Lecture 1. Core Principles and Technologies of Synthetic Biology Flashcards
What is orthogonality?
The ability of a designed and built circuit in a cells to work in parallel, as far as possible to the naturally evolved systems that already exist in the cell
What is biosystem noise?
Random variation
What is robustness?
Reliability under different environmental conditions
What is the typical cycle for synthetic biology?
→ Design → Modelling → Construction → Testing →
What is synthetic biology driven by?
Human design rather than natural evolution
What are the theoretical applications of synthetic biology?
Health
Food Security and Sustainability
Environment
Energy
What do negative feedback circuits typically do?
Generally stabilise system states
What is an example of a machine that uses a negative feedback circuit?
AC
What is the typical structure of a genetic negative feedback circuit?
Repressor → Operator → Promoter → Effector/transcription
What are examples of negative feedback circuits in the body?
Controlling blood sugar levels
Lactose Operon
What do positive feedback circuits typically do?
Generate transient surge-like behaviour within biological systems, leading to excitability, oscillations, bistability
What is the ProP-PhoQ feedback circuit an example of?
Two-component virulence system that allows pathogen survival in the host
What happens in the ProP-PhoQ positive feedback circuit?
Low [Mg2+] causes autophosphorylation of PhoQ (sensor kinase) which, in turn, activates PhoP (response regulator and transcriptional activator of PhoP + other genes, such as those involved in resistance to cationic antimicrobials)
What happens in the sporulation positive feedback circuit?
In Bacillus subtilis
Nutrient limitation causes dramatic morphological and physiological changes under the control of the master regulator Spo0A, which influences the expression of hundreds of developmental genes
When does an AND gate produce an output?
When both A and B produce an output
What is an example of an AND gate in E. coli?
Arabinose and salicylate being required for GFP expression (need both the mRNA and the mutated stop codon to get an output)
When does a NAND gate produce an output?
When only A, only B or neither produce an output
Two inputs both regulate the production of the activation domain
What is the difference between traditional and synthetic biologists when it comes to researching biosystems?
Traditional biologists tend to reverse engineer naturally evolved biosystems
Synthetic biologists tend to forward engineer new behaviours, indeed, even new potential organisms
What are examples of where synthetic biology is making significant contributions?
Stochasticity in gene expression
How genetic circuits generate oscillations and other behaviours
Cell-to-cell communication
How cells can maintain multiple stable steady-states in a dynamical system
Mechanisms intrinsic to gene regulatory networks
Exploring the potential diversity of metabolic networks
Exploring new types of living system that might never have evolved naturally
What are the typical examples of synthetic biology applications?
Engineered microbial strains to produce isoprene (synthetic rubber), acrylic (paint and detergents)
Vaccine development (production of HIV protein antigens)
Biofuels production (sugars to diesel alternatives)
Bipolymer synthesis (for bioplastic production)
What is the set-reset latch similar to?
A light switch
Why is standardisation important?
Needs standards in order to enable: Compatibility Interchangeability Reproducibility Fitness for use Accurate communication of designs Safety Quality assurance Consumer and environmental protection
What is the main purpose of synthetic biology?
Build-to-understand and build-to-apply
