Lecture 3: Secondary Structure

Lecture 3 : Secondary structure
The term “secondary structure” denotes the configurational relationship between residues,
which are about 3–4 amino acids apart in the linear sequence.
For stability of primary structure, hydrogen bonding between the hydrogen of NH and
oxygen of C=O groups of the polypeptide chain occurs, which gives rise to folding or twisting
of the primary structure.
Forces holding Secondary structure

Secondary and tertiary levels of protein structure are preserved by noncovalent forces or
bonds like hydrogen bonds, electrostatic bonds, hydrophobic interactions and van der Waals
forces
i. Hydrogen bond is a weak electrostatic attraction between one electronegative atom
like O or N and a hydrogen atom covalently linked to a second electronegative atom.
Hydrogen atoms can be donated by -NH; -OH (serine, threonine) and -NH2 (arginine,
lysine).
ii. Electrostatic bonds (ionic bonds): Positive charges are donated by amino group of
lysine, arginine and histidine. Negative charges are provided carboxyl groups of aspartic
and glutamic acids.
iii. Hydrophobic bonds are formed by interactions between nonpolar hydrophobic side
chains by eliminating water molecules.
iv. Van der Waals forces are very weak, but collectively contribute maximum towards the
stability of protein structure.
Types of Secondary structures

1. α-helix (Alpha helix):
i. The alpha helix is the most common and stable conformation for a polypeptide chain. In
proteins like hemoglobin and myoglobin, the alpha helix is abundant, whereas it is
virtually absent in chymotrypsin.
ii. The alpha helix is a spiral structure. The polypeptide bonds form the back-bone and the
side chains of amino acids extend outward.
iii. The structure is stabilized by hydrogen bonds between NH and C=O groups of the main
chain.
iv. Each turn is formed by 3.6 residues.
v. The alpha helix is generally right handed.Left handed alpha helix is rare, because amino
acids found in proteins are of L-variety, which exclude left handedness.
vi. Proline and hydroxy proline will not allow the formation of alpha helix, due its rigid ring
structure (no hydrogen atoms remain on the nitrogen atom that takes part in peptide
bonding)
vii. Example/ α-keratin
Types of Secondary structures

2. β-Sheet (Beta-pleated sheet):
i. The polypeptide chains in beta-pleated sheet is almost fully extended.
ii. Beta-pleated sheet is the major in proteins: silk Fibroin (antiparallel),
Flavodoxin (parallel) and Carbonic anhydrase (both).
iii. It is stabilized by hydrogen bonds between NH and C=O groups of neighboring
polypeptide segments.
iv. Adjacent strands in a sheet can run in the same direction with regard to the amino and
carboxy terminal ends of the polypeptide chain (parallel) or in opposite direction (anti-
parallel beta sheet)
v. Beta bends may be formed in many proteins by the abrupt U-turn folding of the chain.
Intrachain disulfide bridges stabilize these bends.
vi. Example/ β-keratin
Difference between α-helix and β-Sheet

• A polypeptide chain in the β-pleated sheet is almost fully extended rather than being
tightly coiled as in the α-helix.
• Unlike α-helix, β-pleated sheets are composed of two or more polypeptide chains.
• β-pleated sheet is stabilized by hydrogen bonds between NH and C=O groups in a
different polypeptide chain whereas in α-helix, the hydrogen bonds are between NH
and CO groups in the same polypeptide chain.
Tertiary structure of protein
❖ Secondary structure denotes the configurational relationship
between residues which are about 3–4 amino acids apart.
❖ The tertiary structure denotes three dimensional structure of the
whole protein.
❖ The arrangements of the polypeptide chain in a protein form a

“fold” and build regions important for the functioning of the
protein, like active site or catalytic site of enzymes.
❖ The three-dimensional folded compact and biologically active
conformation of a protein is called tertiary structure,
❖ example/ myoglobin.
Forces that hold Tertiary structure
The three-dimensional tertiary structure of a protein is stabilized by:
1. Hydrogen bonds
2. Hydrophobic interactions
3. Van der Waals forces
4. Ionic (electrostatic) bonds
5. Disulfide bond
Tertiary and quaternary structure
❖ Each polypeptide chain is called subunit.
❖ Depending on the number of polypeptide chain (subunit) , the
protein may be termed as monomer (1 chain), dimer (2 chains),
tetramer (4 chains ) and so on.
❖ Many proteins consist of a single polypeptide chain and are called
monomeric proteins, e.g. myoglobin. These will have only tertiary
structure.
❖ Only those proteins that have more than one polypeptide chain
(polymeric) have a quaternary structure.
❖ Not all proteins
are polymeric.
❖ Homodimer contains two copies of the same polypeptide chain.

❖ Heterodimer contains two different types of polypeptide chain.
❖ Example/ hemoglobin
2 alpha-chains and 2 beta-chains form the hemoglobin molecule.
Forces that hold Quaternary structure
Protein structure is stabilized by two types of bonds
1. Covalent bond.
• Peptide bonds
• Disulfide bond
2. Noncovalent bond.
• Hydrogen bond
• Hydrophobic bond or interaction
• Electrostatic or ionic bond.
• Van der Waals interactions.

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Lecture 3: Secondary Structure

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Lecture 3 : Secondary structure

Forces holding Secondary structure

Types of Secondary structures

Types of Secondary structures

Difference between α-helix and β-Sheet

❖ The arrangements of the polypeptide chain in a protein form a

❖ Homodimer contains two copies of the same polypeptide chain.

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