Biology Reference
In-Depth Information
conclusion was reached by Rufus Lumry in his “The Protein Primer” available
online (Lumry 2009).
If the content of Table
11.9
is true, there may be an interesting historical analogy
between
blackbody radiation
in physics and
enzymic catalysis
in biology as
summarized in Table
11.13
. Just as the blackbody spectrum led Max Plank in
1900 to postulate the existence of
quantized energy packets
(later called “photons”),
so the single-molecule kinetic data of COx suggest that:
(a) There exists a minimal unit of
c
atalytically
e
ffective
c
onformational
s
trains
(CECS) of an enzyme molecule
(b) The minimal unit of CECS is characterized by its mechanical energy and
evolutionarily conserved amino acid residues
encoding genetic information
(Row 5, Table
11.13
)
The CECSs invoked above can be identified with
conformons
since conformons
are defined as the conformational strains localized at sequence-specific sites within
biopolymers carrying both
mechanical energy
and
genetic information
to drive
words, the
blackbody radiation-enzymic catalysis analogy
entails invoking two
complementary factors underlying catalysis” (a) the
conformational energy
stored
in an enzyme (see Fig.
11.28
) and (b) the
catalytic information
(or negentropy Ji
1974a) encoded in the select set of the amino acid residues constituting the active
site of an enzyme which may be similar to the
evolutionarily coevolving amino acid
residues
of enzymes (Poole and Ranganathan 2006), and Socolich et al. (2005).
The former is necessary to account for the deterministic component of Eq.
11.27
,
and the latter is necessary to account for the nondeterministic, stochastic, and
arbitrary component, X(w). Together, these two factors -
conformational energy
and
genetic information
- completely account for the waiting time distribution of
COx measured by Lu et al. (1998).
In conclusion, the
conformon theory of molecular machines
first invoked to
account for the molecular mechanisms underlying the phenomenon of oxidative
phosphorylation in mitochondria (Green and Ji 1972a, b; Ji 1974a, b, 2000) appears
to provide a most comprehensive and mechanistically and evolutionarily realistic
explanation to date for the single-molecule enzymological data on cholesterol
oxidase measured by Lu et al. (1998).
11.4 The Conformon Model of Molecular Machines
The living cell is a system (or “renormalizable” network; see Sect.
2.4
) of molecular
machines that self-organizes to carry out its varied functions using the free energy
supplied by exergonic chemical reactions or light absorption. Molecular machines
playing essential roles in the cell include ordinary enzymes, molecular motors (e.g.,
myosin, kinesins, dyneins), ion pumps and channels, signal transducing proteins,
DNA polymerase, RNA polymerase, and chaperones. Like macroscopic machines