Biosynthesis is a phenomenon wherein chemical compounds are produced from simpler reagents. Biosynthesis, unlike chemosynthesis, takes place within living organisms and is generally catalyzed by enzymes. The process is a vital part of metabolism.
Secondary metabolism (also called special metabolism) is a term for pathways and small molecule products of metabolism that are not absolutely required for the survival of the organism. Examples of the products include antibiotics and pigments. To distinguish non-secondary (“ordinary”) metabolism, the term basic metabolism is sometimes used. Secondary metabolites are produced by microbes, plants, fungi and animals, but not by all of them.
In biochemistry, a metabolic pathway is a series of chemical reactions occurring within a cell. In each pathway, a principal chemical is modified by chemical reactions. Enzymes catalyze these reactions, and often require dietary minerals, vitamins, and other cofactors in order to function properly. Because of the many chemicals that may be involved, pathways can be quite elaborate. In addition, many pathways can exist within a cell. This collection of pathways is called themetabolic network. Pathways are important to the maintenance of homeostasis within an organism.
The biosynthesis of secondary metabolites Second Edition R.B.Herbert, London; New York: Chapman and Hall, 
Secondary-metabolite biosynthesis and metabolism Richard J. Petroski, Susan P. McCormick, American Chemical Society
Possibility of Bacterial Recruitment of Plant Genes Associated with the Biosynthesis of Secondary Metabolites Helge Björn Bode and Rolf Müller
Secondary Metabolism Second Edition J. Mann. Oxford University Press, 
|KEGG biosynthetic pathways|
|The Secondary Metabolism of Plants: Secondary Defence Compounds|
|Major metabolic pathways|