Paul Magnano: Week 8 Individual Journal: Difference between revisions

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**because the response to oxygen depletion would take time to come into effect
**because the response to oxygen depletion would take time to come into effect
*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).
*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 experiment, TEF4 was reduced as glucose levels decreased. TEF4 is an important part in protien synthesis, so I would hypothesize that when the glucose levels decreased, the yeast cells would show reduction in TEF4 to reduce the rate of protein synthesis. This would save energy, and would allow the yeast cells to survive longer if they were continually deprived of glucose (food).
*11. (p. 120) Why would TCA cycle genes be induced if the glucose supply is running out?
*11. (p. 120) Why would TCA cycle genes be induced if the glucose supply is running out?
**Because the TCA cycle allows energy production without glucose. Its the yeast response to sensing they "might starve".
**Because the TCA cycle allows energy production without glucose. Its the yeast response to sensing they "might starve". By activating the TCA cycle when they sense glucose is low, they can produce as much ATP as possible through the cycle, before glucose runs out.
*12. (p. 120) What mechanism could the genome use to ensure genes for enzymes in a common pathway are induced or repressed simultaneously?
*12. (p. 120) What mechanism could the genome use to ensure genes for enzymes in a common pathway are induced or repressed simultaneously?
 
The cells could use the same repressors or promoters to control the pathway, that way the control of the pathway is through one promoter or repressor.
*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?
*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?


Revision as of 19:39, 14 March 2013

Paul Magnano BIOL398-03/S13 User: Paul Magnano

Class Journals

Assignments/Individul Journals

Questions from ch 4

  • 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: 1.0 > black, 2.2 > medium red, 1.0 > black, 0.15 > bright green
    • gene Y: 1.0 > black, 4.5 >bright red, 0.95 > dim green, 0.05 > bright green
    • gene Z: 1.0 > black, 1.5 > dim red, 2.0 > medium red, 2.0 > medium red
  • 7. (p. 110) Were any of the genes in Figure 4.7b transcribed similarly?
    • All three genes transcribed similarly up to hour three, showing an increase. Genes X and Y transcribed similarily after hour 3 showing an overall decrease, although gene Y was more drastic in the reduction. Gene Z was transcribed differently after 3 hours, showing a continued increase.
  • 9. (p. 118) Why would most spots be yellow at the first time point?
    • because the response to oxygen depletion would take time to come into effect
  • 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 experiment, TEF4 was reduced as glucose levels decreased. TEF4 is an important part in protien synthesis, so I would hypothesize that when the glucose levels decreased, the yeast cells would show reduction in TEF4 to reduce the rate of protein synthesis. This would save energy, and would allow the yeast cells to survive longer if they were continually deprived of glucose (food).
  • 11. (p. 120) Why would TCA cycle genes be induced if the glucose supply is running out?
    • Because the TCA cycle allows energy production without glucose. Its the yeast response to sensing they "might starve". By activating the TCA cycle when they sense glucose is low, they can produce as much ATP as possible through the cycle, before glucose runs out.
  • 12. (p. 120) What mechanism could the genome use to ensure genes for enzymes in a common pathway are induced or repressed simultaneously?

The cells could use the same repressors or promoters to control the pathway, that way the control of the pathway is through one promoter or repressor.

  • 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?
  • 14. (p. 121) What color spots would you expect to see on the chip when the transcription factor Yap1p is overexpressed?
  • 15. (p. 121) Could the loss of a repressor or the overexpression of a transcription factor 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?
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