Biology Reference
In-Depth Information
(Sect. 8.4 ). Some of the key ideas generated from the conformon theory are
described below:
1. The ability for cells to self-replicate is encoded in a set of genes numbering in the
hundreds, if not thousands. It should be recalled that the human cell contains
approximately 25,000 structural genes constituting only less than 3% of the total
DNA mass. The timing of the expression of these genes are controlled by
regulatory genes postulated to reside in “noncoding” regions of DNA that
constitute more than 90% of the DNA mass in the human genome (Ji 1999b,
2002b).
2. The cell can be viewed as a “supramolecular machine” that is constructed out of
a set of n molecular machines, mostly enzymes, but including DNA and RNA
(where n
10 6 -10 9 ), each having a diameter about 10 5 times as large as the
diameter of atoms. Interestingly, the diameter of the cell itself is about 10 5 times
as small as the diameter of the human body, suggesting that the cell may possess
the right physical size to mediate the world of atoms and that of the human body.
3. For the cell to be able to self-replicate, it must (1) utilize the free energy
provided by chemical reactions which do not proceed inside the cell spontane-
ously without catalysis performed by molecular machines (also called enzymes)
and (2) control the utilization of free energy in accordance with the genetic
information stored in DNA and the information received from its environment.
4. Molecular machines are capable of carrying out both the utilization of the free
energy generated from chemical reactions (called “rate-dependent dynamics” by
Pattee) and the control of free energy utilization based on genetic information
(called “rate-independent genetic symbols” by Pattee), ultimately because
¼
(a) Biopolymers possess the right physical sizes/dimensions to be thermally
deformed, thereby transiently storing thermally derived kinetic and potential
energies in the form of conformational strains, called “virtual conformons”
(Ji 2000) or “conformational substates” (Frauenfelder 1987).
(b) The genetic information encoded in the internal structures of biopolymers
provide the necessary constraints to synchronize (or control the timing of)
the entrapping of virtual conformons at sequence-specific loci and the
catalysis triggered by the virtual conformons, leading to the dissipation of
the requisite chemical-free energy into heat, thus paying back the thermal
energy borrowed from the environment (in the form of virtual conformons)
quickly enough to avoid violating the second law (Ji 1979, 2000) (Sect.
2.1.2 ) .
The combination of the synchronized partial processes (a) and (b) is necessary
and sufficient to convert virtual conformons into real conformons. As long as this
conversion is completed within the cycling time
of the molecular machine, no
laws of thermodynamics is violated (Sect. 2.1.2 ) (McClare 1971; Ji 2004a). It
should be pointed out that realistic molecular mechanisms for synchronizing
processes (a) and (b) were proposed almost three decades ago based on the
“generalized Franck-Condon principle” (Sect. 2.2.3 ) (Ji 1974b, 2000). The critical
t
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