Biology Reference
In-Depth Information
The possible mechanism employed by the cell to accomplish the micro-meso
coupling on the mass scale is suggested by the molecular tactics used by the cell to
control its DNA molecule during cell division, namely, the chunk-and-control
mechanism discussed in Sect. 2.4.2 . The figure showing the chunking of DNA
double helix into a chromosome is reproduced from Fig. 2.9 on the right-hand side
of Fig. 11.14 . As indicated in Sect. 2.4.2 , the chunking operation not only
compactifies DNA by a factor of 10 9 but also constrains the motional degrees of
freedom of DNA components such as atoms, nucleotides, and DNA segments. In
addition, since the frequency of an oscillator is inversely proportional to the square
root of its reduced mass ( http://en.wikipedia.org/wiki/Molecular_vibration ), it is
here postulated that the chunking operation (which increases mass) applied to
biopolymers can lead to slowing down of their global oscillatory motions.
For convenience, this idea will be referred to as the principle of “slowing down
oscillation by increasing mass” (SDOBIM). Hence, the principle of SDOBIM
defined here can provide the theoretical foundation for the principle of “chunk-
and-control” (C&C) (Sect. 2.4.2 ) , and these two principles may be viewed as the
two sides of the same coin. As will be discussed in Sect. 11.3 , the principle of
SDOBIM appears to apply to single-molecule enzyme mechanics, i.e., to the low-
frequency oscillations of cholesterol oxidase measured with a single-molecule
manipulation technique (Lu et al. 1998).
It is interesting to note that the chunk-and-control operation depicted in
Fig. 11.14 involves a single molecule consisting of a set of monomeric units
covalently linked in a linear chain. It is postulated here that the chunk-and-control
operation can be applied to a set of molecules that are not covalently linked to one
another but nevertheless interact through noncovalent bonds such as electrostatic
bond, hydrophobic bond, and the van der Waals force. Thus it may be necessary to
distinguish between two kinds of chunk-and-control operations: (a) the covalent-
chunk-and-control (CC&C) operation and (b) the non-covalent-chunk-and-control
(NC&C) operation. The DNA packaging shown in Fig. 11.14 embodies both CC&C
(e.g., covalent linking of thousands of structural genes and regulatory regions into a
chromatin) and NC&C (e.g., beads-on-a-string to form a chromatin).
11.3 Single-Molecule Enzymology
Single-molecule measurements can provide mechanistic information on enzymic
catalysis that is not available through conventional ensemble-averaged enzyme
kinetic studies (Xie 2001; Ishii and Yanagida 2007; Deniz et al. 2008). A good
example of single-molecule enzyme experiments is provided by Lu et al. (1998)
who monitored the fluorescence emission from a single molecule of the flavin
adenine dinucleotide (FAD) bound to the active site of cholesterol oxidase (COx)
as it went through catalytic cycles (Figs. 11.15 , 11.17 ). The principle underlying the
phenomenon of fluorescence emission is explained in Fig. 11.16 .
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