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Amino Acids – Types, Classification, Genetic Code and Applications
#1
Amino acids, the tiny building blocks of proteins occupies a prominent position among all the other nutrients and are reported as the molecule of source of life in theories discussing the mysteries behind origin of life. There are 20 naturally occurring amino acids and Asparagine was the first discovered amino acid in the year 1806 followed by Cysteine, Leucine and Glycine. All the 20 amino acids involved in the construction of proteins were identified in the year 1935 and this discovery marked phenomenol significance in understanding the proteins, its structure and functions. Amino acid, as the name implies has amine (-NH2) group and carboxylic acid (-COOH) with additional functional R group which acts as a side chain. Thus amino acids possess molecules of carbon, nitrogen oxygen and hydrogen. The R group alone varies from one amino acid to the other thus contributing to 20 different natural amino acids.

Types
The 20 amino acids involved in the construction of proteins are Glycine, Valine, Leucine, Isoleucine, Arginine, Cysteine, Lysine, Proline, Threonine, Methionine, Histidine, Tyrosine, Serine, Alanine, Phenylalanine, Glutamine, Glutamate, Asparagine, Aspartic acid and Tryptophan. These 20 amino acids based on their mode of availability are divided into essential (dietary intake) and non essential amino acids (synthesized in the body through metabolic process). Out of the 20 amino acids, Glycine, Arginine, Cysteine, Proline, Tyrosine, Alanine, Glutamine, Glutamate, Arginine, Asparagine and Aspartic acid are the amino acids synthesized in the body and hence falls under the category non-essential amino acids and the rest 9 amino acids are essential that is to be supplemented through diet.

Classification
Based on the type of functional group (R group) present amino acids are classified as aliphatic, aromatic, acidic, basic, acid amide, sulfur and cyclic amino acids. Based on the characteristic of the functional group amino acids are classified as polar and non-polar amino acids. They are also classified as alpha, beta, gamma and delta amino acids based on the site of attachment of the functional group.

Genetic Code
The base sequences of DNA ( A- Adenine, G-Guanine, C-Cytosine, T-Thymine) are information centers which are copied to RNA (A-Adenine, G-Guanine, C-Cytosine, U-Uracil) through transcription and the resulting RNA with complementary base sequences to that of the DNA translates the information into proteins. The sequence of bases in the RNA dictates the type of amino acid to be synthesized and as a rule three bases codes for one aminoacid and such set of three bases is called as codon. Except for the amino acids Methionine and Tryptophan all the other amino acids are represented by more than one codon and such condition is termed as degeneracy and the different set of codons representing the same amino acid are called as Synonyms. Below are the natural amino acids and the codons specific for each amino acid.

Glycine - GGU,GGC, GGA,GGG
Valine -GUU,GUC,GUA,GUG
Leucine -CUU,CUC,CUA,CUG,UUA,UUG
Isoleucine -AUU, AUC, AUA
Arginine -CGU,CGC,CGA,CGG,AGA,AGG
Cysteine-UGU,UGC
Lysine-AAA,AAG
Proline-CCU,CCC,CCA,CCG
Threonine-ACU,ACC,ACA,ACG
Methionine-AUG
Histidine-CAU,CAC
Tyrosine-UAU,UAC
Serine-UCU,UCC,UCA,UCG,AGU,AGC
Alanine-GCU,GCC,GCA,GCG
Phenylalanine -UUU,UUC
Glutamine-CAA, CAG
Glutamate-GAA, GAG
Asparagine-AAU, AAC
Aspartic acid-GAU, GAC and
Tryptophan-UGG

Apart from these codons coding specific amino acid there are three codons which do not code for any amino acid but acts as stop signal in the protein synthesis are called as Stop codons and they are UAG, UGA and UAA. The codon AUG which codes for Methionine is also called as Start codon for it initiates the protein synthesis.

Various researches carried out in order to explore the amino acid present in different food types states the correlation between the type of amino acid present in the food and the taste of the food. For example Glutamate and Aspartic acid contribute to the sour taste of the food, Glycine, Alanine, Threonine, Proline, Serine and Glutamine are sweet factors in the food and Bitter taste of the food is contributed by Phenylalanine, Tyrosine, Arginine, Leucine, Isoleucine, Valine, Histidine and Methionine.

Applications
Amino acids are used in the preparation of feed for animals. The chelating property of the amino acid makes it a suitable element enhancing the absorption of minerals from the food by the animals. Various amino acids are used in the food industry as a flavor enhancer and also used in pharmaceuticals and cosmetic preparations. The chelating nature of the amino acids when used along with fertilizers enhances the absorption of minerals from the soil by the cultivated crops. With all these applications amino acids are on its way into the synthesis of biodegradable polymers.
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#2
Though there are ‘n’ numbers of amino acids present there are only twenty amino acids which are proved as essential amino acids and their genetic codes have been derived successfully. To this existing list of twenty amino acids enters the “Selenocysteine” the 21st amino acid whose genetic code has been identified. Selenocysteine makes its presence in almost all forms of lives from prokaryotes to eukaryotes.

Selenocysteine codon: UGA

UGA is one among the three stop codons (UAG, UGA and UAA) and these three codons acts exclusively as stop signal in protein synthesis and do not code for any other existing 20 amino acids.
Hence there must be a unique pathway in the protein synthesis involving selenocysteine which requires the regulation of UGA codon in the synthesis of selenocysteine by inhibiting its original function of termination. Yes, there are separate mechanisms for the synthesis of selenoproteins (protein containing the amino acid selenocysteine) identified in prokaryotes and eukaryotes where presence of selenium is significant.

In prokaryotes, the incorporation of selenocysteine in the protein is made possible by two factors like,
1. Stem loop structure in the 3 prime region of mRNA (untranslated)
2. Sel operon with Sel A, Sel B, Sel C and Sel D genes each of which functions uniquely aiding the synthesis of selenocysteine incorporated proteins .

In Eukaryotes, the mechanism is regulated by three factors,
1. SECIS (SeC insertion sequence)
2. SBP2 (SECIS binding protein)
3. eEFSeC (a translational factor enhances ribosomal binding)

Different selenoproteins

Iodothyronine deiodinases (3 types like DIO1,DIO2 & DIO3)
Glutathione peroxidases (5 types)
Selenophosphate synthetase (2 types)
Thioredoxin reductases (3 types)
Selenoproteins like Sel-H, I, K, M, N, O, P, R, S, T, V, W

There are about 25 different selenoproteins (contains selenium) identified which signifies the requirement of selenium by the human body. Selenium is essential as it protects cardiovascular system and muscular system, acts as a hurdle to cancer cells and also boosts immune system. But again high intake of selenium will pave way for selenium poisoning.

Selenocysteine Biotechnological application

The differently labeled selenocysteine are used in the fields like positron emission tomography, labeling radioactive elements and X-ray crystallography.
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#3
Amino acid: Pyrrolysine

Year of discovery: 2002

Abbreviation: Pyl

In short: O

Position in the standard amino acid list: 22nd Amino acid next to Selenocysteine

Codon: UAG, which is actually a stop codon but codes for the amino acid Pyrrolysine in the presence of PYLIS element.

PYLIS: Pyrrolysine Insertion sequence found in some mRNA as a stem loop structure and when UAG codon is followed by this structure it will signal the production of the amino acid Pyrrolysine instead of the actual terminating function of the codon.

Found in the Organism: Methanosarcinaceae barkeri (Archaea species)

First Located: In methyl transferase enzyme’s active site and hence Pyrrolysine makes its significance in most of the methane producing pathways.

Some of the enzymes containing Pyrrolysine: Methyltransferases MtmB, MtbB and Mttb

Structure: Methylated pyroline carboxylate is bridged to the amino group of L- Lysine where the amide group acts as the bridge.

Chemical formula: C12H21N3O3

Side chain: -(CH2)4NHCOC4H5NCH3

pH: Pyrrolysine is a weak Basic

Presence in human proteins: 0 percent

Bioproduction of Pyrrolysine: The synthesis of Pyrrolysine requires two molecules of the amino acid L- Lysine. One molecule transforms into Methylornithine before binding itself to the second molecule which is followed by several steps like deamination and cyclization resulting in the formation of the amino acid Pyrrolysine.

Genes involved in the synthesis of Pyrrolysine and its incorporation into proteins are pylT, pylS, pylB, pylC, pylD.

pylT: pylT which encodes tRNA is an important unit in the decoding of the codon UAG into the aminoacid Pyrrolysine.

pylS: This gene codes for pyrrosyl t-RNA synthetase which charges the pylT encoded tRNA with Pyrrolysine (tRNApyl).

In a research study the recombinant E.coli carrying the genes pylT, pylS, pylB, pylC and pylD derived from methanogenic archaea has been observed for the insertion of the synthesized pyrrolyisne into the proteins.

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#4
Hence there must be a unique pathway in the protein synthesis involving selenocysteine which requires the regulation of UGA codon in the synthesis of selenocysteine by inhibiting its original function of termination. Yes, there are separate mechanisms for the synthesis of selenoproteins (protein containing the amino acid selenocysteine) identified in prokaryotes and eukaryotes where presence of selenium is significant.
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#5
The basic constituents of living cells, the amino acids, participate in the body’s most significant biochemical reactions. These are extremely essential to life. The building blocks of protein in structural tissues are the amino acids. In free linked form such as peptides, amino acids play important roles in activities such as regulation of pH balance, neurotransmitter function, metabolism of cholesterol, detoxification, pain control, control of various inflammations etc. Some important amino acids that vital role in the body are methionine, taurine, cysteine, lysine, arginine, tryptophan, and glutamine. Amino acids are quite importantly used in food technology, nutrition supplements, fertilizers, and in industrial production of biodegradable plastics, drugs. Immense advances in the field of amino acid research are provided with a wealth of information on its various applications such as in enzyme functionality, protein and nutrient cofactor adequacy, wasting syndromes, predisposing to some degenerative disorders, neurological disorders, gastrointestinal dysfunction, cardiovascular disease, ammonia toxicity, impairments in detoxification, inborn errors of metabolism, and a vast array of clinical conditions. Results can be applied in the certain replacement therapy design, needed to restore proper balance. Analysis of amino acid provides desirable information regarding the nutritional requirement that includes amino acid supplements, based upon urine or blood plasma levels. Calculations of these levels are based on the measured versus the reference range, the individual’s age, and tabulation of human needs obtained from the National Research Council’s amino acids requirements table. Such amino acid supplements should be packaged and formulated by qualified pharmacy, prescribed by the specialists, and administered orally to patients.

Various biotechnological applications widely require amino acids. They can be safely applied in some pharmaceutical applications, such as solvent additive during purification of protein and also applied in protein formulations and as an excipient in drug preparation required for oral administration. Certain amino acids maintains the intracellular osmotic pressure during high salinity of the surrounding medium. They do not affect function of macromolecules due to which they are also known as “compatible solutes”. Apart from increasing the osmotic pressure, the amino acids also increase protein stability. Certain amino acids also enhance the stability of protein stability after isolating them from natural environments. Arginine is an amino acid which has the ability to assist in the phenomenon of recombinant protein refolding. Arginine suppresses protein aggregation during refolding, as a result increases the efficiency of refolding. Due to this mechanism, arginine is widely applied in recent times in the fields of protein research and development than anticipated, particularly in pharmaceutical applications.
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Amino Acids – Types, Classification, Genetic Code and Applications00