Lecture 3 Part 2 Notes – Protein Folding, Structure, and Complexes

Lecture 3 Part 2 Notes – Protein Folding, Structure, and Complexes

• Overview

  • Builds on the idea that amino acids determine not just primary sequence but also how proteins fold and function.
  • Proteins can form complexes by bringing separate polypeptides together via non-covalent interactions.

• Primary structure and polypeptides

  • A short polypeptide as a model for protein folding (much shorter than typical proteins, which are ~50–200 amino acids, though the exact number varies).
  • Proteins are unbranched, linear chains linked head-to-tail by peptide bonds (covalent bonds).
  • The chain has polarity with an N-terminus (left) and a C-terminus (right); translation proceeds from N to C, with methionine usually the first incorporated amino acid.
  • Side chains (R groups) project outward from the backbone in a linear sequence; this sequence constitutes the primary structure.
  • Although shown linearly, proteins fold into complex three-dimensional shapes; the identity and properties of amino acids in the primary sequence influence folding, secondary structure formation, and the overall tertiary structure.

• Backbone geometry and phi/psi angles

  • Focus on a single amino acid in the chain to illustrate backbone geometry.
  • Each amino acid contributes three backbone bonds:
  • The peptide bond linking amino acids (backbone linkage).
  • The bond between the amide nitrogen and the central alpha carbon (N–Cα).
  • The bond between the alpha carbon and the carbonyl carbon (Cα–C′).
  • Rotations around these bonds define two key angles:
  • The phi angle $$\