Primary and secondary structures

Describe the primary structure of a polypeptide

• Amino acid sequence in polypeptide chain

• Linked by peptide bonds

Describe properties of a peptide bond

Have some features of a ‘double bond’

• Shorter C-N bond length

• Delta negative oxygen

• Delta positive nitrogen

Resonance

• Occur when a double bond is next to another bond that has the potential to be a double bond

• Shared electrons in a covalent bond fluctuate

  • Go between the C=O & C=N bond

• Rigid C-N bond = no rotation around the peptide bond

Planar

• Side chains alternate on different sides of the polypeptide chain

Side chains alternate

• Side chains have fixed orientation

  • Trans arrangement - don’t clash

  • Explained using the Ramachandran plot

Describe the secondary structure

• Hydrogen bonding

• Form alpha helix and beta pleated sheets

Alpha helix

• H bonds in the same polypeptide chain

• Between oxygen on C=O and hydrogen on N-H

  • Every 4th peptide bonds

• 3.6 residues per turn - verticals length of 1 full turn (pitch) = 0.54nm

• R-groups point outwards

• Rigid cylinder shape

Describe the tertiary structure of the polypeptide

• Overall structure of the folded polypeptide chain

• Ionic bonds

• Disulphide bridges

• Hydrogen bonds

Describe the quaternary structure of the polypeptide

• 2 or more folded polypeptide chains

  • Assembly of subunits