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Chapter: Basic Concept of Biotechnology - Biomolecules

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Amino Acids and Classification of Amino Acids

The hydrolysis of each polypeptide yields a set of amino acids, referred to as the molecule’s amino acid composition.

Amino Acids

The hydrolysis of each polypeptide yields a set of amino acids, referred to as the molecule’s amino acid composition. The structures of the 20 amino acids that are commonly found in naturally occurring polypeptides. Amino acids are the most versatile small biomolecules. They fulfil a number of extremely important roles in biology. These include: building blocks of proteins which are polymers of amino acids, precursors of hormones, and precursors of molecules with specialized physiological functions, e.g., the neurotransmitter dopamine and the hormone thyroxine are both derivatives of the amino acid tyrosine. As the name implies, amino acids contain amino and carboxyl groups. They can be divided into groups based on acidic, basic, and neutral properties when dissolved in water. They are also classified according to solubility, e.g., hydrophilic and hydrophobic. There are 20 so-called amino acids in proteins; however, one of these, proline, is in fact an imino acid. Nineteen of the 20 amino acids are optically active, i.e., they are capable of rotating plane polarized light either to the right (dextrorotary) or left (levorotary).


Classification of Amino Acids

  Amino acids are classified as acidic, basic or neutral depending upon the relative number of amino and carboxyl groups in their molecule. Equal number of amino and carboxyl groups makes it neutral; more number of amino than carboxyl groups makes it basic and more carboxyl groups as compared to amino groups makes it acidic. The amino acids, which can be synthesized in the body, are known as nonessential amino acids. On the other hand, those which cannot be synthesized in the body and must be obtained through diet are known as essential amino acids (marked with asterisk in Table 14.2). Amino acids are usually colorless, crystalline solids. These are water-soluble, high melting solids and behave like salts rather than simple amines or carboxylic acids. This behavior is due to the presence of both acidic (carboxyl group) and basic (amino group) groups in the same molecule. In aqueous solution, the carboxyl group can lose a proton and amino group can accept a proton, giving rise to a dipolar ion known as twitter ion. This is neutral but contains both positive and negative charges.

     In twitter ionic form, amino acids show amphoteric behavior as they react both with acids and bases. Except glycine, all other naturally occurring α-amino acids are optically active, since the α-carbon atom is asymmetric. These exist both in ‘D’ and ‘L’ forms. Most naturally occurring amino acids have L configuration. L-Amino acids are represented by writing the –NH2 group on left hand side.

Non-proteinogenic amino acids:

Amino acids are multifunctional organic compounds that contain at least one amino and one carboxyl group attached to a central carbon atom, whose side chains may vary in length and branching as well as in content of other functional groups or aromatic rings. Amino acids may form numerous molecular structures, where the relative position of the amino and carboxyl function allows their general classification as 2-, 3-, 4- etc. (also referred to as α, β, γ, etc.) amino acids. Most amino acids have at least one asymmetric carbon and are chiral. Amino acids are classified as non-protein when they are not part of the 22 such molecules that are translated into proteins by the standard genetic code. Aside from the twenty standard amino acids and the two special amino acids, there are a vast number of "Non-proteinogenic amino acids (NPA)". Two of these can be encoded in the genetic code, but are rather rare in proteins. Selenocysteine is incorporated into some proteins at a UGA codon, which is normally a stop codon. Pyrrolysine is used by some methanogenic bacteria in enzymes that they use to produce methane. It is coded for with the codon UAG (Krzycki, 2005).

Examples of nonstandard amino acids that are not found in proteins include lanthionine, 2-aminoisobutyric acid, dehydroalanine and the neurotransmitter gamma-aminobutyric acid. Nonstandard amino acids often occur as intermediates in the metabolic pathways for standard amino acids - for example ornithine and citrulline occur in the urea cycle, part of amino acid catabolism (Curis et al., 2005). Nonstandard amino acids are usually formed through modifications to standard amino acids. For example, homocysteine is formed by the transsulfuration pathway from cysteine or as an intermediate in S-adenosyl methionine metabolism (Brosnan and Brosnan, 2006).

Of the thousands of known non-protein amino acids (NPA), about 300 occur in plants. They are found mostly in a small number of families, such as the Leguminosae, Cucurbitaceae, Sapindacae, Aceraceae and Hippocastenaceae. Many of these NPA are structurally similar to the components of common proteins. The incorporation of NPAs into proteins may be associated with autoimmune diseases in humans. Furthermore, there is evidence of a phenotypic conversion of ras-transformed human cells to normal due to incorporation of the tyrosine analogue, azatyrosine, into cellular protein. One NPA that has received some attention is canavanine, (L-2-amino-4-(guanidinooxy) butyric acid), the guanidinooxy structural analogue of arginine.



Role of Non-proteinogenic amino acids

In cells, especially autotrophs, several non-proteinogenic amino acids are found as metabolic intermediates. However, despite the catalytic flexibility of PLP-binding enzymes, many amino acids are synthesised as keto-acids (e.g. 4-methyl-2-oxopentanoate to leucine) and aminated in the last step, thus keeping the number of non-proteinogenic amino acid intermediates fairly low. Ornithine and citrulline occur in the urea cycle, part of amino acid catabolism (Curis et al., 2005). In addition to primary metabolism, several non-proteinogenic amino acids are precursors or the final production in secondary metabolism to make compounds such as toxins.

Non-protein amino acids have been implicated in plant defense against insect pests. Direct toxic effects occur through interference with animal amino acid metabolism. Nitrogen is stored in a form that ismetabolically inaccessible to herbivores. Some specialist herbivores have specific detoxification mechanisms.

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