Some basic knowledge about protein with its structural and functional variety!!!!!

1. WEL COME
TOPIC – PROTEIN
BY - DEBABRATA BEHERA
+3 3rd YEAR (ZOOLOGY HONOURS)
GUIDED BY – SHAKTI RANJAN BEHERA
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2. 2
WHAT IS A PROTEIN…?
• Proteins are the most abundant biological macromolecules which
mediate virtually every process that takes place in a cell.
• Proteins (molecular instrument ) are functional part of the genetic
information.
• Proteins are made up of 20 Amino acids , building blocks of proteins.
• Hormones , Enzymes , Antibodies , Transporters , Muscle fibers ,
Spider webs , Milk proteins are constructed by different protein
molecules.

3. 3
AMINO ACIDS (BUILDING BLOCKS OF PROTEINS)
• Proteins are , macromolecules , composed of monomers called Amino acids.
• It can be made up of as few as 100 amino acids to as many as four thousand amino
acids.
• Amino acids are a group of organic compounds containing two functional groups , the
Amino group(-NH₂) , basic in nature , & Carboxylic group(-COOH) , acidic in nature.
• Two functional groups and one H-atom & one R-group(alkyl group) are attached to the
same -carbon atom.
H
NH₂ - C – COOH
R

4. 4

5. 5 ZWITTER ION
• Amino acid has a property that it present in state of dipolar ion state.
• It is a hybrid mol. Containing both +ve & -ve ionic group.
• The amino acid rarely exist in a neutral form with free carboxylic and free
amino group.
Strong acid pH (low pH) - +ve charge amino acid (Cation)
Strong alkaline pH (high pH) - -ve charge amino acid (Anion)
Each amino acid has a characteristic pH value at which it carries both +ve & -ve
charge & exist as Zwitter ion.

6. 6
WHERE AND HOW PROTEIN FORMS ?
• The process in which amino acids are decoded by the codons of m-
RNA to synthesize specific protein is known as protein synthesis.
• Ribosome is the site of protein synthesis.
• Synthesis of protein is known as Translation.
TRANSCRIPTION TRANSLATION
DNA m-RNA Protein
(NUCLEUS) (CYTOPLASM)
RNA polymerase Peptidyl transferase

7. 7

8. 8 PRIMARY STRUCTURE OF PROTEIN
• The primary structure of protein refers to linear arrangement of
constituent monomers which is fixed for each protein.
• The primary structure of a protein is largely responsible for its function
& genetic expression of DNA.
• The amino acid composition of protein determines its physical &
chemical properties.
H3N+–Ala–Lys–Ala–Ala–COO-

9. 9 PEPTIDE BOND
• Amino acids are linked in a chain form while forming peptides and
proteins.
• The amino and carboxylic groups react to form an amide bond ,
called as peptide bond.
• Both amino & carboxylic group are polar in nature & are involved in
H-bond formation.
• These bonds are rather strong and serve as cementing material
between the individual amino acids.

10. 10

11. 11 SECONDARY STRUCTURE
The confirmation of polypeptide chain by twisting & folding is
reffered as secondary structure of protein.
SECONDARY STRUCTURE
-helix β-pleated sheet

12. 12 -helix
It is the most common spiral structure of protein with
rigid arrangement of polypeptide chain.
It was proposed by Pauling & Corey in 1951 which
was regarded as one of the milestone in bio-
chemistry.

13. 13 FEATURES OF -helix
• It is a tightly packed coiled structure with
amino acid side chain extending outward
from central axis , which is stabilized by H-
bonding.
• All the peptide bonds except 1st & last in a
chain participate in H-bonding.
• Each turn of a helix contains 3.6 amino acids
residues travel a distance of 54Å & the
spacing of each amino acid is 15Å.
• It is a stable confirmation forms spontaneous
with lowest energy.
• Right handed -helix is more stable than the
left hand helix.

14. 14 β Pleated sheet
Another form of secondary structure is called β sheet in which the H-
bonding is between –CO and –NH of adjacent polypeptide strands (parallel
& anti parallel) giving an appearance of a pleated structure.
β Pleated sheet
ANTIPARALLEL PARALLEL

15. 15 ANTIPARALLEL SHEET
Adjacent strands run in
opposite direction.
H bonds between NH & CO
groups connect each amino
acid to a single amino acid on
an adjacent strand.

16. 16 PARALLEL SHEET
Adjacent strands run in same
direction.
H bonds connect each amino acid
on one strand with two different
amino acids on adjacent strand.

17. 17 RAMACHANDRAN PLOT

18. 18 TERTIARY STRUCTURE
• The 3-D arrangement of protein structure is reffered as
tertiary structure.
• It is a compact structure with hydrophobic side chain
held interior when the hydrophilic groups are on the
surface of protein molecule.
• This type of arrangement ensure stability of molecule.
overall folded conformation of the polypeptide

19. 19
INSULIN

20. 20
Physical forces affect tertiary structure
(a) Hydrophobic forces - hydrophobic residues orient to
inside & hydrophilic orient out
(b) electrostatic forces
(c) Van der Waals radii
(d) Hydrogen bonds
(e) Disulfide bridges

21. 21
QUARTERNARY
STRUCTURE
A great majority of protein are composed of single
polypeptide chain.
Some of the protein however consist of two or more
polypeptide called oligomer and posses quarternary
structure.
Same force drive quarternary structure.

22. 22
HEME MOLECULE OF HEMOGLOBIN

23. 23
Physical forces govern 3-D structure of proteins
(Pauling and Corey)
1. bond lengths and angles should be distorted as little
as possible
2. structures must follow Van der Waal’s rules for atomic
radii
3. peptide bond is planar and trans
4. noncovalent bonding stabilizes structure
5. conformation can change without breaking bonds
(flexibility)

24. 24 Types of non-covalent forces important to protein
conformation
1. Hydrophobic forces
(a) hydrophobic residues orient to inside
(b) hydrophilic residues orient out
2. Van der Waal’s potential:
includes electron shell repulsion, dispersion forces, and
electrostatic interactions
3. Disulfide bonds
4. Hydrogen bonds

25. 25 PROPERTIES
• Variety- There are thousands of proteins present in each organism due
to specific arrangement of amino acid.
• Specificity- Each species has specific proteins not found in others help in
evolution.
• Colloids- Being large sized , many proteins function as colloids and
colloidal solution.
• Shape- Wide variation in protein shape it may be globular(Insulin)
oval(Albumin) elongated(Fibrinogen).
• Mol. Wt.- Proteins are vary in their mol. wt. from Insulin(5,700 D) to
Serum albumin(69,000 D).
• Amphoteric Nature- Like amino acids , proteins are amphoteric.
• Permeation- Cell membranes do not allow permeation of proteins. They
can pass through exocytosis and endocytosis. Every cell synthesis its own
proteins from amino acids.

26. 26
Proteins are involved in various cellular
process and fulfill many functions such
as
Enzyme catalysis
Transport
Mechanical Support
Storage
Metabolic Control
Immunity
Function of protein

27. 27

28. 28
FIBRONIN
• Protein of silk , is produced by insects and spiders.
• Its polypeptide chains are predominantly in β confirmation.
• Rich in alanine and glycine residues permitting a close packing of sheets
and alkyl groups.
• H-bond , Vander waal radii like weak interaction make it flexible rather
than stretch.

29. 29
ATP synthase
ADP + Pi ATP

30. 30KINESIN
HEMOGLOBIN ALSO ACTS AS TRANSPORT
PROTEINS.

31. 31
ANTIBODY

32. 32COLLAGEN

33. 33APOPTOSOMES

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