Lecture 17 Ear and sinus infections caused by viruses most use antibiotic treatment but should not but if you wait it out and take pain medication you will feel just as good For your lab exercise a single gene had been chemically synthesized o Gfp size 800 base pairs It is possible to do DNA synthesis on a MUCH larger scale o For example Venter and colleagues of JVI have successfully synthesized an entire bacterial chromosome by Chemically synthesizing 1 078 segments each 1 080 base pairs long Using yeast genetics to assemble these segments into a single circular chromosome 1 077 947 base pairs o The genome they made is a naturally occurring genome They have recreated a whole organism genome Have JCVI scientists created life Are they playing God Standardization iGEM wants this o Unified set of protocols o Unified set of pieces BioBricks sections of DNA you could buy that could only be put together in certain ways o Order custom made genes Genetic Code Expansion o Naturally occurring code 20 amino acids o Use existing tRNA to add novel aa to peptides Synthetic aa tagged with florescent molecules Always phosphorylated residues always know what sort of response you are getting Antibodies tagged with DNA o New codes 4 base code from 3 base codes to 4 base codes this enables you to expand the amount of amino acids that sequence codes for Synthetic Biological circuits o Organism with programmed response to conditions o Biological computers you put input in and know what output you will get o Oscillating systems naturally occurring or synthetically occurring can be used for marking time Synthetic oscillations in bacteria o Naturally occurring e coli with a genetically modified circuit that allows them to have an oscillations with a gfp that makes them synchronize their glow Metabolic Engineering o Complete understanding of cell physiology Create virtual cells literally means on the computer save time with experiments to model cellular behavior and keep scaling this up Create virtual systems o Rearrange the spatial arrangement in cells to make metabolism more efficient Synthetic Biology can accomplish great things Jay Keasling UC Berkley o Ex he engineered e coli to produce large amount of antimalarial drug artermisinin at a cost of 10 cents per gram from e coli compared to 1 per gram drug extracted from plants What is the function of the protein products of lacI relative to the gene of this plasmid Basically what does Plac do Answer Suppression of genes downstream of Plac o Why LacI makes a protein the repressor that binds downstream of Plac What needs to be added to the medium to allow expression from Plac Answer Lactose o Why The lacI gene responds to lactose when lactose is present it binds to lactose and no longer binds downstream of Plac Which of the methods of horizontal gene transfer could occur in the Rumen o Conjugation DNA travels through pili to another cell E coli we put in the cell is f Needs to come in contact with an f bacteria F cell puts out pilus and f DNA goes into f cell that cell then becomes f If there is recombination between the two plasmids you can then have transfer of the ampicillin gene then if it comes in contact with an f cell it can send a pilus again and give the recombinant DNA o Transformation the uptake of naked DNA from the environment Its possible if the e coli cell were lyse the plasmid would then be free in the environment and there were naturally competent microorganism the plasmid could then be transformed into one of these organisms o Transduction phage sucking up tiny bits of host chromosome and giving it to other cells There are phage in every environment where there are bacteria if a bacteria phage infects a cell that contains are plasmid if it the plasmid somehow gets incorporated in the phage the phage could then go on to infect a new cell with this DNA Virus o Just bad news wrapped in a protein o Obligate intracellular parasites o Innert in an environment until they come in contact with a host organism Novel properties of viruses Viruses Inert macromolecules outside of a cell but become active inside a cell Do not divide or grow Acellular not cellular Contain either DNA or RNA never both Genome can be dsDNA ssDNA dsRNA or ssRNA ds double stranded ss single stranded Ultramicroscopic in size ranging from 10 nm to 400 nm Have a proteinaceous capsid around genome some have an envelope around the capsid Cells Metabolize on their own Divide and grow Cellular Contain both DNA and RNA Genome is dsDNA 200 nm to 12 cm in diameter Surround by a phospholipids membrane and often a cell wall Replicate in an assembly line manner using the enzymes and organelles of a host cell Self replicating by asexual and or sexual means Synthesis strategies of animal viruses Feature of virus Contain nucleic acid inside a capsid o Most simple virus is just a protein encapsulating DNA Eukaryotic viruses often contain an envelope sometimes a lipid bilayer with proteins embedded into it lipid bilayer is often taken from cells they have infected Bacterial viruses phage can go through 1 of 2 life cycles o 1 Lytic cycle encounters a cell and recognizes its surface proteins injects its DNA into the cell this DNA takes over the host DNA replication machinery to basically make more phages between 5 200 once enough phage are made there is a signal to basically cause cell rupture phage then go out into the environment to infect new organisms pathway requires living cells cells that are actively growing won t take place with cells in a stationary phase Host recognition host range some virus can only recognize certain bacteria Recognition of cell surfaces by virus cell surface proteins Cell wall proteins Flagella Fimbriae Glycoproteins Restriction modification systems in bacteria how bacteria protect itself Restriction enzymes destroy DNA that has not been modified not native to the cell phage DNA will not of been methylated o 2 Lysogenic pathway phage attaches to cell and its DNA enters the cell and recombines itself with the host chromosome Prophage in chromosome Phage DNA hangs out like a plasmid and waits until a certain environmental signal occurs then it starts its lytic cycle Once it replicates into the chromosome it replicates like a normal cell When the environmental signal is given induction occurs and assembly of phages happen lytic cycle the cell eventually burst and the phages go on to infect other cells If the cell happens to already be one of the cells infected by