Peptides

Question 1

Amide bond structure

Answer 1

• The nitrogen lone pair is conjugated to the C=O double bond, creating a partial double-bond between the N and the C
• Due to orbital constraints, no free rotation about the C-N bond - this group is planar

Question 2

Protein synthesis - how to draw polypeptides

Answer 2

• Always write from the N-terminus to the C-terminus
• N-terminus is the amine group, C-terminus is the carboxylic acid group

Question 3

How to work out the isoelectric point

Answer 3

1. Write out the pKa’s from highest to lowest
2. Start at the most acidic pH (lowest) and choose a pH which is more acidic than the lowest pKa, acidic ones will be neutral but the basic one will be protonated because it is a basic amine giving it a charge of +1
3. Then choose a pH between the two lower pKa’s and do the process again (if the pH is higher than the pKa it will be deprotonated (negative), if it is higher it will stay neutral and the amine group will still be protonated)
4. Take the average of the two pKa values where the charge is 0