Chapter 2 - autoregulation Flashcards
What is a network motif
A building block pattern that occurs more often than it would on chance.
What is a randomized network?
A network with the same characteristics as a real one but with node connections are random.
What is autoregulation?
When the gene product of a gene regulates itself.
Generating ER random network
Probability is simply A (number of arrows) / N (number of nodes) of a particular type of interaction.
Why is NAR smart?
It can keep the same Yst while still maintaining a high production rate.
In simple regulation Yst = beta/alpha
In NAR Yst = K
What is the steady state level of a protein undergoing negative autoregulation?
Basically the repression coefficient (K) of the protein effect on itself.
What happens if K changes in NAR
If K increases the steady state level will increase.
What happens if beta changes in NAR?
If beta increases the steady state will increase faster
What is the T0.5 ofa NAR?
T_1/2 = K/(2*beta)
What is a rate plot?
On the X-axis: protein level
On the Y-axis: the rate of production and the rate of degredation
What is a fixed point?
A steady state value that protein levels converges to.
Explain using rate plots why NAR is faster than simple regulation.
We know:
1) simple regulation has constant production (beta) and degredation that is dependent on concentration (alpha*X)
2) we know that in NAR has a decreasing beta as the concentration increases (max for no X) and linear alpha.
3) They have the same steady state levels.
The amount of Y is the rate of production minus the degredation. We know that the production rate must be bigger first and then decrease and the diffrence must be bigger in the beginning for the NAR compared to the simple reg if they are to end up at the same stable point.
Name the second benefit of NAR:
Robustness of steady state levels at varying beta rates.
The beta can change but because the steady state is not dependent on the beta it will not change.
