Whole Cells - Molecular Theory of the Living Cell - page 413

1 2 3 4

5

6

7

Fig. 12.16 A molecular model of the genotype-phenotype coupling based on the concepts
of dissipative structures and conformons, the key elements of the Bhopalator model of the cell
(Ji 1985, 2002b) (see Fig. 2.11 ) . This scheme is consistent with the multilevel representation of the
cell depicted in Fig. 9.2

( transcription , translation , and enzymic catalysis ) are relatively well understood,
but the fourth process connecting OPCPs to cell functions is not yet well known,
because it is difficult to study OPCPs due to the paucity of appropriate experimental
techniques. That OPCPs do occur inside the living cell is now beyond doubt. One of
the first clear demonstrations of OPCPs was published by D. Sawyer et al. in 1985
as already mentioned in Sect. 3.1.2 . Unlike the intracellular calcium ion gradients in
human neutrophils measured by Sawyer et al. (1985), which are chemical concen-
tration gradients in the three-dimensional Euclidean space (requiring x, y, and z
coordinates for specification), the time-dependent intracellular RNA levels such as
those measured by Garcia-Martinez et al. (2004) in budding yeast undergoing
glucose-galactose shift exemplify a chemical concentration gradient in the time
dimension . That is, the intracellular concentrations of RNA molecules can change
with time - rising or falling within minutes to hours, depending on the functions of
RNA molecules involved. What was most significant was that these time or
temporal gradients of RNA levels are associated with activation or inhibition of
select cell functions (e.g., glycolysis and oxidative phosphorylation, see Panel a in
Fig. 12.2 ), thereby linking OPCPs to cell functions. This observation has led to the
formulation of the IDS-Cell Function Identity Hypothesis given in Statement 12.1.
So we have two examples - one involving “spatial gradients” of chemical
concentrations and the other “temporal gradients” - that demonstrate the causal
relation between OPCPs and cell functions. These observations provide the empiri-
cal basis for the postulate that what drives the cell functions are OPCPs. It is
important to keep in mind that OPCPs in Fig. 12.15 cannot exist without continuous
dissipation of free energy and hence are examples of dissipative structures or
dissipatons . Thus, we can replace the operationally defined OPCPs in Fig. 12.15
with the thermodynamics-based concept of “intracellular dissipative structures” or
IDSs (Sect. 3.1 ) as shown in Fig. 12.16 .
Processes 1, 2, and 3 are catalyzed by enzymes and Process 4 is suggested to be
an identity relation (see Statement 12.1 in Sect. 12.5 ). Since functions of enzymes
are postulated to be driven by internal mechanical stresses localized in sequence-
specific sites referred to as conformons (Chap. 8 and Sect. 11.4 ), it can be concluded
that Processes 1-3 and 5-7 are all driven by conformons generated within enzymes
catalyzing exergonic chemical reactions. Thus, it may be concluded that the
Bhopalator model of the cell provides molecularly realistic mechanisms for
effectuating the genotype-phenotype coupling.