Johnllopez Week 6

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Reading Questions

  1. Week6.png
  2. For Gene X: Black, Dim Red, Black, Dim Green. For Gene Y: Black, Medium Red, Bright Green, Dim Green. For Gene Z: Black, Dim Red, Dim Red, Dim Red
  3. I would say that none of these genes were transcribed similar. Although X and Y share color patterns, with the exception of the third ratio, none of the transcription patterns align that well.
  4. Because the yellow color comes from the indication that there is no change within the genes, it would indicate that the reason most spots are yellow at their first time point is due to the fact that no change has occurred.
  5. The image indicated that TEF4 was repressed due to the light green color. This might be the case due to an increasing lack of glucose. Since glucose is necessary for translation to occur in this scenario (as it is the only available food source), the cell would respond to this by having perofrming less translation in order to preserve glucose.
  6. With the supply of glucose decreasing, the cells begin to perform cellular respiration in order to preserve what supply remains so that the cell might have energy.
  7. The guilt by association method is a way for the genome use to that ensure genes for enzymes in a common pathway are induced or repressed simultaneously because despite not knowing what that gene is, the same induction/repression can occur.
  8. In a scenario 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, I would expect the spots that represented glucose-repressed genes to be in the later time points of this experiment to be colored red.
  9. In a scenario 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, I would expect the spots that represented Yap1p target genes to be in the later time points of this experiment to be colored red.
  10. By performing enough of the same experiments to confirm that there is in fact a pattern, you could verify that you had truly deleted TUP1 or overexpressed YAP1 in the experiments described in questions 8 and 9.

Acknowledgements and References

Acknowledgements

I worked with my partner Mary Balducci in class. We exchanged contact information on Thursday. On Monday we met in the LSB to go over the assignment and review the material. I also looked up TCA to understand what it was and I found a Khan Academy article to help me answer a question. While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source. Johnllopez616 (talk) 18:57, 9 October 2017 (PDT)

References

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.
LMU BioDB 2017. (2017). Week 6. Retrieved October 9, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_4
The Citric Acid Cycle. Khan Academy. Retrieved October 9, 2017, from https://www.khanacademy.org/test-prep/mcat/biomolecules/krebs-citric-acid-cycle-and-oxidative-phosphorylation/a/the-citric-acid-cycle-2

Links to Other Pages

Individual Journal Entries and Assignments

Class Assignments

Class Weekly Journal Entries / Project Weekly Journal Entries

My Page

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