Difference between revisions of "Emmatyrnauer Week 6"

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(answering more questions)
(answering more questions; getting rid of questions themselves)
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#(Question 5, p. 110) Choose two genes from Figure 4.6b (PDF of figures on Brightspace) and draw a graph to represent the change in transcription over time. Create your plot in Excel (or other program that can do plots) and display the image up on your wiki page. Alternately, you can do it by hand, scan or take a photo of the plot, and display the image on your wiki page.
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#The ratio is calculated by dividing one gene’s activity in cells gradually consuming all the available oxygen by its activity in control cells with unlimited oxygen. Therefore, Gene X goes from black to dim red to black to medium green. Gene Y goes from black to medium red to dim green to bright green. Finally, Gene Z goes from black to dim red and stays at dim red. (In the order of 1 hour, 2 hour, 3 hour, and 4 hour, respectively)
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#(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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#Genes X and Y were transcribed similarly.
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#*The ratio is calculated by dividing one gene’s activity in cells gradually consuming all the available oxygen by its activity in control cells with unlimited oxygen. Therefore, Gene X goes from black to medium red to black to medium green. Gene Y goes from black to bright red to dim green to medium green. Finally, Gene Z goes from black to dim red to medium red and then stays at medium red.
 
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#(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?
 
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#*Genes X and Y were transcribed similarly.
 
 
#(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?
 
#(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?
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#*At time 0, no/very little change has occurred in terms of expression or repression of the gene. Spots with equal expression and repression compared to the reference sample appear yellow because red and green mix to make yellow.   
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#At time 0, no/very little change has occurred in terms of expression or repression of the gene because the cells have just been exposed to the experimental growth conditions. Spots with equal expression and repression compared to the control sample appear yellow because red and green mix to make yellow.   
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#(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).
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#TEF4 was repressed over the course of the experiment indicated by the green color. TEF4's change in expression was part of the cell's response to a reduction in available glucose. Glucose is the source of energy for cells and in the absence of glucose, actions that expend the cells energy (such as translation) may be limited.
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#*TEF4 was repressed over the course of the experiment indicated by the green color. TEF4's change in expression was part of the cell's response to a reduction in available glucose. Glucose is the source of energy for cells and in the absence of glucose, actions that expend the cells energy (such as translation) may be limited.
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#The TCA cycle does not use glucose directly--glucose is converted into pyruvic acid prior to its entrance into the TCA cycle.
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#(Question, 11, p. 120) Why would TCA cycle genes be induced if the glucose supply is running out?
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#These genes in the common pathway could all be induced or repressed by the same transcription factor (pg. 119).
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#*The TCA cycle does not use glucose directly--glucose is converted into pyruvic acid prior to its entrance into the TCA cycle.
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#I would expect these spots to be red because since the repressor is absent, the cells would continue to express the gene even in the absence of glucose.
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#(Question 12, p. 120) What mechanism could the genome use to ensure genes for enzymes in a common pathway are induced or repressed simultaneously?
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#I would expect the spots to be red since Yap1p target genes allow for increased resistance to environmental stresses. Therefore, a depletion of glucose in the environment would induce more expression of these genes.  
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#*These genes in the common pathway could all be induced or repressed by the same transcription factor (pg. 119).
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#Deletion of TUP1 and YAP1 would result in a red spot on the microarray for Tup1p compared to a green spot and a brighter red spot for Yap1p (indicating more expression).
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#(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?
 
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#*I would expect these spots to be red because since the repressor is absent, and the cells would continue to use up the glucose.
 
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#(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?
 
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#*I would expect the spots to be green since Yap1p target genes allow for increased resistance to environmental stresses. Therefore, a depletion of glucose in the environment would not have as significant of an effect on these cells.
 
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#(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?
 
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Revision as of 04:11, 10 October 2017

  2. The ratio is calculated by dividing one gene’s activity in cells gradually consuming all the available oxygen by its activity in control cells with unlimited oxygen. Therefore, Gene X goes from black to dim red to black to medium green. Gene Y goes from black to medium red to dim green to bright green. Finally, Gene Z goes from black to dim red and stays at dim red. (In the order of 1 hour, 2 hour, 3 hour, and 4 hour, respectively)
  3. Genes X and Y were transcribed similarly.
  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?
  5. At time 0, no/very little change has occurred in terms of expression or repression of the gene because the cells have just been exposed to the experimental growth conditions. Spots with equal expression and repression compared to the control sample appear yellow because red and green mix to make yellow.
  6. TEF4 was repressed over the course of the experiment indicated by the green color. TEF4's change in expression was part of the cell's response to a reduction in available glucose. Glucose is the source of energy for cells and in the absence of glucose, actions that expend the cells energy (such as translation) may be limited.
  7. The TCA cycle does not use glucose directly--glucose is converted into pyruvic acid prior to its entrance into the TCA cycle.
  8. These genes in the common pathway could all be induced or repressed by the same transcription factor (pg. 119).
  9. I would expect these spots to be red because since the repressor is absent, the cells would continue to express the gene even in the absence of glucose.
  10. I would expect the spots to be red since Yap1p target genes allow for increased resistance to environmental stresses. Therefore, a depletion of glucose in the environment would induce more expression of these genes.
  11. Deletion of TUP1 and YAP1 would result in a red spot on the microarray for Tup1p compared to a green spot and a brighter red spot for Yap1p (indicating more expression).
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