Biology Reference
In-Depth Information
Fig. 5. Petri net model simplification.
and
k
r
is the rate of consumption of biochemical reaction. GPC denotes the concentration of the binding
complex of gene, TFs, RNA ploymerase etc. DNA is a stable molecule, but mRNA and proteins are
constantly being degraded by cellular machinery and then to be recycled. Specifically, mRNA is degraded
by a ribonuclease (RNase), which competes with ribosomes to bind to mRNA. If a ribosome binds, the
mRNA will be translated, if the RNase binds, the mRNA will be degraded. Proteins are degraded by
cellular machinery including proteasomes signaled by ubiquitin tagging. Protein degradation is regulated
by a variety of more specific enzymes (which may differ from one protein target to another). In practice,
the first-order rate constant of degradation kd often is replaced by a half life
H
, and the degradation rate
is expressed as
dC
dt
0
.
693
=
−
H
C
, where
H
=
0.693/
k
d
.
mRNAs have specific half-lives ranging from
hours to days.
Regarding the model of binding procedures which also are common phenomena in signal transduction,
say,
-
converting inactive proteins into active proteins, and vice versa.
-
binding of proteins to genes, proteins
-
binding of RNA polymerase to genes and gene-protein complex
-
binding of receptors to transcription factors
a general model
[
Complex
]=
K
b
·
i−
1
[
A
i
]
, where
K
b
is the binding constant, is presented for systems
consisting of one subject
A
i
binding with other subjects.
