Alex A. Cardenas Week 10
- 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 of molecules. The images can be found here.
- 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. The images can be found here.
Answered Questions from Chapter 4
- 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.
- 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.
- Number 7 from p. 110: Were any of the genes in Figure 4.7b transcribed similarly?
- Gene X and Y somewhat transcribe similarly except for the last hour 9. At this point Gene Z ratio is 0.15 and appears green, while Gene Z is 2.0 and appears red. Gene X and Y probably undergo aerobic function and Gene Z -->anaerobic.
- Number 9 from p. 118: Why would most spots be yellow at the first time point?
- Most spots would be yellow at the first time point because the mRNA would have not time to change transcription. When first exposed --> no time to transcribe and it shows yellow. There would be no glucose because the cell does not need it for regulation.
- 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).
- When compared to the first points the TEF4 expression showed a decrease for the last part of the data. The cell is most likely conserving energy because TEF4 is used in cell growth.
- Number 11 from p. 120: Why would TCA cycle genes be induced if the glucose supply is running out?
- The TCA cycle would be induced if glucose was running out because it reverses the overall flow of carbon toward glucose-6-phosphate. Which in turn induceds glycogen synthase and trehalose synthase which make storage sugars by converting glucose-6-phoshate.
- 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?
- They could all have the same transcription factors which allows for the genes to all be expressed at once or not at all. This could play a role in a common pathway when different enzymes that all induce or repress the genes.
- 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?
- You would see a red color on a DNA chip when cells had their represor gene TUP1 deleted.
- Number 14 from p. 121: What color spots would you expect to see on the chip when the transcription factor Yap1p is overexpressed?
- Red spots would most be expected because the transcription factor Yap1p is overexpressed.
- 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?
- Yes due to different gene pathways that inhibit or stimulate expression of other genes. Gene 1 could inhibit or be dependent on Gene 2, thus if Gene 2 is not expressed then Gene 1 will not be expressed either.
- 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?
- Control spots should be unaffected by the the gene interactions with repressors and transcription factors. This is why it is called a 'control spot' because it does not show variation and does not show to be affected by the transcription factors. The microarray data should include the gene that codes for the transcription factor to verify that we had truly deleted or overexpressed a particular gene --> it will be shown along with other genes that are expressed.