Subcellular Systems - Molecular Theory of the Living Cell - page 358

Table 11.13 A suggested historical analogy between blackbody radiation and single-molecule
enzymology. COx ¼ cholesterol oxidase

Blackbody radiation Single-molecule enzymology

1. Data Blackbody spectrum Waiting time distribution of COx

2. Early theory Wien's law Probability distribution function for

waiting times derived on the basis of
the Michaelis-Menten kinetics (Lu et al.
1998; Kurzynski 2006; Qian and Xie
2006; Prakash and Marcus 2007)

Rayleigh-Jeans law

3. Final theory Planck's law Probability distribution function for

waiting times derived from the
blackbody radiation-enzymic catalysis
analogy (Ji 2008b)

4. Improvement Better fit in the low frequency

region of the blackbody
spectrum

Better fit for the “noisy” or “rugged”
portions of the waiting time distribution
by introducing the X(w) factor as a
measure of evolutionary information
carried by catalytic residues

5. New concept Energy quantization (photons) Conformons as carriers of (a) quantized

energy and (b) catalytic information
or catalytic negentropy (Ji 1974a)

distribution for waiting times derived by Lu et al. (1998), Eq. 11.25 , may be
comparable to Wien's law and Rayleigh-Jeans law (Kragh 2000; Nave 2009),
just as that derived on the basis of the analogy between blackbody radiation
and enzymic catalysis, Eq. 11.27 (Ji 2008b), is comparable to Planck's law,
Eq. 11.26 . These and other analogies between blackbody radiation and enzymic
catalysis are summarized in Table 11.13 .

If the blackbody radiation-enzymic catalysis analogy turns out to be true, the
single-molecule waiting time distribution measured by Lu et al. (1998) may be
viewed as the first direct experimental evidence for demonstrating that an enzyme
molecule must absorb heat before it can carry out catalysis, thus establishing the
fundamental role of heat in molecular biology , consistent with the “thermal barrier”
hypothesis of molecular machines (Ji 1991, pp. 29-31) and the Second Law of
Molecular Biology, Statement 11.43. Although biochemists have known for a long
time that raising temperature leads to an increase in catalytic rates (the so-called
Q 10 value of an enzymic reaction being in the 2-4 range), these rates are ensemble
averages that are affected by many physicochemical steps, making it difficult to
pin down the precise catalytic process affected by heat. This difficulty is largely
overcome in single-molecule kinetic experiments where one elementary step (e.g.,
the electron transfer from cholesterol to FAD, Scheme 11.16 ) can be studied.
Unlike in chemical reactions where heat provides all of the energy required to
overcome the activation energy barrier, an enzyme molecule appears to supplement
the heat energy absorbed from its environment with its intrinsic ground-state
potential energy stored in local conformational strains (called static or intrinsic
conformons ; see (6) above) in activating its substrate to form the product. A similar