Protein structure

• Proteins are the polymers of L-alpha-amino acids.

• The structure of proteins is rather complex which can be divided into 4 levels of
organization
• 1. Primary structure : The linear sequence of amino acids forming the backbone
of proteins (polypeptides).
• 2. Secondary structure : The spatial arrangement of protein by twisting of the
polypeptide chain.
• 3. Tertiary structure : The three dimensional structure of a functional protein.
• 4. Quaternary structure : Some of the proteins are composed of two or more
polypeptide chains referred to as subunits.
• The spatial arrangement of these subunits is known as quaternary structure.
• The term protein is generally used for a polypeptide containing more
than 50 amino acids.
• In recent years, however, some authors have been using
‘polypeptide’ even if the number of amino acids is a few hundreds.
• They prefer to use protein to an assembly of polypeptide chains with
quaternary structure
• PRIMARY STRUCTURE OF PROTEIN
• Each protein has a unique sequence of amino acids which is
determined by the genes contained in DNA.
• The primary structure of a protein is largely responsible for its
function.
• A vast majority of genetic diseases are due to abnormalities in the
amino acid sequences of proteins i.e. changes associated with
primary structure of protein
• Peptide bond
• The amino acids are held together in a protein by covalent peptide
bonds or linkages.
• These bonds are rather strong and serve as the cementing material
between the individual amino acids (considered as bricks).
• Formation of a peptide bond : When the amino group of an amino
acid combines with the carboxyl group of another amino acid, a
peptide bond is formed
• Characteristics of peptide bonds : The peptide bond is rigid and
planar with partial double bond in character.
• Writing of peptide structures : The peptide chains are written with
the free amino end (N-terminal residue) at the left, and the free
carboxyl end (C-terminal residue) at the right.
• The amino acid sequence is read from N-terminal end to C-terminal
end.
• Incidentally, the protein biosynthesis also starts from the N-terminal
amino acid.
• SECONDARY STRUCTURE OF PROTEIN
• The conformation of polypeptide chain by twisting or folding is
referred to as secondary structure.
• The amino acids are located close to each other in their sequence.
Two types of secondary structures, Alpha helix and Beta-sheet, are
mainly identified
• Alpha -Helix is the most common spiral structure of protein.
• It has a rigid arrangement of polypeptide chain.
• Alpha-Helical structure was proposed by Pauling and Corey (1951)
which is regarded as one of the milestones in the biochemistry
research.
• The salient features of Alpha-helix are given below
• It is a right handed coiled structure
• It is stabilized by extensive hydrogen bonding
• Hydrogen bonds are individually weak, but collectively large number
of hydrogen bonds maintains the helical structure in stable form
• Each turn of the helix contains 3.6 amino acid residues and each
amino acid is separated by a distance of 1.5 A .So the pitch of the
helix is 5.4 A
• BETA PLEATED SHEET STRUCTURE
• It is an extended structure
• It is stabilised by hydrogen bonding
• Bonding chains lie side by side
• Hydrogen bonds are perpendicular to the polypeptide chains
• Beta pleated structures can be parallel or antiparallel depending of
the bonding chains
• If the bonding chains run in same direction ,it is parallel
• If the bonding chains run in opposite direction, it is antiparallel
• TRIPLE HELIX(COLLAGEN HELIX)
• It is a right handed super coil seen in collagen
• Collagen is made up of 3 polypeptide chain ,which are wound around
each other to form a right hand helical conformation called triple
helix or collagen helix
• Tertiary structure
• Tertiary structure of protein refers to the further folding of secondary
structure of polypeptide chain giving the compact three dimensional
conformation
• Bonds stabilizing tertiary structure are hydrogen bond, van der waals
forces, ionic bonds and hydrophobic bonds
• Even though these bonds are weak, large number of these bonds
gives stability to the structure
• Quaternary structure
• Proteins having more than one polypeptide chain show one more
level of higher structure called the quaternary structure
• It refers to the spatial arrangement of the subunits of an oligomeric
protein
• Hemoglobin has four globin chains.so it shows quaternary structure
• Other examples are aspartate transcarbamoylase,lactate
dehydrogenase etc..
• Bonds stabilizing quaternary structure
• Hydrogen bonds, van der waals forces, ionic bonds, hydrophobic
bonds, and also few covalent disulphide bonds
• Examples of protein structure
• Structure of human insulin : Insulin consists of two polypeptide
chains, A and B.
• The A chain has glycine at the N-terminal end and asparagine at the
C-terminal end.
• The B chain has phenylalanine and alanine at the N- and C-terminal
ends, respectively.
• Originally, insulin is synthesized as a single polypeptide preproinsulin
which undergoes proteolytic processing to give proinsulin and finally
insulin
• Denaturation
• The process of disorganization of native protein structure is called
denaturation
• Denaturation involves the loss of secondary, tertiary and quaternary
structures without breaking the primary structure