Msaeedi23 Week 7

From LMU BioDB 2015
Jump to: navigation, search
  1. (Question 5, p. 110) Choose two genes from Figure 4.6b (PDF of figures on MyLMUConnect) and draw a graph to represent the change in transcription over time. You can either create your plot in Excel and put the image up on your wiki page or you can do it in hard copy and turn it in in class.
    • Graph.png
  2. (Question 6b, p. 110) Look at Figure 4.7, which depicts the loss of oxygen over time and the transcriptional response of three genes. These data are the ratios of transcription for genes X, Y, and Z during the depletion of oxygen. Using the color scale from Figure 4.6, determine the color for each ratio in Figure 4.7b. (Use the nomenclature "bright green", "medium green", "dim green", "black", "dim red", "medium red", or "bright red" for your answers.)
    • Gene X at 1,3,5, & 9 hours: black, dim green, black, dim red. Gene Y at 1,3,5, & 9 hours: black, medium green, black, slightly red, medium red. Gene Z at 1,3,5, & 9 hours: black, black slightly green, dim green, dim green.
  3. (Question 7, p. 110) Were any of the genes in Figure 4.7b transcribed similarly? If so, which ones were transcribed similarly to which ones?
    • Gene Z was transcribed a little similarly to SPS100, because it went from black to a dark green, that gradually became greener.
  4. (Question 9, p. 118) Why would most spots be yellow at the first time point? I.e., what is the technical reason that spots show up as yellow - where does the yellow color come from? And, what would be the biological reason that the experiment resulted in most spots being yellow?
    • The technical reason a yellow spot shows at the first time point is because yellow indicates no change in gene induction/repression. The genes are arranged so that they are near other genes with similar expression patterns.
  5. (Question 10, p. 118) Go to the Saccharomyces Genome Database and search for the gene TEF4; you will see it is involved in translation. Look at the time point labeled OD 3.7 in Figure 4.12, and find the TEF4 spot. Over the course of this experiment, was TEF4 induced or repressed? Hypothesize why TEF4’s change in expression was part of the cell’s response to a reduction in available glucose (i.e., the only available food).
    • The gene appears slightly green, with some yellow, which would allow us to determine that the TEF4 gene is repressed. With less available glucose expression of this gene is repressed as a result because it is the transcription elongation factor.
  6. (Question, 11, p. 120) Why would TCA cycle genes be induced if the glucose supply is running out?
    • TCA cycle genes are induced if the glucose supply is running out because the TCA cycle is a key component involved in the glycolysis pathway necessary for glucose production.
  7. (Question 12, p. 120) What mechanism could the genome use to ensure genes for enzymes in a common pathway are induced or repressed simultaneously?
    • Through regulating various amounts of glucose and, subsequently, observing the genes that are induced or repressed at various amounts of glucose could differentiate them in a common pathway simultaneously.
  8. (Question 13, p. 121) Consider a microarray experiment where cells deleted for the repressor TUP1 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 glucose-repressed genes to be in the later time points of this experiment?
    • I would expect the glucose-repressed gene spots to be green later in the experiment because these genes will be repressed when there is plenty of glucose available.
  9. (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?
    • Later in the experiment, I would expect the Yap1p target gene spots to be red because these cells overexpress this specific transcription factor.
  10. (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?
    • With the use of the microarray data we are able to verify whether TUP1 was deleted or YAP1 was overexpressed in the experiments described by comparing the results of these experiments with the microarray data to verify these results.

Mahrad Saeedi

Class Whoopers Team Page
Assignment Links
Individual Journals
Shared Journals
Retrieved from "https://xmlpipedb.cs.lmu.edu/biodb/fall2015/index.php?title=Msaeedi23_Week_7&oldid=2844"