3.      AMINO ACIDS     

Molecule amino acids are which have amino group carboxylate group along with a side chain (R group) and one side chain all together bounded with alpha carbon which makes the carbon a chiral carbon. A chiral carbon is a carbon which has four different groups at their all four valences. All amino acids show this signature characteristic of chiral carbon.

For each amino acid, the R group is different. At physiological pH, the amino acid present as the zwitterion means the backbone of amino acids does not contribute to the net charge of the protein. 
The primary function of the amino acids is working as the monomers for the synthesis of the proteins. Proteins are the highly versatile bio-molecules in structure and function; the versatility of a protein is the combined result of the all amino acid. Unlike the other monomers of the bio-macromolecules (DNA, RNA, carbohydrate, lipid) amino acid is 20 in number with a different side chain, which possesses unique features that makes proteins so much exclusive in structure and functions. To study the protein structure one should aware of the structures of amino acid and to study amino acids one should aware of side chain of the amino acids because the side chain is the structural part of an amino acid which make an amino acid different from other and the unique feature of the side chain contribute for the unique nature of amino acid. 
3.1.    Major groups of amino acids
There are 7 major groups present in the amino acid side chain.

3.1.1.    Carboxylate group    
It is present in two amino acid aspartate and glutamate. The presence of this carboxylate group in these two amino acids make themselves as acidic amino acids and contribute to making negative charge at physiological pH on the protein and there are other advantages for having negative charge that it can make salt bridges with positively charged amino acids and another is they can  bind with the metals ions because metal ions posses positive charge so they easily bind e.g.  glutamate binds with zinc.

3.1.2.    Amides    :   

In the protein building amino acids, there are two amino acids that have amide group in their side chain. eg asparagine and glutamine.  The amide containing amino acids are neutral and polar in physiological PH. Asparagine and glutamine amino acids are known for the hydrogen bonding as the presence of two electronegative atom oxygen and nitrogen makes the amide containing amino acid both as acceptor (oxygen) and donor (Amino group) which can easily make a hydrogen bond with each other.  These amino acids can make hydrogen bonds with the water molecule which make them soluble in the water. 
3.1.3.    Amines (NH3+)

There are three amino acids which posses the amine group in their side chain named as lysine, arginine and histidine. These amino acids are basic in nature and have a positive charge. Both the acidic and basic amino acids increase the solubility of the protein and peptides. The negative charge amino acid binds with positive charge amino acid and forms salt bridges.

3.1.4.    Aliphatic –CH2

A larger proportion of amino acid is structurally aliphatic in nature. Out of twenty-five amino acids possess aliphatic side chain these are alanine, valine, leucine, Isoleucine, and methionine. All aliphatic amino acids are hydrophobic in nature thus they are actively present in the core of the globular proteins and they are present in the large number in the membrane-spanning region of the protein.

3.1.5.    Aromatic carbon ring

There is three amino acid which has an aromatic carbon ring named as phenylalanine, tyrosine and tryptophan. The carbon ring absorbs the light of wavelength 260 nm. These absorbance properties are used for the protein quantification by spectrophotometry.

3.1.6.    Alcoholic -OH

There is three amino acid which contains alcohol group in their side chain. They are serine, threonine and tyrosine. More interestingly tyrosine is an amino acid which has an alcohol group associated with the benzene carbon ring.

3.1.7.    Thiol Side Chain – (SH)

Cysteine amino acid is having Thiol side chain. Cysteine and methionine are sulphur containing amino acid. Moreover only cysteine form disulphide bonds with other cysteine amino acid.

3.1.8.    Special amino acids

The glycine and proline are the two special categories of amino acids because of their very different nature. 

Glycine doesn’t have side chain instead glycine only have hydrogen thus glycine are unable to interact with other amino acids with their side chain and thus minimal role on the tertiary folding of a protein. The second special amino acid is proline. Proline is a nonpolar aliphatic amino acid. The cyclic structure of proline gives rigidity to the peptide chain, unlike glycine which gives flexibility to the peptide chain. 
3.1.9.    Proline

Contain amino\alpha group, a \alphacarboxylic group and a side chain pyrrolidine. Proline is an imino acid. Proline affects the rate of peptide bond formation between proline and another amino acid. As the nitrogen of proline cannot act as hydrogen bond donor but can be a hydrogen bond acceptor. This shift in nature is because hydrogen is not attracted to \alpha-nitrogen of proline. Thus the proline-proline peptide bond is slowest of all peptide bond.
Proline provides conformational rigidity to proline and that's why in the thermophilic organism the percentage of proline in all protein is relatively high.
3.2.    Biologically Active Amino Acids
In addition to their primary function as components of protein, amino acids also have several other biological roles.
(i)    Neurotransmitter :
The neurotransmitter is a chemical messenger which transmit a signal through the chemical synapse. Neurotransmitters are either alpha-amino acids or its derivatives. Like lycine, glutamate, \gamma-aminobutyric acid (GABA, a derivative of glutamate), and serotonin and melatonin (derivatives of tryptophan) all are neurotransmitters. 
(ii)     Hormones -
Thyroxine (a tyrosine derivative produced in the thyroid gland of animals) and indole acetic acid (a tryptophan derivative found in plants) are hormones.
Amino acids are precursors of nucleotides, heme and chlorophyll. Several standards and non-standard amino acids act as metabolic intermediates. For example, arginine, citrulline, and ornithine are components of the urea cycle 
3.3.    Modified Amino Acids
After the translation, the amino acids present in the polypeptide chain are modified by certain enzymes. These modifications are posted translation modification.
In the blood-clotting protein prothrombin, a calcium-binding amino acid residue is found that is known as gamma carboxyglutamic acid. Both 4-hydroxyproline and 5-hydroxylysine are important structural components of collagen
Phosphorylation is the most common post-translation modification. Phosphorylation of the hydroxyl-containing amino acids serine, threonine, and tyrosine is often used to regulate the activity of proteins. 
3.4.    Titration of Amino Acids
Amino acids contain ionizable groups. The ionic forms of amino acid depending upon the pH. The effect of pH on the amino acid structure can be studied by titration. A titration is also a useful tool in determining the reactivity of amino acid side chains. The simple amino acid is alanine. It has two titratable groups. 
In the strong acidic pH, the alanine is present mainly in the form in which the carboxyl group is unchanged. Under this circumstance, the molecule’s net charge is +1 because the ammonium group is protonated. As we increase the OH ion concentration by adding NaOH during titration the carboxyl group loses its proton to become a negatively charged carboxylate group. Further addition of NaOH resulted into loss of H+ from ammonium also.

Once the carboxyl group lost its proton, alanine has no net charge and is electrically neutral. The pH at which the net charge on amino acid is zero is called as isoelectric point (pI). The isoelectric point for alanine may be calculated as follows:

3.4.1.    The pI of amino acid that has an ionizable side chain
In a polyprotic acid, the protons are first lost from the group with the lowest pKa. The pI of an amino acid is the average of the pKa values of the similarly ionizing groups (a positively charged group ionizing to an uncharged group or an uncharged group ionizing to a negatively charged group). For example, the pI of lysine is the average of the pKa values of the two groups that are positively charged in their acidic form and uncharged in their basic form. The pI of glutamate, on the other hand, is the average of the pKa values of the two groups that are uncharged in their acidic form and negatively charged in their basic form.

3.5.    Peptide Bonds
The covalent amide bonds that link amino acid residues are called peptide bonds. By convention, peptides and proteins are written with the free amino group (the N-terminal amino acid) on the left and the free carboxyl group (the C-terminal amino acid) on the right.

3.5.1.    Cis and Transpeptidase Bond

In naturally occurring protein almost all peptide bonds are in trans configuration however if an amino acid is followed by proline (X-proline, X can be any amino acid) then it acquires a cis configuration.

A peptide bond is partial double bond and it has about 40% double-bond character because of electron delocalization. The trans configuration to be more stable than the cis configuration due to steric hindrance. Thus the a-carbons of adjacent amino acids are trans to each other.

The partial double-bond character does not allow free rotation of peptide bond. The carbon and nitrogen atoms of the peptide bond and the two atoms to which each is attached are held rigidly in a plane. This regional planarity affects the way of a chain of amino acids can fold, so it has important implications for the three-dimensional shapes of peptides and proteins.

The omega (w) torsion angle of proline will be close to zero degrees for the cis configuration. And It is 180° for trans configuration. Thus X–prolixe peptide bond normally occur in cis form.
Examples of Peptides:

1.     Dipeptide (two amino acids joined by one peptide bond):

Example: Aspartame which acts as the sweetening agent being used in replacement of cane sugar. It is composed of aspartic acid and phenylalanine.

2.    Tripeptides (3 amino acids linked by two peptide bonds).

Example: GSH which is formed from 3 amino acids: glutamic acid, cysteine and glycine. It helps in absorption of amino acids, protects against haemolysis of RBC by breaking H2O2.

3.     Octapeptides: (8 amino acids)

Examples: Two hormones; oxytocin and vasopressin (ADH).

4.    Polypeptides: 10- 50 amino acids: e.g. Insulin hormone

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