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The use of biochemistry in taxonomic studies. Living organisms produce many types of natural products in varying amounts, and quite often the biosynthetic pathways responsible for these compounds also differ from one taxonomic group to another. The distribution of these compounds and their biosynthetic pathways correspond well with existing taxonomic arrangements based on more traditional criteria such as morphology. In some cases, chemical data have contradicted existing hypotheses, which necessitates a reexamination of the problem or, more positively, chemical data have provided decisive information in situations where other forms of data are insufficiently discriminatory. See Animal systematics
Modern chemotaxonomists often divide natural products into two major classes: (1) micromolecules, that is, those compounds with a molecular weight of 1000 or less, such as alkaloids, terpenoids, amino acids, fatty acids, flavonoid pigments and other phenolic compounds, mustard oils, and simple carbohydrates; and (2) macromolecules, that is, those compounds (often polymers) with a molecular weight over 1000, including complex polysaccharides, proteins, and the basis of life itself, deoxyribonucleic acid (DNA).
A crude extract of a plant can be separated into its individual components, especially in the case of micromolecules, by using one or more techniques of chromatography, including paper, thin-layer, gas, or high-pressure liquid chromatography. The resulting chromatogram provides a visual display or “fingerprint” characteristic of a plant species for the particular class of compounds under study.
The individual, separated spots can be further purified and then subjected to one or more types of spectroscopy, such as ultraviolet, infrared, or nuclear magnetic resonance or mass spectroscopy (or both), which may provide information about the structure of the compound. Thus, for taxonomic purposes, both visual patterns and structural knowledge of the compounds can be compared from species to species. See Spectroscopy
Because of their large, polymeric, and often crystalline nature, macromolecules (for example, proteins, carbohydrates, DNA) can be subjected to x-ray crystallography, which gives some idea of their three-dimensional structure. These large molecules can then be broken down into smaller individual components and analyzed by using techniques employed for micromolecules. In fact, the specific amino acid sequence of portions or all of a cellular respiratory enzyme, cytochrome c, has been elucidated and used successfully for chemotaxonomic comparisons in plants and especially animals.
Cyctochrome c is a small protein or polypeptide chain consisting of approximately 103–112 amino acids, depending on the animal or plant under study. About 35 of the amino acids do not vary in type or position within the chain, and are probably necessary to maintain the structure and function of the enzyme. Several other amino acid positions vary occasionally, and always with the same amino acid substitution at a particular position. Among the remaining 50 positions scattered throughout the chain, considerable substitution occurs, the number of such differences between organisms indicating how closely they are related to one another. When such substitutional patterns were subjected to computer analysis, an evolutionary tree was obtained showing the degree of relatedness among the 36 plants and animals examined. This evolutionary tree is remarkably similar to evolutionary trees or phylogenies constructed on the basis of the actual fossil record for these organisms. Thus, the internal biochemistry of living organisms reflects a measure of the evolutionary changes which have occurred over time in these plants and animals. Since each amino acid in a protein is the ultimate product of a specific portion of the DNA code, the substitutional differences in this and other proteins in various organisms also reflect a change in the nucleotide sequences of DNA itself. See Genetic code, Phylogeny
In the case of proteins, it is often not necessary to know the specific amino acid sequence of a protein, but, rather, to observe how many different proteins, or forms of a single protein, are present in different plant or animal species. The technique of electrophoresis is used to obtain a pattern of protein bands of spots much like the chemical fingerprint of micromolecules. Because each amino acid in a protein carries a positive, negative, or neutral ionic charge, the total sum of charges of the amino acids constituting the protein will give the whole protein a net positive, negative, or neutral charge.
By using other techniques of molecular biology, such as DNA hybridization and genetic cloning, the specific gene function of individual fragments may be identified. Their nucleotide sequences can be determined and then compared for different taxa. Such data may prove useful at several different taxonomic levels. See Genetic engineering
While the organellar DNA does not contain the number of genetic messages of the organism that nuclear DNA does, and its transmission from parent to offspring may vary somewhat depending on the organism, the convenient size of organellar DNA and its potential for direct examination of the genetic code suggest that it is a potent macromolecular approach to chemosystematics. See Genetic code