Team:ITB Indonesia/Modeling/Cytochrome

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.

This set of equation is can be applied to another protein synthesis phenomena :
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).

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.

Website like bionumbers.org can be really useful to gather this kind of data.

Parameters involved in this phenomena are :

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