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.
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. 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) 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. Cell-free protein synthesis not only is a robust and efficient system compared to in vivo methods, in which yields are comparatively lower, but if we go in terms of flexibility and experimental variables, there’s a lot of control to be had here given that we only use the components that are essential, this means that variables such as metabolism, possible toxicity, and laborous work such as transformation, transfection, just the whole genetically enginering part (and the assays that come with it, such as, verifying if my organism is indeed genetically modified!) is something to not worry about anymore. Now, because of all the previously mentioned, we do have more control too on elements needed for protein synthesis, such as, nucleotides, salts, DNA concentration, pH; said elements would typically be directed towards other cellular processes, but not here because there is no cell.
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.
Week 11 — Bioproduction & Cloud Labs
Homework Part A: The 1,536 Pixel Artwork Canvas | Collective Artwork Assignees for this section MIT/Harvard students Required Committed Listeners Required Contribute at least one pixel to this global artwork experiment before the editing ends on Sunday 4/19 at 11:59 PM EST. Make a note on your HTGAA webpages including: what you contributed to the community bioart project (e.g., “I made part of the DNA on the bottom right plate”) If I recall correctly, I was helping on the HTGAA spelling in the bottom left corner!