Biology Reference
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Table 12.11 The relative rate constants of the transcriptosome-degradosome (TD) complexes
predicted on the basis of the conformational (or quantum) states (1, 2, 3, 4, and 5) of their T and D
components. These numbers can also be viewed as the “quantum numbers” of transcriptosome
(n T ) and degradosome (n D ). The following symbols are used: n
¼
no change; d
¼
down regula-
tion or decrease; u
up regulation or increase in the rate of change in the level of RNA molecules
x and y. The subscripts indicate the relative magnitudes of the rates of changes in TL, i.e.,
u 1
¼
d 4 . The numbers above these symbols are the difference
between the quantum numbers of the transcriptosome and degradosome, i.e.,
<
u 2
<
u 3
<
u 4, and d 1
<
d 2
<
d 3
<
n
¼
n T - n D , that
D
are associated with the changes in TL levels, i.e., dTL/dt, indicated in parentheses
1
2
3
4
5
1
0
(n)
1
( d 1 )
2
( d 2 )
3
( d 3 )
4
( d 4 )
2
1
( u 1 )
0
(n)
1
( d 1 )
2
( d 2 )
3
( d 3 )
3
2
( u 2 )
1
( u 1 )
0
(n)
1
( d 1 )
2
( d 2 )
4
3
(u 3 )
2
( u 2 )
1
( u 1 )
0
(n)
1
( d 1 )
5
4
( u 4 )
3
( u 3 )
2
( u 2 )
1
( u 1 )
0
(n)
and the rate of its degradation depends on the Gibbs free energy level of the associated
degradosome (see Steps 2 and 5 in Fig. 12.27 ). Thus, the kinetics of the Xth RNA
trajectory “catalyzed” byT X andD X, either acting as separate entities or as components
of a functional unit (to be denoted as (T X D X ); see Step 7 inFig. 12.27 ), is determined by
the Gibbs free energy levels (or the quantum states) of T X and D X .
The analysis of the TL vs. TR plots such as Fig. 12.6 indicates that transcriptosomes
and degradosomes can exhibit at least five distinct turnover rates, i.e., (1) slow
decrease, (2) rapid decrease, (3) no change, (4) slow increase, and (5) rapid increase.
For example, in (a), Fig. 12.6 , during the first phase (i.e., 0-5 min), TL decreases
despite the fact that TR increases. This can be accounted for only if we can assume
that, during this phase, the rate of transcript degradation (TD) decreases more than TR
does. If each enzyme system has five conformational (or quantum) states with free
energy levels arbitrarily labeled as 1-5 as in Fig. 12.29 , there are 25 possible
conformational (or quantum) states for the (T X +D X ) system, each associated with
a rate of change in TL given in parenthesis as described in Table 12.11 .These25
different entries group into 9 classes (to be denoted as 1, 2, 3, 4, 5, 6, 7, 8, and 9) as
indicated by the dotted lines, and these dotted lines are associated with the relative
frequencies of 1, 2, 3, 4 , 5, 4, 3, 2, and 1 for the classes 1-9, respectively. For example,
the relative frequencies of the occurrence of the (dTL/dt) classes, n, d 1 ,d 2 ,d 3 , and d 4
(or n, u 1 ,u 2 ,u 3 , and u 4 ) are 5, 4, 3, 2, and 1 (counting the number of cells along the
dotted lines). Thus, if all the possible couplings between the quantum states of T and D
have an equal probability of occurrence (as assumed in Table 12.11 ), RNA trajectories
are five times more likely to remain unchanged, i.e., dTL/dt
¼
0 (or n), than to
decrease (or increase) rapidly with dTL/dt
d4 (or u4 ). However, the experimentally
observed data (see Series 9 in Fig. 12.30a ) deviate from the theoretically predicted
¼
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