Homework
Weekly homework submissions:
Week 1 HW: Principles and Practices
- Bioengineering Application / Product to Be Developed Bioengineering Product A bioplastic derived from organic waste that is composed of 100% biopolymers, food-grade, and naturally biodegradable. This product is designed as an alternative to fossil-based polymer plastics that are widely used today, particularly for single-use packaging applications. Key Product Specifications • Main raw materials Sourced from underutilized organic waste, such as: o cassava peels
Week 10 HW: Advanced Imaging & Measurement Technology
Waters Part I — Molecular Weight The amino acid sequence of the His-tagged eGFP was analyzed using the ExPASy Compute pI/Mw tool. The results showed: Theoretical molecular weight (Mw) = 28,006.60 Da Theoretical pI = 5.90 This indicates that the predicted molecular mass of the intact eGFP protein, including the linker and His-tag, is approximately: 28.01 kDa This theoretical molecular weight will be used as the reference value for comparison with the experimentally determined mass from LC-MS analysis.
Part A: The 1,536 Pixel Artwork Canvas | Collective Artwork 1. Contribution Honestly, I did not contribute anything to the canvas, as I was already too late to participate in the artwork. However, that is okay. I feel that I still have a lot to learn about this kind of project, and I was genuinely excited to see how enthusiastic everyone was while working on it.
Week 2 HW: DNA Read, Write & Edit
Part 1: Benchling & In-silico Gel Art PART 3: DNA Design Challenge 3.1 Choose your protein Erythropoietin is a hormone that stimulates red blood cell production. Selected because: Vital in anemia therapy High-value biotechnology protein Relevant to the pharmaceutical industry Erythroproietin : sp|P01588|EPO_HUMAN Erythropoietin OS=Homo sapiens OX=9606 GN=EPO PE=1 SV=1 MGVHECPAWLWLLLSLLSLPLGLPVLGAPPRLICDSRVLERYLLEAKEAENITTGCAEHC SLNENITVPDTKVNFYAWKRMEVGQQAVEVWQGLALLSEAVLRGQALLVNSSQPWEPLQL HVDKAVSGLRSLTTLLRALGAQKEAISPPDAASAAPLRTITADTFRKLFRVYSNFLRGKL KLYTGEACRTGDR
Published Paper on Opentrons Automation The paper entitled AssemblyTron: flexible automation of DNA assembly with Opentrons OT-2 lab robots, published in the journal Synthetic Biology (2023), reports the development of AssemblyTron, a software platform that automates DNA assembly workflows using the Opentrons OT-2 liquid-handling robot. The system integrates DNA construct design (for example, from design software such as j5) with automated execution on the OT-2 to perform molecular biology procedures in a precise and standardized manner. AssemblyTron is designed to support the Design–Build–Test–Learn (DBTL) cycle in synthetic biology by automating PCR optimization, Golden Gate assembly, and in vivo assembly (IVA).
Week 4 HW: Protein Design Part I
A. Conceptual Question Molecules of Amino Acids in 500g Meat A typical 500 g serving of lean meat contains about 125–150 g of protein (≈25–30% by weight). Taking 130 g as an average and assuming an average amino acid residue mass of ~110 g/mol, this corresponds to: 130 g ÷ 110 g/mol ≈ 1.18 mol of amino acid residues. Multiplying by Avogadro’s number (6.022 × 10²³ mol⁻¹) gives: ≈ 7 × 10²³ amino acid molecules.
Week 5 HW: Protein Design Part II
PART 1 Generate Binders with PepMLM The human SOD1 protein sequence was retrieved from the UniProt database (P00441). To model a disease-associated variant, the A4V mutation was introduced by substituting alanine with valine at residue position 4 of the protein sequence. This mutation is known to be associated with amyotrophic lateral sclerosis (ALS). The resulting mutant SOD1 sequence was then used as the input for subsequent peptide binder generation using the PepMLM model.
Week 6 HW: Genetic Circuits I: Assembly Technologies
- Components in Phusion High-Fidelity PCR Master Mix and Their Purpose One of the main enzymes used is Phusion High-Fidelity DNA Polymerase, a DNA polymerase with an extremely low error rate (high fidelity), making it ideal for mutagenesis and cloning experiments. The main components in Phusion High-Fidelity PCR Master Mix and their functions are: Components Function Phusion DNA Polymerase Enzyme that synthesizes new DNA from primers during the extension phase. It has proofreading activity (3’→5’ exonuclease), resulting in very low replication errors. dNTPs (dATP, dTTP, dGTP, dCTP) Substrates or “building blocks” used by the polymerase to form the new DNA strand. Reaction Buffer Provides optimal chemical conditions (pH, salts, enzyme stability) for polymerase activity. Mg²⁺ ions (MgCl₂) Essential cofactor required by DNA polymerase to catalyze phosphodiester bond formation between nucleotides. Stabilizing agents Maintain enzyme stability during PCR. The master mix is typically at 2X concentration, so only primers, template DNA, and water need to be added.
Week 7 HW : Genetic Circuits Part II: Neuromorphic Circuits
PART 1: INTRACELLULAR ARTIFICIAL NEURAL NETWORKS Advantages of IANNs over Boolean Genetic Circuits Intracellular Artificial Neural Networks (IANNs) provide key advantages over traditional Boolean logic-based genetic circuits. Conventional circuits produce discrete input-output relationships, limited to simple ON or OFF states, which restricts their information-processing power. In contrast, IANNs operate in an analog fashion, using molecular concentrations as continuous variables. This allows cells to generate nuanced, graded responses to fluctuating biological inputs.
PART 1 — General Homework Questions
- What are the main advantages of cell-free protein synthesis over in vivo methods, particularly in terms of flexibility and control of experimental variables? Provide at least two cases where CFPS is more beneficial. Cell-free protein synthesis (CFPS) offers significantly greater flexibility compared to in vivo systems because it is not constrained by cellular viability. In this system, biological components are extracted from cells, allowing researchers to directly manipulate reaction conditions such as ion concentrations (Mg²⁺, K⁺), energy molecules (ATP), and enzymatic composition. This enables precise experimental control without interference from complex cellular regulatory networks. Furthermore, CFPS operates as an open system, meaning components can be added or removed dynamically during the reaction, enhancing experimental tunability. CFPS is particularly advantageous in several scenarios, including: