1. Amino acids: Chemical and Physical Properties
Debalina Mukhopadhyay

2. Introduction: Containing carbon, hydrogen, nitrogen, oxygen
Building blocks of protein
Contain Amino group (NH2+) , carboxyl group (COO-) , Alkyl group (R ) / H
alpha carbon contains the functional groups.
All amino acids bear same functional group only differs by R group

3. Alkyl Group/Side Chains:
The greater the electronegativity difference between atoms in a bond, the more polar the bond. Partial negative charges are found on the most electronegative atoms, the others are partially positive.
Amino acids with Non-Polar and Neutral side chain:
Side chains which have pure hydrocarbon alkyl groups (alkane branches) or aromatic (benzene rings) are non-polar. Examples include valine, alanine, leucine, isoleucine, phenylalanine.
The number of alkyl groups also influences the polarity. The more alkyl groups present, the more non-polar the amino acid will be. This effect makes valine more non-polar than alanine; leucine is more non-polar than valine .

4. Amino acids with Non-Polar and Neutral side chain (R):
Alanine
Leucine
Isoleucine
Valine
Phenylalanine

5. amino acids with Polar Neutral Side Chain (R):
Amino acid side chain with  amide, alcohol, -SH (Cysteine) group is said to be polar.
Because water is a polar solvent, and like dissolves like, these polar amino acids are hydrophilic, and tend to occur more commonly on the exterior of proteins in contact with aqueous cell environments.

6. amino acids with Polar Neutral Side Chain (R):

7. amino acids with Polar Acidic Side Chain (R):
If the side chain contains an acid functional group, the whole amino acid produces an acidic solution. Normally, an amino acid produces a nearly neutral solution since the acid group and the basic amine group in amino acid neutralize each other in the zwitterion. If the amino acid structure contains two acid groups and one amine group, there is a net acid producing effect.
The two acidic amino acids are aspartic and glutamic.

8. amino acids with Polar Acidic Side Chain (R):

9. amino acids with Polar Basic Side Chain (R):
If the side chain contains an amine functional group, the amino acid produces a basic solution because the extra amine group is not neutralized by the acid group.
Amino acids which have basic side chains include: lysine, arginine, and histidine.

10. amino acids with Polar Basic Side Chain (R):

11. Difference among the amino acids according to their side chain:

12. Don’t get confused with amines and amides
                                                            
An amine doesn't have a carbonyl group.
Don’t get confused with amines and amides
Amino acids with an amide on the side chain do not produce basic solutions i.e. asparagine and glutamine.
An amine doesn't have a carbonyl group.
Amide is a Nitrogen with a carboxylic acid
An amine can be written like this:   R-NH3, or CH3-CH2-CH2-NH3
But an amide is written like this:  R(CO)NH2 or CH3-C=O-NH3 or CH3CONH3 or RCONH3

13. Amino Acid can act as Acids and Bases:
When amino acid is dissolved in water, it exists in solution as the dipolar ion or Zwitterion.
A zwitterion can either act as an acid (Proton donor) or a base (Proton acceptor)
Hence amino acid is an Amphoteric molecule.

14. Titration of Amino acid:
Depending on the pH of the solution the amino acid functional groups (COOH- and NH3+) leaves H+ ion and produces COO- and NH2 respectively.
 Hence, pKa can be defined as the pH at which the concentrations of the protonated [HA] and unprotonated [A-] forms of a particular ionisable species are equal. Then, log [HA] / [A-]= 0, pKa = pH
The isoelectric point (isoelectric pH; pI) is the pH at which the amino acid has a net zero charge.
For a simple diprotic amino acid, the pI falls halfway between the two pK values. For acidic amino acids, the pI is given by ½(pK1 + pK2) and for basic amino acids it’s given by ½(pK2 + pK3).

15. Titration of Glycine: pI= ½ (pK1+pK2) pI= ½ (2.34+9.60) pI= 5.97
The net charge is 0

16. Chiral carbon and its configuration:
Chiral carbon can be in two configuration that are non- superimposablemirror image of each other.
Configurations are called enantiomers of each other.
Majorly L-amino acids are incorporated in protein by ribosome.

17. Optical Properties of Amino Acid:
Except Glycine all the amino acids are optically active.
Optically active molecule has Chiral carbon.
Ac optically active compound can rotate the plane of polarized light. Either clockwise (Dextrorotatory [+]]) or counter clock/anticlockwise (Levorotatory [-]).
Optical activity is measured by Polarimeter.
The mathematical expression of measuring the degree of rotation of the plane of polarized light is given below:

18. Absorption of UV ray by Amino acid:
Aromatic amino acid such as Tryptophan, Tyrosin (both absoorv UV at 280nm), Phenylalanine (257 nm).
Absorbance at 280nm is used to detection and quantification of amino acid.
Absorbance of each rotein depends on the number and position s of its aromatic amino acid residue.
Mathematical Expression:
A = εcl A = absorbance c = concentration of the substance I = l = length of the path of light through the sample or the thickness of the cell (cuvette) E = absorption coefficient or absorptivity

19. UV absorbance spectra of Amino Acid:

20. Ninhydrin Test to detect amino acid peptide and protein: