Difference between revisions of "Team:RHIT/GeneticsModel"
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<p>Plasmid 1 uses an AraC and pBAD promoter to regulate expression of PETase and MHETase. The transcription factor made from AraC usually binds and represses the pBAD promoter, halting transcription of the plasmid. The inducer, Arabinose, can be added to the media, and this molecule binds to the AraC transcription factor on the DNA strand and changes it conformation so that transcription can occur [bmcsys]. The reaction scheme on the left explains a more complete mechanism of the transcription/translation of these proteins. The creation of AraC protein is related to a constitutive promoter which we assume enters the system as a constant rate, K. This method was also used by the UC Davis team in 2012. We assumed fast-equilibrium hypothesis on the formation of the dimer and that there is essentially a constant pool of arabinose in the environment. We can also streamline the binding of the two arabinose to the AraC dimer into one reaction determined by the rate parameters k3+ and k3-. Since the amount of RNA polymerase does not change relative to these molecules and the frequent assumption used literature to group the transcription and translation rate into one overall rate of protein production, we simplify the system further. From these assumptions, we can simplify the system down into the system shown on the right.</p> | <p>Plasmid 1 uses an AraC and pBAD promoter to regulate expression of PETase and MHETase. The transcription factor made from AraC usually binds and represses the pBAD promoter, halting transcription of the plasmid. The inducer, Arabinose, can be added to the media, and this molecule binds to the AraC transcription factor on the DNA strand and changes it conformation so that transcription can occur [bmcsys]. The reaction scheme on the left explains a more complete mechanism of the transcription/translation of these proteins. The creation of AraC protein is related to a constitutive promoter which we assume enters the system as a constant rate, K. This method was also used by the UC Davis team in 2012. We assumed fast-equilibrium hypothesis on the formation of the dimer and that there is essentially a constant pool of arabinose in the environment. We can also streamline the binding of the two arabinose to the AraC dimer into one reaction determined by the rate parameters k3+ and k3-. Since the amount of RNA polymerase does not change relative to these molecules and the frequent assumption used literature to group the transcription and translation rate into one overall rate of protein production, we simplify the system further. From these assumptions, we can simplify the system down into the system shown on the right.</p> | ||
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| + | <center> | ||
| + | <img src="https://static.igem.org/mediawiki/2018/9/96/T--RHIT--Plasmid1Eq.png"> | ||
| + | </center> | ||
| + | |||
| + | <p>Model Equations:</p> | ||
| + | |||
| + | <center> | ||
| + | <img src="https://static.igem.org/mediawiki/2018/8/8a/T--RHIT--Plasmid1Model.png"> | ||
| + | </center> | ||
| + | |||
| + | <p>https://bmcsystbiol.biomedcentral.com/articles/10.1186/1752-0509-5-111 useful description and numbers for AraC promoter</p> | ||
Revision as of 19:42, 28 June 2018
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Genetics Model
The DNA coding for the 6 enzymes required for breakdown and assimilation of PET was too long to fit on one plasmid. To rectify this and to be able to test smaller subsystems the PETase and MHETase genes were placed on Backbone 1, Plasmid 1. The Glycolaldehyde Reductase, Glycolaldehyde Dehydrogenase, and Glycolate Oxidase, and Malate Synthase were placed in sequence on the backbone 2, Plasmid 2.
Plasmid 1 uses an AraC and pBAD promoter to regulate expression of PETase and MHETase. The transcription factor made from AraC usually binds and represses the pBAD promoter, halting transcription of the plasmid. The inducer, Arabinose, can be added to the media, and this molecule binds to the AraC transcription factor on the DNA strand and changes it conformation so that transcription can occur [bmcsys]. The reaction scheme on the left explains a more complete mechanism of the transcription/translation of these proteins. The creation of AraC protein is related to a constitutive promoter which we assume enters the system as a constant rate, K. This method was also used by the UC Davis team in 2012. We assumed fast-equilibrium hypothesis on the formation of the dimer and that there is essentially a constant pool of arabinose in the environment. We can also streamline the binding of the two arabinose to the AraC dimer into one reaction determined by the rate parameters k3+ and k3-. Since the amount of RNA polymerase does not change relative to these molecules and the frequent assumption used literature to group the transcription and translation rate into one overall rate of protein production, we simplify the system further. From these assumptions, we can simplify the system down into the system shown on the right.
Model Equations:
https://bmcsystbiol.biomedcentral.com/articles/10.1186/1752-0509-5-111 useful description and numbers for AraC promoter