Matthew E. Jurek Week 8

Matthew E. Jurek BIOL398-03/S13

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• BIOL398-03/S13:Week_2
• BIOL398-03/S13:Week 3
• BIOL398-03/S13:Week 4
• BIOL398-03/S13:Week_5
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• BIOL398-03/S13:Week_8
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• BIOL398-03/S13:Week_13
• BIOL398-03/S13:Week_14

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• Matthew E. Jurek Week 2
• Matthew E. Jurek Week 3
• Matthew E. Jurek Week 4
• Matthew E. Jurek Week 5
• Matthew E. Jurek Week 6
• Anthony J. Wavrin/Matthew E. Jurek Metabolic Pathways Project
• Matthew E. Jurek Week 8
• Matthew E. Jurek Week 9
• Matthew E. Jurek Week 11
• Matthew E. Jurek Week 12
• Matthew E. Jurek Week 13
• Matthew E. Jurek Week 14
• Final Presentation

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.

• Submitted in class on Thursday morning

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.

• Hour 1 / 3 / 5 / 9
  • gene X black / dim red/ black/ dim green
  • gene Y black / red/ black-some green/ bright green
  • gene Z black / dim red/ dim red/ dim red

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

• The colors from 6b can be used to determine if any genes were transcribed similarly. At hour 1 all genes were transcribed similarly. During hour 3 gene X and gene Z were transcribed somewhat similarly even though their shades of red will be slightly different. At hour 5 gene X and gene Y were also transcribed similarly.

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

• I believe this question relates to figure 4.11. This figure illustrates a microarray showing gene expression based on glucose consumption. The yellow indicates no change, meaning there was no change in the expression of genes. This is seen at the first time point as there hasn't been a drastic change in the control vs. experimental environments. All conditions are normal at this point.

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).

• According to the database, TEF4 is a translational elongation factor that ultimately assists in protein synthesis. In Figure 4.12, the TEF4 spot is green meaning it's been repressed. If the food source is low, it makes sense that protein synthesis would be reduced as there is a decline in available energy.

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

• If glucose is running out, yeast will switch to aerobic respiration. This switch requires the TCA cycle as it is a part of aerobic respiration. As a result of this, TCA cycle genes would be induced if the glucose supply was running low.

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

• Along the lines of "guilt by association" a transcription factor can target several genes. This if a a transcription factor is induced, the genes it pertains to will also be induced. If the transcription factor is repressed, the genes it relates to will also be repressed.

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?

• A large number of red spots would be seen as a repressor gene has been deleted leading to "un-repressed" expression.

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

• Overexpression would result in a large number of red 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 because the transcription factor could be for a repressor which would result in the repression of a particular gene.

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?

• One of the neatest things about this type of science is the amount of available information stemming from previous work. All microarray results are available online as there is so much information to analyze. With that being said, there's been a lot of analyzation done on numerous microarrays already. Previous results could be used as a control to ensure your experiment is working properly. In order to verify the deletion or expression of a particular gene, reverse transcription PCR could be used. This would help to ensure genes had actually been deleted or overexpressed.