Classified by Group

Amino Acids Classified by Group

In this section we will look at categories of amino acids based on the nature of their side groups. As individual amino acids the amino group and acid group dominate the properties of the molecules. However, when amino acids combine to form proteins it is the properties of the side chains only that determines the properties of the protein. For that reason, let's look at them arranged by group. These amino acids are listed by group in Example 2 of your workbook.

Nonpolar Alkyl Groups

Glycine, alanine, valine, leucine and isoleucine all contain alkyl side chains. Glycine's side chain consists of a single hydrogen atom, making glycine the only common amino acid that is not optically active. Alanine contains a methyl side chain. Valine contains an isopropyl side chain. With leucine and isoleucine, again you can see alkyl side chains.

Structures of amino acids with nonpolar side groups (Ex. 2 - Gly, Ala, Val, Leu, Ile). [68006.jpg]

Since their side chains are all nonpolar and therefore hydrophobic, these amino acids are referred to as hydrophobic amino acids. This is true in spite of the fact that the carboxylic acid and amine groups make the individual amino acid molecules polar rather than nonpolar.

Hydroxyl Groups

The second group of amino acids consists of the two with hydroxyl groups on their side chains: serine and threonine. Because hydroxyl groups are polar and capable of hydrogen bonding, these amino acids are hydrophilic.

Structures of amino acids with hydroxyl side groups (Ex. 2 - Ser, Thr). [68007.jpg]

Sulfur Groups

The third group shows the two amino acids with sulfur atoms in their side chains: cysteine and methionine.

Structures of amino acids with sulfur side groups (Ex. 2 - Cys, Met). [68008.jpg]

The amino acid cysteine can, under appropriate conditions, bond to a second molecule of cysteine through its side chain. The resulting bond is between the sulfur atoms of the two cysteine molecules and is called a disulfide bridge. The new molecule that forms is called cystine. This ability of cysteine to form disulfide bridges will turn out to be important in maintaining the structure of some proteins.

Equation with structures showing conversion of cysteine to cystine. [68009.jpg]

Note that this reaction involves the removal of two hydrogen atoms along with their electrons. It is therefore an oxidation reaction. The reaction can be reversed by replacing the two hydrogen atoms and splitting apart the two sulfur atoms. The reverse of this reaction is, of course, a reduction reaction. Anyone who has had a hair permanent has been a participant in this reversible reaction. I'll explain that later, when we get to hair protein and the tertiary structure of proteins.

Annotated equation showing conversion of cysteine to cystine. [68010.jpg]

Carboxylic Acid Groups

The next group consists of the amino acids that have a second carboxylic acid group as part of the side chain. These are aspartic acid and glutamic acid. Because of the acidity of the carboxylic acid group on the side chain, these amino acids are not only polar, but can become negatively charged because, in solution, the acidic proton is transferred to a water molecule, leaving a negatively charged carboxylate ion.

Structures of amino acids with carboxylic acid side groups (Ex. 2 - Asp,Glu). [68011.jpg]

Monosodium glutamate (MSG) is a salt of glutamic acid that is formed when one of the acidic hydrogen atoms is lost and replaced by a sodium ion.

Structure of MSG. [68012.jpg]

Amide Groups

These two amino acids are very similar to the previous, but the side chains contain amide groups instead of carboxylic acid groups. The amide group is customarily written -CONH₂ in condensed structural formulas. The amide formed from glutamic acid is called glutamine and the amide formed from aspartic acid is called asparagine.

Structures of amino acids with amide side groups (Ex. 2 - Asn, Gln). [68013.jpg]

These two amino acids are easily converted to the original acidic amino acids via hydrolysis reactions that occur in the presence of moderate concentrations of hydronium (or hydroxide ions to make aspartate and glutamate).

Structures of amino acids showing hydrolysis of Asn and Gln to Asp and Glu (Ex. 2 - Asn, Gln, Asp, Glu). [68014.jpg]

Amino Groups

The sixth group consists of the three amino acids that contain one or more amino groups in the side chain: lysine, arginine and histidine. (unfortunately lysine got left out of this picture.) Because amine groups can accept protons, they are bases and these amino acids are considered basic amino acids. In solution they can accept a proton from water to become positively charged. In arginine and histidine it is the double bonded nitrogen atom that accepts the proton.

Structures of amino acids with amino side groups (Ex. 2 - Arg, His). [68015.jpg]

Aromatic Groups

The next group consists of three amino acids whose side chains contain aromatic ring structures: phenylalanine, tyrosine and tryptophan. Because of its hydroxyl group, tyrosine is polar. Tryptophan, on the other hand, is non-polar in spite of the nitrogen atom in its ring. This is because of the large size of the two combined rings. Phenylalanine is also non-polar.

Sometimes the aromatic rings are drawn in this style. Either way they are the same compounds.

Structures of aromatic amino acids (Phe, Tyr, Trp). [68018.jpg]

Looped Group

The last amino acid, proline, is unusual in that the side chain bends around to form a ring by bonding to the amine group. Actually this makes the molecule an imino acid rather than an amino acid. That is a distinction that we will not worry about. It is non-polar and wherever it occurs in a protein, it causes a sharp bend in the chain of amino acids.

Structure of Pro (Ex. 2). [68019.jpg]

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