Homework
Weekly homework submissions:
Week 1 HW: Principles and Practices
1.First, describe a biological engineering application or tool you want to develop and why. As a pharmacy student, I have become increasingly interested in how drugs move from an initial idea to clinical use, and how many potential compounds fail long before they could reach patients. Drug development is an expensive and time consuming subject, and an ethically complex process, specifically in early stages. But many drugs are left behind as they fail to show strong enough effects or because the costs for further testing is too high.
Week 2 HW: DNA- Read, Write and Edit
Pre-Lecture HW: 1.Nature’s machinery for copying DNA is called polymerase. What is the error rate of polymerase? How does this compare to the length of the human genome. How does biology deal with that discrepancy? The error rate of polymerase estimates to be made errors once every 10x4–10x5 nucleotides polymerized. This compared to the length of the human genome that’s approximately 3.2 billion base pairs long, that would account up to 32 thousand mutations every time a single cell divided. Biology fixes this gap with multiple systems that check for these errors. Its first system is proofreading; a function found in most polymerases. When they add a wrong base, they recognize this error, backtrack and fix it cutting the wrong base and replacing it. Another way, is mismatch repair (NMR), after polymerase is done, a second group of proteins scan the new DNA for any remaining errors.
I designed a drawing with the website that was made available to us https://opentrons-art.rcdonovan.com/. It made it easier to get used to the way the points would be done inside the plate to create our art. Personally I decided to create a flower, took the exact points for each color, green (sfGFP) and red (mrFP1). I integrated the points to the base code, and customized it for the design to be possible, especially with the high quantity of points and the limit of the 20ul pipette.
Week 4 HW: Protein Design Part 1
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) To calculate this we have to make some equivalences. 1 aminoacid = 100 Da = 100g/mol Meat= 20% protein Look only for the protein mass 500g of meat x 0.20 = 100g of protein Moles of aminoacid
Week 5 HW: Protein Design Part 2
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 1
Protocol Questions 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? Phusion High-Fidelity PCR Master Mix with HF Buffer is a 2X master mix consisting of Phusion DNA Polymerase, deoxynucleotides and reaction buffer that has been optimized and includes MgCl2. All that is required is the addition of template, primers and water. (New England Biolabs, 2026)
Week 7 HW: Genetic Circuits Part 2: 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? While Booleann circuits produce on/off outputs, IANNs generetae continuous and graded reposnes allowing us to detect subtle changes in input signals. They also can intigrate multiple inputs that are adjustable, making them more flexible and better to mimic natural cellular desicion processes.
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. CFPS offers several key advantagesin felxibility and experimental control over traditional in vivo protein expression. In terms on flexibility, unlike living cells, we have an open reaction enevironment as we are not constrained by structures or the viability of the cell. We can add and remore components at any time. As we dont depend on the cell, there is no need for cloning or transformation, allowing the qucik testing of multiple gene constructs at the same time. We can express proteins that coudl be toxic or unstable in livign things because nothing is alive. Comparing the benefits for control of the experimental values, CFPS systems are superior as we cna tightly control conditions, directly manipulate the gene expression and define the environment for production.
Week 10 HW: Imaging and Measurement
Homework: Final Project 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 11 HW:Bioproduction & Cloud Labs
Part A: Art Pixel I was not able to complete this portion because I did not receive the email containing the project link. By the time I realized the issue, it was too late to contribute. Part B: Cell-Free Protein Synthesis | Cell-Free Reagents Referencing the cell-free protein synthesis reaction composition (the middle box outlined in yellow on the image above, also listed below), provide a 1-2 sentence description of what each component’s role is in the cell-free reaction.