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Chapter: Biochemistry: Proteins

Classification of amino acids

The amino acids are classified based on the nature of their R groups, in particular their polarity or tendency to interact with water at biological pH.

Classification of amino acids

The amino acids are classified based on the nature of their R groups, in particular their polarity or tendency to interact with water at biological pH. The polarity of the R groups varies widely, from totally non polar to highly polar.


1. Non-polar, aliphatic R-group

The R-group in this class of amino acids are non polar (or) hydrophobic. Six amino acids come under this class, which are glycine, alanine, valine, leucine, isoleucine and methionine.

Glycine has the simplest structure. Methionine is one of the two sulphur containing aminoacids and has a non polar thio ether group in its side chain.


2. Aromatic R groups

Phenylalanine, tyrosine and tryptophan, with their aromatic side chains, are relatively non-polar. All can participate in hydrophobic interactions. The hydroxyl group of tyrosine can form hydrogen bond with other compounds and it is an important functional group in some enzymes. Tyrosine and tryptophan are significantly more polar than phenyl alanine because of the hydroxyl group of tyrosine and the nitrogen of the indole ring in tryptophan.


3. Polar-uncharged R groups

The R groups of these amino acids are more soluble in water or more hydrophilic, than those of the non polar amino acids because they contain functional groups that form hydrogen bonds with water. This class of amino acids includes serine, threonine, cysteine, proline, asparagine and glutamine.

The polarity of serine and threonine is contributed by their hydroxyl groups; that of cysteine by its sulphydryl (-SH) group; and that of asparagine and glutamine by their amide groups. Proline has a distinct cyclic structure and is only moderately polar. Proline has an imino group. Cysteine is readily oxidized to form a covalently linked dimeric amino acid called cystine, in which two cysteine molecules are joined by a disulphide bond.


4. Positively charged (basic) R-groups

The most hydrophilic R groups are those that are either positively (-NH3+) or negatively (-C00-) charged. The amino acids in which the R groups have significant positive charges at pH 7.0 are lysine, arginine and histidine.


5. Negatively charged (Acidic) R groups

The two amino acids having R groups with a net negative charge at pH 7.0 are aspartate and glutamate.

Based on their inclusion in the diet, amino acids are classified into two groups, namely essential amino acids and non-essential amino acids.


6. Essential amino acids

Certain amino acids can not be synthesized by the living organisms. They must be compulsarily included in the diet for normal health.These amino acids are called essential amino acids. For human being about 10 amino acids are considered as essential.eg,

1. Arginine 

2. Histidine 

3. Isoleucine 

4. Leucine 

5. Lysine 

6. Methionine

7. Phenyl alanine

8. Threonine

9. Tryptophan

10. Valine


7. Non-essential amino acids

Certain amino acids can be synthesized in the cells from essential amino acids or from other compounds. So these amino acids need not be included in the diet. They are called non-essential amino acids.


8. Non protein amino acids

Certain amino acids which do not exist in proteins are called non protein amino acids eg.

Ornithine and b-alanine etc..


9. Peptide bonds

In proteins, amino acids are linked together by linkages called peptide bonds. The carboxyl group of one amino acid is joined to the α amino group of another amino acid by a peptide bond.

The peptide bond is also called as the amide bond. The two amino acids, joined by a peptide bond, constitute a dipeptide. The dipeptide is formed by simple condensation reaction.

The product formed by a peptide bond is called a peptide. The compound formed by the linking of three amino acids is called as tripeptide. A peptide formed of less than 10 amino acids constitute an oligopeptide. More than 10 amino acids join together to form a polypeptide chain (Fig. 5.2).

Protein is made up of one or more polypeptide chains

Many proteins, such as myoglobin, consist of a single polypeptide chain. Others contain two or more chains, which may be either identical or different. For example haemoglobin is formed of 4 polypeptide chains, of which two a chains are of one kind and the other two b chains are of another kind.

N and C terminal ends of protein

An amino acid in a polypeptide is called a residue. A polypeptide have two ends, namely amino and carboxyl terminal end. The end of the polypeptide chain containing amino group is called amino terminal or N-terminal. The end of the polypeptide chain containing carboxyl group is called carboxyl terminal or C-terminal. The terminal amino acid with the free amino group is called N-terminal amino acid and the terminal amino acid with the free carboyl group is called C-terminal amino acid.


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