BIOL368/F14:Nicole Anguiano Week 10

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HIV Structure Redux

  • To get more information on the individual subjects and clones studied, see Week 9. The presentation this information is coming from can be found here.
  • Note: Upon further investigation, it appears that I studied the actual beta sheet proteins instead of the protein in the beta sheet listed by PsiPred. As a result, instead of the information coming from the sequence "FYT", as PsiPred called for, I found the information for "RAF", which is the actual beta sheet in the V3 tip.
Shows the six proteins studied from the AIDS diagnosed patients.
Figure 1: Image displaying the amino acids talked about in the presentation, their locations, and the amino acid substitutions that exist in that location. The arrow points to the amino acid. The first word is the amino acid that is located at that particular spot. After come the substitutions, which are the mutations that were found in the V3 sequences studied in the presentation. The one or two possible alternatives are listed.
  • It is likely that the majority of the amino acids that switch out may not be necessarily relevant to the function of the gp120 protein. Due to the fact that all of the substitutions existed in viable clones, all of the substitutions create a functional protein that is capable of infection. Beginning on the right hand side at the bottom near the V3 tip, the substitution of Arginine for Lysine would likely had no effect. However, the substitution of Arginine for Serine would likely have an effect due to the dramatic change in size. The substitution of the Alanine for Threonine or Valine would likely cause some change in function, as Alanine is a very small molecule and Threonine and Valine are much larger. Phenylalanine, Tyrosine, and Leucine are all large, bulky molecules. The substitutions of Phenylalanine for Tyrosine would likely cause no effect, as they are both benzene rings. A substitution with Leucine would also likely have no effect due to its large size and lack of polarity, both traits that it shared with phenylalanine. The substitution of Aspartic Acid for Asparagine, due to its location in the already disordered random coil of the returning strand, likely would have little no effect. The substitution of Glutamine with Lysine, due to the large size, would also likely have little effect. Lastly, the substitution of alanine with arginine would likely have a dramatic effect. Alanine is a small, non-polar molecule and Arginine is an extremely large, basic molecule. As a result, it is highly likely that a change in function would occur as a result of this substitution.

Introduction to DNA Microarrays

  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.)
  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?
  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?
  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).
  6. (Question, 11, p. 120) Why would TCA cycle genes be induced if the glucose supply is running out?
  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?
  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?
  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?
  10. (Question 15, p. 121) Could the loss of a repressor or the overexpression of a transcription factor result in the repression of a particular gene?
  11. (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?

Finding a Journal Club Article

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Nicole Anguiano
BIOL 368, Fall 2014

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