Keasling: Synthetic Biology Class/Questions

Questions for 1/25/2006:

Questions for Engineering E. coli to see light:

1. What is the purpose of the system? What are the "parts" of the system? What are the inputs and outputs of each part? What are the inputs and outputs of the overall system? How could you use each of the "parts" for other applications?

Questions for Engineering a mevalonate pathway in E. coli for production of terpenoids:

2. What is the purpose of the system? What are the "parts" of the system designed? What are the inputs and outputs of each part? What are the inputs and outputs of the overall system?

3. What are the advantages of splitting the biosynthetic genes into multiple operons? What could be the disadvantages?

4. What were some of the problems encountered while engineering E. coli to produce amorphadiene? How did the authors overcome those problems? How was the system optimized for production of amorphadiene in E. coli?

5. What other types of applications could you build based on this system?

Questions for 2/1/2006:

Questions for Reconstruction of genetic circuits:

1. In Fig 2a, what is the purpose of the system? What are the "parts" of the system? What are the inputs and outputs of each part? What are the inputs and outputs of the overall system? How could you use each of the "parts" for other applications?

2. In Fig 2b, what is the purpose of the system? What are the "parts" of the system? What are the inputs and outputs of each part? What are the inputs and outputs of the overall system? How could you use each of the "parts" for other applications?

3. In Fig 2c, what is the purpose of the system? What are the "parts" of the system? What are the inputs and outputs of each part? What are the inputs and outputs of the overall system? How could you use each of the "parts" for other applications?

4. In Fig 2d, what is the purpose of the system? What are the "parts" of the system? What are the inputs and outputs of each part? What are the inputs and outputs of the overall system? How could you use each of the "parts" for other applications?

5. In Fig 3a, what is the purpose of the system? What are the "parts" of the system? What are the inputs and outputs of each part? What are the inputs and outputs of the overall system? How could you use each of the "parts" for other applications?

6. In Fig 3b, what is the purpose of the system? What are the "parts" of the system? What are the inputs and outputs of each part? What are the inputs and outputs of the overall system? How could you use each of the "parts" for other applications?

7. In Fig 3c, what is the purpose of the system? What are the "parts" of the system? What are the inputs and outputs of each part? What are the inputs and outputs of the overall system? How could you use each of the "parts" for other applications?

8. In Fig 1c, what is the purpose of the system? What are the "parts" of the system? What are the inputs and outputs of each part? What are the inputs and outputs of the overall system? How could you use each of the "parts" for other applications?

Questions for 2/8/2006:

Questions for Programming cellular function:

1. What are some of the ethical issues associated with each of the applications for synthetic biology discussed in the paper? Are there some applications that might be easier to adopt than others from an ethical perspective? Which ones? Why?

2. For the applications you thought might be difficult to adopt, discuss some of the ways you might persuade policy makers to approve the application. If you do not believe that certain applications should be adopted, then discuss why you believe that the application should not be adopted.

Questions for Metabolic engineering for drug discovery and development:

3. Discuss some the issues (scientific, engineering, ethical, etc.) that make metabolic engineering challenging. How might one try to resolve these issues?

4. What are the limitations of metabolic engineering? Are there any disadvantages? Are there scenarios where chemical synthesis might be a better solution for producing a small molecule?