Biology Reference
In-Depth Information
12.15 Time-Dependent Gibbs Free Energy Landscape
(TGFEL): A Model of Whole-Cell Metabolism
When two RNA trajectories exhibit a linear Pearson correlation coefficient greater
than 0.7 or smaller than
0.7, these trajectories are
positively
or
negatively linearly
correlated, respectively.
The degree of such linear correlations differs from one
metabolic pathway to another, ranging from 39% to 98% (see the bold numbers in
Table
12.12
). The degree of
nonlinear correlation
among RNA pairs was deter-
mined by calculating the percentage of the intra-pathway or inter-pathway RNA
pairs, the Euclidean distances between whose trajectories fit the blackbody radia-
tion-like equation (BRE) (see the numbers in parentheses in Table
12.12
).
To account for these observations based on the molecular mechanisms
postulated to underlie the coupling between transcriptosomes and degradosomes
(see Sect.
12.14
), I have been led to invoke what is here called the
time-dependent
Gibbs free energy landscape
(TGFEL) model of whole-cell metabolism as depicted
in Fig.
12.32
and explained below:
1. Just as the atom is associated with a set of atomic orbitals representing
the energy levels of electrons, the living cell is thought to be associated with
a set of space- and time-dependent
Gibbs free energy levels
of biopolymers
to be called the
time-dependent Gibbs free energy landscape (TGFEL)
of
the cell
.
2. The TGFEL model is formulated in terms of Gibbs free energy (G) and not just
energy (E) as in the “energy landscape” concept frequently employed in
chemistry and biology (see Eq.
2.1
for the difference between E and G),
in order to emphasize the potential role of
entropy
in determining the ground-
state of enzymes. Thus two enzymes, both at their lowed energy levels, can still
be at two different Gibbs free energy levels, if entropy contributions are
different. The five different Gibbs free energy levels of the TD complexes
shown in Figs.
12.30
and
12.31
may all be associated with the same internal
energy levels due to the same environmental temperature but still can exist at
different ground-state Gibbs free energy levels mainly due to different entropy
(or negentropy) contents of the complexes (Ji 1974a).
3. The TGFEL model can be represented as a five-dimensional surface since it
takes five numbers to specify the position of a biopolymer in it - the three
dimensions of the Euclidean space, time, and the Gibbs free energy level of
a biopolymer. In Fig.
12.32
, the three Euclidean dimensions are collapsed
to (or compactified into) one dimension on the
x
-axis, the Gibbs free energy
levels are encoded on the
y
-axis, and the time dimension is represented by
the
z
-axis.
4. TGFEL is composed of valleys and a set of sub-valleys within a valley
(see Valleys 1 and 2, and sub-valleys labeled 1-5 for T and 1
0
-5
0
for D).
The transcriptosomes (T) and degradosomes (D) catalyzing the transcription
and degradation of a set of RNA molecules belonging to a metabolic pathway
