Peptide Bond

PEPTIDE BOND
 PRIMARY STRUCTURE OF PEPTIDE

 The squence of amino acvid in a poly peptide is
referred to as its primary structure.
 Chemically method are required to determine the
primary structure.
 Physical technique such as X- ray crystallography
are employed for higher order of protein structure.
 The N- terminal amino acid is always shown at the
left and C- terminal amino acid at the right of the
polypeptide chain.
 Even small change in the primary structure of
protein may produce remarkable physological
effects.


 Substitution of a single amino acid for another in a
sequence of 100 or more amino acid may abolish
biologic activity.

 Determination of the primary structure of peptides
A) Peptide are purified before analysis
 1. The classic purification procedure include
precipitation with varying salt concentration(
ammonium or sodium sulfate) or solvent(
acetone or ethanol), differential centrifugation,
Gel filtration and electrophoresis.
2. Selective absorption and elution of protein
from the cellulose anion exchanger.

 Determination of amino acid composition.

 The peptide bond linking amino acid residue are first
broken by hydrolysis.
 The liberated amino acid are separated and
identified by HPLC or Ion exchange
chromatography.
Determination of sequence of polypeptide by
Sanger method
Sanger approach was first to separate the two
polypeptide chain A and B if insulin and then to
convert them by specific enzymatic cleavage
into smaller peptide that contained region of
overlapping sequence
Using 1,2,4 dinitro benzene

 STRUCTURE OF PROTEIN
 The structure of protein is considered by several level
of organization on the basic of modern view.

 The level of organization are:
 1. Primary Level Of Organization
 2. Secondary Level Of Organization
 3. Tertiary Level Of Organization
 4. Quarternary Level Of Organization


 1. Primary Level Of Organization
 The sequence of amino acid and location of any disulfide
bond in a protein is called primary structure of protein.

 NH3
+
-CH-CO-NH-CH-CO-NH-CH-CO-NH-CH-COO


R

R R
 The primary level of structure in a protein is th
linear sequence of amino acid as joined
together by peptide bonds.


 The sequence of amino acid in the primary structure is
determined by sequence of nucleotide bases in the gege
coding protein.

 Primary structure also show the location of any other
covalent bond.
 There are primary disulfide bond between cysteine residue
that are near to each other in space but away from each
other in linear amino sequence.
 These disulfide covalent cross link can take place between
two separate poly peptide chain between different parts of
the same chain.
 They are formed on oxidation of SH group on cysteine
residue that are exposed to each other in space.



 SECONDARY STRUCTURE

 The conformation of the polypeptide chain or the
conformation of the primary structure of protein
constitutes their secondary structure.

 For stability of primary structure hydrogen bonding between
the hydrogen of NH( amide) and oxygen of C=O) carbonyl)
group with in the polypeptide chain occur which give rise to
folding or twisting of the primary structure.

 Thus regular folding and twisting of the poly peptide chain
brought about. By hydrogen bonding is called secondary
structure of protein.

 The different kinds of secondary structure are.

 1. Alpha helix
2. Beta – pleated Sheet
3. Loop region
4. Beta –bend
5. Triplex helix

 1. Alpha helix
It is called alpha because it was the first structure
predicted by Linus Pauling and Robert Corey.
If a backbone of polypeptide chain twisted by an equal
amount about each alpha carbon it form a coil or helix.
The helix is stabilized by hydrogen bond between the
NH and Co group.
These hydrogen bond have an essentially optimal
Nitrogen to oxygen (N-O) distance of 2.8A
The distance travelled per turn is 0.54nm
The spacing / amino acid residue is 0.15nm
There are 3.6 amino acid residue per of the helix.
The right handed helix when occur in protein is
significantly more stable than the left handed helix.


 1. Beta Pleated sheet
Pauling and Robert Corey discovered another type of
structure which they named beta pleated sheet( beta
because it was the second structure predicted).
The surface of beta sheet appeared pleated and these
structure are therefore often Beta Pleated sheet.
The Beta Pleated sheet differ markedly from the
alpha helix in that
It is a sheet rather than a rod a polypeptides chain
in the in the Beta Pleated sheet is almost fully
extended rather than being tightly coiled as in the
alpha helix.

 The axial distance between adjecent amino acid is 3.5A in
contrast with 1.5 A for the alpha helix.
 Unlike alpha helix Beta Pleated sheet are composed of two or
more polypepteide. Chain.
 Beta Pleated sheet is stabilized by hydrogen bond between NH ad
C=O group in a different or the same polypeptide chain.