Week 10 Homework
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Week 10 Homework

Homework Part A

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?
    1. How can I model every circuit in the body as one model, that takes in all vibrations around and inside of me? Meaning we can predict what will happen at atomic level clarity what happens when a bee stings us, when we eat an apple, when we go to the gym and the music is too loud, when we are listening to negative conversation that is affecting our subconscious negatively. We want clarity into our environmental <> internal feedback loop, and what proteins are created, what is out of balance, and the overall physics of mental health.
  2. If you could make metric tons of any protein, what would you make and what positive impact could you have?
    1. No single one- design a system that caters to the ones that are needed, where that info is obtained via the method above. We want all proteins needed at all times- a live market of everything needed by a single person. That demand will drive supply and you’ll know what is needed from that. It hinges on clarity of information- what the individual human needs at any given time, then groups of humans, then all humans.

Homework Part B

  1. Which genes when transferred into E. coli will induce the production of lycopene and beta-carotene, respectively?
    1. Lycopene: crtE, crtB, crtI
    2. Beta-carotene: crtE, crtB, crtI, crtY

      3. These come from Erwinia herbicola and are carried on the pAC-LYC and pAC-BETA plasmids.

  2. Why do the plasmids that are transferred into the E. coli need to contain an antibiotic resistance gene?
    1. So that only the bacteria with the plasmid survive. The antibiotic kills all the cells without the plasmid.
  3. What outcomes might we expect to see when we vary the media, presence of fructose, and temperature conditions of the overnight cultures?
    1. Media (LB vs 2YT): richer media = more growth and pigment
    2. Fructose: less acetate, higher yield (especially lycopene)
    3. Temperature: 30C is better for folding/stability, 37C is better for faster growth, but at the expense of pigment (stretched out)
  4. Generally describe what “OD600” measures and how it can be interpreted in this experiment.
    1. It measures cell density (turbidity). At 600 nm, the light scattering indicates the bacterial concentration. We can use it to normalize pigment output per cell.
  5. What are other experimental setups where we may be able to use acetone to separate cellular matter from a compound we intend to measure?
    1. Any hydrophobic pigments/metabolites:
      1. chlorophyll
      2. lipids
      3. essential oils
      4. small hydrophobic drugs that denature proteins, dissolve hydrophobic chemicals
  6. Why might we want to engineer E. coli to produce lycopene and beta-carotene pigments when Erwinia herbicola naturally produces them?
    1. It grows fast and we have better control over quantity- our tools are designed around E Coli, thus we can better engineer it. This will change as our tooling becomes general purpose.