Homework
Weekly homework submissions:
Week 1 HW: Principles and Practices
BIO QR CODES My Synthetic Biology proposal is to create Biological QR codes that update based on the body's internal signals. (Think Biomarkers). They act as unique IDs. This is based on the dermal abyss study done by researchers at MIT and Harvard, back in 2017. "Living" tattoos take in the body's metabolic signals as inputs. (This image is from Fluxey, Deviant art: link)
Week 2 HW: DNA Read, Write & Edit
Professor Jacobson: The error rate of DNA polymerase differs in organisms and also because there are different types of polymerase enzymes. Usually this accuracy is 1 in 100,000 bp before proof reading and error correction. (I used an AI prompt to confirm, the prompt: 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 length of the human genome is around 3.2 billion bp. To compare, without error correction, this would cause around 32,000 errors if the entire genome is replicated .To correct for this, biology employs DNA repair mechanisms and proof reading that massively reduce the error rate.
Automation Art Now following from previous week’s idea. This gives me more freedom to make the chrome dino art work. I uploaded the chrome dino image into the automation art website. In the end I came up with this design. This is the link to the automation art page
Week 4 HW: Protein Design Part-i
Part A : Conceptual Questions 1. How many molecules of amino acids do you take with a piece of 500 grams of meat? (on average an amino acid is ~100 Daltons) Some of the leanest cuts of meats have ~155gm of protein for 500gm of meat. The number of moles= Total weight/molecular weight = 155/100 – 1.55 moles .
Week 5 HW: Protein Design Part-ii
Part A: SOD1 Binder Peptide Design (From Pranam) Part 1: Generate Binders with PepMLM Before mutation sp|P00441|SODC_HUMAN Superoxide dismutase [Cu-Zn] OS=Homo sapiens OX=9606 GN=SOD1 PE=1 SV=2 MATKAVCVLKGDGPVQGIINFEQKESNGPVKVWGSIKGLTEGLHGFHVHEFGDNTAGCTSAGPHFNPLSRKHGGPKDEERHVGDLGNVTADKDGVADVSIEDSVISLSGDHCIIGRTLVVHEKADDLGKGGNEESTKTGNAGSRLACGVIGIAQ After A4V mutation MATKVVCVLKGDGPVQGIINFEQKESNGPVKVWGSIKGLTEGLHGFHVHEFGDNTAGCTSAGPHFNPLSRKHGGPKDEERHVGDLGNVTADKDGVADVSIEDSVISLSGDHCIIGRTLVVHEKADDLGKGGNEESTKTGNAGSRLACGVIGIAQ I used the pepMLM colab to generate 4 binders Part 2: Evaluate Binders with AlphaFold3 Each of the above binders are number 0 to 3 and the binder_ex is the known SOD1-binding peptide FLYRWLPSRRGG
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