Homework
Weekly homework submissions:
Week 1 HW: Principles and Practices
Question 1: I propose a digital, governance-aware health data platform designed to support a population-level understanding of cancer and tumor prevalence in Iraq. At present, most medical records in Iraq are paper-based and fragmented across hospitals or retained by patients, making them vulnerable to loss and preventing the creation of a reliable national picture of cancer types, trends, and possible contributing factors. As a result, medical research, evidence-based policymaking, and long-term public health planning are severely limited. This proposed tool would not collect full patient records, enable diagnosis, or identify individuals. Instead, it would focus on aggregated, de-identified clinical and contextual data that can be used to understand broader cancer patterns while respecting patient privacy, consent, and cultural sensitivities. The primary goal of this platform is to address a critical infrastructure gap in Iraq’s health system by enabling ethical research and informed decision-making, while explicitly avoiding surveillance, stigmatization, or misuse of sensitive medical information. While neurological and psychological conditions represent equally serious challenges in Iraq, they are intentionally excluded from the initial scope of this design due to heightened ethical, privacy, and stigma-related risks.
Week 2 HW: DNA read, write, and edit
Homework Questions from Professor Jacobson: According to the Lecture 2 slides, the intrinsic error rate of biological DNA polymerase is approximately 1 error per 10⁶ base pairs. The slides also indicate that the human genome is approximately 3.2 × 10⁹ base pairs in length. At this error rate, replication of the human genome would result in thousands of errors per replication cycle if no additional correction mechanisms existed. The slides explain that biology addresses this discrepancy through error-correcting mechanisms, including proofreading activity associated with DNA polymerase and post-replication mismatch repair systems, such as the MutS pathway. Together, these mechanisms reduce the effective mutation rate and allow large genomes to be stably maintained.
Post-Lab Questions Find and describe a published paper that utilizes the Opentrons or an automation tool to achieve novel biological applications. Article: “Automation of protein crystallization scaleup via Opentrons-2 liquid handling” Jacob B. DeRoo, Alec A. Jones, Caroline K. Slaughter, Tim W. Ahr, Sam M. Stroup, Grace B. Thompson, Christopher D. Snow, SLAS Technology, Volume 32, 2025, 100268, ISSN 2472-6303, https://doi.org/10.1016/j.slast.2025.100268 General overview: Protein crystallization is a complex and time-consuming process that is essential for determining protein structures in structural biology. Producing well-formed protein crystals requires careful optimization of multiple conditions, including protein concentration, precipitant composition, and mixing accuracy. Because these parameters cannot be predicted in advance, crystallization is largely a trial-and-error process that demands repeated setup of crystallization plates. Traditionally, this process is performed manually, making it labor-intensive and susceptible to human error and variability. In addition, viscous protein solutions are difficult to handle consistently, which further complicates crystallization experiments.
Week 04 – Protein Design Part I
Part A: Conceptual Questions For an average amino acid, the molecular weight is about 100 Daltons, which is equivalent to 100 g/mol. If I assume meat is about 20% protein, then 500 g of meat contains roughly 100 g of protein. The relationship is: number of moles = mass (g) / molar mass (g/mol) So, 100 g ÷ 100 g/mol ≈ 1 mole of amino acids. One mole corresponds to approximately 6×1023molecules. Therefore, consuming 500 g of meat corresponds to on the order of 1023amino acid molecules.
Week 05 – Protein Design Part II
Image source: Genetic Lifehacks. https://www.geneticlifehacks.com/sod1-gene-polymorphisms/ Part 1: SOD1 Binder Peptide Design “MATKAVCVLKGDGPVQGIINFEQKESNGPVKVWGSIKGLTEGLHGFHVHEFGDNTAGCTSAGPHFNPLSRKHGGPKDEERHVGDLGNVTADKDGVADVSIEDSVISLSGDHCIIGRTLVVHEKADDLGKGGNEESTKTGNAGSRLACGVIGIAQ” This is the SOD1 original sequence The mutation A4V means: Alanine (A) at position 4 → Valine (V) But UniProt includes the starting M, so the alanine that changes is the 5th residue in the sequence. 1 M 2 A 3 T 4 K 5 A ← this is the one that changes 6 V We change from this MATKAV to this MATKVV
Week 06 – Genetic Circuits Part I
DNA Assembly Phusion High-Fidelity PCR Master Mix contains DNA polymerase, dNTPs, buffer, and Mg²⁺. The polymerase has proofreading activity (3′→5′ exonuclease), which reduces errors during DNA amplification. The dNTPs act as building blocks, while the buffer and Mg²⁺ maintain optimal conditions for enzyme activity. This is important in cloning because even small mutations can affect protein function. https://www.neb.com/en/products/e0553-phusion-high-fidelity-pcr-kit?srsltid=AfmBOooI-JWWTJ01XuZL3foWSnvq5kqQol7r8q61xRo95a6S7amAGeiH
Week 07 – Genetic Circuits Part II
Part 1: Intracellular Artificial Neural Networks Q.1. Traditional genetic circuits mostly behave like Boolean logic, meaning everything is either ON or OFF. That works for simple designs like AND or OR gates, but it doesn’t really match what actually happens inside cells. In real biology, nothing is strictly binary. Gene expression can be low, medium, or high, and signals are noisy and constantly changing. So forcing everything into ON/OFF makes the system too limited.
Part A: General and Lecturer-Specific Questions Q.1. One of the main advantages of cell-free protein synthesis over traditional in vivo methods is the flexibility and level of control over the system. In normal in vivo systems, cells are still trying to survive, grow, divide, regulate metabolism, and maintain their own functions. Because of that, researchers are working with the cell’s own priorities and limitations.
Week 10 – Imaging and Measurement
Homework: Final Project I would mainly want to see whether the redesigned GR-LBD protein is successfully produced and whether introducing the Q642K mutation improves cortisol selectivity compared with cortisone. Since the DNA construct was designed and ordered through Twist Bioscience, I would first verify the received construct sequence before moving into expression studies.
For the collaborative bioart project, I contributed to several wells including K10, K11, K12, K13, K15, K16, L14, and L15. Most of my contributions appeared in the right-side region of the artwork. What I liked most about this project was seeing how many people from different backgrounds worked together to create one large scientific artwork. It honestly felt chaotic at first, but super cool once the final pattern started forming. I also liked how science and art were combined together in a very interactive way. One thing that could make the project even more fun next year is adding a little more guidance or visualization for first-time participants to better follow how the final image develops collectively over time. I really enjoyed the project overall, but at the beginning it took me some time to fully understand how everything was coming together. I wish I have participated more and on time!