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Bio 322 > Unit 5 > Flashcards

Unit 5 Flashcards

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Biology 101 flashcards
1
Q

5 phyla of Archaea

A

Euryarchaeota
Thaumarchaeota
Nanoarchaeota
Korarchaeota
Crenarchaeota

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2
Q

what is the phylogenetic tree based on?

A

16S r RNA

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3
Q

what is the evolution of Archaea driven by?

A

HGT between phyla

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4
Q

what are the common traits shared by all Archaea?

A
  • ether linked lipids
  • lack of peptidoglycan in cell walls
  • structurally complex RNA polymerases
  • RNA polymerase resemble eukaryotic enzymes
  • extreme metabolic diversity
  • chemoorganotrophic or chemolithotrophic organisms
  • aerobic and anaerobic organisms
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5
Q

Euryarchaeota

A

halophilic (salt-loving obligate aerobes)
methanogens (strictest anaerobes)
hyperthermophilic
acidophilic
extremophilic and non-extremophilic

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6
Q

what are the 2 organisms representing halophilic archaea and their characteristics?

A

halococcus
haloquadratum
- usually aerobic
- anaerobic is possible
- no fermentation

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7
Q

halococcus

A

largest plasmids in nature
plasmid is 30% of total cellular DNA

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8
Q

haloquadratum

A

gas vesicles for floating in hypersaline enviro

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9
Q

what do organisms do in high solute enviro?

A

either accumulate or synthetize solutes intracellularly (compatible solutes)

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10
Q

function of compatible solutes?

A

prevent dehydration under conditions of high osmotic strength

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11
Q

what do certain Euryarchaeota do if they do not synthesize or accumulate organic compounds?

A

pump large amounts of K+ from enviro into cytoplasm
- different in K+ levels maintains pos water balance

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12
Q

hyperthermophilic organisms

A

thermococcus
thermoplasma

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13
Q

thermoplasma

A
  • cell wall lacking
  • small genome
  • DNA in globular eukaryotic-like structures
  • 55C
  • pH 2
  • sulfate respiration
  • No sterols
  • Lipoglyan cell wall
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14
Q

methanogens

A

produce methane as integral part of energy metabolism
- major source of biogenic methane in nature

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15
Q

Methanocaldococcus jannaschii

A

model methanogen
enzymes for methanogenesis
central metabolic enzymes and cell division machinery- resembles bacterial structures
transcription and translation genes resembles eurkayotic organisms

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16
Q

acidophilic organisms

A

ferroplasma
picrophilus

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17
Q

Ferroplasma

A

cell-wall lacking
strong acidophile
non thermophile
Fe2+ as e donor

18
Q

Picrophilus

A

phylogenetic relative Ferroplasma
more acidophilic than Ferrroplasma

19
Q

Methanopyrus

A

hyperthermophilic methanogen
unique lipids- bacterial and archaeal features
archaeal- glycerol side chain with saturated phytanyl
bacterial- glycerol side chain with fatty acids
- unusual lipids may help stabilize the cytoplasmic membrane at its high growth temps

20
Q

Thermococcus

A

organic substrates
sulfur respiration

21
Q

Nitrosopumilus maritimus

A
  • Thaumarchaeota
    AOA
    CO2 fixation
  • grows at NH3 concentrations that are 100x lower than those required by bacterial nitrifiers
  • all isolated species are chemolithotrophic ammonia-oxidizers
  • can grow at v low concentrations of NH3
  • unique lipid called crenarchaeol
  • major role in controlling NH3 levels in oceans
22
Q

Nanoarchaeum equitans

A
  • Nanoarchaetoa
  • one of the smallest
  • no growth in pure culture
  • growth only when attached to surface of host
  • host - Ignicoccus hospitalis (hyperthermophilic species of Crenarchaeota- hospitable fireball)
  • grows at high temps
  • metabolically dependent on host
23
Q

ignicoccus

A

performs H2 oxidation and S^0 reduction along with CO2 fixation

24
Q

what genes did Nanoarchaeum equitans lose?

A
  • amino acids biosynthesis
  • nucleotides production
  • coenzymes
  • ATPase genes
25
Q

what genes remained in Nanoarchaeum equitans?

A
  • lipids biosynthesis
  • glycolysis
  • molecular machinery
  • DNA repair enzymes
26
Q

Korarchaeum cryptofilum

A
  • Korarchaeota
  • cryptic filament of youth
  • obligately anaerobic chemoorganotroph
  • hyperthermophile
  • inability of K. cryptofilum to synthesize molecules essential for its own growth may be explained by evolution of mutual dependence as described by Black Queen hypothesis
  • incapable to synthetize necessary molecules for their growth
  • evolution of mutual dependence
27
Q

Black Queen hypothesis

A

evolutionary strategy to lose costly functions in favor of improving growth efficiency
- results in mutants becoming obligately dependent upon provider to produce necessary resource

28
Q

Crenarchaeota

A
  • hyperthermophiles
  • species that grow optimally above boiling point of water
  • chemolithotrophic autotrophs
  • primary producers in extremes
29
Q

Eocyte tree

A
  • 2D
  • 2 domains
  • ancestor of eukaryotes was thermophilic organism that did not have nucleus
  • organisms called eocytes
  • 1 branch with nucleus separated (Karyocytes)
  • branch 2 was prokaryotic (B and A)
  • unrooted
30
Q

3D tree

A
  • prokaryotes branched to B and A
  • eukaryotes developed as separate lineage
  • all biochemical data, DNA and RNA polymerases that were added late onto the tree were in favor of model
  • unrooted
31
Q

what do Eukarya and Archaea have in common?

A

ancestral branch

32
Q

was the branch the same for eukarya, archaea and bacteria?

A

no

33
Q

are archaea distantly related to bacteria?

A

yes

34
Q

what are archaea and bacteria?

A

not monophyletic groups

35
Q

what was the last group that bridged A and E?

A

Asgard

36
Q

what group has sequence homology to core domains in eukaryotic endosomal sorting complexes proteins?

A

Cell division machinery in Crenarchaeota

37
Q

what was discovered in Asgard arachae?

A

homolog of eukaryotic ESP

38
Q

ESCRT

A
  • simple, ancient origins
  • many archaeal have homologues of ESCRT-III and Vps4
39
Q

roles of ESCRT-III and Vps4

A

role in cytokinesis, extracellular vesicle formation and viral exit

40
Q

what is an example of homologue systems in Ascard archaea?

A

ESCRT machinery

Bio 322 (11 decks)

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