Biology Reference
In-Depth Information
1. RNA trajectories can be correlated in two ways - (1) linearly and (2) nonlinearly.
The former indicates that, when the concentration of the ith RNA molecule is
increased by a factor of x and that of the jth is increased or decreased also by the
same factor, the ith and jth RNA concentrations are said to exhibit a positive and
a negative linear correlation, respectively. However, when the concentration of
the ith RNA is increased (or decreased) by two different factor, say, x and x
n
,
respectively, where the absolute value of n is greater than or less than 1, we are
dealing with nonlinear correlations.
2. It is evident that the correlated changes in the intracellular concentrations of any
pair of RNAmolecules are impossible if the two enzyme systems, each supporting
its associated RNA trajectory, are not coupled. That is, a linear correlation between
[mRNA]x and [mRNA]y in Fig.
12.27
would be impossible without the functional
coupling between the (TXDX) complex and the (TYDY) complex, where T is
transcriptosome and D is degradosome, and X and Y are the two different RNA
molecules, the correlation between whose trajectories are under consideration
(see Steps 9 in Fig.
12.27
). We can represent this idea symbolically as follows:
T
Y
D
Y
b
!
ð
ð
T
X
D
X
a
þð
T
X
D
X
Þð
T
Y
D
Y
Þ
D
G
(12.38)
c
3. In principle, there are two distinct mechanisms for coupling two enzymes or
enzyme complexes - (1) the
cis-mechanism
whereby two enzyme systems form a
higher-order structure or complex through direct physical binding interactions and
(2) the
trans-mechanism
whereby two enzyme systems are coupled indirectly by
sharing diffusible substrates (e.g., mRNA) or regulators (e.g., ATP, ADP, glucose).
Similar
cis-
and
trans-mechanisms
operate in the control of gene expression
mechanisms. Since no spontaneous interaction can occur without the associated
Gibbs free energy decrease (under the conditions of constant temperature and
pressure), Eq.
12.39
holds, where G is Gibbs free energy and the subscripts indicate
the reactants and the products appearing in Reaction (
12.38
):
D
G
¼
G
c
ð
G
a
þ
G
b
Þ<
0
(12.39)
4. The Gibbs free energy levels of (T
X
D
X
), (T
Y
D
Y
) and (T
X
D
X
)(T
Y
D
Y
) in Reac-
tion (
12.38
) are represented diagrammatically as G
i
,G
j
, and G
ij
in Fig.
12.31
.
It is assumed that the transition state of all these enzyme systems is common as
indicated by the red dotted line labeled G
{
. Once the higher-order complex
(T
X
D
X
)(T
Y
D
Y
) is formed spontaneously, it may act as a functional unit (or
of mRNA
X
and mRNA
Y
in a
coordinated manner
so that their trajectories are
correlated either linearly or nonlinearly as shown in Table
12.12
. Just as the
function-related behavior of an mRNA trajectory (or ribon) signals the underly-
ing coupling between its transcriptosome and degradosome (see Steps 7 and 8 in
Fig.
12.27
), the nonrandom correlations found between two mRNA trajectories
