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Structure of Proteins

Proteins are building blocks of a human as well as animal body. Protein plays a very important role in building up of muscles, which in turn protects the bone structure from breaking, thereby providing stability to an animal body.

Enzymes are bio molecules which are essential for catalyzing most of the biological processes. All enzymes are proteins. Therefore, knowledge of proteins is essential from bio-organic point of view. Proteins are polypeptides with molecular weight greater than 10,000. Thus, they are macromolecular and are condensation polymers of amino acid.

 

Levels of Protein Structure

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Protein structure can be divided into four levels. Their structures have been classified as
  1. Primary structure
  2. Secondary structure
  3. Tertiary structure
  4. Quaternary structure
Arrangement of amino acids, their numbers and nature in poly peptide chain makes up for the primary structure of proteins. Covalent peptide bond is only type of bond in the primary structure of protein. Peptide bond is resonance stabilized.
Peptide Bond


Primary structure of proteins or the sequence of amino acids, is very important from biological point of view. If even a single amino acid in a protein is replaced its properties are totally changed. For example, if in hemoglobin glutamic acid is replaced by Valine, a different hemoglobin called Hemoglobin - s is formed which causes genetically inherited disease called sickle cell anemia during which red blood cells which are normally rounded become sickle shaped.This disease is caused by mutant genes.

Polypeptide chain from hemoglobin
His- Val - Leu- Leu - Thr - Pro - Glu - Glu - Lys

Polypeptide chain from hemoglobin - s
His- Val - Leu- Leu - Thr - Pro - Val - Glu - Lys

Primary Structure of a Protein

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Secondary structure of protein deals with conformation of peptide chain present in protein molecule. There are two important possible ways in which peptide chain is arranged viz. $\alpha$-helix and $\beta$-conformation or pleated sheet.

Because of double bond character of C-N bond there is no free rotation about the axis of this bond. But, polypeptide chain can rotate on either side of peptide bond, that is on C-N and C-C axis. Extent of rotation at the bond between nitrogen and $\alpha$-carbon (N-C) of the chain is known as $\phi$(phi) and the rotation between $\alpha$-carbon and carbonyl carbon (C-C) is called as $\psi$(psi).
The configuration of polypeptide chain can be determined if the value of $\phi$ and $\psi$ for each amino acid residue are known. In a fully stretched polypeptide chain amino acid residues are known. Certain combinations are not possible due to stearic reasons.

G.N Ramachandran recognized that amino acids residue in a polypeptide chain can not have any pair of values of $\psi$ angles.
  1. In secondary structure of protein peptide chains are held together by hydrogen bonding, intra molecular forces and electrostatic fores as well as intermolecular forces. Hydrogen bonding is between oxygen of carboxylic group and hydrogen of -NH group.
  2. Electrostatic force of attraction and repulsion also operate between charged polar groups. Inter and intra molecular forces due to bonds like disulphide bonds are also there.
  3. $\alpha$-helical structure was proposed by Pauling in 1951 which was confirmed by x-ray analysis. Hydrogen bonds between -C=O and -NH group of the same chain hold the helix. In Helix 3.7 residues per turn give most stable helix.
  4. Hydrogen bonding is between -(C=O) group of one residue and -N-H group of fourth residue in the helix. For L-amino acid peptide chain there is right-handed helix which is more stable than left handed helix. Stability of $\alpha$-helix is due to resonance between -C=O and N-H group.

Secondary structure of protein


Secondary Structure of a Protein
→ Read More Tertiary structure of protein is three dimensional picture of protein which depends upon folding (or coiling) of long polypeptide chain. Thus tertiary structure gives an account of actual shape of a protein. Tertiary structure involves forces like hydrogen bonding, ionic, chemical and hydrophobic bonds. Tertiary structure is the structure under normal conditions of temperature and pH and is most stable structure of that protein. This is also known as native conformation of that protein. This is tertiary structure of protein that undergoes unfolding during denaturation.

Fibrous structure contains large helical contents and acquire rod-like shape. Globular proteins contain helical chain coiled to give spherical shape. Polypeptide chains in globular protein are folded in such a way that polar groups are on the surface and side chains inside. Tertiary structure may be determined by X- ray analysis, light-scattering, diffusion, viscosity determination, ultra centrifuge method and electron microscopy.

Denaturation

  1. Besides hydrogen bonding, ionic, chemical and hydropholic bonds other types of bonds like disulphide bonds are also present in tertiary structure of protein.
  2. Denaturation is the unfolding of secondary and tertiary structures of proteins by the application of light, heat, ultra-violet rays, chemicals, acids, alkalies and solvents like acetone, alcohol, etc.
  3. Denaturation can be reversible as well as irreversible. An example of reversible denaturation is by the treatment of protein ribonuclease with urea and mercapto ethanol during which disulphide bonds are broken.
  4. In protein ribonuclease tertiary structure can be regained by slow re oxidation without urea. An example of irreversible denaturation is boiling of egg during which tertiary structure of protein is completely destroyed.

Tertiary Structure of Protein
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Quaternary Structure of Protein

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  1. Several identical or non-identical polypeptide chain may be linked together to form protein. Individual polypeptide chain is known as subunit. Each sub-unit has its own primary, secondary and tertiary structure.
  2. Fibrous as well as globular proteins consists of only one or more than one polypeptide chain.
  3. Proteins consisting of more than one subunits are called oligomeric proteins whereas individual chain is called promoters (or sub-unit).
  4. The complete three dimensional structure including interactions between polypeptide chains are called Quaternary structure of protein.
  5. Quaternary structure of hemoglobin consists of four subunits (two identical α-chains ad two identical β-chains). Each chain binds to heme group. There are minor differences in folding of α and β chains.
  6. Four chains are held together through vander walls forces (hydrophobic forces) to give spherical quaternary structure. In myoglobin single polypeptide chain consists of eight segments (α - helical units) folded in regular manner.

Chemical Structure of Protein

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Protein has an alpha helix structure, with amino acid links. Amino acids are building blocks of proteins. When amino acids condense together, water molecule is removed from -NH2 group of one molecule of amino acid and -COOH group of another molecule of amino acid, to form the primary structure of protein.
More topics in Structure of Proteins
Primary Structure of a Protein Secondary Structure of a Protein
Tertiary Structure of Protein
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