The Biological Molecules:

Proteins

BYBY
 Introduction
• Proteins are the most abundant biological macromolecules,
occurring in all cells.
• All proteins contains C, H, O, N and S.
• Some proteins also contain phosphorus, iodine and traces of metals
like Fe, Cu, Zn, Mn.
• They are high molecular mass complex biopolymers made up of
smaller units called amino acids.
• Proteins are the polymers of amino acids covalently linked by the
peptide bonds.
• Thus, all proteins on hydrolysis first give polypeptides and finally
give amino acids.
Amino acids
• There are over 300 amino acids that exist in nature. Of these, only 20 have
been found in proteins.

• The difference among them is the structure of the R group.

• The R group determines the individual chemical properties of each amino

acid.
• Amino acids contain the
reactive groups: amino
group (-NH2) and
carboxylic group (-COOH).

• In addition to that they also

contain a hydrogen atom
and an R side chain/group.
Classification of Amino acids
• Depending upon:
1. The relative number of amino and carboxyl groups in their
molecule.
• Amino acid may be categorized as:
i. Neutral: These are the amino acids containing equal number of
NH2 and COOH groups.
ii. Acidic: These are the amino acids containing more COOH groups
than NH2 groups.
iii. Basic: These are the amino acids containing more NH2 groups than
COOH groups.
2. Depending upon their synthesis, amino acids can be categorized
as:
i. Essential Amino Acids: The amino acids which cannot be
synthesized in the body and must be obtained through diet, are
known as essential amino acids.
✓ Examples: Valine, Leucine.
ii. Non-essential Amino Acids: The amino acids, which can be
synthesized in the body, are known as non-essential amino acids.
✓ Examples: Glycine, Alanine
• Amino acid contains both acidic (carboxyl group) and basic (amino
group) groups in the same molecule.
• In aqueous solution, the carboxyl group loses a proton which is
accepted by the NH2 group which results in the formation of a
dipolar ion known as Zwitter ion.
• This is neutral but contains both positive and negative charges.

• In zwitter ionic form, amino acids show amphoteric behaviour as

they react both with acids and bases.
Peptide
• A peptide is a short chain of amino acids joined by peptide bonds.
• They are classified by the number of amino acids joined in the
chain, we have:
✓ Dipeptide: It is a peptide composed of two amino-acid residues.
✓ Tripeptide: It is a peptide composed of three amino-acid
residues.
✓ Polypeptide: It is a peptide composed of more than ten amino-
acid residues.
Peptide Bonds and Amino Acid linkages
• Peptide bonds are the bonds that form between amino acids
thereby linking them.
• They are formed when the acidic group (COOH) of one amino acid
joins the amino group of a second amino acid.
• The are formed through condensation and broken through
hydrolysis
Formation of a peptide bond via condensation
 Characteristics of Proteins

1.The backbone of all protein molecules is made up of a linear

chain of polypeptides, which are made up of amino acids.
• The number of amino acids in the polypeptide may vary
considerably. For example, The smallest protein ‘insulin’ has 51
amino acids and the bigger protein ‘hemoglobin’ has 574
amino acids.
2. They are colorless

3. Tasteless (except serine which is sweet)

4. They are affected by temperature and pH

 Testing for Proteins
• Reagent used is the biuret reagent.
• Biuret test is the name of a chemical test that utilises the Biuret reagents,
which contains a 1% solution of Copper II sulphate (CuSO₄).
• It is the Cu₂⁺ in the Biuret reagent that forms a complex with the peptide
bonds found in proteins.
• In the presence of alkaline, when Biuret is reacted with dilute copper
sulphate, a purple coloured substance is formed.
• The reason behind this colour is the formation of a chelate complex or
the copper coordination complex.
• Cu (II) or cupric ions create a chelate complex of violet colour, using
oxygen of water and the unshared electron pairs of peptide nitrogen.
• The colour intensifies as the number of peptide bonds increases in
protein.
 Classification of Proteins

• Proteins can be classified into different categories based on a

number of criteria.
1. Based on Composition
i. Simple proteins
• The are composed entirely composed of only amino acids.
• Examples include: Albumin, Globulin
ii. Conjugated proteins
• These are made up of amino acids and other organic compounds.
• The non-amino acid group is termed as the prosthetic group.
• Examples include: Nucleoproteins, Lipoproteins, Glycoproteins,
Metalloproteins
2. Based on Function
• Proteins can also be classified into different categories based on the
roles they play in bodies of living organisms.
• Examples include:

✓Structural proteins ✓Contractile proteins

✓Enzymes ✓Storage Structural

✓Hormones ✓Toxins

✓Pigments ✓Transport Structural

3. Based on Molecular shape
• On the basis their molecular shape, proteins can be classified as:
i. Fibrous proteins: The polypeptide chains run parallel and are held
together by hydrogen and disulphide bond forming a fiber like
structure.
• They are generally insoluble in water.
• For example: Keratin (present in hair, wool, silk) and myosin
(present in muscles)
ii. Globular proteins: The polypeptide chains coil around to give a

spherical shape.

• These are soluble in water.

• For example: Insulin and albumins.

Primary structure
• The sequence of amino acids is said to be the primary structure of
a protein.
• Amino acids are covalently linked by peptide bonds.
• Each component amino acid in the polypeptide is called a residue
or moiety
Secondary structure
• This comes about due to folding of the primary protein.
• Peptide bonds contain polar amide hydrogen atoms (with a partial
positive) and polar carbonyl oxygen atoms (with a partial negative
charge).
• This allows hydrogen bonds to form between peptide parts of the
chain.
• There are two types of secondary structures:
✓ Alpha (α)-Helix and Beta (β) pleated-Helix sheets
Alpha (α)-Helix Beta (β) pleated-Helix sheets

• The polypeptide chain coil itself into a • In this structures, the peptide chains
right handed screw with the −NH are stretched out to nearly maximum
group attached to the −C=O of an extension and then laid side by side,
adjacent turn of the helix by the held together by intermolecular
hydrogen bonding. hydrogen bonds.

• It generally exists when R- group is • It generally exists when R- group is

large small.
Tertiary structure
• Tertiary structure of a protein refers to its overall three-dimensional
conformation.
• The types of interactions between amino acid residues that
produce the three dimensional (3D) shape of a protein include
hydrophobic interactions, electrostatic interactions, and hydrogen
bonds, all of which are non-covalent.
• Covalent disulfide bonds also occur.
• It is produced by interactions between amino acid residues that
may be located at a considerable distance from each other in the
primary sequence of the polypeptide chain.
• Hydrophobic amino acid residues tend to collect in the interior of
globular proteins, where they exclude water, whereas hydrophilic
residues are usually found on the surface, where they interact with
water.
Quaternary structure
• All proteins have the primary, secondary and third structures.
• Some of the proteins are composed of two or more polypeptide
chains referred to as sub-units.
• The spatial arrangement of these subunits with respect to each
other is known as quaternary structure.
• We can only find the quaternary structure in some proteins. Not all
proteins.
Denaturation
• The most stable conformation of a protein at a given temperature
and the pH is known as its native state.
• The loss of biological activity of proteins when a protein in its
native form, is subjected to physical change like change in
temperature or chemical change like change in pH, is called
denaturation of protein.
• Proteins can be denatured by agents such as heat and urea that

cause unfolding of polypeptide chains without causing hydrolysis of

peptide bonds.

• The denaturing agents destroy secondary and tertiary structures,

without affecting the primary structure.

• For example:

i. Coagulation of egg white on boiling

ii. Curdling of milk which is caused due to the formation of lactic acid

by the lactobacillus bacteria present in milk.

• If a denatured protein returns to its native state after the

denaturing agent is removed, the process is called renaturation.

 Functions of Proteins
1. Enzyme catalysis/metabolism. enzymes, which are biological catalysts that
facilitate specific chemical reactions.
2. Defense. Other globular proteins use their shapes to “recognize” foreign
microbes and cancer cells. These cell surface receptors form the core of the
body’s hormone and immune systems e.g Immunoglobulins i.e Antibodies
3. Transport. A variety of globular proteins transport specific small molecules
and ions. The transport protein hemoglobin, for example, transports oxygen
in the blood, and myoglobin, a similar protein, transports oxygen in muscle.
Iron is transported in blood by the protein transferrin.
4. Support. Fibrous, or threadlike, proteins play structural roles; these structural
proteins include keratin in hair, fibrin in blood clots, and collagen, which
forms the matrix of skin, ligaments, tendons, and bones and is the most
abundant protein in a vertebrate body.
5. Motion. Muscles contract through the sliding motion of two kinds of protein
filament: actin and myosin. Contractile proteins also play key roles in the
cell’s cytoskeleton and in moving materials within cells.
6. Storage. Storage of ions in the body i.e Ferritin (stores iron especially in
spleen), Casein stores ions in milk, Calmodulin binds calcium ions).
7. Regulation. Small proteins called hormones serve as intercellular
messengers in animals.
8. Proteins also play many regulatory roles within the cell, turning on and
shutting off genes during development, for example. In addition, proteins
also receive information, acting as cell surface receptors.
9. Proteins are the molecular instruments through which genetic information is
expressed.
 Protein disorders
• What happens when you take in too much/excessive proteins or you or you
have insufficient proteins in your body?
• The adverse effects associated with long-term high protein/high meat intake in
humans include:
i. Disorders of bone and calcium homeostasis
ii. Disorders of renal function
iii. Increased cancer risk
iv. Disorders of liver function
v. Precipitated progression of coronary artery disease
• On the other hand, having an insufficient amount of proteins in your body can
lead to:
i. Disorders like kwashiorkor and marasmus

Kwashiorkor Marusmus
• Hypoproteinemia (having low levels of protein), can be identified by the
following signs and symptoms:
i. Fatigue
ii. Weakness
iii. Susceptibility to infection
iv. Thinning and breaking of hair
Enzymes

BYBY
 Introduction
• Enzymes are one of the classes of proteins.
• By definition, enzymes are biological catalysts that speeds up rates
of chemical reactions without being permanently changed.
• Enzymes are globular proteins, with a three-dimensional shape that
fits snugly around the chemicals they form complexes with.
• Enzymes have a specific site on them called the active site on which
substances get attached on for a reaction to take place.
• Compounds that attached onto the active site to be worked on are called
substrates.
 Characteristics of Enzymes
1.They are highly specific.
• This specificity be in terms of:
✓Substrate specific- some enzymes will catalyze reactions
involving one particular kind of substrate.
✓Group specific- some enzymes will catalyze reactions
involving a particular group of substrates.
✓Reaction type specific- some enzymes will catalyze reactions
of a particular type.
2. Enzymes are very sensitive to temperature
3. They are sensitive to pH
4. Some can catalyze both forward and backward reactions
 Factors affecting enzyme activity
• Enzymes are affected by a number of factors which include:
1. Temperature
2. pH
3. Inhibitors
4. Activators
5. Substrate concentration
6. Enzyme concentration
1. Temperature
• The rate of an enzyme-catalyzed reaction also increases with
temperature, but only up to a point called the optimum temperature.
• Below this temperature, the hydrogen bonds and hydrophobic
interactions that determine the enzyme’s shape are not flexible enough to
permit the induced fit that is optimum for catalysis.
• Above the temperature optimum, these forces are too weak to maintain
the enzyme’s shape against the increased random movement of the
atoms in the enzyme hence the enzyme denatures
2. pH
• Ionic interactions between oppositely charged amino acid residues, such as
glutamic acid (–) and lysine (+), also hold enzymes together.
• These interactions are sensitive to the hydrogen ion concentration of the fluid
the enzyme is dissolved in, because changing that concentration shifts the
balance between positively and negatively charged amino acid residues.
• The favorable pH at which an enzyme works best is called the optimum pH.
• The enzyme pepsin, for example, digests proteins in the stomach at pH 2, a very
acidic level salivary amylase, an enzyme in the mouth works at the pH of 8.
3. Inhibitors
• A substance that binds to an enzyme and decreases its activity is
called an inhibitor.
• Enzyme inhibition occurs in two ways:
i. competitive inhibitors ii. Non-competitive inhibitors
• These compete with the substrate for • These bind to the enzyme in a
the same binding site, displacing a location other than the active site,
percentage of substrate molecules changing the shape of the enzyme
from the enzymes. and making it unable to bind to the
substrate.
4. Activators
• Enzyme function is often enhanced by additional chemical components known
as cofactors (A Non-protein chemical compound that tightly or loosely binds
with an enzyme or other protein molecules.
• Coenzyme = non-protein organic molecule that carries chemical groups
between enzymes e.g. NAD & FAD. Many vitamins are parts of coenzymes.
• Apoenzyme = An in-active enzyme.
• Holoenzyme = An apoenzyme together with its cofactor.
5. Substrate concentration
• In the presence of a given amount of enzyme, the rate of enzymatic
reaction increases as the substrate concentration increases until a
limiting rate is reached, after which further increase in the substrate
concentration produces no significant change in the reaction rate.
• At this point, so much substrate is present that essentially all of the
enzyme active sites have substrate bound to them.
• In other words, the enzyme molecules are saturated with substrate.
• The excess substrate molecules cannot react until the substrate
already bound to the enzymes has reacted and been released (or
been released without reacting).
6. Enzyme concentration
• As the concentration of the enzyme is increased, the velocity of the
reaction proportionately increases.
 Mechanisms of enzyme activity

• Two theories govern the mechanism of action of enzymes;

i. Lock and key theory ii. Induced fit theory

• The binding of a substrate induces the
• Substrate fits into the active site
enzyme to adjust its shape slightly,
perfectly.
leading to a better induced fit between
enzyme and substrate.
• Enzymes lower the activation energy of reactions they catalyze.
• Activation energy is the minimum amount if energy needed for a reaction to
take place.
• By stressing particular chemical bonds of a substrate, an enzyme lowers the
activation energy required for new bonds to form.
• The reaction thus proceeds much more quickly than it would without the
enzyme.
• Substrates bind to the enzyme at these active sites, forming an enzyme-
substrate complex.
• For catalysis to occur within the complex, a substrate molecule must fit
precisely into an active site.
• When that happens, amino acid side groups of the enzyme end up in close
proximity to certain bonds of the substrate.
• These side groups interact chemically with the substrate, usually stressing or
distorting a particular bond and consequently lowering the activation energy
needed to break the bond.
• The substrate, now a product, then dissociates from the enzyme.
 Classification of Enzymes
• Enzymes can be classified into different classes based on different criteria.
• According to the International Union of Biochemists (IUB), enzymes are
divided into six functional classes and are classified based on the type of
reaction in which they are used to catalyze.
1. Oxidoreductases
• These are enzymes that catalyze the transfer of electrons from
one molecule (reductant) to another (the oxidant)
2. Transferases
• Enzymes that catalyze the transfer of specific functional groups
from one molecule to another.
3. Hydrolases
• These use water to break a chemical bond, resulting in dividing a
larger molecule into smaller molecules.
4. Lyases
• These catalyze the breaking of chemical bonds by other means
other than hydrolysis or oxidation (usually via addition &
elimination).
5. Isomerases
• These enzymes that convert a molecule from one isomer to
another.
• Facilitate intramolecular rearrangements in which bonds are broken
or formed.
6. Ligases
• The are enzymes that catalyze the joining of two molecules by
forming a new chemical bond.
 Uses of Enzymes
• Analytical tests: Diabetics use strips of paper fertilized with aldohexose
enzyme to observe their glucose.
• They can also be used as Deworming agents. Example: Papain
• Enzymes act as anti-clotting agents like Fibrinolytic and Thrombolytic.
Examples: Urokinase and Streptokinase.
• They can also be used in the diagnosis purpose. Example: Glucose oxidase
along with peroxidase to detect the level of glucose (colorimetric estimation
• Therapeutic accelerators: Enzymes are typically used as medicines to
interchange enzyme deficiencies in patients like is that the use of blood
coagulation factors to treat bleeder’s disease.
• Enzymes can be used as surface disinfectants. Example: Trypsin
• Drug manufacture: The chemical synthesis of complicated medicine is usually
troublesome, and corporations apply enzymes to perform chemical
conversions
• In a semi-therapeutic way, enzymes are accustomed to aid digestion, to
supplement the natural amylase, lipase and protease produced by the
pancreas. People with lactose intolerance lose the enzyme lactase. Lactase
supplements facilitate to avoid abdomen upsets for these folks.
• Proteases are accustomed to clean wounds and thus accelerate the healing
method.