Sarah Carratt: Week 8

Formatting

 * Store this journal entry as "username Week 8" (i.e., this is the text to place between the square brackets when you link to this page).
 * Create the following set of links. (HINT: you can do all of this easily by adding them to your template and then using the template on your pages.)
 * Link to your journal entry from your user page.
 * Link back from your journal entry to your user page.
 * Link to this assignment from your journal entry.
 * Don't forget to add the "BIOL398-01/S11" category to the end of your wiki page.

Discovery Questions from Chapter 4

 * (p. 110) Choose two genes from Figure 4.6 (PDF of figures on MyLMUConnect) and draw a graph to represent the change in transcription over time.  * Note: Dr. Dahlquist said that this will be done on a seperate piece of paper to be submitted in class on Thursday.
 * (p. 110) Look at Figure 4.7, which depicts the loss of oxygen over time and the transcriptional response of three genes.  These data are the ratios of transcription for genes X, Y, and Z during the depletion of oxygen.  Using the color scale from Figure 4.6 (bright, medium, dim green, black, dim, medium, or bright red), determine the color for each ratio in Figure 4.7b.
 * (p. 110) Were any of the genes in Figure 4.7b transcribed similarly?
 * (p. 118) Why would most spots be yellow at the first time point?
 * (p. 118) Go to http://www.yeastgenome.org and search for the gene TEF4; you will see it is involved in translation.  Look at the time point labeled OD 3.7 in Figure 4.12, and find the TEF4 spot.  Over the course of this experiment, was TEF4 induced or repressed?  Hypothesize why TEF4’s gene regulation was part of the cell’s response to a reduction in available glucose (i.e., the only available food).
 * (p. 120) Why would TCA cycle genes be induced if the glucose supply is running out?
 * (p. 120) What mechanism could the genome use to ensure genes for enzymes in a common pathway are induced or repressed simultaneously?
 * (p. 121) Given rule one on page 109, what color would you see on a DNA chip when cells had their repressor gene TUP1 deleted?
 * (p. 121) What color spots would you expect to see on the chip when the transcription factor Yap1p is overexpressed?
 * (p. 121) Could the loss of a repressor or the overexpression of a transcription factor result in the repression of a particular gene?
 * (p. 121) What types of control spots would you like to see in this type of experiment?  How could you verify that you had truly deleted or overexpressed a particular gene?

Online Sources

 * Campbell, A.M. and Heyer, L.J. (2003), "Chapter 4: Basic Research with DNA Microarrays", in Discovering Genomics, Proteomics, and Bioinformatics, Cold Spring Harbor Laboratory Press, pp. 107-124. (Available on MyLMUConnect; the color figures are also posted there)
 * DeRisi, J.L., Iyer, V.R., and Brown, P.O. (1997)  Exploring the Metabolic and Genetic Control of Gene Expression on a Genomic Scale.  Science  278:  680-686.
 * This animation from Malcolm Campbell may also be helpful.

Entry on Due Date



 * Color ratios for Figure 4.7 after 1, 3, 5 & 9 hours
 * Gene X: black, medium red, black, medium green
 * Gene Y: black, bright red, dim green, bright green
 * Gene Z: black, dim red, medium red, medium red
 * Gene X and Gene Y were transcribed similarly.
 * There is no change in gene expression at the beginning, so most spots are yellow (aka not induced or repressed yet).
 * TEF4 is repressed in a response to a reduction in glucose. This illustrates the ability of a cell to respond to low food sources and prioritize. Protein synthesis, the end result of TEF4 (an elongation factor), is less important that survival. Energy is diverted to inducing other genes.
 * The TCA cycle has the same promoter sequence as another gene that is induced by a lack of glucose. These promotors are recognized by ribosomes at the same time (since they have the same sequence). This is "guilt by association."
 * Give them the same promoter/binding factors to recognize under set conditions.
 * Red (induced) when TUPi is deleted
 * Red (induced) when Yap1 is over-expressed
 * The loss of a repressor/over-expression of a transcription factor could cause the expression of a gene only if something else was induced by the conditions that allowed for the first two changes.
 * Green spots (repressed); verify by comparing with a control microarray

Revisions After Class Discussion

 * Cell represses proteien synthesis gene because want to conserve ATP and carbon. Turn off energy intensive processes when running out of fuel. Turn off non-esential functions.
 * Dioxic shift occurs and ethanol is converted to CO2 inorder to keep producing ATP. It would switch to TCA if the energy source for glycolysis was running out. Meanwhile, it would have plenty of substrates for TCA to make ATP.
 * Mechanism for making sure they are induced and repressed simultaneously by transcription factors. Two kinds of transcription factors are general (bind to promoter to find location of gene) and regulatory DNA sequences (tell cell "when" and "how much"). Yeast have about 200 regulatory transcription factors for 6,000 genes. Regulate as a set by having same motif for same regulatory transcription factor. Either activators or repressors.