Biology Reference
In-Depth Information
Table 12.12 The fraction of the RNA pairs showing linear or nonlinear correlations among intra-
pathway and inter-pathway RNA Pairs. Both members of an
intra-pathway RNA pair
belong to one
metabolic pathway, whereas an
inter-pathway RNA pair
involves two pathways, each contributing
one of the two members of a pair. The extent (or fraction) of the linear correlations (numbers in
bold) were determined by counting the RNA pairs whose Pearson correlation coefficients were
greater than 0.7 or less than
0.7, and the fraction of the nonlinear correlations (numbers in italics)
were determined by counting the RNA pairs whose phenotypic distances fit the
blackbody
radiation-like equation
(BRE), Eq.
12.26
. The number of RNA molecules per pathway ranged
from 12 to 50. P1
¼
protein folding
,P2
¼
cytoskeleton
,P3
¼
protein glycosylation
,P4
¼
oxida-
tive phosphorylation
,P5
¼
respiration
,P6
¼
glycolysis
,P7
¼
nuclear protein targeting
,P8
¼
DNA repair
,P9
¼
protein degradation
, P10
¼
meiosis
P1
P2
P3
P4
P5
P6
P7
P8
P9
P10
P1
0.88
0.70
0.99
P2
0.54
(
0.13
)
0.57
P3
0.74
0.99
P4
0.72
0.20
P5
0.44
(
0.17
)
P6
0.47
(
0.91
)
P7
0.98
0.76
P8
0.59
P9
0.609
(
0.43
)
P10
rate behaviors, i.e., dTL/dt classes (denoted as
1, 0, 1, 2, 3, 4, and 5)
(see the interior of the table in Panel c, Fig.
12.30
), that result from the interactions
between T and D, each of which is postulated to exist in one of the five quantum states
(denoted as
4,
3,
2,
1, 0, 1, and 2 in Panel b, Fig.
12.30
). If we identify the value of
dTL/dt during Phase I in Fig.
12.30
with the most rapid decrease, i.e.,
2,
4, the quantum
states of the underlying T and Dwould be predicted to be
2 and +2, respectively (see
the dotted line labeled I in Panel b, Fig.
12.30
). During Phases II and V, TL is not
decreasing as rapidly as during Phase I, so we may infer the quantum states of T and D
during these phases to be
2 and 0 for Phase V as indicated
by the dotted lines in Panel b, Fig.
12.30
. Phase IV is characterized by a relatively rapid
increase in TL and hence the quantum states of T and D may be inferred to be 2 and
2and1forPhaseIIand
2. During Phase III, TL remains more or less unchanged and hence the quantum
states (and the Gibbs free energy levels) of T and D are likely to be the same, leading to
the equality of their rate constants, according to Eq.
12.42
.
The
quantization of the Gibbs free energy levels of enzymes
in cells provides
a possible explanation for the pathway-dependent correlations found among
some of the RNA trajectories in budding yeast during glucose-galactose shift
(see Table
12.12
). This conclusion is based on the following reasoning.
