Homework
Weekly homework submissions:
Week 1 HW: Principles and Practices
First, describe a biological engineering application or tool you want to develop and why. This could be inspired by an idea for your HTGAA class project and/or something for which you are already doing in your research, or something you are just curious about. Response I’m interested in developing synthetic biology and pharmaceutical based platforms that use engineered bacteria to address major environmental and health challenges, more specifically I want to to explore the effectiveness of bacteria as therapeutic agents to prevent or treat certain type of conditions such as malaria or cancer. These engineered bacteria can live in the human as part of the normal flora but is also cheaper and less harmful as normal pharmaceutical medications. Another part of the engineering bacteria ambitions is related to climate change and carbon footprint, as it looks synthesising bacteria that could decrease human wastes then give us oxygen and decrease carbon dioxide seems as hopeful goal and contributing to the long lasting of human civilisations and human health. This connects my pharmaceutical field of study with synthetic biology to create solutions that are global irrelevant, beneficial and scalable.
Week 2 pre-Lecture HW: DNA Read, Write and Edit
Questions from Professor Jacobson: 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? Response DNA polymerases make about 1 error per 10⁶ bases during DNA synthesis when proofreading is included (≈10⁻⁶ per base). Given that the human genome is ~3.2 × 10⁹ base pairs (haploid), If replication relied only on a 10⁻⁶ error rate, each cell division would cause thousands of mutations (≈3,200 errors per replication), which would be biologically dangerous. However, cells have multiple error reduction mechanisms: such as Polymerase proofreading (3′→5′ exonuclease activity) that removes most misincorporated bases during synthesis. And post-replicative mismatch repair (MMR) detects and fixes remaining mismatches after replication. Also, it’s important to remember that DNA have intersting properties such diploidy, noncoding DNA and kill switches
Week 2 HW: DNA read, write and edit
Part One Benchling & In-silico Gel Art! this was a very intersing journy, starting with Ronan’s website to get some inspiration i was very unsaure of the type of artpiece i want to make, and even with a lot of inspiration, my eyes feel on the most famous trend for 2025, the 67 meme! so i got to work, this was my first draft using ronans website, and after checking the website enzymes used, i found these below
How cool it is to desgin the logo of SAB at AUIB? the python scripit is uplouded for the questions? Q1: a paper that utilizes Openrons for biological purposes:? I’ve came across this paper Titled: Automation of protein crystallization scale-up via Opentrons-2 (2025) In Summary: it Uses an Opentrons OT‑2 robot to automate protein crystallization experiments, which are normally manual and laborious. The robot handles precise reagent dispensing, gradient formulation, and 96-well plate setup, increasing throughput and reproducibility. This is rare because low-cost robots are rarely used in structural biology workflows.
Week 4 HW: Protien Design Part I
HW Questions Assuming that the meat is ~20% protein, thus for 500 g meat ≈ 100 g protein. Average amino acid ≈ 100 Da = 100 g/mol, we can find the Moles of amino acids by ≈ 100 g (protein) ÷ 100 g/mol = 1 mol. According to Avogadro’s Number of molecules ≈ 6.02 × 10²³ amino acids in 1 mol. Why eating beef doesn’t turn me into a cow? Proteins are digested into amino acids in the stomach and intestine and broken down before absorption, then transferred in the blood and reassembled in each cell based on our DNA and mRNA commands into different proteins. food’s structure is always broken down, that’s why insulin can’t be taken orally.