6 - Polypeptides and protein folding

Question 1

Primary structure

Answer 1

The sequence in which the amino acids are arranged

Question 2

Explain how peptide bonds form

Answer 2

The carboxyl group of the first amino acid reacts with the amino group of the second
The reaction produces water and is called a condensation reaction

Question 3

directional nature of polypeptides

Answer 3

proteins have a free amino group at their start and a free carboxyl group at their end
The amino acid sequence of proteins is ALWAYS written in the N -> C direction

Question 4

Why is there no free rotation around the peptide bond?

Answer 4

• Because of electron distribution within the peptide unit
• peptide bond has partial double bond character which means rotation is restricted
  – THE PEPTIDE UNIT IS RIGID AND PLANAR
• hydrogen and oxygen atoms are on opposite sides

Question 5

PSI (ψ)

Answer 5

Rotation around Cα-C bond

Question 6

PHI (Φ)

Answer 6

Rotation around N-Cα bond

Question 7

Protein Conformation

Answer 7

Most combinations of psi and phi angles are not allowed because of steric collisions between the side chains and the main polypeptide chain
The shape of the entire protein is determined by the values of the psi and phi angles for each amino acid

Question 8

Describe the behaviour of hydrophobic and hydrophilic groups in protein conformation

Answer 8

• For water soluble proteins it is essential to pack hydrophobic side chains into the interior of the protein to ‘hide’ them from the surrounding water molecules.
• forms a hydrophobic core (similar process to oil forming droplets in water).
• main polypeptide chain is hydrophilic because of the polar C=O and N-H groups, protein must adopt structures which ‘neutralise’ these groups by hydrogen bonding.

Question 9

Is the process of protein folding random?

Answer 9

No! Equivalent to 1.6 x 1027 years to try every conformation