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188 PROCEEDINGS OF THE CALIFORNIA ACADEMY OF SCIENCES
Series 4, Volume 60, No. 10
CHAPTER I
BIOSYNTHESIS AND BIOTRANSFORMATION
Part 1: Biosynthesis
The ability of organisms to synthesize primary metabolites must have originated very early in
the history of life. Indeed, we might go so far as to say that the origin of life and the origin of
biosynthetic capacity are the same basic phenomenon. When a functional unit has arisen that is able
to control and orchestrate a system of chemical reactions that sustain its existence and further its
reproduction, we have what may reasonably be considered an organism. Much earlier, during what
is considered prebiotic evolution, the precursors of such organized systems are supposed to have
taken advantage of materials that were furnished by chemical reactions in the environment. The
transition from the prebiotic to the biotic stage would then have involved the increasing ability to
fabricate and transform a limited number of primary metabolites. Cells as we know them contain
systems of biochemical pathways, such as the Krebs cycle, that make such metabolites available
for the basic activities of the organism. Such activities are facilitated by enzymes, which are catalysts.
Catalysts do not allow an organism to do anything contrary to the laws of nature. Instead they
affect the rate at which reactions occur. In a biosynthetic pathway metabolites are modified step by
step, with each step under enzymatic control.
It has been speculated that the earliest enzymes were RNA molecules. Like DNA, which is the
hereditary material in most organisms, RNA can be replicated within the cell. But unlike DNA,
RNA has also been shown to function as a catalyst or enzyme. According to the “RNA world” theory,
DNA gradually replaced RNA as the hereditary material, and proteins took over most (but not
quite all) of the enzymatic activity. So, at present, the main activity of RNA is that of transforming
amino acids into polymers (including enzymes) using the hereditary material in the DNA as a template.
The evolution of biosynthetic pathways can occur by changes of the genes that control the
structure of the enzymes. A mutation of a gene may alter the enzyme for which it codes such that
it catalyzes another reaction and consequently gives rise to a different product. But that means losing
the original product, which is not necessarily a good thing. New genes may also arise by duplication
of a pre-existing one. Such gene duplication makes an identical enzyme available, which can
then be modified, perhaps catalyzing reactions that did not occur previously. The pathway can
thereby be changed by adding a new step at the end, or by giving rise to two different end products
(Fischbach & Clardy, 2007). The history of the evolution of biosynthetic pathways can be reconstructed
as a series of duplications and subsequent divergent modifications of the molecules and
the genes that code for them. However, that is not the only thing that goes on, and we must avoid
oversimplifying. In addition to genes that code for proteins, there are regulatory genes that affect
what product is produced when, and where, and in what quantity. And the activities of cells and
organs also come into play.
The opportunistic character of evolutionary change in general provides an important basis for
reconstructing evolutionary history. New features arise from the modification of pre-existing ones.
Darwin’s follower Anton Dohrn (1840-1909) created the magnificent marine laboratory at Naples
for the study of evolution among marine organisms. He also propounded what he called the principle
of the succession of functions (Dohrn, 1875; translation in Ghiselin, 1994). According to
Dohrn, new organs arise from earlier ones in an orderly and gradual sequence. A part begins having
an initial main function, then it comes to have both the main function and a minor, additional
one. With the passage of time the new function becomes increasingly important, finally replacing