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The simplest and smallest of the standard AAs is glycine, abbreviated Gly or G , which can be viewed by clicking the left or right "button" here in order to produce an image in the lowerleft or the lower right window below, respectively. The image of glycine corresponds to its predominant ionization state at pH = 7 where the amino nitrogen is protonated (pKn = 9.2) and therefore positively-charged and the carboxyl oxygen is deprotonated (pKc = 2.2) and therefore negatively-charged.

The "alpha-carbon" is, by convention, the central carbon atom to which both the amino- and carboxyl-groups are covalently-linked, thus, these groups are the alpha-amino and alpha-carboxyl groups of the AA. Because the remaining two covalent bonds of the alpha-carbon of glycine are with hydrogen atoms, glycine is a symmetrical structure where mirror images are chemically and spatially identical. Thus, glycine is the only standard AA with a symmetric alpha-carbon and, as a result, it not stereoisometric and is technically not an "L-amino acid," as discussed later in the next lesson.

Alanine, abbreviated Ala or A , is slightly more complex in terms of its structure and chemistry as compared to glycine. Once you have replaced glycine with alanine in one of the windows below, note that one of the alpha-carbon-linked hydrogen atoms of glycine has been effectively replaced by a methyl group in alanine. The spatial location of the methyl group, relative to the alpha-amino and alpha-carboxyl groups, defines this as an L-amino acid (as opposed to a D-amino acid; see section 2A ). Thus, alanine is sometimes referred to as L-alanine (or L-Ala) even though "alanine" and "Ala" both connote this particular stereoisomer whenever reference to a standard amino acid is being made.

The methyl group of Ala is referred to as its "sidechain" or "R-group."Whereasthe R-group of glycine is a hydrogen atom, the other AAs exhibit different chemical groups in the corresponding location therefore defining the essential structural differences between different AAs. The AAs are often grouped or classified according to the chemical and/or physical properties of their corresponding R-groups. For example, Ala is considered to be one of the "small" and "nonpolar" amino acids. Obviously, Ala itself is polar given the strong charge polarization between its positive alpha-amino and negative alpha-carboxyl groups. However, these charged groups disappear when AAs are covalently assembled into polypeptides where adjacent AAs "condense" forming a neutral a peptide bond with the loss of a water molecule (and the corresponding charges). Thus, the chemical contribution each AA "residue" makes to a polypeptide is defined primarily by the properties of its corresponding R-group as discussed in the next two sections.