"
Team:ITB Indonesia/Modeling/Cytochrome
From 2013.igem.org
(Created page with "{{:Team:ITB_Indonesia/template/header}} <html> <div id="main"> <div class="content-left"> <div class="post post-single"> <h2 class="title">CYP synthesis</h2> ...") |
|||
| Line 9: | Line 9: | ||
<!-- Masukkan Data Artikel Disini --> | <!-- Masukkan Data Artikel Disini --> | ||
<p>CYP450 3A4 is a very important catalyst to transform the neutral form of aflatoxin to become DNA damaging form of aflatoxin oxide. CYP that constituvely produced in the cell is represented by a set of equation below.<br /> | <p>CYP450 3A4 is a very important catalyst to transform the neutral form of aflatoxin to become DNA damaging form of aflatoxin oxide. CYP that constituvely produced in the cell is represented by a set of equation below.<br /> | ||
| - | <img src=" | + | <img src="https://static.igem.org/mediawiki/igem.org/1/19/2013_ITB_Indonesia-cyp1.jpg" /></p> |
| - | + | ||
| - | + | ||
<div style="border:solid #F90">This set of equation is can be applied to another protein synthesis phenomena :<br /> | <div style="border:solid #F90">This set of equation is can be applied to another protein synthesis phenomena :<br /> | ||
1. RNA is transcribed from DNA. (DNA appeared on both side to state that DNA is not consumed nor produced because of this reaction)<br /> | 1. RNA is transcribed from DNA. (DNA appeared on both side to state that DNA is not consumed nor produced because of this reaction)<br /> | ||
| - | <img src=" | + | <img src="https://static.igem.org/mediawiki/igem.org/3/3f/2013_ITB_Indonesia-cyp2.jpg" /> <br /> |
2. Protein then translated from RNA<br /> | 2. Protein then translated from RNA<br /> | ||
| - | <img src=" | + | <img src="https://static.igem.org/mediawiki/igem.org/3/3f/2013_ITB_Indonesia-cyp3.jpg" /> <br /> |
3. RNA degrade by time. (Symbol on the right side represent ‘null’)<br /> | 3. RNA degrade by time. (Symbol on the right side represent ‘null’)<br /> | ||
| - | <img src=" | + | <img src="https://static.igem.org/mediawiki/igem.org/9/9d/2013_ITB_Indonesia-cyp4.jpg" /></div> |
<p>From literature, transcription polimerase rate of E. coli is approximately 55 nucleotide/s [1] and ribosomal translation rate of E. coli is approximately 18 residue/s [2]. With the length of CYP450 gene is 2000 nucleotide, we can calculate the transcription rate constant of CYP gene (ktrc) and the translation rate constant of CYP gene (ktrl).</p> | <p>From literature, transcription polimerase rate of E. coli is approximately 55 nucleotide/s [1] and ribosomal translation rate of E. coli is approximately 18 residue/s [2]. With the length of CYP450 gene is 2000 nucleotide, we can calculate the transcription rate constant of CYP gene (ktrc) and the translation rate constant of CYP gene (ktrl).</p> | ||
<div style="border:solid #F90">We calculate our transcription and translation rate simply by dividing the rate of transcption polimerase rate or ribosomal translation rate with the length of involved gene.<br /> | <div style="border:solid #F90">We calculate our transcription and translation rate simply by dividing the rate of transcption polimerase rate or ribosomal translation rate with the length of involved gene.<br /> | ||
| - | <img src=" | + | <img src="https://static.igem.org/mediawiki/igem.org/e/e8/2013_ITB_Indonesia-cyp5.jpg" /> <br /> |
| - | + | ||
Website like bionumbers.org can be really useful to gather this kind of data. </div> | Website like bionumbers.org can be really useful to gather this kind of data. </div> | ||
<p>Parameters involved in this phenomena are :</p> | <p>Parameters involved in this phenomena are :</p> | ||
Revision as of 03:02, 28 September 2013
CYP synthesis
CYP450 3A4 is a very important catalyst to transform the neutral form of aflatoxin to become DNA damaging form of aflatoxin oxide. CYP that constituvely produced in the cell is represented by a set of equation below.
1. RNA is transcribed from DNA. (DNA appeared on both side to state that DNA is not consumed nor produced because of this reaction)
2. Protein then translated from RNA
3. RNA degrade by time. (Symbol on the right side represent ‘null’)
From literature, transcription polimerase rate of E. coli is approximately 55 nucleotide/s [1] and ribosomal translation rate of E. coli is approximately 18 residue/s [2]. With the length of CYP450 gene is 2000 nucleotide, we can calculate the transcription rate constant of CYP gene (ktrc) and the translation rate constant of CYP gene (ktrl).
Website like bionumbers.org can be really useful to gather this kind of data.
Parameters involved in this phenomena are :
| Variable | Definition |
Value |
Source |
ktrc |
Transcription rate constant of CYP gene |
0,0275 s-1 |
Calculated |
ktrl |
Translation rate constant of CYP gene |
0,009 s-1 |
Calculated |
kdeg |
Degradation rate of mRNA CYP |
0,00256 s-1 |
[3] |
Reference
[1] Vogel U, Jensen KF. The RNA chain elongation rate in Escherichia coli depends on the growth rate. J Bacteriol. 1994 May176(10):2807
[2] Bremer, H., Dennis, P. P. (1996) Modulation of chemical composition and other parameters of the cell by growth rate. Neidhardt, et al. eds. Escherichia coli and Salmonella typhimurium: Cellular and Molecular Biology, 2nd ed. chapter 97, pp. 1559
[3] Global analysis of mRNA decay and abundance in Escherichia coli at single-gene resolution using two-color fluorescent DNA microarrays. Jonathan A. Bernstein, Arkady B. Khodursky, Pei-Hsun Lin, Sue Lin-Chao, and Stanley N. Cohen. Departments of Genetics and Biochemistry, Stanford University School of Medicine, Stanford, CA 94305; and Institute of Molecular Biology, Academia Sinica, Nankang, Taipei 115, Taiwan. May 27, 2002
