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Revision as of 20:26, 18 September 2015
UNIQ handout
Synthetic Biology
Aims
- To introduce the jargon of synthetic biology
- To become familiar with the concepts of synthetic biology
- To introduce gene structural elements and their function
Tasks
Discuss the answers to the following questions in your group.
- Define a Biobrick.
- Is there specific order that BioBricks needs to be arranged?
- Discuss the types of inputs to which a promoter can respond.
- How are the biological circuits constructed?
- In which cases might terminators be necessary in the biological part?
Sets of Group Questions
Group A: BioBrick Constructs
Aims:
- To understand how multiple BioBricks can be used to build a biological circuit
- To explain the flexibility of the terms ‘BioBrick’ and ‘system’ in synthetic biology
Tasks:
Study the follow biological system and answer the questions in your group. Plan a 2 minute talk to the rest of the class that includes:
- Description of the part
- Functions and applications
Info 1: Dichloromethane (DCM) is a highly volatile solvent which finds application in a wide variety of industrial and commercial processes
Q1: Why might it be important to remove solvents like DCM from the environment?
Q2: Does DCM need to stimulate or inhibit transcription of the coding sequence downstream ofthe promoter?
Q3: What might the function of the protein dcmA be?
Q4: Which part of the biological part needs to be sensitive to DCM?
Q5: Why might a strong RBS be used?
Q6: When would it be useful to include a reporter protein?
Q7: What parts could be changed or added to remove different contaminants from the environment?
Group B: BioBrick Constructs
Aims:
- To understand how multiple BioBricks can be used to build a biological circuit
- To explain the flexibility of the terms ‘BioBrick’ and ‘system’ in synthetic biology
Tasks:
Study the follow biological system and answer the questions in your group. Plan a 2 minute talk to the rest of the class that includes:
- Description of the part
- Functions and applications
Info 1: Bacteria produce and secrete certain signaling molecules, such as AI2, to communicate with neighbouring bacteria. This is called quorum sensing. The quorum sensing molecules that bacteria release increase in concentration as a function of cell density.
Q1: What is the function of the “AI2 induced” promoter?
Info 2: Holins are proteins produced by viruses that infect bacteria (bacteriophages) that cause the bacterial cell to burst (cell lysis)
Q2: Why might a weak RBS be used?
Q3: What is the function of GFP?
Q4: What is the function of the overall system?
Q5: What are the applications of this system and how might it be changed and expanded?
Group C: BioBrick Constructs
Aims:
- To understand how multiple BioBricks can be used to build a biological circuit
- To explain the flexibility of the terms ‘BioBrick’ and ‘system’ in synthetic biology
Tasks:
Study the follow biological system and answer the questions in your group. Plan a 2 minute talk to the rest of the class that includes:
- Description of the part
- Functions and applications
This biological system breaks down blood clot under hypoxic conditions.
Info 1: Hypoxia Response Element (HRE) responds to a lack of oxygen in the environment
Info 2 : Fibrin is a fibrous protein and is a major component for the blood clotting.
Info 3: Plasmin is produced by tissue plasminogen activator (tPA) and cuts the fibrin mesh at various places to break down a blood clot
Q1: What is the function of the HRE induced promoter?
Q2: Why would blood clots forming in blood vessels be a problem?
Q3: Why do you think it’s important to target an inactive enzyme rather than to express an enzyme which will act directly on the fibrin mesh?
Q4: What are the applications of this system and how might it be changed and expanded?
Group D: BioBrick Constructs
Aims:
- To understand how multiple BioBricks can be used to build a biological circuit
- To explain the flexibility of the terms ‘BioBrick’ and ‘system’ in synthetic biology
Tasks:
Study the follow biological system and answer the questions in your group. Plan a 2 minute talk to the rest of the class that includes:
- Description of the part
- Functions and applications
Info 1: PgolB senses toxic gold in the environment
Q1: What might the function of GolB protein be?
Q2: Why might you have a strong RBS?
Q3: What is the function of RFP?
Q4: Why can’t the arrow for GolB point in the other direction?
Q5: What are the applications of this system and how might it be changed and expanded?