Homework
Weekly homework submissions:
Week 1 HW: Principles and Practices
Bioindicator for Microplastic Contamination in Agricultural Soils 1. Biological Engineering Application Project Description The proposed biological engineering application is the development of a bioindicator for detecting contamination by microplastics and their chemical additives in agricultural soils.
Week 2 HW: DNA read, write and edit.
Part I: Benchling & In-silico Gel Art Begin by importing your DNA sequence and use the Digests tool to test the effects of different restriction enzyme(s). Export your final design as a png and compare with your lab results on your Notion page. See the images below for where to find the Digests tool, selecting the “NEB 2-log” ladder in the Virtual Digest tab, and how to have multiple Digests appear in the same Virtual Digest.
WEEK 3 — LAB AUTOMATION LAB PROTOCOL 1. Review of Materials First, I reviewed the available documentation on HTGAA (LAB–Week 3 – Opentrons Art). Key information required to prepare the design was found at the beginning of the Google Colab notebook, including technical constraints and recommended parameters for droplet spacing and volume.
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? First, I researched how much protein the meat contains. I assumed it was beef, and I saw that the amount of protein per gram varies depending on the cut (FEN, 2012). I calculated the average protein content of 10 cuts and got 19.46, which I rounded up to 20g per 100g.
Week 5 HW: Protein Design Part II
Part 1: Generate Binders with PepMLM 1. Begin by retrieving the human SOD1 sequence from UniProt (P00441) and introducing the A4V mutation. Superoxide Dismutase 1 (SOD1) is a human enzyme that plays a critical role in protecting cells from oxidative stress by catalyzing the conversion of superoxide radicals into oxygen and hydrogen peroxide. It is a small, 154-amino-acid protein that typically forms a stable homodimer and contains a β-βarrel core structure with metal cofactors, copper and zinc, essential for its catalytic activity. Mutations in SOD1, such as the A4V variant, are associated with familial amyotrophic lateral sclerosis (ALS), a neurodegenerative disorder. SOD1 is widely expressed in the cytoplasm and is a key model protein for studying protein folding, aggregation, and targeted protein degradation strategies.
Week 6 HW: Genetic Circuits: Part I
Answer these questions about the protocol in this week’s lab:
- What are some components in the Phusion High-Fidelity PCR Master Mix and what is their purpose? Components of the Phusion High-Fidelity PCR Master Mix and their purpose: Phusion DNA polymerase – a high-fidelity DNA polymerase that synthesizes new DNA strands with a low error rate during PCR. Primers (forward and reverse) – short DNA sequences that bind to the target DNA and define the region that will be amplified. dNTPs (dATP, dTTP, dCTP, dGTP) – the nucleotide building blocks used by the polymerase to synthesize new DNA strands. Reaction buffer – maintains optimal pH and ionic conditions for proper enzyme activity. Mg²⁺ ions – an essential cofactor required for DNA polymerase catalytic activity. Nuclease-free water – maintains the correct reaction volume and prevents degradation of DNA. 2. What are some factors that determine primer annealing temperature during PCR?