Amino acid and protein
Amino acids are compounds containing carbon ,hydrogen ,Oxygen, and nitrogen and serve as monomers of proteins. As the name implies, this compounds contain both and amino group and carboxylic group. In an Alpha Amino acid, the amino and carboxyl groups and attached to the same carbon atom, which is called called the Alpha carbon. The various Alpha amino acids difffer with respect to the side chain.(R group) attached to their alpha carbon. The R group or side chain attach to the Alpha carbon is different in each Amino acid. In the simplest case, the R group is hydrogen atom and amino acid is glycine. With the exception of proline, all Alpha amino acids have same general structure. Prolin is unique among the standard Alpha Amino acids because it is not a primary amino acid. But rather is secondary amino acid, sometimes called an imino acid
unlike the primary and acid which contain a primary amino group (-NH2), proline is secondary amine which contains a secondary amino group (-NH).
In alpha amino acid,both the amino group and carboxyl group are attached to the same alpha carbon atoms. However, many naturally occurring amino acids not found in protein, have structures that differ from Alpha Amino acids. In these compounds the amino group is attached to the carbon atom other than the Alpha carbon atom and they are called beta, Gama , delta, Or epsilon amino acids depending upon the location of the C- atom to which amino group is attached.
Standard and Non standard amino acid.... There are hundreds of different amino acids present in the living organisms; however, only 22 different amino acid participate in protein synthesis, which are incorporated ribosomically into proteins. Such a amino acids are called standard or proteinogenic amino acids. Amino acids that occur naturally in the cell but not incorporated ribosomically into proteins are called Non standard amino acids. Some non standard amino acids are constituents of ribosomically synthesized protein, but they are generated by post translation modification of standard amino acids which are incorporated ribosomically into proteins. Examples of some of these amino acids are 4 hydroxyproline (a derivative of proline), 5- hydroxylysine (a derivative of lysine) ,desmosine ( a derivative of lysine) ,N - formylmethionine ( a derivative of methionine) and gamma carboxyglutamate ( a derivative of glutamate).
All standard amino acids are L - alpha amino acid. This amino acids are specified by simple 3 letters codon. Standard amino acids can be classified on the properties of their side chain or R group, in particular, their polarity or tendency to interact with water at physiological PH (near pH7). The polarity of the side chains varies widely, from nonpolar and hydrophobic to highly polar and hydrophilic.
Amino acid with non polar side chain
Among standard amino acids, 9 amino acids contain nonpolar side chain. These are glycine, alanine, valine, leucine, isoleucine, proline, methionine, phenylalanine and tryptophan. Proline differs from other members in having its side chain bonded to both the nitrogen and the Alpha carbon atoms. Phenylalanine and tryptophan have aromatic side chain. The side chain of phenylalanine contain a phenyl ring wheras tryptophan has an indole ring.
Amino acids with uncharged polar side chain.
6 Amino acids contain uncharge polar side chain- serine,threonine,cysteine,aspargine, glutamine,and tyrosine . Three amino acid,serine, threonine and tyrosine contain hydroxyl group attached to the side chain. Cysteine is structurally similar to serine but contain sulfhydryl or thiol group (- SH ) in place of hydroxyl group.
Amino acids with charge polar side chains
Positively charged side chain - lysine and arginine have side chain that contains positively charged group at neutral pH or physiological pH. Lysine has an amino group where as arginine contain a guanidinium group. Histidine contain an imidazole aromatic ring( a planner five members heterocyclic ring). The imidazole ring can be uncharged or positively charged near neutral pH , depending on its local environment.
Negatively charged side chain : Amino acids aspartate and glutamate contain acidic side chain that contain negatively charged carboxyl group at neutral pH.
Selenocystein (Sec or U ) is the 21 st standard amino acid. It has a structure similar to that of cysteine,but it contains selenium rather sulphur. It is incorporated into polypeptide during translation. However,it is specified by a triplet codon,UGA (a stop codon). Selenocystein has its own tRNA containing the anticodon UCA and it is formed by modifying a serine that has been attached to selenocystein tRNA . Enzymes like glutathione peroxidase and formate dehydrogenase contain selenocystein in their catalytic center. Pyrrolysine ( pyl or O ) is the 22 nd standard amino acids. It is similar to lysine and is present in some bacterial proteins. It is coded by UAG codon.
