Biology Reference
In-Depth Information
Table 12.1 A summary of the kinetics of the TL (transcript level) and TR (transcription rate)
depicted in Fig.
12.2a
, b. The upward and downward arrows indicate an increase and a decrease,
respectively
Time, min
0-5
5-120
120-360
360-450
450-850
Phase (or time period)
I
II
III
IV
V
Transcript level (
TL
)
# #
#
"
Glycolysis
No change
Oxidative
phosphorylation
# "
"
"
#
Transcription rate (
TR
) Glycolysis
" #
#
"
"
Oxidative
phosphorylation
" #
#
"
"
Output
Input
9
10
Gradients
5
6
4
Proteins
Amino
Acids
3
7
2
Ribo-
nucleotides
RNA
1
8
Genes
Fig. 12.4 A simplified version of the Bhopalator model of the cell (see Fig.
2.11
)
. Gradients in this
figure can be equated with “Dissipative Structure of Prigogine” in the Bhopalator or Intracellular
Dissipative Structures (IDSs) (Ji 1985, 2002). It is important to note that what DNA arrays
commonly measure is not the
rates
of transcription or gene expression (Step 1), as is widely
believed, but the intracellular
levels
of RNA molecules (the balance between Steps 1 and 2) at any
given time. In other words, the latter is determined by both the rate of synthesis (Step 1) and the rate
of transcript degradation (Step 2). Ignoring this simple fact has led to erroneous interpretations of
DNA microarray data since the beginning of the DNA microarray era in the mid-1990s
(see Sect.
12.6
) (Ji et al. 2009a)
The qualitative features of the temporal behaviors of TL and TR displayed
in Fig.
12.2a
, b are summarized in Table
12.1
. In order to understand the molecular
mechanisms underlying these dynamic behaviors of TL and TR, it is necessary to
have a simplified model of the cell as shown in Fig.
12.4
. As indicated in the first two
rows in Table
12.1
, the total observational period of 850 min can be divided into five
phases, labeled I-V. During Phase I, the transcript levels of both glycolytic and
