Subcellular Systems - Molecular Theory of the Living Cell - page 371

electronic rearrangements entailed by chemical reactions by a factor of 10 3 -10 6 (see
data in Ishii and Yanagida 2000, 2007; Xie and Lu 1999; Xie 2001). Therefore,
Rules (1), (2), and (3) presented above appear to provide a sound theoretical
framework for grounding the newly emerging single-molecule stochastic mechanics
(SMSM).

11.4.4 Biopolymers as Molecular Machines: Three Classes
of Molecular Machines and Three Classes of Their
Mechanisms of Action

All biopolymers (proteins, RNA, and DNA) have two properties in common:
(a) sequence information and (b) sequence-preserving mechanical deformability
(also called “conformational changes”), which enables biopolymers to store
mechanical energy as conformational strains. These properties were first clearly
recognized in enzymes and were postulated to play essential roles in the molecular
mechanisms underlying enzymic catalysis (Lumry 1974; Ji 1974a, b, 1991, 2000,
2012) as embodied in the concept of the conformon , the conformational strains
storing mechanical energy and genetic information to drive all goal-directed
molecular motions in living cells (see Chap. 8 ) . The main objective of this section
is to propose that
The principles and mechanisms of molecular machines discovered in proteins are univer-
sally applicable to all biopolymers, including RNA and DNA to varying degrees. (11.54)

We may refer to Statement 11.54 as the Principle of the Universality of Molecular
Machines (PUMM) and represent its content

in a tabular form as shown in

Table 11.15 .
Molecular machines can be divided into passive and active machines depending on
whether their outputs approach to or move away from equilibria, respectively.
Examples of the former include voltage- and ligand-gated ion channels and those of
the latter include active transporters such as the Na + /K + ATPase, H + pumps and Ca ++
pumps. The active machines in turn divide into two classes - primary active machines
and secondary active machines - depending on whether the form of the free energy
driving the machine is chemical (e.g., Na + /K + ATPase) or nonchemical, i.e., osmotic
(e.g., Na + /Ca ++ antiporter) or mechanical (e.g., DNA supercoil-driven regulation of
gene expression; see Sect. 8.3 ), respectively. Thus these dual dichotomous divisions
lead to three distinct types of molecular machines (a) primary active (or Type I)
machines, (b) secondary active (or Type II) machines, and (c) passive (Type III)
machines and each type is divided into three classes based on molecular types, i.e.,
proteins, RNAs and DNAs, on the one hand, and based on whether the processes
involved are Victoria or scalar, thus resulting in a total of 18 classes of molecular
machines as summarized in Table 11.15 .The9 2 matrix constituting the content of

Table 11.15 maybeviewedasthe periodic table of molecular machines (PTMM),
and, as was the case with its chemical counterpart, many cells or blocks are left vacant