Khwaja Yunus Ali University, Sirajganj

Proteins

What are Proteins?

Proteins are the most abundant biological macromolecules, occurring in all cells. It is also
the most versatile organic molecule of the living systems and occurs in great variety;
thousands of different kinds, ranging in size from relatively small peptides to large
polymers. Proteins are the polymers of amino acids covalently linked by the peptide
bonds. The building blocks of proteins are the twenty naturally occurring amino
acids. Thus, proteins are the polymers of amino acids.

Properties of Proteins

Solubility in Water
• The relationship of proteins with water is complex.
• The secondary structure of proteins depends largely on the interaction of peptide
bonds with water through hydrogen bonds.
• Hydrogen bonds are also formed between protein (alpha and beta structures)
and water. The protein-rich static ball is more soluble than the helical structures.
• At the tertiary structure, water causes the orientation of the chains and
hydrophilic radicals to the outside of the molecule, while the hydrophobic chains
and radicals tend to react with each other within the molecule (hydrophobic
effect).
Denaturation and Renaturation
• Proteins can be denatured by agents such as heat and urea that cause the
unfolding of polypeptide chains without causing hydrolysis of peptide bonds.
• The denaturing agents destroy secondary and tertiary structures, without
affecting the primary structure.
• If a denatured protein returns to its native state after the denaturing agent is
removed, the process is called renaturation. Some of the denaturing agents
include

Physical agents: Heat, radiation, pH

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Chemical agents: Urea solution which forms new hydrogen bonds in the protein, organic
solvents, detergents.

Isoelectric point
• The isoelectric point (pI) is the pH at which the number of positive charges equals
the number of negative charges, and the overall charge on the amino acid is zero.

• At this point, when subjected to an electric field the proteins do not move either
towards anode or cathode, hence this property is used to isolate proteins.

Protein Structure
• The linear sequence of amino acid residues in a polypeptide chain determines the
three-dimensional configuration of a protein, and the structure of a protein
determines its function.
• All proteins contain the elements carbon, hydrogen, oxygen, nitrogen, and sulfur
some of these may also contain phosphorus, iodine, and traces of metals like
ions, copper, zinc, and manganese.

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• A protein may contain 20 different kinds of amino acids. Each amino acid has an
amine group at one end and an acid group at the other and a distinctive side
chain.
• The backbone is the same for all amino acids while the side chain differs from
one amino acid to the next.

The structure of proteins can be divided into four levels of organization:

1. Primary Structure
• The primary structure of a protein consists of the amino acid sequence along the
polypeptide chain.
• Amino acids are joined by peptide bonds.
• Because there are no dissociable protons in peptide bonds, the charges on a polypeptide
chain are due only to the N-terminal amino group, the C-terminal carboxyl group, and
the side chains on amino acid residues.
• The primary structure determines the further levels of organization of protein molecules.

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2. Secondary Structure
• The secondary structure includes various types of local conformations in which the atoms
of the side chains are not involved.
• Secondary structures are formed by a regularly repeating pattern of hydrogen bond
formation between backbone atoms.
• The secondary structure involves α-helices, β-sheets, and other types of folding patterns
that occur due to a regularly repeating pattern of hydrogen bond formation.
• The secondary structure of protein could be :
1. Alpha-helix
2. Beta-helix
• The α-helix is a right-handed coiled strand.
• The side-chain substituents of the amino acid groups in an α-helix extend to the outside.
• Hydrogen bonds form between the oxygen of the C=O of each peptide bond in the strand
and the hydrogen of the N-H group of the peptide bond four amino acids below it in the
helix.
• The side-chain substituents of the amino acids 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 hydrogen bond 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.

3. Tertiary Structure
• The tertiary structure of a protein refers to its overall three-dimensional conformation.
• The types of interactions between amino acid residues that produce the three-dimensional
shape of a protein include hydrophobic interactions, electrostatic interactions, and
hydrogen bonds, all of which are non-covalent.
• Covalent disulfide bonds also occur.
• It is produced by interactions between amino acid residues that may be located at a
considerable distance from each other in the primary sequence of the polypeptide chain.
• Hydrophobic amino acid residues tend to collect in the interior of globular proteins,
where they exclude water, whereas hydrophilic residues are usually found on the surface,
where they interact with water.

4. Quaternary Structure
• Quaternary structure refers to the interaction of one or more subunits to form a functional
protein, using the same forces that stabilize the tertiary structure.
• It is the spatial arrangement of subunits in a protein that consists of more than one
polypeptide chain.

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Classification of Proteins
Based on the chemical nature, structure, shape, and solubility, proteins are classified as:
1. Simple proteins: They are composed of only amino acid residue. On hydrolysis, these
proteins yield only constituent amino acids. It is further divided into:
• Fibrous protein: Keratin, Elastin, Collagen
• Globular protein: Albumin, Globulin, Glutelin, Histones
2. Conjugated proteins: They are combined with non-protein moiety. Eg. Nucleoprotein,
Phosphoprotein, Lipoprotein, Metalloprotein, etc.
3. Derived proteins: They are derivatives or degraded products of simple and conjugated
proteins. They may be :
• Primary derived protein: Proteans, Metaproteins, Coagulated proteins
• Secondary derived proteins: Proteosesn or albunoses, peptones, peptides.

Functions of Proteins
Proteins are vital for growth and repair, and their functions are endless. They also have an
enormous diversity of biological functions and are the most important final products of
the information pathways.
• Proteins, which are composed of amino acids, serve in many roles in the body
(e.g., as enzymes, structural components, hormones, and antibodies).
• They act as structural components such as keratin of hair and nail, collagen of
bone, etc.
• Proteins are the molecular instruments through which genetic information is
expressed.
• They execute their activities in the transport of oxygen and carbon dioxide by
hemoglobin and special enzymes in the red cells.
• They function in the homeostatic control of the volume of the circulating blood
and that of the interstitial fluids through the plasma proteins.
• They are involved in blood clotting through thrombin, fibrinogen, and other
protein factors.
• They act as the defense against infections by means of protein antibodies.
• They perform hereditary transmission by nucleoproteins of the cell nucleus.
• Ovalbumin, glutelin, etc. are storage proteins.
• Actin, myosin act as a contractile protein important for muscle contraction.