Team:Paris/Modeling/Molecular Reactions

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{{Paris/Menu}}
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{{Paris/Header|Molecular Reactions}}
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We show here the elementary reactions that served us as basis. They intend to be "exhaustive" in the sense that every step of the [[Team:Paris/Modeling/Protocol_Of_Characterization|system]] is described. Each of these reactions has to be "mathematically interpreted", in a [[Team:Paris/Modeling/FromMolReactToNLOde|model]] which accounts for the observable phenomena, and, in the same time, allows us to well estimate [[Team:Paris/Modeling/Protocol_Of_Characterisation|experimentally]] all the involved parameters.
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We starts from elementary reactions that are "exhaustives" in the sense that every steps of the system is described. Each of those reactions has to be "mathematically interpreted", in a model (see [[Team:Paris/Modeling/FromMolReactToNLOde|the model]]) that accounts for the important phenomenon, and in the same time allows us to find experimentally (see [[Team:Paris/Modeling/Protocol_Of_Caracterisation|the protocol]]) every involved parameters.
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'''The system we are studying is the "Core System with three genes of interest"''' that we can represent in the scheme below (with all alternatives ''pFlhDC'' or ''pTet'' and ''TetR'' or ''envZ'' or ''OmpR<sup>*</sup>'')
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<div style="text-align: center">
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{{Paris/Toggle|Core System|Team:Paris/Modeling/More_Mol_Reac_System|200px}}
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'''The System we are studying is the "Core System" ''' (see [[Team:Paris/Modeling/PRECISERLADRESSE|PRECISERLADRESSE]]) that we can represent in the following, with all alternatives (''pFlhDC/pTet'' ; ''TetR/EnvZ/OmpR<sup>*</sup>'') : [[Image:CoreSystemf5.jpg|thumb|center|The Full System<br>The interaction surrounded in red (f5) is the one of the detailed example]]
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{| border="1" width="100%" style="text-align: center"
{| border="1" width="100%" style="text-align: center"
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| width="75%" | '''Complexation Reactions''' <br>
| width="75%" | '''Complexation Reactions''' <br>
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The double triangle (|><|) is a symbol for complexations : <br>
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The double triangle ('''><''') is a symbol for complexations : <br>
[[Image:compl.jpg|110px]] means ''n<sub>1</sub>'' molecules of ''FlhDC'' complexed with a ''pFliA'' promoter<br><br>
[[Image:compl.jpg|110px]] means ''n<sub>1</sub>'' molecules of ''FlhDC'' complexed with a ''pFliA'' promoter<br><br>
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<html><iframe height="300" width="600" src="https://static.igem.org/mediawiki/2008/3/3a/Complexation_Reactions.pdf"></iframe></html>
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<div style="text-align: center">
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{{Paris/Toggle2|Complexation Reactions|Team:Paris/Modeling/Compl_React}}
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</div>
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| width="25%" | '''On the Example''' <br>
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| width="25%" | '''On the Example :''' <br>
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The complexation of ''FlhDC'' on ''pFliL'' : <br>
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<small> How given amounts of ''FlhDC'' and ''FliA'' would produce ''FP1'' ? </small><br>
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* ''FlhDC'' and ''FliA'' bind to ''pFliL'' : <br>
[[Image:DCiLcompl.jpg]]
[[Image:DCiLcompl.jpg]]
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The complexation of ''FliA'' on ''pFliL'' : <br>
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[[Image:AiLcompl.jpg]]
[[Image:AiLcompl.jpg]]
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| width="75%" | '''Production Reactions''' <br>
| width="75%" | '''Production Reactions''' <br>
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The double triangle (|><|) is a symbol for complexations : <br>
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The double triangle ('''><''') is a symbol for complexations : <br>
[[Image:compl.jpg|110px]] means ''n<sub>1</sub>'' molecules of ''FlhDC'' complexed with a ''pFliA'' promoter<br><br>
[[Image:compl.jpg|110px]] means ''n<sub>1</sub>'' molecules of ''FlhDC'' complexed with a ''pFliA'' promoter<br><br>
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<html><iframe height="300" width="600" src="https://static.igem.org/mediawiki/2008/e/ef/Production_Reactions.pdf"></iframe></html>
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<div style="text-align: center">
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{{Paris/Toggle2|Production Reactions|Team:Paris/Modeling/Prod_React}}
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</div>
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| width="25%" | '''On the Example''' <br>
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| width="25%" | '''On the Example :''' <br>
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The production of ''FP1'' by ''FlhDC><pFliL'' and ''FliA><pFliL'' : <br>
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<small> How given amounts of ''FlhDC'' and ''FliA'' would produce ''FP1'' ? </small> <br>
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<br>
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* ''FlhDC><pFliL'' and ''FliA><pFliL'' causes "production" of ''FP1'' : <br>
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[[Image:bFP1.jpg]]
[[Image:bFP1.jpg]]
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| width="75%" | '''Degradation/Dilution Reactions''' <br><br>
| width="75%" | '''Degradation/Dilution Reactions''' <br><br>
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<html><iframe height="300" width="600" src="https://static.igem.org/mediawiki/2008/f/f7/Degradation_Dilution.pdf"></iframe></html>
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<div style="text-align: center">
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{{Paris/Toggle2|Degradation/Dilution Reactions|Team:Paris/Modeling/D_React}}
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</div>
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| width="25%" | '''On the Example''' <br>
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| width="25%" | '''On the Example :''' <br>
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The disappearance of ''FP1'' because of its degradation/dilution : <br>
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<small> How given amounts of ''FlhDC'' and ''FliA'' would produce ''FP1'' ? </small><br>
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<br>
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* ''FP1'' disappears because of its degradation and dilution : <br>
[[Image:dFP1.jpg]]
[[Image:dFP1.jpg]]
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<div style="text-align: right">For complete PDF with all Reactions and Numbered References : [https://static.igem.org/mediawiki/2008/6/61/Equa_Core_System.pdf complete list of reactions and equations] </div>
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<div style="text-align: right">for complete .pdf with all reactions and references : [[https://static.igem.org/mediawiki/2008/6/61/Equa_Core_System.pdf|complete list of reactions/equations]] </div>
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{{Paris/Navig|Team:Paris/Modeling/Workflow_Example}}

Latest revision as of 03:39, 30 October 2008

Molecular Reactions


We show here the elementary reactions that served us as basis. They intend to be "exhaustive" in the sense that every step of the system is described. Each of these reactions has to be "mathematically interpreted", in a model which accounts for the observable phenomena, and, in the same time, allows us to well estimate experimentally all the involved parameters.


The system we are studying is the "Core System with three genes of interest" that we can represent in the scheme below (with all alternatives pFlhDC or pTet and TetR or envZ or OmpR*)

↓ Core System ↑


core system

The "core systeme"
* Every interactions are modelised by a ƒX function
* The detailed example FP1 = ƒ5([FlhDC],[FliA]) is surrounded in red


Complexation Reactions

The double triangle (><) is a symbol for complexations :
Compl.jpg means n1 molecules of FlhDC complexed with a pFliA promoter

↓ Complexation Reactions ↑


Equa Complex.jpg
 On the Example :

How given amounts of FlhDC and FliA would produce FP1 ?

  • FlhDC and FliA bind to pFliL :

DCiLcompl.jpg

AiLcompl.jpg

Production Reactions

The double triangle (><) is a symbol for complexations :
Compl.jpg means n1 molecules of FlhDC complexed with a pFliA promoter

↓ Production Reactions ↑


Prod React.jpg
 On the Example :

How given amounts of FlhDC and FliA would produce FP1 ?

  • FlhDC><pFliL and FliA><pFliL causes "production" of FP1 :



BFP1.jpg

Degradation/Dilution Reactions

↓ Degradation/Dilution Reactions ↑


D React.jpg
 On the Example :

How given amounts of FlhDC and FliA would produce FP1 ?

  • FP1 disappears because of its degradation and dilution :

DFP1.jpg

For complete PDF with all Reactions and Numbered References : complete list of reactions and equations



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