Homework
Weekly homework submissions:
HW.1: Class assignment 1. 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.
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. 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”.
https://2026a.htgaa.org/2026a/course-pages/weeks/week-03/index.html 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. 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
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:
https://2026a.htgaa.org/2026a/course-pages/weeks/week-07/index.html Part 1: Intracellular Artificial Neural Networks (IANNs) What advantages do IANNs have over traditional genetic circuits, whose input/output behaviors are Boolean functions? They can compute continuous values, not just discrete ones. 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. A feedback-response mechanism, for example how the pancreas runs a sort of PID controller / control system for managing glucose levels in the body - through two hormones that move glucose levels in opposite directions - insulin and glucagon.
https://2026a.htgaa.org/2026a/course-pages/weeks/week-08/index.html There was no week 8 - GOTCHA On to week 9
https://2026a.htgaa.org/2026a/course-pages/weeks/week-09/index.html General homework questions Explain the main advantages of cell-free protein synthesis over traditional in vivo methods, specifically in terms of flexibility and control over experimental variables. Name at least two cases where cell-free expression is more beneficial than cell production. Cell-free protein synthesis is technology where proteins are produced using lysed cell machinery (ribosomes, enzymes) rather than living cells.
https://2026a.htgaa.org/2026a/course-pages/weeks/week-10/index.html Homework: Final Project Identify at least one aspect of your project to measure (protein mass, sequence, biomarker presence/quantity, etc.). For this homework, let’s say my project is to produce human insulin (INS_HUMAN) via recombinant synthesis (cell-based system - E. Coli). The aspect I want to measure is purification/presence of the insulin protein.
https://2026a.htgaa.org/2026a/course-pages/weeks/week-11/index.html Part A: The 1,536 Pixel Artwork Canvas | Collective Artwork Contribute at least one pixel to the global artwork experiment before editing ends. Discuss on the Discourse forum. I missed the deadline for this, sorry! Part B: Cell-Free Protein Synthesis | Cell-Free Reagents Provide 1–2 sentence descriptions of each component’s role in the cell-free reaction: E. coli Lysate: BL21 (DE3) Star Lysate (includes T7 RNA Polymerase) Provides the core machinery for translation and transcription of proteins.
https://2026a.htgaa.org/2026a/course-pages/weeks/week-12/index.html No HW this week.
https://2026a.htgaa.org/2026a/course-pages/weeks/week-13/index.html Work on final project
https://2026a.htgaa.org/2026a/course-pages/weeks/week-14/index.html Finish and present final project