# Alyssa N Gomes Week 9 Journal

Alyssa N Gomes

MATH 388-01: Survey of Biomathematics Loyola Marymount University

## Week 9 Assignment

1. (Question 5, p. 110) Choose two genes from Figure 4.6b (PDF of figures on MyLMUConnect) 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 in hard copy and turn it in in class.

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.)
• Gene X
• Hour 1: Black
• Hour 3: Medium Red
• Hour 5: Black
• Hour 9: Medium Green
• Gene Y
• Hour 1: Black
• Hour 3:Bright Red
• Hour 5: Dim Green
• Hour 9: Bright Green
• Gene Z
• Hour 1: Black
• Hour 3: Dim Red
• Hour 5: Medium Red
• Hour 9: Medium Red<
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?
• Of the three genes, Gene X and Gene Y were most similarly transcribed. Gene Z ranged mostly on the red side, but both X and Y started out black, transcribed to red and eventually transitioned to green. Although the two were slightly different in hour 5, they are comparable.
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?
• Most spots would be yellow at the first time point because yellow indicates no change from initial readings. Yellow will serve as the conglomeration of the red and green gene expressions, as both converge to the initial DNA transcription levels.
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).
• Looking at the TEF4 spot in the yeast genome database, we see that TEF4 is repressed as glucose within the yeast decreases. There is a correlation between the two amounts decreasing at parallel rates. TEF4 helps bind tRNA to ribosomes; seeing as tRNA is needed to send messages and ribosomes are used primarily for the genes to be translated upon, repressing TEF4 would decrease translation. Because there is less glucose, the decreased rates of translation allow the cell to conserve its resources.
6. (Question, 11, p. 120) Why would TCA cycle genes be induced if the glucose supply is running out?
• When glucose supply runs out, TCA cycle genes would be induced in order use other genes for energy, to conserve the cell's resources. The cell would find other food resources and means to survive.
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?
• For the genome to ensure genes for enzymes in common pathways are induced or repressed simultaneously, the genome may employ similar activation or repression factors. There are a wide array of factors for both activation and repression, we can use prior studies of the effects of these factors upon the yeast genome and attribute that to ensure simultaneous reaction.
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?
• Upon a microarray experiment where cells deleted for repressor TUP1 are subject to same glucose depletion, I would expect the glucose-repressed genes to be a variation of the red color, because as demonstrated in previous examples, a depletion of glucose will lead to an increased expression of these genes, and an increased amount of activity.
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 YAP1 target genes to be in the later time points of this experiment?
• If the transcription factor YAP1 was subjected to the same procedure of glucose depletion, I would also expect the spots representing YAP1 genes to be red. YAP1 is made to resist external environmental stresses, so even though glucose is limited in this experiment, YAP1 resists these stresses and will continue to be overexpressed with increasing activity in the genome.
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?
• Using the microarray data, you can verify deletion of TUP1 or overexpresion of YAP1 in the above experiments by looking at: for TUP1, after time, the spots will remain black for TUP1, showing no signicant changes in the transcription, meaning that it has finished and been deleted. For overexpression of YAP1, the spots will be a bright red, exemplifying the >20 fold expression.