Homework
Weekly homework submissions:
Week 1 HW: Principles and Practices
Describe a biological engineering application or tool you want to develop and why. I want to engineer a bacteria to produce enzymes to convert plastic and glass wastes to a fertilizer. Microbes secrete extracellular enzymes—such as PETase, MHETase, cutinases, lipases, and esterases—to hydrolyze (break) the chemical bonds of plastics, releasing monomers (e.g., ethylene glycol, terephthalic acid) and oligomers. For glasses (phosphate-based), bacteria such as Bacillus ascheri and Burkholderia eburnea can aid in dissolving and releasing silicon and other plant-growth-promoting nutrients. I want to create a bacteria that can combine these two functions by engineering it to produce enzymes for break down of both plastics and glasses and convert to useful biofertilizers for plants. I want to develop such an organism because both plastic and glass seem to pose serious threats as being non biodegradable for ages.
Week 2 HW: DNA-Read Write and Edit
Part 1: Benchling & In-silico Gel Art Import lambda DNA Courtesy:NCBI - O’Leary NA, Cox E, Holmes JB, Anderson WR, Falk R, Hem V, Tsuchiya MTN, Schuler GD, Zhang X, Torcivia J, Ketter A, Breen L, Cothran J, Bajwa H, Tinne J, Meric PA, Hlavina W, Schneider VA. Exploring and retrieving sequence and metadata for species across the tree of life with NCBI Datasets. Sci Data. 2024 Jul 5;11(1):732. doi: 10.1038/s41597-024-03571-y. PMID: 38969627; PMCID: PMC11226681.
Create a Python file to run on an Opentrons liquid handling robot. Find and describe a published paper that utilizes the Opentrons or an automation tool to achieve novel biological applications. Journal Article Cell-free biosensor with automated acoustic liquid handling for rapid and scalable characterization of cellobiohydrolases on microcrystalline cellulose Taeok Kim, Eun Jung Jeon, Kil Koang Kwon, Minji Ko, Ha-Neul Kim, Seong Keun Kim, Eugene Rha, Jonghyeok Shin, Haseong Kim, Dae-Hee Lee, Bong Hyun Sung, Soo-Jung Kim, Hyewon Lee, Seung-Goo Lee, Cell-free biosensor with automated acoustic liquid handling for rapid and scalable characterization of cellobiohydrolases on microcrystalline cellulose, Synthetic Biology, Volume 10, Issue 1, 2025, ysaf005, https://doi.org/10.1093/synbio/ysaf005
Week-04-hw-protein-design-part-1
Homework: Protein Design I Part A. Conceptual Questions 1.Why are there only 20 natural amino acids? The 20 natural amino acids evolved as optimal sets very early, during the RNA world (4 billion years ago). The format was not changed and became frozen because it would disrupt all proteins and also due to tRNA recognition limitations further expansion was prohibited. 2.Where did amino acids come from before enzymes that make them, and before life started?