Synthetic biology Flashcards
Synthetic biology has a bottom-up approach. What does this mean?
It tries to assess whether complex systems can be made from parts, and whether they can be redesigned.
Give examples of synthetic biology.
- Engineered enzymes
- Gene circuits
- Custom genomes
- Unnatural substrates
In synthetic biology systems are broken down into parts. What might serve as the ‘chassis’?
The organism of interest, e.g. bacteriophages, bacteria, yeast etc.
Define a BioBrick.
DNA sequences that conform to a restriction-enzyme assembly standard.
What are BioBricks used for?
To design and assemble synthetic biological circuits. These are then incorporated into living cells to build new systems.
How are new parts introduced, i.e. how are BioBricks joined?
Wit restriction endonucleases. The original restriction site changes with each addition of a new brick.
What do the assembled parts generate?
A device, which itself is a composite part.
Where are new parts added?
At the ends of the starting device/part.
basically can only be added in order
Parts can be tested to evaluate robustness and reproducibility before they are integrated into living cells. True or false?
True.
Define a logic gate.
It performs a logical function on one or more inputs. This produces a single output that is a logical function of the inputs.
Logic gate equivalents are used in synthetic biology, what are the components?
Paths for biological molecules to travel down (wires equiv.) and places where they can pass or be blocked.
Complex circuits are just as robust as simple circuits. True or false?
False: complex circuits are far less robust than simple circuits.
Can devices be integrated between cells?
Yes.
Give 2 advantages of BioBricks.
- Standardised parts can be created and shared
2. Much of the design process can be automated, causing fewer errors
Give 3 disadvantages of BioBricks.
- When all parts are viewed as independent modules then context is ignored, meaning there is less robustness
- Scars are created at junctions when different BioBricks are ligated together.
- Serial assembly is slow even when automated.
Define a scar.
When BioBricks with different RE sites are joined, both palindromic sequences are destroyed. Thus the 2 bricks can never be cut apart. This mixing of RE sites forms a scar.
When can scars be a problem?
If the device is being used to create a single polypeptide. The scar is a bit of mis-sense DNA.
Define a Type IIS RE.
Cut outside of their asymmetric, non-palindromic recognition sites.
How can Type IIS REs be used in scarless cloning?
They do not create scars when 2 BioBricks are joined as the recognition sites are non-palindromic. Plus it does not require the introduction of new cutting sites.
Define Gibson assembly.
Allows the joining of multiple DNA fragments in a single isothermal (temperature remains constant) reaction.
What 3 kinds of enzymes, other than REs, does Gibson assembly require? Briefly state why they are needed.
- Exonucleases: unmask compatible ends
- Polymerases: fills in gaps between free 3’ and 5’ ends
- Ligases: assembles the construct into a single molecule
Gibson assembly produces scars. True or false?
False.
Gibson assembly allows multiple fragments to be joined at once. True or false?
True.
Gibson assembly is used to assemble small constructs. True or false?
False: it is used for larger constructs.
What is the term ‘Synthia’ used to describe?
Synthetic life.
Multiple fragments can be assembled in vivo. How?
Using yeast recombination machinery.
Biological systems result from evolutionary processes. Why are components in their current arrangement? There are 2 possibilities.
- Intrinsic limitation
- Frozen accident
Synthetic biology seeks to find out and thus improve upon systems.
Information is stored in DNA but only accessible via RNA. True or false?
True.
All 3 chemical groups of a nucleotide - the sugar, the nitrogenous base and the phosphate - contribute to its structure and function. True or false?
True.
What is XNA?
‘Xenobiotic nucleic acids’: synthetic nucleotides whereby one or more of the 3 distinct chemical groups have been modified.
XNA have variable properties and compatibility with biological systems. True or false?
True.
Define an episome.
Non-integrated, extra-chromosomal DNA.
If XNA is used as the genetic material, what may we be able to create in the future?
XNA episomes.
Why might an XNA episome be useful? Give 2 examples.
- Can store extra information: if we establish a coding/decoding mechanism with synthetic enzymes whereby XNA and DNA are interchangeable.
- Can be maintained stably as is not part of the chromosomes.
On what condition would and XNA episome need to work?
Orthogonality: XNA would need to be inaccessible to current biological systems (basically so it doesn’t fuck your cells up), i.e. they can both occur without interfering with each other.
Define Xenobiology.
Unnatural biological systems.
What are the risk of GMOs resulting for xenobiology? Give 2 examples.
- Ecological: GMOs may interfere with other animals and their niches.
- Informational: the risk that part of the GMed genome could spread to natural organisms, which would disrupt ecosystems.
Reports of controlled GMO release have so far conferred what?
GMOs released for bioremediation have not established themselves in the tested niches and pose no threat to the environment.
XNA can be viewed as a ‘dead man’s switch’. Why?
Because it requires synthetic prescursors and xenobiology is purposely isolated from natural biology, it does not require an organisms to be alive to be activated, e.g. does not require precursors to be synthesised etc.
Containment failure of XNA relies on the ‘shortest evolution distance’. What does this mean?
The smallest change could cause it to be uncontained: for example a single mutation is archaea with XNA caused the production of XNA reverse transcriptase, causing RNA to be produced from XNA.
