Bioorganic Chemistry: An Introduction to Bioorganic Chemistry

This article provides an introduction to bioorganic chemistry.

Bioorganic Chemistry :

As life comes from previous life, it was believed for a long that the carbon compounds of organisms (hence the name organic) arose from life only.

This is referred to as vital force theory. Friedrich Wohler (1825) first discovered that urea (NH₂—CO—NH₂), the organic compound, could be prepared by heating ammonium cyanate (NH₄NCO), in the laboratory. Thereafter, thousands and thousands of organic compounds have been synthesized outside the living system.

Organic chemistry broadly deals with the chemistry of carbon compounds, regardless of their origin. Biochemistry, however, is concerned with the carbon chemistry of life only. The general principles of organic chemistry provide strong foun­dations for understanding biochemistry. However, biochemistry exclusively deals with the reactions that occur in the living system in aqueous medium.

Most Common Organic Compounds Found in Living System:

The organic compounds, namely carbohydrates, lipids, proteins, nucleic acids and vitamins are the most common organic compounds of life.

Common Functional Groups in Biochemistry:

Most of the physical and chemical properties of organic compounds are determined by their functional groups. Biomolecules possess certain functional groups which are their reactive centres. The common functional groups of importance in biomolecules are presented in Table 64.1.

Common Ring Structures in Biochemistry:

There are many homocyclic and heterocyclic rings, commonly encountered in biomolecules. A selected list of them is given in Fig. 64.1.

Homocyclic rings:

Phenyl ring derived from benzene is found in several biomolecules (phenylalanine, tyrosine, catecholamine’s). Phenanthrene and cyclopentane form the backbone of steroids (cholesterol, aldosterone). Coenzyme Q is an example of benzoquinone while vitamin K is a naphthoquinone.

Heterocyclic rings:

Furan is the ring structure found in pentoses. Pyrrole is the basic unit of porphyrins found in many biomolecules (heme) while pyrolidine is the ring present in the amino acid, proline. Thiophen ring is a part of the vitamin biotin. The amino acid histidine contains imidazole.

Pyran structure is found in hexoses. Pyridine nucleus is a part of the vitamins-niacin and pyridoxine. Pyrimidine’s (cytosine, thymine) and purines (adenine, guanine) are the constituents of nucleotides and nucleic acids. Indole ring is found in the amino acid tryptophan. Purine and indole are examples of fused heterocyclic rings.

Isomerism:

The compounds possessing identical molecular formulae but different structures are referred to as isomers. The phenomenon of existence of isomers is called isomerism (Greek: isos—equal; meros— parts). Isomers differ from each other in physical and chemical properties. Isomerism is partly responsible for the existence of a large number of organic molecules.

Consider the molecular formula—C₂H₆O. There are two important isomers of this — ethyl alcohol (C₂H₅OH) and diethyl ether (CH₃OCH₃) as shown below:

Isomerism is broadly divided into two categories — structural isomerism and stereo­isomerism.

Structural isomerism:

The difference in the arrangement of the atoms in the molecule (i.e. molecular framework) is responsible for structural isomerism. This may be due to variation in carbon chains (chain isomerism) or difference in the position of functional groups (position isomerism) or difference in both molecular chains and functional groups (functional isomerism).

Structural isomerism, as such, is more common in general organic molecules. Tautomerism, a type of structural isomerism, occurs due to the migration of an atom or group from one position to the other e.g. purines and pyrimidine’s.

Stereoisomerism:

Stereoisomerism (Greek: stereos—space occupying) is, perhaps, more relevant and important to biomolecules. The differential space arrangement of atoms or groups in molecules gives rise to stereoisomerism. Thus, stereoisomers have the same structural formula but differ in their special arrangement.

Stereoisomerism is of two types—geometric isomerism and optical isomerism.

Geometrical isomerism:

This is also called cis- trans isomerism and is exhibited by certain molecules possessing double bonds. Geometrical isomerism is due to restriction of freedom of rotation of groups around a carbon-carbon double bond (C = C). Maleic acid and fumaric acid are classical examples of cis-trans isomerism.

When similar groups lie on the same side, it is called cis isomer (Latin: cis—on the same side). On the other hand, when similar groups lie on the opposite sides, it is referred to as trans isomer (Latin: trans—across). As is observed from the above structure, maleic acid is a cis form while fumaric acid is a trans form. Geometric isomerism is also observed in sterols and porphyrins, cis-trans isomers differ in physical and chemical properties.

Optical isomerism:

Optical isomers or enantiomers occur due to the presence of an asymmetric carbon (a chiral carbon). Optical isomers differ from each other in their optical activity to rotate the plane of polarized light.

What is an asymmetric carbon?

An object is said to be symmetrical if it can be divided into equal halves e.g. a ball. Objects which cannot be divided into equal halves are asymmetric, e.g. hand. An asymmetric object cannot coincide with its mirror image. For instance, left hand is the mirror image of right hand and these two can never be superimposed.

In contrast, a symmetrical object like a ball superimposes its image. A carbon is said to be chiral (Greek: hand) or asymmetric when it is attached to four different groups. Their mirror images do not superimpose with each other.

The number of possible optical isomers of a molecule depends upon the specific number of chiral carbon (n). It is given by 2ⁿ.

What is optical activity?

The ordinary light propagates in all directions. However, on passing ordinary light through a Nicol prism, the plane of polarized light vibrates in one direction only (Fig. 64.2).

Certain organic compounds (optical isomers) which are said to exhibit optical activity rotate the plane of polarized light either to the left or to the right. The term levorotatory (indicated by 1 or (-) sign) is used for the substances which rotate the plane of polarized light to the left.

On the other hand, the term dextrorotatory (indicated by d or (+) sign) is used for substances rotating the plane of polarized light to right (Fig. 64.2). The term racemic mixture represents equal concentration of d and I forms which cannot rotate the plane of polarized light.

Configuration of chiral molecules:

While representing the configuration of chiral molecules, the configuration of glyceraldehyde is taken as a reference standard.

It must, however, be remembered that D- and L- do not represent the direction of the rotation of plane of polarized light.

Existence of chiral biomolecules:

As you know, you can never come across anybody who is your mirror image. The same is true with biomolecules. Only one type of molecules (D or L) are found in the living system. Thus, the naturally occurring amino acids are of L-type while the carbohydrates are of D-type.