Homework
Weekly homework submissions:
Week 1 HW: Principles and Practices
Class Assignment 1. First, describe a biological engineering application or tool you want to develop and why. I want to develop a membraneless organelle within plant cells that is able to detect breakage of the cell membrane by a foreign organism. This organelle, which is comprised of intrinsically disordered proteins (IDPs), would trigger immune system responses upon detection. The purpose of this organelle is to detect and shut down fungal plant pathogens that infect through breaching cell membranes. This novel application would lower yield loss in rice plants (primarily Oriza Sativa) from fungal diseases like Rice Blast (Magnaporthe grisea) which is responsible for 10%-30% yield losses every year for rice, preventing the possibility of feeding about 60 million people.
Week 2 HW: DNA Read, Write, & Edit
Part 1: Benchling & In-silico Gel Art Info This is a picture of the gel art I designed on Benchling. The bands in the 1-6 ladders create the word “Hi” on completion. The restriction enzymes used on the Lambda DNA are listed above the diagram.
Assignment: Python Script for Opentrons Artwork This is a link to the code for my Opentrons Artwork. AI Contributions: I used AI to generate large portions of my code as I am largely unfamiliar with python programming. I used Gemini AI and asked it to integrate my coordinates for my artwork into the code in Colab.
Week 4 HW: Protein Design Part I
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) Assuming that meat contains about 20% protein, 500 grams of meat translates to ~100 grams of protein. If an amino acid weighs 100 Daltons, this will translate to 100 grams per mole of amino acids. Knowing this, we calculate 500 grams of meat to have one mole of amino acids. Using Avogadro’s constant, we can calulate the number to be 6 x 1023 molecules of amino acids in 500 grams of meat.
Week 5 HW: Protein Design Part II
Part A: SOD1 Binder Peptide Design (From Pranam) Part 1: Generate Binders with PepMLM This is the human SOD1 sequence containing the A4V mutation: MATKVVCVLKGDGPVQGIINFEQKESNGPVKVWGSIKGLTEGLHGFHVHEFGDNTAGCTSAGPHFNPLSRKHGGPKDEERHVGDLGNVTADKDGVADVSIEDSVISLSGDHCIIGRTLVVHEKADDLGKGGNEESTKTGNAGSRLACGVIGIAQ Binder Pseudo Perplexity 0 WHYYATGARWGE 16.929015 1 WRYGAVALELKK 12.714672 2 WRSPAAAARWWK 9.155765 3 WRYPATAAALKX 4.843841 4 FLYRWLPSRRGG N/A Info The table generated by PepMLM detailing possible peptides to bind to mutant SOD1 along with their pseudo perplexity scores. Peptide 4 is an already known SOD1-binding peptide.
Week 6 HW: Genetic Circuits Part I: Assembly Technologies
Assignment: DNA Assembly What are some components in the Phusion High-Fidelity PCR Master Mix and what is their purpose? The Phusion High-Fidelity PCR Master Mix consists of Phusion DNA Polymerase, deoxynucleotides, and a reaction buffer (including MgCl2). The Phusion DNA Polymerase is a high-fidelity enzyme that is used to synthesize new, complementary nucleotides to the 3’ end of a DNA strand. Deoxynucleotides are present within the master mix to be added to the cloned DNA strand. The reaction buffer facilitates enzymatic function and stabilizes the DNA polymerase, allowing the PCR reaction to proceed smoothly.