HDelgadi Week 7

5. (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. *

   Note: You can do this by hand and submit a hard copy in class on Thursday, October 10 (morning after the midnight deadline) or you may do it by computer and upload it to your individual journal page by the midnight deadline.

Done by Hand

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 Medium 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?

I would say gene X and gene Y were transcribed similarly since their ratios increase by the third hour, decrease by the fifth hour, and decrease even more significantly by the ninth hour, so their transcription activity fluctuates similarly with the depletion of oxygen.

9. (p. 118) Why would most spots be yellow at the first time point?

An equal amount of genes are being repressed (green spots) and reduced (red spots); therefore yellow spots appear.

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 this experiment, TEF4, is being repressed. Since there was a reduction of glucose, some of the genes had to become repressed and these genes would be those involved in protein production, so TEF4 was ultimately reduced while energy metabolism genes were induced.

11. (p. 120) Why would TCA cycle genes be induced if the glucose supply is running out?

The TCA cycle genes are induced by glucose since they would try to use up the depleting glucose due to its importance. Glucose turns into glycolysis and ultimately pyruvate which promotes the TCA cycle.

12. (p. 120) What mechanism could the genome use to ensure genes for enzymes in a common pathway are induced or repressed simultaneously?

The addition or depletion of glucose for example can cause genes that share a common pathway to be induced or repressed simultaneously if they share the same transcription factor binding sites.

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?

The color would be bright red for a strong induction.

14. (p. 121) What color spots would you expect to see on the chip when the transcription factor Yap1p is overexpressed?

I would expect to see a bright red color if the transcription factor Yap1p is over-expressed.

15. (p. 121) Could the loss of a repressor or the overexpression of a transcription factor result in the repression of a particular gene?

The loss of a repressor or the over-expression of a transcription factor can 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?

I would like to see repressed control spots. I could verify the deletion or over-expression of a particular gene by looking at the consequential colored spots, so if they are bright red then there has been a great induction by a deletion or over-expression of a gene. Comparing the colored spots before and after the deletion or over-expression of a particular gene would help with the verification of the desired results.

HDelgadi (talk) 21:08, 9 October 2013 (PDT) Class Journal Week 1