Protein Structure

The Amino Acid Building Blocks
Proteins and polypeptides are composed of linked amino acids. That amino acid
composition of the polymer is known as the primary structure or sequence for
short.
Basic Cα Unit
Each amino acid consists of a central tetrahedral carbon known as the alpha (α)
carbon (Cα) attached to four units: a hydrogen atom, a protonated amino group
(NH+3 ), a dissociated carboxyl group (COO−), and a distinguishing sidechain, or
R group.

This dipolar or zwitterionic form of the amino acid (COO− and NH+3 ) is typical
for neutral pH (pH of 7). The un-ionized form of an amino acid corresponds
to COOH and NH2 end groups. Different combinations involving ionized/unionized
forms for each of the side groups can occur for the amino acid depending
on the pH of the solution.

Acidic and Basic Amino Acids

There are three amino acids that have basic side chains at neutral pH. These are arginine (Arg), lysine (Lys), and histidine (His). Their side chains contain nitrogen and resemble ammonia, which is a base. Their pKa’s are high enough that they tend to bind protons, gaining a positive charge in the process.
Two amino acids have acidic side chains at neutral pH. These are aspartic acid or aspartate (Asp) and glutamic acid or glutamate (Glu). Their side chains have carboxylic acid groups whose pKa’s are low enough to lose protons, becoming negatively charged in the process.
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