Ajvree 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. (Submitting in class)
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 hr- black
3 hr- red
5 hr- black
9 hr- green
Gene Y:
1 hr- black
3 hr- red
5 hr- green
9 hr- green
Gene Z:
1 hr- black
3 hr- red
5 hr- red
9 hr- red
7. (p. 110) Were any of the genes in Figure 4.7b transcribed similarly?
Gene X and Y were transcribed similarly. They were both induced hour 3 and repressed hours 5 and 9.
9. (p. 118) Why would most spots be yellow at the first time point?
At the first time point, no change has yet occurred. Rapid change does not happen until later in time.
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).
The TEF4 gene was repressed, as it went from yellow in one time frame to green in the next time frame.
11. (p. 120) Why would TCA cycle genes be induced if the glucose supply is running out?
TCA cycle genes would be simultaneously induced with the genes Trehalose synthase and glycogen synthase, which are used to convert glucose-6-phosphate into storage sugars. Since these genes are induced/repressed in concert, then if one is induced, the other would be, too.
12. (p. 120) What mechanism could the genome use to ensure genes for enzymes in a common pathway are induced or repressed simultaneously?
Simultaneous inducing or repressing could occur by using similar transcription factors for all genes involved.
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?
You would see a red spot.
14. (p. 121) What color spots would you expect to see on the chip when the transcription factor Yap1p is overexpressed?
You would expect to see green spots.
15. (p. 121) Could the loss of a repressor or the overexpression of a transcription factor result in the repression of a particular gene?
Yes. A repressor can function as a sort of defense for a gene, blocking unwanted stresses that may affect the functionality. Overexpression of a transcription factor could also harm a gene's ability to function properly, and alter the way transcription occurs.
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?
I would think that control spots should be yellow, since that means the genes were not over or under expressed. If the spots change to red or green, it is a safe bet that they were successfully deleted or overexpressed.
