Carmen E. Castaneda: Week 8

Answer the following Discovery Questions from Chapter 4
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: Dr. Dahlquist said that this will be done on a seperate piece of paper to be submitted in class on Thursday.

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
 * at 1 hr it sould be black
 * at 3 hrs it should be medium red
 * at 5 hrs it should be black
 * at 9 hrs it should be bright green


 * gene y
 * at 1 hr it sould be black
 * at 3 hrs it should be bright red
 * at 5 hrs it should be dim green
 * at 9 hrs it should be bright green


 * gene z
 * at 1 hr it sould be black
 * at 3 hrs it should be dim red
 * at 5 hrs it should be medium red
 * at 9 hrs it should be medium red

7. (p. 110) Were any of the genes in Figure 4.7b transcribed similarly?

No, none of the genes in the figure were transcribed similarly because the rows did not have the same values.

9. (p. 118) Why would most spots be yellow at the first time point?

Most spots would be yellow at the first point because since they are at the beginning of the process, they have yet to be induced or repressed so their red to green ration is 1:1.

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).

Over the course of the expirement, the TEF4 gene was repressed because we see it go from yelloww to a dim green that becomes brighter as the expirement continued. TEF4's gene regulation was part of the cell's reponse to the reduction in available glucose because since it requires energy to do the binding of aminoacyl-tRNA (AA-tRNA) to the ribosome as explained TEF4 we know it will need to consume the only available food which in this case is the glucose.

11. (p. 120) Why would TCA cycle genes be induced if the glucose supply is running out?

The TCA cycle genes would be induces if the glucose supply is running out because since they are involved in the glycolisis process they would feel as if they were starving and thus react in such a way.

12. (p. 120) What mechanism could the genome use to ensure genes for enzymes in a common pathway are induced or repressed simultaneously?

The mechanism the genome could use to ensure genes for enzymes in a common pathway are induced or repressed simultaneously is the guilt by association method which leads to predictions which later can be tested.

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?

Given rule one on page 109, the color we would see on a DNA chip when cells had their repressor gene TUP1 deleted would be red since this is a cell grown in experimental conditions.

14. (p. 121) What color spots would you expect to see on the chip when the transcription factor Yap1p is overexpressed?

The color spots we would expect to see on the chip when the transcription factor Yap1p is overexpressed is also red since once again this would be grown under experimental conditions.

15. (p. 121) Could the loss of a repressor or the overexpression of a transcription factor result in the repression of a particular gene?

The loss of the repressor or the overexpression of a transcription factor could result in the repression of a particular gene because as this is a discovery since it is not for sure until the question is asked and put onto the test in the lab, but as stated in the book we know that as Yap1p was overexpossed, the putative aryl-alcohol was reduced or in other words repressed. (pg.122)

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 types of contorl spots we would like to see in this type of experiment are green because as we are dealing with a controlled enviorement and according to rule 1 on page 109, that's what it should be. The only way we can verify that we truly deleted or overexpossed a particular gene is if we find no change in our system because it would treat our experimental as a controlled system.