Protein Structure and Function

  • Proteins catalyze reactions, bind to molecules and transport molecules
  • Proteins can do these diverse functions because of their complex shapes and the precise positioning of various chemical groups.
    • The twenty amino acids have a variety of functional groups: acidic, basic, hydrophobic, hydrophilic, cyclic, large, small, etc.

  • Four levels of protein structure - primary, secondary, tertiary and quaternary
    • Primary - the linear order of the amino acids in the polypeptide chain
      • The amino group of one amino acid reacts with the carboxyl group of the next amino acid to form the peptide bond
      • There is a free amino group at one end (where synthesis starts) and a free carboxyl group at the other end (where synthesis ends)

A more extensive tutorial on amino acid and peptide structure can be found at the Amino Acid tutorial, however, you will need the Chime plugin to view this tutorial.

  • Secondary structure refers to stable structures formed in regions of the polypeptide chain. The most important are the alpha helix and the beta-pleated sheet
    • There are also turns, random coils, etc.
    • The alpha helix is stabilized by hydrogen bonds
      • bonds go length ways, not across as in DNA
      • 3.6 amino acids per turn
      • side groups stick out, not in as in DNA
      • Amphipathic helix has hydrophobic groups on one side, hydrophilic on the other

For those with the chime plugin there is a much more extensive example of protein strucutre at Carnigie Mellon University

  • Beta-pleated Sheets
    • Two stretches of the polypeptide chain lie parallel to one another and are held together by hydrogen bonds
    • can be parallel or antiparallel
    • multiple chains held together this way create a sheet
    • sheets can be very strong and inflexible
  • Tertiary Structure - the three dimensional conformation of the entire chain
    • Can be measured using NMR or X-Ray crystallography
    • Held together by covalent disulfide bonds between cysteines, hydrogen bonds in alpha helix and beta-pleated sheets, and the tendency of hydrophilic groups to face the water and hydrophilic groups to clump together in the interior
    • Many proteins need chaperones to help them fold properly

Beta subunit of hemoglobin with heme co-factor in red

or, with the alpha helixes highlited

  • Quaternary Structure
    • Many proteins are composed of multiple polypeptide chains, some also include co-factors
    • hemoglobin is a tetramer of two _ chains and two _ chains
      • each chain also includes a heme group
      • cooperative binding of oxygen is very important for proper hemoglobin function

For the chime enabled there is much more at this hemoglobin site

This document is copyright of Jeff Bell
Last Update: Wednesday, March 28, 2001