Amino Acids

The basic subunit of proteins are amino acids. Amino acids are molecules that contain two functional groups:

• A carboxyl group (-COOH)

• An amino group (-NH2)

These two groups are attached to the same carbon. This carbon is termed the alpha carbon. Every amino acid has 4 atoms/groups coming off the alpha carbon:

• A carboxyl group

• An amino group

• A hydrogen

• An R group (This is called the side chain. It is different for every amino acid which helps in the identification of each amino acid.)

When amino acids are dissolved in water, they take the form of a zwitterion. These are molecules that have both a postitive and a negative charge resulting in an overall neutral molecule.

The structure of the amino acid varies depending on the environment it is exposed to. In an acidic environment (low pH), the zwitterion acts as a base and accepts a proton. Specifically, the carboxylate group accepts a proton (hydrogen ion) to become a carboxy group:

In a basic environment the zwitterion acts as an acid and donates a proton from the nitrogen:

As zwitterions can act as both a weak acid and a weak base if means that they can act as a buffer. They are also referred to as internal salts and can engage in strong ionic interactions with other amino acids forming a crystalline solid with very high boiling points.

Proteins

Proteins are large biopolymers that are made of several alpha amino acids. Amino acids form proteins by engaging in several condensation reactions.

A condensation reaction is where two molecules combine by the loss of a small molecule, that is usually water. For Example:

When two amino acids react the carboxyl group of one amino acid and the amino group of the other interact and there is a loss of water to form a peptide bond (also called an amide bond):

Around 500 amino acids have been identified in nature, however for this course you are to consider the 20 amino acids that make up proteins found in the human body (don’t worry you do not have to remember them, you can find them on pages 6 and 7 of your data booklet).

When considering the amino acid sequence of a polypeptide, it is easier to consider each amino acid as a three-letter-abbreviation. For example, alanine is abbreviated to Ala, arginine to Arg, asparagine to Asn and aspartic acid to Asp.

In addition, when naming this chain, it begins from the free amino group referred to as the N terminal, all the way to the free carboxyl group referred to as the C terminal.

When polypepyides (proteins) reach a large enough size, they form primary, secondary and tertiary structures. The Primary Structure is simply the sequence of amino acids. This includes the type, number, and order of the amino acids.

The Secondary Structure results when there is hydrogen bonding between the N-H and C=O bonds in either the backbone of the same peptide chain or with neighbouring chains. When there are internal hydrogen bonds an alpha helix is formed:

When there are intermolecular hydrogen bonds beta-pleated sheets are formed:

The Tertiary Structure refers to the overall three-dimensional shape of the protein. It is dependent upon the interactions between the amino acid side chains in the protein:

The types of interactions you can have between the amino acid side chains:

• Ionic Bonding

• Disulphide Linkages

• Hydrogen Bonding

• Dispersion Forces