Homework
Weekly homework submissions:
Week 1 HW: Principles and Practices
First, describe a biological engineering application or tool you want to develop and why. The engineering of extracted hematopoietic stem cells so their B-cell progeny produces bnAbs (broadly neutralizing antibodies), so after exposure to an immunogen (a highly mutable virus like HIV, Influenza, and so on) they can provide protection for a long time after autologous engraftment. The reason why I want to develop this is because it is near within our reach to be able to create a method of viral protection against a lot of viruses which we thought we’d never be able to get rid of.
Week 2 HW: DNA Read, Write, & Edit
Part 0: Basics of Gel Electrophoresis Attend or watch all lecture and recitation videos. Optionally watch bootcamp. Done :checkmark: Part 1: Benchling & In-silico Gel Art See the Gel Art: Restriction Digests and Gel Electrophoresis protocol for details. Overview:
Homework Assignment: Python Script for Opentrons Artwork — DUE BY YOUR LAB TIME! Committed Listeners Required Your task this week is to Create a Python file to run on an Opentrons liquid handling robot.
Week 4 HW: Protein Design Part I
Week 4 — Protein Design Part I This week focuses on how sequence, structure, and energetics can be modeled and manipulated to create or optimize proteins with specified functions. 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) Meat contains at around 26g of protein per 100g of meat, so, in 500g of meat, this would be 26 g x 5 = 130g of protein
Week 5 HW: Protein Design Part II
Homework DUE BY START OF MAR 10 LECTURE 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 — Genetic Circuits Part I: Assembly Technologies
Answer these questions about the protocol in this week’s lab: What are some components in the Phusion High-Fidelity PCR Master Mix and what is their purpose? As stated in the thermofisher website, “Phusion DNA Polymerase, nucleotides, and optimized reaction buffer including MgCl2” The Phusion DNA Polymerase will be the one replicating the DNA at a really high fidelity The nucleotides will be ‘inserted’ into the replicated DNA strands And the reaction buffer (Including MgCl2, which is a co-factor needed for the enzyme), which is optimized, meaning, it has the favorable conditions for the enzyme such as pH.
Week 7 HW: Genetic Circuits Part II: Neuromorphic Circuits
Assignment Part 1: Intracellular Artificial Neural Networks (IANNs) What advantages do IANNs have over traditional genetic circuits, whose input/output behaviors are Boolean functions? Scalability for one, and for second, way more outputs; comparing this to, for example, the lac operon, if I recall correctly it only has a represor, an operator, and the lactose gene. IANNs would have way more repressor, operators, and so way more outputs, and ways said outputs are regulated, by multiple inputs.
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. Describe the main components of a cell-free expression system and explain the role of each component. Why is energy provision regeneration critical in cell-free systems? Describe a method you could use to ensure continuous ATP supply in your cell-free experiment. Compare prokaryotic versus eukaryotic cell-free expression systems. Choose a protein to produce in each system and explain why. How would you design a cell-free experiment to optimize the expression of a membrane protein? Discuss the challenges and how you would address them in your setup. Imagine you observe a low yield of your target protein in a cell-free system. Describe three possible reasons for this and suggest a troubleshooting strategy for each.
Week 10 — Advanced Imaging & Measurement Technology
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.