Ksherbina Week 7
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| Final Project | Team H(oo)KD Project Page | Journal Club Presentation | Project Individual Journal |
Answers to Discovery Questions from Chapter 4 of Discovering Genomics, Proteomics, and Bioinformatics
5. Graph of transcription of DMC1 and SPS100 over time:
6b. Gene X 1 hour: black
- Gene X 3 hour: dim red
- Gene X 5 hour: black
- Gene X 9 hour: medium green
- Gene Y 1 hour: black
- Gene Y 3 hour: medium red
- Gene Y 5 hour: dim green (almost black)
- Gene Y 9 hour: bright green
- Gene Z 1 hour: black
- Gene Z 3 hour: dim red
- Gene Z 5 hour: dim red
- Gene Z 8 hour: dim red
7. Gene X and Gene Y were transcribed similarly. The genes were induced after 3 hours, went back to the control state (no fold change) after 5 hours, and were repressed after 9 hours.
9. At the first time point, the cell density is very low. Consequently, there is no appreciable depletion of the source of glucose. Since there is no stress present, as there would be if the availability of glucose was significantly decreasing, most of the genes are not being induced or repressed. Thus, most of the spots are yellow.
10. As the experiment progressed, the depletion of glucose, the starting material for glycolysis, inhibited aerobic respiration. As a result, the cells produced little ATP. Since a cell needs ATP to perform translation, the depletion of glucose inhibited translation. Therefore, over the course of the experiment, TEF4 was repressed.
11. If the glucose supply is running out, TCA cycle genes will be induced in order to produce oxaloacetate. The cell can then use oxaloacetate to perform gluconeogenesis in order to produce glucose.
12. To ensure that genes for enzymes in a common pathway are induced or repressed simultaneously, these genes would have to share a promoter.
13. If the repressor gene TUP1 is deleted, then whatever cells controlled by the TUP1 transcription factor would no longer be repressed. As a result, the spots on a microarray corresponding to those genes would appear red.
14. If the transcription factor Yap1p is overexpressed, then the spots on the microarray corresponding to the genes regulated by this transcription factor would appear red.
15. If the transcription factor that is overexpressed is a repressor, then a particular gene controlled by that transcription factor would be repressed. The loss of a repressor may result in the repression of a gene if that lost repressor inhibited a transcription factor that repressed that particular gene.
16. For this type of experiment, I would like to see yellow spots for control spots because these spots correspond to genes that did not have a change in expression between the control and experimental populations. The spot on the microarray for a gene that was truly deleted should appear black. To verify that a gene was truly overexpressed, I would normalize the microarray data and then see what spots would still appear bright after the normalization.
