Chapter 13 - optimal gene circuit design Flashcards
What does optimality mean?
The ability of a biological system to maximize fitness by converging on specific circuit designs.
bacterial growth rate formula:
N(t) = N(0) * e^Ft
F is rate
What is a fitness function?
A function that describes how well a system is doing - in bacteria this is most often growth.
What is a cost function?
Something that hinders fitness.
What is genetic drift?
In small populations random mutations and noise can cause big differences in the genetics of a population.
What is a gratituous inducer?
Something that induces expression but gives no benefit to the system.
What is the fitness equal to?
The benefit minus the cost.
What is the Benefit function for lacZ?
b(Z,L) = b0 * Z* L / K + L
b0 = maximal growth rate advantage per LacZ Z = LacZ concentration L = Saturating function of lactose concentration K = michaelis menten constant -the rate limiting step
What is the cost function of LacZ?
c(Z) = c0 * Z / 1 - Z/M
c0 = cost of single protein Z = concentration of LacZ M = the maximal amount of LacZ possible.
Optimal fitness can be found when conditions do not change - how do cells reacct when coditions dochange?
Gene regulation.
Name 3 ways a gene can be regulated (evolutioonary):
1) Constitutive expressions
2) Regulated -only produce in proper conditions
3) no expression
List the fitness function for a gene with constitutive expression:
F = pb - c
probability of benifit minus constant cost
State the fitness function a regulated gene:
F = pb - pc - r
probability of benfit, probability of cost and cost of regulation.
State the fitness function of the lack of an expression system:
F = 0
When will regulation be selected?
when
p < 1 - r/c
AND
p > r / (b - c)
Generally for an intermediate value of p.
