Part A

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’d like to discover the maximum speed that I can run biological pathways at. Genetic circuits take hours or days to produce the output, which is rather slow if I’m trying to do biological computation. I’d like to see if I can speed it up to minutes.

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

Apparently, the blood of Atlantic horseshoe crab (Limulus polyphemus) is incredibly expensive, because it clots in reaction to bacterial endotoxins, and it can do so extremely sensitively, so the blood is very valuable for pharmaceutical testing to detect contamination.

There are a bunch of proteins involved in endotoxin-induced blood clotting, but the first in the sequence is Limulus clotting factor C, so it’d be pretty valuable if we could make a metric ton of that.

Part B

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

For lycopene:

Sugar metabolism → Geranylgeranyl diphosphate synthase (crtE) → Phytoene synthase (crtB) → Lycopene beta cyclase (crtL) →Lycopene.

For beta-carotene:

Sugar metabolism → Geranylgeranyl diphosphate synthase (crtE) → Phytoene synthase (crtB) → Lycopene beta cyclase (crtL) →Lycopene beta-cyclase (crtY).

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

Because any given E. coli bacterium may or may not take up the plasmid. We want only the bacteria that have taken up the plasmid to grow and reproduce, so we grow the bacteria in an antibiotic medium, and so only the bacteria with the plasmid get resistance and survive.

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

The bacteria might grow faster or slower with those variables.

Or the bacteria might just die, e.g. if one of the temperatures is just too high for them.

If one of the reagents like fructose is a component of the pathway for making pigment, then limiting the reagent will also limit how much pigment we produce.

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

It’s how much light is absorbed by a sample when you shine a 600 nm light on it. This is the standard wavelength for measuring bacteria concentration, so it tells you how much bacteria has grown in your sample.