Individual Journal Week 8

Answer the following Discovery Questions from Chapter 4

5. (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.

• Will be turned in Tuesday.

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.

• .05 ratio: Bright Green
• .15 ratio: Medium Green
• .95 ratio:Dim Green
• 1.0 ratio: black
• 1.5 ratio:Dim Red
• 2.0 ratio:Dim Red
• 2.2 ratio:Dim Red
• 4.5 ratio:Medium Red

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

• X and Y seem similar, their ratios progress in a similar manner and they are repressed.

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

• The spots are mostly yellow at the first point, because little change has occurred. Few changes have made in the yeasts environment, the oxygen levels are still relatively high and unchanged.

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).

• In Figure 4.12, TEF4 appears to be green and thus repressed. TEF4 repression was possibly part of the cell's response to a reduction in available glucose because the gene requires energy. TEF4 is involved in translation, as suggested by yeastgenome.org, and thus requires energy, glucose, to function. A decrease in glucose would mean that the cell would not have enough energy to continue the translation instigated by the TEF4 gene.

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

• In order to encourage the production of ATP, TCA cycle genes would be induced with declining glucose. Given a low level of glucose, the TCA cycle will optimize the use of glucose, at least in comparison to the possible outcomes of fermentation.

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

• The genome could use the same promotor or binding factors to identify in specific conditions to ensure genes for enzymes in a common pathway are induced or repressed simultaneously.

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 TUP1 a red color changed will be induced on a DNA chip.

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 a red color changed will be induced on a DNA chip.

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

• Repression of a particular gene could be caused by the loss of a repressor or the over-expression of a transcription factor. This is because the repressor or over-expression may create conditions that activates a particular gene. When these conditions change, the gene may be repressed.

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?

• You would like to see green repressed control spots, that can be verified by comparing to another control microarray in which deleted genes will be absent and over-expressed genes will be indicted by red spots.