This document provides information about proteins. It begins with an introduction stating that proteins are abundant organic molecules that are found in all parts of cells and make up about 50% of cellular dry weight. It then discusses the origin of the word "protein" and the elemental composition of proteins. The document outlines the bonds responsible for protein structure, including peptide bonds, disulfide bonds, and non-covalent bonds. It describes the four levels of protein structure - primary, secondary, tertiary, and quaternary. Key properties of proteins and methods of determining protein structure are summarized. The document concludes by discussing clinical aspects of proteins, including prion diseases and Alzheimer's disease.

1. PRESENTED BY:-
Sanjeev Kumar
BSC MLT 2ND year
DEPARTMENT OF BIOCHEMISTRY
1

2. INTRODUCTION
Most abundant organic molecules of the living
system.
Occur in every part of cells.
Constitute about 50% of cellular dry weight.
Form the fundamental basis of structure &
function of life.
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3. Origin of Word ‘Protein’
Greek word ‘proteios’ meaning ‘holding the
first place’.
Berzelius (swedish chemist) suggest the name
proteins to the group of organic compound.
Dutch chemist Mulder in 1838 used the term
‘protein’ for high molecular weight nitrogen
rich and most abundant substance present in
animals & plants.
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4. Elemental composition of proteins
Carbon = 50-55% Hydrogen = 6-7.3%
Nitrogen = 13-19% Sulfur = 0-4%
Oxygen = 19-24%
Protein may also contain other element such
as P, Fe, Cu, I, Mg, Zn etc.
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5. Bonds responsible for protein structure
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Covalent bonds: The peptide and disulfide
bonds are the strong bonds in protein
structure.
Disulfide bonds: A disulfide bond
(S-S) is formed by the sulfhydryl
groups(-SH) of two cysteine
residues, to produce cystine. The
disulfide bonds may be formed in
a single polypeptide chain or
between different polypeptides.
These bonds contribute to the
structural conformation and
stability of proteins.
Peptide Bond: The –COOH
group of one amino acid can
be joined to the –NH2 group
of another by a covalent
bond called as peptide bond.

6. 6
Disulfide Bond
Peptide Bond

7. 7
Non-Covalent Bonds
Hydrogen bonds:
formed by sharing
of hydrogen atoms
b/w nitrogen &
carbonyl oxygen of
different peptide
bonds.
Hydrophobic
bonds: the non
polar side chains of
neutral amino acids
tend to be closely
associated with
each other in
protein.
Electrostatic
bonds: formed by
the interaction b/w
negatively charged
groups (COO-) of
acidic amino acid
with positively
charged group of
basic amino acids
(NH3
+).

8.  Vander Waals forces: are formed by the electrostatic
interactions due to permanent or induced dipoles.
Hydrogen Bonds
Hydrophobic Bonds
Electrostatic Bond
8

9. DIFFERENT STRUCTURE
OF A PROTEIN
(a) Primary structure.
(b) Secondary structure.
(c) Tertiary structure.
(d) Quaternary structure.
9

10. 10
Diagrammatic representation of protein structure

11. PRIMARY STRUCTURE OF A
PROTEIN
Primary structure comprises the sequence or
specific order of amino acids in the
polypeptide chains and location of peptide
bonds in them.
Peptide bond is the main force which
maintains primary structure:
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12. THE POLYPEPTIDE CHAIN
(i) One ‘N’ terminal amino acid (Ist amino acid on left
terminal of polypeptide chain having free amino
group). The protein biosynthesis starts from this end.
(ii) One ‘C’ terminal amino acid (last amino acid
having free carboxyl group).
• In between the amino acids are joined by peptide
bonds.
• Each amino acid in a polypeptide is called a “residue”
because it is the portion of the amino acid remaining
after the atoms of water are lost in the formation of
the peptide bond.
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13. DIMENSIONS OF PEPTIDE BOND
• The two adjacent α-carbon atoms are placed at a
distance of 0.36nm. The inter atomic distances and
bond angles are also shown in this figure.
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14. DETERMINATION OF PRIMARY
STRUCTURE
Determination of amino acid
composition
Degradation of Protein or poly
peptide into smaller fragment
Determination of the amino acid
sequence.
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15. Determination of Amino Acid
composition
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Acid and Alkali treatment to cleave the
peptide bond to release individual amino
acid.
Amino acid cleaved by acid and alkali
treatment can be determined by
chromatographic technique.
A mixture of amino acids is applied to a
column that contains a res into which a
negatively charged group is tightly attached.

16. 16
The amino acids bind to the column and
seperate with different affinities ,
depending on their charges ,
hydrophobicity, and other characterstics
The separated amino acids contained in
column are quantitated by heating them
with ninhydrin.
The amount of each amino acid is
determined spectrophotometrically by
measuring the amount of light absorbed
by the ninhydrin.
CONTI..

17. Degradation Of Protein Into Smaller
Fragment
• Treatment with urea or
guanidine hydrochloride.
Libration of
polypeptide
• Treatment with dansyl chloride.
• The number of dansyl amino acid
produced is equal to number of
polypeptide chain in protein.
Number of
polypeptide
• Enzymatic Cleavage.
• Chemical Cleavage.
Breakdown of
polypeptide into
fragments
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18. 18
Reaction of Dansyl Choloride with
polypeptide

19. Determination Of Amino Acid Sequence
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Sanger’s Reaction Edman Reaction

20. SECONDARY STRUCTURE OF A
PROTEIN
• The conformation of polypeptide chain by
twisting or folding is referred to as secondary
structure.
• The amino acids are located close to each other
in their sequence.
• Two types of secondary structures, a-helix and
β-sheet, are mainly identified.
• Proposed by Pauling & Corey (1951).
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21. α–HELIX
The a-helix is a tightly packed coiled structure
with amino acids side chains extending outward
from the central axis.
The a-helix is stabilized by extensive hydrogen
bonding.lt is formed between H atom attached to
peptide N and O atom attached to peptide C .
All the peptide bonds, except he first and last in a
polypeptide chain, participate in hydrogen
bonding.
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22. Each turn of alpha-helix contains 3 .5 amino
acids and travels a distance of 0.54nm. The
spacing of each amino acidi s 0.15nm.
Certain amino acids( particularly proline)
disrupt the alpha helix. Large number of acidic
(Asp, Glu) or basic (Lys, Arg, His) amino
acids also interfere with alpha helix structure.
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23. 0.54nm distance b/w one
turn & 3.6 AA per turn.
Secondary structure of protein
Alpha helix structure
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24. β– PLEATED SHEET
β-Pleated sheets (or simply β-sheets) are
Composed of two or more segments of fully
extended peptide chains.
In the β-sheets, the hydrogen bonds are formed
between the neighboring segments of Polypeptide
chain(s).
The distance between adjacent A.A is 3.5 Å.
Sheets are composed of two or more than two
polypeptide chains.
β-pleated sheets is parallel and anti-parallel
sheets.
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25. Parallel β-pleated sheet Anti-Parallel β-pleated sheet
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26. TERTIARY STRUCTURE OF A PROTEIN
The looping and winding of the secondary
structure of a protein by other associative
forces between the amino acid residues which
give three dimensional conformation is called
tertiary structure.
In the tertiary structure, proteins fold into
compact structure. The tertiary structure
reflects overall shape of the molecule.
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27. Forces involved in the tertiary structure
(a) Hydrogen bonds.
(b) Hydrophobic interactions.
(c) Van der Waal’s forces.
(d) Disulphide bonds.
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28. Quaternary Structure of a Protein
When proteins consist of two or more
polypeptides which may be identical or
unrelated. Such proteins are termed as
oligomers and possess quaternary structure.
Bonds in quaternary structure:
The monomeric sub units are held together by
non-convalent bonds i.e. hydrogen bonds,
hydrophobic interactions and ionic bonds.
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29. PROPERTIES OF PROTEINS
Solubility: Proteins form colloidal solutions
instead of true solutions in water. This is due to
huge size of protein molecules.
Molecular weight: The proteins vary in their
molecular weights, which is dependent on the
number of amino acid residue.
Insulin - 5,700 Myoglobin-1700
Hemoglobin -64,450 Serum albumin-69,000.
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30.  Shape: There is a wide variation in the protein shape. lt
may be globular (insulin), oval (albumin), fibrous or
elongated (fibrinogen).
 Isoelectric PH: The pH at which a protein possesses
equal number of positive and negative charges (net
charge is zero) is called isoelectric pH with respect to
that protein.
At isoelectric pH, the proteins exist as zwitterions or
dipolar ions.
They are electrically neutral (do not migrate in the
electric field) with minimum solubility, maximum
precipitability and least buffering capacity.
Isoelectric PH of several protein:-
Pepsin – 1.1 Casein – 4.6
Human albumin – 4.7 Urease – 5.0
Hemoglobin – 6.7 lysozyme – 11.0
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31. Acidic and basic proteins : Proteins in which
the ratio (ε Lys + ε Arg)/(ε Glu + ε Asp) is
greater than 1 are referred to as basic proteins.
For acidic proteins, the ratio is less than 1.
Precipitation of proteins: Proteins exist in
colloidal solution due to hydration of polar
groups( - COO-, -NH3
+, -OH) . Proteins can be
precipitated by dehydration or neutralization of
polar groups.
Colour reaction of proteins: The proteins
give several colour reactions which are often
useful to identify the nature of the amino acids
present in them. E.g.: Biuret reaction.
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32. Denaturation
 The phenomenon of disorganization of native protein
structure is known as denaturation.
 Denaturation results in the loss of secondary, tertiary
and quaternary structure of proteins.
 This involves a change in physical, chemical and
biological properties of protein molecules.
 Agents of denaturation
Physical agents: Heat, violent shaking, X-ravs, UV
radiation.
Chemical agents: Acids, alkalies, organic solvents
(ether, alcohol), salts of heavy metals(Pb, Hg), urea,
salicylate.
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33. Denaturation of protein
33

34. Classification of proteins
Functional classification
of protein
Based on chemical nature
& solubility
Nutritional classification
of protein
1. Structural proteins : Keratin of hair and nails, collagen of bone.
2. Enzymes or catalytic proteins: Hexokinase, pepsin.
3. Transport proteins: Hemoglobin, serum albumin.
4. Hormonal proteins: Insulin, growth hormone.
5. Contractile proteins: Actin, myosin.
6. Storage proteins: Ovalbumin, glutelin.
7. Genetic proteins: Nucleoproteins.
8. Defense proteins: Snake venoms, lmmunoglobulins.
9. Receptor proteins for hormones, viruses.
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35. Classification of Proteins Based on
Chemical Nature & Solubility
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Fibrous protein

36. Nutritional classification of protein
1.Complete proteins: These proteins have all the ten
essential amino acids in the required proportion by the
human body to promote good growth. e.g. egg albumin,
milk casein.
2.Partiatly incomplete proteins: These proteins are
partially lacking one or more essential amino acids and
hence can promote moderate growth. e.g. wheat and
rice proteins (limiting Lys, Thr).
3.Incomplete proteins: These proteins completely lack
one or more essential amino acids.Hence they do not
promote growth at all e.g. gelatin( lacks Trp), zein
(lacks Trp, Lys).
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37. Function of proteins
Structural functions: Certain proteins perform
brick and mortar roles and are primarily
responsible for structure and strength of body.
These include collagen and elastin found in
bone matrix, vascular system and other organs
and α-keratin present in epidermal tissues.
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38. Dynamic functions: The dynamic functions of
proteins are more diversified in nature. These
include proteins acting as enzyme, hormones,
blood clotting factors, immunoglobulins,
membrane receptors, storage proteins, besides
their function in genetic control, muscle
contraction, respiration etc
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39. Proteins are the main structural components of the
cytoskeleton. They are the sole source to replace
Nitrogen of the body.
Biochemical catalysts known as enzymes are
proteins.
Proteins known as immunoglobulins serve as
the first line of defence against bacterial and viral
infections.
Several hormones are protein in nature.
Structural proteins furnish mechanical support
and some of them like actin and myosin are
contractile proteins and help in the movement of
muscle fibre, microvilli, etc.
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40.  Some proteins present in cell membrane, cytoplasm
and nucleus of the cell act as receptors.
 The transport proteins carry out the function of
transporting specific substances either across the
membrane or in the body fluids.
 Storage proteins bind with specific substances and
store them, e.g. iron is stored as ferritin.
 Few proteins are constituents of respiratory
pigments and occur in electron transport chain or
respiratory chain, e.g. cytochromes, hemoglobin,
myoglobin.
 Under certain conditions proteins can be catabolised
to supply energy.
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41. Proteins by means of exerting osmotic pressure help
in maintenance of electrolyte and water balance in
body.
Storage proteins bind with specific substances
and store them, e.g. iron is stored as ferritin.
Few proteins are constituents of respiratory
pigments and occur in electron transport chain or
respiratory chain, e.g. cytochromes, hemoglobin,
myoglobin.
Under certain conditions proteins can be
catabolised to supply energy.
Proteins by means of exerting osmotic pressure help
in maintenance of electrolyte and water balance in
body.
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42. CLINICALASPECT
1. Prions and Prion Diseases: Prions are infectious
proteins that contain no nucleic acid. This infectious
protein-prions was discovered in 1982 by Stanley
Prusiner.
 Abnormal or pathological prions cause several fatal
neurodegenerative disorders known as “transmissible
spongiform encephalopathies” (TSEs) or Prion
Diseases.
 The basic defect involves alteration of α-helical structure
into β-pleated sheet.
 Prion proteins have normal primary structure and
abnormal secondary, tertiary, and quaternary.
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43. 2. Alzheimer’s Disease: It is neuropsychiatric
disease frequently encountered in the elderly
persons(>60 years).
Alzheimer’s Disease is characterized by
progressive impairment in intellectual
capabilities, loss of memory, confusion, behavior
disturbances, hallucinations etc.
It is now believed that a protein namely amyloid
peptide deposited in the brain, cause Alzheimer’s
Disease.
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44. 44Thank You