Homework
Weekly homework submissions:
Week 1 HW: Principles and Practices
Lab Documentation Pipetting Lab Objective: Practice accurate pipetting techniques while preparing bacterial cultures and media for in-vitro experiments. Procedure: Selected appropriate pipettes and tips for working with bacterial suspensions. Measured and transferred culture media and bacterial samples. Mixed bacterial suspensions gently to avoid damaging cells. Changed tips between samples to prevent cross-contamination. Challenges and Fixes:
Post-Lab Question 1: Published Paper Description Automated High-Throughput DNA Assembly using Opentrons For this assignment, I researched how the Opentrons OT-2 is utilized to automate Golden Gate Assembly for synthetic biology applications. A prime example of this is the widespread use of the OT-2 in laboratories to assemble combinatorial genetic libraries. Instead of researchers manually pipetting thousands of small-volume reactions—which is highly prone to human error and fatigue—the Opentrons robot is programmed to precisely distribute vector backbones, inserts, buffers, and enzymes into 96-well or 384-well plates.
Week-04-HW:Protein Design Part I
Part I of Protein Design 1. How many molecules of amino acids do you take with a piece of 500 grams of meat? Meat is approximately 20% protein. 500g $\times$ 0.20 = 100g of protein. Average amino acid weight $\approx$ 100 Daltons. 100g / 100 g/mol = 1 mole of amino acids. You consume approximately $6.022 \times 10^{23}$ molecules of amino acids. 2. Why do humans eat beef but do not become a cow, or eat fish but do not become fish? During digestion, enzymes break down foreign proteins into individual amino acids. Our cells then use our own DNA blueprint to reassemble those amino acids into human proteins. We use the same “bricks” to build a different “house.”
Week-05-HW: Protein Design & Engineering Part II
Final Project Report: Computational Protein Engineering 🧬 PART A: Therapeutic Peptide Design for SOD1 (ALS) 1. Objective Amyotrophic Lateral Sclerosis (ALS) is often linked to mutations in the SOD1 protein, such as the A4V variant, which leads to toxic protein aggregation. Our goal was to design a synthetic peptide binder to act as a “molecular shield,” stabilizing the protein and preventing aggregation.