PROTEINS

Dr Sonam Chhoden R
 AA

AA

AA

AA

Amino Acid
 Amino Acids

General structure:

-an amino group (-NH2)

-a carboxyl group (-COOH)
-side chain (varies between
different amino acids bonded
to α- (alpha) carbon)
-a hyrogen atom

α- amino acid, the amino and carboxyl groups are

attached to the same carbon atom, which is called the α–
carbon.
300 AA

20 AA
constitute the monomer unit of mammalian protein and the Genetic Code
Specifies 20 L-Amino Acids

Selenocysteine
Pyrrolysine
 CLASSIFICATION
by the properties of their side chain into four groups.

non-polar AA polar AA Acidic side AA Basic side AA

-Hydrophobic (oily or Hyrophilic side These are proton These accept
lipid like side chain) chain. donor and at neutral proton and at
-no charge on R group -side chain have zero pH fully ionized body PH they are
-does not bind or give net charge at neutral contain negatively positively charged
up proton or participate pH but can lose charged carboxylate
in hydrogen ion binding proton at alkaline group (-COO-) e.gHistidine
solution and lysine
e.g. Glycine, alanine, participate in e.g. Aspartic acid Arginine.
leucine. Isoleucine, hydrogen binding. and glutamic acid
valine, methionine,
phenylalanine, e.g. Serine, threonine,
tryptophan and proline tyrosine, asparagines,
cysteine and
glutamine
 Nutritional classification

Essential amino acids Semi essential amino acids: Non essential amino
can not be synthesized in They are partially acids:
the body synthesized by adult humans. -synthesized in the body
e. g. Arginine and histidine
e.g.- Valine, leucine , e.g. Glysine, alanine,
isoleucine, methionine, serine, cysteine, aspartic
acid, asparagine, Glutamic
phenylalanine, threonine,
acid, glutamine, tyrosine
lysine and tryptophan. and proline.
 Classification on the basis of metabolic fate

Absolute Absolute ketogenic Both glucogenic and

glucogenic amino amino acid ketogenic
acids amino acid
Ketone bodies can be
Precursor for glucose or synthesised from them.
glycogen Synthesize glucose and
e.g. Leucine
e.g. Alanine
Lysine
fat(KB)
Aspartate
Glycine
e.g. phenylalanine
Threonine Isoleucine,
Tryptophan
Tyrosine
 Chemical properties
Acid-Base Properties:
Acid-Base properties of amino acids depend on
Physical properties
the weakly basic amino and weakly acidic
Colourless carboxyl group attached to the α-carbon atom.
Crystalline
Water soluble Electrical charges:
High melting point Amino acids have positive, negative or zero net
charge and have definite isoelectric PH

At acidic condition both carboxyl and amino

groups are protonated and cationic and are carry
Isoelectric PH
positively charged
It is the PH at which AA
exist as zwitter ion.
At alkaline condition the amino group is
Possess same amount of deprotonated, and molecule is anionic and are
positive and negative negatively charged
charge on the surface
with net charge zero At physiological pH range 7.35 – 7.45, the
carboxyl and the amino group carry equal
charge.
“Molecules that contain an equal numbers of ionizable
groups of opposite charge and bear no net charge are
termed zwitterions”.
Zwitterions or dipolar ions
Amino acids rarely exist in a neutral form with free carboxylic (-
COOH) and free amino (-NH) groups.

At physiological pH range 7.35 – 7.45, the carboxyl group is

dissociated and the amino group is protonated forming negatively
charged carboxylate ion (--COO-) and amino group is protonated
(--N+H3).
This kind of ionized molecule, coexisting negative and positive
charges and is called a dipolar ion or ampholyte.

An amino acid in its (1) unionized and (2) zwitterionic forms

Optical properties:
Of the standard α-amino acids, all but glycine can exist
in either of two optical isomers, called L or D amino
acids, which are mirror images of each other.

While L-amino acids represent all of the amino acids

found in proteins during translation in the ribosome, D-
amino acids are found in some proteins produced by
enzyme posttranslational modification after translation
and translocation to the endoplasmic reticulum.
 Functions of amino acids

Are the structural units that make up proteins

They join together to form short polymer chains called
peptides or longer chains called either polypeptides or
proteins

Supplies energy
Precursor for synthesis of enzymes, hormones,
neurotransmitters, hormone releasing factors.
Separation technique of amino acids

The differing solubilities and acid-base properties are basis of

separation.
.

-Electrophoresis
-Partition chromatography
-Ion exchange
chromatography
 Proteins

Proteins are the polymers of L-α-amino acids linked by peptide bond

OR
The proteins are macromolecular compound of high molecular
weight generally formed by polypeptides containing more than 40
amino acids.

Peptide bond
The chemical bond formed between the carboxyl groups and amino groups of
neighboring amino acids, constituting the primary linkage of all protein structures

In protein amino acids are joined covalently which are amide linkage or peptide
bonds

bond is rigid and planer, covalent, partial double bond in character

Peptide
Short polymers of amino acids are called peptide.
Each component of amino acid in a polypeptide is called
residue or moiety.
Dipeptide
Have two amino acids and one peptide bond.
Oligopeptide
Have up to five amino acids in a chain.

Polypeptide
Linkage of more than 10 amino acid residue through peptide bonds
result in an unbranched chain is called polypeptide.
 Chemical properties

-Amphoteric (ampholyte) in nature and

can act as buffer
Physical properties -Heat labile
Solubility:soluble and form - Express charge on the surface and
have definite isoelectric PH
colloidal solution.
Molecular weight: Proteins are - Gives colour reaction with ninhydrin,
high molecular compound biuret reagent
ranging from 400-400,000
dalton.
Classification of proteins
-Functional classification
-On size, shape and solubility
-Nutrional classification
A. Functional classification:
-Structural proteins: Collagen, elastin.
-Catalytic proteins: Enzymes;Hexokinase
-Transport proteins: Transferrin, serum albumin.
-Hormone protein:Insulin, Glucagon
-Contractile proteins: Actin, myosin
-Protective proteins: Immunoglobulins
-Genetic proteins: Nucleoproteins
-Receptor protein: LDL receptor
B. Classification on size, shape, solubility
1. Simple proteins: Composed of amino acid residues
without non protein
-Globular protein-albumin, globulins.
-Fibrous proteins-collagens, elastins, keratin

2.Conjugated proteins: Composed of amino acids with non

protein moiety.
Nucleoprotein, Glycoproteins, Lipoproteins

3.Derived proteins: Denatured or degraded products of

simple or conjugated proteins.
C. Nutritional classification:
1. Complete protein: Contain all essential amino acids
e.g. albumin, milk casein.

2. Partially incomplete protein: Partially lack one or more

of essential amino acids
e.g. wheat and rice proteins.

3. Incomplete proteins: Completely lack essential amino

acids
e.g. gelatin.
PROTEIN STRUCTURE

The complex structure of protein can be divided into

4 levels of organization.
PRIMARY STRUCTURE
SECONDARY STRUCTURE
The linear sequence of
It is the helical or pleated sheet lie conformation
amino acids in a protein
of protein produced by peroidic folding
forming the backbone is
twisting or coiling of its primary structure
called the primary structure
of protein
eg α-Helix, β-Sheet and β-Bends.
Secondary structures are stabilized by
eg. valine and alanine can
hydrogen bonding.
form the dipeptide
valylalanine through the
formation of a peptide bond
with release of one molecule
of water.
Tertiary structure
It is three dimensional globular
form of protein produced
by further folding and
twisting of secondary
structure with hydrophobic
side chains buried interiorly
and hydrophilic groups
exposed out side
It is stabilised by
disulfide bonds, hydrogen
bonds and ionic interactions
or bonds
Found in albumin, globulin,
antibody etc
 Quaternary structure of proteins
Many proteins consist of single, two or more polypeptide
chains are called subunits.
The arrangement of more than one polypeptide chains in
protein is called the quaternary structure of protein.
If protein contain one polypeptide chain or one subunit is
called monomeric proteins.
Protein misfolding

Amyloidoses
• Improperly folded molecules accumulate spontaneously
aggregating proteins, called amyloid that implicate
degenerative disease. Exam- Neurodegenerative disorder-
Azheimer disease

Prion disease:
• Altered folding form prion protein (lack nucleic acids)
cause transmissible spongioform encephalopathies
including Creutzfeldt–jakob disease
Denaturation of protein:
The phenomenon of disorganization of native protein
structure is known as denaturation of protein.
Denaturing agents:
1. Physical agents:
• These are heat, mechanical mixing, X-rays and UV
radiation.
2. Chemical agents:
• Organic solvents (ether, alcohol), strong acids or bases,
detergents and ions of heavy metals such as lead and
mercury.
• Protein denaturation results in the unfolding of the
secondary, tertiary and quaternary structure but not primary
structure
• Denatured proteins are often insoluble and precipitate and
in ideal condition it is reversible but may irriversible.
• Biomedical importance of proteins:
• 1. Sructural components:
Proteins form the structural component of body e.g.
collagen and elastin in bone matrix, vascular system,
other organs and α-keratin in epidermal tissues.
Proteins are the constituents of biological membrane and
maintain cellular shape and physical integrity.
• 2. Dynamic functions
• Protein have diverse functions
• a) As catalysis of chemical reactions for energy supply –
enzymes.
• b) Regulatory functions– hormones.
• c) Protective function - blood clotting factors,
immunoglobulins.
• d) Signal transduction - membrane receptors.
• e) Storage proteins
• f) Genetic control – nucleoprotein.
• g) Contractile function- muscle contraction, respiration.
• h) Transport function -hemoglobin & lipoproteons,
channels.
• i) Synthesize and degrade biomolecules.
• Diagnostic & prognostic uses: Estimation of proteins in
different body fluids are useful in diagnosis and prognosis
several diseases. e.g.- Serum albumin in CLD, Urinary
protein for renal diseases.
Separation of proteins:
Ultracentrifugation.
Electrophoresis.
Isoelectric focusing.
Immunoelectrophoresis.
Ion exchange chromatography.
Gel filtration.
High performance liquid Chromatography
(HPLC)
• Determination of amino acids composition of
polypeptide:
• Primary structure is broken by acid hydrolysis at 110◦C for
24 hours and alkali hydrolysis at 100◦C for 5-8 hours.
• Amino acids are separated by different types of
chromatography.
• Amino acid sequences are determined first by Sagner by
applying a reagent called Sagner’s reagent.
• He used 1-fluro 2. 4- dinitrobenzene to determine insulin
structure.
• Sequencing of peptides and proteins from its N-terminal
in stepwise by phenylisothiocyanate known as Edman’s
reagent and by sequanator.
• Amino acid are estimated by amino acid analyzer by
reagent ninhydrin.
• By Mass spectrometry.
• Primary structure is determined by DNA cloning and
molecular biology.