The Peptide Chain

Question 1

How are peptide bonds formed?

Answer 1

Formed through a condensation reaction between 2 amino acids
Water is a product
Reaction between OH on carboxylic acid on one amino acid and H on Amino group on another amino acid

Question 2

What does protein synthesis require?

Answer 2

Requires an input of free energy

Question 3

What is a peptide?

Answer 3

A peptide is a chain of 2 or more amino acids

Question 4

How many bonds and angles are there along the main chain?

Answer 4

3 bonds along main chain for each peptide and 3 torsional angles for these 3 bonds

Question 5

Describe the torsional angles

Answer 5

There are 3 torsional angles
Omega is the torsional angles between CO-N
Phi is the angle between NH-C
Psi is the angle between C-CO

Question 6

Which torsional angles can rotate?

Answer 6

Only phi and psi can rotate

Omega is fixed

Question 7

What dominates protein folding?

Answer 7

Folding is dominated by van fee waals repulsions- related to steric hindrance
This means the protein folds in a way that prevents steric conflicts

Question 8

What are van der waals repulsions?

Answer 8

Two substituents in a molecule approach each other with a distance less than the sum of their van der waals radii

Question 9

What are the values of psi and phi and what is optimised at these angles?

Answer 9

There are only two possible values for phi and psi which prevent steric conflicts
Van der waals attractions and H bonds are optimised at these allowed values of psi and phi

Question 10

What is a ramachandran plot?

Answer 10

This shows which values of psi and phi are allowed

Visualise energetically allow regions for dihedral angles (psi and phi)

Question 11

Describe the backbone conformation and why is it like this?

Answer 11

It is a regular back bone conformation
This is due to repeating values of psi and phi
This gives secondary structures alpha helix and B strand

Question 12

Is alpha helix and B strand chiral or not chiral?

Answer 12

They are chiral

This is because L alpha amino acids are chiral

Question 13

What prohibits certain conformations?

Answer 13

Conformations may be prohibited by van der waals radio due to steric conflicts

Question 14

Is trans or cis preferred?

What is the exception to this?

Answer 14

Trans is preferred
This is because their are less van der waals repulsions which leads to less steric conflict
Proline is an exception- some proline cis residues are found in proteins

Question 15

What are the possibilities for the position of electron density in the peptide bond?
Which one is true?

Answer 15

3 possibilities
Pure C=O and free rotation around the C-N bond. Omega is not fixed

No rotation around C-N double bond but too much charge separation

In reality, the true electron density is intermediate. Partial double bond character in both C-O and C-N

Question 16

Why is amide bond planar?

Answer 16

Omega is fixed
There is partial double bond character in C-N as electron density in amide bond is intermediate
High barrier to rotation which means too much energy is required to rotate C-N so bond is fixed

Question 17

Why is the C-N observed bond length different to expected?

Answer 17

This is because the electron density in the amide bond is intermediate which means C-N has partial double bond character
This explains why is it short than the expected single bond length of C-N

Question 18

Describe the hybridisation of N in amide bond

Answer 18

It is sp2 rather than sp3