Protein 1

Table of Contents
Biomolecules Gateway Page
Jmol Tutorial

In this module:

Amino Acids
Hydrophobic and Polar Amino Acids
Acidic and Basic Amino Acids
Peptide Bonds
Planarity of Peptide Bonds
Protein Sequences
Sickle Cell Anemia

Amino Acids

Proteins are polymers of amino acids . An amino acid is a carbon atom (called the a carbon) bonded to a hydrogen atom, an amine group, a carboxylic acid group, and one of 20 different side chains. The structure of an amino acid is shown at right (R is a generic letter used to take the place of the side chain). All 20 amino acids have three-letter abbreviations for their names. For example, Val is the abbreviation for valine.

The 20 amino acids are sorted into 4 groups, hydrophobic, polar but uncharged, basic, and acidic, depending on the nature of their side chains (R groups).

On the structure of valine (Val) at the right, try clicking on the following groups:

a carbon

The other groups are bonded to the a carbon

Side chain

The side chain is usually represented by an R.


Amine groups contain nitrogen


The acid is a carboxylic acid (COOH)

The amine group of an amino acid has a relatively high pKa, so at physiological pH (about 7), it will tend to bind a proton, becoming positively charged. Similarly, the acid group has a relatively low pKa, so around pH 7 it will tend to donate its proton to water, becoming negatively charged. Thus, amino acids usually have both a positive charge on the amine group and a negative charge on the acid group. This form of an amino acid is called the zwitterion form (German for "double ion").

Amino Acids