Simonwro120 Week 6
From LMU BioDB 2017
Contents
BioLogical Database Reading Questions
Question 1
Question 2
Gene X
- Hour 1: 1.0 ratio, black.
- Hour 3: 2.2 ratio, very dim red.
- Hour 5: 1.0 ratio, black.
- Hour 9: 0.15 ratio, medium green.
Gene Y
- Hour 1: 1.0 ratio, black.
- Hour 3: 4.5 ratio, dim red.
- Hour 5: 0.95 ratio, still black.
- Hour 9: 0.05 ratio, very bright green.
Gene Z
- Hour 1: 1.0 ratio, black.
- Hour 3: 1.5 ratio, very dim red.
- Hour 5: 2.0 ratio, very dim red.
- Hour 9: 2.0 ratio, very dim red.
Question 3
- Yes, genes X and Y were transcribed similarly. They both have a spike in transcriptions and then quickly fall nearing 0 by the end of hour 9.
Question 4
- A 1:1 ratio of the green and red cDNAs is indicated by a yellow pigment when the images merge. The yellow color comes from the images merging their own color on the computer. Figure 4.13 clearly shows that some genes change their expression levels when they realize they are starving, so as oxygen is reduced the ratio will either change to green or red. However, until those signals are sent, the merged image has a close ratio of 1:1.
Question 5
- According to OD 3.7 in Figure 4.12, TEF4 is depicted as repressed. This is possibly because TEF4 needs glucose to be able to transcribe, so as glucose supplies are reduced, the TEF4 gene's ability to transcribe reduce as well.
Question 6
- As glucose supplies are depleted, an increase in the production of acetyl-CoA is caused by alcohol dehydrogenase. This results in more molecules entering into the TCA cycle. To handle the increase in molecules, TCA cycle genes would be induced.
Question 7
- The genome is able to ensure induction or repression simultaneously if all the genes for enzymes in a common pathway are regulated by a similar transcription factor.
Question 8
- Tup1p represses glucose-repressed genes. Without Tup1p, these genes would not be repressed, regardless of the presence/absence of glucose. This would cause the rate of transcription to increase which would result in more red coloration.
Question 9
- Assuming that the cells which over express the transcription factor of Yap1p were subjected to the same experiment, in which glucose is depleted over time, the spots that represented Yap1p target genes would show up green as time moves forward in this experiment. This is because Yap1p confers environmental stress. This answer makes the assumption that glucose depletion is an environmental stress factor.
Question 10
- Well, to start you would acquire a microarray of the genome in a controlled setting. Next you would acquire a microarray of the genome as glucose is depleted and compare the colors. If the Tup1p related genes were red in the presence of glucose, then you could verify that you had deleted Tup1p in the glucose depletion experiment. Similarly, if Yap1p related genes were brighter red as the glucose was depleted, this would indicate an over expression of YAP1.
Acknowledgements
Worked in a group with Zach Van Ysseldyk to answer the questions in assignment 6.
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