Homework
Weekly homework submissions:
Week 1 HW: Principles and Practices
- Introduction With a rather limited background in the field of synthetic biology and bioengineering, I sketched out my initial scope of interest in closed-loop controllers, in which they are autonomous and adjust to the environment around. While I’m also interested in the bidirectional communication via the gut-brain axis. I want to explore the idea of engineering a gut bacterium with a synthetic genetic circuit that could detect biomarkers in the gut and conditionally produce neuroactive compounds that modulate brain activity via the GBA.
Week 2 HW: DNA Read, Write, and Edit
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. I have selected PIEZO1 as my protein, that is a protein sitting in the cell membrane and opens when the membrane is physically stretched, compressed, or deformed, basically detecting the membrane tension.
Post Lab Questions Write a description about what you intend to do with automation tools for your final project. You may include example pseudocode or Python scripts, procedures you may need to automate, 3D printed holders you may need, and more. Example ideas that you can create a protocol for: Use the cloud laboratory to screen an array of biosensors constructs that you design, synthesize, and express using cell-free protein synthesis Use Opentrons to dispense microorganisms onto fabric to design “living textiles” as “bio artwork”
Week 4 HW: Principles and Practices
Part A. Conceptual Questions 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.