Homework
Weekly homework submissions:
Week 1 HW: Principles and Practices
Table of Contents 1) Biological engineering application / tool 2) Governance / policy goals 3) Governance actions 4) Scoring governance actions 5) Governance Prioritization and Recommendation 1) Biological engineering application tool I want to develop and why Engineered probiotics for therapeutic compound delivery
Homework Questions from Professor Jacobson Question 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? DNA polymerase has an error rate on the order of 1 error per 106 bases. Compared to the size of the human genome, about 3 × 109 base pairs, this would imply thousands of errors per genome replication. Biology addresses this mismatch by adding layers of correction: polymerases can proofread during synthesis, and additional mismatch repair pathways correct many of the errors that still escape proofreading.
Week 4 HW: Protein Design Part I
Due Date Due by start of Mar 3 Lecture A. Conceptual Questions Answer any NINE of the following questions from Shuguang Zhang: 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) Why do humans eat beef but do not become a cow, eat fish but do not become fish? Why are there only 20 natural amino acids? Can you make other non-natural amino acids? Design some new amino acids. Where did amino acids come from before enzymes that make them, and before life started? If you make an α-helix using D-amino acids, what handedness (right or left) would you expect? Can you discover additional helices in proteins? Why are most molecular helices right-handed? Why do β-sheets tend to aggregate? What is the driving force for β-sheet aggregation? Why do many amyloid diseases form β-sheets? Can you use amyloid β-sheets as materials? Design a β-sheet motif that forms a well-ordered structure. B. Protein Analysis and Visualization In this part of the homework, you will be using online resources and 3D visualization software to answer questions about proteins. Pick any protein (from any organism) of your interest that has a 3D structure and answer the following questions: