PROTEINS

Proteins are the most abundant biological macromolecules, occurring in all cells and all parts of cells.
Amino acids are the building blocks of proteins. All proteins are constructed from the same set of 20
amino acids. What is most remarkable is that cells can produce proteins with strikingly different properties
and activities by joining the same 20 amino acids in many different combinations and sequences. From these
building blocks different organisms can make such widely diverse products as enzymes, hormones,
antibodies, transporters, muscle fibers, feathers, spider webs, rhinoceros’ horn, milk proteins, and other
substances having distinct biological activities.

1.0 AMINO ACIDS

Proteins are polymers of amino acids, with each amino acid residue joined to its neighbor by a specific type
of covalent bond. Proteins can be broken down (hydrolyzed) to their constituent amino acids the free
amino acids derived from them. The 20 amino acids are divided into essential and non- essential as
reflected in table 4.1 below.

Essential amino acids are "essential" not because they are more important to life than the others, but
because the body does not synthesize them. They must be present in the diet or they will not be present in
the body.
A nonessential amino acid is that which can be made by human humans and so is not essential to human
diet.

1.1 Amino Acids are Chiral Molecules

An α-amino acid consists of a central carbon atom, called the α carbon, linked to an amino group, a
carboxylic acid group, a hydrogen atom, and a distinctive R group. The α-carbon atom is thus a chiral
center. A chiral molecule is non-supposable on its mirror image. The mirror images of a chiral molecule/ion
are called enantiomers or optical isomers. Enantiomeric molecules display a special property called optical
activity – the ability to rotate the plane of polarization of plane-polarized light.
Fig. 1.1: General structure of an amino acid. This structure is common to all but one of the α-amino acids.
(Proline, a cyclic amino acid, is the exception.) The R group or side chain attached to the α carbon is
different in each amino acid.

Fig. 1.2: The L and D Isomers of Amino Acids. R refers to the side chain. The L and D isomers are mirror
images of each other.

1.2 Structure of a Typical Amino

Acid Amino acids in solution at neutral pH exist predominantly as dipolar ions (also called zwitterions). A
zwitterion is a neutral molecule with positive and negative charges. Amino acids can exist as zwitterions -
substances containing equal numbers of positive and negative charge due to their carboxyl and amine
groups, which can be negatively and positively charged, respectively. In the dipolar form, the amino group is
protonated (NH3+) and the carboxyl group is deprotonated (COO–). The ionization state of an amino
acid varies with pH. Amino acids differ from each other in their side chains, or R groups, which vary in
structure, size, and electric charge, and which influence the solubility of the amino acids in water.

1.3 Amino Acids can join via Peptide Bonds

The crucial feature of amino acids that allows them to polymerize to form peptides and proteins is the
existence of their two identifying chemical groups: the amino (NH3+) and carboxyl (COO) groups. The
amino and carboxyl groups of amino acids can react in a head-to-tail fashion, eliminating a water molecule
and forming a covalent amide linkage, which, in the case of peptides and proteins, is typically referred to as
a peptide bond.

2.0 PROTEIN
Proteins are a diverse and abundant class of biomolecules, constituting more than 50% of the dry weight of
cells. This diversity and abundance reflect the central role of proteins in virtually all aspects of cell structure
and function. Biologically occurring polypeptides range in size from small to very large, consisting of two or
three to thousands of linked amino acid residues.

Peptides are chains of amino acids: two amino acid molecules can be covalently joined through a
substituted amide linkage, termed a peptide bond (Figure 1.3), to yield a dipeptide. Such a linkage is formed
by removal of the elements of water (dehydration) from the α-carboxyl group of one amino acid and the α-
amino group of another. Peptide bond formation is an example of a condensation reaction, a common class
of reactions in living cells. Three amino acids can be joined by two peptide bonds to form a tripeptide;
similarly, amino acids can be linked to form tetrapeptides, pentapeptides, and so forth. When a few
amino acids are joined in this fashion, the structure is called an oligopeptide. When many amino acids are
joined, the product is called a polypeptide. Proteins may have thousands of amino acid residues.

Fig. 1.3: Peptide bond formation between two amino acids Alanine and Serine.

Proteins can be assigned to one of three global classes on the basis of shape and solubility: fibrous, globular,
or membrane.
• Fibrous proteins have relatively simple, regular linear structures. These proteins often serve
structural roles in cells e.g to construct connective tissues, tendons, and bone and muscle fiber.
Typically, they are insoluble in water or in dilute salt solutions.

• Globular proteins are roughly spherical in shape. These tend to form ball- like structures where
hydrophobic parts are towards the centre and hydrophilic parts are towards the edges, which
makes them water soluble. These usually have metabolic roles e.g. enzymes in all organisms, plasma
proteins and antibodies in mammals.

• Membrane proteins are found in association with the various membrane systems of cells. For
interaction with the nonpolar phase within membranes, membrane proteins have hydrophobic
amino acid side chains oriented outward. As such, membrane proteins are insoluble in aqueous
solutions.

2.1 THE LEVELS OF PROTEIN STRUCTURE

The various levels of protein structural organization are defined as follows;
a) Primary Structure
Proteins are made up of polypeptide chains, which are amino acids joined together with peptide
bonds. The unique sequence of amino acids that make up a protein or polypeptide chain is called
the primary structure.

b) Secondary Structure
After synthesis, polypeptide chains are folded or pleated into different shapes, called secondary
structure. A secondary structure is the way in which the primary structure of a polypeptide chain
folds. Two common examples of secondary structure are Alpha Helices and Beta pleated sheets.
Secondary structure is held together by hydrogen bonds, overall giving the shape great stability.

c) Tertiary Structure
The final 3D structure of a protein is its Tertiary structure, which pertains to the shaping of the
secondary structure. This may involve coiling or pleating, often with straight chains of amino acids
between. Tertiary structure is held together by four different bonds and interactions:
- Disulphide bonds: where two Cysteine amino acids are found together, a strong double bond
(S=S) is formed between the Sulphur atoms within Cysteine monomers.
- Ionic Bonds: If two oppositely charged ‘R’ groups (+ve and -ve) are found close to each other,
and ionic bond forms between them.
- Hydrogen bond
- Hydrophobic and hydrophilic interactions - some amino acids may be hydrophobic while
others are hydrophilic. In a water-based environment, a globular protein will orientate itself
 such that its hydrophobic parts are towards the centre and its hydrophilic parts are towards the
edges.

d) Quaternary Structure
This is the structure formed when two or more polypeptide chains join together, sometimes with
an inorganic component, to form a protein. Many proteins consist of two or more interacting
polypeptide chains, each of which is commonly referred to as a subunit of the protein for example,
a haem group in haemoglobin called a Prosthetic group. These proteins will only be able to function
if all subunits are present.

DENATURATION
Changing the structure of proteins will affect its function. Often that means the function is lost.
Therefore, denaturation of a protein means loss of the protein’s function due to structural change in
the protein caused by some chemical or physical factor such as high temperature or unfavorable pH or
exposure to organic solvents.
- Heat; As the temperature of a solution containing proteins is raised, the extra heat causes twisting,
rotating, and bending of bonds and functioning groups within the molecule; the higher the
temperature, the more of this there is.
- pH: ionic interactions occur between charged amino and carboxyl groups in the side chains of
some amino acids in the folded protein. If the pH of the solution is changed, some of these
functional groups will gain or lose a proton and, therefore, will lose their charge or become
charged, depending on which pH is changed and by how much. That will eliminate some or many of
the ionic interactions that were necessary for maintenance of the folded shape of the protein.
- Organic solvents; such as alcohol. In the tertiary structure the hydrophobic ends occupy the
interior and the hydrophilic ends are found at the surface of the protein. When an organic solvent
such as alcohol is mixed with the aqueous solution, the amino acid side chains on the surface don’t
dissolve in the water-alcohol mixture as well. The protein molecule twists or flexes as the
hydrophilic side chains shun the alcohol. At the same time some interior hydrophobic side chains
twist to the surface where they interact favourably with the organic solvent. The net effect is as
though the protein molecule were trying to turn itself inside out in response to the change in the
surrounding solvent. In the process H-bonds and ionic interactions will be broken. The result is a
structurally altered protein molecule.

FUNCTIONS OF PROTEINS
- Repair and maintenance; protein is termed the building block of the body. It is termed so
because protein is vital in the maintenance of body tissue, including development and repair. Hair,
skin, eyes, muscles, and organs are all made from protein.
- Energy: protein is a major source of energy. If more protein is consumed than needed for body
tissue maintenance and other necessary functions, the body uses it for energy. If it is not needed
due to sufficient intake of other energy sources such as carbohydrates, the protein will be used to
create fat and becomes part of fat cells.
- Hormones: protein is involved in creation of hormones e.g. insulin, a protein, is an example of a
hormone that regulates blood sugar. Secretin is another example of a protein hormone and assists
in the digestive process by stimulating the pancreas and the intestine to create necessary juices.
- Enzymes: these are proteins that increase the rate of chemical reactions in the body.
- Transportation: Protein is a major element in transportation of certain molecules for example
hemoglobin is a protein that transports oxygen throughout the body.
- Storage of molecules: protein is also used to store certain molecules; Ferritin is an example of a
protein that combines with iron for storage in the liver.
- Antibodies: protein forms antibodies that help prevent infection, illness and disease. These
proteins identify and assist in destroying antigens such as bacteria and viruses.