14. The three domains of life

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14. The three domains of life
2011-11-08 13:38:17
PMB 112 midterm2

general microbiology midterm 2
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  1. phylogenetic trees
    • hypotheses about the evolutionary relationships between organisms
    • groups organisms based on inherited characteristics
  2. When are trees a good model of relationships?
    • DNA is passed from "parents"
    • genes change by accumulation of point mutations
  3. When can trees be inaccurate/misleading?
    • genes are duplicated- which to use in sequence comparison?
    • genes are lost as a species inhabits a highly specialized niche
    • DNA is acquired from sources other than "parents"
  4. difficulties in determining phylogenetic relationships among bacteria
    • relative lack of complex structures
    • little fossil record
    • metabolic characteristics may change according to how a strain is cultured
    • observable characteristics often result in conflicting trees
    • bacteria are haploid and do not undergo sexual reproduction - can't define a species as a group capable of interbreeding and having fertile offspring
  5. Why is 16S (18S in eukaryotes) ribosomal RNA (rRNA) DNA sequence used to construct phylogenetic trees?
    • performs the same function in ALL organisms
    • has highly conserved regions good for alignment and other regions with more variability where sequence divergence occurs
    • abundant, thousands/cell
  6. one method for comparing 16S rRNA sequences of two or more organisms
    • 1) isolate genomic DNA from organisms to be compared
    • 2) PCR 16S rRNA gene from each organism using universal primers based on conserved nucleotides
    • 3) align two sequences
    • 4) compute number of sequence differences/total nucleotides
    • 5) repeat for other pairs of organisms to create a distance matrix
    • 6) use these distances to make a tree that reflects evolutionary relationships
  7. correction factor
    • designed to account for the fact that a sequence may have changed more than once to get to the observed sequence
    • sequence changes we see are considered to be the minimum
  8. endosymbiosis
    hypothesis that mitochondria and chloroplasts originated as proteobacteria or cyanobacteria that were engulfed by a primitive organism and came to live as permanent symbionts
  9. horizontal gene transfer
    • acquisition of DNA from an organism other than one's "parents"
    • mechanism of spreading antibiotic resistance among pathogens
    • phylogenetic tree based on gene sequence may accurately represent history of that gene, but not history of the entire organism
    • two trees based on different genes could be contradictory but both could be true
  10. Crenarchaeota
    • extreme thermophiles
    • all are facultative or obligate anaerobes
    • some are acidophiles - grow best at pH 2
    • both autotrophs and heterotrophs
    • lipid monolayers protect against extreme heat
  11. Euryarchaeota - Methanogens
    • synthesize methane during energy conservation
    • obligate anaerobes and autotrophs
    • global distribution despite intolerance for O2
    • found in stagnant water, sewage treatment plants, intestinal tracts, ocean bottom, hot springs
  12. Euryarchaeota- Extreme halophiles
    • require > 2M NaCl, with 4-5M being optimal
    • found on ocean borders with salty inland waters
    • aerobic heterotrophs (require organic C source)
  13. Origin of Earth
    • had to cool down before organic molecules could exist stably
    • life probably began below the surface of the ocean near hydrothermal vents where energy source of reduced inorganic compounds like H2, FeS and S0 would have been abundant
  14. Current ideas about the origins of life
    porous mounds of precipitated pyrite (FeS), silicates and carbonates near hydrothermal vents could have provided surface area for reactions, possible catalysis for formation of first organic molecules and primitive compartments for accumulation of these molecules

    RNA is thought to have been first organic catalyst and self-replicating information storage molecule

    organic molecules had to become encased in lipid bilayers, proto-organisms would be able to disperse from the mounds and would be separate entities for resources, become subject to natural selection/evolution
  15. possible energy-generating scheme for primitive cells
    • splitting of H2 by a primitive hydrogenase could provide protons to drive an ATPase
    • H2 could come from exergonic reaction of pyrite (FeS) with H2S or from reduction of H+ by Fe2+ and UV
    • electrons from splitting of H2 reduce S0, also an exergonic reaction
  16. cyanobacteria
    • perform oxygenic photosynthesis
    • their metabolism gradually oxygenated the atmosphere after much Fe2+ was oxidized to Fe3+ compounds - enabled the evolution of organism that used oxygen as an electron acceptor in respiration
    • also created oxone layer - shields earths' surface from UV
  17. "Nucleus hypothesis"
    • nucleus developed in a branch of the Archaea
    • these primitive Eukarya then engulfed proteobacteria/cyanobacteria to make mitochondria/chloroplasts
    • problem is that Archaea and Eukarya don't share similar membrane lipids while Eukarya and Bacteria do
  18. "Hydrogen hypothesis"
    • An H2-producing bacterium was engulfed by an H2-consuming archaeaon
    • the bacterium became the mitochondrian
    • genes for lipid synthesis were transferred to the "host" archaeaon and the nucleus developed later
    • this model accounts for the similarity between B and E in membrane lipids but similarity between E and A in aspects of transcription and translation