Jwoodlee 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.
   • Hard copy
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.)
   • Chart With Answers
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?
   • X and Y were transcribed mostly the same because their ratios of limited oxygen transcription to unlimited oxygen transcription are mostly the same.
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 comes from no change in the expression of the gene, red indicates an induced gene and green indicates a repressed gene. Yellow is from a mixing of the green and red dyes. Most spots were yellow because there was not a big enough change in transcription to warrant a change in color.
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).
   • Based on the bright green color I would say that the gene was repressed. It is obvious that in the absence of energy cells will repress certain genes in order to save energy, I'm just not sure why the cell chose this gene. Based on the fact that this gene is involved with translation I would say that in an attempt to save energy the cell chose to slow down the rate of translation.
6. (Question, 11, p. 120) Why would TCA cycle genes be induced if the glucose supply is running out?
   • So I didn't realize that the Krebs cycle was also called the TCA cycle. After a quick google search this answer was pretty obvious. The cell is increasing energy production in an attempt to make as much ATP as it can before the glucose goes completely away. This would be advantageous because the cell could potentially survive a period of time with little or no food.
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 textbook mentions transcription factors, and that using "guilt by association" researchers can figure out similarities between genes if they are both repressed or both induced.
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?
   • The cDNA produced in the control population is green and the experimental condition is red. That simple rule on page 109 effectively means it is red because it would become the experimental condition. TUP1 represses glucose repressed genes and if it is gone the glucose-repressed genes would be induced.
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 is known to give cells resistance to their environments, the target genes of Yap1p are therefore genes that aid the cell in this environmental resistance. A bigger necessity for environmental resistance(less glucose) means genes that aid in environmental resistance will be expressed. So an increase in Yap1p means an increase in Yap1p target gene expression which means that the target genes would be red at later time points.
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?
    • For YAP1p over expression: checking if the Yap1p target genes are induced at an earlier time than what is normal. For TUP1 deletion: check if the gene is absent from the micro array.

BIOL 367, Fall 2015, User Page, Team Page

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