BIOMOLECULES AND CELLS:

BIO 111
Mr. Derrick Banda MSc, BSc
 How to get hold of Mr Derrick Banda

•Office: School of Sciences, Engineering and

Technology, Mulungushi University Main Campus

•E-mail: dbanda@mu.ac.zm dbanda45@yahoo.com

•Phone Number: +260974420585

: +260955556060
Proteins
 Introduction
• They are natural polymer molecules consisting of
monomers called amino acids.
• Proteins are the most diverse molecules in living
organisms and among the most important.

• Hair, antibodies, blood clots, egg whites, and

fingernails they are all made of protein.

• Protein-rich foods include beef, poultry, fish,

beans, eggs, nuts, and dairy products such as
milk, yogurt, and cheese.
Proteins accomplish more tasks than any other group
of biological molecules, and they make up more than
50% of the dry mass of most cells.
 Introduction
• Proteins contain elements such as Carbon,
Oxygen, Hydrogen, Nitrogen and also Sulphur.

• 20 naturally occurring amino acids are identified in

proteins.

• Different sequences of amino acids result in wide

variety of protein
 Amino acids
• Are building units (monomers) of proteins.
• All amino acids have the same functional structure.
 Amino acids
• Amino acid consist of a central asymmetric Alpha Carbon with
the following attachments;
1. A Hydrogen atom (H).
2. An Amino functional group (-NH2); Has the capacity to receive
free protons (H+) and become a amino group (-NH3+).
3. A Carboxyl functional group (-COOH) ; It can donate protons
and become a negatively charged carboxylic group (-COO-).

4. R group (R); Referred to as the amino “side chain”. The nature of

the R group determines the character and chemical properties of
an amino acid.
 Chemical Classes of Amino acids
• The 20 amino acids are grouped into four chemical
classes based on the R group types.

1. Non-polar Hydrophobic Side Chains amino acids

2. Polar but uncharged side chains (Hydrophilic) amino acids

3. Charged side chains (Hydrophilic) amino acids

4. Special cases class amino acids

 Chemical Classes of Amino acids
• The 20 amino acids are grouped into four chemical
classes based on the R group types.
1. Non-polar Hydrophobic Side Chains amino acids: R group
contains CH2 or CH3 e.g Alanine,leucine,
Phenylalanine,Isoleucine,Methionine,Tryptophan and
Valine
 Chemical Classes of Amino acids
2. Polar but uncharged side chains (Hydrophilic)
amino acids: R group contain oxygen or (-OH)
e.g threonine, serine, asparagine, glutamine and tyrosine
 Chemical Classes of Amino acids
3. Charged side chains (Hydrophilic) amino acids: R
group contains an acid or base that can ionize e.g
Arginine, histidine,lysine, glutamic and aspartic acids.
 Chemical Classes of Amino acids
4. Special cases class amino acids: This group
includes Cysteine, Glycine and Proline
 Properties of Amino acids
1. As Dipolar (Zwitterion) ion
• Contains both an acid group (-COOH) and a
basic group (-NH2) hence Amphoteric.

• At isoelectric point (pH 7), net charge of amino

molecules is Zero (0) because it has both the
positive charge and negative charge.
 Amino acid as Dipolar (Zwitterion ion)
• At the pH values commonly found in cells, both
the carboxyl and amino groups of amino acids are
ionized: the carboxyl group has lost a hydrogen
ion, and the amino group has gained one. Thus
amino acids are simultaneously acids and bases.
2. As buffers
• Buffers tends to resist change in pH and try to
maintain pH close to neutral.
• Amino acid have the ability to donate or receive
protons depending on the pH.
• At low pH (acidic condition e.g HCl, pH < 6) the
carboxylic group is neutralised by binding with a
proton (H+) due to excess hydrogen and the amino
acid becomes positively charged.
• At high pH (alkaline condition e.g NaOH, pH >
7) the amino group is neutralised by giving away
a proton (H+) to excess hydroxide and the amino
acid becomes negatively charged.
3. Solubility
• Solubility of amino acids depends on the
type of the side chain.
• Extent of solubility depend on nature and
size of the ‘R’ group.
• Some R groups are hydrophobic while
others are hydrophilic
4. High melting point
• Amino acids normally exist as dipole
molecules (Zwitterion).
• Hence the stronger ionic attraction between
one ion and its neighbor.
• The ionic attraction take more energy to
break hence the high melting point.
 Essential Amino acids
• Human beings can synthesize 10 of the 20 naturally
occurring amino acids.

• The other 10 amino acids cannot be synthesized by

the human body and hence should be obtained from
the diet.

• Amino acids which can not be synthesized by the

body are referred to as essential amino acids.
• Unlike animals, plants and prokaryote can make all
the necessary amino acids.
 Amino acids
Produced by human Essential from diet
Alanine Arginine
Asparagine Histidine
Aspartic acid Isoleucine
Cysteine Leucine
Glutamic acid Lysine
Glutamine Methionine
Glycine Phenylalanine
Proline Threonine
Serine Tryptophan
 Peptide bonds
• The bonds that hold the amino acids together are
called peptide bonds.

• Peptide bonds are formed by a condensation

reaction.

• The bond is between the amino group of one amino

acid and the carboxyl group of an adjacent amino
acid.
 Peptide bond formation
• The chemical reaction is a condensation or
dehydration synthesis as water is produced.
 Polymerization of Amino Acids
• A long chain of amino acids is called a polypeptide
and the addition of more amino acid to a chain is
called polymerization.

• At one end, the polypeptide is called the amino

terminus (or N-terminus). The other end, is known
as the carboxyl terminus (or C-terminus).
 Proteins and amino acids
• The sequencing of amino acids determines
the shape of proteins, and the shape
determines the biological function of a
particular protein
 Levels of protein structure
• Polymerisations of amino acids occurs in the
ribosomes of cells.
• Protein structures can be classified into four levels
of organisation.

1.Primary Structure
2.Secondary Structure
3.Tertiary Structure
4.Quaternary Structure
Levels of protein structure
 Levels of protein structure
1. Primary structure
• It is the unique sequence of amino acids in a
polypeptide chain.

• Each of the amino acids in a polypeptide is

referred to as a residue.

• Different proteins consist of different arrangement

of the 20 amino acids.
 1. Primary structure
The specific amino acid sequence of a protein is its primary
structure.
 2. Secondary structure
• Refers to local folded structures that form within a
polypeptide due to interactions between atoms.

• Hydrogen bonds that form with nearby amino acids

coil and fold the polypeptide into α helix and the β
pleated sheet secondary structures.

• Both structures are held in shape by hydrogen

bonds, which form between the Oxygen of one
amino acid and the Hydrogen of another.
2. Secondary structure
 a. Alpha helix
•Takes the shape of the spring, twisting around
(clockwise) like a loosely coiled spring.
•The coiling results from hydrogen bonds that form
between the δ+ hydrogen of the N—H of one amino
acid and the δ– oxygen of the C=O of another.
 Alpha helix of Protein Secondary structure

The alpha helix causes the protein to be elastic. An example

of a protein with alpha helix structure is Keratin (i.e hair,
wool, nails, feathers, claws, beaks and horns).
 b. Beta pleated sheet
• Consist of polypeptide chains arranged in
parallel to one another.
• Chains are usually running in the opposite
direction.
• Chains are held together by the hydrogen bond
between the amide group of one chain and
carboxyl group of the adjacent chain.
Beta sheet of Protein Secondary Structure

Chains are usually running in the opposite direction.

 Beta sheet of Protein Secondary Structure

For example, fibroin a protein found in silk is mainly

beta pleated sheet (i.e produced by silkworm).
 3. Tertiary structure
• It is the overall three-dimensional structure of a
polypeptide.
• The tertiary structure is primarily due to interactions
between the R groups of the amino acids that make up the
protein.

• Important to tertiary structure are hydrophobic

interactions, in which amino acids with nonpolar,
hydrophobic R groups cluster together on the inside of the
protein, leaving hydrophilic amino acids on the outside
to interact with surrounding water molecules.
3. Tertiary structure
 A Disulfide bridge
Two close Cysteine amino acids in a polypeptide chain can
form a disulfide bridge (—S—S—) by oxidation (removal of
H atoms).
 Disulfide bridges
• Chain A and B are linked together by disulfide
bond (S-S) formed from two Cysteine amino acids
occurring on both chains.
 Quaternary structure
• A quaternary structure consist of more than one
polypeptide chain.

• The individual chains are the subunit of the protein.

• Each subunit can be made of many of the same

type or different type of proteins in varying
proportion.

• The aggregate of polypeptide chains are held

together by hydrophobic interactions, hydrogen
bonds, van der Waals forces and ionic bonds.
Quaternary structure
 Quaternary Structure of a Protein
• Keratin (the fibrous protein in hair), and hemoglobin,
the globular protein that transports oxygen in red blood
cells are examples of proteins in quaternary structure.
 Denaturation of Protein
• Denaturation is the loss of the specific three
dimensional shape of a protein molecule.
• When denaturation occurs the protein unfolds
and lose their capacity to perform their specific
function.
 Denaturation of Protein
• Change of shape of protein may be reversible or
irreversible, but the primary sequence remains intact.

• Loss of three-dimensional structure (secondary and

tertiary) of a protein as a result of denaturation. This
process may be reversible in some instances.
Denaturation of Protein
Environmental conditions affect protein
structure
• Factors that can alter protein shape include extreme
temperature, pH or chemicals.
• Increase in temperature cause more rapid molecular
movements and thus can break hydrogen bonds and
hydrophobic interactions.

• Alterations in pH can change the pattern of ionization of

exposed carboxyl and amino groups of amino acids, thus
disrupting the pattern of ionic attractions and repulsions.

• Chemicals such as strong detergents causes the proteins to

lose their functional structures, and precipitate
 Functions of Proteins
Proteins can be classified into major groups based on
their function.
1. Enzymes
• Biological catalysts that control biological reactions
(metabolism) e.g amylase

2. Structural proteins
• Form part of the body of an organism e.g keratin and
collagen.

3. Receptor proteins receive and respond to molecular

signals from inside and outside the organism.
 Functions of Proteins
4. Contractile protein
• Facilitate body movement in organism e.g myosin and
actin of muscles

5. Storage
• Help in the storage of protein e.g egg albumin.

6. Defense proteins
• Help to fight infections in the body e.g antibodies.

7. Transport proteins
• Facilitate transportation of material in the body e.g
Haemoglobin and carrier proteins. Myoglobin, a
similar protein, transports oxygen in muscle.
 Functions of Proteins
8. Hormonal and regulatory proteins such as
insulin control physiological processes.
END OF LECTURE!
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