Isaiah M. Castaneda Week 10

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HIV Structure Redux


Histidine is a surface protein. An amino acid change that occurred was from Asp to His. Aspartic is acidic, whereas Histidine is basic. For this reason, I believe that such a substitution may affect protein function.


Leucine is buried. In this position, a change from Glysine to Aalanine occured. Both amino acids have small side-chains which are non-polar hydrophobic. Therefore, it is possible that this substitution would not affect protein function.

Introduction to DNA Microarrays

  1. I chose genes SSP100 and DIT1. Time is in hours on the x-axis & change is on the y-axis. Negative values are associated with repression whereas positive values indicate induction. The graphs may be seen in THIS excel document.
  2. I created a nice chart in excel to organize the information. A ratio of 1 is black, above 1 is red, and below 1 is green. The file is HERE
  3. After 3 hours had passed, all genes' transcription increased. Gene Z appeared to have a consistent induction going on, whereas Genes X and Y eventually experienced repression.
  4. A yellow spot is indicative of no change in gene expression. Gene expression changes are not immediate. After appropriate amounts of time have elapsed, the colors are more likely to change in accordance with gene induction/repression.
  5. The spot for TEF4 in figure 4.12 appears to be green, which would mean that the gene was repressed. This repression could be a result of the low glucose levels. Without an energy source, there is nothing to drive the eEF1A releasing that TEF4 is responsible for.
  6. Glucose is broken down for energy in the TCA cycle. If this supply is running out, the same level of expression will not suffice in maintaining energy production. Rather, TCA genes would need to be induced to do the most they can with the low sources of fuel available.
  7. To repress or induce two different genes similarly, the genome may want them to have similar promoter sequences. Furthermore, the genes should be regulated by the same transcription factors. Genes that are regulated in the same way tend to be regulated by the same transcription factors.
  8. Rule 1 states that "the cDNA produced from the control population of cells is green and cDNA from cells grown in the experimental condition is red." The deletion of a gene is clearly an experimental condition, it should then follow that the cells under these conditions should be red.
  9. Over-expression leads to increased transcription. This induction would be verified by a red spot on the chip
  10. If a repressor is lost, it cannot repress the genes it was meant to repress. But perhaps over-expression of a particular transcription factor may cause another gene to be repressed. Over-expression of one gene may trigger the repression of another.
  11. Control spots would need to be yellow because as the control, the gene should not undergo any change. If you successfully deleted a gene, it should not appear in the experimental microarray chip and if you truly over-expressed a gene, the spot should turn red.

Journal Club

For this next Journal Club, I shall be working with the great, Samantha Hurndon. We will be researching the microarray dataset from species Helicobacter Pylori. Our paper is HERE