Primary Structure of Proteins

Question 1

What is the L form of the amino acid?

Answer 1

R is vertical and H comes out of the plane towards you. COOH is on the left.

Question 2

What is the D form of the amino acid?

Answer 2

R is vertical and H comes out of the plane towards you. COOH is on the right.

Question 3

Is the C-N bond in the peptide backbone a single or double bond?

Answer 3

It is inbetween. There is resonance of electrons between the C=O of the neighbouring amino acid and the C-N bond.

Question 4

Why is a peptide chain planar?

Answer 4

There is resonance between C-N and the C=O of the neighbouring aa, so there is restricted rotation around the double bond

Question 5

Where can the peptide chain rotate?

Answer 5

The Cἀ-N bond , called the Phi bond (ϕ)

The Cἁ-C bond , called the Psi bond (⫛ upside down)

Question 6

Which configuration of the peptide chain is favoured? What are the exceptions?

Answer 6

Trans is favoured when the R groups are as far apart as possible. Cis is only acceptable for glycine or proline.

Question 7

How do you know when an amino acid is deprotonated?

Answer 7

pH is 1.5 units larger than the pKa

Question 8

How do you know when an amino acid is protonated?

Answer 8

pH is 1.5 units less than pKa

Question 9

How do you calculate pKa of an aa?

Answer 9

An average of the pKa of the NH2 and COOH.

Question 10

When pH>isoelectric point, what is the charge?

Answer 10

Negative

Question 11

When pH is less than the isoelectric point, what is the charge?

Answer 11

Positive