Lecture 16 Notes.docx

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Department
Molecular Genetics and Microbiology
Course
MGY377H1
Professor
William Navarre
Semester
Fall

Description
Lecture 16- Transcript MGY377 (Oct.19 recording) Slides that were skipped means that the prof just read off of them and didn’t add anything new. They should still be considered testable. Microbial Genomics 2 (Cont’d) “I’ve got my genome…now what?” Quiz How are horizontally acquired genes identified? A). Compare closely related strains as well as nucleotide compositions b). Horizontally acquired gene are not integrated into the genome therefore you can identify them as they would be on extra-chromosomal plasmid c). Horizontally acquired genes display significant homology to bacteriophage genes d). They would be a different size in comparison to the host gene in the host genome Review from lecture 15 -Bacterial genomes vary from bacterial species to bacterial species. This does not refer to the house keeping genes which tend to be very conserved due to their similar function -Ended talking about gene loss and Mycobacterium leprae versus it relatives M. mariunum and M. TB. M. Leprae has only adapted to live in humans (specialist) and strangely armadillos. Turns out that M. Leprae is still indemic in texas (people who eat armadillo meat still get leprosy) Slide 33-37 -Mitochondria used to be a bacteria (alpha-proteobacteria) got inside another cell and over evolutionary time it became part of the eukaryotic cell. The mitochondria shed a vast amount of its DNA but maintained this remnant chromosome (the mitochondrial DNA) and lost most of its mitochondrial genes. Some of these genes were shipped off to the host nucleus, so there’s horizontal gene transfer to the host nucleus. This causes the endosymbiont to be in a predicament: cannot survive without the host. However, there are benefits to this. Constantly receives food, shelter etc. -Half of the insects out there carry these endosymbionts within their cell as well -E. Coli and salmonella are commonly related to many of the common endosymbionts we see in insects. The strategy that these endosymbionts got inside of eukaryotic cell is very similar to how bacteria which cause disease get into host cells -these cells didn’t kill their hosts and set up residence to co-survive with their hosts. Note that these genomes are very small in comparison to their single bacteria counterparts. “You use it or you lose it” analogy (remember when we looked at gene loss) You don’t need these genes, takes energy to maintain them remember. Overtime, these genes mutate and get loss and there is no fitness value from them. Furthermore, there is a fitness benefit from removing these genes as you’re streamlining your genome and making relevant genes more easily accessible Slide 38 -Mitochondrial genome codes for its own ribosome. But the rest of it is reserved for oxidative phosphorylation) recall the ETC -The mitochondrial DNA (this circular DNA) that looks like a bacterial plasmid. There are antibiotic resistance genes in mitochondria! Similar to bacteria wow.. Slide 39 -The genome of generalists are much larger than genomes of specialists. This is because they require a broad array of mechanisms for survival.The genome of endosymbionts tend to be the smaller of the three and very specific. Slide 40-41- Revisiting Phylogeny -relatedness between species -Phylogeny of microbes that evolve is hard to classify. Animals (let’s consider mammals for instance) we can define species as organisms which can breed with each other to form viable offspring. You can’t talk about that in bacteria because there is so much gene transfers going on (horizontal transfer for instance) Hard to classify -If we compare a human to a blowfish we can find 75% of the same genes -If we compare this uropathogenic strain (infects the urinary bladder) with this common laboratory strain, we see that 65% genes are the same (with a significantly less amount of time) horizontal gene transfer causes a lot of variation with these bacteria between the same species. -So how do you define a species of bacteria based on their genomes? -Ribosomal sequences tend to be a more conserved component in cells Lecture 17- Transcript MGY377 (Oct.19 recording) Slides that were skipped means that the prof just read off of them and didn’t add anything new. They should still be considered testable. Bacterial Transcription Slide 2 -Central dogma (If you don’t know this, kill yourself) DNARNA, DNA DNA, RNA DNA, RNARNA (DNA dependent RNA polymerase, DNA dependent DNA polymerase, RNA dependent DNA polymerase, RNA dependent RNA polyermase, respectively) -ribosome creates proteins -RNA and proteins create functions in the cell Slide 3 -How does the process of gene regulation occur, when you have 8000 genes and you don’t want to turn them all on at the same time? (If you did it’d be a waste of resources and the genes would compete against one another) Slide 4 -What is a gene? A stretch of DNA in a genome that encodes a discrete and individual protein of RNA Slide 5 -Bacterial genes are very streamline -Bacterial genes that have the same function overall tend to cluster together on chromosomes I.e. If you had a cluster of 5 genes (that coded for 5 enzymes) to metabolize a sugar; those 5 genes would be clustered next to each other on the chromosome. -an operon is a group of genes that carries the same function I.e. gene 1,2,3,4  operon -operator: DBP (DNA binding protein) -gene 2,3,4 are co-transcribed (if they have very similar function) polycistronic whereas gene1 creates a monocistronic transcript Slide 6 -Regulons: If you look at the chromosome as a whole, contains several different operons. We need to coordinate the regulation of these I.e. anerobic versus aerobic respiration in bacteria that have a fluctuating environment -There is a single regulator or control protein that can go to each of these operons to activate or repress the expression of the genes -the regulon is shown in the pink Slide 7 -promoter: region of DNA that does not code for RNA but controls the expression of an adjacent gene. The promoter allows the binding of RNA polymerase to initiate transcription of the adjacent gene. Allows cell to know how to turn on and off the adjacent gene for transcription Slide 8 -We can start to look at bacterial promoters and the signals present in these promoter Slide 9 -Here is a typical E. Coli, house keeping pr
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