Note: this is drawn "flat" for clarity, but the C_a are still tetrahedral (the H atom on the C_a is also not shown in this diagram)

Key structural features:

• A "
peptide bond" is formed by a condensation reaction between the carboxylic acid of one amino acid with the amino group of the next amino acid
• The amino acid R1, at the "amino terminus" of the polymer is the "first" amino acid. The residue (R₃ in the above diagram) at the carboxyl terminal is known as the "last" amino acid. These termini define the directionality of the protein.

There are 20 common amino acids. They are composed of C, H, O, N and S atoms. They are structurally and chemically different, and also differ in size and volume. Some are branched structures, some are linear, some have ring structures. One of the 20 common amino acids is actually an imino acid. A typical grouping of their chemical nature is as follows:

• Nonpolar (hydrocarbons and one sulfur-containing amino acid).
Dispersion forces and hydrophobic effects predominate in their interactions. They cannot H-bond with water and these side chains have a characteristic hydrophobic effect in water.
• Polar uncharged. Contain functional groups that
can H-bond with water and other amino acids. Include C, H, O, N and S atoms.
• Acidic. Contain a carboxylic acid functional group with a
negative charge at neutral pH. Can H-bond with water, can form ionic interactions, and can also serve as nucleophiles or participate in acid-base chemistry.
• Basic. Nitrogen containing bases (e.g. guanidino, imidazole or amino groups) with a net
positive charge at neutral pH. Can serve as proton donors in chemical reactions, and form ionic interactions.

The amino acids have a name, as well as a three letter or single letter mnemonic code:

In addition to the 20 common amino acids, there are several uncommon ones found:

• Hydroxylysine and hydroxyproline. These are found in the protein collagen. Collagen is a fibrous protein made up of three polypeptides that form a stable assembly, but only if the proline and lysine residues are hydroxylated. (requires vitamin C for reduction of these amino acids to hydroxy form)
• Thyroxine, an iodinated derivative of tyrosine, found in thyroglobulin (produced by thyroid gland; requires iodine in diet)
• g
-carboxyglutamic acid (i.e. glutamic acid with two carboxyl groups) found in certain blood clotting enzymes (requires vitamin K for production)
• N-methyl arginine and n-acetyl lysine. Found in some DNA binding proteins known as histones

Amino acid derivatives not found in proteins

Some amino acids are made that are not intended for incorporation into proteins, rather they have important functionalities on their own

• Serotonin (derivative of tryptophan) and
g-amino butyric acid (a derivative of glutamic acid) are both neurotransmitters
• Histamine (derivative of histidine) involved in allergic response
• Adrenaline (derivative of tyrosine) a hormone
• Various antibiotics are amino acid derivatives (penicillin)

Acid-base Chemistry of Amino Acids

Amino acids by themselves have amino (pKa ~9.0-10.5) and carboxyl groups (pKa ~2.0-2.4) that can be titrated

• At neutral pH the amino group is protonated, and the carboxyl group is deprotonated

The side chains of acid and basic amino acids, and some polar amino acids can also be titrated:

• Physiological pH is near neutral. It would appear that only histidine is of physiological relevance. However, pKa values can be shifted significantly by neighboring charged groups in complex molecular structures.

Reactions of amino acids

• Free amino acids (excluding proline) share similar chemical reactivities due to the common amino and carboxyl groups.
• Different amino acid side chains have different chemical reactivities. Therefore,
reactivities of different proteins reflects the composition of the unique sequence of amino acids in their structure.

Some common carboxyl-group reactivities:

NOTE: This can covalently link two polypeptide chains in a "disulfide bond" crosslink

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