Chapter 1 - Transcription networks basic concepts

Question 1

Function of transcription factors:

Answer 1

1) Represents the environmental state the cell is in so it can adapt its gene expression to it.

Question 2

What does transcription networks describe?

Answer 2

The interactions between transcription factors and genes. Transcription factors can be a product of other transcription factors mm.

Question 3

What is a promotor?

Answer 3

Region that interacts with transcription factors and controls the amount of mRNA per time made.

Question 4

RNAp

Answer 4

RNA polymerase

Question 5

What does X -> Y mean?

Answer 5

X is a TF for Y.

Question 6

What is Sx?

Answer 6

A signal S on TF X that changes its DNA affinity (e.g. it activates it.

Question 7

What is X*

Answer 7

An activated form of the TF X.

Question 8

What is a dynamical system?

Answer 8

A system that is changing e.g. after a signal occurs TF activity changes and thus protein levels of the target changes.

Question 9

What is seperation of timescales?

Answer 9

The different components of transcription networks (TF activation by signal, TF binding, transcription, protein concentration change) work on different timescales (msec, sec., min and hours for the examples listed)

Question 10

Whaat does seperation of timescales mean for signal activation?

Answer 10

When considering protein levels we can consider protein activation as steady stae since the time scales are so different.

Question 11

What is modularity?

Answer 11

The way transcription networks can be changed by introducing or removing components e.g. by knocking out a gene.

Question 12

Explain activation vs repression

Answer 12

activation increases levels of transcription and repression hinders it.

Question 13

What is an input function?

Answer 13

Describes the strength of effect a transcription factor has on transcription.

Question 14

What is a hill function?

Answer 14

for an activator:

f(X) = beta * ( X^n/(K^n + X*^n))

K is the activation coefficient. Describes the concentration of active X* needed to activate expression.

Beta is the maximal promoter activity.

n is the hill coefficient describes function steepness.

Question 15

What is the basal expression level?

Answer 15

a base level of expression can be added to the input function by adding a constant beta0.

Question 16

What is a logical approximation?

Answer 16

Instead of viewing input functions as actual functions they are seen as step function were transcription rate is maximal when X* > K or minimal X* < K for repressors.

Question 17

What are multi-dimensional input functions?

Answer 17

For genes regulated by multiple transcription factors their expression has more than one input function. Often approximated with logic function forming AND or OR gates. Can also be sum.

Question 18

What is the degradation rate?

Answer 18

How fast protein is degraded:

alpha = alpha_dilution - alpha_degredation

Question 19

How is the amount of Y changing over time?

Answer 19

dY/dt = Beta - Alpha*Y

Question 20

What is the Y steady state?

Answer 20

Yst = Beta/alpha

Question 21

If no Y is produced how fast does Y disappear?

Answer 21

Y(t) = Yst * exp(-alpha*t)

Question 22

What is the response time?

Answer 22

T_1/2 = log>(2)/alpha

Describes the half time of the exponentially decaying Y(t)

Question 23

WHat is the benefit of a large beta large alpha system?

Answer 23

Fast response times for similar steady state levels.

Question 24

Equation of Level of Y starting at Y = 0 and inducing a signal:

Answer 24

Y(t) = Yst*(1-exp(-alpha))

The response time is the same as the deay - T1/2 = log(2)/alpha