Information Technology Reference
In-Depth Information
Table 4.1 Biochemical reactions that model an inverter.
k
xlate
−−−−→
translate
mRNA
A
+
rRNA
mRNA
A
+
rRNA
+
A
(1)
k
dec(mrna)
−−−−→
decay
mRNA
A
(2)
k
dim(a)
−−−−→
k
dec(a)
−−−−→
decay
A
+
A
dimerization
A
2
(3)
A
(5)
k
sngl(a)
−−−−→
single
k
dec(a2)
−−−−→
decay
A
+
A
A
2
(4)
A
2
(6)
k
rprs(a2)
−−−−→
repress1
k
dec(ga4)
−−−−→
decay
P
Z
+
A
2
P
Z
A
2
(7)
P
Z
A
4
P
Z
A
2
(10)
k
dis(a2)
−−−−→
k
rprs(a4)
−−−−→
repress2
P
Z
A
2
dissociation
P
Z
+
A
2
(8)
P
Z
A
2
+
A
2
P
Z
A
4
(11)
k
dec(ga2)
−−−−→
decay
k
dis(a4)
−−−−→
P
Z
A
2
P
Z
(9)
P
Z
A
4
dissociation
P
Z
A
2
+
A
2
(12)
k
xscribe
−−−−→
P
Z
+
RNA
p
transcribe
P
Z
+
RNA
p
+
mRNA
Z
(13)
k
dec(mrna)
−−−−→
decay
mRNA
Z
(14)
mRNA
A
is the input and mRNA
Z
the output.
control, translation of mRNA, repression through cooperative binding, and
degradation of proteins and mRNA transcripts.
Table 4.1 presents one possible chemical model of the reactions involved
in biochemical inversion. In particular, this model incorporates characteristics
from the bacteriophage
cI
repressor operating on the P(R) promoter and the
O
R
1 and O
R
2 operators. The mRNA
A
molecule represents the input signal, and
the mRNA
Z
molecule represents the output signal. Ribosomal RNA (rRNA)
translates mRNA
A
into the input protein repressor
A
, and
A
2
denotes the dimeric
form of
A
.
P
Z
denotes the concentration of the active form of the promoter for
Z
. A promoter is active only when its associated operator is unbound by a
repressor.
P
Z
A
2
and
P
Z
A
4
represent the repressed (i.e., inactive) forms of the
promoter, where either one or two dimers is bound to the promoter, respectively.
RNA polymerase (RNAp) initiates transcription from the active form of the
promoter,
P
Z
, into mRNA
Z
, the gene transcript.
2
This gene transcript typically
codes for other signals (e.g., protein repressors or activators), or for structural
and enzymatic proteins that perform certain cellular tasks.
λ
2
The simulations in this section assume that the concentrations of RNA
p
and rRNA are fixed. Chapter 7 discusses
how to measure the effect of fluctuations in these concentrations, as well as other factors, on the inverter's behavior.
Once these effects have been quantified, robust gates can be designed.
