Amino acids are the building blocks used to make proteins and peptides. The different amino acids have interesting properties because they have a variety of structural parts which result in different polarities and solubilities Although we are studying only about 20 amino acids, there are about six more found in the body. Many others are also known from a variety of sources.

Each amino acid has at least one amine and one acid functional group as the name implies. The different properties result from variations in the structures of different R groups. The R group is often referred to as the amino acid "side chain". Amino acids are generally divided into groups on the basis of their side chains (R groups). Amino acids have special common names, however, a three letter abbreviation for the name is used most of the time.

Zwitterion
Amino acid physical properties indicate a "salt-like" behavior. Amino acids are crystalline solids with relatively high melting points. In solution, the amino acid molecule appears to have a charge which changes with pH.
An intramolecular neutralization reaction leads to a salt-like ion called a zwitterion. The accepted practice is to show the amino acids in the zwitterion form.
(1) The carboxyl group can lose a hydrogen ion to become negatively charged.
(2) The amine group can accept a hydrogen ion to become positively charged

Principles of Polarity
The greater the electronegativity difference between atoms in a bond, the more polar the bond. Partial negative charges are found on the most electronegative atoms, the others are partially positive.

Non-Polar Side Chains
Side chains which have pure hydrocarbon alkyl groups (alkane branches) or aromatic (benzene rings) are non-polar. Examples include valine, alanine, leucine, isoleucine, phenylalanine.
The number of alkyl groups also influences the polarity. The more alkyl groups present, the more non-polar the amino acid will be. This effect makes valine more non-polar than alanine; leucine is more non-polar than valine.

Polar Side Chains
Side chains which have various functional groups such as acids, amides, alcohols, and amines will impart a more polar character to the amino acid. The ranking of polarity will depend on the relative ranking of polarity for various functional groups. In addition, the number of carbon-hydrogens in the alkane or aromatic portion of the side chain should be considered along with the functional group.
Example: Aspartic acid is more polar than serine because an acid functional group is more polar than an alcohol group.
Example: Serine is more polar than threonine since threonine has one more methyl group than serine. The methyl group gives a little more non-polar character to threonine.
Example: Serine is more polar than tyrosine, since tyrosine has the hydrocarbon benzene ring.

Acid - Base Properties of Amino Acids

Acidic Side Chains
If the side chain contains an acid functional group, the whole amino acid produces an acidic solution. Normally, an amino acid produces a nearly neutral solution since the acid group and the basic amine groups on the root amino acid neutralize each other in the zwitterion. If the amino acid structure contains two acid groups and one amine group, there is a net acid producing effect. The two acidic amino acids are aspartic acid and glutamic acid.

Basic Side Chains
If the side chain contains an amine functional group, the amino acid produces a basic solution because the extra amine group is not neutralized by the acid group. Amino acids which have basic side chains include: lysine, arginine, and histidine.

Neutral Side Chains
Since an amino acid has both an amine and acid group which have been neutralized in the zwitterion, the amino acid is neutral unless there is an extra acid or base on the side chain. If neither is present then the whole amino acid is neutral. Amino acids with an amide on the side chain do not produce basic solutions i.e. asparagine and glutamine. An amide starts out looking like an amine, but has the carbon double bond oxygen which changes the property. Amides are not basic. Even though tryptophan has an amine group as part of a five member ring, the electron withdrawing effects of the two ring systems do not allow nitrogen to act as a base by attracting hydrogen ions.

Peptide bond
Two individual amino acids can be linked to form a larger molecule, with the loss of a water molecule as a by-product of the reaction.
The newly created C-N bond between the two separate amino acids is called a peptide bond. The term 'peptide bond' implies the existence of the peptide group which is commonly written in text as -CONH-