Multicellular Systems - Molecular Theory of the Living Cell - page 516

control of production and degradation, and (2) that there exists a hierarchy among
these three processes:

Production > Degradation > Control (15.4)

>

where the symbol, “ A B”, reads as “A must precede B”or“A is a prerequisite

for B”. Scheme (15.4), when applied to Fig. 15.2 , suggests (1) that X must be
produced before it can be degraded, and (2) that the production and degradation
processes of X must be in place before they can be controlled. This is reminiscent of
a similar hierarchical relation that obtains among the three fundamental aspects of
reality that Peirce referred to as Firstness, Secondness, and Thirdness (Sect. 6.2.2 ) .
If the system under consideration is the cell, then the function of the cell is
postulated to depend on the presence of a set X of molecules and ions inside the cell.
If the system under consideration is a subcellular compartment of a developing
embryo such as the peripheral compartment of a syncytial blastoderm, then the
function of such a compartment is thought to depend on the set X of molecules and
ions present in that compartment as a balance between their input into and output
from the compartment. The concentrations or levels of the members of X can be
controlled by regulating their rates of production (or input) and degradation (or
output). The vertical double-headed arrow indicates an identity relation. The
horizontal arrows indicate irreversible processes driven by free energy dissipation.
The numerals 1, 2, and 3 refer to the hierarchical relation shown in Inequality
(15.4): Without 1, no 2; without 2, no 3. The source of the control signals is
postulated to be the cell itself which communicate with its neighbors and environ-
ment as indicated above.
The nature of X in Fig. 15.2 can be any material or physical entities controlled by
the system under consideration, including activated genes, pre-mRNAs, mRNAs,
nc-RNAs (Amaral et al. 2008, Mattick 2003, 2004), microRNAs (Hobert 2008,
Makeyev and Maniatis 2008), small-molecular-weight entities such as glucose,
ATP, P i , NADH, and metal ions. X need not be confined to the cell and can
represent any material entities that play fundamental role in living systems such
as blood level of hormones, glucose, and other metabolites, blood content of an
organ, and the space- and time-dependent number of electrically active neurons in
the brain, etc. In Table 15.2 , the triadic control mechanism is applied to five
different levels of biological organization, listing specific examples of the key
components of the mechanism in a self-explanatory manner.
Enzymes may be viewed as one of the simplest material systems whose
behaviors can be accounted for in terms of the triadic control mechanism depicted
in Fig. 15.2 . Enzymes can exist in at least two conformational states, ground state
and activated state (characterized by the presence of sequence-specific conforma-
tional strains, i.e., conformons ; see Figs. 11.30 and 14.7 ) . The activated state of
an enzyme is produced by substrate binding (Jencks 1975) and/or exergonic
chemical reactions through generalized Franck-Condon mechanisms (see Fig. 8.1
and Sect. 11.4 ). The activated state of an enzyme is caused to relax back to its
ground state when it performs a molecular work, be it catalysis (i.e., lowering the