PROTEIN

1. Proteins (also known as polypeptides) are

organic compounds made of amino acids
arranged in a linear chain and folded into a
globular form.
2. The amino acids in a polymer are joined together
by the peptide bonds between the carboxyl and
amino groups of adjacent amino acid.
3. The sequence of amino acids in a protein is
defined by the sequence of a gene, which is
encoded in the genetic code.
4. In general, the genetic code specifies 20 standard
amino acids.

5. A protein is a biologically functional molecule

made up of one or more polypeptides, each folded
and coiled into a specific three dimensional structure.
 AMINO ACIDS.
1. Amino acids are molecules containing an amino
group, a carboxylic acid group , a hydrogen atom
and a side chain (R group) that varies between
different amino acids.
2. These molecules contain the key elements of
Carbon, Hydrogen, Oxygen, and Nitrogen.
3. Amino acids are critical to life, and have many
functions in metabolism. One particularly important
function is as the building blocks of proteins.
4. There are 20 amino acids which occurs
naturally in the proteins of living organisms.
The general structure of an amino acid

The physical and chemical

properties of the side chain
determine the unique
characteristics of a particular
amino acid, thus affecting its
functional role in a polypeptide
A)NONPOLAR AMINO ACID
• Principles of Polarity:
• The greater the electronegativity difference between atoms
in a bond, the more polar the bond.
• Non-Polar Side Chains
• Side chains which have pure hydrocarbon alkyl groups
(alkane branches) or aromatic (benzene rings) are non-
polar. Examples include valine, alanine, leucine,
isoleucine, phenylalanine.
• The number of alkyl groups also influences the
polarity. The more alkyl groups present, the more
non-polar the amino acid will be.
• This effect makes valine more non-polar than
alanine; leucine is more non-polar than valine.
• Hydrophobic and do not form hydrogen bond with
water
• Not electrically charged
• Importance in maintaining the three dimensional
structures of proteins
B) POLAR AMINO ACID
🞭 Polar Side Chains:
🞭 Side chains which have various functional groups
such as acids, amides, alcohols, and amines will
impart a more polar character to the amino acid.
🞭 Eg. Serine, cysteine, tyrosine.
🞭 Hydrophilic, form hydrogen bond with water, have
affinity with water and take part on chemical
reaction
🞭 Presence of polar amino acids increases the
solubility of proteins
C) ELECTRICALLY CHARGED
1. Electrically Charged (negative and hydrophilic)
🞭 aspartic acid , glutamic acid .
🞭 Acidic Side Chains:
🞭 If the side chain contains an acid functional group, the
whole amino acid produces an acidic solution.
C) ELECTRICALLY CHARGED
2. Electrically Charged (positive and hydrophilic)
🞭 lysine ,arginine , histidine .
🞭 Basic Side Chains:
🞭 If the side chain contains an amine functional group, the
amino acid produces a basic solution because the extra
amine group is not neutralized by the acid group.
PEPTIDES AND POLYPEPTIDES
🞭 Peptides are short polymers formed from the
linking, in a defined order, of amino acids. The
link between one amino acid residue and the next
is called a peptide bond.

🞭 Polypeptides are chains of amino acids. Proteins

are made up of one or more polypeptide
molecules.
PROPERTIES OF PROTEIN
A colloid is a mixture in which one
substance of microscopically dispersed
insoluble particles are suspended
throughout another substance. However,
some definitions specify that the particles
must be dispersed in a liquid, and others
extend the definition to include substances
like aerosols and gels.
🞭 Colloid
🞭 Milk is an emulsified colloid of liquid butterfat
globules dispersed within a water-based liquid.
🞭 A colloid is a type of mixture in which one
substance is dispersed evenly throughout
another.
🞭 A colloidal system consists of two separate
phases: a dispersed phase and a dispersion
medium.
Classification of protein.
a) Level of organisation – primary, secondary,
tertiary and quaternary structures.
b) Structure – fibrous and globular proteins.
c) Composition – simple and conjugated
proteins.
d) Functions – structure, catalysis, signals,
movement, defence and storage.
 LEVELS OF ORGANISATION
PRIMARY STRUCTURE.
🞭 The primary structure of a
protein is its linear sequence
of amino acids and the
location of any disulfide
(-S-S-) bridges.
E.g Lysozyme

Lysozyme.
 PRIMARY STRUCTURE
🞭 The primary structure of a protein is its sequence of amino acids.
🞭 As an example, let’s consider transthyretin, a globular blood protein that
transports vitamin A and one of the thyroid hormones throughout the body.
🞭 Transthyretin is made up of four identical polypeptide chains, each
composed of 127 amino acids.
🞭 Shown here is one of these chains unraveled for a closer look at its primary
structure.
🞭 Each of the 127 positions along the chain is occupied by one of the 20
amino acids, indicated here by its three letter abbreviation. The primary
structure is like the order of letters in a very long word.
🞭 If left to chance, there would be 20127 different ways of making a
polypeptide chain 127 amino acids long. However, the precise primary
structure of a protein is determined not by the random linking of amino
acids, but by inherited genetic information.
🞭 The primary structure in turn dictates secondary and tertiary structure, due
to the chemical nature of the backbone and the side chains (R groups) of
the amino acids along the polypeptide
• Lysozyme is an enzyme found in egg white, tears,
and other secretions. It is responsible for breaking
down the polysaccharide walls of many kinds of
bacteria and thus it provides some protection against
infection.
• The primary structure of egg white lysozyme -
shown here - is a single polypeptide chain of 129
amino acids. There are four pairs of cysteines that
form disulfide bridges.
• These cross-bridges force us to realize that this
polypeptide is not a straight chain (like cellulose, for
example). Rather the chain must fold to allow these
cysteines to be close to each other.
 SECONDARY STRUCTURE

🞭 Most proteins have segments of their polypeptide chains repeatedly

coiled or folded in patterns that contribute to the protein’s overall
shape.
🞭 These coils and folds, collectively referred to as secondary
structure, are the result of hydrogen bonds between the repeating
constituents of the polypeptide backbone (not the amino acid side
chains).
🞭 Within the backbone, the oxygen atoms have a partial
negative charge, and the hydrogen atoms attached to the nitrogens
have a partial positive charge (see Figure 2.14); therefore, hydrogen
bonds can form between these atoms.
🞭 Individually, these hydrogen bonds are weak, but because there are
so many of them over a relatively long region of the polypeptide
chain, they can support a particular shape for that part of the protein.
 🞭 The other main type of secondary structure
🞭 One such secondary structure is is the 𝛃 pleated
the 𝛂 helix, a delicate coil held sheet.
together by hydrogen bonding 🞭 As shown above, in this structure two or
between every fourth amino acid, more segments of
as shown above. the polypeptide chain lying side by side
🞭 Although each transthyretin (called β strands) are connected by hydrogen
polypeptide has only bonds between parts of the two parallel
segments of the polypeptide backbone.
one α helix region (see tertiary
🞭 β pleated sheets make up the
structure), other globular proteins
core of many globular proteins, as is the
have multiple stretches of α helix case for transthyretin (see
separated by nonhelical regions tertiary structure), and dominate some
(see hemoglobin on the next fibrous proteins, including the silk protein of
page). a spider’s web.
🞭 The teamwork of so many
🞭 Some fibrous proteins, such as hydrogen bonds makes each spider silk fiber
stronger than a steel
α-keratin, the structural protein of
strand of the same weight.
hair, have the α helix structure
over most of their length.
● The α-helix is a right-handed coiled strand
○ side-chain extend to the outside
○ Hydrogen bonds form between the oxygen of each C=O bond in the
strand and the hydrogen of each N-H group four amino acids below it in
the helix.
○ The hydrogen bonds make this structure especially stable.
○ The side-chain fit in beside the N-H groups.
● The hydrogen bonding in a ß-sheet is between strands (inter-strand) rather
than within strands (intra-strand).
○ The sheet conformation consists of pairs of strands lying side-by-side.
○ The carbonyl oxygens in one strand bonds with the amino hydrogens of
the adjacent strand.
○ The two strands can be either parallel or anti-parallel depending on
whether the strand directions (N-terminus to C-terminus) are the same or
opposite.
○ The anti-parallel ß-sheet is more stable due to the more well-aligned
hydrogen bonds.
ALPHA HELIX

MYOGLOBIN
 TERTIARY STRUCTURE
🞭 Superimposed on the patterns of secondary structure is a protein’s tertiary structure,
shown above in a ribbon model of the transthyretin polypeptide. While secondary
structure involves interactions between backbone constituents,
🞭 tertiary structure is the overall shape of a polypeptide resulting from interactions
between the side chains (R groups) of the various amino acids.
🞭 One type of interaction that contributes to tertiary structure is called—somewhat
misleadingly— a hydrophobic interaction.
🞭 As a polypeptide folds into its functional shape, amino acids with hydrophobic
(nonpolar) side chains usually end up in clusters at the core of the protein, out of
contact with water.
🞭 Thus, a “hydrophobic interaction” is actually caused by the exclusion of nonpolar
substances by water molecules.
🞭 Once nonpolar amino acid side chains are close together, van der Waals
interactions help hold them together.
🞭 Meanwhile, hydrogen bonds between polar side chains and ionic bonds between
positively and negatively charged side chains also help stabilize tertiary structure.
🞭 These are all weak interactions in the aqueous cellular environment, but their
cumulative effect helps give the protein a unique shape.
● Myoglobin contains only one heme unit surrounded by a
globular protein, containing seven α-helical and six non
helical segments, made up of 153 amino acids .
QUATERNARY STRUCTURE

🞭 Some proteins consist of two or more polypeptide chains

aggregated into one functional macromolecule.
🞭 Quaternary structure is the overall protein structure that
results from the aggregation of these polypeptide subunits.
🞭 For example, shown above is the complete globular transthyretin
protein, made up of its four polypeptides.
🞭 Another example is collagen, shown below, which is a fibrous
protein that has three identical helical polypeptides intertwined
into a larger triple helix, giving the long fibers great strength.
🞭 This suits collagen fibers to their function as the girders of
connective tissue in skin, bone, tendons, ligaments, and other body
parts. (Collagen accounts for 40% of the protein in a human body.)
🞭 tertiary structure - The bonding relationships
between distant amino acids which determine the
larger three-dimensional bending and folding of the
protein into its complex functional shape; the third
level in the hierarchy of protein structure. Eg.
Enzyme.
🞭 quaternary structure - In the hierarchy of protein
structure, the fourth level, composed of two or more
polypeptide chains of tertiary structure exhibit
quaternary structure. Eg. Haemoglobin.
DENATURATION OF PROTEIN
Denaturation is a process in which proteins or nucleic acids lose their
tertiary structure and secondary structure by application of some external
stress or compound, such as a strong acid or base, a concentrated
inorganic salt, an organic solvent (e.g., alcohol or chloroform), or heat. If
proteins in a living cell are denatured, this results in disruption of cell
activity and possibly cell death. Denatured proteins can exhibit a wide
range of characteristics, from loss of solubility to communal aggregation.
• When food is cooked, some of its proteins become denatured. This is
why boiled eggs become hard and cooked meat becomes firm.
• A classic example of denaturing in proteins comes from egg whites,
which are largely egg albumins in water. Fresh from the eggs, egg whites
are transparent and liquid. Cooking the thermally unstable whites turns
them opaque, forming an interconnected solid mass. The same
transformation can be effected with a denaturing chemical. Pouring egg
whites into a beaker of acetone will also turn egg whites opaque and
solid. The skin which forms on curdled milk is another common example
of denatured protein.
Protein Functions
1. Protection (Defensive Proteins) - Antibodies - are
specialized proteins involved in defending the body from
antigens (foreign invaders). One way antibodies destroy
antigens is by immobilizing them so that they can be destroyed
by white blood cells.
2. Movement - Contractile Proteins - are responsible for
movement. Examples include actin and myosin. These proteins
are involved in muscle contraction and movement.
3. Nutrition - Digestive Enzymes - are proteins that facilitate
biochemical reactions. They are often referred to as catalysts
because they speed up chemical reactions. Examples include
the enzymes lactase and pepsin. Lactase breaks down the sugar
lactose found in milk. Pepsin is a digestive enzyme that works
in the stomach to break down proteins in food.
4. Coordination and sensitivity - Hormones- are messenger proteins
which help to coordinate certain bodily activities. Examples include
insulin, oxytocin, and somatotropin. Insulin regulates glucose
metabolism by controlling the blood-sugar concentration. Oxytocin
stimulates contractions in females during childbirth. Somatotropin is
a growth hormone that stimulates protein production in muscle cells.

5. Structural Proteins- Structure and support - are fibrous and stringy

and provide support. Examples include keratin, collagen, and elastin.
Keratins strengthen protective coverings such as hair, quills,
feathers, horns, and beaks. Collagens and elastin provide support for
connective tissues such as tendons and ligaments.

6. Storage Proteins - Store amino acids. Examples include ovalbumin

and casein. Ovalbumin is found in egg whites and casein is a milk-
based protein. Myoglobin stores oxygen in muscles.
7. Transport Proteins – are carrier proteins which
move molecules from one place to another around
the body. Examples include haemoglobin and
cytochromes. Hemoglobin transports oxygen
through the blood. Cytochromes operate in the
electron transport chain as electron carrier proteins.
8. Homeostasis.
9. Growth.
10. Excretion.
11. Reproduction.
12. Toxins.
HOW TO TEST FOR PROTEIN IN FOOD
• Instructions
• Things You'll Need:
• Biuret Reagent Solution, Test tube, Fork or spoon, Bowl,
Eye dropper, Distilled water, Various food products

• Step 1: Select the food you'd like to test and remove just
a small portion of it.
• Step 2: Place it in a bowl with about a tablespoon of
distilled water and crush with a fork (or spoon). You're
trying to make an almost liquefied version of the food.
• Step 3: Transfer the liquid into a test tube by using a eye
dropper.
• Step 4 Squeeze 3 to 4 drops of Biuret Reagent Solution,
cover tube and shake.
• Step 5 Wait for the color to change. If it turns either pink
QUESTION.
1.a) With the aid of diagram, show how a peptide bond
is formed between two amino acids.
b) Explain how the structures of keratin and
haemoglobin are related to their functions.
2. a) Explain the meaning of the terms primary structure,
secondary structure, tertiary structure and quaternary
structure of protein.
b) Describe the types of bonding which hold an enzymes
molecule in shape.
3. a) Some common method used to group proteins
are based on the four levels of organisation of
protein structure, composition and functions.
Name six types of proteins based on their
functions in the living organisms.