HW #2 F 2023

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University of Toronto *

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18

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Chemistry

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Oct 30, 2023

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1

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Professor Wood 1 ChE 340 Homework #2 Due 9-5-23 1. Bacterial database (20 pts). E. coli is the workhorse for synthetic biology since genes from almost any source are readily converted into proteins in this host (and many are active). In this bacterium, there are about 40 toxin/antitoxin systems that allow the cell to become dormant (reduce protein synthesis) which is important for sleeping through antibiotic treatments and is relevant for disease. Also, most cells are starving in the environment so bacteria have to have ways to reduce their metabolism. Use the website: ecocyc.org to answer the following questions. a. What does the acronym “HokA” stand for? b. What is the antitoxin for this toxin? c. How many aa’s is HokA? d. What genes flank (i.e., are upstream/downstream) of hokA ? 2. Polymerase Chain Reaction (20 pts) Determine the products (number of DNA strands) you expect to see after 4 cycles of PCR, i.e., indicate the total number of original template strands, intermediate-sized strands, and small-sized strands. It is recommended that you keep track of the 3 sizes of DNA (perhaps via color) and the direction of each strand (i.e., 5’ or 3’). Rules: a. You only can elongate on the 3’ end with DNA polymerase. b. DNA polymerase cannot “guess” what nt to add so once it runs out of template, it stops (i.e., it has no imagination!). 3. Short answer (35 pts) a. What cellular entity is sequenced (idea from Carl Woese ca. 1977, U of IL) in order to classify living things (give the answer for bacteria)? Indicate clearly if it is RNA or DNA for full credit. b. True/False: SARS-CoV-2 is a DNA-based virus. c. True/False: Bacteria could be used to prove faster Darwin’s evolution ideas (since they have 30 generations/day, if well- fed). d. True/False: Adding phosphates makes the polar head of lipids more charged. e. True/False: Most bacteria are growing rapidly in the environment. f. True/False: NO (nitric oxide) may be used to disperse biofilms. g. True/False: Cells use RNA building blocks as internal signals by converting them into cyclic compounds (e.g., c-di-GMP, cAMP).
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