Difference between revisions of "Eyoung20 journal week 6"
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===(Question, 11, p. 120) Why would TCA cycle genes be induced if the glucose supply is running out?=== | ===(Question, 11, p. 120) Why would TCA cycle genes be induced if the glucose supply is running out?=== | ||
| + | The TCA cycle genes would be induced because the TCA cycle is a cycle that can be temporarily run without the presence of glucose, the use of this cycle will allow the cell to produce some energy while it starves. In essence it helps to keep the cells alive a little bit longer. | ||
| + | |||
===(Question 12, p. 120) What mechanism could the genome use to ensure genes for enzymes in a common pathway are induced or repressed simultaneously?=== | ===(Question 12, p. 120) What mechanism could the genome use to ensure genes for enzymes in a common pathway are induced or repressed simultaneously?=== | ||
===(Question 13, p. 121) Consider a microarray experiment where cells deleted for the repressor TUP1 were subjected to the same experiment of a timecourse of glucose depletion where cells at t0 (plenty of glucose available) are labeled green and cells at later timepoints (glucose depleted) are labeled red. What color would you expect the spots that represented glucose-repressed genes to be in the later time points of this experiment?=== | ===(Question 13, p. 121) Consider a microarray experiment where cells deleted for the repressor TUP1 were subjected to the same experiment of a timecourse of glucose depletion where cells at t0 (plenty of glucose available) are labeled green and cells at later timepoints (glucose depleted) are labeled red. What color would you expect the spots that represented glucose-repressed genes to be in the later time points of this experiment?=== | ||
Revision as of 16:49, 9 October 2019
Contents
- 1 Purpose
- 2 Questions
- 2.1 (Question 5, p. 110) Choose two genes from Figure 4.6b (PDF of figures on Brightspace) and draw a graph to represent the change in transcription over time. You can either create your plot in Excel and put the image up on your wiki page or you can do it by hand and upload a picture or scan.
- 2.2 (Question 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, determine the color for each ratio in Figure 4.7b. (Use the nomenclature "bright green", "medium green", "dim green", "black", "dim red", "medium red", or "bright red" for your answers.)
- 2.3 (Question 7, p. 110) Were any of the genes in Figure 4.7b transcribed similarly? If so, which ones were transcribed similarly to which ones?
- 2.4 (Question 9, p. 118) Why would most spots be yellow at the first time point? I.e., what is the technical reason that spots show up as yellow - where does the yellow color come from? And, what would be the biological reason that the experiment resulted in most spots being yellow?
- 2.5 (Question 10, p. 118) Go to the Saccharomyces Genome Database 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 change in expression was part of the cell’s response to a reduction in available glucose (i.e., the only available food).
- 2.6 (Question, 11, p. 120) Why would TCA cycle genes be induced if the glucose supply is running out?
- 2.7 (Question 12, p. 120) What mechanism could the genome use to ensure genes for enzymes in a common pathway are induced or repressed simultaneously?
- 2.8 (Question 13, p. 121) Consider a microarray experiment where cells deleted for the repressor TUP1 were subjected to the same experiment of a timecourse of glucose depletion where cells at t0 (plenty of glucose available) are labeled green and cells at later timepoints (glucose depleted) are labeled red. What color would you expect the spots that represented glucose-repressed genes to be in the later time points of this experiment?
- 2.9 (Question 14, p. 121) Consider a microarray experiment where cells that overexpress the transcription factor Yap1p were subjected to the same experiment of a timecourse of glucose depletion where cells at t0 (plenty of glucose available) are labeled green and cells at later timepoints (glucose depleted) are labeled red. What color would you expect the spots that represented Yap1p target genes to be in the later time points of this experiment?
- 2.10 (Question 16, p. 121) Using the microarray data, how could you verify that you had truly deleted TUP1 or overexpressed YAP1 in the experiments described in questions 8 and 9?
- 3 Acknowledgements
- 4 References
Purpose
This assignment is designed to give students an informative and active introduction to DNA microarrays, allowing students to gain a familiarity that will be useful in future projects.
Questions
(Question 5, p. 110) Choose two genes from Figure 4.6b (PDF of figures on Brightspace) and draw a graph to represent the change in transcription over time. You can either create your plot in Excel and put the image up on your wiki page or you can do it by hand and upload a picture or scan.
(Question 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, determine the color for each ratio in Figure 4.7b. (Use the nomenclature "bright green", "medium green", "dim green", "black", "dim red", "medium red", or "bright red" for your answers.)
| gene | 1 hour | 3 hour | 5 hour | 9 hour |
|---|---|---|---|---|
| gene x | 1.0 | 2.2 | 1.0 | 0.15 |
| gene Y | 1.0 | 4.5 | 0.95 | 0.05 |
| gene z | 1.0 | 1.5 | 2.0 | 2.0 |
| gene | 1 hour | 3 hour | 5 hour | 9 hour |
|---|---|---|---|---|
| gene x | Black | dim red | black | dim green |
| gene Y | Black | medium red | black | dim green |
| gene z | Black | dim red | dim red | dim red |
(Question 7, p. 110) Were any of the genes in Figure 4.7b transcribed similarly? If so, which ones were transcribed similarly to which ones?
Yes, gene x and gene y appear to have been transcribed similarly.
(Question 9, p. 118) Why would most spots be yellow at the first time point? I.e., what is the technical reason that spots show up as yellow - where does the yellow color come from? And, what would be the biological reason that the experiment resulted in most spots being yellow?
most spots would be yellow at the first time point because a yellow spot is the result of no change occurring in the regulation of the gene. The yellow color is a combination of the green and red colors in equal parts. This yellow color is a result of no change in regulation due to a cell not being stressed, which is why the first point is yellow because the cell has not experienced the stressor yet.
(Question 10, p. 118) Go to the Saccharomyces Genome Database 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 change in expression 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 repressed as seen by the green color it has in Figure 4.12 at the time point labeled as OD 3.7. The cell mostlikly repressed the gene due to the reduction in glucose and the cell conserving energy reduced it's transcription levels.
(Question, 11, p. 120) Why would TCA cycle genes be induced if the glucose supply is running out?
The TCA cycle genes would be induced because the TCA cycle is a cycle that can be temporarily run without the presence of glucose, the use of this cycle will allow the cell to produce some energy while it starves. In essence it helps to keep the cells alive a little bit longer.
