Homework
Weekly homework submissions:
Week 1 HW: Principles and Practices
Class Assignment — DUE BY START OF FEB 10 LECTURE (1) 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.
Homework Week 2 Part 1: Benchling & In-silico Gel Art Import the Lambda DNA. Simulate Restriction Enzyme Digestion with the following Enzymes: EcoRI HindIII BamHI KpnI EcoRV SacI SalI Create a pattern/image in the style of Paul Vanouse’s Latent Figure Protocol artworks.
Homework Week 3 Post-Lab Questions One of the great parts about having an automated robot is being able to precisely mix, deposit, and run reactions without much intervention, and design and deploy experiments remotely. For this week, we’d like for you to do the following:
- Find and describe a published paper that utilizes the Opentrons or an automation tool to achieve novel biological applications.
Week 4 HW: Protein Design Part I
Part A. Conceptual Questions Answer any NINE of the following questions from Shuguang Zhang: (i.e. you can select two to skip)
- How many molecules of amino acids do you take with a piece of 500 grams of meat? (on average an amino acid is ~100 Daltons) Assuming the meat is a red meat like beef, there would be approximately 20-25g of protein per 100g of meat [1, 2].
Week 5 HW: Protein Design Part II
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. Mutations in SOD1 cause familial Amyotrophic Lateral Sclerosis (ALS). Among them, the A4V mutation (Alanine → Valine at residue 4) leads to one of the most aggressive forms of the disease. The mutation subtly destabilizes the N-terminus, perturbs folding energetics, and promotes toxic aggregation.
Week 6 HW: Genetic Circuits Part I: Assembly Technologies
Assignment: DNA Assembly 1. What are some components in the Phusion High-Fidelity PCR Master Mix and what is their purpose? The template DNA is the mUAV plasmid at Used at 20 ng/µL, with 0.8 µL added to the reaction. The primers are “colour forward” and “colour reverse”. Give that the stock concentration is 5 µL, using 2.5 µL of each primer in a total reaction volume of 25 µL results in a final primer concentration of 0.5 µM.
Week 7 Genetic Circuits Part II
Assignment Part 1: Intracellular Artificial Neural Networks (IANNs)
- What advantages do IANNs have over traditional genetic circuits, whose input/output behaviors are Boolean functions? The advantages of IANNs over traditional circuits include: (i) Continuous processing which allows them to constantly measure changes in concentration gradients of cellular inputs rather than just their absolute presence or absence. (ii) Relatively easier to scale up. That is, new inputs can be programmed by integrating additional weighted connections to existing nodes without completely rewiring the circuit.
Week 9 Week 9 — Cell-Free Systems
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. Advantages of cell-free protein synthesis (CFPS) over traditional in-vivo methods: (i) Greater flexibility and control: Given that cells do not need to stay “alive” and the absence of a cell wall, it is possible to manipulate cells in real time; add chaperones, cofactors etc [1].
Week 10 — Imaging and measurement
Homework: Waters Part I — Molecular Weight We will analyze an eGFP standard on a Waters Xevo G3 QTof MS system to determine the molecular weight of intact eGFP and observe its charge state distribution in the native and denatured (unfolded) states. The conditions for LC-MS analysis of intact protein cause it to unfold and be detected in its denatured form (due to the solvents and pH used for analysis).