Amino acids and its Classification | Online Biotech Notes

Online Biotech Notes

Amino acids

• Amino acids are a group of organic compounds containing two functional groups— amino and carboxyl. The amino group (—NH2) is basic while the carboxyl group (—COOH) is acidic in nature.

General structure of amino acids

• The amino acids are termed as α-amino acids, if both the carboxyl and amino groups are attached to the same carbon atom, as depicted below

• The α-carbon atom binds to a side chain represented by R which is different for each of the 20 amino acids found in proteins. The amino acids mostly exist in the ionized form in the biological system (shown above).

General structure of amino acids

Optical isomers of amino acids

• If a carbon atom is attached to four different groups, it is asymmetric and therefore exhibits optical isomerism. The amino acids (except glycine) possess four distinct groups held by α-carbon. Thus all the amino acids (except glycine where R = H) have optical isomers.
• The structures of L-and D-amino acids are written based on the configuration of L-and D-glyceraldehyde as shown in Fig.4.1. The proteins are composed of L-α-amino acids.

Optical isomers of amino acids

Classification of amino acids

• There are different ways of classifying the amino acids based on the structure and chemical nature, nutritional requirement, metabolic fate etc.

A Amino acid classification based on the structure :

A comprehensive classification of amino acids is based on their structure and chemical nature.

• Each amino acid is assigned a 3 letter or 1 letter symbol. These symbols are commonly used to represent the amino acids in protein structure. The 20 amino acids found in proteins are divided into seven distinct groups.

1. Amino acids with aliphatic side chains : 

• These are monoamino monocarboxylic acids. This group consists of the most simple amino acids—glycine, alanine, valine, leucine and isoleucine. The last three amino acids (Leu, Ile, Val) contain branched aliphatic side chains,
• hence they are referred to as branched chain amino acids.

2. Hydroxyl group containing amino acids : 

• Serine, threonine and tyrosine are hydroxyl group containing amino acids. Tyrosine—being aromatic in nature—is usually considered under aromatic amino acids.

3. Sulfur containing amino acids : 

• Cysteine with sulfhydryl group and methionine with thioether group are the two amino acids incorporated during the course of protein synthesis. Cystine, another important sulfur containing amino acid, is formed by condensation of two molecules of cysteine.

4. Acidic amino acids and their amides : 

• Aspartic acid and glutamic acids are dicarboxylic monoamino acids while asparagine and glutamine are their respective amide derivatives. All these four amino acids possess distinct codons for their incorporation into proteins.

5. Basic amino acids : 

• The three amino acids lysine, arginine (with guanidino group) and histidine (with imidazole ring) are dibasic monocarboxylic acids. They are highly basic in character.

6. Aromatic amino acids : 

• Phenylalanine, tyrosine and tryptophan (with indole ring) are aromatic amino acids. Besides these, histidine may also be considered under this category.

7. Imino acids : 

• Proline containing pyrrolidine ring is a unique amino acid. It has an imino group (=NH), instead of an amino group (–NH2) found in other amino acids. Therefore, proline is an α-imino acid.

Heterocyclic amino acids

• Histidine, tryptophan and proline.

B Classification of amino acids based on polarity :

Amino acids are classified into 4 groups based on their polarity. Polarity is important for protein structure.

1. Non-polar amino acids :

These amino acids are also referred to as hydrophobic (water hating). They have no charge on the ‘R’ group. 

The amino acids included in this group are — alanine, leucine, isoleucine, valine, methionine, phenylalanine, tryptophan and proline.

2. Polar amino acids with no charge on ‘R’ group

These amino acids, as such, carry no charge on the ‘R’ group. They however possess groups such as hydroxyl, sulfhydryl and amide and participate in hydrogen bonding of protein structure. The simple amino acid glycine (where R = H) is also considered in this category. The amino acids in this group are— glycine, serine, threonine, cysteine, glutamine, asparagine and tyrosine.

3. Polar amino acids with positive ‘R’ group :

The three amino acids lysine, arginine and histidine are included in this group.

4. Polar amino acids with negative ‘R’ group : 

The dicarboxylic monoamino acids— aspartic acid and glutamic acid are considered in

this group.

C Nutritional classification of amino acids :

• The 20 amino acids are required for the synthesis of variety proteins, besides other biological functions. However, all these 20 amino acids need not be taken in the diet.

• Based on the nutritional requirements, amino acids are grouped into two classes—essential and nonessential.

1. Essential or indispensable amino acids : 

• The amino acids which cannot be synthesized by the body and, therefore, need to be supplied through the diet are called essential amino acids. They are required for proper growth and maintenance of the individual. The ten amino acids listed below are essential for humans (and also rats) :

Arginine, Valine, Histidine, Isoleucine, Leucine, Lysine, Methionine, Phenylalanine, Threonine, Tryptophan.

[The code A.V. HILL, MP., T. T. (first letter of each amino acid) may be memorized to recall essential amino acids.The two amino acids namely arginine and histidine can be synthesized by adults and not by growing children, hence these are considered as semi–essential amino acids (remember Ah, to recall). Thus, 8 amino acids are absolutely essential while 2 are semi-essential.

2. Nonessential or dispensable amino acids :

• The body can synthesize about 10 amino acids to meet the biological needs, hence they need not be consumed in the diet. These are—glycine, alanine, serine, cysteine, aspartate, asparagine, glutamate, glutamine, tyrosine and proline.

D Amino acid classification based on their metabolic fate : 

The carbon skeleton of amino acids can serve as a precursor for the synthesis of glucose (glycogenic) or fat (ketogenic) or both. From metabolic view point, amino acids are divided into three groups.

1. Glycogenic amino acids :

• These amino acids can serve as precursors for the formation of glucose or glycogen. e.g. alanine, aspartate, glycine, methionine etc.

2. Ketogenic amino acids :

• Fat can be synthesized from these amino acids. Two amino acids leucine and lysine are exclusively ketogenic.

3. Glycogenic and ketogenic amino acids : 

• The four amino acids isoleucine, phenylalanine, tryptophan, tyrosine are precursors for synthesis of glucose as well as fat.

Selenocysteine – the 21st amino acid

• As already stated, 20 amino acids are commonly found in proteins. In recent years, a 21st amino acid namely selenocysteine has been added. It is found at the active sites of certain enzymes/proteins (selenoproteins). e.g. glutathione peroxidase, glycine reductase, 5′-deiodinase, thioredoxin reductase. 
• Selenocysteine is an unusual amino acid containing the trace element selenium in place of the sulfur atom of cysteine. Incorporation of selenocysteine into the proteins during translation is carried out by the codon namely UGA. It is interesting to note that UGA is normally a stop codon that terminates protein biosynthesis. Another unique feature is that selenocysteine is enzymatically generated from serine directly on the tRNA (selenocysteinetRNA), and then incorporated into proteins.

Pyrrolysine – the 22nd amino acid?

• In the year 2002, some researchers have described yet another amino acid namely pyrrolysine as the 22nd amino acid present in protein. The stop codon UAG can code for pyrrolysine.

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