Homework

Weekly homework submissions:

• Week 1 HW: Principles and Practices

  A Living Anti-Corrosion System for Ocean Infrastructure:

• Week 2 pre HW: DNA Read, Write and Edit

  Homework Questions from Professor Jacobson: Nature’s machinery for copying DNA is called polymerase. What is the error rate of polymerase? How does this compare to the length of the human genome. How does biology deal with that discrepancy? Ans: DNA polymerase has an inherent error rate of approximately 1 in 10⁶ bases. Given the human genome size of about 3.2 billion base pairs, this would lead to thousands of mutations each time a cell divides if left uncorrected. To maintain genomic stability, cells use a multi-layered error-correction system. First, DNA polymerase performs immediate proofreading through its exonuclease activity. This is followed by post-replication mismatch repair (MMR) mechanisms. Together, these processes greatly enhance replication accuracy, reducing the final error rate to roughly 1 in 10⁹–10¹⁰, meaning fewer than one error typically occurs per genome duplication.

• Week 2 HW: DNA - read, write and edit

  Part 1- Benchling & In-silico Gel Art Simulating Restriction Enzyme Digestion with the following Enzymes: .EcoRI .HindIII .BamHI

• Week 3 HW: lab automation

  My art for Opentrons Artwork Output of the python script. PAPER - Semiautomated Production of Cell-Free Biosensors Journal: ACS Synthetic Biology (2025) PMID: 40073441 Biosensors are biological systems that detect specific chemicals for example, if a substance is present, they might change color or glow. These can be used for:

• Week 4 HW: Protein design part I

  Part A. Conceptual Questions How many amino acid molecules are in 500 g of meat? Ans: Average amino acid ≈ 100 Daltons (100 g/mol) 500 g ÷ 100 g/mol = 5 moles 1 mole = 6.022 × 10²³ molecules So, 5 × 6.022 × 10²³ ≈ 3 × 10²⁴ amino acid molecules Why do humans eat beef but do not become a cow, eat fish but do not become fish? Ans: When we eat beef or fish, our body breaks proteins into amino acids during digestion. Then we rebuild them into human proteins, not cow proteins.

• Week 5: Protein design part II

• Week 6 HW: Genetic Circuits Part I - Assembly Technologies

• Week 7 HW: Genetic Circuits partII: Neuromorphic circuits

  Assignment Part 1: Intracellular Artificial Neural Networks (IANNs)

1. What advantages do IANNs have over traditional genetic circuits, whose input/output behaviors are Boolean functions? Traditional genetic circuits mostly behave like Boolean logic gates (ON/OFF). Intracellular Artificial Neural Networks (IANNs) are more flexible. Advantages: a. Analog (continuous) behavior -> Traditional circuits: only 0 or 1 (OFF/ON)

• Week 9 HW: Cell-Free Systems

  Homework Part A: General and Lecturer-Specific 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. Ans: Cell-free protein synthesis offers significant advantages over in vivo methods due to its open and controllable nature. It allows direct manipulation of reaction components, precise control over parameters such as pH and substrate concentration, and eliminates constraints related to cell viability. As a result, all system resources can be directed toward protein production, enabling rapid optimization and high-throughput experimentation.

• Week 10 HW: Advanced Imaging & Measurement Technology

  Homework: Final Project For your final project: 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. Please describe all of the elements you would like to measure, and furthermore describe how you will perform these measurements. What are the technologies you will use (e.g., gel electrophoresis, DNA sequencing, mass spectrometry, etc.)? Describe in detail.

• Week 11 HW: Bioproduction and Cloud Labs

  Part A: The 1,536 Pixel Artwork Canvas | Collective Artwork Contribute at least one pixel to this global artwork experiment before the editing ends on Sunday 4/19 at 11:59 PM EST. A personalized URL was sent to the email address associated with your Discourse account, and you can discuss the artwork on the Discourse. If you did not have a chance to contribute, it’s okay, just make sure you become a TA this fall! 😉