Biochemistry: Protein Structures and Bonds

Peptide and Peptide Bonds

• Amino acids are covalently linked forming an amide bond between the α-amino and carboxyl groups.
• This bond is called a peptide bond.
• The products formed from amino acid unions are called peptides.
• Linking two amino acids creates a dipeptide (e.g., Gly-Ala).
• This reaction is considered a simple elimination of a water molecule.

Protein Structures and Interactions

• Table of Protein Interactions
  • Type | Mechanism | Energy (kcal/mol) | Interaction Distance (Å) | Interacting groups
  • Covalent | Electron sharing | 30-100 | 1-2 | C-C, C-N, C=O, C-S, C-N-C
  • Electrostatic/Salt Bridges | Coulombic attraction between opposite charges | 10-20 | 2-3 | -NH₃⁺, -COO^-
  • Hydrogen Bonds | Shared hydrogen between electronegative atoms | 2-10 | 2-3 | -N-H···O=C-, -N-H···O-H
  • Van der Waals | Induced dipole moments in polar groups | 1-3 | 3-5 | Polar groups

Protein Denaturation

• Temperature Changes: Heat is a common denaturing agent used in food processing assisting in protein digestion. It also disables inhibitors.
• pH Changes: A change in pH can lead to significant protein conformation modifications due to ionization changes in charged side chains and affect the amount of stabilizing salt bridges.
• Detergents: Denaturing proteins with detergents, (e.g., SDS), is common in lab settings. Detergents' amphiphilic nature helps with this process.