Subcellular Systems - Molecular Theory of the Living Cell - page 300

Dissipative Structures (Glycolysis)

250

YPL075W
YNL199C
YMR205C
YGL256W
YGL253W
YJL052W
YBR221C
YNL071W
YER178W
YMR083W
YDR081C
YGR193C
YCL040W

200

150

100

50

0

-200 0 200 400 600 800 1000

Time (Minutes)

Fig. 11.6 The time-dependent RNA levels (i.e., RNA trajectories, ribbons or RNA waves) of the
glycolytic genes of budding yeast measured with DNA arrays after switching glucose to galactose
at t ¼ 0 (Garcia-Martinez et al. 2004). RNA levels were measured in triplicates at six time points;
t ¼ 0, 5, 120, 360, 450, and 850 min, and the data points are the averages over the triplicates with
coefficients of variations less than 50%. Of the 13 ribbons shown in this figure, the ribbon labeled
YCL040W ( light blue ) exhibits an unusual behavior of increasing (rather than decreasing) its
concentration between 5 and 120 min. This is most likely because the transcription of YCL040W
gene is suppressed by glucose under normal physiological condition and the removal of glucose at
t ¼ 0 leads to glucose derepression of the gene (DeRisi et al. 1997; Johnston 1999; Ashe et al.
2000; Jona et al 2000; Kuhn et al. 2001)

Genes are functions encoded in static structures (e.g., nucleotide sequences) which are
activated into processes (e.g., transcription) by molecular machines that have been selected
by evolution for their ability to fulfill the needs of the cell under a given environmental
condition. (11.1)
For convenience, Statement 11.1 will be referred to as the triadic model of the
gene (TMG) which can be logically derived from combining the concepts and
theories embodied in Figs. 3.4 , 6.10 , and 11.3 .
The concepts of genotype and phenotype were introduced by Johannsen in 1903
(see Row 4, Table 11.1 ). Johannsen was motivated to coin these terms to account
for his finding that genetically identical common beans revealed normally
distributed seed sizes ( http://en.wikipedia.org/wiki/Wilhelm_Johannsen ).
Genotypes are heritable information stored in genes, while phenotypes are the
observable manifestations of genes, on either macroscopic (e.g., morphology,
behavior, biochemical properties of blood) or microscopic (e.g., amino acid
sequences of proteins, RNA trajectories in cells) scale. Referring to Fig. 11.5 ,we
can identify genotypes with the Watson-Crick form of genetic information and
phenotypes with the Prigoginian form.
Phenotypes are commonly associated with stable structures such as the shape of
seeds, height of plants, etc., while dissipatons (of which the Prigoginian form of
genetic information is an example) are associated with unstable, dynamic structures