Chemistry - Molecular Theory of the Living Cell - page 76

Table 3.2 The classification of structures into four groups based on the principle of the
kinematics-dynamics complementarity (Sect. 2.3.5 ). Equilibrons dissipate no free energy, that is,
dG/dt ¼ 0, while dissipatons do, that is, dG/dt < 0, where dG is Gibbs free energy change

Equilibrons (E)
Random motions
dG/dt

Dissipatons (D)
Directed motions
dG/dt

Dynamics

Kinematics
Local (L) motions

¼ 0 < 0

LE (Local Equilibrons) (e.g.,
thermal fluctuations of bonds )

LD (Local Dissipatons)
(e.g., DNA supercoils,
molecular motors )

Global (G) motions GE (Global Equilibrons) (e.g.,

Brownian motions of molecules )

GD (Global Dissipatons)
(e.g., enzyme complexes,
action potentials )

energy dissipation. Second, thermal motions are divided into local and global
thermal motions, the former being identified with “thermal fluctuations,” essential
for enzymic catalysis (see Sect. 7.1.1 ) (Welch and Kell 1986; Ji 1974a, 1991), and
the latter with “Brownian motions,” which may play an essential role in the regula-
tion of cell metabolism and motility. Another example of local versus global
equilibrons is provided by individual bond vibrations versus domain or segment
motions of an enzyme involving hundreds and thousands of covalent bonds whose
vibrational motions can be coupled into coherent modes.
The cell can be viewed as a dynamic system of molecules (biochemicals,
proteins, nucleic acids, etc.) that are organized in space and time to form local
dissipatons (e.g., enzyme turnovers driven by conformons; Chaps. 7 and 8 ) and
global dissipatons (e.g., cell cycles, cell motility driven by local dissipatons). Since
all organizations in the cell are driven by the free energy supplied by chemical
reactions catalyzed by enzymes, which in turn are driven by conformons, examples
of local dissipatons, it would follow that all global dissiptons of the cell are
ultimately driven by local dissipatons , which may be a case of the local-global
coupling. Local-global couplings are important in biology in general and cell
biology in particular, and are likely controlled by the generalized Franck-Condon
principle or the Principle of Slow and Fast Processes discussed in Sect. 2.2 .

3.1.7 Activities versus Levels (or Concentrations)
of Bioploymers and Biochemicals in the Cell

The molecular entities (or biomolecules) of the cell may exist in two distinct states -
active and inactive . For example, genes are inactive when they are buried deep inside
chromosomes and active only when they are unpacked and brought out onto the
surface of chromatins so that they can interact with transcription factors and
enzymes. Another example would be RNA molecules that are free versus bound to
other molecules to affect their actions. Biomolecules need not be stable structures