Proteins
The word protein is derived from Greek word, proteious meaning primary. So, proteins are the
major components of any living organism.
Proteins are natural substances with high molecular weights ranging from 5,000 to many
millions. Besides Carbon, Hydrogen and Oxygen, they also contain Nitrogen, and sometimes,
Sulfur and Phosphorous.
Proteins are most important constituent of cell membranes and cytoplasm. Muscle and blood
plasma also contain certain specific proteins.
Protein containing foods are essential for living organism, because protein is the most important
biological molecules in building up and maintenances of the structure of body, giving as much
energy as carbohydrates in the course of metabolism in the body. Many of the body proteins
perform innumerable chemical reactions constantly taking place inside the body.
Proteins are the molecular instruments in which genetic information is expressed; hormones,
antibodies, transporters, muscle, the lense protein, antibiotics, mushroom poisons, and a myriad
of other substances having distinct biological activities are derived.
Definition
Proteins are macromolecules with a backbone formed by polymerization of amino acids in a
polyamide structure.
Classification
Even though there is no universally accepted classification system, proteins may be classified
on the basis of their composition, solubility, shape, biological function and on their three
dimensional structure.
I. Composition:
A. Simple protein:
Yields only amino acids and no other major organic or inorganic hydrolysis products i.e. most of
the elemental compositions.
B. Conjugated Proteins
Yields amino acids and other organic and inorganic components
E.g. Nucleoprotein (a protein containing Nuclei acids)
Lipoprotein (a protein containing lipids)
Phosphoprotein (a protein containing phosphorous)
Metalloprotein (a protein containing metal ions of Fe2+)
Glycoprotein (a protein containing carbohydrates)
II. Solubility
a) Albumins: These proteins such as egg albumin and serum albumin are readily
soluble in water and coagulated by heat.
b) Globulins: these proteins are present in serum, muscle and other tissues and are
soluble in dilute salt solution but sparingly in water.
c) Histones:
Histones are present in glandular tissues (thymus, pancreas etc.) soluble in water;
they combine with nucleic acids in cells and on hydrolysis yield basic amino acids
III. Overall Shape
A. Fibrous proteins
In these protein, the molecule are constituted by several coiled cross-linked
polypeptide chains, they are insoluble in water and highly resistant to enzyme
digestion. The ratio of length to breath (axial ratio) is more than 10 in such protein. A
few sub groups are listed below.
1. Collagens: the major protein of the connective tissue, insoluble in water,
acids or alkalis. But they are convertible to water-soluble gelatin, easily
digestible by enzymes.
2. Elastins: present in tendons, arteries and other elastic tissues, not convertible
to gelatin.
3. Keratins: protein of hair, nails etc.
B. Globular proteins:
These are globular or ovoid in shape, soluble in water and
constitute the enzymes, oxygen carrying proteins, hormones etc. the axial ratio is 3
to 4 or less. Subclasses include:- Albumin, globulins and histones.
IV. On their Biological Functions:
Proteins are sometimes described as the "workhorses" of the cell because they do
So many things Like:
Enzymes: kinases, transaminases etc.
Storage proteins myoglobin, ferretin
Regulatory proteins peptide hormones, DNA binding proteins
Structural protein collagen, proteoglycan
Protective proteins blood clotting factors, Immunoglobins,
Transport protein Hemoglobin, plasma lipoproteins
Contractile or motile Proteins Actin, tubulin
V. On their level of organization
Primary, secondary, tertiary and quaternary.
a) Primary Structure of Proteins
The primary structure of a protein is defined by the linear sequences of amino acid
residues. Protein contain between 50 and 2000 amino acid residues.
The mean molecular mass of an amino acid residue is bout 110 Dalton units (Da).
Therefore the molecular mass of most proteins is between 5500 and 220,000 Da.
The amino acid composition of a peptide chain has a profound effect on its physical
and chemical properties of proteins.
Protein rich in polar amino acids are more water soluble. Proteins rich in aliphatic or
aromatic amino groups are relatively insoluble in water and more soluble in cell
membranes (can easily cross the cell membrane).
• The primary structure cannot represent the 3D-nature of a protein molecule since
the extended chain of amino acids is co-planar as the covalent bind of peptide is
right.
b) Secondary Structure
The secondary structure of a protein refers to the local structure of a polypeptide
chain, which is determined by Hydrogen bond. The Interactions are between the
carbonyl oxygen group of one peptide bond and the amide hydrogen of another near
by peptide bond.
There are two types of secondary structure, the ∝ - helix and the β- pleated sheet.
The α - helix
The α - helix is a rod like structure with peptide chains tightly coiled and the side chains of
amino acid residues extending outward from the axis of spiral. Each amide carbonyl group is
hydrogen bonded to the amide hydrogen of a peptide bond that is 4 - residues away along the
same chain. There are 3.6 amino acids residues per turn of the helix the complete turn has 0.54
mm pitch. (1nm = 10-9 m) including nearly 3.6 amino acid residues. This enable every = NH
group to bind with a carbonyl O, fourth in line behind the primary structure and the helix winds in
a right handed manner in almost all natural protein, i.e. turns in a clockwise fashion around the
axis.
Since all the carbonyl oxygen and peptide nitrogen are thus involved in the hydrogen bonds, the
hydrophilic nature of the helical region is greatly minimized. As the free energy involved in
hydrogen bond is very low, it is formed spontanemsly being weak bonds these are disrupted
easily when the chain is extended by a little force and reformed when force is released.
Fig 5.16. The α helix (a) and the β-pleated sheet (b)
c) Tertiary Structure
The three dimensional, folded and biologically active conformation of a protein is referred to as
tertiary structure. The structure reflects the overall shape of the molecule. The three -
dimensional tertiary structure of a protein is stabilized by interactions between side. Chain
functional group, covalent, disulfide bonds, hydrogen bonds, salt bridges, and hydrophobic
interactions.
In the tertiary structure the side chains of Tryptophan and Arginine serve as both hydrogen bond
donors and acceptors. Lysine, aspartic acid Glutamic acid, tyrosine and Histidine also can serve
as both donors and acceptors in the formation of ion-pairs (salt bridges). Two opposite -
charged amino acids, such as glutamate with a γ -carboxyl group and lysine with an ε - amino
group, may form a salt bridge, primarily on the surface of proteins.
Fig.5.17. Elements that stabilize the tertiary structure of a protein
Fig 5.18.The three dimensional structure of Myoglobin
d) Quaternary Structure
Quaternary structure refers to a complex or an assembly of two or more separate peptide
chains that are held together by non- covalent or, in some case, covalent interactions.
If the subunits are identical, it is a homogeneous quaternary structure; but if there are
dissimilarities, it is heterogeneous. For instance insulin consists of A and B chain which are
different. Hemoglobin has 4 chains, two of them are α and two are β. these, the polymers may
be dimers, trimers, tetramers and so on.
Fig 5.19: Hemoglobin as an example of tertiary structure of a protein
Hemoglobin structure shown above is as an example of quaternary structure of a Protein. Cu,
Zn - superoxide dismutase from spinach is a good example of quaternary structure of a protein
The β- pleated sheet
The β – pleated sheet is an extended structure as opposed the coiled ∝ - helix. It is pleated
because the (C-C) bonds are tetrahedral and cannot exist in a planar configuration. If the
polypeptide chain runs in the same direction, if forms a parallel β – sheet. It is said to be
parallel, and when in opposite direction, antiparallel. A protein molecule may have both type of
secondary configuration in different parts of its molecule. Gylcine (Gly) and proline (Pro)
residues often occur in β -turns on the surface of globular proteins. Most immunoglobulins have
such β-pleated conformation and some enzymes like Hexokinase contain a mixed α-β
conformation.
Diagrammatic represntation of hydrogen bonds between -NH and C=O groups on adjacent
strands in a β -pleated sheet is as shown above in the Fig 5.16.