 3 DA

Question 1

What are the benefits of genetic code redundancy (2)?

Answer 1

Offers some protection against mutation.

Can also mean mutation replaces an amino acid with a similar amino acid to minimise change.

Question 2

Is proline an actual amino acid?

Answer 2

Is really a secondary amino acid, has a cyclic structure, better known imino acid.

Question 3

When are proteins most stable?

Answer 3

At their lowest gibbs free energy.

Question 4

Proteins are only marginally more stable in their native form vs another. Why?

Answer 4

Difference in energy between functional and non-functional protein forms is very small. So proteins are only marginally more stable.

Question 5

What kind of interaction dominates the tertiary structure of proteins?

Answer 5

Weak interactions outnumber strong ones, so they determine folding.

Question 6

Does the peptide bond have a neutral charge?

Answer 6

Carbonyl oxygen has a partial negative charge, while the amide nitrogen has a partial positive one. Results is a small dipole.

Question 7

What is the smallest amino acid? What feature does this confer?

Answer 7

Glycine is the smallest amino acid. Allows the most flexibility.

Question 8

In amino acid flexing, where does the flexibility occur? Is the peptide bond flexible?

Answer 8

Flexing occurs around the alpha carbons. The peptide bond is rigid.

Question 9

What kind of backbone can proline form?

Answer 9

Cis-backbone.

Question 10

What can proline’s unique structure and cis-backbone capability allow the formation of?

Answer 10

Can form turns and corners, present in beta sheet turns.

Question 11

What are the flexibility angles called? What limits movement?

Answer 11

Phi and psi are the angles. Stearic hindrance limits movement, electron clouds, like charges etc.

Question 12

How many amino acids present in a turn of an alpha helix?

Answer 12

3.6 amino acids.

Question 13

How long is a turn of an alpha helix? How long per amino acid?

Answer 13

is 5.4A long, means 1.5A per amino acid.

Question 14

An alpha helix turn takes 3.6 amino acids. Which amino acids interact with each other to form the helix?

Answer 14

The 1st and 4th amino acids interact.

Question 15

Why do alpha helices form more readily vs other conformations?

Answer 15

It doesnt involve specific residues, is due to interactions between the amide and carbonyl.

Question 16

There are left and right handed helices. Which is more stable? Which is found in nature?

Answer 16

Left handed is less stable, and usually isnt observed in proteins.

Question 17

Which amino acid most readily forms a helix and why?

Answer 17

Alamine, it has the least free energy.

Question 18

Which amino acids are the most difficult in forming alpha helices (2)?

Answer 18

Glycine and proline.

Question 19

Does beta sheet formation require side chains?

Answer 19

No.

Question 20

What conformation can a beta sheet have (3)?

Answer 20

Parallel or anti-parallel.

Multiple sheets stacked are called pleated beta sheets.

Question 21

How many amino acids does a beta turn require? Which conformation is a beta turn found in? what amino acids does it usually involve (2)?

Answer 21

4 amino acids found. Found in the anti-parallel conformation. Usually involves glycine and proline.

Question 22

A beta turn requires 4 amino acids. Which amino acids interact? What interaction is it?

Answer 22

1st and 4th amino acids have a H bond between them.

Question 23

How many residues does a left handed alpha helix require?

Answer 23

3 per turn.

Question 24

Which amino acid is found in left handed alpha helices, not normally found in right handed ones, and why?

Answer 24

Glycine, typically present on the inside as it needs to be tight and rigid.