Individual hw week 7
5. (p. 110) Choose two genes from Figure 4.6 (PDF of figures on MyLMUConnect) and draw a graph to represent the change in transcription over time. *
Note: You can do this by hand and submit a hard copy in class on Thursday, October 10 (morning after the midnight deadline) or you may do it by computer and upload it to your individual journal page by the midnight deadline.
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 (bright, medium, dim green, black, dim, medium, or bright red), determine the color for each ratio in Figure 4.7b. Gene X 1 hour -black 3 hours - red 5 hours - black 9 hours - green
Gene Y 1 hour - black 3 hours - red 5 hours - green 9 hours - green
Gene Z 1 hour - black 3 hours - red 5 hours - red 9 hours - red
7. (p. 110) Were any of the genes in Figure 4.7b transcribed similarly? I would say that Gene X and Gene Y would have a similar transcription because their trends over time reflect a repression
9. (p. 118) Why would most spots be yellow at the first time point?
It would be yellow at the first time point because it hasn't had time to respond to the change through a repression or induction of the desired genes.
10. (p. 118) Go to http://www.yeastgenome.org 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 gene regulation was part of the cell’s response to a reduction in available glucose (i.e., the only available food).
TEF4 was repressed due to the lack of available glucose. I hypothesize that it was repressed because more proteins would not help the cell in saving energy if the energy source is being limited
11. (p. 120) Why would TCA cycle genes be induced if the glucose supply is running out?
The TCA cycle is induced even though the glucose supply is running out because the cell is converting the sugars away from metabolism and towards storage.
12. (p. 120) What mechanism could the genome use to ensure genes for enzymes in a common pathway are induced or repressed simultaneously?
The cell could simultaneously induce and repress enzymes in a similar metabolic pathway through the use of similar transcription factors used
13. (p. 121) Given rule one on page 109, what color would you see on a DNA chip when cells had their repressor gene TUP1 deleted?
When the repressor is deleted the DNA spot would be red
14. (p. 121) What color spots would you expect to see on the chip when the transcription factor Yap1p is overexpressed?
When the transcription factor is deleted it would show up as multiple red spots on the micro array
15. (p. 121) Could the loss of a repressr or the over expression of a transcription factor result in the repression of a particular gene? Since similar transcription factors encode similar proteins with similar functions it is possible that the loss of a single repressor or transcription factor could still trigger a repression of a gene
16. (p. 121) What types of control spots would you like to see in this type of experiment? How could you verify that you had truly deleted or overexpressed a particular gene? The control spots I would like to see in this experiment would be the ethanol metabolism genes and the glucose synthesis genes. If you had truly deleted or overexpressed a gene then the micro array of the metabolic pathway would be all the same color.
