Homework Part A

<aside> <img src="/icons/exclamation-mark_orange.svg" alt="/icons/exclamation-mark_orange.svg" width="40px" /> These homework questions are based on lecture questions! Mandatory for Committed Listeners.

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Patrick Boyle’s Lecture Questions:

  1. Assume that all of the molecular biology work you'd like to do could be automated, what sort of new biological questions would you ask, or what new types of products would you make?

    I would want to work towards building multicellular systems. I would like to try to create trees that can grow into the furniture they will become. I would like to have butterflies with custom patterns on their wings. I would want to explore the intersection of art and life. However, this could very quickly go into the realm of unethical, and so I would have to be very careful.

  2. If you could make metric tons of any protein, what would you make and what positive impact could you have?

    IF I could make metric tons of any protein, I would want to manufacture spider silk proteins on an industrial scale. We could use these ultra-high-strength fibers in place of petroleum based textiles.

Homework Part B

<aside> <img src="/icons/exclamation-mark_orange.svg" alt="/icons/exclamation-mark_orange.svg" width="40px" /> These homework questions are based on the Bio Production Lab! Mandatory for both Committed Listeners and MIT/Harvard students.

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<aside> <img src="/icons/push-pin_green.svg" alt="/icons/push-pin_green.svg" width="40px" /> Key Links: http://docs.google.com/document/d/15-tlrejgbbr4FMpA6rKogTjlv6qXJhFqQm7o_Ppfh-I/edit?tab=t.0#heading=h.jyt74412izch

Key Papers:

  1. Gene expression pattern analysis of a recombinant Escherichia coli strain possessing high growth and lycopene production capability when using fructose as carbon source

  2. Improvement of Biomass Yield and Recombinant Gene Expression in Escherichia coli by Using Fructose as the Primary Carbon Source </aside>

  3. Which genes when transferred into E. coli will induce the production of lycopene and beta-carotene, respectively?

    three genes from Erwinia herbicola: CrtE, Crtl, and CrtB induce the production of lycopene. The addition of a fourth gene, CrtY, induces the production of beta-carotene.

  4. Why do the plasmids that are transferred into the E. coli need to contain an antibiotic resistance gene?

    The E. coli strain that we are using is not antibiotic resistant. By transforming a plasmid with antibiotic resistance into the E. coli, we can select for cell colonies that resulted from successful transformation.

  5. What outcomes might we expect to see when we vary the media, presence of fructose, and temperature conditions of the overnight cultures?

    Media composition: Richer media (e.g., LB vs. minimal) generally boost biomass and may dilute per‑cell pigment concentration, while minimal or carbon‑limited media can slow growth

    Fructose (inducer): We might expect a higher overall biomass with fructose, and a higher turbidity.

    Temperature: Higher temperature may increase cell growth, while lower temperatures may allow for better protein stability.

  6. Generally describe what “OD600” measures and how it can be interpreted in this experiment.

    OD600 measures the microbe concentration of a given sample.

  7. What are other experimental setups where we may be able to use acetone to separate cellular matter from a compound we intend to measure?

  8. Why might we want to engineer E. coli to produce lycopene and beta-carotene pigments when Erwinia herbicola naturally produces them?