Molecular Biology Lecture 4

The Physical Structure of Protein Molecules

See figure 2.1 for the basic structure of an amino acid

See figure 4.1 and 4.2 for peptide bond formation.

The peptide bond has a partial double-bond character, thus it is planar and rigid.

Amino acids have an “average” molecular weight of about 110 daltons

Remember that the “primary” structure of a protein is its amino acid sequence

Some of the general tendencies of protein folding are:

1. the polar amino acids tend to be on the surface of the folded molecule

2. the non-polar amino acids tend to be buried inside

3. H-bonds form between C=O and H-N of different amino acids in the polypeptide chain à this goes to form the secondary structures (the alpha-helix and the beta-pleated sheets (figure 4-4 and 4-5))

4. the –SH groups of the cysteines form covalent disulfide bonds (figure 4-3)

The final 3-dimensional structure of a polypeptide is called its “tertiary” structure (figure 4-6 and 4-7)

A “quaternary” structure describes a protein that is made up of several distinct polypeptides (each of these polypeptides is also called a subunit).

Antibody molecules with two heavy chains and two light chains are a good example of a protein with 4^o structure. (See figures 4-8, 4-9, 4-10 and 4-11).

Be sure to look at Fig 4-12 for a description of an enzyme-substrate interaction.

Also Fig 4-17 for the model showing how a substrate interacts with the much larger enzyme molecule

Also look at the discussion of lysozyme (what is lysozyme?) and Figs 4-13 and 4-14. Note that the enzyme’s active site is made up of amino acids that are actually widely separated on the linear (1^o sequence) molecule, but after folding, these amino acids are all congregated in the same area (active site) of the final protein conformation (2^o and 3^o structure).