topics made easy for post graduate life science entrance exam amino acids- definition, classification,naming, standard and non standard amino acids, optical properties and some examples of amino acids

2. Amino acids
 Are compounds containing carbon,
hydrogen, oxygen and nitrogen
 Serves as monomers(building blocks) of
proteins and are composed of an amino
group, a carboxyl group, a hydrogen atom,
and a distinctive side chain, all bound to a
carbon atom, the α carbon
 In an α amino acid, the amino and
carboxylate groups are attached to the
same carbon atom, which is called the α
carbon

3. Amino acids
 The general structure of an amino acid
is

4. Amino acids
 They can act as acids and bases
 They contain both an amino NH2 and a carboxyl COOH group
 Amino group is basic proton acceptor and carboxyl group is
acidic proton donor therefore amino acids are amphoteric in
nature
 An amphoteric molecule can either donate or accept a proton
thus acting either as an acid or a base
 At high concentrations of proton (low pH) the carboxyl group
accepts a proton and becomes uncharged so the overall charge
on the molecule is positive
 At low concentrations of proton (high pH) the carboxyl group
loses a proton and becomes uncharged so the overall charge
on the molecule is negative
 At specific value of pH called isoelectric point (pI), every amino
acid exists as dipolar ion or zwitter ion
 A zwitter ion is a compound with no overall electric charge, but
contain positively and negatively charged groups

5. Acid base behavior of an amino
acid in a solution

6. Optical properties
 All amino acids except glycine are optically active
that is they rotate the plane of plane polarized light
 Optically active molecules contain chiral carbon and
can rotate the plane of polarized light either
clockwise(right) or counterclockwise( left)
 Optically active compounds that rotate the plane of
polarized light clockwise are said to be dextrorotatory
and is designated by + sign
 Optically active compounds that rotate the plane of
polarized light counterclockwise are said to be
levorotatory and is designated by – sign
 And also + and – forms have also been termed d and
l respectively

7. Optical properties

8. Optical properties

9. Optical properties
 Optical activity is measured by polarimeter
 Optical rotation – is a quantitative measure of the rotation
of light caused by the compound
 Optical rotation of an optically active compound depends
on concentration of the compound, temperature,
wavelength of light used, solvent used to dissolve the
sample and light path length
 Specific rotation- is the reference value of optical rotation
for a given concentration of compound at a given
temperature and fixed wavelength
 A t a given temperature and for a given wavelength of
light the specific rotation is defined as the observed value
of optical rotation when plane polarized light is passed
through a sample with a path length of 1 decimeter and a
sample concentration of 1 g per milliliter

10. Absolute configuration
 An amino acid with a chiral carbon can exist in 2 configurations
that is non super imposable mirror images of each other. These
2 configurations are called enantiomers
 An enantiomers is identified by its absolute configuration
 Ex. Absolute configuration of amino acids are specified by D-
and L-system
 The designation of D and L to an amino acid refers to its
absolute configuration relative to the structure of D and L
glyceraldehyde
 All amino acids except glycine exist in these 2 different
enantiomeric forms
 All amino acids which ribosomically incorporated into proteins
exhibit L configuration therefore they are all L-α- amino acids
 D-form of amino acids are found in some peptide antibiotics and
peptidoglycan cell wall of eubacteria

11. Standard amino acids
 There are hundreds of amino acids present in living
organisms however only 22 different amino acids
participate in protein synthesis which are
incorporated ribosomically into proteins
 Such amino acids are called standard/ proteinogenic
amino acids
 Some amino acids are more abundant in proteins
than other amino acids. 4 amino acids – leucine,
serine, lysine, glutamic acid are the most abundant
amino acid residues in a typical protein
 Tryptophan and methionine are rare amino acids in a
protein
 Standard L-α-amino acids are specified by simple 3
letter codons

12. Classification of amino
acids

13. Classification of amino
acids

14. Classification of amino
acids
 Based on chemical nature of R group
Chemical nature of R group Example
Aliphatic Gly, ala, val, leu
Aromatic Phe, tyr, trp
Hydroxyl Ser, thr
Carboxylic Asp, glu
Sulphur containing Cys, met
Imino Pro
Amino Lys, arg
Amide Asn, gln

15. Classification of amino
acids
Amino acid with non
polar side chain
Amino acid with
uncharged polar side
chain at ph 7
Amino acid with charged
polar side chain at ph 7
Glycine
Alanine
Valine
Leucine
Isoleucine
Proline
Methionine
Phenylalanine
Tryptophan
Serine
Threonine
Cysteine
Asparagine
Glutamine
Tyrosine
Lysine
Arginine
Histidine
Aspartate
Glutamate

16. Non standard amino acids
 Apart form 22 standard amino acids, all other amino acids
are not ribosomically incorporated into proteins and are
called non standard
 In addition to standard amino acids, some proteins may
contain non standard amino acid residues formed by pos-
translational modification of standard amino acids residue
already incorporated into a polypeptide
 These modifications are essential for function or
regulation of a protein
 Ex. 4 hydroxyproline, 5- hydoxylysine, desmosine, N-
acetylserine, N-formylmethionine , ᵧ - carboxyglutamate
 Selenocysteine is the 21st standard amino acid it is
specified by a triplet codon UGA stop codon
 Pyrrolysine is the 22nd standard amino acid it is coded by
UAG codon

17. Selenocysteine and
pyrrolysine