Homework

Weekly homework submissions:

• Week 1 HW: Principles and Practices

  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. I am interested in creating biosensors by using modified bacterial cultures to detect toxins and contaminants in the environment. Currently, to test for substances such as heavy metals, biotoxins, and organic pollutants, we often need expensive and often inaccessible detection tools, such as mass spectrometers and analytical chemistry kits. By creating biosensors out of bacteria, we can simplify contaminant detection.

• Week 5 HW: Protein Design Part 2

  Part A: SOD1 Binder Peptide Design (From Pranam) Assignees for the following sections MIT/Harvard studentsRequired Committed ListenersRequired 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 Assignees for the following sections MIT/Harvard studentsRequired Committed ListenersRequired What are some components in the Phusion High-Fidelity PCR Master Mix and what is their purpose? as per 1 High fidelity DNA polymerase (50 times more accurate than “standard” Thermus aquaticus DNApoly) Phusion HF buffer Mg2+ as 1.5mM MgCl2 for DNApoly to function dNTPs What are some factors that determine primer annealing temperature during PCR?