Exam 3 Terms Flashcards
biological species concept
organisms that create fertile offspring are the same species
phylogical species concept
based on shared evolutionary history (DNA)
16S rRNA
is a chronometer to measure relatedness, ribosomal genes must be ancient, compared via PCR and alignment (reveals 3 branches of life)
informational genes
transcription and translation, generally passed on vertically
operational genes
metabolism, pathogenicity, can be traded horizontally
gene sharing
more commons between organisms in different environments
pan genome
all genes found in any strain
core genome
all genes found in all strains
pathogenicity island
region of the genome that contains virulence factors (the genetic information transferred into it to make it infect others), may contain skewed GC ratio or codon bias
shigella
genus with 4 species, all are pathogenic (S. dysenteriae, S. flexneri, S. sonnel, S. boydii, can cause body flux and kidney failure
how shingella differs from E. coli?
non-motile, does not ferment lactose, indole, lysine-decarboxylase negative, more insertion sequences, virulence plasmin, causes similar but more severe disease
how is shigella similar to E. coli
the sequencing shows they are very closely related:
- 94% same open reading frames
- causes similar diseases
- PINV plasmid, can invade other species
form species
observable characteristics
morphology
size and shape
biochemistry
composition and metabolism
ecology
habitat and tolerances
pathogenicity
ability to cause disease
paralog
same gene in same species duplicated (happens by HGT or errors in DNA repair)
reduction
organism lives in a stable, predictable environment and loses genes to reduce energy (common in nutrient poor environments and symbiosis)
evolution determinants
growth rate and strength of selection
MRSA
- treated with two rounds of antibiotic due to weakened immune system, developed small colony variant/multiple drug resistant
- mutation to S. aureus made ppGpp, normally triggered by stress
- ppGpp binded to polymerase, creating slow growth of bacteria and recycle instead of growth (shows regulatory mechanisms have large impact)
takeaway: benefit of being antibiotic resistant was greater than the cost of slow growth
E. coli long term growth experiment
takeaways: cultures evolved, every point mutation occurred
-molecular clock: mutations happen at a steady rate
-all populations evolved faster growth rates and larger cells size (rate dramatically increased more early on)
-after 33,000 generations, one culture was notably denser (cit+ mutation)
Cit+ mutation
-can use citrate as a C source, Cit- phenotype had gone extinct
-duplication copied citrate anti-porter, making citrate come in and succinate go out (behind a different promoter, CitT is usually not produced in aerobic conditions
why is CitT mutation bad?
loss of succinate, only good with gltA mutation