Homework
Weekly homework submissions:
Week 1 HW: Principles and Practices
Class Assignment š Ø First, describe a biological engineering application or tool you want to develop and why. I want to develop a 3D Bio-Art Platform that merges biological growth with interactive synthetic biology. The idea is to use 3D-printed molds and structured agar media to create āliving sculpturesā that donāt just sit there but actually āfeelā and react.
Week 2 HW: DNA read, write & edit
Week 2 Lecture Prep Homework Questions from Professor Jacobson: 1) Natureās 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? The error rate of polymerase is 1 in 106 compared to the ~3.2 billion bp of the human genome. This means that the polymerase makes 3200 errors each time it replicates. Biology manages this discrepancy through DNA repair mechanisms, such as real-time proofreading and post-replication mismatch repair (MutS Repair system).
Homework Assignment: Python Script for Opentrons Artwork Your task this week is to Create a Python file to run on an Opentrons liquid handling robot. Generate an artistic design using the GUI at opentrons-art.rcdonovan.com. For my first design I made a colorful butterfly! I first used the Opentrons art page to design it by using the upload image option. Initially the design
Week 4 HW: Protein Design - Part I
Homework: Protein Design I Objective: Learn basic concepts: amino acid structure 3D protein visualization the variety of ML-based design tools Brainstorm as a group how to apply these tools to engineer a better bacteriophage (setting the stage for the final project). Part A. Conceptual Questions Answer any NINE of the following questions from Shuguang Zhang: (i.e. you can select two to skip)
Week 5 HW: Protein Design - Part II
Homework 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.
Week 6 HW: Genetic Circuits Part I
Homework Assignment: DNA Assembly Answer these questions about the protocol in this weekās lab: What are some components in the Phusion High-Fidelity PCR Master Mix and what is their purpose? Some components in the Phusion High-FideƱity PCR Master Mix include the Phusion DNA Polymerase, which is the enzyme that actually builds the new DNA strands with high accuracy. It also contains dNTPs, which are the building blocks (A, T, C, and G) used to synthesize the DNA. There are also buffer salts and magnesium ions (Mg^2+) that provide the right chemical environment for the enzyme to stay stable and work efficiently.
Week 7 HW: Genetic Circuits Part II
This week covers neuromorphic genetic circuits, showing how engineered gene networks can implement neural-network āperceptronā-like computation and learning. Homework Assignment Part 1: Intracellular Artificial Neural Networks (IANNs) What advantages do IANNs have over traditional genetic circuits, whose input/output behaviors are Boolean functions? Traditional Boolean circuits are limited because they only understand āonā or āoffā (0 or 1), which doesnāt reflect the noisy and analog reality of a cell. IANNs allow for weighted inputs and non-linear integration, meaning the cell can make decisions based on the concentration of signals rather than just their presence. This allows for complex pattern recognition, like identifying a specific metabolic state or a signature of multiple biomarkers, making the decision-making process much more robust and āintelligentā than a simple AND/OR gate.
This week introduces synthesis of proteins using cellular machinery outside of a cell. Homework Homework Part A: General and Lecturer-Specific Questions General homework questions Explain the main advantages of cell-free protein synthesis over traditional in vivo methods, specifically in terms of flexibility and control over experimental variables. Name at least two cases where cell-free expression is more beneficial than cell production. The biggest advantage of cell-free systems is that they offer an open environment where you have total control over experimental variables like pH and salt concentrations without a cell membrane getting in the way. This flexibility is especially beneficial when producing antimicrobial peptides or lysis proteins that would normally kill a living host, as well as for high-throughput screening of genetic circuits where you need to test many DNA variants in hours rather than waiting days for cultures to grow.
Week 10 HW: Imaging and Measurement
Homework Homework is partly based on data that will be generated in the Waters Immerse Lab in Cambridge, MA. Students will characterize green fluorescent protein (eGFP, a recombinant protein standard) structure (primary, secondary/tertiary) in the lab using liquid chromatography and mass spectrometry, as well as Keyhole Limpet Hemocyanin (KLH) oligomeric states using charge detection mass spectrometry (CDMS). Data generated in the lab needed to do the homework is included both within this document and in the Appendix of the laboratory protocol.