Dwilliams week 7 assignment

6b. Gene X

1 hour: black
3 hours: dim red
5 hours: black
9 hours: medium green

Gene Y

1 hour: black
3 hours: medium red
5 hours: dim green (almost black)
9 hours: bright green

Gene Z

1 hour: black
3 hours: dim red
5 hours: dim red
8 hours: dim red

7. It appeared to me that both Gene X and Gene Y were transcribed in a similar fashion. The genes were induced after 3 hours, then they went back to the control state -- and produced no fold change after 5 hours, and were repressed after 9 hours.

9. At the first time point, the cell density is very low, and there is no real depletion of the cells source of glucose. Because the cell is not under any stress, a majority of the genes are not being induced or repressed. This results in a majority of the spots being yellow.

10. As the experiment progressed, glucose became more and more depleted. This in turn crippled glycolysis and therefore inhibited aerobic respiration. Naturally, the cells could not produce ATP as a result. Without ATP to perform translation, the translation process was inhibited. This resulted in TEF4 being repressed.

11.TCA cycle genes would be induced because the cell would be metabolizing other cellular components. The cell can use this energy gained by consuming the other cellular components to complete the cycle, but is now missing those other non-essential components.

12. In order to ensure genes for enzymes in a common pathway are induced or repressed simultaneously, the cell could use the same set of transcription factors for all genes in the pathway.

13. If the repressor gene TUP1 is deleted, then the TUP1 transcription factor would no longer be able to be repressed. Because of this, the spots on a microarray corresponding to those genes would simply appear red.

14. If the transcription factor Yap1p is overexpressed, the spots corresponding to the genes regulated by this specific transcription factor would simply appear red.

15. If the transcription factor that is overexpressed happens to be a repressor, then the specific gene controlled by that transcription factor would be repressed as a result. The loss of a repressor would likely result in the repression of a gene, assuming that the lost repressor was responsible for inhibiting a transcription factor that repressed that specific gene in question.

16. For this type of experiment, I would like to see clear yellow control spots, meaning that there would be no change between control and experimental groups. One way to verify if a gene had been overexpressed would be if the color appeared to be green after being normalized. If the gene in question was entirely removed it would appear black on the microarray, which would mean that no protein was detected. A bright red would be produced when combined with the control.