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<p>Plasmid 2 uses a LacI and pTrc promoter is its backbone, which is requires a slightly different model structure from the other promoter. The transcription factor constitutively expressed by the LacI sequence creates a homotetramer and binds to the pTrc sequence repressing transcription of the Reductase, Dehydrogenase, Oxidase, and Synthase genes. We used a similar expression equation for this protein to the repressor protein in plasmid 1. However when IPTG, a lactose analog, is added to the cells, two of these molecule binds to the LacI protein causing it to change conformation and fall off the promoter. This then allows RNA polymerase to bind and start transcription. We used the same assumption as in plasmid 1, grouping the transcription and translation rate into one rate parameter, which simplified to the system on the right. We also grouped the binding of 2 IPTG to the LacI tetramer into one reaction instead of two separate events. Finally, since we are uncertain about the ordering of binding or the rate parameters of the formation of the LacI tetramer, we kept it with separate rate parameter for each subunit binding. This was important to include as the tetramer is the molecule that actually represses the genes. The last thing to note is that for there to be a functional Glycolaldehyde Reductase protein it needs two copies of itself to dimerize. This explains the factor multiplying its transcription rate.</p> | <p>Plasmid 2 uses a LacI and pTrc promoter is its backbone, which is requires a slightly different model structure from the other promoter. The transcription factor constitutively expressed by the LacI sequence creates a homotetramer and binds to the pTrc sequence repressing transcription of the Reductase, Dehydrogenase, Oxidase, and Synthase genes. We used a similar expression equation for this protein to the repressor protein in plasmid 1. However when IPTG, a lactose analog, is added to the cells, two of these molecule binds to the LacI protein causing it to change conformation and fall off the promoter. This then allows RNA polymerase to bind and start transcription. We used the same assumption as in plasmid 1, grouping the transcription and translation rate into one rate parameter, which simplified to the system on the right. We also grouped the binding of 2 IPTG to the LacI tetramer into one reaction instead of two separate events. Finally, since we are uncertain about the ordering of binding or the rate parameters of the formation of the LacI tetramer, we kept it with separate rate parameter for each subunit binding. This was important to include as the tetramer is the molecule that actually represses the genes. The last thing to note is that for there to be a functional Glycolaldehyde Reductase protein it needs two copies of itself to dimerize. This explains the factor multiplying its transcription rate.</p> | ||
Revision as of 19:16, 9 July 2018