An amino acid is the simplest unit of a protein and has distinct structural characteristics that are responsible for the different types of interaction it can participate in inside the body. It is important to study the structure of amino acids as the function of a protein is highly affected by the type of amino acids that constitute the protein. In this article, the structural features and properties of amino acids will be discussed. Further, the classification of amino acids based on their side chains is reviewed, in addition to the ionization of amino acids.
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Amino acids Structure


Amino Acids

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 comprise them are unique. Changes in the arrangement of the amino acids can lead to the improper function of polypeptides.

general structure of amino acids

General Structure of Amino Acids, prepared by Mark Xavier Bailon

An amino acid is any compound whose structure contains an amino group and a carboxyl group. In the context of biomolecules, α-amino acids are more important. For α-amino acids, the amino group is attached to the α-carbon or the carbon adjacent to the carboxyl carbon. In this article, the term amino acids will be used to generally refer to α-amino acids.

Since all amino acids contain an amino group and a carboxyl group, the structural differences in amino acids arise from the variety of R groups that can be present. Different R groups have varying degrees and types of interaction with the environment and other components. Understanding the chemistry of amino acid side chains is important for understanding the properties of individual amino acids and the proteins they form.

Twenty-one α-amino acids are commonly found in all proteins or polypeptides. Humans synthesize some of these amino acids, while the others are obtained via diet. The ones obtained from diet are called essential amino acids. There are 9 essential amino acids and these include:

  1. Histidine
  2. Isoleucine
  3. Leucine
  4. Lysine
  5. Methionine
  6. Phenylalanine
  7. Threonine
  8. Tryptophane
  9. Valine

The rest of the amino acids will be mentioned later in the article.

Amino acids can be classified in many ways. One common method of classification is based on their interaction with water. Amino acids are considered hydrophobic (water-repelling), hydrophilic (water-attracting), or ionic. Depending on the type of R group, it can be determined whether an amino acid will belong to any of the 3 groups.

Hydrophobic Amino Acids

Hydrophobic amino acids have side chains that are considered non-polar. Since water is a polar molecule, the non-polar side chains repel water 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.

Hydrophobic Amino Acids

Hydrophobic Amino Acids, prepared by Mark Xavier Bailon

Glycine

The smallest amino acid is glycine. Glycine is considered a hydrophobic amino acid because its side chain is just a single hydrogen atom. Unlike most amino acids where the α-carbon is chiral (i.e., has 4 different substituents around it), glycine is the only one with no chiral center.

Other amino acids in this group have hydrocarbon side chains, and include:

  • Isoleucine
  • Alanine
  • Leucine
  • Valine

Hydrocarbon side chains are also considered non-polar due to the 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 included 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

Hydrophilic Amino Acids, Prepared by Mark Xavier Bailon

Hydrophilic amino acids have polar side chains that are not readily ionizable. Common functional groups present in these side chains are carboxamide, sulfhydryl, and hydroxyl groups. Six amino acids are members of this group.

The amino acids with carboxamide functional groups are asparagine and glutamine. They are amide derivatives of aspartate and glutamate, respectively.

Cysteine has sulfhydryl groups and when cysteine molecules are oxidized, they 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 amino acids are ionized depending on the reaction condition. They are divided into the 2 following groups:

  1. Basic
  2. Acidic

Basic amino acids contain side chains that tend to accept protons. They have additional amino groups in their side chains that make them more basic. Amino acids in 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 have side chains that contain additional carboxyl groups. Depending on the pH of the solution, these side chains can be deprotonated. Amino acids in this group include aspartic acid and glutamic acid. Below the structures of the different ionic amino acids are highlighted.

Ionic Amino Acids

Ionic Amino Acids. Prepared by Mark Xavier Bailon

Ionization

The carboxyl and amino groups have almost the same strength with respect to acidity and basicity, respectively. At a neutral pH of 7, the carboxyl group of the amino acid is in its deprotonated form, while the amino group is in its protonated form. When this occurs, the amino acid forms a zwitterion or 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 more soluble in water than in ether or dichloromethane. They have large dipole moments compared to normal amines and carboxylic acids, and are less acidic than normal carboxylic acid and less basic than normal amines. Because amino acids possess basic and acidic parts in their structure, they are also considered as amphoteric compounds, exhibiting both basic and acidic properties.

At a neutral pH, both the amino and carboxyl groups exist in their ionic form. When the pH of a solution is lowered, the –COO tends to accept a proton to form the –COOH group. However, when the pH of the solution is increased, the –NH3+ tends to release a proton to produce the –NH2 group. In this way, amino acids tend to be cationic in acidic solution, and anionic in basic solution. The presence of another carboxyl, amino, or hydroxyl group in the side chains also contributes to the degree of ionization in varying pH values.

Review Questions

The correct answers can be found below the references.

1. Which amino acid can form a disulfide linkage when oxidized?

  1. Methionine
  2. Cysteine
  3. Lysine
  4. Arginine

2. What do you call the ionic form of an amino acid where the carboxylic acid group is deprotonated while the amino group is protonated?

  1. Carboxylate
  2. Amino
  3. Zwitterion
  4. Bipolarity
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