Introduction

Introduction

1. Genetics

   • 5'-3' orientation
     • N terminal --> C terminal
   • Protein chains always begin with Met

2. Amino acids

   • Negative side chains
     • Aspartic acid
     • Glutamic acid
   • Positive side chains
     • Arginine
     • Lysine
     • Histidine
   • Uncharged polar side chains
     • Asparagine
     • Glutamine
     • Serine
     • Threonine
     • Tyrosine
   • Nonpolar side chains
     • Alanine
     • Glycine
     • Valine
     • Leucine
     • Isoleucine
     • Proline
     • Phenylalanine
     • Methionine
     • Tryptophan
     • Cysteine
   • Handedness
     • L-type
       • CORN crib

3. Proteins

   • Polymers of amino acid monomers
   • Peptide bonds
   • Properties
     • Shared
     • Unique to each amino acid
   • Secondary structure
     • Alpha helix
     • Beta sheet
     • Determinants
       • Backbone bonds
         • Phi angles
         • Psi angles
       • Hydrogen bonds between main chain atoms
     • Supersecondary structure
       • The arrangement of secondary structural regions
   • Tertiary structure
     • The way in which secondary structures associate
   • Quaternary structure
     • The overall protein molecule
     • Larger association
     • Folding
   • Bond types
     • Backbone-backbone
       • Hydrogen bonds between atoms of two peptide bonds
     • Backbone-side chain
       • Hydrogen bond between atoms in peptide bond and amino acid side chain
     • Side chain-side chain
       • Hydrogen bonds between two amino acid side chains
     • Van der Waals
     • Electrostatic attraction
   • Structure types
     • Transmembrane
       • Bacteriorhodopsin
     • Globular
       • Myoglobin
     • Fibrous
       • Collagen

4. Chaperonins

   • Specialised proteins which protect folding
     • Cylindrical
       • Unfolded protein enters cylinder from one end
         • Cap attaches to that end
           • Cylinder changes shape
             • Hydrohilic environment conducive to folding created
     • Properly folded proteins released

5. Influences on folding

   • Size
   • Amino acid content
     • Hydrophilic/hydrophobic
   • Strength of intramolecular interactions
   • Number of S-S bonds
   • Domain architecture