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.

  • Week 3 HW: AUTOMATION

    1. 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.
  1. Final project automation plan Project: “Living Ice Cream” A temperature-responsive dessert system with:

  • Week 4 HW: Protine Design

    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.

  • Week 9 HW: Cell-Free Systems

    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.