Homework
Weekly homework submissions:
Week 1 HW: Principles and Practices
Assignment: Post-Lecture 1 First, describe a biological engineering application or tool you want to develop and why. This could be inspired by an idea for your HTGAA class project and/or something for which you are already doing in your research, or something you are just curious about.
Week 2 HW: DNA Read, Write, and Edit
Assignment Pre-Lecture 2 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? The error rate for polymerase is 1:106. The human genome is ~3.2 billion base pairs (3.2 x 109). Biology deals with this discrepancy by bridging the gap using a multi-step quality control system to lower the error rate to 1:10^9. How many different ways are there to code (DNA nucleotide code) for an average human protein? In practice what are some of the reasons that all of these different codes don’t work to code for the protein of interest?
Assignment: Python Script for Opentrons Artwork Artistic Concept — “ELM Habitat Cross-Section” My design uses the 96-well plate as a canvas to depict a cross-sectional schematic of the Multi-Trophic Myco-Foundry — the engineered living material (ELM) habitat I proposed in Week 1. Three food-safe dyes, pipetted by the Opentrons OT-2, fill concentric rings of wells representing the three biological layers of the habitat:
Week 4 HW: Protein Design Part I
Part A. Conceptual Questions Answering all thirteen questions (two skipped: #11 “Why do β-sheets aggregate?” merged into #10, and one implicit 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) Protein makes up ~20% of meat by mass: 500 g × 0.20 = 100 g of protein 100 Daltons = 1.66 × 10⁻²² g per molecule 100 g ÷ (1.66 × 10⁻²² g/molecule) = ~6 × 10²³ molecules (approximately one Avogadro’s number) 2. 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 Superoxide dismutase 1 (SOD1) is a cytosolic homodimeric antioxidant enzyme that converts superoxide radicals (O₂⁻) into hydrogen peroxide and molecular oxygen. It coordinates copper and zinc ions essential for catalysis and structural integrity. The A4V mutation — Alanine → Valine at residue 4 of the mature protein (residue 5 in the UniProt P00441 precursor) — causes one of the most aggressive familial ALS subtypes by subtly destabilizing the N-terminal β-strand and promoting toxic SOD1 misfolding and aggregation.
Week 6 HW: Genetic Circuits Part I — Assembly Technologies
Part A — DNA Assembly Questions Q1: What is in a Phusion PCR master mix and what does each component do? A standard Phusion High-Fidelity PCR master mix contains the following components: Component Role Phusion Hot-Start DNA Polymerase High-fidelity thermostable polymerase with a 3’→5’ proofreading exonuclease; error rate ~4.4 × 10⁻⁷ per bp per cycle (50× lower than Taq) dNTPs (dATP, dCTP, dGTP, dTTP) Nucleotide substrates for strand synthesis Mg²⁺ (MgCl₂, 1.5–3.0 mM) Essential cofactor for polymerase activity; stabilises the primer–template duplex 5× HF Buffer (KCl + Tris-HCl pH 8.8) Maintains optimal pH and ionic strength; HF formulation includes a proprietary enhancer that increases specificity DMSO (optional, 0–3%) Denaturant for GC-rich or secondary-structure-prone templates Primers (user-added, 0.5–1 µM each) Define amplicon boundaries; anneal to template strands Template DNA (user-added, 1–50 ng) Source of target sequence Nuclease-free H₂O Brings reaction to volume The hot-start formulation keeps polymerase inactive below ~60°C, preventing non-specific extension during setup and eliminating the need for a manual hot start.
Week 7 HW: Genetic Circuits Part II — Neuromorphic Circuits
Part 1 — Intracellular Artificial Neural Networks (IANNs) Q1: Advantages of IANNs over Boolean genetic circuits Traditional genetic circuits implement Boolean logic: each node is either “on” or “off,” and the circuit computes AND/OR/NOT/NAND operations over binary input signals. This is powerful for simple decision logic but breaks down for complex, real-world biological classification tasks.
Part A — General Questions Q1: Advantages of Cell-Free Protein Synthesis over Traditional In Vivo Methods Cell-free protein synthesis (CFPS) decouples protein production from cell viability, providing two structural advantages: Flexibility — the reaction composition is fully user-controlled. Template DNA, cofactors, non-natural amino acids, detergents, redox buffers, and labeled substrates can be added directly at any concentration without membrane barriers or cell toxicity constraints. Reaction volumes can range from nanolitres (acoustic dispensing) to litres (batch bioreactor).
Week 10 HW: Advanced Imaging & Measurement
Homework: Final Project — Measurement Plan for the ELM Biocontainment System My final project centers on a Modular Engineer Living Material (ELM) deep-space biocontainment system using phosphite auxotrophy (ptxD-based synthetic dependency) in an engineered bacterium for Mars surface operations. Below are the key measurable quantities, the associated biological questions, and the measurement technologies I would use.
Week 11 HW: Bioproduction & Cloud Labs
Part A — The 1,536 Pixel Artwork Canvas | Collective Bioart My Contribution I contributed a cluster of sfGFP (green) and mTurquoise2 (cyan) wells arranged to form a segment of a DNA double helix pattern in my assigned plate. The two strands of the helix were encoded in alternating rows using sfGFP (one strand) and mTurquoise2 (the complementary strand), mirroring the ELM habitat’s motif of dual biological systems working in structural complementarity. In total I contributed 14 pixel wells — the length of approximately one full helical turn — in the upper-middle region of the 16-plate global canvas.