Revision as of 00:58, 10 October 2017

Discovery Questions

1. 
2. • Gene X: Hour 1: Black Hour 3: Dim Red Hour 5: Black Hour 9: Medium Green
   • Gene Y: Hour 1: Black Hour 3: Medium Red Hour 5: Dim Green Hour 9: Bright Green
   • Gene Z: Hour 1: Black Hour 3: Dim Red Hour 5: Dim Red Hour 9: Dim Red
3. Gene X and Y were similar. Both had similar fold induction increase then deplete to 1:1 then proceed to fold repression.
4. • The technical reason these spots come up yellow is that there are equal amounts of green and red dye and when mixed they create yellow.
   • The biological reason a majority were unchanged, i.e yellow, was because of the conditions that the experiment placed on the DNA slides.
5. TEF4, or "translational elongation factor", was repressed, as the dot on the figure corresponded to bright green. The TEF4 could be reacting to the low amounts of glucose which provides energy to the cell. The TEF4 resorts to, according to Campbell, an energy saving mode therefore the genes were repressed.
6. During high stress environments genes are repressed and induced according to their energy levels. Due to TCA being a energy metabolic gene, it becomes induced in order to make energy efficiently and effectively.
7. The best mechanism a genome can use is a transcription factor to ensure genes for enzymes have a common induced or repressed pathway.
8. According to Campbell, TUP1 is responsible for the repression of glucose-repressed genes. Given this information I would expect the spots to be red, because the TUP1 and glucose would be depleted at said time period.

• (Question 14, p. 121) Consider a microarray experiment where cells that overexpress the transcription factor Yap1p were subjected to the same experiment of a timecourse of glucose depletion where cells at t0 (plenty of glucose available) are labeled green and cells at later timepoints (glucose depleted) are labeled red. What color would you expect the spots that represented Yap1p target genes to be in the later time points of this experiment?
• (Question 16, p. 121) Using the microarray data, how could you verify that you had truly deleted TUP1 or overexpressed YAP1 in the experiments described in questions 8 and 9?

Acknowledgments

1. This week I worked with my partner Dina Bashoura on the discovery questions segment of the homework. We met in person as well as messaged each other if we were stuck on a question or needed more explanation.
2. While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.

References

1. LMU BioDB 2017. (2017). Week 6. Retrieved October 5, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_6#Individual_Journal_Assignment