Of the twenty standard amino acids (AAs),
the simplest and smallest is glycine,
which can be viewed below by clicking on one
Gly
or G, the
standard three-letter or one-letter abbreviation for this AA. The resulting images of
glycine correspond to its predominant ionization state at pH =
7 where its amino nitrogen is protonated (pKn = 9.2) and therefore
positively-charged, and its
carboxyl oxygen is deprotonated (pKc = 2.2)
and therefore negatively-charged.
The "alpha-carbon"
(Cα) is,
by convention, the central carbon atom to which both the amino and carboxyl groups are
covalently linked. Thus, these groups are designated the alpha-amino
(α-NH3+) and
the alpha-carboxyl (α-COO-)
groups. The remaining two covalent bonds of glycine's Cα
carbon are are linked to hydrogen atoms. Thus,
glycine is a symmetrical
structure where all mirror images are chemically and spatially identical. Glycine is the
only standard AA with a symmetric Cα-carbon
and, thus, it not stereoisometric
and is technically not an "L-amino acid," as
discussed below.
Of the remaining twenty standard AAs,
alanine, is slightly more complex in terms of its structure and
chemistry compared to glycine. The structure of alanine can be
viewed below by clicking on
Ala or
A, the
standard three-letter or one-letter abbreviations for this AA, Note that one of the
two Cα-linked hydrogen atoms
found in glycine is replaced by an α-methyl
group. The spatial location of the methyl group, relative to the
α-amino
and α-carboxyl groups
creates an asymmetric structure that is distinct in structure (i.e., non-superimposable)
compared to its mirror image isomer. By definition, alanine is an L-amino acid (as
opposed to a D-amino acid; see
Amino Acid Stereochemistry). Thus, alanine is occasionally referred to as L-alanine
(or L-Ala) but "alanine," "Ala,"
and "A," all implicitly connote the "L" stereoisomer when
referring to the standard AA.
The
α-methyl group of
Ala is
referred to as its "sidechain" or "R-group,"
in contrast to the R-group of glycine which is a hydrogen atom. All the other
standard AAs have α-amino
(except proline)
and α-carboxyl groups,
as well as one α-hydrogen,
but they all distinguished by having R-groups with different chemical
compositions. The R-groups represents the
essential structural differences between different standard AAs. Thus, as
discussed in the next two sections, AAs are frequently categorized or
classified according to their R-group chemistry and/or physical properties. For example, Ala is considered to be one of the "smaller" and
"nonpolar" amino acids. This classification seems to contradict
the fact that Ala itself is very polar with strong charge polarization
of its positive α-amino and negative α-carboxyl
groups at neutral pH. However, when AAs are covalently assembled into
polypeptides, amino acids "condense" to form neutral peptide bonds covalently
linking one amino acid "residue"
to the next in a linear polypeptide chain. In this process, the
charged α-amino and
α-carboxyl
groups disappear with the formation of the peptide bond and the release of a water molecule. Thus, the R-group of each
AA residue in a polypeptide
chain defines its major chemical contribution to the polypeptide. For
example, the interactions between R-groups of the AA residues of a protein,
which is usually no more than a long polypeptide chain, determines exactly how
that protein will fold up into a specific shape and create surfaces for specific
interactions with other molecules in its surroundings.
