LauraTerada Individual Journal Assignment Week 8

• Laura Terada
• BIOL398-03/S13:Week 8

1. (p. 110) Choose two genes from Figure 4.6 https://mylmuconnect.lmu.edu/webapps/portal/frameset.jsp?tab_tab_group_id=_2_1&url=%2Fwebapps%2Fblackboard%2Fexecute%2Flauncher%3Ftype%3DCourse%26id%3D_57614_1%26url%3D (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.
2. (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.
   • 0.05: bright green, 0.15: green, 0.95: dim green, 1.0: black, 1.5: dim red, 2.0: dim red, 2.2: dim red, 4.5: medium red
3. (p. 110) Were any of the genes in Figure 4.7b transcribed similarly?
   • Yes, genes X and Y have similar patterns as shown by their values.
4. (p. 118) Why would most spots be yellow at the first time point?
   • The first time point is 0 hours, which means that the ratio between genes repressed and induced is 1. Since the quantity of genes repressed and induced are equal, the spots must be yellow. There would be no change in gene expression because expression changes on a level of hours.
5. (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 this experiment, the TEF4 spot was green, which means the gene was respressed due to low glucose levels. A reason why TEF4 gene regulation occurred from low glucose is because the yeast cell must induce other genes when in a starvation mode. Therefore, there is not enough energy for the yeast cell to induce TEF4 and so it must be repressed.
6. (p. 120) Why would TCA cycle genes be induced if the glucose supply is running out?
   • In the paper, the genes in the pathway were either induced or repressed together. Ald2 and Acs1 convert products of alcohol dehydrogenase into acetyl-CoA, a compound that enters the TCA cycle. Meanwhile, other genes regulating the TCA cycle become induced or repressed, and the outcome causes pyruvate toward oxalacetate into the TCA cycle. Phosphoenolpyruvate carboxykinase, fructose 1,6-biphosphatase, trehalose synthase, and glycogen synthase are also induced. This causes the overall flow of carbon to reverse toward glucose-6-phosphate. When glucose is running out, the yeast cells would want to convert that glucose to as many ATPs as it can via the TCA cycle, thus TCA cycle genes would be induced.
7. (p. 120) What mechanism could the genome use to ensure genes for enzymes in a common pathway are induced or repressed simultaneously?
   • An approach called guilt by association can be used to predict gene functions and to test these predictions through experimentation. The guilt by association method follows that genes with similar expression profiles have similar promoters, and genes with similar promoters have similar expression profiles. Therefore, one can use this method to determine if specific clustered genes, which have the same promoters, are being either repressed or reduced simlultaneously. Secondly, yeast have 200 regulatory transcription factors for 6,000 genes, which means that many genes can be induced or repressed simultaneously by one transcription factor.
8. (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?
   • The DNA chip would be red.
9. (p. 121) What color spots would you expect to see on the chip when the transcription factor Yap1p is overexpressed?
   • The chip would be red.
10. (p. 121) Could the loss of a repressor or the overexpression of a transcription factor result in the repression of a particular gene?
    • Yes, the loss of a repressor or overexpression of a transcription factor could result in the repression of a specific gene if the transcription factor induces the gene.
11. (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 are the genes that are not affected by the deletion or overexpression, which means the spots should be bright red (induced). Moreover, this can be verified by performing a microarray chip, and it should not show up on the chip.