Proteins are polymers of the bifunctional monomer, amino acids. The twenty common naturally-occurring amino acids each contain an α-carbon, an α-amino group, an α-carboxylic acid group, and an α-side chain or side group. These side chains (or R groups) may be either nonpolar, polar and uncharged, or charged, depending on the pH and pKa of the ionizable group. Two other amino acids occasionally appear in proteins. One is selenocysteine, which is found in Archaea, eubacteria, and animals and just recently found is pyrrolysine, found in Archaea. We will concentrate on only the 20 abundant, naturally-occurring amino acids.
Introduction to Amino Acids
Amino acids form polymers through a nucleophilic attack by the amino group of an amino acid at the electrophilic carbonyl carbon of the carboxyl group of another amino acid. The carboxyl group of the amino acid must first be activated to provide a better leaving group than OH-. (We will discuss this activation by ATP later in the course.) The resulting link between the amino acids is an amide link which biochemists call a peptide bond. In this reaction, water is released. In a reverse reaction, the peptide bond can be cleaved by water (hydrolysis).
- Structure and Property of the Naturally-Occurring Amino Acids (Too large to include in text: print separately)
When two amino acids link together to form an amide link, the resulting structure is called a dipeptide. Likewise, we can have tripeptides, tetrapeptides, and other polypeptides. At some point, when the structure is long enough, it is called a protein. There are many different ways to represent the structure of a polypeptide or protein, each showing differing amounts of information.
Figure: Different Representations of a Polypeptide (Heptapeptide)
Figure: Amino Acids React to Form Proteins
(Note: above picture represents the amino acid in an unlikely protonation state with the weak acid protonated and the weak base deprotonated for simplicity in showing removal of water on peptide bond formation and the hydrolysis reaction.) Proteins are polymers of twenty naturally occurring amino acids. In contrast, nucleic acids are polymers of just 4 different monomeric nucleotides. Both the sequence of a protein and its total length differentiate one protein from another. Just for an octapeptide, there are over 25 billion different possible arrangements of amino acids. Compare this to just 65536 different oligonucleotides of 8 monomeric units (8mer). Hence the diversity of possible proteins is enormous.
Shultz et al. have gone one step farther by engineering bacteria to incorporate two new amino acids, O-methyl-tyrosine and p-aminophenylalanine. More recently, they (Chin et al.) have engineered the yeast strain Saccharomyces cerevisiae to incorporate five new unnatural amino acids (using the TAG nonsense codon and new, modified tRNA and tRNA synthetases) with keto groups that allow chemical modifications to the protein. We will concentrate on only the 20 abundant, naturally-occurring amino acids.