Proteins are the high molecular mass complex biopolymers of amino acids and organic compounds that are most important to life. They are essential for growth and maintenance of life. They are high molecular weight, nitrogen rich substances that are present all living cells of animals and plants. They occur in every part of the cell. They are composed of 20 amino acids, which are repeatedly found in the structure of proteins. These amino acids are liberated when proteins are hydrolyzed. Proteins are the polymers of -amino acids.

conversion of proteins to amino acids

All proteins contain the elements carbon, hydrogen, oxygen, nitrogen and sulphur some of these may also contain phosphorus, iodine, and traces of metals like ion, copper, zinc and manganese.

The name protein is derived from the Greek word proteios meaning of prime importance. As enzymes, they catalyze biochemical reactions, as hormones they regulate metabolic processes and as antibodies they protect the body against toxic substances.

Structure of amino acids

Amino acids are the building blocks of proteins. There are 300 amino acids that occur in nature. Among these only 20 are known as standard amino acids that commonly occur in proteins. Amino acids contain two functional groups. They are - amino and carboxyl groups. The amino group (-NH2) is basic and the carboxyl group (-COOH) is acidic in nature.

General structure

The carboxyl group and amino group are attached to the same carbon atom, hence amino acids are termed as -amino acids.

structure of a- amino acid

a-amino acid

Nomenclature of amino acids

All amino acids have trivial names. IUPAC names which even if not cumbersome are not used. For e.g., H2N CH2COOH is better known as glycine rather then a-amino acetic acid or 2-amino ethanoic acid.

These trivial names usually reflect the property of that compound or its source. Example: Glycine is so named since it has sweet taste (in Greek glykos means sweet) and tyrosine was first obtained from cheese (in Greek, tyros means cheese).

Classification of amino acids based on polarity

Amino acids are classified into different ways based on polarity, structure, nutritional requirement, metabolic fate, etc. Generally used classification is based on polarity.

Based on polarity amino acids are classified into four groups.

Non-polar amino acids

They have equal number of amino and carboxyl groups and are neutral.

These amino acids are hydrophobic and have no charge on the 'R' group. The amino acids in this group are alanine, valine, leucine, isoleucine, phenyl alanine, glycine, tryptophan, methionine and proline.

alanine valine leucine

 isoleucine glycine tryptophan

phenyl alanine methionine proline

Polar amino acids with no charge

These amino acids do not have any charge on the 'R' group. These amino acids participate in hydrogen bonding of protein structure. The amino acids in this group are - serine, threonine, tyrosine, cysteine, glutamine and aspargine.

serine threonine gultamine

cycteine aspargine tyrosine

Polar amino acids with positive charge

Polar amino acids with positive charge have more amino groups as compared to carboxyl groups making it basic.

The amino acids, which have positive charge on the 'R' group are placed in this category. They are lysine, arginine and histidine.

lysine is a polar amino acid
histidine is a polar amino acid

arginine is a polar amino acid

Polar amino acids with negative charge

Polar amino acids with negative charge have more carboxyl groups than amino groups making them acidic.

The amino acids, which have negative charge on the 'R' group are placed in this category. They are called as dicarboxylic mono-amino acids. They are aspartic acid and glutamic acid.

aspartic acid and glutamic acid
Classification of amino acids based on nutrition
According to the classification based on nutrition, they are divided into two types:

They are:

  • Essential amino acids and
  • Non-essential amino acids.

Essential amino acids

The amino acids that are to be supplied through diet are called as essential amino acids. They cannot be produced by the body. The essential amino acids are arginine, valine, histidine, isoleucine, leucine, lysine, methionine, phenylalanine, threonine and tryptophan.

Arginine and histidine are called semi-essential amino acids as they can be partly synthesized in the human body.

Non-essential amino acids

The amino acids that can be synthesized by the body are called non essential amino acids. They are: Glycine, alanine, serine, cysteine, aspartic acid, glutamic acid, aspargine, glutamine, tyrosine and proline.

Physical properties of amino acids

Amino acids are colourless, crystalline solids. They are water-soluble high melting solids and behave like salts. The a-carbon atom has 'R' which is a side chain. This side chain is different for different amino acids. The carboxyl and amino groups interact resulting in the transfer of proton from carboxyl group to amino group. Thus the amino acid exists in ionised form known as zwitter ion. This explains the physical properties of these a-amino acids.

zwitter ion

In aqueous solution, the carboxyl group can loose a proton and amino group can accept a proton giving rise to a dipolar ion which is neutral but has both positive and negative charges.

In zwitter ionic form, amino acids slow amphoteric behavior as they react both with acids and bases. In acidic solution, the carboxylate function (- COO-) accepts a proton and gets converted to carboxyl substituent (- COOH) while in basic solution the

ammonium substituent (+NH3) changes to amino group (-NH2) by losing a proton.

In acidic solution, an amino acid exists as a positive ion and migrates towards the cathode in an electric field, while in alkaline solution it exists as a negative ion and migrates towards anode. At a certain hydrogen ion concentration (pH), the dipolar ion exists as a neutral ion and does not migrate to either electrode. This pH is known as the isoelectric point of the amino acid.

Iso-electric point

It is defined as the point at which a molecule exists as zwitter ion with no net charge. Thus, at this point the molecule is electrically neutral. The molecules have minimum solubility, maximum precipitability and least buffer capacity. The acidic amino acids and basic amino acids strongly influence the iso-electric point (PI). The PI value of protein is determined by the nature of ionizable groups of amino acids. By taking average Pka values of ionisable groups PI value can be calculated.

The minimum solubility of amino acids in water at the isoelectric point is utilised in the separation of different amino acids obtained on hydrolysis of proteins.

For e.g., Leucine has 2 ionizable groups and its iso-electric pH is 6.0. Leucine exists as cation at pH below 6.0 and as anion at pH above 6.0. It exists as a zwitter ion at pH 6.0.

Proteins are generally least soluble at iso-electric pH. In acidic medium proteins are present as cations acid in alkaline medium they are found as anions.

If an a-carbon atom has four different groups attached to it. Then it is asymmetric and it exhibits optical isomerism. Except glycine all amino acids exhibit optical activity. Therefore two stereo isomers are formed and they are mirror images to each other. They appear as shown below.

asymmetric and optical isomerism of amino acid

Their Fischer projection formulae are written with carboxyl group, on the top. In the 'D' form amino group (NH2) is written on the right side and in the 'L' form on the left side. 'D' and 'L' refers to the configuration of the amino acid molecule about the asymmetric carbon atom. Most naturally occurring amino acid have L-configuration.

Peptide Bond Formation

When two amino acids combine with each other, the amino group of one amino acid combines with carboxyl group of other amino acid. This leads to peptide bond formation. The combination of the amino group of one molecule with the carboxyl group of the other results in the elimination of a water molecule and forms a -CO-NH-bond.

The bond formed above is a peptide bond. The dipeptide contains two amino acids and one peptide bond.

formation of dipeptide bond

Glycylalanine (Gly-Ala) has structure

structure of glycylalanine

The same two amino acids may also form Ala-Gly where the amino group of glycerin may react with the carboxyl group of alamine. Both those dipeptides have 3 free functional groups which further react with relevant groups of other amino acids forming tri, tetra, penta peptides and so on.

Both -CO and -NH groups of peptide bonds are polar. They are involved in hydrogen bond formation. In a protein the amino acids are held together by peptide bonds. The peptides with more than 10 amino acids are called polypeptides. Peptide chains are written with free amino end at left and free carboxyl end at right. Any amino acid sequence is read from N-terminal end to C-terminal end.

Peptide bonds are strong, rigid and planar. They have partial double bond characteristics. They serve as cementing material between individual amino acids. The polypeptide chain is shown below:

 distance between two adjacent a-carbon atoms is 0.36 nm

The distance between two adjacent a-carbon atoms is 0.36 nm.

Poly peptides

Peptides containing more than 10 amino acids are called poly peptides. Poly peptides are formed by the linear sequence of amino acids. Some proteins are composed of two or more poly peptide chains. Relatively shorter peptides are known as oligopeptides whereas longer polymers are called polypeptides. Polypeptides containing more than 100 amino acids having molecular mass higher then 10,000 are generally called as proteins. However the distinctive between a polypeptide and a protein is not sharp.

As a matter of convention, the structure of peptides is written in a way that the amino acid with the free amino (-NH2) group known as N-terminal residue is written on the left hand side of the polypeptide chain and the amino acid with the free carboxyl group (c terminal residue) written on the right hand side of the chain. Thus a tripeptide, alanylglycylphenyl alamine is represented as

representation of alanylglycylphenyl alamine

The name of any polypeptide is written starting from the N-terminel residue. The suffix ine in the name of the amino acid is replaced by '-yl' (as glycine to glycl, alanine to alanyl etc) for all amino acids except the C-terminal acid.

The usual nomenclature is the thee letter on the one letter abbreviation for the amino acid. For e.g., the above tripeptide is named as Ala-Gly-Phe or A-G-F.

Polypeptides are amphoteric because of the presence of terminal ammonium and carboxylate ions as well as the ionized side chains of amino acid residues. Therefore, they titrate as acids or bases and have an isolectric point at which they are frequently least soluble and have the greatest tendency to aggregate.

The functions of proteins are important and valued in bio systems however the smaller peptides also have important functions though their total content in tissues is smell compared to proteins. Some of them are very potent. Most of the toxins (poisonous substances) in animal venoms and in plant sources are polypeptides. Minute amount of some oligopeptides with as few as three modified amino acid residues as effective as hormones. A derivative of dipeptide aspartylphenylalenine methyl ester (aspartame) is 160 times as sweet as sucrose and is used as a sugar substitute.

Denaturation of proteins

Proteins found in a biological system with definite configuration and biological acts is called a native protein.

Denaturation is a process by which the native form of protein structure is disorganized. This causes drastic changes in a protein molecule. Denaturation is caused by some physical and chemical agents. Denaturation causes loss in biological activity of protein. The peptide bonds in the primary structure are not hydrolyzed, but helical structure of the protein is lost. Protein is soluble in water but after denaturation it is insoluble and easily digested.

Denaturation is usually a irreversible process, but it is sometimes reversible. The coagulation of egg white on boiling of egg protein is an example of irreversible protein denaturation. The reversible process is called the reverse of denaturation i.e., renaturation. This is when the disruptive agent is removed and the protein recovers its original physical and chemical properties and biological activity.

Biological functions of protein

Proteins perform essential and specialized functions in living cells.

  • Proteins are primarily responsible for the structure and strength of the body.
  • Some proteins act as enzymes, hormones, blood clotting factors, etc. These are the dynamic functions of proteins.
  • Proteins performing dynamic functions are known as the working horses of cell.
  • Peptides that are biologically important are Glutathione, oxytocin, vasopressin, etc.

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