protein structure

protein structure

1. Primary structure

   • Sequence of amino acids
     • peptide bonds (Amide linkage b/n Amino acid)
       • Formed by dehydration synthesis (removes water)
       • Can be broken by hydrolysis (addition of water)
       • Restricted rotation due to partial double bonds
         • Small electric dipole
           • Due to partial negative charge on carbonyl oxygen and partial positive charge on amide notrogen
         • Two rotatable single bonds w/low energy/high probablilty
           • phi (φ) rotation b/n N-Calpha
           • psi (ψ) rotation b/n Calpha -C
       • GEOMETRY (Based on the bulkiest groups --steric hindrance)
         • CIS
           • C alpha on same sides of the partial double bond)
         • TRANS
           • C alpha on opposite sides of the partial double bond)
           • For all peptide bonds EXCEPT PROLINE
       • Monomer + Monomer = Polymer Example: polypeptide ( >10 AA)
         • Polymer + Polymer = Protein (>50AA)
       • Composed of 6 atoms
     • 1-letter code from N-terminal (Left) to C- terminal (RIGHT)
   • Conserved (similar properties)
     • Leads to protein function
   • Not conserved (Different properties)
     • Loss of function (mutation, deleterious)

2. Not random

   • hydrogen bond (NH donor and C=O acceptor)
   • Backbone steric

3. Random

   • Hydrophobic side chain fold back on itself