Protein

By
Dr. Mohammad Umair
• Proteins are the most abundant organic
molecules of the living system.
• The term protein is derived from a Greek word
proteios, meaning holding the first place.
• Proteins perform a great variety of specialized
and essential functions in the living cells.
These functions may be broadly
• 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
D-keratin present in epidermal tissues.
• Structural Proteins: Some proteins have a
primarily structural role, providing support
and stability to cells and tissues. For example,
collagen is a fibrous protein that forms the
main component of connective tissues like
tendons, ligaments, and skin. It gives these
tissues their strength and resilience.
• Dynamic functions :
The dynamic functions of proteins are more
diversified in nature. These include proteins
acting as enzymes, hormones, blood clotting
factors, immunoglobulins, membrane receptors,
storage proteins, besides their function in genetic
control, muscle contraction, respiration etc.
Proteins performing dynamic functions are
appropriately regarded as the working horses of
cell.
• Enzymes: Enzymes are specialized proteins
that catalyze (speed up) chemical reactions in
the body. They act as biological catalysts,
facilitating a wide range of essential
biochemical reactions that are necessary for
metabolism, digestion, energy production,
and more. Enzymes are crucial for maintaining
the chemical processes required for life.
• Hormones: Some hormones, such as insulin,
are proteins that regulate various
physiological processes in the body, including
metabolism, growth, and reproduction
• Antibodies: Antibodies, also known as
immunoglobulins, are proteins produced by
the immune system to identify and neutralize
harmful substances such as bacteria, viruses,
and toxins. They play a crucial role in immune
defense.
• Signal Transduction Proteins: These proteins
are involved in transmitting signals within and
between cells. They help coordinate various
cellular processes and responses to external
stimuli. Protein kinases, for example, are
involved in the transfer of phosphate groups
to other proteins, which can activate or
deactivate them.
• Transport Proteins: These proteins are
responsible for transporting molecules across
cell membranes and throughout the body.
Hemoglobin, for instance, is a protein that
binds to oxygen in the lungs and carries it to
tissues throughout the body.
• Gene Regulation Proteins: Proteins are
involved in controlling gene expression by
binding to DNA and regulating the
transcription of genes into messenger RNA
(mRNA). This process determines which
proteins are synthesized by the cell.
• Proteins are predominantly constituted by five
major elements in the following proportion.
Carbon : 50 – 55%
Hydrogen : 6 – 7.3%
Oxygen : 19 – 24%
Nitrogen : 13 – 19%
Sulfur : 0 – 4%
 Proteins are polymers of amino acids
• Proteins on complete hydrolysis (with
concentrated HCl for several hours) yield L-D-
amino acids. This is a common property of all
the proteins. Therefore, proteins are the
polymers of Alpha-D-amino acids.
• There are 300 amino acids occur in nature—
Of these, only 20—known as standard amino
acids are repeatedly found in the structure of
proteins, isolated from different forms of
life— animal, plant and microbial.
• when the proteins are synthesized in the cells.
The process in turn is controlled by DNA, the
genetic material of the cell.
 Amino acids
• Amino acids are a group of organic
compounds containing two functional
groups— amino and carboxyl.
• The amino group (—NH2) is basic while the
carboxyl group (—COOH) is acidic in nature.
 General structure of amino acids
• The amino acids are termed as D-amino acids,
if both the carboxyl and amino groups are
attached to the same carbon atom, as
depicted below
• The Alpha-carbon atom binds to a side chain
represented by R which is different for each of
the 20 amino acids found in proteins. The
amino acids mostly exist in the ionized form in
the biological system
 Classification of amino acids
• There are different ways of classifying the
amino acids based on the structure and
chemical nature, nutritional requirement,
metabolic fate etc.
 NON-STANDARD AMINO ACIDS
Besides the 20 standard amino acids
(described above) present in the protein
structure, there are several other amino acids
which are biologically important. These
include the amino acid derivatives found in
proteins, non-protein amino acids performing
specialized functions and the D-amino acids.
A. Amino acid derivatives in proteins :
The 20 standard amino acids can be
incorporated into proteins due to the
presence of universal genetic code. Some of
these amino acids undergo specific
modification after the protein synthesis
occurs. These derivatives of amino acids are
very important for protein structure and
functions. Selected examples are given here
under
• Collagen—the most abundant protein in
mammals—contains 4-hydroxyproline and 5-
hydroxylysine.
• Histones—the proteins found in association
with DNA—contain many methylated,
phosphorylated or acetylated amino acids
Gamma-Carboxyglutamic acid is found in
certain plasma proteins involved in blood
clotting.
 B. Non-protein amino acids :
These amino acids, although never found in
proteins, perform several biologically
important functions. They may be either D-or
non-D-amino acids. A selected list of these
amino acids along with their functions
 C. D-Amino acids :
The vast majority of amino acids isolated from
animals and plants are of L-category. Certain
D-amino acids are also found in the antibiotics
(actinomycin-D, valinomycin, gramicidin-S).
D-serine and D-aspartate are found in brain
tissue. D Glutamic acid and D-alanine are
present in bacterial cell walls
 Amino acids useful as drugs
There a certain non-standard amino acids that are
used as drugs.
D-Penicillamine (D-dimethylglycine), a metabolite
of penicillin, is employed in the chelation therapy
of Wilson’s disease. This is possible since D-
penicillamine can effectively chelate copper.
N-Acetylcysteine is used in cystic fibrosis, and
chronic renal insufficiency, as it can function as an
antioxidant.
Gabapentin (Gamma-aminobutyrate linked to
cyclohexane) is used as an anticonvulsant.
Proteins are the polymers of L-D-amino acids.
The structure of proteins is rather complex
which can be divided into 4 levels of
organization.
1. Primary structure : The linear sequence of
amino acids forming the backbone of proteins
(polypeptides).
2. Secondary structure : The spatial
arrangement of protein by twisting of the
polypeptide chain.
3. Tertiary structure : The three dimensional structure
of a functional protein.
4. Quaternary structure : Some of the proteins are
composed of two or more polypeptide chains
referred to as subunits. The spatial arrangement of
these subunits is known as quaternary structure.
The term protein is generally used for a polypeptide
containing more than 50 amino acids. In recent
years, however, some authors have been using
‘polypeptide’ even if the number of amino acids is a
few hundreds. They prefer to use protein to an
assembly of polypeptide chains with quaternary
structure.
 PRIMARY STRUCTURE OF PROTEIN
 Each protein has a unique sequence of amino
acids which is determined by the genes
contained in DNA.
 The primary structure of a protein is largely
responsible for its function.
 A vast majority of genetic diseases are due to
abnormalities in the amino acid sequences of
proteins
 Peptide bond
The amino acids are held together in a protein
by covalent peptide bonds or linkages. These
bonds are rather strong and serve as the
cementing material between the individual
amino acids (considered as bricks).
 Formation of a peptide bond :
When the amino group of an amino acid
combines with the carboxyl group of another
amino acid, a peptide bond is formed.
• Peptides containing more than 10 amino acids
(decapeptide) are referred to as polypeptides.
 Characteristics of peptide bonds :
• The peptide bond is rigid, having double bond
in structure. It generally exists in trans
configuration. Both -C=O and -NH groups of
peptide bonds are polar and are involved in
hydrogen bond formation.
Determination of primary structure
 SECONDARY STRUCTURE OF 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, Alpha-helix and B-sheet,
are mainly identified.
 Alpha-Helix
• Alpha-Helix is the most common spiral structure of
protein. It has a rigid arrangement of polypeptide
chain.
• Alpha-Helical structure was regarded as one of the
milestones in the biochemistry research.
• The Alpha-helix is a tightly packed coiled structure
with amino acid.
• The Alpha-helix is stabilized by extensive hydrogen
bonding. It is formed between H atom attached to
peptide N, and O atom attached to peptide C.
Each turn of Alpha-helix contains 3.6 amino
acids and travels a distance of 0.54 nm. The
spacing of each amino acid is 0.15 nm.
The right handed Alpha-helix is more stable than
left handed helix
 B-Pleated sheet
• B-Pleated sheets (or simply B-sheets) are
composed of two or more segments of fully
extended peptide chains
• In the B-sheets, the hydrogen bonds are
formed between the neighbouring segments
of polypeptide chain(s).
 Parallel and anti-parallel B-sheets
• The polypeptide chains in the B-sheets may be
arranged either in parallel (the same
direction) or anti-parallel (opposite direction).
• Besides the Alpha-and Beta-structures
described above, the Beta-bends and non
repetitive (less organized structures)
secondary structures are also found in
proteins
TERTIARY STRUCTURE OF PROTEIN
The three-dimensional arrangement of protein
structure is referred to as tertiary structure.
It is a compact structure with hydrophobic side
chains held interior while the hydrophilic
groups are on the surface of the protein
molecule.
This type of arrangement ensures stability of the
molecule.
 Bonds of tertiary structure :
• Besides the hydrogen bonds, disulfide bonds (
S S), ionic interactions (electrostatic bonds),
hydrophobic interactions and van der Waals
forces also contribute to the tertiary structure
of proteins.
• Domains : The term domain is used to
represent the basic units of protein structure
(tertiary) and function.
QUATERNARY STRUCTURE OF PROTEIN
• A great majority of the proteins are composed
of single polypeptide chains. Some of the
proteins, however, consist of two or more
polypeptides which may be identical or
unrelated. Such proteins are termed as
oligomers and possess quaternary structure.
The individual polypeptide chains are known
as monomers, protomers or subunits. A dimer
consits of two polypeptides while a tetramer
has four.
 Bonds in quaternary structure :
• The monomeric subunits are held together by
non convalent bonds namely hydrogen bonds,
hydrophobic interactions and ionic bonds.
 Methods to determine protein
structure
For the determination of secondary and tertiary
protein structures, X-ray crystallography is
most commonly used. Nuclear magnetic
resonance (NMR) spectra of proteins provides
structural and functional information on the
atoms and groups present in the proteins.
 Methods for the isolation and
purification of proteins
• Several methods are employed to isolate and
purify proteins. Initially, proteins are
fractionated by using different concentrations
of ammonium sulfate or sodium sulfate.
Protein fractionation may also be carried out
by ultracentrifugation. Protein separation is
achieved by utilizing electrophoresis, ion-
exchange chromatography, gel-filtration,
(HPLC) etc
 PROPERTIES OF PROTEINS
• 1. Solubility : Proteins form colloidal solutions instead of
true solutions in water. This is due to huge size of protein
molecules.
• 2. Molecular weight : The proteins vary in their molecular
weights, which, in turn, is dependent on the number of
amino acid residues. Each amino acid on an average
contributes to a molecular weight of about 110. Majority of
proteins/polypeptides may be composed of 40 to 4,000
amino acids with a molecular weight ranging from 4,000 to
440,000. A few proteins with their molecular weights are
listed below : Insulin-5,700; Myoglobin-17,000;
Hemoglobin64,450; Serum albumin-69,000.
• 3. Shape : There is a wide variation in the protein shape. It
may be globular (insulin), oval (albumin) fibrous or
elongated (fibrinogen).
 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-rays,
UV radiation.
• Chemical agents : Acids, alkalies, organic
solvents (ether, alcohol), salts of heavy metals
(Pb, Hg), urea, salicy
 Characteristics of denaturation
• The primary structure of a protein with
peptide linkages remains intact i.e., peptide
bonds are not hydrolysed.
• The protein loses its biological activity.
• Denatured protein becomes insoluble in the
solvent in which it was originally soluble.
• The viscosity of denatured protein (solution)
increases
 CLASSIFICATION OF PROTEINS
• Proteins are classified in several ways. Three
major types of classifying proteins based on
their function, chemical nature and solubility
properties and nutritional importance are
discussed here.
Functional classification of proteins
• Based on the functions they perform, proteins
are classified into the following groups (with
examples)
• 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
Functional classification of proteins
• Genetic proteins : Nucleoproteins.
• Defense proteins : Snake venoms,
Immunoglobulins.
• Receptor proteins for hormones, viruses.
 Protein classification based on
chemical nature and solubility
• This is a more comprehensive and popular classification
of proteins. It is based on the amino acid composition,
structure, shape and solubility properties. Proteins are
broadly classified into 3 major groups
• 1. Simple proteins : They are composed of only amino
acid residues.
• 2. Conjugated proteins : Besides the amino acids, these
proteins contain a non-protein moiety known as
prosthetic group or conjugating group.
• 3. Derived proteins : These are the denatured or degraded
products of simple and conjugated proteins.
 Simple proteins
• (a) Globular proteins : These are spherical or
oval in shape, soluble in water or other
solvents and digestible.
• (i) Albumins : Soluble in water and dilute salt
solutions and coagulated by heat. e.g. serum
albumin, ovalbumin (egg), lactalbumin (milk).
• (ii) Globulins : Soluble in neutral and dilute
salt solutions e.g. serum globulins, vitelline
(egg yolk).
• Histones : Strongly basic proteins, soluble in
water and dilute acids but insoluble in dilute
ammonium hydroxide e.g. thymus histones.
• Globins : These are generally considered along
with histones. However, globins are not basic
proteins and are not precipitated by NH4OH.
• Protamines : They are strongly basic and
resemble histones but smaller in size and soluble
in NH4OH. Protamines are also found in
association with nucleic acids e.g. sperm proteins
• Lectins are carbohydrate-binding proteins,
and are involved in the interaction between
cells and proteins. They help to maintain
tissue and organ structures.
 (b) Fibrous proteins :
• These are fiber like in shape, insoluble in water
and resistant to digestion.
• (i) Collagens are connective tissue proteins
lacking tryptophan. Collagens, on boiling with
water or dilute acids, yield gelatin which is
soluble and digestible
• (ii) Elastins : These proteins are found in elastic
tissues such as tendons and arteries.
• (iii) Keratins : These are present in exoskeletal
structures e.g. hair, nails, horns. Human hair
keratin contains as much as 14% cysteine
 2. Conjugated proteins
• (a) Nucleoproteins : Nucleic acid (DNA or RNA) is
the prosthetic group e.g. nucleohistones,
nucleoprotamines. (b) Glycoproteins : The
prosthetic group is carbohydrate, which is less
than 4% of protein. The term mucoprotein is used
if the carbohydrate content is more than 4%. e.g.
mucin (saliva), ovomucoid (egg white).
• (c) Lipoproteins : Protein found in combination
with lipids as the prosthetic group e.g. serum
lipoproteins.
• (d) Phosphoproteins : Phosphoric acid is the
prosthetic group e.g. casein (milk), vitelline
(egg yolk).
• (e) Chromoproteins : The prosthetic group is
coloured in nature e.g. hemoglobins,
cytochromes. (f) Metalloproteins : These
proteins contain metal ions such as Fe, Co, Zn,
Cu, Mg etc., e.g. ceruloplasmin (Cu), carbonic
anhydrase (Zn).
• 3. Derived proteins : The derived proteins are of two
types. The primary derived are the denatured or
coagulated or first hydrolysed products of proteins. The
secondary derived are the degraded (due to
breakdown of peptide bonds) products of proteins. (a)
Primary derived proteins (i) Coagulated proteins :
These are the denatured proteins produced by agents
such as heat, acids, alkalies etc. e.g. cooked proteins,
coagulated albumin (egg white). (ii) Proteans : These
are the earliest products of protein hydrolysis by
enzymes, dilute acids, alkalies etc. which are insoluble
in water. e.g. fibrin formed from fibrinogen. (
• iii) Metaproteins : These are the second stage
products of protein hydrolysis obtained by
treatment with slightly stronger acids and alkalies
e.g. acid and alkali metaproteins. (b) Secondary
derived proteins : These are the progressive
hydrolytic products of protein hydrolysis. These
include proteoses, peptones, polypeptides and
peptides. C. Nutritional classification of proteins
The nutritive value of proteins is determined by
the composition of essential amino acids
(described already).
• From the nutritional point of view, proteins are classified
into 3 categories.
• 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. Partially incomplete proteins : These proteins partially
lack one or more essential amino acids, and 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).