Proteins consist of amino acids linked together via peptide bonds. In this way, polymers ranging in size from just a few amino acids to thousands of amino acids can be created. A peptide bond is formed by condensing the carboxyl group of one amino acid with theamine group of another amino acid to form a special type of amide bond known as a peptide bond. This condensation reaction eliminates water and requires an input of energy.Once an amino acid has been covalently linked to form a polypeptide it is referred to as an
amino acid residue (usually abbreviated to residue). Thus, it is incorrect to use the
terminology “50 amino acid protein”; the correct usage is “50-residue protein”.
Do the amino acids form chemical series?
Unfortunately (especially from a pedagogical viewpoint!), the sidechains of the amino acids do
not form a natural series. At a very early stage of evolution, certain sidechains were selected for a
variety of reasons, some of them possibly random. The sidechains are not easy to remember, but
they can be conveniently subdivided into several classes based on their chemical properties.
Aliphatic nonpolar amino acids: Gly, Ala, Met, Val, Val, Leu, and Ile
These amino acids become progressively more nonpolar (hydrophobic) as one moves from Gly to
Leu/Ile. They also differ substantially in shape and relative bulkiness. These amino acids prefer to
be buried within the interior of protein molecules to minimize their exposure to water. Proline has
a cyclic sidechain in which the end is covalently linked to the amine group of the amino acid.
Thus, strictly speaking, Pro is an imino acid. The Gly aC is achiral.
Aromatic nonpolar amino acids: Phe, Tyr, and Trp
Phe is the most hydrophobic amino acid. Tyr and Trp, on the other hand, are amphipathic; they
have both polar and nonpolar portions. The polar groups (–OH in Tyr and >NH in Trp) can
engage in hydrogen bonding. The aromatic amino acids, like most conjugated compounds, absorb
light strongly in the near ultraviolet region of the spectrum. The approximate absorption maxima
in this region for each of these amino acids is 257 nm (Phe), 275 nm (Tyr), and 280 nm (Trp).
