Homework
Weekly homework submissions:
Week 1: Principles, Ethics, & Practices
Sensory Bio: HOLM 1. The Big Idea: What & Why? HOLM: Hormone-Linked Ocular Monitoring The Why: An often ignored and under-discussed impact of menstruation is its effect on ocular comfort and vision. Millions of women experience eye strain, blurry vision, dry eyes, and light sensitivity during different phases of their menstrual cycle. These symptoms are frequently dismissed with generic advice such as “rest your eyes,” despite being real, recurring, and disruptive.
Week 02: Read, Write, Edit DNA
Part 1 — Benchling and In-Silico Gel Art Objective Simulate restriction enzyme digests using lambda DNA and generate gel electrophoresis patterns. Tools Used Benchling Restriction enzyme digest simulation Lambda DNA reference sequence Restriction Enzymes EcoRI HindIII BamHI KpnI EcoRV SacI SalI XohI Part 3 — DNA Design Challenge Selected Protein Protein Name BDNF (Brain-Derived Neurotrophic Factor)
Python Script for opentron 1. Generate an artistic design using the GUI at opentrons-art.rcdonovan.com. 2. Writing the python script and results Post-lab Questions Find and describe a published paper that utilizes the Opentrons or an automation tool to achieve novel biological applications.4 Paper: Technical upgrade of an open-source liquid handler to support bacterial colony screening del Olmo Lianes et al., Frontiers in Bioengineering and Biotechnology, 2023. DOI: 10.3389/fbioe.2023.1202836
Week 04: Protein Design Part-1
Part A: Conceptual Questions 1. How many molecules of amino acids in 500g of meat? Meat is roughly 20% protein by weight. To find the total number of molecules, we can use the following estimation: Protein Mass: 500g × 0.20 = 100g Molar Mass: On average, an amino acid is 100 Da (which is equivalent to 100 g/mol). Moles: 100g / 100 g/mol = 1 mole Molecules: Using Avogadro’s number ($6.022 \times 10^{23}$), 500g of meat contains approximately 600 sextillion ($6 \times 10^{23}$) amino acid molecules. 2. Why don’t humans become cows or fish after eating them? When we consume protein, our digestive system does not keep the original structure intact. Instead, it breaks the long polymer chains down into individual amino acids.
Week 06: Genetic Circuits Part I
Assignment 1 — DNA Assembly Questions Q1. Components of Phusion High-Fidelity PCR Master Mix Components Phusion DNA Polymerase Thermostable, high-fidelity enzyme with proofreading activity that synthesizes new DNA strands.
Week 07: Genetic Circuits Part-II
Assignment Part 1: Intracellular Artificial Neural Networks (IANNs) Q1. Advantages of IANNs over traditional Boolean genetic circuits Traditional genetic circuits are limited to discrete ON/OFF outputs — they can only compute simple logic like AND, OR, NOT. IANNs go beyond this by processing continuous, graded inputs and computing weighted sums across multiple signals simultaneously, just like neurons. This means a single cell can integrate many environmental signals at once and produce nuanced, analog responses rather than just a binary switch. IANNs can also be trained — their weights (gene expression levels) can be tuned to classify complex input patterns. This makes them far more powerful for tasks like disease detection inside a cell, where multiple biomarkers need to be weighed together rather than evaluated individually.
General Homework Questions 1. Advantages of Cell-Free Protein Synthesis Over In Vivo Methods Cell-free protein synthesis (CFPS) eliminates the need to maintain viable cells, giving direct access to the reaction environment. You can tune pH, redox state, temperature, and add cofactors like chaperones or lipids directly — impossible inside a living cell.
Week 10: Imaging and Measurement
Part I — Molecular Weight Q1 — Theoretical MW from Sequence The eGFP sequence was entered into the ExPASy Compute pI/Mw tool. The resulting molecular weight was: 28,006.60 Da However, eGFP undergoes autocatalytic chromophore cyclization, which removes approximately 20 Da from the protein.
Cell-Free Protein Synthesis (CFPS) CFPS recreates transcription and translation outside a living cell using a lysate supplemented with all the molecular machinery needed to produce a protein from a DNA template. No cell wall means direct control over every component. The Lysate The BL21(DE3) Star lysate provides ribosomes, tRNAs, elongation factors — and crucially, T7 RNA Polymerase, which transcribes any gene under a T7 promoter with high speed and efficiency.