Homework
Weekly homework submissions:
Pre-HW Week 2 From Dr. LeProust
My Homework What’s the most commonly used method for oligo synthesis currently? The phosphoramidite method using solid-phase synthesis is the most commonly used approach for oligonucleotide (oligo) synthesis today. This method builds oligos in the 3’ to 5’ direction on solid supports like controlled pore glass (CPG) or polystyrene, allowing automation and high efficiency. It involves four key steps per cycle: detritylation to expose the 5’-OH, coupling with activated phosphoramidite monomers, capping unreacted sites, and oxidation to stabilize phosphite triesters into phosphates. Commercial synthesizers make it scalable from small research batches to large therapeutic production.
Pre-HW Week 2 From George Church
My Homework Prompt in Perplexity : Can you identify the ten essential amino acids in animals, and explain how this relates to your understanding of the “Lysine Contingency”? What are the 10 essential amino acids in all animals and how does this affect your view of the “Lysine Contingency”? There are nine universally essential amino acids for all animals, including lysine, which they must obtain from their diet since they cannot synthesize them. The “Lysine Contingency” from Jurassic Park is scientifically implausible because lysine is abundant in nature. All animals, including humans, require nine essential amino acids—histidine, isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan, and valine that their bodies cannot synthesize and must obtain from food sources like meat, plants, or prey. While some species need a tenth like arginine, these nine are universal across animals for protein building and vital functions. The “Lysine Contingency” in Jurassic Park portrayed dinosaurs genetically engineered to lack lysine synthesis as a failsafe, meant to kill them by withholding the nutrient, but this is scientifically flawed since lysine is already an essential amino acid for all animals, abundantly available in nature from sources like soybeans, grains, and animal tissues. Dinosaurs could easily survive by eating wild plants or animals, rendering the contingency useless and highlighting poor genetic engineering logic in the story. This doesn’t change my view of it as entertaining but implausible fiction, real biotech safeguards would need novel dependencies, not mimicking natural nutritional limits.
Pre-HW Week 2 From Professor Jacobson
My Homework 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? DNA polymerase, the enzyme that copies DNA, makes a mistake roughly once every 10⁴ to 10⁵ nucleotides synthesized, which sounds small but would lead to about 300,000 errors per round of human‑genome replication (about 3 billion bases) if left unchecked. Biology solves this by stacking multiple layers of quality control: the polymerase active site is selective for correct base pairs, the enzyme can proofread its own work by removing mispaired bases (3′→5′ exonuclease activity), and after replication specialized mismatch repair proteins scan and fix errors, bringing the effective mutation rate down to about 1 per 10⁷ to 10⁹ bases per cycle, which keeps the overall mutation load low enough for the organism to function reliably.
Week 1 HW: Principles and Practices
From Genes to Neurons : CRISPR as a Breakthrough for Ischemic Stroke Describe a biological engineering application or tool you want to develop and why? Stroke, or cerebrovascular accident (CVA), is a leading cause of mortality and morbidity in my country, Indonesia. Compared to other Southeast Asian countries, Indonesia has the highest age- and sex-standardized mortality rate and the greatest loss of disability-adjusted life years. Reducing stroke incidence is key to lowering stroke-related disability. This condition is generally classified as either ischemic—caused by arterial blockage from thrombi, emboli, or hemorrhagic, due to intracranial bleeding. Ischemic stroke, the most common type, often stems from atherosclerosis or thromboembolism. Given these issues, I want to learn more about the problem and what solutions we can develop through biological engineering. Despite advances in acute management, current therapeutic options remain limited, highlighting the need for innovative strategies. In this context, CRISPR genome-editing technology has emerged as a promising biological engineering approach, offering the potential to modulate genes involved in inflammation, neuroprotection, and vascular repair, thereby opening new avenues for ischemic stroke research and therapy.
Week 2 HW : Benchling and In-silico Gel Art
Part 1: Benchling & In-silico Gel Art step 01 : I have already made my benchling account step 02 : copy lambda_NEB sequence and import the sequence in my benchling Part 3: DNA Design Challenge my protein data from –> https://www.uniprot.org 498 AA | EC=3.2.1.1 | Full=1,4-alpha-D-glucan glucanohydrolase A | amyA | Aspergillus awamori (Black koji mold) | UniProtKB:P0C1B3
Python Script for Opentrons Artwork Actually I really struggle with python :( , I’ll try very soon. This picture below is my trial for generate an artistic design from https://opentrons-art.rcdonovan.com/ I make this design without picture This one with picture preference desc : 0,75 uL