Metabolism 1 - Intro to Protein Structure

Question 1

What is the simplest amino acid?

Answer 1

Glyciene - the only amino acid with no R group, it is not an L-ismoer.

Question 2

What amino acid codes for glycolysation?

Answer 2

Asparagine, codon AAT.

Question 3

How does electrophoresis separate proteins?

Answer 3

On the basis of charge, allowing us to distinguish between normal and mutant forms of protein that have gained or lost charge.

Question 4

What is chirality in amino acids?

Answer 4

The central carbon is chiral - meaning that it can fom optical isomers as it is bound to 4 different groups. All amino acids but glycine are in the L-form.

Question 5

Draw a tripeptide

Answer 5

(Drawing of 3 amino acids joined with peptide bonds, loss of 2 water molecules. Represent the R groups.)

Question 6

Which amino acids have charged side chains? What is their charge at physiological pH?

Answer 6

Aspartate and glutamate. They are always negatively charged in the body due to proton donation.

Question 7

What are th characteristics of the peptide bond?

Answer 7

There is no free rotation, the C=O and N-H are in the same plane of the molecule. The other two bonds in the backbone can rotate.

Question 8

What bonds hold a protein together?

Answer 8

• Covalent (peptide and disulfide bridges)
• Hydrogen bonds (intramolecular OR intermolecular)
• Ionic interactions
• Van der Waals forces (between two atoms that are quite close)
• Hydrophobic interactions (hydrophobic groups point inwards)

Question 9

Describe the structure of an alpha-helix

Answer 9

A right handed helix caused by hydrogen bonds within the peptide a few residues apart.

Question 10

What is proline?

Answer 10

A kinky amino acid which loses th NH group upon joining a polypeptide chain. This prevents hydrogen bonding and puts a kink in alpha-helices.

Question 11

Describe the structure of the beta-pleated sheet.

Answer 11

Hydrogen bonds are many more residues apart. They may run in the same direction (parrallel) or in different directions (antiparrallel).

Question 12

Summarise the structural levels of proteins.

Answer 12

• Primary structure is the sequence of amino acids.
• Secondary structure is the local structural motifs of a protein (alpha-helices and beta-pleated sheets)
• Tertiary structure is the arrangement of the secondary structure motifs into compact globular structures called domains.
• Quarternary structure is the three dimentional structure of a multimeric protein composed of several subunits.

Question 13

Give an example of post-translational modification of proteins.

Answer 13

• N-linked glycolysation occurs in LHR to ensure it has correct membrane conformation. (This is the addition of sugar groups to asparagine residues).
• Mutation of two asparagines to glutamine can therefore be picked up in electrophoresis as a reduction in molecular weight of the LHR.