Biology Reference
In-Depth Information
1.
DNA level.
In Sect.
2.3.6
, I have presented detailed analysis of the structure
and function of the DNAmolecule, leading to the conclusion that DNA embodies
three kinds of complementarities - (a) the
Watson-Crick base pair complemen-
tarity
, (b) the
information-energy complementarity
, and (c) the
kinematics-
dynamics complementarity
which includes the
wave-particle complementarity
(Sect.
2.3.5
) (Murdoch 1987). Of these three kinds of complementarities, the
information-energy complementarity and kinematics-dynamics complementar-
ity may be viewed as belonging to the same family of what I often call the
global-local or (forest-tree) complementarity
which may be considered as the
generalization of the wave-particle complementarity, wave being global and
particle being local.
2.
Catalysis Level.
Single-molecule enzymic activity data (i.e., waiting time distri-
bution) of cholesterol oxidase measured by Lu et al. (1998) fit the equation,
y
a(Ax + B)
5
/(exp (b/(Ax + B))
1), where a, b, A and B are constants
equation discovered by M. Planck in 1900 when x
¼
the
spectral energy density (i.e., the intensity of radiation emitted or absorbed at
wavelength
l
by the blackbody wall when heated to T K), a
¼
wavelength
l
,y
¼
hc/kT
(where h is the Planck constant, c is the speed of light, and k is the Boltzmann
constant), A
¼
8
p
hc, b
¼
0. This unexpected finding strongly indicates that
enzyme molecules exhibit both particle (e.g., their
nucleotide sequences
) and
wave properties (e.g., the electromagnetic waves generated by the
vibrational
motions
of covalent bonds within proteins) as symbolized by the first triangle
appearing in Table
2.13
.
It appears possible that the enzymic activity of a protein
is the result of the electronic transitions (or quantum jumps) triggered by the
coincidence of the phase angles of a set of vibrating bonds within an
enzyme-substrate complex.
3.
Control Level.
The Planck radiation law-like equation described above also fit
the microarray data measured in budding yeast undergoing glucose-galactose
shift (Ji and So 2009d). Garcia-Martinez et al. (2004) measured the genome-
wide RNA levels of budding yeast at six time points (0, 5, 120, 360, 450, and
850 min after the nutritional shift) which showed pathway-specific trajectories
(see Fig.
12.1
). It is well known that the RNA levels inside the cell are
determined by the balance between two opposing processes, i.e.,
transcription
and
transcript degradation
(Ji et al. 2009a) (see Steps 4 and 5 in Fig. 12.22, Sect.
12.11
). When these RNA level data are mapped onto a six-dimensional mathe-
matical space (called the “concentration space”), each RNA trajectory (also
called an “RNA expression profile”) is represented as a single point and the
whole budding yeast genome appears as a cluster of approximately 6,000 points.
There are about 200 metabolic pathways in budding yeast, and each one of these
pathways occupies a more or less distinct region in the 6-D concentration space.
If a metabolic pathway contains n genes, n being typically 10-50, it is possible to
calculate the distances between all possible RNA pairs belonging to a given
metabolic pathway as n(n
¼
1, and B
¼
1)/2. When these distances are “binned” (i.e.,
grouped into different “bins” based on the different classes of distance values,
