Alex A. Cardenas Week 10: Difference between revisions

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==Mutation Pictures==
==Mutation Pictures==
*Structure 2F58 - Amino Acid Position 315. This amino acid appears to be on the outside of the protein. Substitution could affect the function --> could lead to hydrophobic region buried inside protein --> thus affecting the function for binding and interaction.
*Structure 1F58 - Amino Acid Position 327. This amino acid appears to be on the surface of the protein which could affect the function due to different bonding and side chain interactions.


==Answered Questions from Chapter 4==
==Answered Questions from Chapter 4==

Revision as of 16:00, 2 November 2011

Mutation Pictures

  • Structure 2F58 - Amino Acid Position 315. This amino acid appears to be on the outside of the protein. Substitution could affect the function --> could lead to hydrophobic region buried inside protein --> thus affecting the function for binding and interaction.
  • Structure 1F58 - Amino Acid Position 327. This amino acid appears to be on the surface of the protein which could affect the function due to different bonding and side chain interactions.

Answered Questions from Chapter 4

  1. Number 5 from 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.
    • Show in graph later.
  2. Number 6b. from 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, determine the color for each ratio in Figure 4.7b.
    • For Hour 1 All genes expressed are at a ratio of 1 = all yellow --> no change in transcription.
    • For Hour 3 Gene X ratio is 2.2 = red , Gene Y ratio is 4.5 = red , Gene Z ratio is 1.5 = red.
    • For Hour 5 Gene X ratio is 2.2 = red , Gene Y ratio is 0.95 = green, Gene Z ratio is 2.0 = red.
    • For Hour 9 Gene X ratio is 0.15 = green , Gene Y ratio is 0.05 = green, Gene Z ratio is 2.0 = red.
  3. Number 7 from p. 110: Were any of the genes in Figure 4.7b transcribed similarly?
    • Gene X and Z somewhat transcribe similarly except for the last hour 9. At this point Gene X ratio is 0.15 and appears green, while Gene Z is 2.0 and appears red.
  4. Number 9 from p. 118: Why would most spots be yellow at the first time point?
  5. Number 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).
  6. Number 11 from p. 120: Why would TCA cycle genes be induced if the glucose supply is running out?
  7. Number 12 from p. 120: What mechanism could the genome use to ensure genes for enzymes in a common pathway are induced or repressed simultaneously?
  8. Number 13 from 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?
  9. Number 14 from p. 121: What color spots would you expect to see on the chip when the transcription factor Yap1p is overexpressed?
  10. Number 15 from p. 121: Could the loss of a repressor or the overexpression of a transcription factor result in the repression of a particular gene?
  11. Number 16 from 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?

Links

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