Homework

Weekly homework submissions:

  • Week 1 Homework: Principles and Practices

    View Image Credits Image courtesy of Vincent Muir Q1. Describe a biological engineering application or tool you want to develop and why: Concept: Bio-Circuit for CO₂ Sensing and Reduction

  • Week 2 Homework: DNA Read, Write & Edit

    3.1. Choose your protein Question: In recitation, we discussed that you will pick a protein for your homework that you find interesting. Which protein have you chosen and why? Using one of the tools described in recitation (NCBI, UniProt, google), obtain the protein sequence for the protein you chose. The protein I have chosen is Rubisco, the protein responsible for fixing carbon dioxide during photosynthesis. I have chosen this protein because one of my final project ideas was to create a system that is more efficient at fixing carbon.

  • Week 3 Homework: Lab Automation

    Published Automation Research Question: Find and describe a published paper that utilizes the Opentrons or an automation tool to achieve novel biological applications. The Paper Title: An automated cell-free platform for the rapid characterization of genetic regulators Journal: Scientific Reports (2024) Source: https://www.nature.com/articles/s41598-024-52642-x Description This research utilizes the Opentrons OT-2 to automate the setup of cell-free protein synthesis (CFPS) reactions. The authors focused on characterizing genetic parts like promoters and riboswitches. By using automation, they were able to test over 1,000 different conditions in a fraction of the time it would take a human, with much higher reproducibility across plates.

  • Week 4 Homework: Protein Design Part I

    HW – Part A: Amino Acids and Protein Folding 4.1. Quantitative Consumption Question: 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). 1 gram is equal to Avogadro’s number of daltons (6.022E23 Da). To find the total molecules in 500g of meat:

  • Week 5 Homework: Protein Design Part II

    Part 1: Generate Binders with PepMLM The target for this study is the human SOD1 protein (UniProt P00441), specifically focusing on the A4V mutation, which is a common cause of Amyotrophic Lateral Sclerosis (ALS). Mutant SOD1 Sequence (A4V): ATKVVCVLKGDGPVQGIINFEQKESNGPVKVWGSIKGLTEGLHGFHVHEFGDNTAGCTSAGPHFNPLSRKHGGPKDEERHVGDLGNVTADKDGVADVSIEDSVISLSGDHCIIGRTLVVHEKADDLGKGGNEESTKTGNAGSRLACGVIGIAQ Using PepMLM-650M, four peptides of 12 amino acids were generated and compared against the known SOD1-binding peptide FLYRWLPSRRGG.

  • Week 7 Homework: Genetic Circuits Part II

    Assignment Part 1: Intracellular Artificial Neural Networks (IANNs) What advantages do IANNs have over traditional genetic circuits, whose input/output behaviors are Boolean functions? Analog Processing: IANNs process continuous, multi-level inputs to produce graded, proportional responses, rather than being restricted to rigid binary (ON/OFF) states. Complex Integration: A single IANN layer can compute complex, non-linear functions by tuning biological “weights” (like promoter strength), whereas Boolean logic requires fragile, metabolically expensive cascades of multiple gates to achieve the same complexity. Robustness: Because they use graded signals and distributed pathways, IANNs are more resistant to biological noise and mutation, showing gradual performance decline (graceful degradation) instead of catastrophic failure. Describe a useful application for an IANN; include a detailed description of input/output behavior, as well as any limitations an IANN might face to achieve your goal. A potential application could be an environmental risk biosensor that measures the combined threat of multiple water pollutants (e.g., arsenic and pesticides) and outputs a color-coded, continuous risk scale.

  • Week 9 Homework: Cell-Free Systems

    Part 1: General Homework Questions 1. Advantages of Cell-Free Synthesis Cell-free protein synthesis (CFPS) offers an “open” architecture, allowing for direct control over the chemical environment. Unlike in vivo methods, CFPS is not limited by cell toxicity or metabolic competition. Toxic Protein Production: CFPS can produce proteins that would otherwise kill a living host cell. High-Throughput Screening: It allows for the rapid testing of genetic libraries without the need for time-consuming cloning and cell culture. 2. Main Components Cell Extract: The catalytic machinery (ribosomes, polymerases). DNA Template: The genetic instructions. NTPs & Amino Acids: The energy and building blocks. Energy Regeneration: Essential for recycling ATP to sustain translation. 3. Energy Provision Energy regeneration is critical because ATP is consumed rapidly and phosphate byproducts inhibit the reaction. The Creatine Phosphate/Creatine Kinase system is often used to maintain an ATP supply by transferring phosphate groups to ADP.

  • Week 10 Homework: Imaging and Measurement

    Homework: Final Project Integration Please identify at least one (ideally many) aspect(s) of your project that you will measure. It could be the mass or sequence of a protein, the presence, absence, or quantity of a biomarker, etc. I will be measuring a couple of aspects to assay my experiments. For example, i will be using a spectrophotometer to quantify NADH exchange to validate that the malate products are being formed. I will be looking at turbidity and optical density to evaluate calcium chloride precipitate quantity and formation rate to analyze the efficacy of carbonic anhydrase. Additionally, I ordered some inorganic carbon sats made with heavy carbon, which I plan to compare to a standard to showcase additional evidence of reaction success and product formation.