Topic 3 - Archaea

Question 1

archaea look like eukarya/bacteria?

Answer 1

bacteria

Question 2

are archaea and bacteria genetically similar?

Answer 2

NO

Question 3

any known archaeal human pathogens?

Answer 3

NO

Question 4

archaea can form ___ shapes

Answer 4

bizarre

Question 5

Who began archaeal studies (phylogenetic trees)

Answer 5

Woese and Fox

Question 6

what did archaea used to be called?

Answer 6

Archaeobacteria

Question 7

what were the first “archaea” discovered?

Answer 7

methanogens

Question 8

are archaea the only ones that can do methanogenesis?

Answer 8

YES

Question 9

how big are archaea?

Answer 9

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

Question 10

shapes of archaeal cells

Answer 10

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

Question 11

do archaea have chloroplasts?

Answer 11

NO they could be gas vacuoles but NO chloroplasts!

Question 12

archaea: cytoplasm

Answer 12

• 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)

Question 13

Archaea: what is gas vacuole an example of?

Answer 13

inclusion bodies

Question 14

difference between eukaryal and archaeal nucleosomes?

Answer 14

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

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

Question 15

archaea: cytoskeleton

Answer 15

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

Question 16

archaea: cell envelope

Answer 16

• 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

Question 17

archaea vs. eukarya/bacteria bilayer plasma membrane

Answer 17

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

Question 18

monolayers in some archaea (stability)

Answer 18

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

Question 19

archaea: cell wall

Parts + made of?

Answer 19

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)

Question 20

archaea: cell surface

Answer 20

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

Question 21

flagellus vs archaellum

Answer 21

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

Question 22

Ignicoccus

Answer 22

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

Question 23

4 major phyla of archaea

Answer 23

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

Question 24

Crenarchaeota characteristics

Answer 24

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

Question 25

Crenarchaeota adaptations for survival

Answer 25

- 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

Question 26

mesophile meaning

Answer 26

thrives in moderate temp

Question 27

Euryarchaeota characteristics

Answer 27

- 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))

Question 28

hypo/hyper/isotonic solution?

Answer 28

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

Question 29

Euryarchaeota adaptations

Answer 29

- 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)

Question 30

Bacteriorhodopsin

Answer 30

- 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

Question 31

Euryarchaeota

Answer 31

- 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

Question 32

Volta experiment

Answer 32

- Volta performed this exp ~200 ya - inverted funnel traps CH4 from methanogenic freshwater sediments - fire ignites

Question 33

methanogen habitats (6)

Answer 33

- 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

Question 34

TACK superphylum

Answer 34

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

Question 35

mesophiles vs psychrophiles

Answer 35

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

Question 36

DPANN superphylum

Answer 36

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?)

Question 37

Ignicoccus (Crenarchaeota) and Nanoarchaeum (Nanoarchaeota)

Answer 37

- 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?)

Question 38

Asgard superphylum

Answer 38

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

Question 39

Lokiarchaeota/Thorarchaeota

Answer 39

- 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?

Question 40

proposed origin of eukaryotes?

Answer 40

- Eukaryote-Asgard common ancestor - Eukaryote-alphaproteobacterium common ancestor those two combine (endosymbiosis)