Homework
Weekly homework submissions:
Week 1 HW: Principles and Practices
- First, describe a biological engineering application or tool you want to develop and why. I am interested in developing materials that recover over time by mimicking fungal evolutionary conservatism and continuity. I am currently developing a pollen sensor intended to be placed in children’s playgrounds, while simultaneously reading Merlin Sheldrake’s Entangled Life. Together, these are inspiring me to think about design in a different way.
Week 2 HW: DNA Read, Write, Edit Life
Part 1: Benchling & In-silico Gel Art Navigating to Lambda sequence and saving as text. file Importing Lambda file by saving FASTA Format of Sequence file Simulate Restriction Enzyme Digestion with the following Enzymes: EcoRI Testing Virtual digest example Adding more restrcition enzymes Simulate Restriction Enzyme Digestion with all the Enzymes
Generate an artistic design using the GUI at opentrons-art.rcdonovan.com I wanted to draw Punch, the famous baby Japanese macaque from the zoo in Japan. The GUI created an approximate outline which I used as a base and added more details of different colour on top. This was the end result This was the settings with the coordinates.
Week 4 HW: Protein Design Part I
Part A. Conceptual Questions Answer any NINE of the following questions from Shuguang Zhang: (i.e. you can select two to skip) 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) Why do humans eat beef but do not become a cow, eat fish but do not become fish? Why are there only 20 natural amino acids? Can you make other non-natural amino acids? Design some new amino acids. Where did amino acids come from before enzymes that make them, and before life started? If you make an α-helix using D-amino acids, what handedness (right or left) would you expect? Can you discover additional helices in proteins? Why are most molecular helices right-handed? Why do β-sheets tend to aggregate? What is the driving force for β-sheet aggregation? Why do many amyloid diseases form β-sheets? Can you use amyloid β-sheets as materials? Design a β-sheet motif that forms a well-ordered structure. Part B: Protein Analysis and Visualization