Homework 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?

Dynamic and Interactive Biological Colors, that can change based on environmental stimuli or user input. This could be used in fashion, art, or even as a form of communication. For example, clothing that changes color based on temperature or mood, or living art installations that respond to viewer interaction. another use case would be in patient monitoring, where clothing or wearable devices change color to indicate health status or stress levels. or even in home decor, where furniture or wall coverings change color to match the ambiance or time of day. or in forests, where trees or plants change color to indicate environmental conditions like pollution levels or soil health. This could provide a visual representation of ecosystem health and help in conservation efforts.

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

Spider Silk Proteins. Spider silk is known for its incredible strength, elasticity, and biocompatibility. If we could produce it in large quantities, it could revolutionize various industries. In medicine, spider silk could be used for sutures, wound dressings, and even as scaffolds for tissue engineering and artificiial tendons. In textiles, spider silk could lead to the development of lightweight, durable, and environmentally friendly fabrics. Additionally, spider silk could be used in construction materials, providing a sustainable alternative to traditional materials while reducing environmental impact.

Homework Part B

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

For Lycopene, We need the genes crtE, crtB, and crtI. These three enzymes convert the endogenous precursors (FPP) into Lycopene. For Beta-Carotene, one additional gene is required: crtY (lycopene cyclase). This enzyme takes the Lycopene produced by the previous three enzymes and forms Beta-Carotene.

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

To be able to select the bacteria that have successfully taken up the plasmid through adding the relative antibiotic to the growth media.

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

• Providing Rich Media may lead to higher biomass and less pigment production, since the cells may prioritize growth over secondary metabolite production. Minimal media may result in slower growth but higher specific productivity and possibly pigment production.
• Fructose metabolism yields more precursors for the MEP pathway, which may enhance the pigment production.
• Temperature can affect enzyme activity and membrane fluidity. Lower temperatures may slow growth but can sometimes enhance the stability of certain enzymes involved in pigment biosynthesis, potentially leading to higher pigment yields, unlike higher temperatures which may denature enzymes or prevent proper folding.

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

OD600 stands for Optical Density at 600 nm. It acts as a proxy measurement for biomass (cell density). Bacteria act like tiny mirrors, They scatter light, so if you shine a light through the tube, the less light that comes out the other side, the more bacteria are in the way.

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?

Acetone is an amphiphilic solvent ideal for extracting hydrophobic compounds while precipitating proteins and hydrophilic cellular debris. Some experimental setups where acetone can be used include Chlorophyll Extraction from plant tissues or Lipid Extraction.

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

• E. coli is a well studied, fast growing, and easy to manipulate organism. Engineering E. coli to produce these pigments allows for easier genetic modifications, potentially higher yields, and more controlled production conditions compared to using Erwinia herbicola.
• Also Erwinia herbicola is a plant pathogen and can be a human opportunistic pathogen, so E. coli especially the K12 strains are generally considered biologically safer for industrial applications.

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