Whole Cells - Molecular Theory of the Living Cell - page 431

experiment (see Sect. 11.3 ) is not the heat re-emitted by an enzyme (as in blackbody
radiation) but the consequence of heating, i.e., the catalysis (e.g., the disappearance
of the fluorescence of FAD, the coenzyme of cholesterol oxidase, due to reduction)
proceeding in times shorter than t 0 .
h During whole-cell metabolism two or more metabolic pathways (or SOWAWN
machines) are coupled (e.g., transcription and transcript degradation pathways; see
Fig. 12.22 ) to maintain a certain cell state (e.g., RNA levels) and meet the metabolic
demand of the cell. It is postulated here that thermal (also called Brownian) motions
of biopolymers are essential for the cell to explore and access the right
biopolymeric complexes among a large repertoire of the biopolymeric complexes
available to it. In this view, what is measured in whole-cell metabolic experiments
(e.g., the genome-wide RNA measurements in budding yeast undergoing
glucose-galactose shift) is not the activities of individual enzymes but the balance
of all the activities of the coupled metabolic pathways, i.e., the system properties of
a group of dozens or more enzymes and other biopolymers.
i The discrete units of light, a member of the family of quantum objects
(Plotnitsky 2006) that include all microscopic entities such as electrons, protons,
and neutrons. According to quantum mechanics (Morrison 1990; Plotnitsky 2006),
light can be viewed as streams of particles (i.e., photons) or as waves.
j The discrete units of mechanical energy stored as sequence-specific conforma-
tional strains of biopolymers (see Chap. 8 ) .
k The dynamic and transient systems of biopolymers (e.g., SOWAWN machines;
Sect. 2.4 ) and associated small molecules that are coupled together to perform
elementary metabolic functions inside the cell such as glycolysis, transcription, and
RNA degradation. There are many different kinds of dissipatons just as there are
many different kinds of molecules .
l The fitting of the blackbody radiation data into Planck's radiation law (see
Eq. 11.27 ) established the concept that the physical quantity known as action,
defined as the product of energy and time, is not continuous but quantized, ushering
in the era of quantum revolution in physics beginning in 1900 (Nave 2009). One
consequence of the quantization of action is the establishment of the energy levels
in an atom between which electrons are constrained to undergo transitions. Thus,
quantization of action and the electronic energy levels within an atom are the two
sides of the same coin.
m The idea that the conformational energy of biopolymers plays essential roles in
catalysis (Lumry 1974, 2009), gene expression (Benham 1992) and molecular
motions (Ji 1974b; Astumian 2001) is gaining general acceptance among biologists
(Frauenfelder 1987; Frauenfelder et al. 2001; Ji 2000). But the idea that conforma-
tional energy levels of biopolymers may be quantized just as the electronic energy
levels are in atoms is novel and suggested here (see Sect. 11.3.3 ) for the first time on
the basis of the finding that the single-molecule enzymic data of Lu et al. (1998) fit
the Planck radiation law-like equation, Eq. 11.26 , which, when applied to atoms,
leads to the “quantization” of the electronic energy levels in atoms. The term