This presentation intends to explore the beauty of the polypeptide and its various attributes in the magic of the reality of life.

1. PROTEIN:
UNIQUE MOLECULE

2. Presented by
Dr. N. Sannigrahi,
Associate Professor,
Department of Botany,
Nistarini College, Purulia ( W.B)
India

3. Life is a millions of biochemical reactions and the four elements
build up the most of the molecules essentially required for the
execution of life since the origin of life started in this blue planet.
Besides carbohydrates and lipids along with nucleic acids, another
macromolecule essentially required to build up the life is protein.
As garland made up of flower like protein are made up of amino
acids joined to one another by means of chemical thread called
peptide bonds. Irrespective of the structural complexity and
functional attributes, it is difficult to find out the beat of life
without protein. From acellular virus to multicellular most complex
human beings via unicellular prokaryotes like bacteria, protein is
everywhere. Staring from physical and chemical activities,
biological membrane, enzymes, hormones, muscular contraction,
cell to cell transport, motion to flexibility, defence along with to
overcome unavoidable stress, the saga of protein must be sung. In a
word, from birth to death, protein is the main actor in the magic of
the reality of life.

5. AMINO ACIDS: Proteins, a kind of macromolecules are mostly
treated as the polymer of amino acids. Thus, amino acids are
building block materials or structural units of all proteins and these
monomer are joined to each other by peptide bonds as stated earlier.
The name protein was first suggested by Berzelius (1838). The
amino acids are basically of 20 types and they almost constitute at
1011 different kind of proteins . Human beings 40000 different kind
of proteins while E. coli has 3000 kinds of proteins. The polymer
contains the elements in the following percentage:
C= 50-55%, H= 6-8%, O= 20-23%, N=15-18%, S= 0-4%
The distribution of amino acids ins not uniform in all proteins.
Nearly 40% by weight of fibroin and 25% by weight of collagen are
accounted for by glycine. Serine and threonine predominate in
casein and phosvitin.

6. STRUCTURE OF AMINO ACIDS
Amino acids consist of -NH2 and – COOH group bonded to
the same carbon,
Amino acid both basic and acidic in nature,
The carbon adjacent to carboxyl group is called α-carbon to
which the amino group is attached,
The α-carbon of most amino acid is joined by covalent bonds
to 4 different groups- carboxyl group, amino group, residue ®
and hydrogen atom,
The R stands for side chains that are different for each amino
acids. R can be simply as only one H as in glycine amino acid or
may be a methyl group as in alanine or more complex structure,
α-carbon in all amino acids is asymmetric except in glycine .

7. For this reason, all amino acids except glycine exhibit optical
isomerism- Dextro and Levo form just like monosaccharide &
D- glyceraldehydes,
Isolecucine and threonine have two asymmetric carbon atoms,
hence each have4 2*2=4 optical isomers.
Most of the naturally occurring amino acids are L-isomers.
At neutral pH, the amino and carboxyl groups of an amino acids
are ionized, the amino group with + charge and carboxyl group
with –ve charge. Thus in aqueous solution, at pH 7.0, an amino
acid behaves like a dipole. This dipolar ion is known as
Zwitterions.
The molecular structure of the 20 amino acids are arranged on
the basis of the polarities of R groups as follows:

8. On the basis of the composition of side chain or R group, amino acids
are as followed:
i. Simple amino acids-no functional group in the side chain like
glycine, alanine, valine, leucine, isoleucine,
ii. Hydroxy-amino acids- one hydroxy group in the side chain like
serine, threonine,
iii. Sulphar containing amino acids- A single sulfur atom in the side
chain like cysteine, methionine,
iv. Acidic amino acids- A carboxyl group in the side chain like aspartic
acid & glutamic acid,
v. Amino acids amides- derivatives of acidic amino acids in which one
of the carboxyl group has been transformed into an –amide group (-
CO.NH2),
vii. Basic amino acids- amino group in the side chain like lysine &
arginine,
viii. Heterocyclic amino acids- side chain consists a ring having one
atom other than carbon like tryptophan, histidine, proline

9. viiii. Aromatic amino acids- Have a benzene ring in the side chain
like Phenylalanine, tyrosine .
B. On the basis of the number of amino & carboxyl group-
1. Mono-amino mono-carboxylic amino acids-
a. Unsubstitted- Glycine, alanine, Valine, Leucine, Isoleucine
b. Heterocyclic- Proline,
c. Aromatic- Phenylalanine, Tyrosine, Tryptophan,
d. Thio-ether- Methionine
e. Hydroxy- Serine, Threonine
f. Mercapto- Cysteine
g. Carboxyamide- Asparagines, Glutamine.
Thus amino acids are classified on the basis of the number of the
functional groups required for the same.

10. C. On the basis of the polarity of the side chains----
i. With non-polar (hydrophobic) R group (insoluble ) in water-
Here the R group simply Hydrocarbon in nature and thus
hydrophobic. This group includes both aliphatic (alanine,
valine, leucine, isoleucine And methionine) and aromatic
(Phenylalanine and tryptophan) amino acids along with
glycine.
ii. With uncharged polar R group- This group contain amino
acids having R group as a. Hydroxyl (-OH) as in serine,
threonine and tyrosine, b. Sulf-hydryl group( -SH) as in
cysteine, c. amide (-NH2) as in asparagine and glutamine.
iii. Amino acids with + vely charged R groups( Basic amino
acids)- This group includes with + vely charged R groups
such as Lysine, arginine and histidine. These are basic in
nature as they contain 2 or more + vely charged and one –
vely charge making ultimately positive.

11. iv. With –vely charged R group (acidic amino acids)- this group
includes two carboxylic acids like aspartic acid and glutamic acid.
These contain two acidic (-ve) and one basic (+vely ) group thus
making the net charge –ve and acidic in nature.
NONSTANDARD AMINO ACIDS
There is a wide distribution in proteins , several other amino acids
exist. These have4 a limited distribution but may be present in
high amounts in a few proteins and hence deserve mention.
Hydroxyproline has limited distribution in nature but constitutes
12% of the composition of collagen, important animal protein .
Similarly hydroxylysine in collagen, N- methyllysine as found in
myosin also belong to this category.
NON-PROTEIN AMINO ACIDS –About 250 different amino
acids have been detected are not proteniceous in nature like L-
ornithine, L-citruline, Creatine, GABA, Histamine, Dopamine,
Thyroxine . Their function is important and have allelopathic
effect.

13. PEPTIDE BOND
A peptide bond is a chemical bond produced in between two
amino acids. Formation of peptide bonds leads to the synthesis
of oligopepetide and polypeptides that are converted into protein.
If 2 –amino acids are linked by peptide bond, it is called
dipeptide,
If 3 amino acids are joined by peptide bond , it is called
tripeptide,
If 10 or less than 10 amino acids are joined by peptide bonds are
called oligopeptides,
If more than 10 amino acids are joined together by peptide bonds
are called polypeptides.
A peptide bond is generated when the alpha carboxylic acid
group of one amino acids is joined to the α-amino group of
another amino acids by secondary linkage with the liberation of
one molecule of water.

15. 1. A peptide bond is a specialized amide linkage and is actually
a bond between C and N.
2. Peptide bond is the backbone of the protein polypeptide3
chain,
3. A peptide chain has the amino group at the one end (left) and
the carboxyl group (right) at the other end,
4. The amino acid end is known as the amino terminus or N-
terminus and the carboxyl end is called carboxyl terminus or
C-terminus,
5. The N-terminus amino acid residue is the first amino acid
and the C-terminus amino acid is the last amino acid of the
polypeptide chain,
6. The C-N bond is a strong bond and only to be hydrolyzed by
the action of the enzyme-peptidase and can be artificially
synthesized at normal temperature and pH by the action of
enzyme peptidyl transferase.

16. PROTEIN CLASSIFICATION
Proteins on the basis of source traditionally divided into two well-
defined groups-animal proteins and Plant proteins. Animal proteins
are treated as higher –quality proteins having the adequate amount
of all the essential amino acids while the plant proteins are called
lower quality as they have a low content of one or more of the
essential amino acids like methionine, lysine, threonine and
tryptophan.
On the basis of the shape of the protein molecule, proteins have
grouped under two categories- Globular & fibrous.
GLOBULAR or CORPUSCULAR : Due to less axial ratio (length:
width) of less than 10, appear spherical or ovoid in shape, soluble in
water or aqueous medium containing acids, bases, salt, alcohol,
complex in conformation, mostly tertiary & quaternary belong to
this group; enzymes , plant hormones, blood transport proteins,
antibodies and storage proteins belong to this group.

17. FIBROUS OR FIBRILLAR PROTEIN:
Here, the axial ratio more than 10, long ribbons or fibers shape,
mainly animal in origin, insoluble in almost all common solvents
like water, acids, salt, alcohol; strong and possess two important
properties of elastomers-
They can stretch and later recoil to their original length,
They have the tendency to creep i.e if stretched for a long time,
their basic length increases and equals the stretched length but if the
tension of the two ends of the fiber is relaxed, they creep to their
shorter and shorter length. It is heterogeneous groups and includes
the proteins of connective tissues, bones, blood vessels, hairs, nails,
wool, silk etc.
The most important are- Collagens that build up the total protein in
the mammalian body, Elastine being the major constituents of
yellow elastic tissues like ligaments, Keratin with large amount of
sulfur in the form of human hair and Fibroin being the principal
constituent of fibers of silk

18. CLASSIFICATION ON THE BASIS OF SOLUBILITY
3 major groups- Simple or Holoproteins, Conjugated or complex
or Heteroproteins and Derived.
SIMPLE PROTEIN
Mostly globular includes proteins containing only amino acids as
structural components and their decomposition with acids liberate
constituent amino acids, It may be different as per solubility like
Protamines & histones ( Salamine and nucleohistones), albumins(
Ovalbumin), Globulins(serum globulin), Glutelins (Glutelin from
corn), Prolamines (gliadin from wheat), scleroproteins or
albuminoids Collagen from bones)etc.
CONJUGATED PROTEIN: Proteins linked with a separable non-
protein portion called prosthetic group either metal or compound
and on decomposition with acids produce amino acids &
prosthetic group.
They may be metalloprotein, chromoproteins, glycoprotein,
phosphoproteins, lipoproteins, nucleoproteins etc.

19. 1. Metalloproteins -Proteins linked with various metals like hg,
Au, Cu, Zn strongly bind with collagen, albumins. Ca binds
weakly with proteins but Na & K do not couple with proteins.
Siderophilin, ceruloplasmin are the two examples in this
regard
2. Chromoproteins - Proteins coupled with colored pigment,
mostly found in enzymes like cartalase, perxidase and
flavoproteins. Myglobin, hemoglobin, cytochromes.
Haemocyanin are some examples.
3. Glycoprotein- Proteins containing carbohydrate as prosthetic
group. Glycoprotein like albumin, elastin and mucoproteins
like mucin, ovomucoid are belonged to this group.
4. Phosphoproteins- proteins linked with phosphoric acid like
casein from milk and ovovitelin from egg yolk belong to this
group.
5. Lipoproteins- Proteins associated with lipid like cephalin,

20. lecithin, cholesterol , highly insoluble in water. Lipoproteins
may be VHDL, HDLs, LDLS, VLDLs belong to this group.
6. Nucleoproteins-Compounds containing nucleic acid like
protamines and histones, usually salt like compounds either
present in nuclear substances or cytoplasm.
DERIVED PROTEINS
Derivatives of protein resulting from the action of heat, enzymes or
chemical agents and it also includes artificially induced
polypeptides.
i. Primary derived proteins like proteans, metaproteins and
coagulated proteins belong to this.
ii. Secondary derived proteins-These are derivatives of protein in
which the hydrolysis has certainly considered. Proteases,
Pep[tones, polypeptides belong to this group.
Thus, on the basis of source and the degree of the occurrence
of the different other components, proteins can be studied in
the different forms.

21. LEVELS OF PROTEIN STRUCTURE
The proteins have specific molecular configurations leading to four
types of structural levels of organization - primary, Secondary, Tertiary
and Quaternary, the first three types of structures composed of one
polypeptide chain only while the quaternary structures exist in protein
molecule composed of more than two polypeptides chain in a complex
manner.
In the secondary, tertiary and quaternary structure of the protein, apart
from the normal polypeptide bond, a variety of chemical bonds bonds
exist either in the same polypeptide chain or in between different
polypeptide chain. These chemical bonds are
Hydrogen bond,
Ionic or electrostatic bond,
Non-polar or hydrophobic bond
Disulphide bond. Protein conformation basically speaks about
combined secondary, tertiary and quaternary structure.

22. PRIMARY STRUCTURE
I. It is the linear sequence and the number of amino acid residues
that make the polypeptide chain
II. Ii. The amino acids residues are linked by polypeptide bonds
formed between α-carboxyl group of one amino acid residue to
the α amino group of the other.
III. The peptide bond is a special amide linkage and it construct the
backbone of the protein chain,
IV. The primary structure of a protein is to start from the amino-
terminus (N) end to the carboxyl-terminal (C) end.
V. All peptide bonds in proteins occur in trans configuration
Glycine, Proline etc.

24. SECONDARY STRUCTURE
The primary structure of the protein chain is folded by hydrogen
bonds to produce secondary structure which may be helical structure
as in α-helices and β-helices. As observed in an atomic-resolution
structure. In this structure, the hydrogen bond is formed in between
the amine hydrogen of one amino acid residue with the carboxyl
oxygen atom of a different amino acid residue of the same chain. The
α-helix and β pleated sheet structure were first proposed by Nobel
prize winner, Linus Pauling et al in 1951. The α-helix is a rod like
structure whose inner part is formed by the tightly coiled polypeptide
chain. All the main chain carboxyl and amino groups are hydrogen
bonded. All the naturally occurring α-helices are right handed. Each
complete coil in each helix consists of 3.6 amino acid residues and the
rise of the helix per turn is 5.4Å (ii) β-plated sheet is different from
the α-helix in that it is a sheet rather than being tightly coiled. The
several polypeptides are being parallel to one another in a plane , with

26. Hydrogen bonds between the adjacent chains. The β-pleated sheets
may have two structures-parallel and anti-parallel. If the chains
run in the same direction, then it is treated as parallel and if it run
in alternate opposite direction, then it is known as anti-parallel β-
sheet.
Examples : α-helix: Keratin wool,
β-pleated sheet: silk, certain synthetic fibres like nylon,
orlon etc.
Many long helices form a multi-stranded rope like structure.
i. Protofibril of hair having 3-right handed helices round around
each other to form a left-handed super-coil of 20Å in
diameter.
ii. Coiled coil having identical α-helices and non-polar repeating
side chains twist around in each other to produce a stable
structure as in α-keratin fiber.

27. TARTIARY STRUCTURE
In this structure of [protein, a polypeptide chain is extensively
coiled and folded to produce a complex and rigid structure . The
folding are due to interact between the amino acid residues
relatively present far apart in the primary sequence , produce
different type of bonding such as hydrogen bond,
hydrophobic(non-polar), ionic and disulphide bond.
The tertiary structure of a protein involves folding of its
secondary structural elements and specifies the position of atoms,
bonds other than normal bonds of residue. And those of the side
chains. The helices in globular protein undergo folding sequences
due to the above four additional bonds and in turn, they achieve a
globular or spherical structure. A protein having tertiary structure
with a large polypeptide chain containing more than 200 amino
acids residues fold into globular spherical clusters to form
domains that give the protein bi- or multi –lobed appearance.

29. A domain may consists of around one-two hundred residues having
diameter approximately 25Å. The adjacent domains are also well
connected by chemical bond. However, small spherical proteins
have many independent domains.
EXAMPLES:
I. Myoglobin- a hem protein found in muscle tissue contains 153
residues and a single Fe porphyrin group in horse heart with
molecular weight 16, 700.
ii. Ribonuclease - of bovine pancreas contains 124 residues having
4 disulphide bridges,
iii. Lysozyme has 129 residues with 40 α-helices and 12 β-
structures,
iv. Cytochrome C with 104 residues,
v. Chymotrypsin with 247 residues,
vi. Carboxypeptidase with 307 residues having 38 α-helices & 17
β-structures

30. QUATERNARY SATRUCTURE
Here, the very complex structure are formed due to the protein-
protein interactions and develop two or more than two interacting
polypeptide chains. Each of then known as subunit . Thus, a large
size globular protein is formed giving a quaternary structure. The
same bonds involved in the formation of tertiary structure like H
bond, ionic, disulphide bonds and also involved to link the various
polypeptide chains in the quaternary structure.
EXAMPLES:
I. Tobacco Mosaic Virus (TMV) protein containing 158 residues
are rod like, tubular structure measuring 3000 Å in length and
180 Å in diameter,
II. Blood hemoglobin containing 4 polypeptide chains of two types-
α and β chains roughly spherical in shape with mol. wt. 64,450;
α-chain with 141 residues & β chains with -146 residues, the two
chains are joined together with ionic & hydrogen bond. The 2
pairs are then joined to each other by H, ionic and hydrophobic
bond.

31. iii. Glutamate dehydrogenase of bovine liver: consists of 40 chains
with 83000 residues having molecular weight 1000000.
iv. Glutamate synthetase of E. coli having 12 subunits,
v. Ribulose bis-phosphate carboxylase oxygenase (RUBISCO) –a
kind of dual enzymes performs oxidation and reduction during
photosynthesis and photorespiration contains 16 sub units ; 8 in
upper view and 8 in lower view.
DNA polymerase, I, II, III associated with DNA replication

32. ISOELECTRIC POINT
As in amino acids, we have observe that in aqueous solution,
proteins are either positively or negatively charged and migrate
towards positive or negative pole. But at certain condition, they
neither behave positively or negatively charged , rather behaves like
a dipole just like Zwitterions form of dipolar amino acids. The
Isoelectric pH of the proteins depend upon the number of basic (+
ve ) and acidic (- ve) group which are provided by the amino acids
residues. Proteins like Pepsin, ovalbumin like substances contain
more acidic amino acids and this make the isoelectric pH of 2.7 and
4.6 respectively. Lysozyme of egg white has high number of basic
amino acids and the isoelectric pH is 11.0.some proteins like milk
casein readily precipitated at or near the isoelectric point and this
phenomenon is called isoelectric precipitation. The isoelectric point
is a valuable information to the biochemists and some of the
proteins and their isoelectric point are attached herewith.

33. Sl.
No.
Proteins along with no. of
chains
Molecular
weight
Isoelectric point
1. Cytochrome C (1) 12,500 9.8
2. Myglobin of horse (1) 16,700 7.0
3. Fibrinogen 4,50, 000 5.5
4. Catalase 2,50,000 5.6
5. Insulin of bovine 5,733 5.4
6. Urease 4,80,000 5.0
7. Pepsin 35,500 2.7

34. DENATURATION OF PROTEIN
Spatial arrangement of polypeptides chain within protein molecules
can be altered for diverse purposes. Protein denaturation is the
process of the alteration of the spatial arrangement of the
polypeptide chain within a protein molecule with an aim to keep
the primary structure retained. It was first coined by Kauzamann
(1959). The physical and chemical properties of the native protein
is altered. In many cases , it is followed by coagulation when the
denatured protein molecules form large aggregate and precipitate in
the solution. The different types of agents are employed for the
denaturation process as followed:
1. PHYSICAL AGENTS- This process include mechanical action
like shaking, rubbing, heat treatment , high hydrostatic pressure
varying from 5000-10000 atm., ultraviolet rays, ionizing
radiations etc are used for the same. Heating and the pH
alteration changes the conformation of protein leading to the
denaturation.

35. 2. CHEMICAL AGENTS- Different types of chemical agents like
acetone, alcohol, aromatic anions like salicylates, anionic detergents
like sodium dodecyl sulphate, mineral acid and alkynes, picric acid,
trichloroacetic acid, tangustic acid are some of the compounds used
for the chemical denaturation of protein. These agents generally
cleave the hydrogen and salt linkages or other chemical bonds
present in the protein to unfold the polypeptide chain. The unfolding
of the polypeptide chain by denaturation causing disorganization of
the protein structure . The denaturized proteins are more easily
hydrolyzed as the denaturation causes freed the hydrogen bond in
between the two polypeptide chains and the free sulphohahydryl
group (-SH) are set free by the denaturation process. Denaturation
causes the cessation of biochemical activity of enzymes and
hormones; decrease solubility; change the size and shape along with
the increase of activity of some radicals present in protein molecule
like –SH, -S-S-, -COOH group etc.

36. TYPES OF DENATURATION
Depending on the nature of the denaturation, it may be of the
following types-
i. Irreversible type- Denatured proteins by external agents can not
be brought back to its previous original position and conformation.
ii. Reversible type- In some cases, denatured proteins can be
brought back to its original position called reversible type. The
process of regaining the normal state of the protein from the
denatured one is called renaturation. In some cases, antibodies may
cause refolding of the protein chains restoring the original bonds to
bring back the original state.
Examples:i.Trypsin- If trypsin is exposed to the high temperature (
80-90℃), it denatures but when cooled at room temperature (37℃),
the solubility and the activity of the enzyme is restored.
ii. RNAase- The enzyme RNAase can be denatured by keeping it in
8M urea solution containing 2-mercaptoethnol. If after dialyzing the
urea and mercaptoethanol, RNAase activity is regained at pH 8 in
O2 exposure.

37. FUNCTION OF PROTEINS
Proteins extend a number of biological role as a part of the structural
and functional mode as stated below:
i. Components of tissues- As a part of the structural attributes,
protein serve as components of tissues like skeletal systems and
collagen as connective tissues.
ii. It acts as central key components in the architecture of
organisms,
iii. Catalysts-acts as catalysts to perform diverse biological
functions,
iv. Biological membranes- key components of cell membrane,
v. Transport functions-The mechanism of active transport into cell
and out of cell requires protein expedited by energy,
vi. Hormones-mostly proteins act as chemical messenger to
control multiple physiological functions,

38. vii. Signal transduction-Communication in between cells during
signal transduction takes place by proteins,
Viii .Chromosomes - Histone and non- histone proteins build up
the structure of chromosomes,
ix. Cellular toxicity- Under different stress condition, the cell
accumulates the different toxic substances and these are the
accumulation of the different denatured protein components,
x. Interferon-these are low molecular weight, regulatory,
glycoprotein's produced by many eukaryotic cells in
response to numerous inducers like virus infection, dsRNA ,
endotoxins, antigenic stimuli, mutagenic agents, and many
more.

39. References:
1. Google for images,
2. Different open sources of information of WebPages
3. Biochemistry- Lehninger
2. Biomolecules & Cell Biology- Arun chandra Sahu,
3. A textbook of Botany (Vol. II) Ghosh, Bhattacharya,
Hait
4. Fundamentals of Biochemistry- Jain, Jain, & Jain,
5.A Textbook of Genetics- Ajoy Paul
DISCLAIMER:
This presentation has been made to enrich open source of
learing without any financial interest. The presenter
acknowledges Google for images and other open sources of
information to develop this PPT.