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Proteins Proteins are numerous large, complex naturally

produced molecules composed of one or more long chains of amino acids, in which the amino acid groups are held together with peptide bond.

Proteins properties depends upon the amino acid composition.Amino acids are the building blocks of proteins.

Amino acids can be classified by the presence of R group.

Function of R groups

Aromatic R group• Tryptophan

Provide hydrophobicity• form hydrogen bonding

Non-polar R group•Ala,Val,Leu And Iso

•Pro

Stabilize the proteinSide chains cluster together and stabilize

Provide rigidity

Polar uncharged R group•Cysteine

Make them soluble in watermake disulfide bond

Negatively charged R group Provide negative charge

Positively charged R group Provide positive charge

Ionization behaviour

The acid-base behavior of a peptide can be predicted from its free alpha amino and alpha carboxyl groups and the nature and number of its ionisable R groups.

Isoelelectric point(PI)-It is the pH at which amino acid have no net charge, thus it is electrophoretically immobile.

In solution amino acid exist in zwitter ionic form. Which provide them physical properties characteristics of ionic compounds. i.e., high melting point, water solubility and low solubility in organic solvents.

Ionisation pattern is different for different amino acid

There are more ionisable groups in amino acids other than carboxyl and amino group.

groups include a phenolic group (tyrosine), guanidino group (arginine), imidazolyl group (histidine) and sulphydryl group (cysteine) .

ionisable groups are on the outside of the molecule,

can interact with the surrounding aqueous medium some located within the structure may be involved in electrostatic attractions that help to stabilise the three-dimensional structure of the protein molecule

These properties use for electrophoretic and ion exchange chrometographic seperation of mixture of amino acids.

at the isoelectric protein has minimum solubility, since it is the point at which there is the greatest opportunity for attraction between oppositely charged groups of neighboring molecules and consequent aggregation and easy precipitation.

Shape Enzymes, hormones, structural protein, receptor,

antibody all are protein .but how they are distinct from each other?

This is of because of their structure.

There are four levels of protein structure.

Other interaction for protein folding

Protein denaturation When temperature of a protein solution is increased there

is breaking of weak interaction (primarily hydrogen bonds) resulting in denaturation of protein.

denaturation: Partial or complete unfolding of the specific native conformation of a polypeptide chain,

such. that the function of the molecule is lost

Proteins can also be denatured by extremes of pH, by certain miscible organic solvents such as alcohol or acetone, by certain solutes such as urea and guanidine hydrochloride, or by detergents. Each of these denaturing agents represents a relatively mild treatment in the sense that no covalent bonds in the polypeptide chain are broken

Solubility in water

Typically a protein contains multiple charged group, so its solubility depends on the concentrations of dissolved salts , the polarity of solvent, the pH and the temperature.

The solubility of a protein at low concentration increase as salt is added, a process called Salting in.

The additional ion shield the protein charged group, thereby weakening the attractive force between individual protein molecules.

However ,when more salt is added , the solubility of protein decrease. This Salting out effect is primarily a result of competition between added salt ions and protein molecules for water.

At very high salt concentration so many of the added ions are solvated that there is significantly less bulk solvent available to dissolve other substance including protein.

Since protein precipitates at different salt concentration s, salting out is the basis of most commonly used protein purification procedure.

(a) Primary structure. The primary structure of a protein is a sequence of amino acids linked together by peptide bonds, forming a polypeptide.

Each type of protein also has a unique amino acid sequence. And the function of a protein depends on its amino acid sequence so if the primary structure is altered , the function of that protein also be change.

(b) Secondary Structure. The secondary structure of a protein describes local regions of structure that result

from hydrogen bonding between NH and CO groups

along the polypeptide backbone. These local interactions

result in two major structural patterns, referred to as the

helix and sheet conformations

an a helix is spiral in shape, consisting of a backbone of amino acids linked by peptide bonds with the specific R groups of the individual amino acid residues jutting out from it.

Another form of common secondary structure in proteins is the beta sheet, this structure is an extended sheet like conformation with successive atoms in the polypeptide chain located at the “peaks” and “troughs” of the pleats. The R groups of successive amino acids jut out on alternating sides of the sheet. Because the carbon atoms that make up the backbone of the polypeptide chain are successively located a little above and a little below the plane of the b sheet, such structures are sometimes called beta pleated sheets.

(c) Tertiary structure is the complete three-dimensional structure of a polypeptide chain. There are two general class of proteins based on tertiary structure: fibrous and globular.

Fibrous proteins, which serve mainly structural roles,

have simple repeating elements of secondary structure.

Globular proteins have more complicated tertiary structures, often containing several types of secondary structure in the same polypeptide chain..

(d)Quaternary structure results from interactions between the subunits of multisubunit (multimeric) proteins or large protein assemblies . Some multimeric proteins have a repeated unit consisting of a single subunit or a group of subunits