Homework
Weekly homework submissions:
Week 1 HW: Principles and Practices
First, describe a biological engineering application or tool you want to develop and why. I want to develop a highly efficient bacterial chassis for rapid intracellular biosynthesis of novel PHA (polyhydroxyalkanoate) copolymers. More than 150 different hydroxyalkanoate monomers have been identified, and they can be combined into co-polymers (and potentially ter-/quad-polymers) with variable composition and sequence/microstructure, leading to an astronomical design space.
Week 11 HW: Bioproduction & Cloud Labs
Part A: The 1,536 Pixel Artwork Canvas | Collective Artwork Part B: Cell-Free Protein Synthesis | Cell-Free Reagents Each component’s role is in the cell-free reaction. E. coli Lysate (BL21 (DE3) Star): Provides the essential biological “hardware,” including ribosomes, tRNAs, and various translation factors; it specifically includes T7 RNA Polymerase to drive high-level transcription from T7 promoters. Salts and Buffers: Potassium Glutamate: Acts as the primary potassium source and a major intracellular salt, which is critical for maintaining proper osmotic pressure and supporting protein-DNA interactions during transcription and translation. HEPES-KOH pH 7.5: Serves as a chemical buffering agent to maintain a stable physiological pH throughout the reaction, preventing acidification from metabolic byproducts. Magnesium Glutamate: Provides essential $Mg^{2+}$ ions that act as necessary cofactors for ribosome assembly and the enzymatic activity of polymerases. Potassium Phosphate (Monobasic & Dibasic): Maintains phosphate homeostasis and contributes to pH stability, while also providing inorganic phosphate for nucleotide recycling. Energy and Nucleotide System:
Week 2 HW: DNA Read, Write, and Edit
Part 1: Benchling & In-silico Gel Art 🦠 Create a pattern/image in the style of Paul Vanouse’s Latent Figure Protocol artworks: Part 3: DNA Design Challenge I chose poly(3-hydroxyalkanoate) polymerase / PHB synthase (PhaC) from Cupriavidus necator (UniProt accession P23608) because it is a key enzyme in microbial bioplastic production. PhaC catalyzes the polymerization of (R)-3-hydroxybutyryl-CoA monomers to form poly(3-hydroxybutyrate) (PHB), and engineered variants of PhaC are widely used to broaden substrate specificity and produce other polyhydroxyalkanoates (PHAs). I obtained the amino-acid sequence from UniProt (entry P23608) in FASTA format.
Python Script for Opentrons Artwork: https://colab.research.google.com/drive/14m54uLCM5UtsggVjU2Ucxh5hhtNELWD2#scrollTo=pczDLwsq64mk&line=4&uniqifier=1 Find and describe a published paper that utilizes the Opentrons or an automation tool to achieve novel biological applications. I found the paper ¨Opentrons for automated and high-throughput viscometry¨ very interesting. ¨The operating protocol involves measuring the amount of liquid dispensed over a set time for given dispense conditions. Data collected at different set dispense flow rates was used to train an ensemble machine learning regressor to predict Newtonian liquid viscosity¨. They demonstrated the ability of the proxy viscometer to characterize the rheological behavior of two types of power-law fluids.
Week 4 HW: Protein Design - Part 1
Part A. Conceptual Questions 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) Assumptions: Meat ≈ 20% protein. 500 g meat → ~100 g protein. Average amino acid residue mass ≈ 100 Da ≈ 100 g/mol. So: 100 g ÷ 100 g/mol ≈ 1 mole of amino acid residues. 1 mole = 6.022 × 10²³ molecules. 👉 You ingest on the order of 6 × 10²³ amino acid residues in 500 g of meat. Why do humans eat beef but do not become a cow, eat fish but do not become fish? Because digestion destroys biological structure. Proteins are hydrolyzed into amino acids. The original sequences (information) are lost. Your body reassembles amino acids according to human DNA instructions. Biological identity is encoded in sequence and genomic regulation — not in the raw amino acid building blocks. You absorb matter, not identity. Note: While reading this response, I was prompted to ask ChatGPT the following question: “Do the 20 amino acids explain all the DNA of all species? Are there more evolved species that use more amino acids?” ChatGPT’s response was: Yes, the same 20 amino acids (with two rare exceptions) account for virtually all proteins in all known living organisms. There are no “more evolved” species that use a greater number of standard amino acids.
Week 5 HW: Protein Design - Part 2
Part A. SOD1 Binder Peptide Design The perplexity scores for the candidate peptides were: ‘SDGAVLLGSDGE’ (Candidate 1): 16.25 ‘LLGSDGALQVGS’ (Candidate 2): 14.65 ‘SGVAVLCSDGQG’ (Candidate 3): 25.34 ‘AVGVCGVAVLGN’ (Candidate 4): 17.20 Lower perplexity scores suggest that the model finds a sequence more “familiar” or “expected,” potentially correlating with higher biological plausibility, conformational stability, or likelihood of interaction. Candidate 2, with a perplexity of 14.65, appears to be the most promising candidate from the mutated SOD1 sequence for further investigation, being closest to the known binding peptide’s score.
Week 6 HW: Genetic Circuits Part I: Assembly Technologies
Part A. DNA Assembly What are some components in the Phusion High-Fidelity PCR Master Mix and what is their purpose? Phusion High-Fidelity DNA Polymerase: A Pfu-like enzyme fused to a dsDNA-binding domain (Sso7d). This increases processivity and ensures an error rate 50 times lower than Taq polymerase. 5X Phusion HF Buffer (including $MgCl_2$): Maintains optimal pH and provides Magnesium ions, which act as essential cofactors for the polymerase to catalyze the addition of dNTPs. dNTPs (Deoxynucleotide Triphosphates): The molecular “bricks” (dATP, dTTP, dCTP, dGTP) used to synthesize the new DNA strand. Stabilizers: Often including glycerol or mild detergents to maintain enzyme stability through repeated thermal cycling.
Week 7 HW: Genetic Circuits Part II: Neuromorphic Circuits
Part 1: Intracellular Artificial Neural Networks (IANNs) What advantages do IANNs have over traditional genetic circuits, whose input/output behaviors are Boolean functions? Traditional genetic circuits operate like a light switch (0 or 1). IANNs, however, behave like a signal processor, offering several critical advantages: Analog vs. Digital Processing. Boolean circuits only detect if a signal is “present” or “absent.” IANNs process signals analytically, so they can distinguish between low, medium, and high concentrations. This allows the cell to respond to gradients, which is much closer to how natural biological systems actually function.
Part 1: General and Lecturer-Specific Questions 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. The fundamental advantage of cell-free protein synthesis (CFPS) lies in the removal of the cellular membrane, which effectively transforms a “black box” biological process into an open, accessible engineering platform. By eliminating the cell wall, researchers gain unprecedented flexibility and direct control over experimental variables; the reaction environment can be precisely manipulated by adding non-natural amino acids, specific chaperones, or tailored energy sources without the constraints of cellular transport or homeostasis. Furthermore, CFPS decouples protein production from host viability, allowing for the synthesis of highly cytotoxic proteins that would otherwise trigger cell death and halt production in traditional in vivo systems.Beyond throughput, the “open” nature of the system significantly enhances real-time monitoring and process optimization. Unlike the opaque interior of a living E. coli cell, a cell-free reactor allows for millisecond-scale sampling and mid-process adjustments of critical concentrations—such as magnesium levels or pH—to maximize yields. Perhaps most importantly for rapid prototyping, CFPS enables a drastically accelerated iteration cycle. By bypassing time-consuming steps like transformation, plating, and overnight culturing, researchers can transition from a linear DNA template (such as a PCR product) to a functional protein in just a few hours, representing a paradigm shift in the speed of biological design.