Protein Structure: Four Levels Explained

Level 1 — Primary Structure:

• The linear sequence of amino acids
• Bond: covalent peptide bond (-CO-NH-)
• Most stable level; NOT disrupted by denaturation
• Completely determines higher-order structures

Level 2 — Secondary Structure:

Alpha-helix:

• Right-handed coil, 3.6 residues/turn
• Stabilised by intramolecular H-bonds: C=O(i) ··· H-N(i+4)
• All H-bonds roughly parallel to helix axis
• Example: Keratin (hair, nails)
• Proline disrupts helices (no N-H; rigid pyrrolidine ring)

Beta-pleated sheet:

• Extended polypeptide chains side by side
• Stabilised by intermolecular H-bonds between adjacent chains
• Can be parallel (weaker) or antiparallel (stronger, more stable)
• Example: Silk fibroin (antiparallel beta-sheets)

Level 3 — Tertiary Structure:

• Overall 3D conformation of a single polypeptide
• Stabilising forces (weakest to strongest):
  1. Hydrophobic interactions (non-polar R groups cluster inside)
  2. Hydrogen bonds (polar R groups)
  3. Ionic bonds / salt bridges (-$NH_{3}^{+}$ ··· ^{-}OOC-)
  4. Disulfide bonds (covalent: Cys-SH + HS-Cys → Cys-S-S-Cys + 2$H^{+}$ + 2$e^{-}$)
• Example: Myoglobin (single-chain globular protein)

Level 4 — Quaternary Structure:

• Association of 2 or more polypeptide subunits
• Same forces as tertiary (between subunits)
• Not all proteins have quaternary structure
• Example: Haemoglobin (2α + 2β subunits)

Denaturation summary: