Biology Reference
In-Depth Information
element (inducible enzyme) will enable the transcription process. However, the effector element will
activate the activator element. Both elements will build a protein complex which enables the transcription
process. The formal description of the positive control is:
P
=
{
activator inactive, effector, activator active, protein
}
}
F
=
{
(
activator inactive, conformation
), (
effector, conformation
),
(
conformation, activator active
), (
activator active, transcription
),
(
transcription, protein
)
}
With regard to repressive positive control, the effector element will repress the transcription process.
The catalytic element is inducible for the transcription process until the effector element will appear.
The effector element will inactivate the activator.
P
=
{
T
=
{
conformation, transcription
activator active, effector, activator inactive, protein
}
}
F
=
{
(
activator active, conformation
), (
effector, conformation
),
(
conformation, activator inactive
), (
activator active, transcription
),
(
transcription, protein
)
}
The negative control will be controlled by a repressor element which will repress the transcription
process. Regarding the inducible negative control, an active repressor will suppress the transcription
process. The enzyme complex of the active repressor and the operator will prevent the transcription
process. The effector element inactivates the repressor that will enable the transcription process.
P
=
{
T
=
{
conformation, transcription
repressor active, repressor/operon, inductor, repressor inactive, active operon, protein
}
}
F
=
{
(
repressor active, connection
), (
connection, repressor/operon
),
(
repressor/operon, docking/RNA polymerase
), (
inductor, docking/RNA polymerase
),
(
docking/RNA polymerase, repressor inactive
), (
docking/RNA polymerase, active operon
),
(
active operon, transcription
), (
transcription, protein
)
}
The last type of gene regulation processes discussed here is the repressible negative control. The main
feature of this control mechanism is that the appearance of the inductor will suppress the transcription
process. Without the inductor the operon is active. The repressor is inactive and will be activated by the
inductor element. The activated repressor will deactivate the operon, the transcription process will be
blocked up.
P
=
{
T
=
{
connection, docking/RNA polymerase, transcription
repressor inactive, inductor, repressor active, repressor/active operon, active operon, protein
}
T
=
{
}
F
=
{
(
inductor, conformation
), (
repressor inactive, conformation
),
(
conformation, repressor active
), (
repressor active, docking repressor
),
(
docking repressor, repressor/active operon
), (
active operon, transcription
),
(
transcription, protein
)
}
conformation, docking repressor, transcription
Cell communication
Regarding cell communication processes, which are based on exocytose and endocytose or cellular
gaps, the formalization by using Petrinets is simple. Uptake of metabolites by a cell can be formalized
using a transition without incoming arrows. On the other hand, if substances leave the cell, we use
transitions without outgoing arrows. Regarding specific receptor activities new transitions have to be
added.
