Homework
Weekly homework submissions:
Week 1 HW: Principles and Practices
AI Cite Prompts were directly based on the homework questions provided. Homework Questions from Professor Jacobson 1. What is the error rate of polymerase? How does this compare to the human genome length, and how does biology address the discrepancy? Polymerase error rate: ~10⁻⁵ per base without proofreading; ~10⁻⁷–10⁻⁸ with proofreading; ~10⁻⁹–10⁻¹⁰ with mismatch repair.
Week 2 HW: DNA Read, Write, & Edit
3.1 mCherry I was thinking about observation under UV illumination — red fluorescence seems easier to detect compared to blue or green light. It also has stronger visual impact. Protein Sequence MVSKGEEDNMAIIKEFMRFKVHMEGSVNGHEFEIEGEGEGRPYEGTQTAKLKVTKGGPLPFAWDILSPQFMYGSKAYVKHPADIPDYLKLSFPEGFKWERVMNFEDGGVVTVTQDSSLQDGEFIYKVKLRGTNFPSDGPVMQKKTMGWEASSERMYPEDGALKGEIKQRLKLKDGGHYDAEVKTTYKAKKPVQLPGAYNVNIKLDITSHNEDYTIVEQYERAEGRHSTGGMDELYK Source: https://www.fpbase.org/protein/mcherry/ 3.2 Original DNA Sequence atggtgagcaaaggcgaagaagataacatggcgattattaaagaatttatgcgctttaaa gtgcatatggaaggcagcgtgaacggccatgaatttgaaattgaaggcgaaggcgaaggc cgcccgtatgaaggcacccagaccgcgaaactgaaagtgaccaaaggcggcccgctgccg tttgcgtgggatattctgagcccgcagtttatgtatggcagcaaagcgtatgtgaaacat ccggcggatattccggattatctgaaactgagctttccggaaggctttaaatgggaacgc gtgatgaactttgaagatggcggcgtggtgaccgtgacccaggatagcagcctgcaggat ggcgaatttatttataaagtgaaactgcgcggcaccaactttccgagcgatggcccggtg atgcagaaaaaaaccatgggctgggaagcgagcagcgaacgcatgtatccggaagatggc gcgctgaaaggcgaaattaaacagcgcctgaaactgaaagatggcggccattatgatgcg gaagtgaaaaccacctataaagcgaaaaaaccggtgcagctgccgggcgcgtataacgtg aacattaaactggatattaccagccataacgaagattataccattgtggaacagtatgaa cgcgcggaaggccgccatagcaccggcggcatggatgaactgtataaa 3.3 Codon Optimization Why Optimize? The same amino acid can be encoded by multiple codons, but different organisms have different codon usage preferences (tRNA abundance, translation efficiency, mRNA structure, etc.). To allow the host to express the protein more efficiently, codon optimization is necessary.
- Published paper Villanueva-Cañas et al., PLOS ONE (2021) built a multi-station SARS-CoV-2 RT-qPCR testing workflow using Opentrons OT-2 robots. The core novelty is a reusable software + station architecture that makes a complex diagnostic pipeline programmable, modular, and reproducible across setups.
- Final project automation plan Project: “Living Ice Cream” A temperature-responsive dessert system with:
Protein & Amino Acid Questions 1) How many molecules of amino acids are in 500 g of meat? (Assume average amino acid ≈ 100 Da ≈ 100 g/mol) Upper-bound estimate: treat the 500 g as entirely amino acids. Moles of amino acids ≈ 500 g / (100 g/mol) = 5 mol Number of molecules ≈ 5 mol × 6.02 × 10²³ molecules/mol ≈ 3.0 × 10²⁴ amino acid molecules 2) Why do humans eat beef but do not become a cow? Dietary proteins are not incorporated intact into our bodies.
Part A: SOD1 Binder Peptide Design 1. Background and Design Goal Superoxide dismutase 1 (SOD1) is a cytosolic antioxidant enzyme that converts superoxide radicals into hydrogen peroxide and oxygen. In its native state, SOD1 forms a stable homodimer and binds copper and zinc cofactors. Mutations in SOD1 are associated with familial ALS; among them, the A4V variant is one of the aggressive disease-associated variants and has been linked to SOD1 destabilization, altered folding behavior, and toxic aggregation.
DNA Assembly 1. What are some components in the Phusion High-Fidelity PCR Master Mix and what is their purpose? Phusion High-Fidelity PCR Master Mix contains Phusion DNA Polymerase, dNTPs, reaction buffer, and MgCl₂. The DNA polymerase copies the DNA template during PCR. dNTPs are the building blocks used to synthesize the new DNA strand. The buffer keeps the reaction at the correct pH and salt condition. MgCl₂ is an important cofactor that helps the polymerase function properly. Since Phusion is a high-fidelity polymerase, it is useful when the amplified DNA sequence needs to be accurate for cloning or assembly.
Week 7: Genetic Circuits Part II: Neuromorphic Circuits
Part 1: Intracellular Artificial Neural Networks (IANNs) Question 1 - Advantages of IANNs Over Traditional Genetic Circuits Traditional genetic circuits usually work through Boolean logic. An input is treated as either ON or OFF, and the circuit produces an output based on that discrete state. This is useful for simple decisions, but it is limited when the cell needs to respond to gradual or mixed signals.
General homework questions 1. 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 has two major advantages over traditional in vivo expression: flexibility and experimental control.
Week 10: Advanced Imaging & Measurement Technology Homework
Homework: Final Project For my final project, Glowing Ice Cream, the main things I would measure are the identity, quantity, activity, and release behavior of the NanoLuc/substrate system.
- Protein Identity and Purity I need to confirm whether I successfully made the right protein, NanoLuc-GSGS-His₆.
Week 11 HW: Week 11 — Bioproduction & Cloud Labs
Part 1: The 1,536 Pixel Artwork Canvas | Collective Artwork For the collective bioart project, I contributed a small bacteriophage drawing in the upper-right corner of the canvas. (Later seemed to have been modified by someone else） What I liked about this project is that it made the artwork feel genuinely collective. Instead of everyone making a separate image, the final result became a shared and evolving biological canvas. The fact that my pixel contribution could be changed by someone else was a little unexpected, but it also made the project feel more alive.
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