Metabolism 1: An Introduction to Protein Structure

Question 1

What are the 4 groups in an amino acid

Answer 1

Hydrogen
Amino group
Carboxyl group
R side chain

Question 2

What is a chiral centre

Answer 2

four different substituents bound- gives form to optical isomers

Question 3

What optical form are all AA

Answer 3

L

Question 4

Which is the only none chiral AA

Answer 4

Glycine- R chain is H

Question 5

How are peptides formed

Answer 5

CONDENSATION REACTIONS

Question 6

Characteristics of the Peptide Bond

Answer 6

There is no free rotation around the peptide bond

C=O and N-H are in the same plane

Other two bonds in the backbone of the peptide are able to rotate

Only conformation in which the side chains do not clash with the main chain (steric hindrance) are allowed

Question 7

What holds a protein together?

Answer 7

Covalent Bonds
Hydrogen Bonds
Ionic Interactions
Van der waals
Hyderphobic interactions

Question 8

How are helices stabilised by Hydrogen Bonds

Answer 8

Hydrogen bonds between the C=O of one residue and the N-H of another residue, 4 amino acids along the helix, stabilised the entire structure

Question 9

How is proline kinky

Answer 9

When proline is joined to a polypeptide chain - the NH group of the amino acid is LOST

This prevents the side chain from hydrogen bonding with C=O groups of another residue within the helix

This distorts the helical conformation

Puts a kink into it

Question 10

Describe beta pleated sheets

Answer 10

Alternate beta strands can run in the same direction to give a parallel beta-pleated sheet

Or in opposite directions to give an anti-parallel beta-pleated sheet

The pleating in each case allows for the best alignment of the hydrogen bonded groups

Question 11

Describe folding of protiens

Answer 11

Proteins generally fold into the single conformation of lowest energy

Chaperones may be involved to make sure that folding occurs in the most energetically favourable way

By breaking bonds that hold the protein together, we can denature the protein into the original flexible polypeptide

Common Denaturants used in the lab:

Urea (breaks hydrogen bonds)

2-mercaptoethanol (breaks disulphide bonds)

Question 12

Describe the primary to Quaternary structure of proteins

Answer 12

Primary= Linear sequence of amino acids that make up the protein

Secondary= Defined as local structural motifs within a protein (alpha helices/ beta pleated sheets)

Tertiary= The arrangement of the secondary motifs into compact domains

Quaternary structure= The three dimensional structure of a multimeric protein composed of several subunits