Biology Reference
In-Depth Information
(1) Primary AMM
(PAMM)
Active Molecular Machines
(AMM)
(2) Secondary AMM
(SAMM)
Molecular Machines
(3) Passive Molecular Machines
(PMM)
Fig. 12.23 Three kinds of molecular machines.
Active molecular machines
(e.g., ATP-dependent
ion pumps) are autonomous in that they can generate mechanical forces directly from exergonic
chemical reactions that they catalyze.
Passive molecular machines
(e.g., passive ion channels)
cannot perform any active processes such as ion movements against their concentration gradients.
Active molecular machines divide into two groups - the
primary
and the
secondary.
The
primary
active molecular machines
(PAMM) can generate mechanical forces or conformons directly from
the chemical reactions catalyzed by them (e.g., myosin). The
secondary active machines
(e.g., Ca
+
+
-ion driven Na
+
-ion channel, DNA supercoils) cannot generate mechanical forces or conformons
from any chemical reactions but depend on the energy or conformon transfer from primary active
molecular machines
12.12 The Isomorphism Between Blackbody Radiation
and Whole-Cell Metabolism: The Universal Law
of Thermal Excitations (ULTE)
The genotypic similarity vs. phenotypic distance (GSvsPD) plots such as shown in
Fig.
12.17
were useful in gauging the overall behaviors of the kinetic differences
between all possible RNA pairs within a metabolic pathway but did not reveal any
clear patterns of distribution of the points within the main body of the plots.
However, when the data points in a GSvsPD plot are graphed in the form of what
is called the phenotypic distance vs. frequency (PDvsF) plot by displaying the
number of points found within an arbitrary interval (or a bin) of the phenotypic
distance against the phenotypic distance class, unexpected patterns or regularities in
frequency distribution emerged as shown in Fig.
12.24
. This contrasts with the
seemingly random distributions found in the corresponding GSvsPD plots shown in
the bottom two panels in Fig.
12.21
. The following observations can be made:
1. The PDvsF plots are energy-dependent. When budding yeast cells undergo a state
transition from the energy-poor early phase to the energy-rich late phase, the
mean and the variance of the PDvsF plot of the oxphos pathway remain unchanged
and increase, respectively (see the table in the bottom panel of Fig.
12.24
).
In contrast, the mean and the variance of the glycolytic pathway both decreased
during the same cell-state transition. These changes are most likely the results of
the metabolic transitions from the respiratory to the glycolytic mode induced by the
glucose-galactose shift (Ronne 1995; Winderickx et al. 2002).
2. A decrease in the variance of a pathway-specific PDvsF plot indicates a more
coherent behaviors of RNA trajectories in the yeast cell secondary to the activation
