Homework

Weekly homework submissions:

  • Week 1 HW: Principles and Practices

    Question 1 – Application & why First, describe a biological engineering application or tool you want to develop and why. Introduction

  • Week 2 HW: DNA Read, Write, & Edit

    Part 1 – Benchling & In-silico Gel Art I used Benchling to design an in‑silico restriction digest of Lambda DNA. In Benchling, I created a customized restriction enzyme list for smoother later operations that included all the enzymes provided in the Week 2 HTGAA homework

  • Week 3 HW: Lab Automation

    Assignment 1: Python Script for Opentrons Artwork This week we are creating a Python file to run on an Opentrons OT-2 liquid handling robot to create flourescent designs. Using provided website I created a small “Cherry” pattern. I have little experience in coding on such platofrms, so Google Gemini was a big help to assist while writing a code: https://colab.research.google.com/drive/1kZZStiHlPdG17vqHZPM2IhAQ3vTWkMRb#scrollTo=pczDLwsq64mk&line=76&uniqifier=1

  • Week 4 HW: Protein Design

    Part A Answer any NINE of the following questions from Shuguang Zhang: (i.e. you can select two to skip) 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) Since meat is not entirely made of proteins, lets assume 20% of the whole meat mass = around 100 g. An amino acid is ~100 Da (=~100g/mol). 100 g/ (100 g/mol) = 1 mol = 6.022* 10^23 AA.

  • Week 5 HW: Protein Design. Part 2

    Part A Some background: Mutations in SOD1 cause familial Amyotrophic Lateral Sclerosis (ALS) ALS is a heterogeneous, severe neurodegenerative disorder, the hallmark of which is an adult-onset loss of upper and lower motor neurons. It leads to a progressive paresis and atrophy of skeletal muscles, resulting in quadriplegia and fatal respiratory failure. The mutation subtly destabilizes the N-terminus, perturbs folding energetics, and promotes toxic aggregation. Task: Design short peptides that bind mutant SOD1 & then decide which ones are worth advancing toward therapy.

  • Week 6 HW: Genetic Circuits Part I: Assembly Technologies

    DNA Assembly What are some components in the Phusion High-Fidelity PCR Master Mix and what is their purpose? Phusion DNA Polymerase* Chimeric enzyme that catalyzes the synthesis of ew DNA strand in the 5 -> 3 direction with high-fidelity dNTPs four chemical building blocks ($dATP, dTTP, dCTP, dGTP$) used to construct the DNA. They provide both the physical material and the energy required for the polymerase to grow the new strand Reaction Buffer