Notes in MGY377 Lec 4

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Published	09/23/2023	Bacterial strain names are {{c1::unreliable::reliable/unreliable}} for definition.
Published	09/24/2023	How does the way eukaryotic DNA is stored different from bacterial/archaeal DNA?
Published	09/24/2023	How do eukaryotic vs bacterial/archaeal chromosomes differ?
Published	09/24/2023	What is the disadvantage of linear chromosomes?
Published	09/24/2023	Genome sizes can range from {{c1::~130 bil to ~2.8 mil}} base pairs
Published	09/24/2023	Most bacteria have {{c1::1}} chromosome
Published	09/24/2023	Borrelia burgdorfei, cause of lyme disease, has 21 plasmids but most of the plasmids are {{c1::linear, non-circular plasmid::linear/circular?}}
Published	09/24/2023	The bulk of bacterial genomes tend to fall between {{c1::1-6}} mil base pairs, with E.coli being on the larger end.
Published	09/24/2023	Bacterial genomes encode about {{c1::1}} open reading frame for every 1000 base pairs of DNA.
Published	09/24/2023	Why is the endosymbiont genome so small compared to other bacteria?
Published	09/24/2023	Large bacterial genomes tend to have larger % {{c1::GC}} content
Published	09/24/2023	Large genomes are disproportionately {{c2::enriched}} in {{c1::regulation and secondary metabolism}} genes and {{c2::depleted}} in protein translation…
Published	09/24/2023	Endosymbionts (small genome) are 95% essential genes. Why aren't large genomes the same?
Published	09/24/2023	Why does salmonella, which is AT/GC neutral (~50% GC) choose cta codons over ctg?
Published	09/24/2023	What forces shape microbial genomes?
Published	09/24/2023	Pros/cons of mutating an existing bacterial gene
Published	09/24/2023	In gene duplication, a copy of gene keeps the ancestral function and the other copy ({{c1::paralog::called what?}}) is free to change by mutation.&nbs…
Published	09/24/2023	Pros/cons of gene duplication?
Published	09/24/2023	Pros/cons of horizontal (lateral) gene transfer?
Published	09/24/2023	Large blocks of newly acquired genes are called "{{c1::genomic islands}}" or, if they are involved in disease, "{{c1::pathogenicity islands}}"
Published	09/24/2023	Salmonella typhimurium encodes 5 major pathogenicity islands called SPI-1 through -5 and has picked up a {{c1::virulence}} plasmid.
Published	09/24/2023	{{c2::SPI-1}}: {{c1::encodes a type III secretion system necessary for invasion into animal cells}}
Published	09/24/2023	{{c2::SPI-2}}: {{c1::encodes a type III secretion system necessary for survival in macrophages}}
Published	09/24/2023	{{c2::SPI-3}}: {{c1::genes here work with SPI-2 to ensure survival in macrophages}}
Published	09/24/2023	{{c2::SPI-4}}: {{c1::encodes an adhesin and works with SPI-1 to help invasion}}
Published	09/24/2023	{{c2::SPI-5}}: {{c1::necessary for survival in macrophages}}
Published	09/24/2023	How can you identify genes acquired by horizontal gene transfer?
Published	09/24/2023	The 5 major pathogenicity islands of Salmonella typhimurium are all more {{c1::AT}}-rich than the rest of the genome
Published	09/24/2023	E.coli CFT073 and E.coli K12 are {{c1::less::more/less}} similar to each other than humans are to a blowfish.
Published	09/24/2023	Out of M. marinum (free-living), M. tuberculosis (almost exclusively lives in human lung and recently diverged), and M. leprae&nbs…
Published	09/24/2023	Typical mtDNA has 37 genes: -13 encode {{c1::proteins}}-22 are for {{c2::tRNA }}-2 encode {{c3::small and large subunits of mt-rRNA}}
Published	09/24/2023	Majority of proteins found in mitochondria are not encoded by mtDNA but instead are encoded in the {{c1::nucleus of the host cell}}. Such proteins hav…
Published	09/24/2023	Endosymbiont genomes are all very {{c1::AT}}-rich.
Published	09/24/2023	Benefits of being an endosymbiont
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