Homework
Weekly homework submissions:
Week 1 HW: Principles and Practices
- Biological engineering application I propose a “DNA Compiler,” a software tool that helps researchers turn DNA designs into safe, synthesis-ready sequences. The main idea is to build safety checks directly into the design process rather than relying only on downstream screening or manual review. The compiler would analyze a DNA sequence, flag potential issues, and suggest safer alternatives (for example, adjusting sequence features or highlighting areas that require review). It would also generate a clear record of how the design was modified or approved. The goal is to make good safety practices automatic and easy to follow.
Week 2 Homework Documentation This week I worked on DNA gel art, restriction digests, and DNA design. I designed a gel art pattern, ran the gel in lab, and prepared a Benchling construct for a spider silk equivalent protein. Part 1: Benchling and In-silico Gel Art For the in-silico gel art part, I used restriction digests of lambda DNA to plan a gel pattern before running the wet-lab version. The main idea was to use different restriction enzymes to create different DNA fragment sizes, so the bands would appear at different positions in the gel.
Final projects were added to the slide and the python file were submitted too. Post-Lab Questions 1. One paper I found is “AssemblyTron: flexible automation of DNA assembly with Opentrons OT-2 lab robots” by Bryant et al. The paper describes a workflow for using an Opentrons OT-2 robot to automate DNA assembly. Instead of manually pipetting every DNA part, enzyme, and reagent, the robot can set up many assembly reactions in a more consistent way. The authors made this system because DNA assembly is a common step in synthetic biology, but it becomes slow and error-prone when many constructs have to be tested.
Part A – Conceptual Questions How many amino acid molecules are in 500 g of meat? A typical amino acid has a mass of about 100 g per mole. If you have 500 g, that corresponds to roughly 5 moles. Since one mole contains about 6 × 1023 molecules, 5 moles would contain about 3 × 1024 amino acid molecules.
Week 5: Protein Design Part II
Week 5: Protein Design Part II Part A: SOD1 Binder Peptide Design Background Superoxide dismutase 1, or SOD1, is an enzyme that helps protect cells from oxidative stress by converting superoxide radicals into hydrogen peroxide and oxygen. SOD1 normally folds into a stable structure and forms a homodimer. It also binds metal cofactors, which are important for its activity.
DNA Assembly Homework Phusion High-Fidelity PCR Master Mix contains a high-fidelity DNA polymerase, dNTPs, MgCl2, buffer salts, and stabilizers. The polymerase copies the DNA template, while its proofreading activity helps reduce mutations. The dNTPs are the building blocks used to make the new DNA strand. MgCl2 is needed for polymerase activity, and the buffer keeps the pH and salt conditions suitable for PCR. The master mix format also makes the reaction more consistent because many components are already premixed.
Week 7 HW: Genetic Circuits Part II: Neuromorphic Circuits
Homework: IANNs and Fungal Materials Assignment Part 1: Intracellular Artificial Neural Networks 1. Advantages of IANNs over traditional genetic circuits IANNs can handle more than simple on/off behavior. Traditional genetic circuits often work like Boolean logic gates, where an input is either present or absent and the output is either low or high. In real cells, signals are usually more gradual than that. An IANN can combine several input levels and produce a more flexible output.
Homework: Cell-Free Systems and Synthetic Minimal Cells General homework questions 1. Advantages of cell-free protein synthesis Cell-free protein synthesis is useful because it is faster and easier to control than expression in living cells. Since there are no cells to keep alive, I can directly change the DNA amount, salts, cofactors, energy source, and reaction conditions.
Final Project Measurement For the development of bio-synthetic spider silk musical strings, I will measure several critical parameters to ensure the protein is synthesized correctly, the fiber is engineered for high tension, and the resulting sound meets professional acoustic standards. Aspects to be Measured Protein sequence and purity: I will verify that the recombinant “Mini-Spidroin” matches the intended genetic design and that all bacterial cellular debris has been removed. Protein concentration: The density of the purified protein in the liquid “spin dope” must be quantified to ensure it has the correct viscosity for extrusion. Fiber diameter and morphology: I will measure the thickness of the thread to ensure it remains consistent and within the 0.20–0.30 mm range required for instrument compatibility. Mechanical properties: Specifically, I will measure the tensile strength and elasticity of the dried fiber to determine if it can withstand the high-tension environment of a violin or guitar. Acoustic frequency and harmonics: I will measure the fundamental resonance and the richness of the overtones produced when the string is under load. Measurement Methods and Technologies
Week 11 Homework: Bioproduction and Cloud Labs Part A: The 1,536 Pixel Artwork Canvas I contributed two pixels on the bottom left of the artwork, but for some reason they did not sync or show up correctly in the final version. I still liked the idea of the project because it turned a biology class assignment into a shared artwork, where everyone’s tiny contribution could become part of a larger image.