Homework

Weekly homework submissions:

• Week 1 HW: Principles and Practices

  Living Modified Organism(LMO) Cotton Textiles That Maintain Hygiene and Emit Pleasant Scents This application envisions a cotton-based textile integrated with genetically engineered microorganisms that are designed to function stably on the fabric surface. These microorganisms would metabolize organic compounds derived from human sweat and skin debris—such as fatty acids, ammonia, and keratin degradation byproducts—thereby maintaining hygiene and reducing odor formation. Unlike conventional approaches that rely on antimicrobial chemicals or synthetic fragrances, this system would operate as an engineered living material, in which biological activity is deliberately programmed to occur only within a non-natural environment (the textile itself). Conventional perfumes and detergents repeatedly introduce chemically stable, exogenous compounds that may unintentionally interfere with human endocrine systems or disrupt the skin microbiome through persistent and non-selective exposure.

• Week 2 HW: DNA Read, Write and Edit

  Part 0: Basics of Gel Electrophoresis #S.S: 부트캠프와 Wk2 수업을 들은 후, 과제를 확인했지만 정확한 개념 정리가 안되어 있어서 뭘 진행하는지 이해하기 어려웠다. 따라서 ChatGPT를 활용, it became clearer once I understood the concept of restriction enzyme(molecular scissors) and gel electrophoresis(DNA size filter). Prompt: "restriction enzyme biology 와 gel electrophoresis에 대해서 아주 간단히 설명해줘" 를 통해 다음과 같은 답변을 얻었다. 1. Restriction enzyme (제한효소) biology 제한효소는 특정한 DNA 염기서열을 인식해서 그 지점을 자르는 효소입니다. 원래는 박테리아의 방어 시스템으로, 침입한 바이러스 DNA를 잘라 파괴합니다. 각 효소는 고유한 인식 서열(예: GAATTC)을 가지며, 그 위치에서 DNA를 정확히 절단합니다. 이 특성 덕분에 분자생물학에서는 DNA를 원하는 조각으로 자르는 도구로 사용됩니다. 2. Gel electrophoresis (겔 전기영동) 겔 전기영동은 DNA 조각을 크기별로 분리하는 실험 방법입니다. DNA는 음전하를 띠므로 전기를 걸면 양극 방향으로 이동합니다. 작은 DNA 조각일수록 겔 속을 더 빨리, 더 멀리 이동합니다. 결과적으로 DNA 조각들이 밴드 형태로 나타나며, 크기를 비교·확인할 수 있습니다. One-line summary -Restriction enzymes: molecular scissors that cut DNA at specific sequences -Gel electrophoresis: a method to separate DNA fragments by size Part 1: Benchling & In-silico Gel Art #S.S: Benchling is such a cool platform that we can edit DNA in-silico. I uploaded ‘Lambda DNA.txt’ and managed digest by choosing each enzyme that cuts DNA strand. My initial thought was to see the ladder that each enzyme makes to decide which figure/shape I’d like on my artwork, but the shown result were not a single bar but of multiple layers. — at this stage, I have no idea how to compose an gel art.

• Week 3 HW: Lab Automation

  A group HW: Design cell-free RNA biosensors RNA toehold switch가 작동하는 원리를 recitation에서 Ana가 설명해 주었는데, 나는 우선 mRNA가 단백질로 translation되는 기전을 이해하고나서 이런 biosensor의 기능을 이해할 수 있었다. mRNA에 ribosome이 와서 결합한다. 찾아다닌다기 보다는 cell내에서 자유롭게 떠다니던 ribosome이 충돌하여 결합하는 것에 가깝다고. Eukaryotes의 경우는 rough endoplasmic reticulum(RER, 세포소기관organelle)에 거칠어 보이도록 ribosome들이 붙어있어서 단백질을 생산, 반면에 Prokaryotes, 즉, bacteria의 경우 ribosome은 free-floating 상태로만 cytoplasm(세포질)에 존재.

• Week 4 HW: Protein Design Part I

  Part A. Conceptual Questions Answer any NINE of the following questions from Shuguang Zhang: (i.e. you can select two to skip) 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) Why do humans eat beef but do not become a cow, eat fish but do not become fish? Why are there only 20 natural amino acids? Can you make other non-natural amino acids? Design some new amino acids. Where did amino acids come from before enzymes that make them, and before life started? If you make an α-helix using D-amino acids, what handedness (right or left) would you expect? Can you discover additional helices in proteins? Why are most molecular helices right-handed? Why do β-sheets tend to aggregate? What is the driving force for β-sheet aggregation? Why do many amyloid diseases form β-sheets? Can you use amyloid β-sheets as materials? Design a β-sheet motif that forms a well-ordered structure. Part B: Protein Analysis and Visualization

• Week 5 HW: Protein Design Part II

  Part A: SOD1 Binder Peptide Design (From Pranam) Superoxide dismutase 1 (SOD1) is a cytosolic antioxidant enzyme that converts superoxide radicals into hydrogen peroxide and oxygen. In its native state, it forms a stable homodimer and binds copper and zinc. Mutations in SOD1 cause familial Amyotrophic Lateral Sclerosis (ALS). Among them, the A4V mutation (Alanine → Valine at residue 4) leads to one of the most aggressive forms of the disease. The mutation subtly destabilizes the N-terminus, perturbs folding energetics, and promotes toxic aggregation.

• Week 6 HW: Genetic Circuits - Part I

  DNA Assembly Answer these questions about the protocol in this week’s lab: What are some components in the Phusion High-Fidelity PCR Master Mix and what is their purpose? What are some factors that determine primer annealing temperature during PCR? There are two methods from this class that create linear fragments of DNA: PCR, and restriction enzyme digests. Compare and contrast these two methods, both in terms of protocol as well as when one may be preferable to use over the other. How can you ensure that the DNA sequences that you have digested and PCR-ed will be appropriate for Gibson cloning? How does the plasmid DNA enter the E. coli cells during transformation? Describe another assembly method in detail (such as Golden Gate Assembly) Explain the other method in 5 - 7 sentences plus diagrams (either handmade or online). Model this assembly method with Benchling or Asimov Kernel! Asimov Kernel

• Week 7 HW: Genetic Circuits - Part II