Alondra Vega: Week 7

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. Will be turned in 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.

7. (p. 110) Were any of the genes in Figure 4.7b transcribed similarly? Yes, gene X and gene Y both have the same transcriptional pattern.

9. (p. 118) Why would most spots be yellow at the first time point? Most spots would be yellow at the first time point because the ratio would be 1:1. This means that there is no change in gene expression, which is expected in the first time point. Gene expression changes over time and then it will eventually turn back to its neutral position.

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). It seems that the spot is green, which means that the control of TEF4 was decreased. Thus, we can say that TEF4 was repressed. TEF4's regulation was part of the cell's response to a reduction in available glucose because the cell probably predicted that it might starve. This means that the cell had to focus on other areas of the cell that could prevent the starvation process, thus not leaving enough energy for translation and repressing TEF4.

11. (p. 120) Why would TCA cycle genes be induced if the glucose supply is running out? The TCA cycle uses to glucose molecules to make ATP as end product. If glucose supply is running out, then the cell will want to make as many ATP molecules as it can before the glucose runs out. This would induce the genes in the TCA cycle to help with the production of ATP.

12. (p. 120) What mechanism could the genome use to ensure genes for enzymes in a common pathway are induced or repressed simultaneously? A method that can be used is the guilt by association method. This method is able to make predictions of possible gene functions and testing these predictions. This means that genes with similar expression profiles might or will have similar promoters. This is very important. If they do not have the same promoter, then they cannot be related. This method also says that genes that have the same promoters also have similar expression profiles, which is what is used to test the predictions. This method will be able to tell us what is being induced and/or repressed when the genes in question are paired or clustered by using the guilt by association method. Also, genes could be found in the same chromosome or be located near each other.

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, the color spots that we would see on a DNA chip when cells had their gene TUP1 deleted is red, which means that glucose-repressed genes would be induced.

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

15. (p. 121) Could the loss of a repressor or the overexpression of a transcription factor result in the repression of a particular gene? Going by the two previous questions, I would answer no, since in both of those cases the genes were induced, not in a repression. I do not have other evidence to say otherwise.

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 should be that of the genes that are no affected by the gene that was deleted or overexpressed. To verify that you have deleted or overexpressed a gene, one can run a microarray chip and check that the gene was truly deleted, thus it would not show up in the chip. In the case of overexpression, the gene would be induced, thus it would have a red color.