More properly known as alpha-amino acids, their general structure is:

Nineteen of the twenty amino acids have the same arrangement around the central alpha-carbon: a. an amino group, b. a carboxyl group, c. a hydrogen, and d. an R group (called the “side chain”) which differs for each amino acid. Recall that when 4 different groups are attached to a carbon atom, stereoisomers are possible. Therefore, amino acids are designated as D- and L-amino acids. Not all the amino acids have D- and L- isomers, but for those that do, only the L- forms are incorporated into proteins.

An important property of amino acids is their net charge, derived from the ionization of weakly acidic or basic groups. The net charge on a group changes as the hydrogen ion concentration (pH) changes because of the association of hydrogen ions with the groups.

Recall that for a weak acid:

RCOOH  <=> H+ + RCOO

This equilibrium is characterized by a constant Ka for each individual group.

This equilibrium shows that lowering the pH (increasing H+) will drive the equilibrium to the left, as written, resulting in decreased RCOO and increased RCOOH. In other words, the fraction of the molecules that are ionized will decrease. Thus the net charge on the group will decrease. For basic groups such as amino groups, the effect is the opposite. That is, the fraction of the molecules that are ionized increases with decreasing pH.

As we will see, proteins have multiple ionizable groups, so their net charge depends on the sum of the charges from all groups.

Categories of Amino Acids

Every amino acid has a 3-letter abbreviation and a one-letter code. I don’t expect you to memorize all the codes, but you will have to memorize a few (see below). Amino acids are classified according to the properties of their side chains.

1. The largest group has non-polar side chains:

a. Some have only H or CH3 in side chains: glycine (gly, G), alanine (ala, A), valine (val, V), leucine (leu, L) and isoleucine (ile, I)

b. Some contain a sulfur atom: cysteine (cys, C), methionine (met, M)

c. Two are aromatic: phenylalanine (phe, F), tryptophan (trp, W)

d. Finally, the one odd one is actually an imino acid (meaning that its immediate synthetic precursor was an imino acid (ie. it contained an imine, or C=NH group): proline (pro, P)

2.Charged side chains: basic or acidic

a. Contain carboxyl groups: glutamic acid (glu, E), aspartic acid (asp, D)

b. Contain basic groups: lysine (lys, K), arginine (arg, R), histidine (his, H)

3. Uncharged polar side chains

a. Contain hydroxyl groups: Serine (ser, S), threonine (thr, T), tyrosine (tyr, Y)

b. Contain amide groups: glutamine (gln, Q), asparagine (asn, N)

Note: You will be expected to know the structure of the following 8 amino acids: glycine (G), alanine (A), cysteine (C), serine (S), proline (P), lysine (K), aspartic acid (D), phenylalanine (F).

While only these 20 amino acids are used to make proteins, other amino acids can be found in proteins due to modifications that happen after the protein is made. This allows the introduction of specialized groups for specific purposes, and often changes the properties of the protein. A common example is phosphorylation of the hydroxyl-containing amino acids ser, thr and tyr. These phosphoamino acids have a phosphate esterified on the hydroxyl group of their side chain. You will come across a variety of other modifications as you study Biochemistry.

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