Homework
Weekly homework submissions:
Week 1 HW: Principles and Practices
I found myself very interested in the aspect of biosynthesis and engineering fabric-like material from microorganisms. The example shown in the first lecture of jackets made from bacterial cellulose piqued my curiosity in particular because it involves possibly making clothes from sustainable and biodegradable material instead of plastic. As a biology student, this application opened my eyes to a new and exciting path I could take in the future that is independent from medicinal applications. For now, I’m very curious about it. But hopefully, I will be able to make this my final project and get hands on experience in synthesizing such materials.
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? response: The error rate of polymerase is one per million bases. Compared to the human genome which is in total 3.2 GBP, which means approximately 3000 errors per genome. The human body deals with this error through a few ways: 1) polymerase proofreading: this utilizes 3’-5’ exonuclease which splices out the wrong mismatched nucleotide from the 3’ end of the strand. This process happens while the DNA replication is active. 2) Mismatch repair: after DNA is finished replicating, proteins like MutS read the strand for incorrect pairings that have escaped the earlier proofreading. It, similarly, cuts out the incorrect nucleotide before resynthesizing that section. How many different ways are there to code (DNA nucleotide code) for an average human protein? In practice what are some of the reasons that all of these different codes don’t work to code for the protein of interest?
part 1:Create a pattern/image in the style of Paul Vanouse’s Latent Figure Protocol artworks. You might find Ronan’s website a helpful tool for quickly iterating on designs! part 3: 3.1. Choose your protein. In recitation, we discussed that you will pick a protein for your homework that you find interesting. Which protein have you chosen and why? Using one of the tools described in recitation (NCBI, UniProt, google), obtain the protein sequence for the protein you chose.
Generate an artistic design using the GUI at opentrons-art.rcdonovan.com. ) Using the coordinates from the GUI, follow the instructions in the HTGAA26 Opentrons Colab to write your own Python script which draws your design using the Opentrons. A) I have obtained the GUI coordinates, but by the time i got around to run the coordinates on the opentron Colab, the website had stopped responding to the codes. and so i was unable to use the website as instructed or access the coordinates again.