Archea Flashcards
What are Archaea?
Prokaryotic cells like BACTERIA, but…
- Several characteristic ‘Archael’ features
- And some features shared with Eukaryotes (to the exclusion of BACTERIA)
- Many are extremophiles
Why are Archaea Prokaryotes
- Usually small cells
- Few internal cell structures
- Usually single circular chromosome w/ operons
- Coupled transcription and translation
Differences from Bacteria
1) cell membrane & envelope composition
2) Some Eukaryote-like features
- Transcription apparatus
- Translation apparatus
- Some histone proteins (in some archaea)
Standard membrane lipids in Bacteria and Eukaryotes
- Glycerol 3-phosphate backbone
- Ester (acid-alcohol) linkages
- Fatty acids
- Archaea membrane lipids are very different
Archaeal cell membrane lipids
Isoprenoids
(assembled from isoprene units)
= ‘branched chain lipids’
Stereochemically opposite backbone (on glycerol 1-phosphate)
Ether linkages (rather than ester linkages)
Archaeal cell envelope
Varied but…
- no true peptidoglycan
- no outer membrane**
‘Pseudopeptidoglycan’ cell wall in a few archaea
‘S-layers’ common
Eukaryote-like features: transcription machinery
- Eukaryote-like many-subunit RNA polymerase
- Eukaryote-like transcription factors
- TATA-binding protein (TBP)
Eukaryote-like features: Translation machinery
- Many Eukaryote + Archaea- specific ribosomal proteins
- Methionine as initiator amino acid
(Bacteria use N-formylmethionine) - Eukaryote-like translation initiation & elongation factors
Eukaryotes and Archaea
- Eukaryote-Archaea similarities reflect a closer phylogenetic relationship
- Recent evidence actually supports Eukaryotes arising within Archaea
Two best-known phylogenetic groups of Archaea
- Crenarchaetoa**
- Euryarchaeota
Archaeal Diversity - best-known biological types
- Thermophiles:
Many crenarchaeotes + some others, including some eurychaeotes
- Crenarchaeota
- Thaumarchaeota
- “Asgards”
- Eukaryotes - Halophiles (Haloarchaea)
- Methanogens
- Many Euryarchaeota (+ a couple of others)
(Hyper-) thermophiles
- Many Archaea (especially many crenarchaeotes)
- Some grow at >90 degrees (‘hyperthermophiles’)
- Many thermophiles are *lithoautotrophs
Habitats for thermophilic Archaea
Primarily, Geothermal sites
- Hot springs, vents
- Deep in Earth’s crust, etc.
Sources of H2, H2S, Sufur (S)
- e.g. oxidize H2, using S as e acceptor (H2 + S = H2S)
Surviving extreme temperatures (membrane)
Membranes - increased integrity and rigidity
- Archaeal membrane lipids (isoprenoid; ether-linked) intrinsically more stable already
- Bonds between isoprenoid tails in thermophiles
e.g. *Tetraethers in some
Surviving extreme temperatures (other features)
Thermostable enzymes and other proteins
- structurally stable (& active) at high temps
DNA stabilization (esp. avoiding denaturation)
- ‘reverse gyrase’ - induces positive supercoils (rather than normal negative supercoils)
- DNA-binding proteins
Non-thermophilic relatives of classical crenarchaeotes (inc. Thaumarchaeota)
- Sea water, soil, etc.
- Common in deep ocean water (~40% of total cells?)
- Many are ammonia oxidizers
- Very few are cultivated
Methanogens
- *Methane (CH4) as end product of energy metabolism
- *Most Euryarchaeota are methanogens
- *Obligate anaerobes (most are VERY strict anaerobes)
Methanogenesis as an energy pathway
- Example substrates: H2, Acetate (e.g. fermentation end products)
- Example: 4 H2 + CO2 -> 2 H2O + CH4 (CO2 acts as an electron acceptor)
- Low energy yield
Methanogens - some habitats
- Marine sediments
- Marshes & other wetlands (inc, rice paddies)
- Animals guts, especially *ruminants & *termites (but also most humans)
- Produce the vast majority of biological methane emissions (methane is a major greenhouse gas)
Haloarchaea
- Mostly extreme halophiles
- Many can grow in saturated brine (~32% NaCl; ~5 molar)
- Almost all aerobic organotrophs; but…
- … also use retinal-based phototrophy
Holoarchaea - how to avoid shrivelling up in saturated salt brine?
- Maintain very high intracellular ion concentrations (esp. potassium chloride ; K+, Cl-)
- ‘Normal’ proteins would denature (-> death), but…
- … Haloarchaeal proteins usually have a highly negative surface charge (many acidic amino acids) - forms ‘a hydration shell’ around protein
