Amino acids and Proteins

Amino acids serve as monomers (building blocks) of proteins and

composed of an amino group, a carboxyl group, a hydrogen atom, and a
distinctive side chain, all bonded to a carbon atom, the -carbon. In an
-amino acid, the amino and carboxylate groups are attached to the
same carbon atom, which is called the -carbon. The various -amino
acids differ with respect to the side chain (R group) attached to their -carbon.

This structure is common to all except one of the -amino acids (proline is the exception).
The R group or side chain attached to the -carbon is different in each amino acid. In the
simplest case, the R group is a hydrogen atom and amino acid is glycine.

Amino acids can act as acids and bases When an amino acid is dissolved in water, it
exists in solution as the dipolar ion or zwitterion due to COO- and NH3+ groups. At high
concentrations of hydrogen ions (low pH), the carboxyl group accepts a proton and becomes
uncharged, so that the overall charge on the molecule is positive. Similarly, at low
concentrations of hydrogen ion (high pH), the amino group loses its proton and becomes
uncharged; thus the overall charge on the molecule is negative. A zwitterion can act as either
an acid (proton donor) or a base (proton acceptor). Hence, an amino acid is an amphoteric
molecule.

Optical properties
All amino acids except glycine are optically active i.e. they rotate the plane of plane polarized
light. Optically active molecules contain chiral carbon. A tetrahedral carbon atom with four
different constituents are said to be chiral. All amino acids except glycine have chiral carbon
and hence they are optically active.
The handedness of a chiral molecule is observable by the ability of a molecule to rotate the
plane of polarized light either to the right (dextrorotatory, + or D) or to the left (levorotatory, or L). The magnitude of optical activity is measured as an angle of rotation or optical rotation
(). Optical rotation of an optically active compound depend on the concentration of the
compound, light path length, wavelength of the polarized light and the temperature. The
optical
rotation of a solition at a given
temperature and wavelength is given
by

[]T =

Where,

A
l C

A= observed rotation in degrees

[]T =specific rotation of the compound at temperature T(degree celcius) and

wavelength (nm).
If the wavelength of light used is 598nm, the symbol D is used
C = is the concentration of solution in g/ml.

[] TD .

= is the optical path length in decimetre.

Problem:- A solution of L-leucine (3.0 g/50 ml of 6 N HCl) had an observed rotation of +1.81 in a 20 cm

polarimeter tube. Calculate the specific rotation of L-leucine in 6 N HCl.

H O
NH2 C C OH
CH3

H O
NH 2

C C OH

CH
H3C CH3

H O
NH2 C C OH

H O
NH2 C C OH
CH CH3

CH2

CH2

CH
H3C CH3

CH3

H O
NH

C C OH

CH2 CH2
CH2

alanine

valine

leucine

isoleucine

proline

ala A

val V

leu L

ile I

pro P

H O

H O
NH2

C C OH

NH 2

C C OH
CH2

CH2

H O
NH2

C C OH

CH2

CH2

NH2

NH

CH3

H O
NH2 C C OH
H O

CH2

C C OH

OH

phenylalanine

methionine

tryptophan

glycine*

serine

phe F

met M

trp W

gly G

ser S

H O
H O
NH2

C C OH

NH2

H O

C C OH
CH2

H O
NH 2

C C OH

CH OH

CH2

CH3

SH

H O
NH2

C C OH
CH2

O C
NH2

OH

NH 2

C C OH
CH2
CH2

O C
NH2

threonine

tyrosine

cysteine

asparagine

glutamine

thr T

tyr Y

cys C

asn N

gln Q

H O
H O
NH2

C C OH
CH2

O C
OH

H O
NH2

C C OH

H O
NH2

CH2

NH 2

C C OH

CH2

CH2

CH2

CH2
O C

C C OH

CH2

NH

NH2

CH2
CH2
CH2

CH2

OH

NH 2

NH
NH

C
NH2

aspartic acid

glutamic acid

histidine

lysine

arginine

asp D

glu E

his H

lys K

arg R

OH

Absolute configuration An amino acid with a chiral carbon can exist in two configurations
that are non-superimposable mirror images of each other called as enantiomers. When the
amino group attached to the chiral carbon is on the left in a Fischer projection, the
configuration is L; when the amino group is on the right, the configuration is D. All amino
acids except glycine exist in these two different enantiomeric forms. However, all the amino
acids ribosomically incorporated into proteins exhibit L-configuration. Therefore, they are all
L--amino acids. D-form of amino acids are not found in proteins, although they exist in
nature. D-form of amino acids are found in some peptide antibiotics and peptidoglycan cell
wall of eubacteria.
Classifications of amino acids

Eight amino acid are called essential (or indispensable) can't be produced by the body

and therefore should be supplied by food: Methionine, Tryptophan, Threonine, Valine,

Isoleucine, Leucine, Phenylalanine, Lysine (MeTTVILPhLy). One more amino acid,
Histidine, is considered semi-essential, as the human body doesn't always need
dietary sources of it.
Amino acids having non-polar aliphatic side chains (GAVa and LIMP):- G= Glycine, A=
Alanine, Va= Valine, L= Leucine, I= Isoleucine, M= Methionine, P= Proline.
HYDROPHOBIC AMINO ACIDS (VIP GAL) V= Valine, I= Isoleucine, P= Proline, G=
Glycine, A= Alanine, L= Leucine.
Hydrophilic Amino acids with positively charged side chain The movie Shallow HAL
has appositive message H=Histidine, A=Arginine, L=Lysine.
Hydrophilic Amino acids with negatively charged side chain:- Hey mate, Guess What?
You are an Asshole. Why are you so negative? Mate= Glutamate, Asshole= Aspartate
Aromatic amino acid:- Tryptophan, phenylalanine, tyrosine.
Polar uncharged side chain containing amino acids Asparagine and Glutamine
Sulphur containing amino acids Cysteine and Methionine

There is no net charge at the isoelectric point, amino acids are electrophoretically non-mobile and least
soluble at this pH.

Absorption of UV radiation by aromatic amino acids aromatic side chains of these amino acids are
responsible for UV absorption. Tryptophan and tyrosine absorb maximum near a wavelength of 280 nm.
However phenylalanine absorbs maximum at 257.4 nm. Absorbance at 280 nm is used for detection and
quantification of purified proteins. The absorbance of each protein depends on the number and positions of
its aromatic amino acid residues.