The Conformon - Molecular Theory of the Living Cell - page 225

Chapter 8
The Conformon
Cells are examples of self-organizing chemical reaction-diffusion systems that
have evolved to perform (or been selected because of their ability to perform)
myriads of goal-directed ( purposive or teleonomic ) motions in space and time. The
goal-directed molecular motions inside the living cell are carried out by
biopolymers acting as molecular machines Albert (1998) Ebright, R. H. and
Strick, and each molecular machine is postulated to be driven by conformons.
Conformons, sequence-specific mechanical strains of biopolymers, can be
generated from the binding energy of ligands as in the Circe effect of Jencks
(1975) or from the free energy of chemical reactions as in stress-induced duplex
destabilizations (SIDDSs) in supercoiled DNA described by Benham (1992, 1996a,
b; Benham and Bi 2004). The living cell can be represented as a system of
molecular machines (e.g., myosin, kinesin, dynein, dynamin, RNA polymerase,
DNA polymerase, topoisomerases, and ion pumps) that are organized in space and
time in various combinations in order to carry out cell functions demanded by a
given environmental condition.
Since the necessary and sufficient conditions for all self-organizations in the
Universe are postulated to be the combination of free energy and control informa-
tion referred to as gnergy (see Fig. 4.8 ) (Ji 1991) (Sect. 2.3.2 ) , the discrete units of
which being referred to as gnergons , cells also must be driven by gnergons . Two
classes of gnergons have been identified inside the cell so far that appear necessary
and sufficient to account for cell functions - (1) conformons (packets of conforma-
tional energy generated from substrate binding and chemical reactions and confined
within biopolymers) and (2) intracellular dissipative structures (IDSs), that is, the
gradients of translationally diffusible chemicals such as glucose, pyruvate, ions,
ATP, and RNA that reside outside biopolymers (Chap. 9 ). Using the piano as a
metaphor, conformons can be compared to the packets of vibrational energies (or
phonons ) of strings and IDSs to the musical sounds generated by vibrating strings.
Using the voice as another metaphor, conformons are akin to the vibrations of
the vocal cord and IDSs to voice produced by vibrating vocal cord. Just as the
vibrational motions of piano strings are responsible for generating sounds as
the inevitable consequence of the laws of physics, so the oscillatory motions of