Homework
Weekly homework submissions:
Week 1 HW: Principles and Practices
- First, describe a biological engineering application or tool you want to develop and why. I want to work with Geobacter bacteria to create a living soil contaminate sensor: where electric signals modulate based on the prescence of heavy metals in the ground. Geobacters are already well studied bacterias that produce electric signals under ground. This makes them a useful organism to modify and use as a biosensor.
Week 2 HW: DNA Read, Write, & Edit
Part 1: Benchling & In-silico Gel Art I made a free account on benchling and then imported the Lambda DNA (see below).
Python Script for Opentrons Artwork I was able to run my opentron script of a rainbow at Lifefabs Institute last year, using paint instead of bacteria. I’m adding a couple images and short video of the process. Python Code This is the code that I used to run my protocol.
Week 4 HW: Protein Design Part I
Part A: Conceptual Questions 1. 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). amino acid = ~100 Daltons meat = 25% protein (according to google between 20 to 30% depending on meat) Daltons = g/mol So 500g/4 is 125g of protein. We’re going to have to use Avogadro's number (6.022 × 10²³) Avogadro’s number helps us to convert Moles to number of molecules.
Week 5 HW: Protein Design Part II
Part A: SOD1 Binder Peptide Design Part 1: Generate Binders with PepMLM Human SOD1 sequence from Uniprot (no Mutation): (https://www.uniprot.org/uniprotkb/P00441/entry) >sp|P00441|SODC_HUMAN Superoxide dismutase [Cu-Zn] OS=Homo sapiens OX=9606 GN=SOD1 PE=1 SV=2 MATKAVCVLKGDGPVQGIINFEQKESNGPVKVWGSIKGLTEGLHGFHVHEFGDNTAGCTS AGPHFNPLSRKHGGPKDEERHVGDLGNVTADKDGVADVSIEDSVISLSGDHCIIGRTLVV HEKADDLGKGGNEESTKTGNAGSRLACGVIGIAQ A4V Mutation refers to Alanine being changed to Valine at the 4th amino acid in the protein.
DNA Assembly 1. What are some components in the Phusion High-Fidelity PCR Master Mix and what is their purpose? According to the New England Biolabs product page, Phusion High-Fidelity PCR Master Mix consists of: Phusion DNA Polymerase deoxynucleotides a reaction buffer that has been optimized and includes MgCl2 The Phusion DNA polymerase is able to synthesize new DNA strands. It is able to “proofread” itself which means it produces much less errors than other polymerase (hence why it is “high fidelity”). Deoxynucleotides refers to the molecules that makeup DNA (ie. A,T,G,C). These building blocks are going to be used in the new DNA strands. The reaction buffer creates the right environment for this process to take place. It ensure there is the right pH and the right amount of ions.
Week 7 HW: Genetic Circuits II - Neuromorphic Circuits
Intracellular Artificial Neural Networks (IANNs) What advantages do IANNs have over traditional genetic circuits, whose input/output behaviors are Boolean functions? IANNs are interesting and different than traditional genetic circuits becuase their inputs are continous molecular concentrations. So a basic artificial neuron can take 2 inputs and have an output that is a constantly changing and evolving based on the changing concentration amounts of the inputs. They are able to therefore handle more complexity than traditional genetic circuits. You might need multiple genetic circuits to create calculations IANNs can do.
General and Lecturer-Specific Questions 1. 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. There are many advantages of cell-free protein synthesis over traditional in vivo methods. Cell-free systems allow you to have more control over the conditions of your experiment (ie. DNA, proteins, small molecules, etc.). Unlike working in vivo methods, where things are a bit more of a “black box”.
Week 9 HW: Advanced Imaging & Measurement Technology
Final Project - Measurements Please identify at least one (ideally many) aspect(s) of your project that you will measure. It could be the mass or sequence of a protein, the presence, absence, or quantity of a biomarker, etc. Please describe all of the elements you would like to measure, and furthermore describe how you will perform these measurements. What are the technologies you will use (e.g., gel electrophoresis, DNA sequencing, mass spectrometry, etc.)? Describe in detail.
Week 10 HW: Bioproduction & Cloud Labs
Part A: The 1,536 Pixel Artwork Canvas | Collective Artwork So I forgot to take a photo but I submitted one green pixel that was above a red heart in the bottom left quadrant. This was early on, when I first received the link to the Pixel Artwork Canvas. However I’m pretty sure the whole heart got erased and replaced multiple times over by the time the deadline ended! haha