Systems Biology Flashcards
How does the wiring diagram of Simple Regulation look like?
How can Simple Regulation be described?
y’ = β - α * y
with:
- β: Production rate
- α: Removal rate
What is the steady-state of simple regulation?
y_st = β / α
with:
- β: Production rate
- α: Removal rate
What is the response time of simple regulation?
t_H = ln(2) / α
with:
- α: Removal rate
How do growth and removal rate affect the steady-state and the response time of simple regulation?
- Higher β –> higher steady-state, does not affect response time
- Higher α –> lower steady-state and lower response time
How do ON and OFF switch of simple regulation look like?
How does the wiring diagram of Negative Auto Regulation (NAR) look like?
How can NAR be described?
y’ = β * 1 / (1 + (y/k)^n) - αy
with:
- β: Production rate
- α: Removal rate
- k: Half-saturation constant
- n: Hill coefficient
What is the steady-state of NAR?
y_st = K
with:
- k: Half-saturation constant
What is the response time of NAR?
t_H = k/2β
with:
- β: Production rate
- k: Half-saturation constant
How does the wiring diagram of Positive Auto Regulation (PAR) look like?
How can PAR be described?
y’ = β * (y/k)^n / (1 + (y/k)^n) - αy
with:
- β: Production rate
- α: Removal rate
- k: Half-saturation constant
- n: Hill coefficient
What is the steady-state of NAR?
If n >= 2:
- It has two steady-states, a low and a high one –> ON and OFF state
- The steady state is history dependant: a third unstable fixpoint is the threshold where system switches from ON to OFF state
–> Bistability
If n = 1:
- Only one steady state
–> Monostability
What is a feed forward loop?
- 3 genes that regulate each other
- 13 possible motives
- Two different types:
- Coherent: Signals reaching product either both activate or repress
- Incoherent: Signals raching product contradict each other
- Arrows reaching product can be connected through different logic gates, eg. AND, OR
How does the wiring diagram of C1-FFL look like?
How can C1-FFL with an AND Gate be described?
y’ = Sx * β - αy
z’ = Sx * β * (y/k)^n / (1 + (y/k)^n) - αz
with:
- β: Production rate
- α: Removal rate
- k: Half-saturation constant
- n: Hill coefficient
- Sx: Input of x (Either 1 or 0)