Structure of protein

• Proteins are the most abundant organic molecules of the

living system.

• They occur in the every part of the cell and constitute about
50% of the cellular dry weight.
• Proteins form the fundamental basis of structure and
function of life.

• In 1839 Dutch chemist G.J.Mulder while investing the

substances such as those found in milk, egg, found that they
could be coagulated on heating and were nitrogenous
compounds.
 Biomedical importance of proteins:

• Proteins are the main structural components of

the cytoskeleton. They are the sole source to
replace nitrogen of the body.

• Bio chemical catalysts known as enzymes are

proteins.

• Proteins known as immunoglobulins serve as the

first line of defense against bacterial and viral
infections.
 Structure of proteins

• Proteins have different level of organization;

• Primary structure: The linear sequence of amino acids
forming the backbone of proteins.

• Secondary structure: The spatial arrangement of protein

by twisting of the polypeptide chain.

• Tertiary structure: The three dimensional structure of a

functional protein.
• 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.
 Structure of proteins

Primary structure: The linear sequence of amino acids

held together by peptide bonds in its peptide chain.

• The peptide bonds form the back bone.

• The free –NH2 group of the terminal amino acid is
called as N-terminal end and the free –COOH end is
called C-terminal end.
• It is a tradition to number the amino acids from N-
terminal end as No.1 towards the C-terminal end.
• Presence of specific amino acids at a specific number
is very significant for a particular function of a
protein.
 Secondary structure

• The spatial arrangement of protein by twisting of the

polypeptide chain

• The amino acids are located close to each other in

their sequence.

• Two chief types of secondary structures, α-Helix and

β-sheet
 α-Helix

• α-Helix is the most common spiral structure of protein

• α-Helical structure was proposed by Pauling and Corey
in 1965.

The salient feature:

• The α-Helix is a tightly packed coiled structure with
amino acid side chains extending outward from the
central axis.
• The α-Helix is stabilized by extensive hydrogen bonding
• Formed between H atom attached to peptide N, and O
atom attached to peptide C.

• The H-bonds are individually weak but collectively,

strong enough to stabilize the helix.
• All the peptide bonds, except the first and last in
polypeptide chain, participate in hydrogen bonding.
• Each turn of helix contains 3.6 amino acids and travels a
distance of 0.54 nm.
• The spacing of each amino acid is 0.15 nm.
• α-Helix is a stable conformation formed spontaneously with
the lowest energy.
• The right handed α-Helix is more stable than the left handed
helix

• Certain amino acids (particularly proline) disrupt the α-Helix.

• Large number of acidic and basic amino acids are also
interfere with α-Helix structure.
 β-pleated sheet

• An another form of secondary structure in which two or more

polypeptides (or segments of the same peptide chain) are linked
together by hydrogen bond between H- of NH- of one chain and
carbonyl oxygen of adjacent chain (or segment).

• β-Pleated sheet may be formed either by separate

polypeptide chains (H-bonds are inter chain) or a single
polypeptide chain folding back on to itself (H-bonds are
intrachain)
Parallel and anti-parallel β-
sheets
The polypeptide chains in
the β-sheets may be
arranged either in parallel
or anti-parallel direction.
 Triple helix
• Collagen is rich in proline and hydroxy proline and
cannot form a α-helix or β-Pleated sheet.

• Collagen forms a triple helix.

• The triple helix is stabilized by both non covalent as
well as covalent bonds.
 Reverse Turns or β-bends
• Since the polypeptide chain of a globular protein
changes direction two or more times when it folds,
the conformation known as Reverse turns or β-bends.

• Reverse turns usually occur on the surfaces of

globular proteins.
Super secondary structures (Motifs)
• Varies combinations of secondary structure, called
super secondary structure, are commonly found in
globular proteins.

These are

• β- α- β unit

• Greek key

• β-meander

• β- barrel
β- α- β unit :
• The β- α- β unit consists of two parallel β-pleated
sheets connected by an intervening strand of α –helix.

Greek key :
• A conformation that takes its name from a design
often found on classical Greek pottery.
β-meander :
• The β-meander consists of five β-Pleated sheets
connected by reverse turns.

• The β-meander contains nearly as many hydrogen bonds

as an α-helix and its common occurrence probably reflects
the stability conferred by this extensive hydrogen bonding.
 Tertiary structure

• The three dimensional structure of a protein.

• It is a compact structure with hydrophobic side chains
held interior while the hydrophilic groups are on the
surface of the protein.

• This type of arrangement ensures stability of the

molecule.
 Bonds of Tertiary structure

• The hydrogen bonds,

• Disulfide bonds(-S-S )
• Ionic interactions (electrostatic bonds) and
• Hydrophobic interactions also contribute to the
tertiary structure of proteins.
Domains: Used to represent the basic unit of protein
structure (tertiary) and function.
• A polypeptide with 200 amino acids normally consists
of two or more domains.
 Quaternary structure
• Majority of the proteins are composed of single
polypeptide chains.

• Some of the proteins, consists 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 consists of two polypeptides while a

tetramer has four.

• Importance of oligomeric proteins:

These proteins play a significant role in the regulation
of metabolism and cellular function.

e.g. hemoglobin, LDH.

 Bonds responsible for protein structure

Two types of bonds

Covalent and non-covalent bonds

Covalent bonds:

• The peptide and disulfide bonds are the strong bonds in

protein structure.
Disulfide bond:
• A disulfide bond (-S-S-) is formed by the sulfhydryl
groups (-SH) of two cystine 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 protein.
 Non-covalent bonds

Hydrogen bonds (H-bonds):

• The H-bonds are formed by sharing of H-atoms
between the Nitrogen and carbonyl oxygen of different
peptide bonds.
• Each H-bond is weak but collectively they are strong.
• A large number of H-bonds significantly contribute to
the protein structure.
 Hydrophobic bonds

• The non-polar side chains of neutral amino acids tend

to be closely associated with each other in proteins.

• These are not true bonds.

• The occurrence of hydrophobic forces is observed in
aqueous environment wherein the molecules are forced
to stay together.
Electrostatic bonds:
• These bonds are formed by interactions between negatively charged
groups of acidic amino acids with positively charged groups of
basic amino acids.
Van der Waals forces:
• These are the non-covalent associations between electrically
neutral molecules.

• They are formed by the electrostatic interactions due to

permanent or induced dipoles
 Methods to determine protein structure

• Determination of secondary and tertiary protein

structures, X-ray crystallography is most commonly
used.
• Nuclear magnetic resonance (NMR) spectroscopy of
proteins provides structural and functional
information on the atoms and groups present in the
proteins
 Properties of proteins
Solubility:
• Proteins form colloidal solutions instead of true solutions
in water.
• This is due to huge size of protein molecule.

Molecular weight:
• The proteins vary in their molecular weights, dependent
on the number of amino acid residues.
• 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.
Shape:
• There is a wide variation in the protein shape.
• It may be globular (insulin), Oval (albumin), fibrous or
elongated (fibrinogen)
Isoelectric pH:
• At isoelectric pH, the proteins exist as zwitterion or dipolar
ions.
• They are electrically neutral with minimum solubility,
maximum precipitability and least buffering capacity.
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

Iso-electric precipitation:
• Proteins are least soluble at their iso-electric pH.
• Some of the proteins are precipitated immediately when
adjusted to their iso-electric pH
e.g. Casein which forms a flocculent precipitate at pH
4.6 and redissolves in highly acidic or alkaline
solutions.
• When the milk is curdled, the casein forms the white
curd, because lactic acid produced by the
fermentation process lowers the pH to the iso-electric
point of casein.
 Classification of proteins

Three major types of classifying proteins based on their

function, chemical nature and solubility and nutritional
importance

• Functional classification of proteins

• Chemical nature and solubility

• Nutritional importance
 Functional classification of proteins

• Structural proteins: Keratin of hair and nails, collagen

of bone

• Contractile proteins: myosin, actin

• Enzymes or catalytic proteins: Hexokinase, pepsin
• Transport proteins: Hemoglobin, serum albumin
• Regulating proteins: Insulin, growth hormone
 Proteins

Simple Conjugated Derived

Globular Scleroproteins Nucleoproteins Primary Secondary

Glycoproteoins
Proteoses
Albumins Collagen Coagulated

Globulins Lipoproteins Peptones

Proteins
Elastins
Glutelins Phosphoproteins Poly
Metaproteins
Keratins peptides
Prolamines Chromoproteins
Histones Peptides
Metalloproteins
Lectins

Protamines
 Simple proteins

A) Globular proteins:
• These are spherical or oval in shape, soluble in water or other
solvents and digestible
Albumins:
• They are soluble in water and coagulated by heat. e.g serum
albumin, ovalbumin (egg), lactalbumin (milk)
Globulins:
• These are insoluble in pure water, but soluble in dilute salt
solutions and coagulated by heat.
• They are precipitated by half saturation with ammonium sulphate or
by full saturation with sodium chloride. e.g., serum globulins, egg
globulins
Glutelins:
• These are plant proteins, insoluble in water or neutral salt solutions,
soluble in dilute acids or alkalies
• They are rich in glutamic acid.
• They are large molecules and can be coagulated by heat. e.g.,
glutelin (wheat), oryzenin (rice).
Prolamines:
• They are soluble in 70-80% alcohol, but insoluble in pure water.
• They are rich in proline but lack in lysine. E.g., gliadin (wheat),
zein (maize)

Histones:
• These are basic proteins, rich in arginine and histidine, with alkaline
isoelectric pH.
• They are soluble in water, dilute acids and salt solutions but
insoluble in ammonia
• They form conjugated proteins with nucleic acids (DNA)
and porphyrins.
e.g., nucleohistones, chromosomal nucleoproteins
Protamines:
• These are soluble in water, dilute acids and alkalies. They are
not coagulated by heating..
• They contain large number of arginine and lysine residues, and are
strongly basic. These are also found in association with nucleic acids
 Scleroproteins or Albuminoids
• These are fibrous proteins with great stability and very low
solubility and form supporting structures of animals
Collagens, are connective tissue proteins lacking tryptophan
Elastins, these proteins are found in elastic tissues such as
tendons and arteries
Keratins, these are present in exoskeletal structures e.g. hair,
nails, horns.

Human hair has a higher content of cysteine.

 Conjugated proteins
They are combinations of proteins with a non-protein part, called
prothetic group
These are
Glycoproteins:
• Glycoproteins are the proteins with carbohydrate moiety as the
prosthetic group.
• The term mucoprotein is used if the carbohydrate content is
more than 4%.
• Blood group antigens and many serum proteins are
glycoproteins
Lipoproteins:

• These are the proteins loosely combined with lipid components.

• They occur in blood and on cell membranes

• Serum lipoproteins, membrane lipoproteins

Nucleoproteins:

• These are the proteins attached to nucleic acids, e.g. Histones.

• The DNA carries negative charges, which combines with positively
charged proteins
 Chromoproteins

•These are the proteins with colored prosthetic groups

Hemoproteins: All hemoproteins are Chromoproteins which carry
heme as the prosthetic group

• Hemoglobin: Respiratory protein found in RBCs

• Cytochromes: These are the mitochondrial enzymes of the
respiratory chain
Catalase:
•This enzyme decomposes H2O2 to water and O2
Flavoproteins:
• Is a cellular oxidation-reduction protein which has riboflavin a
constituent of B-complex vitamin as its prosthetic group.
•This is yellow in color
Visual purple:
• Is a protein of retina in which the prosthetic group is a corotenoid
pigment which is purple in colour
Phosphoproteins:
• These contain phosphorous. E.g. casein and vitellin of egg yolk.
• The phosphoric acid is esterified to the hydroxyl groups of serine
and threonine residues of proteins
Metalloproteins:
• They contain metal ion as their prothetic group.
• Several enzymes contain metallic elements such as Fe, Co, Mn, Zn,
Cu, Mg, etc
E.g., Ferritin (Fe), Carbonic anhydrase (Zn), Ceruloplasmin (Cu)
 Derived proteins
•The derived proteins are of two types
Primary derived proteins:
• These are the denatured or coagulated or first hydrolysed
products of proteins

Secondary derived proteins:

• These are the degraded (due to breakdown of peptide bonds)
products of proteins
 Primary derived proteins

Proteans:
• These are earliest products of protein hydrolysis by enzymes,
dilute acids, alkalis etc.
• They are insoluble in water
•E.g., Myosan (from myosin), Elestan (from elastin)
Meta proteins:
• These are the second stage products of protein hydrolysis by
treatment with slightly stronger acids and alkalis. e.g., acid and
alkali metaproteins.
Coagulated proteins:
• These are the denatured proteins produced by agents such as heat,
acids, alkalis etc, E.g., cooked proteins, coagulated albumin (egg
white )
Secondary derived proteins:
• These are the degraded (due to breakdown of peptide bonds)
products of proteins
Proteoses or albumoses:
• These are hydrolytic products of proteins which are soluble in water
and coagulated by heat and precipitated by saturation with
ammonium sulphate
Peptones:
• These are hydrolytic products of proteoses.
• They are soluble in water, not coagulated by heat and not precipitated
by saturation with ammonium sulphate.

• They can be precipitated by phosphotungstic acid

Peptides:
• Peptides are composed of very small number of amino acids joined as
peptide bonds.
• They are named according to the number of amino acids present in
them
• Dipeptide: made up of two amino acids
• Tripeptides: made up of three amino acids
• Peptides are water soluble and not coagulated by heat
• Hydrolysis: The complete hydrolytic decomposition of a
protein generally follows these stages
• Protein Protean Metaprotein
Peptides Peptone Proteose
Amino acids
 Nutritional classification of proteins
Complete proteins or Nutritionally rich proteins: These proteins
have all the essential amino acids in the required proportion.
• Also called as first class proteins. e.g., egg albumin, casein of
milk

Partially incomplete proteins:

• These proteins are partially lacking one or more essential
amino acids and can promote moderate growth. e.g., wheat and
rice proteins. Limiting amino acids Lysine and Threonine

• Pulses lack Methionine

Incomplete or poor proteins:
• They lack in many essential amino acids
Hence they do not promote growth at all

• e.g., gelatin (lacks Trp), zein ( from corn, lacks Trp, Lys)