Protein Structure Lecture Notes

Introduction to Protein Structure

• Understanding protein structure begins with basics.
• First, describe the structure of a protein by the primary structure.

Primary Structure

• Definition: Sequence of amino acids forming a polypeptide chain.
  • Important for exams.
• Components:
  • Amino acids linked by peptide bonds.
    • Represented by circular symbols.
    • Peptide bond structure: C=O and NH.
• Differences in primary structures:
  • Length of the chain: Different number of amino acids.
  • Sequence of amino acids: Different order despite same length.
• Examples:
  • Two chains with different colors but different structures.
  • Chain A vs. Chain B: Same length, different sequences.

Secondary Structure

• Definition: Formation of coils or folds within a polypeptide chain.
• Formation Causes:
  • Bonds between amino acids that are not close to each other.
  • Hydrogen bonds between C=O (partially negative) and NH (partially positive).
  • Hydrogen bonds cause the chain to curve.
• Types of Secondary Structures:
  • Alpha Helix:
    • Represented as a coil.
  • Beta Pleated Sheet:
    • Resembles folded paper or pleats.
    • Represented as arrows and coils in diagrams.
• Visual Representation:
  • Left chain: Forms alpha helices.
  • Right chain: Forms beta pleated sheets and an alpha helix.
• Exam Note: No need to memorize which chain does what, but understand primary and secondary structures.

Summary

• Primary structure: Linear sequence of amino acids.
• Secondary structure: Coiling or folding of the primary chain due to hydrogen bonding.
• Importance of understanding both structures for exams.