Twenty different amino acids are polymerized to make proteins. A typical protein has hundreds of amino acids in a unique, defined sequence (Figure 5.14). The sequence of amino acids in a protein is called the primary structure of the protein.

Because each amino acid has unique chemical characteristics and a unique shape, the order in which amino acids are linked to make a protein - the primary structure - will determine the chemical characteristics and shape of the protein. Both are essential for a protein's function, so primary structure ultimately determines function. Furthermore, proteins evolve over time by changes in their amino acid sequences. Some changes are called conservative because they maintain the nature of the side chain (e.g., Asp replacing Glu). Others are called nonconservative changes because they alter the nature of the side chain (e.g., Asp replacing Ala).

Ultimately, the primary structure of proteins is encoded in the nucleotide base sequence of DNA. This base sequence is first transcribed into the corresponding base sequence in messenger RNA (mRNA). The base sequence in mRNA, in turn, is translated into the unique amino acid sequence of the protein via the genetic code.

Without a "blueprint," as specified in the nucleic acids, proteins would be made only as random sequences of amino acids. Duplicating a specific sequence of amino acids by random combinations would be extremely rare (1 in 20⁵⁰⁰ for a protein containing 500 amino acids).

Today, giant public databanks of polypeptide sequence information are readily available to anyone with online access. A few popular ones are listed below:

1. Entrez

2. OWL

3. Swiss-Prot

4. Molecules R Us