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14

The Nature of Living Things

such as in the cells of the immune system; cf. Sect. 14.6). Typically, methylation

of the DNA determines which genes are expressed; in the germ cell, only “master

control genes” are unmethylated; these control the demethylases, which progressively

allow other genes to be expressed. As a rule, this development takes place under

much more strongly constrained environmental conditions than those that the fully

developed (adult) organism might expect to encounter. Imprinted genes are those

whose expression is determined by their parental origin, typically according to the

genes’ methylation states (see Sect. 14.8.4).

14.4.2

The Structures of Genome and Genes

Definition. We may provisionally define gene as a stretch of DNA that codes for (i.e.,

is translated into—see Sect. 14.8) a protein. Due to ever more detailed molecular

knowledge, it has become difficult to define “gene” unambiguously. Formerly, the

term “cistron” was used to denote the genetic unit of function corresponding to

one polypeptide chain; the discovery of introns (see below) signified the end of the

“one gene, one enzyme” idea; furthermore, operons group together several proteins

with a common function—are they then to be regarded as a single gene? The genon

concept (see below) may provide a way of reconciling the classical view of a gene as

a function and the molecular biological view of the gene as a coding sequence (with

the ambiguity of whether to include sequences involved in regulating expression).

Definition. The genon has been introduced by Scherrer and Jost (2007) in an attempt

to delineate an object that can be defined unambiguously. The genon is defined as

the coding sequence (which can then revert to being called “gene”, akin to the sense

of cistron, but better (less ambiguously) expressed in terms of the mRNA that is

translated into a protein) together with the additional information that is needed to

fully express the coding sequence. The genon is therefore more akin to a program

that results in a functionally active gene product. The coding sequence together

with its promoter is called the protogenon, and the primary transcript is called the

pregenon. These are comprised within the cisgenon, together with RNA and proteins

necessary for expression. Once the protein is produced, we move into the domain of

the transgenon, which finally denotes the working protein delivered at a particular

time to a particular place in the cytoplasm. Doubtlessly, this concept will be further

refined and its operational implications more fully explored.

Definition. The genome is defined as the entire set of genes in the cell. Intergenomic

sequences and introns (a term suggested by Walter Gilbert in 1978, signifying intra-

genic sequences) were not known when the word was coined. Therefore, it is usually

taken to mean all inheritable polymerized nucleic acids, regardless of their coding

or other function.

The most basic genome parameter is the number of bases (base pairs, since most

genetic DNA is double-stranded). Sometimes, the molecular weight of the DNA is

given (the average molecular weight of the four base pairs is 660). Table 14.2 gives

the sizes of the genomes of some representative organisms.