Proteins

Introduction
• Berzelius: “protein”- ‘proteios’: ‘holding the first
position’.

• Most abundant biological macromolecules that form

the fundamental basis of structure and function of
life.
• functionally diverse molecules.

• Occur in every part of the cell and constitute about

50% of cellular dry weight.
 Functions
• Structural functions:
– Brick and mortar roles eg. Collagen, elastin, a-
keratin

• Dynamic functions:
– Eg. Enzymes, hormones, blood clotting factors,
immunoglobulins, membrane receptors, storage
proteins etc.
– Proteins are the molecular instruments thro’
which genetic information is expressed.
– working horses of cells.
 Elemental composition of proteins
• Carbon: 50-55%
• Hydrogen:6-7.3%
• Oxygen:19-24%
• Nitrogen:13-19%
• Sulfur:0-4%

Besides the above, proteins may also contain other

elements such as P, Fe, Cu, I, Mg, Mn, Zn etc.
 Amino acids
- a group of organic compounds containing two functional
groups- amino and carboxyl.

– Differ from each other in their side chain ie. R group

– Vary in structure, size & electric charge
– At physiologic pH (approximately pH = 7.4), the carboxyl
group is dissociated, forming the negatively charged
carboxylate ion (COO-)and the amino group is protonated
(NH3+)
• Although more than 300 different amino acids have been
described in nature, only twenty are commonly found as
constituents of mammalian proteins: standard amino acids

• Note: These are the only amino acids that are coded for by
DNA, the genetic material in the cell
“Selenocysteine”- 21st aminoacid
• Present in enzymes as glutathione peroxidase,
glycine reductase, 5,-deio- dinase, thioredoxin
reductase
• Selenium atom replaces sulfur of its structural
analogue, cysteine.
Optical properties of amino acids
• The α-carbon of each amino acid is attached to four different
chemical groups: a chiral/ optically active carbon atom.
• Glycine : exception- optically inactive.
• exist in two forms, designated D and L, that are mirror images
of each other
• All amino acids found in proteins are of the L-configuration.
Presentation 1 Date: july 3, 2011
 Classification of amino acids
• Based on
- Structure
- Polarity
- Nutritional importance
- Metabolic fate
Both one- and three-letter abbreviations for each amino acid can be used to
represent the amino acids in peptides.
 Based on polarity
1. Non-polar amino acids :
• also referred to as hydrophobic
• have no charge on the 'R' group.
• alanine, leucine, isoleucine, valine, methionine, phenyl-
alanine,t ryptophan and proline.

2. Polar amino acids with no charge on 'R' group :

• carry no charge on the 'R'group.
• however possess groups such as hydroxyl, sulfhydryl and
amide and participate in hydrogen bonding of protein
structure.
• glycine, serine, threonine, cysteine, glutamine, asparagine
and tyrosine.
3. Polar amino acids with positive 'R' group :
lysine, arginine and histidine

4. Polar amino acids with negative 'R'group :

aspartic acid and glutamic acid
 Based on Nutritional importance
Essential amino acids:
• The amino acids which cannot be synthesized by the body
and, therefore, need to be supplied through the diet
• required for proper growth and maintenance of the
individual.
• Arginine, Valine, Histidine, lsoleucine, Leucine, Lysine,
Methionine, Phenylalanine, Threonine,Tryptophan.

• Arginine and histidine- semi essential

• Non-essential or dispensable amino acids : The body can
synthesize 10 amino acids to meet the biological needs,
hence they need not be consumed in the diet.
• glycine, alanine, serine, cystei ne, aspartate,a sparagi ne,
glutamate, glutamine, tyrosinea nd proline
 Based on metabolic fate
• The carbon skeleton of amino acids can serve as a precursor
for the synthesis of glucose (glycogenic) or fat (ketogenic) or
both.

1. Glycogenic amino acids :

• can serve as precursors for the formation of glucose or
glycogen.
• e.g. alanine,aspartate, glycine, methionine etc.
2. Ketogenic amino acids :
• Fat can be synthesized from these amino acids.
• Eg. leucine and lysine.

3. Glycogenic and ketogenic amino acids :

• precursors for synthesis of glucose as well as fat.
• isoleucine, phenyl- alanine, tryptophan, tyrosine
 Non standard amino acids
• Amino acids besides 20 standard amino acids
present in protein
1. Amino acids derivatives in proteins
2. Non protein amino acids performing
specialised functions
3. D- amino acids
• Some proteins contain additional amino acids that arise by
modification of an amino acid after completion of protein
synthesis.
• Collagen: 4-hydroxyproline and 5-hydroxylysine
• Blood clotting factors: gamma-carboxyglutamate;
• Other modifications: methylation, formylation, acetylation,
prenylation, and phosphorylation of certain aminoacyl
residues.
• These modifications extend the biologic diversity of proteins
by altering their solubility, stability, and interaction with other
proteins.
• D-Amino acids that occur naturally include
 free D-serine and D-aspartate in brain tissue,
D-alanine and D-glutamate in the cell walls of
gram- positive bacteria
D-amino acids in some non-mammalian
peptides and certain antibiotics- bacitracin,
gramicidin
Aminoacids as ampholytes:

• Amino acids act as both acids and bases- ampholytes or

amphoteric substances.

• Therefore, free amino acids can act as buffer

• Amino acids with acidic or basic side chain also act as buffer,
even when present in proteins
• So, amino acids have two ionizable groups (–COOH, NH3 +).
• Both are weak acids. However, R- COOH is much more stronger
than R- NH3.

• At neutral pH both groups are ionized, i.e., the carboxyl group exist
in dissociated form where as amino group exist as associated form.

• Molecules that contain an equal number of ionizable groups of

opposite charge and that therefore bear no net charge are termed
zwitterions(isoelectric/ dipolar form). It is electrically neutral so it
does not move in an electrical field.
Amino acids may have positive, negative or zero net charge:

• The charge of an amino acid always depends on the pH of its

surroundings. In other words, the charge of amino acid is altered by
changing pH of its surroundings.
Isoelectric point or pH:

• the pH at which an amino acid is electrically neutral that is, in

which the sum of the positive charges equals the sum of the
negative charges.

• The pH at which molecule exists as zwitterion

peptide bond formation:
• formed when carboxyl group of an amino acid react with α-
amino group of another amino acid.
• always accompanied by loss of one water molecule
 Overview of protein structure

• Can be viewed at 4 levels/ orders of architecture

-primary, secondary, tertiary and quarternary

 Primary structure

• Sequence of amino acids in polypeptide chain held

by Peptide bonds
• Very important since it provides important
biochemical information - 3D stucture, function,
cellular location
• Change in sequence may cause serious genetic
diseases
 Secondary structure
• Regular repeating arrangement of polypeptide
backbone
• Formed by the folding of short (3- to 30-residue),
contiguous segments of polypeptide into
geometrically ordered units
• Short range strl relationship of amino acids
• Common:alpha helix, beta conformations
• Others: loops, beta bends, turns
Alpha helix:
• Right handed helix
• Stabilised by H- bonds
• R-group protudes outwards
Beta- pleated sheet:
• Zig-Zag/ pleated pattern
• R groups of adjacent residues point in opposite directions.
• Highly extended
• Stabilised by H bonds
• Can be parallel/ antiparallel: depending on amino to carboxy
orientation; similar/ opposite
 Tertiary structure
• 3D arrangement of all atoms in protein/ entire three- dimensional
conformation of a polypeptide.
• Long range structural relationship

• Interactions stabilizing tertiary structural

-disulfide bonds
-hydrophobic bonds
-H bonds
-ionic interactions
 Quaternary structure

• In proteins having two or more polypeptide chains- oligomeric

protein
• Monomers/subunits/ protomers
• Composition and spatial arrangement of subunits

• Eg. Hemoglobin: tetramer- α2β2

• Held by noncovalent bonds
• Function-separate
-co operative
 Forces/ bonds stabilising protein structure

• Primary structures are stabilized by covalent peptide

bonds.

• Higher orders of structure are stabilized by

noncovalent forces
Denaturation of Proteins
• Denaturation is loss of native conformation.
• loss of secondary, tertiary and quaternary structure of proteins

• On denaturation, physical, chemical and biological properties

of a protein are altered
Some of the changes in properties are:
1. Decreased solubility
2. Increased viscosity
3. Unfolding of polypeptide chain- loss of secondary and
tertiary (quaternary too, if present); primary structure
remains intact
4. Decreased or loss of biological activity
5. More susceptible to action of enzymes
6. Usually irreversible
Causes of Denaturation
1.Physical agents:
- High temperature
- UV radiation
- Sonication
- Vigorous shaking

2. Chemical agents:
- Extreme alkaline or acidic pH
- urea and guanidine at high concentration
- Detergent
- organic solvents like ethanol, acetone
- strong acids like trichloroacetic acid, picric acid and tungstic
acid
- heavy metals like Pb2+, Ag2+ and Cu2+
 Biuret test
- Widely used for qualitative/ quantitative detection of protein
in body fluids
Principle
• total protein (peptide bonds) + Biuret reagent (alkaline Cu++)
------> purple colored complex (Cu-peptide bond)
• 2 or more peptide bonds required
 classification of protein
• Based on function

• Based on composition

• Based on nutritional value

 Based on the functions they perform, proteins are classified into following
groups.

• Structural proteins: Examples are keratin of hair and nails, collagen of

connective tissue
• Enzymes or catalytic proteins. Amylase, hexokinase, pepsin etc.
• Transport proteins. Haemoglobin, serum albumin.
• Hormonal/ regulatory proteins. Insulin, glucagon etc.
• Contractile proteins. Actin and myosin.
• Storage proteins. Ovalbumin, glutelin.
• Genetic proteins. Nucleoproteins.
• Protective/ defense proteins. Immunoglobulins (antibodies), clotting
factors
• Receptor proteins: for hormones, viruses.
Protein classification based on composition

• Simple protein
• Conjugated protein
• Derived protein
Simple proteins.
• They are composed of only amino acid residues.
• Further classified on basis of shape
 Globular protein
 Fibrous protein

A. Globular proteins.
• Spherical/ oval; Axial ratio(length to readth ratio): 3-4; <10
• Easy solubility; digestible
• Based on solubility in various solvents (salt solution, alcohol, dilute acid/
alkali); further classified as:
Albumins, Globulins, Glutelins, Histones,Protamine, prolamines,
Scleroproteins

B. Fibrous proteins.
• Elongated; Axial ratio:>10
• Solubility- minimum; resist digestion
• Collagens, elastins, keratins etc.
Conjugated proteins.
• Besides amino acids they contain a non protein moiety known
as prosthetic group.
• the nature of the non-protein or prosthetic groups is the basis
for the subclassification of conjugated proteins.
A. Nucleo proteins like histones.
B. Glycoproteins like mucin, ovomucoid etc.
C. Lipoproteins like serum lipoproteins
and membrane lipoproteins.
D. Phosphoproteins like casein, vitelline.
E. Chromoproteins like haemoglobin, flavoproteins
F. Metalloproteins like ceruloplasmin.
Derived proteins.
• There are the denatured or degraded products of simple
and conjugated proteins.
• Derivatives of proteins due to action of heat, enzymes, or
chemical reagents.
• These are proteins derived by partial to complete hydrolysis
from the simple or conjugated proteins by the action of
acids, alkalies or enzymes.

• These are further classified into

 primary and
 secondary types.
• The complete hydrolytic decomposition of the
natural protein molecule into amino acids
generally progresses through successive
stages as follows:
• Protein -----> Protean -----Metaprotein----
Proteoses ----Peptones -----Peptides ----
amino acids
 Nutritional classification of proteins

• The nutritional value of proteins is determined by the composition

of essential amino acids
a. 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.

b. Partially 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 Lysine,
Threonine)

c. Incomplete proteins: These proteins completely lack one or more

essential amino acids. Hence they do not promote growth at all e.g.
gelatin (lacks Tryptophan ), zein (lacks Tryptophan, Lysine).