Biochemistry - The Chemical Reactions of Living Cells, Volume 1 - D. Metzler 1980

The Molecules of Which We Are Made
Proteins
α-Amino Acids

To understand The properties of Amino Acids both as free metabolites and as components of protein molecules, three simple facts must first be kept in mind.

1. Amino acids exist predominantly in the form of dipolar ions (zwitterions).

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Table 2-2 Structure and Chemical properties of Amino Acid Side Chains

^a Parentheses indicate the three-letter and one-letter Abbreviations for amino acid residues incorporated into Peptides and Proteins.

2. Amino acids are asymmetric and form two families: D and L (Section A.4).

3. Amino acids differ from one another in The structure of their side groups (side chains), which are designated as R in the formulas above. These groups have distinct chemical structures. Projecting from the main chain, they largely shape The surface of the polymer and determine many of the chemical and physical Properties of Proteins.

Table 2-2 presents the structural formulas of the side chains of Amino Acids Commonly Found in Proteins (the formula of Proline is shown in full). It also lists the abbreviated three-letter codes used for writing Amino acid sequences of peptides and proteins, as well as the one-letter abbreviations adopted in Introduction/18.html">Protein Evolution studies and computer programming.

When discussing matters related to Cell/13.html">Protein Structure, amino acids belonging to groups a, b, and c, along with phenylalanine and Methionine, are conventionally grouped together as nonpolar amino acids. They tend to partition into the hydrophobic environment "inside" the protein molecule. The opposite category comprises polar charged molecules (groups e and f), which typically project outward into the aqueous environment of the protein. The remaining ones form the category of polar uncharged amino acids.

An introduction to amino acid structure is best begun with Glycine, Alanine, Serine, aspartic acid, and glutamic acid.

Note that the structure of many Amino acids can be derived from that of alanine by replacing one of the hydrogen atoms with another group. For instance, replacing the ß-hydrogen of alanine yields:

The metabolic interrelationships among amino acids, which will be discussed later, will help in memorizing the structures of the remaining amino acids.

Table 2-2 also includes the pK_a values (see Chapter 4, Section B) for The amino acid side groups. If the terminal amino and carboxyl groups are free, they can also participate in acid-base reactions; the pK_a values for these groups are as follows:

Since at neutral pH the —COOH groups of glutamic and aspartic acids are fully dissociated, it is standard biochemical practice to refer to them as glutamate and aspartate, regardless of the cations present in the medium. This same suffix (-ate) is applied to other acids as well—for example, malate, oxaloacetate, phosphate, adenylate—which is also reflected in Enzyme Nomenclature, such as Lactate dehydrogenase.