Chapter 6 - Building a biological oscilator Flashcards
What is the basic mechanism in an oscilator?
Protein levels that go from high to low and back to high - it oscilates. “move or swing back and forth in a regular rhythm.”
What is the basic biological motif in a biological oscillator?
Negative feedback.
What kind of negative feedback is present in an osciallator?
NAR is not enough as we have seen. We need more elements - e.g X -> Y -| X
What are the requirements for damped (that get smaller) oscialtions?
1) Strong Feedback - preferably ccoperative
2) timescales of the elements must be similar.
What happens if we don’t have similar timscales?
Over-dampening.
When does damped oscillations occur mathematically?
When (alpha_1 - alpha_2)^2 < 4 * beta_1 * beta_2
Where alpha 1 and alpha two are degredation rates and betas are the feedback parameters.
beta_1 * beta_2 is called the feedback strength and is the deriviate of how X and Y acts on each other at steady state.
alpha_1 - alpha_2 is the timescale seperation
When alpha_1 = alpha_2 damped oscilations occur.
What happens with damped oscillations if noise is big enough?
They turn into non-daped osciallations.
How to create undampened oscillations biologically?
feedback loops with 3 or more steps.
What is a repressilator?
A 3 node motif with A -| B -| C -| A
What is needed for all oscillations?
1) Negative feedback
2) delays or noise
What is nonlinearity
Cooperatibity
How can PAR help oscillation?
PAR slows down reactions and therefore adds a delay - osciallations.
