Gene Regulation/Transcription

Question 1

Protein Creation Sequence (Again because why not)

Answer 1

Chromosomal DNA
RNA transcription
Ribosome
Polypetide chain
Translation
Endoplasmic reticulum
Folded protein
Golgi 
Proteins transported within and out of the cell

Question 2

Michalis Menton Equation

Answer 2

E + S ES E + P
E = Enzyme
S = susbstrate
P = Product

Question 3

Michalie Menton Equation Assumptions

Answer 3

Binding step is fast so concentration of all parts reach equilibrium (Conversion of complex [ES] to product is rate limiting step)
At early times where initial velocity (V0) is measured, [P] = 0
Total enzyme concentration = [Etotal] = [E] + [S]
[S]&raquo_space; [Etotal] - Fraction of S which binds to E is negligible and [S] is constant at early timepoints
Rate of formation of ES = Rate of breakdown of ES

Question 4

Transcription factors

Answer 4

Proteins
Excite or inhibit transcription
Signal could be a result of requirement for glucose, DNA repair enzyme etc (maintain balance of the cell by triigering the transcription factors)

Question 5

Transcription factors encoding

Answer 5

Transcription factors are encoded by genes which are regulated by other transcription factors, which can also be regulated by other transcription factors
Set of interactions called a transcription network

Question 6

Transcription network

Answer 6

Encoding of transcription factors which are regulated by other transcription factors
Nodes are genes (genes which encode a transcription factor and other genes)
Arrows represent transcription regulation

Question 7

Information in transcription network

Answer 7

Inputs: Signals which carry information from the environment
Dynamic system
Control production rate of proteins
Many proteins aren’t transcription factors but involved in other cell functions

Question 8

Repressor

Answer 8

Protein which turns off the expression of one or more genes
Binds to gene’s promoter region to prevent the production of mRNA
-
Represented as blunt arrows

Question 9

Activator

Answer 9

Protein which turns on the expression of one or more genes
Must bind to gene’s promoter region to allow for production of mRNA
+
Represented as arrows

Question 10

Time scales

Answer 10

50% change in concentration of the protein

If interested in protein concentration, can assume that all events at earlier times happen instantly

Question 11

Input function

Answer 11

Number associated with an arrow in a transcription network

Question 12

Hill function

Answer 12

Function for describing many gene input functions

Question 13

Michalis Menton equation

Answer 13

[Etotal][S] / Km+[s] = [ES]

Question 14

Michalis Menton with no repressor or activator

Answer 14

Diminishing returns of bound enzyme

Question 15

Importance of transcription networks

Answer 15

Use hill function to understand parameters for transcription by simulating dynamic processes involved in gene expression within transcription networks
Can understand factors which impact responses from cell to environmental factors
Helps understand life/diseases

Question 16

Hill Function Parameters

Answer 16

X - transcription factor concentration
K = activation coefficient (concentration of X required to significantly change expression)
B = maximum promoter activity (maximum production rate)
n = hill coefficient (step function at infinity, MM kinetics at 1, no tf effect)