Synth bio 2

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  • Created by: katie
  • Created on: 21-01-20 14:41
Synthetic Biology
The design and engineering of a biological parts to create a novel device not found in nature
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Abstraction
Engineering principle where you ignore all unneeded details. E.g. Designing wheels and ignoring rest of the bike
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Abstraction levels
Materials, Parts, Devices, Systems
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Part
A functional piece pf DNA, codes a protein
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Device
A gene
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System
Multi-device/multi-gene
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Rational design
Linear process we aspire to: Design, build, test, deliver
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Iterative reterofitting
Realistic current design paradigm: Design, Execute, Test, Deliver
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Bio system
Collection of devices which switch on/off due to enviro factors
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Modularisation/decoupling
Ability to break system into component devices and parts, creates flow chart esc
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Control types
1. Transcriptoional, 2. Translational, 3. RNA, 4. Post-Translational
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Transcription
The process of DNA being copied into RNA. RNA polymerase binds to promoter and creates mRNA sequence
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Translation
mRNA transformation into protein. Ribosome binds, reads codons, attracts tRNA, anti-codon on tRNA binds to mRNA codon. Each tRNA has an amino acid attached. These form a polysaccharid chain=protein
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Constitutive
System constantly produces
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Inducible
System turned on/off environmentally
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Promoter
RNA polymerase bind site= transcription initiator, in DNA
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RBS
Ribosome bind site=translation initiator, in DNA and RNA
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Terminator
Stops transcription
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Operator
=transcription factor bind site=activator or repressor for the regulation of transcription
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Standardisation by functional composition
Grouping of parts by functionality, links to sbol as standard visual description
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Standardisation by physical composition
The creation of a standard physical composition, allowing consistent assembly
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Indempotnece
An operation which always produces the same result no matter how many times it's performed
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Standard Assembly Method- RFC10
Restriction-ligation system, uses BioBrick to combine genome
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BioBrick
Any DNA sequence flanked by E(EcoRI), X(XbaI) and S(SpeI), P(PstI) restriction sites, with PSB1C3 backbone
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Gibson Assembly
Endonuclease to chunk=sticky complementary ends, DNA polymerase fills gaps, DNA ligase reforms backbone
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Chassis
Structural framework of a system which is able to support other parts and device. In bio=cell.
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Metabolic Burden
Amount of resources(Raw materials and energy) removed from hosts normal function to maintain and express foreign DNA and create novel compounds
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Specific Burden
Resources directly taken from host pathways
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Generic Burden
An indirect effect, often due to higher energy consumption within the cell. Reduction of growth rate effecting DNA and cell wall turnover.
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Bottom-up
creation of new synthetic or chemically derived life from basic building blocks which were never alive. Cell free, in vivo function, use lipid vesicles
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Top-down
Add function to existing system, addition/deletion of gene(s), have to avoid cell overload
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Minimum genome
Minimum set of genes to sustain a self sustaining independently replicating organism
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Minimal cell
Cell containing a minimum genome, allowing it to be used as a chassis for synth bio parts/devices/systems. JCVI syn 3.0 = 1st
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Transposone
Mobile genetic element-piece of DNA which insterts itself randomly within the genome
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Transposone mutagenesis
Transposone self inserts and knocks out function-allows testing of gene fucntion
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5 hard truths
1.Many parts unidentified. 2.Circuitry in unpredictable 3.Complexity is unwieldy 4.Many parts incompatible 5.Variability crashes system
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CRISPR
Clustered Regularly Interspaced Short Palindromic Repeats
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CRISPR locus
Spacer DNA + repeats(CRISPR DNA)
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Guide RNA
1 spacer, 1 repeat, 1 aRNA (additional RNA)
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Single guide RNA
Spacer + merged repeat & aRNA
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Other cards in this set

Card 2

Front

Engineering principle where you ignore all unneeded details. E.g. Designing wheels and ignoring rest of the bike

Back

Abstraction

Card 3

Front

Materials, Parts, Devices, Systems

Back

Preview of the back of card 3

Card 4

Front

A functional piece pf DNA, codes a protein

Back

Preview of the back of card 4

Card 5

Front

A gene

Back

Preview of the back of card 5
View more cards

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