BCH 201

General Biochemistry I (2 Units)

 Introductory chemistry of amino acids, their properties,

reactions and biological functions.
 Classification of amino acids: neutral, basic and acidic;
polar and non-polar; essential and non-essential amino
acids.
 Peptides: Introductory chemistry and functions of
proteins.
 Biological functions of proteins.
 Methods of their isolation, purification and
identification.
 Primary, secondary, tertiary and quaternary structures
of proteins.
 Basic principles of tests for proteins, of nucleosides and
nucleotides, effects of acid and alkali on hydrolysis of
nucleic acids.
Lecturers:

Dr O.M. Daniel

Mr K.K. Mustapha

Dr S.A Omar

Dr A.A. Ajadi
Introduction to Proteins
Proteins are large, complex molecules that play many critical
roles in the body. They do most of the work in cells and are
required for the structure, function, and regulation of the body’s
tissues and organs. The Swedish Chemists J. J. Berzelius in 1938
coined the name ’protein’ from the Greek word proteios which
means “of the first rank” or “primary” or “in the lead”.
Proteins are the most versatile macromolecules in living systems
and play important functions in essentially all biological
processes. In nature, over 500 amino acids have been identified,
but only 20 standard α-amino acids are commonly found as
building blocks in proteins across all life forms because they are
coded by genes.
All proteins are essentially linear polymers of these 20 amino
acids, assembled via peptide bonds. Except for glycine, all amino
acids have an asymmetric α-carbon, making them chiral and
optically active. Chirality means they exist in two optically active
asymmetric forms (called enantiomers) that are mirror images
of each other.
This property is conceptually similar to the spatial relationship of
the left hand to the right hand.) One enantiomer is designated D
(dextrorotatory or clockwise rotation) and the other L
(levorotatory or anti-clockwise rotation). It is important to note
that the amino acids found in proteins almost always possess
only the L-configuration. This reflects the fact that the enzymes
responsible for protein synthesis have evolved to utilize only the
L-enantiomers. Reflecting this near universality, the prefix L is
usually omitted. Some D-amino acids are found in
microorganisms, particularly in the cell walls of bacteria and in
several of the antibiotics. However, these are not synthesized in
the ribosome.
All proteins, whether from the most ancient lines of bacteria or
from the most complex forms of life are all made up of from the
same universal set of 20 amino acids that are covalently linked
to form linear sequence. Each of this amino acid has a side chain
that possesses distinctive chemical properties.
Cells can produce proteins with distinctly different properties in
many combinations and sequences. The sequence of amino
acids determines protein’s unique 3-dimensional structure and
its specific function.

Amino acids joined by a series of peptide bonds are said to

constitute a peptide. After they are incorporated into a peptide,
the individual amino acids are referred to as amino acid residues.
Small polymers of amino acids (fewer than 50) are called
oligopeptides, while larger ones (more than 50) are referred to
as polypeptides. Hence, a protein molecule is a polypeptide
chain composed of many amino acid residues, with each residue
joined to the next by a peptide bond.
Properties of Proteins
 Color and Taste: Most proteins are colorless and tasteless.
 Solubility: Most of proteins are hydrophilic compounds and
are soluble in water. Water interacts with the polar groups
of proteins and forms an aqueous membrane - hydration
shell - at the surface of the protein.

Solubility of proteins depends on;

1. presence of the polar groups, including those with
electric charge;
2. presence of the hydration shell;
3. shape of the molecule – the globular proteins are more
soluble then fibrous;
4. Solvent – for example: albumins are soluble both in water
and salt solution of different concentration, but globulins
are not soluble in water and soluble only in weak salt
solution;
5. pH of the medium –Solubility is affected by pH, being
lowest at the isoelectric point (the pH where the protein
has no net charge) and increasing with greater acidity or
alkalinity.
 6. Temperature – mild heating can increase it by helping
proteins unfold and find a more soluble conformation,
while high temperatures cause thermal denaturation,
which leads to aggregation and a significant decrease in
solubility.

 Optical Activity: Protein solutions are levorotatory,

meaning they rotate the plane of polarized light to the left.
 Amphoteric Nature: In aqueous solution, especially at
physiological pH (~7.4), they predominantly exist as
zwitterions (molecules with both positive and negative
charges but electrically neutral overall). This dual nature
allows protein to act as either acids or bases—an
amphoteric property.

 Colloidal Nature: Due to their large size (wt. of 5,000 to

1,000,000 Daltons), proteins exhibit colloidal properties like
very slow diffusion rates and light scattering (Tyndall
effect).
 Denaturation: Heat, chemicals, or pH changes can disrupt
the weak forces holding a protein’s structure together,
causing it to lose its biological activity and decreased
solubility.
The denatured protein can spontaneously return to its
native conformation – renaturation or refolding. This can
take place, but only if the denaturing agent was not strong
enough and its action was of short duration.
 Total electrical charge of proteins: Proteins are amphoteric
polyelectrolytes. The total charge of proteins depends on 2
main factors:
1. amino acid composition
2. pH of the medium
If the protein has more negatively charged amino acids (Glu
and Asp) in aqueous medium its total charge will be
negative (for example - albumin).

If the protein has more positively charged amino acids (Lys,

Arg and His)– its charge will be positive (like in histones).

In acidic medium, the concentration of H+ is high and

neutralizes the COO- - groups of amino acids - the negative
charge decreases; protein becomes positively charged –
becomes a cation, and migrates to the cathode in the
electric field.
In basic medium, the concentration of OH- is high and
neutralizes the positive charge of amino groups -NH3+ - the
positive charge decreases, the protein becomes negatively
charged - becomes an anion, and migrates to the anode in
the electric field.

The state of the protein when its total electrical charge is

equal to zero is called isoelectrical state.
The value of pH when the protein is in the isoelectrical state
is called isoelectrical point.
The proteins in the isoelectrical state have a low solubility
in water medium and can easy precipitate.
  Thermolability: Is the property of protein to maintain the
biological activity in narrow limits of temperature (from 10
to 40°C). If the temperature is higher than 50-60°C the
protein denatures – loses its native conformation. The
destruction of all the structural levels of protein (except the
primary) takes place.

There are several exceptions – the thermostable proteins

(trypsin, lysozyme, tag-polymerase) – stable at high
temperature. If the temperature is low - the protein structure
doesn’t change, but the protein becomes biologically inactive.
Chemical Classification of Proteins
Proteins can be broadly categorized based on their chemical
composition upon hydrolysis.
1. Simple Proteins: These proteins yield only alpha-amino acid
residues, and sometimes occasional small carbohydrate
compounds, when subjected to complete hydrolysis. Examples
include albumins, globulins, and histones.

2. Conjugated Proteins: These macromolecules are composed of

a protein component, known as the apoprotein, complexed with
a non-protein component, referred to as the prosthetic group or
cofactor (inorganic metallic ions or organic coenzymes). Some
proteins contain more than one prosthetic group. The prosthetic
group is often essential for the protein's biological function.
Examples include hemoglobin (which requires the heme group,
containing iron), nucleoproteins, glycoproteins, and
phosphoproteins.
Conjugated proteins are classified on the basis of chemical
nature of their prosthetic group. For instance,
 Glycoproteins: the prosthetic group is carbohydrate
(usually oligosaccharide chains (glycans) covalently
attached to their polypeptide side-chains. The protein part
predominates (60-80% by weight of the molecule)).
 Hemoproteins: the prosthetic group is heme e.g
hemoglobin that transport oxygen in the body.
 Lipoproteins: the prosthetic group is Lipids. Most lipids are
transported in the blood as part of this soluble complexes.
 Similarly, metallo-proteins are so named because they
contain a specific metal prosthetic group.

3. Derived Proteins: These are generated from simple or

conjugated proteins through chemical or physical processes,
such as denaturation or enzymatic cleavage. Examples include
fibrin (from fibrinogen), smaller peptides and denatured
proteins.
Structural Classification: Globular versus Fibrous Proteins
Proteins are also classified based on their characteristic three-
dimensional shape, which directly correlates with their biological
roles.
1. Globular Proteins:
These proteins typically possess compact, nearly spherical
shapes resulting from the polypeptide chain folding tightly back
upon itself. They are generally water-soluble, making them
highly mobile within the aqueous environment of the cell.
Function: Globular proteins usually perform dynamic functions,
such as enzymatic catalysis (e.g., lipase, pepsin), transport (e.g.,
hemoglobin, which transports oxygen), and cellular messaging
(e.g., insulin hormone).
2. Fibrous Proteins:
Fibrous proteins form elongated, rod-like, or filament-like
structures. They are characterized by high stability and are
typically insoluble in water.
Function: Due to their stability and rigidity, they serve primarily
as structural proteins, providing support and protection to
tissues. Key examples include keratin (found in hair and nails)
and collagen (the most abundant protein, forming connective
tissues like bone, tendons, and skin). Elastin, another fibrous
protein, provides elasticity to tissues like the lungs and arteries.
The structural classification underscores a critical principle in
biochemistry: architecture dictates function. The solubility and
compact shape of globular proteins are perfectly suited for
dynamic roles like catalysis and signaling, as their surfaces can
present specific binding pockets for substrates. Conversely, the
stability and insolubility derived from the repeating, elongated
structures of fibrous proteins provide the tensile strength
required for structural integrity in tissues that must withstand
mechanical stress.
Diverse Biological Functions of Proteins
Proteins are central to nearly every physiological process,
accounting for roughly 50% of the dry mass of cells. Their
functional versatility is unparalleled.
1. Enzymatic Catalysis: Proteins acting as enzymes perform
nearly all the thousands of chemical reactions within cells by
significantly accelerating reaction rates (e.g., Phenylalanine
hydroxylase).
2. Structural Support: Structural proteins provide mechanical
support and shape to cells and tissues. Examples include
collagen, which forms the connective framework, and tubulin
and actin, which are essential components of the cytoskeleton.
3. Transport and Storage: Proteins bind and carry atoms and
small molecules throughout the body or within cells.
Hemoglobin transports oxygen, GLUT (glucose transporters)
move glucose, and Ferritin stores iron. Transport proteins
exhibit high specificity, binding only to target substances.
4. Signal Transmission (Messengers): Protein hormones
transmit signals between cells, tissues, and organs to coordinate
physiological processes (e.g., Growth hormone, Insulin,
antidiuretic hormone, ADH).
5. Movement: Proteins are essential for mobility, enabling
muscle contraction (actin working with motor proteins) and
intracellular transport (tubulins).
6. Immune Defense: Antibodies (Immunoglobulin G) are defense
proteins that specifically bind to foreign particles like bacteria
and viruses to facilitate their removal from the body.