Homework
Weekly homework submissions:
Week 1 HW: Principles and Practices
Biological Engineering application Bioremediation with Developmental control General purposal: Engineered bacteria that sculpt the rhizosphere for enhanced bioremediation I want to develop a biological engineering tool designed to enhance the natural process of phytoremediation, where plants are used to extract or break down soil contaminants. The core idea is to create specially engineered soil bacteria that act as biological boosters for ordinary plants. This would enable plants to clean contaminated environments far more effectively. The tool is inspired by natural systems like the plant pathogen Agrobacterium tumefaciens, a microbe that hijacks plant development to create tumors. However, here I would redesign this concept for a beneficial purpose, that involves this: instead of causing disease in the plant, the engineered bacteria would send beneficial signals to the plant, first by these bacteria being able to express morphogens and then instructing the plant to grow a more extensive root system, in addition to further activate internal contaminants uptake and potencial degradation pathways.
Week 2 HW: DNA read, write, and edit
Homework Questions 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? Polymerase has a very low error rate of approximately 10^{-4} to 10^{-6} errors per nucleotide without proofreading. Thus, comparing to the human genome length of approximately 3 billion base pair, it represents a minimal part. Thanks to other molecular features, errors produced by the sythesis machinery can be corrected by mechanisms applied like read proof, including the polymerase’s intrinsic proofreading domain, post-replication mismatch repair (MMR) pathways involving proteins like MutS and MutL that scan and excise mismatches, and DNA damage response mechanisms such as base excision repair (BER) and nucleotide excision repair (NER).
Assignment: Python Script for Opentrons Artwork Python file to run on an Opentrons liquid handling robot Opentrons Colab https://colab.research.google.com/drive/1FSLFjeZfWudyaujskQb60dIuhlPAv9Nq?usp=sharing Python Script from GUI OTDesign_02-24-26_10-43-25.py
Week 4 HW: Protein Design Part I
Homework Questions 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 humans eat beef but do not become a cow, eat fish but do not become fish?