Homework
Weekly homework submissions:
Week 1 HW: Principles and Practices
Class Assignment — DUE BY START OF FEB 10 LECTURE First, describe a biological engineering application or tool you want to develop and why I want to create an antidote for the venom of the Lachesis acrochorda a South American snake, which is currently treated with antivenom serums. But I want to create one that is cheaper and more accessible. This would also help protect this snake species, which is endangered due to habitat loss and because it is potentially deadly to humans.
Week 2 HW: DNA READ, WRITW AND EDIT
Part 1: Benchling & In-silico Gel Art Make a free account at benchling.com Import the Lambda DNA. Simulate Restriction Enzyme Digestion with the following Enzymes: EcoRI HindIII BamHI KpnI EcoRV SacI SalI Create a pattern/image in the style of Paul Vanouse’s Latent Figure Protocol artworks. You might find Ronan’s website a helpful tool for quickly iterating on designs!
Assignment: Python Script for Opentrons Artwork — DUE BY YOUR LAB TIME! I downloaded the script from the GUI website: The script from opentrons import types import string metadata = { ‘protocolName’: ‘{YOUR NAME} - Opentrons Art - HTGAA’, ‘author’: ‘HTGAA’, ‘source’: ‘HTGAA 2026’, ‘apiLevel’: ‘2.20’ } Z_VALUE_AGAR = 2.0 POINT_SIZE = 0.75
Week 4 HW: Protein Design Part I
Part A: Conceptual Questions 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) Why do humans eat beef but do not become a cow, eat fish but do not become fish?
Week 5 HW: Protein Design Part II
Part A: SOD1 Binder Peptide Design (From Pranam) Superoxide dismutase 1 (SOD1) is a cytosolic antioxidant enzyme that converts superoxide radicals into hydrogen peroxide and oxygen. In its native state, it forms a stable homodimer and binds copper and zinc. Mutations in SOD1 cause familial Amyotrophic Lateral Sclerosis (ALS). Among them, the A4V mutation (Alanine → Valine at residue 4) leads to one of the most aggressive forms of the disease. The mutation subtly destabilizes the N-terminus, perturbs folding energetics, and promotes toxic aggregation.
Week 6 HW: Genetic Circuits Part I Assembly Technologies
Assignment: DNA Assembly 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? What are some factors that determine primer annealing temperature during PCR? There are two methods from this class that create linear fragments of DNA: PCR, and restriction enzyme digests. Compare and contrast these two methods, both in terms of protocol as well as when one may be preferable to use over the other.
Week 7 HW: Genetic Circuits Part II: Neuromorphic Circuits
Assignment Part 1: Intracellular Artificial Neural Networks (IANNs) What advantages do IANNs have over traditional genetic circuits, whose input/output behaviors are Boolean functions? Describe a useful application for an IANN; include a detailed description of input/output behavior, as well as any limitations an IANN might face to achieve your goal. Below is a diagram depicting an intracellular single-layer perceptron where the X1 input is DNA encoding for the Csy4 endoribonuclease and the X2 input is DNA encoding for a fluorescent protein output whose mRNA is regulated by Csy4. Tx: transcription; Tl: translation.