Homework
Weekly homework submissions:
- Describe an application Identify a biological engineering tool or application you wish to develop and explain your motivation. I would like to develop a way to make plants grow 100x faster. I find this a very interesting and ambitious question. Perhaps you reverse-engineer the genome, morphological development and constraints, proteins/enzymes/catalysts for growth. Perhaps you design a separate organism (two bacterium?) which produces biomass - a combination of a carbon sequester and a cellulose printer. Perhaps you attempt to design a minimal artificial cell, like a Xenobot / JCVI minimal cells - using new AI design software, you create a minimal genome/DNA, design your own morphological topology through simulation, which is compiled down to gene regulatory networks (GRN’s), transcription factors/thresholds, and DNA.
Week 1 HW.2: Lecture prep for W2
Answer prep questions from three faculty members: Homework Questions from Professor Jacobson: Nature’s machinery for copying DNA is called polymerase. What is the error rate of polymerase? How does this compare to the length of the human genome. How does biology deal with that discrepancy? Error rate refers to errors per nucleotide added per replication. An error could be a misincorporation (wrong base expressed for a pair), for example.
Week 1 HW.3: Setup your website
CHECK IT OUT https://pages.htgaa.org/2026a/liam-edwards-playne/
Week 2 HW.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. Benchling screenshots. Experimental design for Gel art.
Week 2 HW.2: Gel Art - Restriction Digests and Gel Electrophoresis
In the wet-lab perform the lab experiment you designed in Part 1 and outlined in this week’s lab protocol “Gel Art: Restriction Digests and Gel Electrophoresis”. N/A - no access to BioClub Tokyo Lab.
Week 2 HW.3: DNA Design Challenge
3.1. Choose your protein. In recitation, we discussed that you will pick a protein for your homework that you find interesting. Which protein have you chosen and why? Using one of the tools described in recitation (NCBI, UniProt, google), obtain the protein sequence for the protein you chose. Miraculin - https://rest.uniprot.org/uniprotkb/P13087.fasta https://rest.uniprot.org/uniprotkb/P13087.txt >sp|P13087|MIRA_SYNDU Miraculin OS=Synsepalum dulcificum OX=3743 PE=1 SV=3 MKELTMLSLSFFFVSALLAAAANPLLSAADSAPNPVLDIDGEKLRTGTNYYIVPVLRDHG GGLTVSATTPNGTFVCPPRVVQTRKEVDHDRPLAFFPENPKEDVVRVSTDLNINFSAFMP CRWTSSTVWRLDKYDESTGQYFVTIGGVKGNPGPETISSWFKIEEFCGSGFYKLVFCPTV CGSCKVKCGDVGIYIDQKGRRRLALSDKPFAFEFNKTVYF 3.2. Reverse Translate: Protein (amino acid) sequence to DNA (nucleotide) sequence. Using https://www.bioinformatics.org/sms2/rev_trans.html:
Week 2 HW.4: Twist DNA Synthesis Order
Steps to build a plasmid: Import DNA into Benchling. Add promoter, RBS, start/stop codons, 7x His Tag, and terminator Export .fasta and import into Twist. Order Twist clonal gene, using pTwist Amp High Copy vector. Export .gb (genbank) file for plasmid. Import plasmid .gb file into Benchling, open Info>Toplogy and set Circular.
Week 2 HW.5: DNA Read/Write/Edit
DNA Read (i) What DNA would you want to sequence (e.g., read) and why? This could be DNA related to human health (e.g. genes related to disease research), environmental monitoring (e.g., sewage waste water, biodiversity analysis), and beyond (e.g. DNA data storage, biobank). No idea. Possibly my basil plant.
Week 3 HW.1: Python Script for Opentrons Artwork
Review recitation materials and lab documentation. Design artwork using the GUI at opentrons-art.rcdonovan.com. Write a Python script using coordinates from the GUI via the “HTGAA26 Opentrons Colab”. Sign up for a robot time slot and run the script on the Opentrons robot. Submit Python file via provided form. Artwork Design Python Script
Week 3 HW.2: Post-Lab Reflection
2.1. Find and describe a published paper utilizing Opentrons or similar liquid handling automation tools. The paper I have found: Slowpoke: An Automated Golden Gate Cloning Workflow for Opentrons OT‑2 and Flex Slowpoke is a tool which generates Opentron protocols for DNA assembly. DNA assembly is used to assemble larger strings of DNA than can be synthesised in one go, by joining together oligonucleotides.
Week 3 HW.3: Final Project Ideas
Submit 1–3 slides with three individual project concept ideas.
Part A. Conceptual Questions Answer any NINE of the following questions from Shuguang Zhang:
- 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) Meat is roughly 20% protein by weight, so 0.2*500g=100g of protein. This is the only amino acid in meat, as carbs are sugars, and fats are triglycerides (fatty acids + glycerol).
Part A. SOD1 Binder Peptide Design 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.
What are some components in the Phusion High-Fidelity PCR Master Mix and what is their purpose? A Phusion HF PCR Master Mix is a pre-combined PCR reaction system optimised for a specific engineered DNA polymerase. Phusion DNA polymerase — provides the catalytic activity which synthesises DNA, and includes a 3’→5’ exonuclease proofreading to reduce error Reaction buffer MgCl₂ — magnesium ions dNTPs — deoxynucelotide triphosphates: dATP, dCTP, dGTP, and dTTP Stabilizers/additives Water A typical setup only requires after adding: