Vpachec3 Week 7

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.
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   • Figure 1: The graph shows the change of transcription of DMC1 and SPS100. The values were assigned based on the color of the fold repression. For example, SPS100 there are dark green square in the data representing a 3x fold repression. The fold repression is symbolized through a negative sign and fold induced is represented by a positive sign. Thus, in this case, the dark green square was assigned -3 based on the 3x fold repression. The graph shows that there are two instances where DMC1 and SPS100 are similar in result which is at hour 0 and hour 11.
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.)
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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?
   • We see that genes X and Y have similar patterns from hours 1-9. Both genes, although at different quantities, show an increase from hours 1 to 3. After this increase, from hours 5 to 9 both genes show a constant decrease.
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?
   • Yellow is often the color at the first point because yellow means that there is no change in transcription. At the firs point, it is too soon to measure the change which is why it is yellow. The experiment yielded a result of most spots being yellow because the conditions in the experiment did not change enough to have a large impact on the transcription overall. There may have been changes for some pathways but not in the grand scheme of the experiment.
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 TEF4 gene was repressed throughout this experiment. We see that in Growth OD 3.7 the TEF4 gene was a light lime green. According to the scale, the green color ( of various shades depending on magnification) was a signal of fold repression. I hypothesis that because there wasn't enough glucose, food, present the gene was put on a repressed mode in order to survive the conditions. The gene did this by reducing the amount of energy used.
6. (Question, 11, p. 120) Why would TCA cycle genes be induced if the glucose supply is running out?
   • The main goal of the TCA cycle is to amp up the energy production in the cell. So if the glucose supply is running out, the TCA cycle would be induced so the cell can take the energy and store it for extreme conditions like the lack of glucose.
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?
   • The genome could use the same transcription factor for the genes in that particular pathway to ensure the gene for enzymes in a common pathway are induced or repressed 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?
   • Due to the fact that the TUP1's job is to repress glucose- repressed genes, when a cell doesn't have TUP1 it would function simply as glucose-repressed genes causing the spot to be red indicating their inability to take in glucose.
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?
   • Since Yap1p magnifies the expression of the target gene, the spot will be bright red indicating that there is a heavy concentration of expression.
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?
    • If all of the TUP1 and overexpressed YAP1 were deleted, all of the spots would be yellow in the microarray because they would be able to regulate their pathways more efficiently.

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