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Western University
Biology 2382B

Genetics Lecture No. 16: Quantitating Gene Regulation th Monday March 11 , 2013 Introduction: -So far, we have examined gene regulation in a strictly qualitative manner (e.g. the transcriptional levels of the lac operon were either high or low; the presence of glucose in the growth media decreased transcription of the lac operon). Is it possible to examine the transcription of genes in a quantitative manner? If so what could this tell us about transcriptional regulatory networks? Quantitating Gene Regulation: -The goal of quantitating gene regulation is to create working mathematical models of two very simple genetic networks. Here is a model we can use for a given gene Y: Activation: Repression: X -> (+) Y X -> (-) Y X = activator X = repressor Y = target gene Y = target gene -Using this model, we can quantify the rate of mRNA production and degradation for gene Y using a “source and sink” model: Source Sink The Y mRNA is being accumulated in box Y in nmoles: dY/dt = b - aY 1) When production rate > degradation rate, accumulation of Y mRNA in the box. 2) When production rate < degradation rate, loss of Y mRNA in the box. 3) When production rate = degradation rate, levels of Y mRNA stay the same. The level of Y mRNA is dependent on two things: 1) How much Y mRNA is produced through transcription of the source (rate of production) 2) How much Y mRNA is degraded through degradation by nucleases (rate of degradation) Spigots (a and b) control the flow of Y mRNA into the box: 1) When spigot b is open, there is a high production rate of Y mRNA (in nmoles/min) 2) When spigot a is open, there is a high degradation rate of Y mRNA (1/min) Degradation rate depends on the amount of Y mRNA that is present: • If a = 0.1/min, 10% of Y mRNA is degraded every minute • If at an instant in time, there are 1000 nmoles, the rate of degradation is 100 nmol/min • If at another instant in time, there are 100 nmoles, the rate of degradation is 10 nmol/min • a = 10 nmoles / min x 100 nmole = 0.1/min Simulating Gene Transcription: -The transcription of a gene can be simulated with the help of specialized computer programs. For example, it is possible to “create” a gene that is transcribed with a given production and degradation rate within a computer program. In this way, the computer can handle the calculations and you can focus on the results. The levels of Y mRNA will reach a steady state level within a cell based solely on production and degradation rates (in order to quantitate the amount of Y mRNA, you need to know production Steady State Level: Gene F: b = 10 nmoles/min; a = 0.1/min; Yinit and degradation -A concentration of Y mRNA reached over time rates): where the rate of change is zero; calculated by dividing dY/dt = b – a Y the production rate by the degradation rate of the gene. 0 = b – a Y st Gene G: b = 5 nmoles/min; a = 0.1/min; Y init [Y mRNA] (nmol) -b = -a Y st Gene H: b = 5 nmoles/min; a = 0.2/min; Y = 0 init Y stb / a Time (min) The initial levels of Y mRNA will not affect the final steady state levels of the message Gene F: b = 10 nmoles/min; a = 0.1/min
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