Homework

Weekly homework submissions:

• Week 1 HW: Principles and Practices

  First, describe a biological engineering application or tool you want to develop and why. This could be inspired by an idea for your HTGAA class project and/or something for which you are already doing in your research, or something you are just curious about. Response I’m really interested in the development of a new method that decreases the rate of DNA mutations in humans, using one of the genes found in the DNA of whales, the CIRBP (cold inducible RNA building protein) gene provides a significant performance at non homologous end joining, which is a mechanism that cells use to repair damaged DNA, especially when DSB (DNA double strand break) occurs. Although this gene is also found in humans, it doesn’t express the same sufficient amount of the protein as the amount expressed in whales, that explains why whales survive and live longer than humans, although they are bigger in size, which means they have more genes and more divisions that should increase their error prone and susceptibility to cancer. Applying procedures to human cells, where they receive the CIRBP gene from whale cells, could lead to significant development in the field of age-related medical conditions and in cancer resistance, since both are induced by DNA mutations.

• Week 2 HW: dna-read-write-and-edit

  Nature’s machinery for copying DNA is called polymerase. What is the error rate of polymerase? How does this compare to the length of the human genome. How does biology deal with that discrepancy? The error rate of polymerase is 1:106 nucleotides, and the length of the human genome is 3.2 gbp or Gega base pair (=3.2* 109), this means that if we divide the length of the genome by one million, we would get 3 thousand, which represents the number of errors per genome of a single person. Our bodies use polymerase proof reading which is a process done by DNA polymerases, where they have the ability to detect mistakes done in the newly synthesized DNA strand, while simultaneously building it, when such mistakes are detected, they stop their function, send the new strand to a different site, where they preform exonucleases activity on it by cutting out the wrong base that was added, from the 3’ to 5’ side, then the DNA polymerases enzymes return to their original site and continue their function. These modifications are done within the replication process, there are other modifications that are done after the replication process (post-replication modifications) including mismatch repairs where some proteins are able to detect base pair mismatches on the new DNA strand and they cut them out and build the correct matches using the template strand.