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 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

• 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