Class Notes (838,183)
Canada (510,737)
Biology (6,824)
Lecture 20

Biology 2581B Lecture 20: Lecture 20 genetics 2581
Premium

12 Pages
47 Views
Unlock Document

Department
Biology
Course
Biology 2581B
Professor
David R Smith
Semester
Winter

Description
Lecture 20  Craig Venter created the first biosynthetic prokaryotic micro plasmid bacterium = world’s first synthetic organism  Synthesized a complete genome and transferred it to a host cell  Rebooted the host cell so that it was under the control of the introduced synthetic genome  Can introduce synthetic tools into diabetic people to provide “cure”  How can we take all these process that occur in the cell, put it in a computer so that we can manipulate it and make it in a way that it can function the way we want  Example: insulin o Introduce these synthetic devices that will sort of prevent diabetes (to a certain point)  Take the genetic code and translate it to a binary code in the computer → one of the starting points for synthetic biology o Not as simple as taking genes, converting to genetic codes and putting in the computer → recombinant DNA technology = biotechnology  But a biological organism has so many processes organized at a hierarchical level, so it is not as simple as taking these genes and converting them to binary code and putting it into computers  There are certain processes and the genes within the genome code for different regulations  The gene needs to react to the environment and there is also communication between small molecules and proteins o External organisms that cause responses  You have to somehow figure out a way to put all these levels of these processes together and input them into a computer  Synthetic biology is a way to connect all these regulatory, sensory, physical, etc elements in a reliable and predictable way o The term predictable is really important since if you want to put a few genes together, you want them to give a predictable outcome - you want genes that respond to the environment in a predictable fashion o 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  Need to program the cell to function as a whole system  You need to take advantage of a hierarchical system that already exists in biological systems  We already know what the cells are composed of and what proteins, etc they have and how they are designed to react  There is also an organism to ecosystem hierarchy (reacting to the environmental stimulus)  Since the hierarchy already exists in synthetic biology, it makes our job easier  You can alter the existing natural systems and create an entirely new system  Think about it in the context of a pathway, cell, or system as a whole, not just the level of the gene  Connect various elements/layers (regulatory sensory, etc.) in a reliable, predictable way and program a cell to function as an autonomous system, in the highest efficiency with the smallest genome possible (original definition)  Earlier known as recombinant DNA technology or biotech  Construct a biological system (ex. A network or a pathway) using characterized genes and regulatory DNA sequences  GOAL: achieve the highest efficiency in the synthetic cell with minimal genome that a cell can function efficiently for the cell to be able to adapt to any type of circumstance  Method: replicate the following areas “layers” of focus in a synthetic cell, but need to understand how they function first  Regulation: necessary to produce enough protein/RNA in the cell to perform their function properly o Transcriptional, translational, post-translational, modifications, epigenetic o Need to transform the cellular information into technological codes that can be input into computer  Sensory Stimulus: has to sense the signal within and outside the cell in order to perform functions such as glycolysis and photosynthesis o Essentially: how the cell reacts to its environment (both the outside and the inside) o Stimuli are how the cell detects these signals and transmits those to the interior of the cell  Stimuli: chemical, light, force (ex: chemical, kinetic, potential, pressure)  Communication: cell-to-cell communication, protein interactions OR how the cell communicates with other cells and its environment o Layer we are at now in biotechnology – we can create parts and components that do regulation and sensing, but need to create communication between cells to create multicellular organisms o Could be done through small molecules, proteins, viruses  Physical: response to motility, growth (photosynthesis, glycolysis), transport o Most important aspect of synthetic cells  Epigenetic: level of regulation based on the the environmental stimulus that exists  Synthetic Biology: Apply engineering principles to the design and alteration of natural systems or de novo construction of artificial biological devices and systems that exhibit predictable behaviors (new definition)  A computer can actually perform all the functions that a cell can do  Trying to synthesize parts that can function as a system and an organ by itself through technology, with the minimal genetic sequences/materials (genome) required in an efficient & predictable way  Take all the naturally existing system/programming inside a cell & transfer it into the computer  By the end, the synthetic organism must be able to survive in an unique environment that the scientists impose  Synthetic biology can be used at all Hierarchy and Modular Organization  Connects fundamental parts together (proteins) to get a desired outcome (products at the end of a biochemical reaction)  Multiple biochemical reactions together  Network of modules/biochemical pathways together  Multiple cells together to form a network  Parts to modules to complex systems, adapt from other disciplines and implement in biology (analogy)  Proteins and genes are the 1 layer = physical layer  A bunch of parts form gates. If connected together in a reliable fashion biochemical reactions = gates  Can input repressors or inducers that act as gates and produce proteins which act as the output  Gates put together form modules (pathways made up of multiple biochemical reactions)  Pathways make a cell functional  If you want to connect all the computers together, you make a network  If you want to connect all the cells together, you form tissues/cultures  Start by synthesizing/selecting DNA sequences containing the genes that contains desirable protein product  The amount of DNA selected & the order of genes = based on the identity of the desirable protein product  The product should participate in a biochemical reaction that you know would give you the desirable product (see circuit)  Scale for DNA synthesis & assembly:  In the order of genes: 10^2—10^4 bp  A gene circuit’s size: 10^4—10^6  A minimal genome: 10^6—10^7 (a combination of more than one circuits that is required to function, no embellishments)  This process is easy for bacteria = create a traditional recombinant plasmid since the sequences can be fused and inserted  Difficult for eukaryotes especially mammals, need to understand specific functions in each part of the genome  Challenge: unsure if the circuits will function as predicted once fused together in the minimal genome  NOTE: a microplasma = 1.8 mb (megabase) Synthetic Biology Circuits  Sensing, processing, actuation  Sense what is happening in the cell (microRNA, mRNA, and proteins) in the form of a regulatory circuit  If this and that are present, proceed to the next step  If you get to the end, you will get a genome  If you get too much production, you can kill the protein  microRNA, mRNA and proteins can all act as regulatory circuits  The microRNA / mRNA / proteins (physical layers) detect a signal in the environment & react together (circuit)  The final or byproducts serve as stimulus to the targeted molecules, the level of these products affect regulation (regulatory)  The process of proteins reaction together to serve regulatory functions is similar to programming: A+ B → C  If your logigate functions according to the logic command given (A+B), the product yield would be called “activation” (C)  In synthetic biology, the product C must behave in a predictable manner → must control the gate & logic command  Mutations create unpredictability in systems, force them to react to the mutation in different ways 1. Sensing 2. Processing 3. Actuation  Scale for DNA synthesis and assembly  Driving force for more synthetic creations = dropping costs  Trying to create a gene circuit so you put them all together using recombinant DNA technology  Increasing complexity as you go up the hierarchy  Can put in all kinds of stuff (e.g., repressors and genes) but it doesn’t mean it’ll function The Design Cycle  Must conceptualize what your goals, inputs, outputs are – and then you can design it  Select parts and the computer will put it together for you  Then you can start modeling the system – and then you can construct the system  Can use restriction digest to get the system  Once you get the system, you can probe, test, and validate it 1. Conceptualization → identify the system goals, necessary inputs needed to create the designed outputs 2. Design → understand network topologies, kinetic parameters, parts selection (all can be done on computers) 3. Modelling → how do circuits interconnect? Understand network behaviours, robustness, sensitivity 4. Construction → assemble & integrate into a plant 5. Probing, testing and validation → alteration, library screening, directed evolution *1-3 = design ; 4-5 = fabrication* Tools for Design Cycle: 1. Engineering principles for design (simply the process of construction)  Reduce efforts of design cycle  Decoupling: separate / taking apart each level of the cellular component to understand their functions / structures (simplification – rip system apart and see what’s in it)  Abstraction: extract the components from the cell/host, identify how they fit together to produce a viable system (separation into hierarchical levels, see how the pieces fit together)  Standardization: manipulating the separated components in such a way that the components should be able to function properly aka when we put input, an output should come out = putting them back together 2. Components for parts selection  Parts are designed and cataloged onto online databases, then parts are used to build a circuit  Example: anything that is important to gene expression (cis-elements, promoters, exons, protein domains, ORFs, terminators, initiation sites)  Biobricks – things available for purchase  Phytobricks – plants  Challenges: difficult to make sure that transcriptional regulation functions properly and hard to guarantee the precise control of expression in synthetic circuits & time- consuming  Otherwise: could yield unpredictable consequences in a circuit, and doesn’t work the way you want to 3. Computational tools for design and modelling  Help to design network and put parts together  Component design & synthesis (design network))  Can be obtained from the Library of Parts  Composed of the 4 areas of focus (regulation, sensor, communication & physical aspect)  When designing components, need to make sure that these 4 components are satisfied  Topology and network design (put parts together)  Behaviour predictions and simulation (see whether the cell survives)  Registry of Standard Biological Parts – a database where you can get biological parts from  A database from iGEM (international Genetically Engineered Machine)  Has more than 200 000 biological parts that could be used in the designing cycle Synthetic Microplasma Genome  Prokaryotic cell that contains a completely synthetic genome  No matter what changes you introduce to the system, they have to be predictable  Take parts like mRNA, miRNA, etc that are present within the cell and join them through regulatory systems, meaning parts A and B are going to turn on in response to a stimulus and produce an output  In order to build these parts you need DNA  So if you were to create gene circuits then you would have to fuse a few genes and their regulatory elements for the genes - cis elements, promoters, operators, etc that will control the expression and repression of these genes  You would make a plasmid that you would insert  If you're creating an entire genome, you have to consider the amount of DNA that is required (from mb to gb)  You have to take these little parts and stitch them together in a way that they can have a predictable function  To be able to do that, you have to follow a design cycle  First, you want to conceptualize what your end product is supposed to do  Think about your goal, input and outputs  Then you can design your model to reflect the given input and produce a predictable output  Then you have to actually construct and stitch these
More Less

Related notes for Biology 2581B

Log In


OR

Join OneClass

Access over 10 million pages of study
documents for 1.3 million courses.

Sign up

Join to view


OR

By registering, I agree to the Terms and Privacy Policies
Already have an account?
Just a few more details

So we can recommend you notes for your school.

Reset Password

Please enter below the email address you registered with and we will send you a link to reset your password.

Add your courses

Get notes from the top students in your class.


Submit