Biological molecules are the basic building blocks of all biological structures and processes that are the basis of life as we know it. A basic knowledge of the nomenclature and structures of these more common endogenous classes of biological molecules is essential to understanding medicinal chemistry.
There are four major classes of biological momolecules and each is an important component of the cell and performs a wide array of functions. These are:
- Proteins
- Carbohydrates
- Lipids
- Nucleic Acids
Amino acids
Simple amino acids are the basic building blocks of proteins. Their structures contain both an amino group, usually a primary amine, and a carboxylic acid. The relative positions of these groups vary, but for most naturally occurring compounds the amino group is attached to the same carbon as the carboxylic acid.
The structures of amino acids can also contain other functional groups besides the amine and carboxylic acid groups. For example, methionine contains a sulphide group, whilst serine has a primary alcohol group.
Names and Structures of Amino Acids
Peptides and proteins
Peptides and proteins have a wide variety of roles in the human body. They consist of amino acid residues linked together by amide functional groups, which in peptides and proteins are referred to as peptide links. The amide group has a rigid flat structure. The lone pair of its nitrogen atom is able to interact with the π electrons of the carbonyl group.
Some of the biological functions of proteins:
Proteins are often referred to as globular and fibrous proteins according to their conformation. Globular proteins are usually soluble in water, whilst fibrous proteins are usually insoluble. The complex nature of their structures has resulted in the use of a sub-classification, sometimes referred to as the order of protein structures. This classification divides the structure into into primary, secondary, tertiary and quaternary orders of structures.
Carbohydrates
Carbohydrates, or sugars as they are commonly known, are classified as monosaccharides, oligosaccharides and polysaccharides. Monosaccharides are either polyhydroxyaldehydes (aldoses) or polyhydroxyketones (ketoses), which are not converted to any simpler polyhydroxyaldehydes and polyhydroxyketones respectively under aqueous hydrolysis conditions. Carbohydrates also include compounds such as glucosamine, whose structures contain amino groups as well as hydroxy groups. These compounds are known as amino sugars. However, not all polyhydroxyaldehydes and ketones are classified as carbohydrates.
Monosaccharides are classified according to the total number of carbon atoms in their structure. For example, an aldohexose is a monosaccharide that contains a total of six carbon atoms including that of the aldehyde in its structure. Similarly, a ketopentose has five carbons in its structure including the one in the keto group.
Oligosaccharides are carbohydrates that yield from two to about nine monosaccharide molecules when one molecule of the oligosaccharide is hydrolysed. Small oligosaccharides are often classified according to the number of monosaccharide residues contained in their structures.
All monosaccharides have a number of stereogenic centres. The configurations of these centres may be indicated by the use of the R/S nomenclature system. However, the historic system where the configurations of all the chiral centres are
indicated by the stem name of the monosaccharide is generally preferred.
In addition, monosaccharides are also classified as D or L according to the configuration of their pentultimate CHOH group. In the D form this hydroxy group projects on the right of the carbon chain towards the observer whilst in the L form it projects on the left of the carbon chain towards the observer when the molecule is viewed with the unsaturated group at the top.
Polysaccharides (glycans) are carbohydrates whose structures consist of monosaccharide residues joined together by oxygen glycosidic linkages. The links between between monosaccharide residues of a polysaccharide molecule are usually referred to in terms of the type of the numbers of the carbon atoms forming the link and the stereochemistry of the anomeric position.
Lipids
The term lipid is the collective name given to a wide variety of classes of naturally occurring compounds isolated from plant and animal material by extraction with nonpolar solvents. However, not all classes of compound obtained by extraction with nonpolar solvents are classified as lipids.
Fatty acid the most abundant group of compounds that are classified as lipids. They occur as isolated molecules and are more commonly found as residues in other lipid structures.
Fatty acids that are commonly found in lipid:
Acylglycerols are the mono-, di- and tri-esters of glycerol and fatty acids. The fatty acid residues of di- and tri-esters may or may not be the same. Tri-esters are the most common naturally occuring acylglycerols. Complex mixtures of acylglycerols are the major components of naturally occuring fats and oils. Triacylglycerols are the predominant energy store in animals and are mainly located in adipose tissue.
Steroids are compounds based on fused multi-ring carbon skeletons, each ring being referred to by a letter. The rings may be saturated or unsaturated and in some compounds ring A is a benzene ring. Six membered saturated rings usually have a chair conformation whilst the five membered saturated rings have an envelope configuration.
For steroids with saturated A and B rings with chair conformations the substituents at the A/B ring junction can be trans or cis but those of the B/C and C/D ring junction are usually trans.
Phospholipids are essentially disubstituted phosphates. They may be initially classified as phosphatidyl compounds, plasmalogens, ether phospholipids and sphingomyelins depending on the nature of the R1 group attached to the phosphate residue.
Glycolipids are glycosides with a sphingosine derivative (ceramide) acting as the aglycone. They are subdivided according to the nature of the carbohydrate residue.
Nucleic acids
The nucleic acids are the compounds that are responsible for the storage and transmission of the genetic information that controls the growth, function and reproduction of all types of cell.
They are classified into two general types: the deoxyribonucleic acids (DNA), whose structures contains the sugar residue b-D-deoxyribose, and the ribonucleic acids (RNA), whose structures contain the sugar residue b-D-ribose. Both types of nucleic acid consist of long polymer chains based on a repeating unit known as a nucleotide.
Each nucleotide consists of a purine or pyrimidine base bonded to the 1’ carbon atom of a sugar residue by a b-N-glycosidic link. These sugar–base units, which are known as nucleosides are linked, through the 3’ and 5’ carbons of their sugar residues, by phosphate units to form the nucleic acid polymer chain.
A schematic representation of the replication of DNA:
DNA molecules are able to reproduce an exact replica of themselves. The process is known as replication and occurs when cell division is imminent. It is believed to start with the unwinding of the double helix starting at either the end or more usually in a central section, the separated strands acting as templates for the formation of a new daughter strand.
Genes and Human Genome
Each species has its own internal and external characteristics, which are determined by the information stored and supplied by the DNA in the nuclei of its cells. The information is carried in the form of a code based on the consecutive sequences of bases found in sections of the DNA structure.
This code controls the production of the peptides and proteins required by the body. The sequence of bases that act as the code for the production of one specific peptide or protein molecule is known as a gene.
Genes can normally contain from several hundred to two thousand bases. In simple organisms, such as bacteria, genetic information is usually stored in a continuous sequence of DNA bases.
However, in higher organisms the bases forming a particular gene may occur in a number of separate sections known as exons separated by sections of DNA that do not appear to be a code for any process. These noncoding sections are referred to as introns. A number of medical conditions have been attributed to either the absence of a gene or the presence of a degenerate or faulty gene in which one or more of the bases in the sequence have been changed.
The complete set of genes that contain all the hereditary information of a particular species is called a genome.
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