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Amino acids are the building blocks of proteins. Different amino acids may combine to form linear chains called polypeptides. Different polypeptides have different functions and so the type and arrangement of amino acids that comprises them is unique. Changes in the arrangement of the amino acids can lead to having the polypeptide not functioning well for its supposed purpose.
Amino acids are compounds any compounds that contains an amino and a carboxylic acid groups in its structure. In the context of biomolecules, α-amino acids are more important. In α-amino acids, the amino group is attached to the α-carbon or the carbon adjacent to the carboxy carbon. In this article, the general term amino acids will be used to refer to the α-amino acids.
Since all amino acids contain an amino and a carboxy group, the structural differences of amino acids arise from the variety of R groups that can be present. Different R groups will have varying degrees and types of interaction with the environment and other components. Understanding the chemistry of the side chains of amino acids is important in understanding properties of individual amino acids and the proteins they form.
There are 21 common α-amino acids found in all proteins or polypeptides. Humans can synthesize some of these amino acids, while the others are obtained by the diet we have. The ones we obtain from our diet are called essential amino acids. The 9 essential amino acids are histidine, isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan, and valine. The rest of the amino acids will be named later in the article.
Amino acids can be classified in a variety of ways. One common way of classification is based on their interaction with water. There are amino acids that are considered hydrophobic (water-fearing), hydrophilic (water-loving), and or ionic. Depending on the type of R group present, one can classify if the amino acid will belong to any of the three groups.
Hydrophobic Amino Acids
Hydrophobic amino acids are those that whose side chains are considered non-polar. Since the solvent water is a polar molecule, the non-polar side chains do not like to interact the solvent and so in a protein structure, these R groups are usually buried in the core of the protein. Below are the structures of the different amino acids in this group.
The smallest amino acid is Glycine. This is considered a hydrophobic amino acid because its side chain is just a single hydrogen atom. Unlike most amino acid where the alpha carbon is chiral (it has four different substituents around it), glycine is the only one with no chiral center. Other amino acids of this group are those with hydrocarbon side chains. These are isoleucine, alanine, leucine, and valine. Hydrocarbon side chains are also considered non-polar due to presence of only C and H atoms which have close electronegativity values. Amino acids containing aromatic side chains are also part of this group. These are Phenylalanine, tyrosine, and tryptophan. Methionine and Proline are also members of this group because of their unique structural characteristics. Methionine has a thioether group while proline contains a cyclic structure where the amino and the α-carbons are part of the cycle.
Hydrophilic Amino Acids
Hydrophilic amino acids are those whose side chains are polar and not readily ionizable. Common functional group present in these side chains are carboxyamide, sulfhydryl and hydroxyl groups. Six amino acids are members of this group. The amino acids with carboxyamide functional groups are asparagine and glutamine. They are amide derivatives of aspartate and glutamate, respectively. Amino acids with sulfhydryl groups is cysteine. Cysteine molecules when oxidized tend to form disulfide linkages. The amino acids with hydroxyl groups in their side chains are serine, threonine and tyrosine.
Ionic Amino Acids
The last group of amino acids are the ionic amino acids. These are the amino acids that are ionized depending on the reaction condition. These classification is further divided into two groups: basic and acidic. Basic amino acids are those that contain side chains that tends to accept protons. They have additional amino groups in their side chains that makes them more basic. Amino acids of this group include lysine, histidine and arginine. Depending on the pH of the system, the amino groups in the side chains can be protonated. Acidic amino acids are those whose side chains contain additional carboxyl groups. Depending on the pH of the solution, these side chains can be deprotonated. Amino acids of this group include aspartic acid and glutamic acid. Below are the structures of the different ionic amino acids.
Carboxyl and amino groups have almost the same strength of acidity and basicity, respectively. In fact, at neutral pH of 7, the carboxy group of the amino acid is in its deprotonated form, while the amino group is in its protonated form. When this occur, the amino acid form a zwitterion or a dipolar ion. Because of the dipolar nature of amino acids, they tend to exhibit some uncommon properties. Generally, amino acids have high melting points. They are also wat soluble in water than in ether and dichloromethane. They have large dipole moments than normal amines and carboxylic acids. They are less acidic than normal carboxylic acid and less basic than normal amines. Because of having both a basic and acidic part in its structure, amino acids are considered also as amphoteric compounds, that is it both exhibits basic and acidic properties.
At neutral pH, both the amino and carboxylic acid groups exist in its ionic form. When you lower the pH of the solution, the –COO– tend to accept a proton to form the –COOH group. On the other hand, when you increase the pH of the solution, the –NH3+ tend to release a proton to produce –NH2 group. In this way, amino acids tend to be cationic in acidic solution, and anionic in basic solution. Presence of other carboxylic acid, amino, and hydroxyl group in the side chains also contribute in the degree of ionization in varying pH values.
The correct answers can be found below the references.
1. Which amino acid can form disulfide linkage when oxidized?
2. What do you call the ionic form of an amino acid where the carboxylic acid group is deptotonated while the amino group is protonated?