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Lecture 20

Biology 2581B Lecture 20: Synthetic Biology

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Biology 2581B
L.Graham Smith

Lecture 20: Synthetic Biology: Parts, Modules, and Systems - Regulation: transcriptional, translational, post-translational - Sensing: chemical, light, force - Communication: small molecules, proteins, viruses - Physical: motility, growth, transport Synthetic Biology Definition: Connect various elements (regulatory, sensory etc.) in a reliable, predictable way and program a cell to function as a system - In synthetic biology, we’re trying to avoid unpredictable mutations - Goal: to have a predictable end product Hierarchy and modular organization - Even the smallest mutation would result in a sensible phenotypic change - We can take advantage of the fact that everything is hierarchically organized - If we introduce this hierarchy into a synthetic organism, we’d have to start with our first physical layer (analogous to proteins and genes) o Take these individual parts and create gates (if I press switch A or B, this is what should happen…) that can control what each part can do ▪ Equivalent to biochemical reactions in cells We can apply engineering principles to the design and alteration of natural systems or de novo construction of artificial biological devices and systems that exhibit predictable behaviours Synthetic biology circuits - To achieve hierarchy, look at all the individual proteins, mRNAs, and microRNAs o All of these respond to external stimuli, sensing signals from the outside - If we can organize these parts as a module, we’ll end up with a regulatory circuit Let’s say microRNA A regulates expression of gene B, and gene B regulates expression of another gene - We can define how we want this circuit to happen Synthetic biology: start with parts, make the cell react to stimulus and observe the effects - We have to ligate different strands of DNA together The Design Cycle - The first 3 processes start with a computer - Construction of the actual plasmid - Probing, testing, and validation come last Tools for design cycle 1. Engineering principles for design – decoupling, abstraction, standardization a. Abstraction: how do I stitch pieces together to form a good device? 2. Components for parts selection – Cis-elements, promoters, exons, protein-domains, ORFs, terminators, initiation sites (biobricks/phytobricks) a. Challenges: transcriptional regulation and precise control of expression in synthetic circuits b. You have to select parts which are already available c. We already know which parts we’ll need 3. Computational tools for design and modelling a. Component design & synthesis b. Topology and network design c. Behaviour prediction and simulation The Lac Operon Concept - Genes are organized in operons in prokaryotic cells - Regulator gene competes with operator site - If regulatory gene is expressed, it competes for polymerase binding site o No lactose present in this situation - If lactose present, regulator gene can’t bind to operator site because lactose p
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