PROTEIN CHEMISTRY

Dr. SHEFALI PANDEY

 PROTEINS

• Proteins are polymers of L α amino acids.

• They are macromolecules with Complex 3D

structures consisting of multiple polypeptide
chains.

• Different types of proteins includes Enzymes,

receptors, haemoglobin, muscle and organ
tissue etc.

• Improper protein functions cause large

number of diseases e.g. sickle cell anaemia ,
lactosuria, galactosemia etc.
 PEPTIDE BOND FORMATION

1 Carboxyl group Amino group 2

H H

H 2N C COOH + H 2N C COOH
α α

R1 R2

H2O

H H

H 2N C CO NH αC COOH
α Dipeptide

R1 R2
Peptide bond
 PEPTIDE BOND FORMATION

freedom of NO freedom of freedom of

movement movement movement
H H
O H

H2 N
ψ φ
C
C N αC COOH
αC
Angle between Cα and C is ψ angle Angle between Cα and N is φ angle
R1 O H
R2
Peptide bond
φ & ψ are Ramchandran angles
 PEPTIDE BOND FORMATION

1 2
H H

H 2N C CO NH αC COOH
α
N- Terminal C- Terminal
R1 R2
Peptide bond

• Peptide bond is a chemical bond joining the carboxyl group of one amino acid to the amino
group of another amino acid.
• Linkage of many amino acids through peptide bonds result in an unbranched chain called
polypeptide .
• And each amino acid in the polypeptide chain is called as residue.
• Each polypeptide has free amino group at one end called as amino terminal end or N-
Terminal and a free carboxyl group at the other end called as carboxy terminal or C terminal.
• The amino acid with free amino terminal end is the first aa and the amino acid with free
carboxyl group is the last aa.
 CLASSIFICATION OF PROTEINS

1 2 3 4

Function Molecular Solubility Composition

Shape
Structural

Enzyme

Transport

Storage

Contractile

Defense

Regulatory
Structural Immunoglobulins
Actin
Enzyme Growth Hormones
Collagen Pepsin ,Trypsin, amylase ,lipase
Transport
Apoferritin
Transaminase Myoglobin
Storage
Insulin Transferrin Haemoglobin
Dehydrogenase
Contractile Fibrinogen , thrombin
Elastin Cartilage Myosin
Defense
Keratin Albumin Glucokinase

Regulatory
 Collagen in bone

Structural proteins
serve as supporting Cartilage in joints , ear , nose
framework of cells to
give biological
Elastin of ligaments
structure, strength
or protection

Keratin of hair and nails

 Pepsin ,Trypsin, amylase ,lipase
(Hydrolytic enzymes)

Dehydrogenase
Catalytic proteins
or Enzymes
Transaminase

Glucokinase
 Haemoglobin transport oxygen

Transport
Transferrin transport iron
Protein

Albumin carries FA and bilirubin

 Apoferritin Store iron in the form of ferritin

Storage Proteins

Myoglobin store oxygen in muscles

 Actin composed of thin filaments
Contractile
proteins
are responsible for
the contraction of
muscle fibers
Myosin composed of thick filament
 Immunoglobulins or Antibodies
Defense proteins
Involved in defense
mechanism against
invasion of foreign
substances like
bacteria, viruses
Fibrinogen , thrombin
blood clotting proteins
 Insulin regulates blood sugar

Regulatory proteins
Controls and coordinates
various cellular and
physiological processes

Growth Hormones
Controls body growth , cell repair and
influence metabolism
Structural

Enzyme

Transport

Storage

Contractile Fibrous Globular

Defense

Regulatory
 GLOBULAR
No. FIBROUS PROTEINS
PROTEINS
1 Also called Scleroproteins Also called Spheroproteins
Extended along a longitudinal Tightly folded and packed into
2 axis compact structure
Appear like spherical globular
3 Appear like long thin fibers
drops
4 Axial ratio of more than 10 Axial ratio usually 3-4
All secondary and super
They have α helix Β pleated
secondary structures like –
5 sheets as secondary .
α helix Β pleated sheets loops
structures
and turns
• Collagen found in cartilage • Albumin
and tendon • Globulin
• Elastin found in elastic • Enzymes like Insulin
6 tissue • Histones
• Skin , nails , Keratin of hair • Protamine
• Myosin • Actin, Troponin
Structural

Enzyme

Transport

Storage

Contractile Fibrous Globular

Defense

Regulatory
 ALBUMINS GLOBULINS
Product B HISTONES
Product C GLUTELINS

1 • Soluble in water
• coagulated by heat
• Soluble in water,
2 • Not coagulated by
heat
• insoluble in water,
3 • Soluble in dilute
neutral salt solution
• heat coagulated
• Insoluble in neutral
4 solvents
• Soluble in dilute acids
and alkali
 SCLERO PROLAMINSProduct C
PROTEINS

• Soluble in 70-80%
4 alcohol
• Insoluble in water,
neutral solvents or
Absolute alcohol
insoluble in water,
5 neutral salts solutions,
organic solvents dilute
acid and alkali
Structural

Enzyme

Transport

Storage

Contractile Fibrous Globular

Defense Simple conjugated Derived

Regulatory
 Albumins Egg Albumin , Serum Albumin

Globulins Serum Globulin, Myosin of muscle

SIMPLE Glutelin Wheat Glutelin, Oryzenine of rice

PROTEINS
Histones

Protamins
 Nucleoproteins

Glycoproteins &
proteoglycans

CONJUGATED Chromoproteins
PROTEINS

Phosphoproteins

Lipoproteins

Metalloproteins
 Conjugate proteins

Glycoproteins
Type Nucleoproteins &
Proteoglycans

Prosthetic CARBOHYDTRATES
DNA & RNA
Group

Glycoproteins Proteoglycans
(when carbohydrate < 4%) (when carbohydrate > 4%)

Examples • Mucin of saliva Glycosaminoglycans

• Immunoglobulins
 Conjugated Proteins

Type Chromoproteins Phosphoproteins

Prosthetic PHOSPHORIC ACID

HEME
Group

• Hemoglobin
• Casein of milk
Examples • Cytochromes
• Vitellin of egg
• Catalase
yolk
• Peroxidase
 Conjugated Proteins

Type lipoproteins Metalloproteins

Prosthetic Fe Co Mn Zn Cu Mg
LIPID
Group

• Chylomicron • Ceruloplasmin Cu containing

Examples • VLDL • Carbonic anhydrase
• LDL • Carboxypeptidase Zn containing
• HDL • DNA Polymerase
 DERIVED
PROTEINS

Secondary derived
Primary derived Proteins
Proteins

Proteans Meta proteins

Proteoses Peptones Peptides

 Properties of
Proteins

COLLOIDAL SOLUBILITY
NATURE

• Protein molecule exists in the form of colloidal • Globular protein has higher solubility than fibrous
particle protein

• Colloidal protein molecules exerts oncotic pressure • Smaller molecules are more soluble than large
molecule
• Oncotic pressure exerted by protein molecule
important for maintaining blood volume
 Properties of
Proteins

ISOELECTRIC NATURE OF AMPHOTERIC NATURE

PROTEIN

• The pH at which a protein carries no net charge k/as • Proteins can act as both acid and base,
Isoelectric point ( pI) depending upon the pH of the environment
• At this pH solubility of protein is minimum and
• This is due to presence of both acidic and basic
precipitation occurs
groups in their structure that allow them to
• Each protein has a unique pI determined by the specific donate or accept protons
composition and sequence of the amino acids
 Properties of
Proteins

SHAPE OF MOLECULAR
PROTEIN WEIGHT

• Scleroproteins keratin, collagen are in the form of • Proteins are macromolecules

fibers • Have high molecular weight -
Albumin = 69000
γ Globulin = 1,60000

• Globular proteins Albumin, Globulin tend to be of

rounded shape
 Properties of
Proteins

HYDRATION OF Precipitation
PROTEIN

• “A hydration shell” is held around each protein • Organic solvents like Alcohol dehydrates and
particle in an aqueous medium to maintain the precipitates the proteins
proper folding and stabilizes the protein
structure.
PROTEIN CONFORMATION
Number and sequence of Folding and twisting of Three dimensional shape of The arrangement of
amino acids linked by polypeptide chain brought the folded structure multiple polypeptide
peptide bonds to form a about by hydrogen bonding subunits in the protein
polypeptide chain
Primary Structure N C

Number and Sequence of

amino acids linked together by
01 It is the backbone of protein 02
covalent peptide linkage

It has an N terminus (an end It dictates higher levels of

with free amino group) and a protein structure (secondary,
C terminus ( the end with free 03 tertiary, and quaternary) 04
carboxyl group

The primary structure Mutations in DNA can alter

doesn't provide functional the primary structure of
activity; the protein must 05 proteins leading to genetic 06
fold into higher-order diseases
structures to become active.
 Secondary
Structure
• Regular folding and
twisting of the
polypeptide chain
brought about by
hydrogen bonding is
called secondary
structure of protein.

Primary Structure of protein

• Different kinds of
ordered units
α Helix Β pleated secondary structures are
sheets
α Helix
β pleated sheets
Loops and bends
α Helix
structure
• It is called α because it
was the First structure
elucidated by Pauling
and Corey

• The alpha helix is the

most common
secondary structure in
proteins characterized
by a right-handed coil or
spiral.
 α Helix
structure
• It is stabilized by Intra
chain hydrogen bonds
between the carbonyl
oxygen of 1st amino acid
residue and the amide
hydrogen of 4th amino
acid residue ahead in the
sequence
2.8 Å
• Hydrogen bonds have an
optimal distance of about
2.8 Å between the
hydrogen and oxygen
atoms.
 α Helix
structure
• A full turn of an alpha
helix has about 3.6
amino acid residues
and rises about 5.4 Å in
height.
3.6 aa
residue • The axial distance
5.4Å
between adjacent
amino acids is 1.5 Å
 α Helix
structure
• Hemoglobin

• Myoglobin

3.6 aa • α - Keratin
residue
5.4Å
α Helix destabilizing amino acids
Proline
Proline has one hydrogen
atom lesser so it cannot
effectively take part in
hydrogen bonding and Glycine
produces bend in the
structure. Glycine because of its small
size induces bends in the
structure
β Pleated sheet
structure
• β because it was the
second structure
elucidated by Pauling &
Corey.

• Polypeptide chains are

fully extended

• Unlike α-helix, β-pleated

sheets are composed of
two or more polypeptide
chains.
β Pleated sheet
structure
• β-pleated sheet is
stabilized by interchain
hydrogen bonds
between the carbonyl
oxygen of one strand
and the amide hydrogen
of an adjacent strand,

• The axial distance

between adjacent
amino acids in β-
pleated sheet is 3.5Å
 β Pleated sheet
structure
PARALLEL PLEATED
SHEETS
• The arrangement of
polypeptide chains in
β -pleated sheet
conformation can
occur in 2 ways :

• Parallel pleated sheet

ANTI- PARALLEL
PLEATED SHEETS
• Anti – parallel
pleated sheets
Parallel pleated
sheet

• Polypeptide chains lie in

same direction( N
terminal faces to N
terminal)

• Hydrogen bonds are

formed between NH of
one polypeptide chain and
carbonyl hydrogen of a
neighboring chain

• Example: Flavodoxin
Anti - Parallel pleated
sheet

• The polypeptide chains

lie in the opposite
direction ( N-terminal
faces to C-terminal)

• Hydrogen bonds are

formed between NH of
one polypeptide chain
and carbonyl Hydrogen
of a neighboring chain

• Example : Silk fibrion

• Amyloidosis refers to a group of diseases caused by the buildup of
amyloid proteins in tissues and organs.

• Amyloid Proteins have β pleated sheet as secondary structure.

• They misfold and accumulate to form insoluble amyloid fibrils in

tissues and organ disrupting normal physiological function.

• Diseases Under Amyloidosis: Alzheimer's Disease

Type 2 Diabetes
 Super Secondary
Turn/ bend Super structures
secondary
structures loops
• Short segments of
amino acids that join
two units of
secondary structures

• 2 types:
secondary secondary
structures structures  Turns/ Bends
• (β • ( α helix)
pleated  Loops
sheets)
 Turns and bends
TURNS

• If limited number
( short segment)

of amino acids
are used to link
the adjacent
Secondary
structures.
 Loops
LOOPS

• If more number
(long
segment)of
amino acids are
used for linking
the adjacent
secondary
structures .
 Super Super Secondary
secondary structures
structures

• They often form

functional domains
and have hydrogen
bond linkages

Helix -Turn- Helix Helix -Loop- Helix

• Proline and Glycine
are found in super
secondary
MOTIFS structures
 Tertiary structure

• The tertiary structure

of a protein refers to
its three-dimensional
(3D) shape formed by
the folding of the
polypeptide chain.

• It indicates, in 3-
dimentional space,
how secondary
features –helices,
sheets, bends, turns,
Schematic tertiary structure of protein. and loops assemble to
form domains.
 Tertiary structure
Stabilizing forces
formed
N between • Hydrogen bonds
nonpolar
hydrophobic R
groups • Hydrophobic
(side chain) of
amino acids interactions
between two cysteine residues, formed by
the linkage of their
• sulfur atoms
Ionic bonds
(electrostatic)
formed between oppositely charged groups
such as amino (NH3+) terminal and
carboxyl (COO–) •terminal groups of the
Van der Waals forces
peptide and oppositely charged R-groups of
polar amino acid residues.

Schematic tertiary structure of protein. • Di sulfide bonds

 Tertiary structure

Example- INSULIN

• Insulin has SINGLE

polypeptide chain consists of
2 chains A & B which are
connected by disulfide bond.

• These CHAINS are part of

same protein and are not
independent subunits

• first protein in which

complete sequencing of
amino acids was done by
Schematic tertiary structure of Insulin. Sanger
Tertiary structure of myoglobin.
 Quaternary
structure

arrangement of
multiple polypeptide
chains (subunits) into a
functional 3D protein
complex

Quaternary structure of protein.

 Quaternary
structure

The subunits may be -

• Identical
(homopolymer)
or
• Different
(heteropolymer)

Quaternary structure of protein

 Quaternary
structure

Examples-
• Hemoglobin consists
of 4 subunits of two
types – 2 α and 2 β
polypeptide chains
• DNA polymerase
• Creatine kinase
• Lactate
Dehydrogenase
Quaternary structure of Hemoglobin.
 Quaternary
structure stabilizing forces

• Hydrogen bonds

• Hydrophobic
interactions

• Ionic bonds
(electrostatic)

Quaternary structure of protein • Di sulfide bonds

 Peptide bond

Covalent bonds
Disulfide bond
Bonds responsible
For Protein structure

Hydrogen bond
Non covalent bonds
For reference Hydrophobic bond

Ionic bond

Van der Waal forces

 For reference
purpose only
Peptide bond

(–CO-NH–)
Between carbon atom of the carboxyl group
(-COOH) of one amino acid and the nitrogen
atom of the amino group (-NH₂) of another
amino acid.

Covalent bonds

Disulfide bond (-S-S-) between two cysteine residues, formed by

the linkage of their sulfur atoms
 Non Covalent bonds
For reference
purpose only

Interchain hydrogen bond Intrachain hydrogen bond

between the carbonyl hydrogen bonds form between the

oxygen (C=O) of one carbonyl oxygen of one strand and
amino acid and the the amide hydrogen of an adjacent
amide hydrogen (N-H) strand, either in a parallel or
of another, four antiparallel arrangement.
residues ahead in the
sequence.
 Non Covalent bonds
For reference
purpose only

Hydrophobic interaction Ionic bond( Electrostatic)

formed formed between

N between oppositely charged groups N
nonpolar such as amino (NH3+)
hydrophobic R terminal and carboxyl
groups (COO–) terminal groups of
(side chain) of the peptide and
amino acids oppositely charged R-
groups of polar amino acid
residues.
 Non Covalent bonds
For reference
purpose only

Van der wall interaction

These interactions occur

between atoms of polar
and nonpolar side chain
of amino acid residues
that are in close
proximity and help
proteins maintain their
compact 3D shape.
 DENATURATION

• Disorganization of 3D structure of protein

(tertiary and quaternary structure)due to
the disruption of weak bonds, such as
hydrogen bonds, Ionic bonds, hydrophobic
interactions, and van der Waals forces
UNFOLDING
without breakage of peptide linkage.

• The primary structure (the amino acid

sequence) remains intact in denaturation. Native ( active) protein Denatured
(inactive) protein

• e.g. Denaturation of egg protein

Denaturation of proteins lead to

1 Unfolding of natural coils of native

proteins

2 Decrease in solubility& increase in

perceptibility

3 Loss of biological activities ( enzyme

Activity, antigen properties)

4 Increased digestibility
 Denaturing agents

Physical Chemical Mechanical

• Heat • Acid • High pressure

• Ultraviolet rays • Alkalies • Vigorous stirring&

shaking
• Ionizing radiation • Acid solutions of heavy
metals e.g. mercury lead, • Freeze thaw cycles
detergents
• Organic solvents e.g.
Alcohol ,acetone
.