James P. McDonald Week 8

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Questions

Discovery Questions from Chapter 4

5. On paper

6. At 1 hour X, Y, and Z are all black because they had ratios at 1. At 3 hours X, Y, and Z are all a dim red each with a ratio between 1.5-4.5x increase. At 5 hours X and Y go back to black because they are both around a ratio of 1. Z stays at a dim red with a 2x increase. At 9 hours X is a dim/medium green with about a 6x decrease, Y is bright green with about a 20x decrease and Z is still a dim red remaining at a 2x increase.

7. All three of the genes were transcribed similarly up to the 3 hour mark. They all started at a ratio of one and had similar increases. After 3 hours X and Y continued to behave similar at the 5 hour mark as they went back to a ratio around 1. At the 9 hour mark both the X and Y ratios decreased but the Y decreased a lot more than X. Gene Z did not behave anything like X and Y after the 3 hour mark.

9. Initially, the control and experimental cultures have an abundance of glucose so regulation remains constant. Therefore there is no change in the expression of the gene, resulting in the yellow spot. Later in the experiment the glucose is depleted and regulation changes.

10. In the beginning of the experiment the TEF4 expression is constant but over the course of the experiment TEF4 expression was reduced as glucose supplies declined. The glucose is the only available food for the cell so when it was depleted the cell must have sensed that it may starve. It is stated in DeRisi's paper that the cells respond to this by repressing genes involved in protein synthesis. Since TEF4 is a gene used in translation, it is an important part of protein synthesis. I would hypothesize that the cell would repress TEF4 expression and other genes involved in protein synthesis when it detects starvation because the cell needs to save energy.

11. The TCA cycle produces energy in the form of ATP. When glucose runs lows the cell is able to sense that it will starve. The TCA cycle genes are induced because the cell wants to produce as much energy as it can before the glucose runs out. This is a way the cell can prepare itself to live in the absence of a food source for a period of time.

12. The cell could use the same promoter or repressors for a common pathway. That way, when the cell wants to promote or repress all the genes in a common pathway simultaneously, it will be able to do this through a single promoter or repressor rather than coordinate different ones.

13. If the repressor gene TUP1 is deleted the chip would show green in the in the spot for that gene because the gene will not be present in the experimental cells and only in the control. If this repressor gene was deleted it could result in other repressed genes turning red because they are no longer repressed.

14. If the transcription factor Yap1p was over expressed I would expect to see a red spots on the chip.

15. Yes it is possible for a gene to repressed if there is a loss of a repressor or the over expression of a transcription factor. Genes interact with transcription factors, repressors and other genes in many ways. Therefore a loss of a repressor or the over expression of a transcription factor could result in another gene being repressed, such as through a chain reaction of events.

16. The control spots should not be affected by the transcription factors or other gene interactions. The microarray chip should verify if a gene is deleted or over expressed. If a gene is truly deleted it will not appear on the chip. If a gene is over expressed it will appear bright red on the chip. The analysis of the microarray chip allows one to verify the presence and absence of particular genes.

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