4 Positive feedback

Question 1

What is a network?

Answer 1

Nodes connected by edges

Question 2

Define edges in a network

Answer 2

Edges connect nodes = it is an action that occurs

Question 3

Give 4 examples of different networks and what their nodes and edges are

Answer 3

Cell: node = enzymes, substrates, proteins
edges = activation, suppression, cascade
Species interaction: node = organism/species
edges = feeding
Social network: node = people/IDs
edges = info flowing from one person to another
Artificial neural network

Question 4

What is a network motif?

Answer 4

Basic interaction patterns that recur throughout biological networks, much more often than in random networks

Motifs can generate predictable outputs
Motifs are building blocks of networks

Question 5

Define a node

Answer 5

One or more nodes that are interconnected in a specific way with predictive outcome

Question 6

What is the equation for negative autoregulation?

Answer 6

A dot = -rA

Question 7

Describe the graph of negative autoregulation

Answer 7

Exponential decay

Degradation of protein or death of animal = how things disappear on itself over time

Question 8

What is the equation for a self-suppressing gene and why?

Answer 8

A dot = +s - rA

This is because the +s is the external signal to activate the gene A
This signal doesn’t depend on how strong/amount of rA

Product of gene A suppresses its own expression at rate r>0

Question 9

What is the fixed point for A dot = +s - rA?

Answer 9

A* = s/r

Stable fixed point = the rate you get something / rate you lost something

Question 10

What is the outcome of negative autoregulation on response time?

Answer 10

Negative autoregulation ACCELERATES response time

Question 11

What does integrating negative autoregulation equation tell us?

Answer 11

The expression of gene A saturates over time

Question 12

What are the limits for the integration of A dot = +s -rA?

Answer 12

t&raquo_space;> infinity
A&raquo_space;> s/r

Question 13

What factors affect expression level and response time?

Answer 13

s = external stimuli alters level of steady state
Lower expression level at steady state A* = s/r

Stronger auto-suppression = larger r
Leads to faster response time = gene A reaches steady state faster

Question 14

How to ensure both high expression level and fast response time?

Answer 14

High expression level = when s is large
Fast response time = when r is large

Question 15

What is positive autoregulation also called?

Answer 15

Autoactivation

Question 16

What is the Hill Function, give the equation?

Answer 16

Generalized logistic equation

f((x) = x^n / k^n + x^n

Question 17

What are the equations for positive autoregulation, exponential and logistic?

Answer 17

Exponential: A dot = +rA
Logistic: A dot = +rA (K - A)

Question 18

What does k stand for in the Hill function?

Answer 18

Level at which the function f(x) reaches 50% of the max

Question 19

What does n stand for in the Hill function?

Answer 19

Hill coefficient = represents level of association

Question 20

What happens when ‘n’ is large in the Hill function?

Answer 20

Ultrasensitivity

For high n, reaction rate increases drastically

Until it becomes a STEP FUNCTION when n = infinity

Question 21

What happens when k = 1 in the hill equation?***

Answer 21

f(x) is the same as x dot

x dot = x^n / 1 + x^n

Reaction reaches 50% of max rate when x dot = 1 at the same conc of x = 1

Question 22

What does it mean when n=1 as opposed to n= 2? ***

Answer 22

n = 1 means autoactivation only needs one copy of itself

n = 2 means that it could need a dimer to autoactivate

Question 23

What can ultrasensitivity and degradation (removal) enable?

Answer 23

Bistability

If n =1 there is one steady state = constant expression rate of A (LINEAR)

If n>1 (ultrasensitive autoactivation) there are two steady states = eitehr constant expression rate or no expression at all (ON/OFF switch)
NON-LINEAR = S-curve

Question 24

What is cooperativeness and what can it induce? ***

Answer 24

Cooperativeness = when X^n (n>1)

Cooperativeness can induce ultrasensitivity in autoactivation

Question 25

What are the nullclines and trajectories for linear positive feedback?

Answer 25

A dot = +/- rB
B dot = +/- sA

Nullclines: A* and B* = 0

Vectors on nullclines (0, +/-sA) (+/-rB,0)

Question 26

What does linear positive feedback generate with the eigenvectors?

Answer 26

Saddle point = unstable fixed points/nodes

Happens in both mutual activation and mutual repression

Question 27

Examples of mutual activation and repression

Answer 27

Activation = amplification
Repression = exclusion