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BIOL 240 Microbiology > Topic 3 - Archaea > Flashcards

Topic 3 - Archaea Flashcards

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Biology 101 flashcards
1
Q

archaea look like eukarya/bacteria?

A

bacteria

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2
Q

are archaea and bacteria genetically similar?

A

NO

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3
Q

any known archaeal human pathogens?

A

NO

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4
Q

archaea can form ___ shapes

A

bizarre

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5
Q

Who began archaeal studies (phylogenetic trees)

A

Woese and Fox

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6
Q

what did archaea used to be called?

A

Archaeobacteria

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7
Q

what were the first “archaea” discovered?

A

methanogens

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8
Q

are archaea the only ones that can do methanogenesis?

A

YES

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9
Q

how big are archaea?

A

~0.5-5microns in diameter
- varies a lot! (100micron in some species)

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10
Q

shapes of archaeal cells

A
  • rods, cocci, spirals (like bacteria)
  • irregular shapes
  • rectangular shapes
  • squares (high surface area)
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11
Q

do archaea have chloroplasts?

A

NO they could be gas vacuoles but NO chloroplasts!

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12
Q

archaea: cytoplasm

A
  • cytoplasm molecules similar to bacteria
  • inclusion bodies (e.g., gas vacuoles) are in some species
  • single circular chromosomes & no membrane-bound nucleus
  • many of DNA replication enzymes of archaea “look” like eukarya’s
  • development of histones may have been an early “branch point event” in evolution of archaea and eukarya (diff in archaea from eukarya)
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13
Q

Archaea: what is gas vacuole an example of?

A

inclusion bodies

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14
Q

difference between eukaryal and archaeal nucleosomes?

A

Eukaryal:
- 160-nucleotide-pair length of DNA
- octamer of histone proteins

Archaeal:
- 60-nucleotide-pair length of DNA
- tetramer of histone proteins

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15
Q

archaea: cytoskeleton

A
  • cytoskeletal homologues found in both eukarya and bacteria
  • i.e. kind of close to both bacteria and eukarya, but they all have cytoskeletal elements
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16
Q

archaea: cell envelope

A
  • all archaea have a plasma membrane
  • most have cell walls, most do NOT have outer membrane (like G+ve)
  • both structures are different from equivalents in other domains
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17
Q

archaea vs. eukarya/bacteria bilayer plasma membrane

A

archaea:
- glycerol 1-phosphate (isomer of G3P)
- ether linkage (stability!)
- phytanyl (repeating isoprene units - isoprene are 5Cs)
- monolayers in some archaea (stability)

bacteria/eukarya:
- glycerol 3-phosphate
- ester linkage
- fatty acid chain

18
Q

monolayers in some archaea (stability)

A
  • phosphoglycerol molecule on both ends
  • tetra ether lipids
  • v stable, often in archaea living in high temp
  • can include rings too
19
Q

archaea: cell wall

Parts + made of?

A

composed of pseudomurein
- polysaccharide, similar to peptidoglycan
- N-acetylglucosamine (NAG) and N-acetyltalosaminuronic acid (NAT)
- Beta-1,3 linkages; lysozyme insensitive
- L-amino acids

(compared to peptidoglycan; Beta-1,4; NAG + NAM; D-amino acids in bacteria)

20
Q

archaea: cell surface

A
  • S layer (protection against predation/viruses, mediate adhesion)
  • cannulae
    – HOLLOW glycoprotein tubes
    – link cells together to form a complex network “stay in touch”
21
Q

flagellus vs archaellum

A

archaellum = archaeal flagellum
- flagellum (solid)
- grows from base, not tip
- uses ATP

22
Q

Ignicoccus

A
  • has outer membrane and periplasm like in G-ve cells
  • ATP synthase enzymes are housed in outer membrane
  • unusual even for archaea
23
Q

4 major phyla of archaea

A
  • Euryarchaeota
  • Crenarchaeota
  • Thaumarchaeota (low temp, formerly Crenarchaeota, AMMONIA-oxidizing)
  • Nanoarchaetoa (small)
24
Q

Crenarchaeota characteristics

A
  • extreme temp, pressure, acidity
  • many are thermophiles or hyperthermophiles
  • acidophile
  • barophiles (high pressure)
25
Q

Crenarchaeota adaptations for survival

A
  • tetraether lipids/lipid monolayers (pack biphytanyl into monolayer)
  • modified proteins
    – more-helical regions
    – more salt bridges/side chain interactions
    – more arginine/tyrosine
    – less cysteine/serine
    (there are more salt bridges in these more prevalent proteins)
  • strong chaperone protein complexes
  • thermostable DNA-binding proteins
  • reverse DNA gyrase enzyme to increase DNA supercoiling
26
Q

mesophile meaning

A

thrives in moderate temp

27
Q

Euryarchaeota characteristics

A
  • halophiles (SALT), halobacterium (e.g., Great Salt Lake, Dead Sea, evaporation ponds)
  • require NaCl conc > 1.5M
  • varies: 5-34% salinity
  • phototrophic (no chlorophyll, or electron transport chain (no respiration involved))
28
Q

hypo/hyper/isotonic solution?

A

hypotonic = low salt (net water gain)
hypertonic = high salt (net water loss)
isotonic = equiv salt (no net change)

29
Q

Euryarchaeota adaptations

A
  • very high intracellular [K+] offsets very high extracellular [Na+] (K+ acts as a “compatible solute”
  • high intracellular K+ conc can cause protein denaturation, split dsDNA
    – protein denaturation: highly acidic proteins that remain more stable in high salt env
    – DNA denaturation: higher GC content (stronger, 3 Hbond)
30
Q

Bacteriorhodopsin

A
  • Euryarchaeota
  • not red on its own (red pigment - retinal - that captures light)
  • harnesses light energy and produces a proton motive force
  • captures light = cis -> trans
31
Q

Euryarchaeota

A
  • METHANOGENS (only ones that can make methane)
    – reduce CO2 with H2, produce CH4 and H2O; energy released can be used to fix C; strict anaerobes (e.g., in gut, swamp)
    – makes gas in humans and combustible air in swamps
    – methanogens have a lot of diversity but share a common metabolic property
  • halophiles
32
Q

Volta experiment

A
  • Volta performed this exp ~200 ya
  • inverted funnel traps CH4 from methanogenic freshwater sediments
  • fire ignites
33
Q

methanogen habitats (6)

A
  • anoxic sediments (no O2)
    – marshes/swamps, lakes, rice paddies, moist landfill
  • animal digestive tracts (myth: ruminant animals BELCH methane, not fart)
    – ruminant animal rumen (cattle, sheep, elk, etc.)
    – cecal animal cecum (horses, rabbits)
    – large intestine of monogastric (humans, swine, dogs)
  • geothermal H2/CO2 sources
    – hydrothermal vents
  • artificial biodegradation facilities
    – sewage digestors
  • endosymbionts of anaerobic protozoa
  • termite gut symbionts
34
Q

TACK superphylum

A

Thaumarchaeota
- now Nitrososphaerota
- separate phylum for many mesophilic crenarchaeotes
- ammonia oxidizing, fixing CO2 - important in N cycle
- mesophiles and psychrophiles
- important for biogeochemical cycling of C and N in ocean

Aigarchaeota
- none cultivated
- one genome avail - thermophile

Crenarchaeota

Korarchaeota
- distinct 16S rRNA sequence from hydrothermal env
- none cultivated
- one genome avail

35
Q

mesophiles vs psychrophiles

A

mesophiles: 15-40 deg C
psychrophiles: <15 deg C

36
Q

DPANN superphylum

A

Nanoarchaeota (SMALL)
- Nanoarchaeum equitans (riding on back) - sole isolated membrane so far
- distinct 16S rRNA gene sequences

Common features:
- Very small cell size (<1 μm)
- Small genomes (~1 Mb, can be less!)
- Restricted metabolisms, unable to generate basic building blocks
- Interspecies interactions (mutualistic or parasitic?)

37
Q

Ignicoccus (Crenarchaeota) and Nanoarchaeum (Nanoarchaeota)

A
  • Nanoarchaeum equitans -> obligate parasite (debatable) of crenarchaeote, Ignicoccus
    – no metabolic genes, only genes for replication, transcription, translation
    – a lot resources need to come from Ignicoccus (ex. ATP)
    – makes an S layers but Ignococcus can NOT (mutualistic?)
38
Q

Asgard superphylum

A

(all uncultivated)
- Lokiarchaeota
- Thorarchaeota
- Odinarchaeota
- Heimdallarchaeota
- represents the closest prokaryotic relatives of eukaryotes

39
Q

Lokiarchaeota/Thorarchaeota

A
  • thermophilic archaea - distinct from Crenarchaeota
  • group w/eukaryotes on some phylogenies
    (possible closest ancestor to eukaryotes)
  • genome shows euk-like proteins for cell compartmentalization - early stages of complex cell evol?
40
Q

proposed origin of eukaryotes?

A
  • Eukaryote-Asgard common ancestor
  • Eukaryote-alphaproteobacterium common ancestor

those two combine (endosymbiosis)

BIOL 240 Microbiology (10 decks)

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