Intracellular Dissipative Structures (IDSs) - Molecular Theory of the Living Cell - page 255

Whereas Cones 11, 12, 13, 14, 15, 16, and 17 involve many-to-one renormalizations,
we have to invoke a renormalization that involves a one-to-many transitions as
well (see Cone 4) to represent the fact that p53 proteins participate in numerous
functions (Vogelstein et al. 2000).
Cone18 represents all the DNA regions that affect transcription and replication
by acting either as templates (i.e., as “structural genes”) or as regulatory regions
(i.e., as promoters, enhancers, or silencers). As discussed in Sect. 12.11 , we have
recently obtained the microarray evidence that some structural genes in budding
yeast can co-regulate their own transcript levels in conjunction with regulatory
genes (Ji et al. 2009c). Cone 18 in Fig. 9.2 was not present in my original drawing of
the figure but was later added at the suggestion of one of my undergraduate students
at Rutgers, Julie Bianchini, and hence is referred to as the Bianchini cone .
Cone 19 indicates self-replication. The existence of Cone 19 is supported by the
simple fact that DNA acts as the template for DNA synthesis catalyzed by DNA
polymerase which makes a physical contact with the original DNA. The concept of
Cone 19 is also consistent with the hypothesis that the DNA molecule as a whole
can be viewed as a gene (called the d-gene in Sect. 11.2.4 ). It is important to
note that d-genes carry not only genetic information but also mechanical energy in
the form of SIDDSs (stress-induced duplex destabilizations) (see Sect. 8.3 )or
conformons (Chap. 8 ) , thus enabling d-genes to act as molecular machines to
perform goal-directed molecular motions such as strand separations or chromatin
remodeling, very similar to protein molecular machines (Sect. 7.2.1 ) . Since genes
constitute parts of a DNA molecule, and since genes appear to act as molecular
machines (Ji et al. 2009c), it is probably inevitable that a DNA molecule itself
should act as a molecular machine. Also, since according to the conformon theory,
all molecular machines are driven by conformons (Chap. 8 ) (Ji 2000), the following
general statement may be made:
DNA is a coformon-driven molecular machine. (9.1)
Statement 9.1 will be referred to the “DNA-as- Molecular-Machine (DMM)
Hypothesis.”
There are two types of networks in general - equilibrium and dissipative .
Equilibrium networks are those molecular systems that are at equilibrium, requiring
no dissipation of any free energy, whereas dissipative networks are those molecular
systems whose nodes can interact with one another if and only if requisite free
energy is available and dissipated (as in SOWAWN machines; see Sect. 2.4.4 ) .
Examples of the former would include aggregates of heterogeneous proteins in the
cytosol or protein-DNA complexes constituting chromatins in the nucleus, and those
of the latter include sets of activated proteins catalyzing a metabolic process such as
glycolysis, respiration, or gene expression which are destroyed without continuous
dissipation of free energy through, for example, phosphorylation and dephosphory-
lation reactions catalyzed by kinases and phosphoprotein phosphatases.
There are two types of connections in Fig. 9.2 that link one plane to another - (1)
catalysis where a set of objects in one plane cooperates (or acts as a unit) to catalyze the
coupling between one plane and another (as exemplified byCones 4 and 11 through 17)