"
Team:UPO-Sevilla/Project/Basic Flip Flop/Modeling/Basic Bistable
From 2011.igem.org
| Line 101: | Line 101: | ||
<div class="center"> | <div class="center"> | ||
| - | <img src="https://static.igem.org/mediawiki/2011/7/78/UPO-BBEq1.png" alt=" | + | <img src="https://static.igem.org/mediawiki/2011/7/78/UPO-BBEq1.png" alt="Transcription + Represion 1 Rate law" /> |
</div> | </div> | ||
| Line 109: | Line 109: | ||
<div class="center"> | <div class="center"> | ||
| - | <img src="https://static.igem.org/mediawiki/2011/e/e6/UPO-BBEq2.png" alt=" | + | <img src="https://static.igem.org/mediawiki/2011/e/e6/UPO-BBEq2.png" alt="Transcription + Represion 2 Rate" /> |
</div> | </div> | ||
Rate law | Rate law | ||
| Line 115: | Line 115: | ||
<p><strong>Tanslation 1:</strong></p> | <p><strong>Tanslation 1:</strong></p> | ||
| + | |||
| + | <div class="center"> | ||
| + | <img src="https://static.igem.org/mediawiki/2011/f/f3/UPP-BBEq3.png" alt="Translation 1 Rate" /> | ||
| + | </div> | ||
<p><strong>Translation 2:</strong></p> | <p><strong>Translation 2:</strong></p> | ||
| + | |||
| + | |||
| + | <div class="center"> | ||
| + | <img src="https://static.igem.org/mediawiki/2011/d/d0/UPO-BBEq4.png" alt="Translation 2 Rate" /> | ||
| + | </div> | ||
<p><strong>mRNA1/mRNA2 Degradation:</strong></p> | <p><strong>mRNA1/mRNA2 Degradation:</strong></p> | ||
| Line 123: | Line 132: | ||
<p> mRNA1 → null</p> | <p> mRNA1 → null</p> | ||
<p> mRNA2 → null</p> | <p> mRNA2 → null</p> | ||
| + | |||
| + | <div class="center"> | ||
| + | <img src="https://static.igem.org/mediawiki/2011/a/ac/UPO-BBEq5.png" alt="mRNA Degradation Rates" /> | ||
| + | </div> | ||
<p><strong>Repressor1/Repressor2 Degradation:</strong></p> | <p><strong>Repressor1/Repressor2 Degradation:</strong></p> | ||
| Line 128: | Line 141: | ||
<p> Repressor1 → null</p> | <p> Repressor1 → null</p> | ||
<p> Repressor2 → null</p> | <p> Repressor2 → null</p> | ||
| + | |||
| + | <div class="center"> | ||
| + | <img src="https://static.igem.org/mediawiki/2011/c/c5/UPO-BBEq6.png" alt="Repressors Degradation Rates" /> | ||
| + | </div> | ||
</div> | </div> | ||
Revision as of 16:45, 20 September 2011
Basic Bistable
Introduction
To start with the model analysis, we show the reactions in which our plasmid is involved into the ‘E. Coli’ bacteria, and their kinetic laws. Due to the two expressions, each one must have the same rate law. Here we are showing a simplified analysis for every response:
We have the expression of two different proteins, expressions that are regulated by following reactions:
TRANSCRIPTION: RNAp + Promoter → RNAp + Promoter + mRNA
The mRNA production will be described using Michaelis-Menten kinetics.
TRANSLATION: mRNA + Ribosomes → mRNA + Ribosomes + Repressor
The Repressor production will be also modeled using Michaelis-Menten kinetics.
REPRESSION: Promoter + n · Repressor → Promoter_Repressorn
Finally we use a Hill kinetics model for the transcription inhibition, which offers an approximation to the cooperative action.
Diagram
Here we can see all the species involved in the model for the bistable.
Equations
We define the reactions and the parameters involved in the system.
The following list shows a summary of the species:
Species:
- Promoter1
- Promoter2
- mRNA1
- mRNA2
- Repressor1/r1
- Repressor2
- RNAp
- Ribosomes
Parameters:
- Km : Michaelis constant of transcription
- Kmu: Michaelis constant of translation
- δ: mRNA rate of degradation
- λ: mRNA maximum rate of synthesis
- k: Repressor rate of synthesis
- Kiu: Dissociation constant of repression
- γ: Cooperativity of inhibition by the repressor
Before describing the reactions’ equations, we describe the assumptions made:
- Repression is modeled as an inhibition of the mRNA synthesis. Instead of considering the repression as a different process, we include this effect into the Michaelis-Menten equation as a modifier of the Michaelis constant Km, assuming that the protein binds competitively with the RNAp to the promoter site, and knowing that the repressor may form multimers.
- Due to the high values of the RNAp and ribosomes concentration versus promoter concentration, we can assume that the Michaelis-Menten rate law may change into a mass action rate law. Although this assumption is valid for the transcription process, the rate constant changes his value according to the repressor level.
Transcription + Repression 1:
RNAp + Promoter1 + Repressor1 → RNAp + Promoter1 + Repressor1 + mRNA1
Transcription + Repression 2:
RNAp + Promoter2 + Repressor2 → RNAp + Promoter2 + Repressor2 + mRNA2
Tanslation 1:
Translation 2:
mRNA1/mRNA2 Degradation:
mRNA1 → null
mRNA2 → null
Repressor1/Repressor2 Degradation:
Repressor1 → null
Repressor2 → null
Sponsors
