week 10 - archaea Flashcards
(69 cards)
1
Q
Archaea
overview
A
- Single celled prokaryotic microorganisms
- Form one of the three domains of life
2
Q
Archaea
- found in…
A
a wide range of environments
o Oceans, soils, humans, foods
o Also found in extreme environments
3
Q
archaea
pathogenic?
A
- No pathogenic archaea have been identified
o Some may be associated with conditions such as gum disease and diverticulosis
4
Q
archaea
common ancestors
A
- Common ancestor between archaea and euk much more recent than common ancestor with bacteria and archaea
5
Q
KEY FEATURES DISTINGUISHING BACTERIA AND ARCHAEA FROM EUKARYA:
- membrane enclosed nucleus
A
BACTERIA: no
ARCHAEA: no
EUKARYA: yes
6
Q
KEY FEATURES DISTINGUISHING BACTERIA AND ARCHAEA FROM EUKARYA
- membrane enclosed organelles
A
BACTERIA: rarely
ARCHAEA: no
EUKARYA: yes
7
Q
KEY FEATURES DISTINGUISHING BACTERIA AND ARCHAEA FROM EUKARYA
- circular chromosomes
A
BACTERIA: almost always
ARCHAEA: yes
EUKARYA: no
8
Q
KEY FEATURES DISTINGUISHING BACTERIA AND ARCHAEA FROM EUKARYA
- paired chromosomes
A
BACTERIA: no
ARCHAEA: no
EUKARYA: yes
9
Q
KEY FEATURES DISTINGUISHING BACTERIA AND ARCHAEA FROM EUKARYA
- ribosomes size
A
BACTERIA: 70S
ARCHAEA: 70S
EUKARYA: 80S
10
Q
KEY FEATURES DISTINGUISHING BACTERIA AND ARCHAEA FROM EUKARYA
- introns in genes
A
BACTERIA: not usually
ARCHAEA: no
EUKARYA: yes
11
Q
KEY FEATURES DISTINGUISHING BACTERIA AND ARCHAEA FROM EUKARYA
- genes organised in operons
A
BACTERIA: yes
ARCHAEA: yes
EUKARYA: not usually (much more complex)
12
Q
KEY FEATURES DISTINGUISHING BACTERIA AND ARCHAEA FROM EUKARYA
- growth above 70 degrees
A
BACTERIA: yes
ARCHAEA: yes
EUKARYA: no
13
Q
KEY FEATURES DISTINGUISHING BACTERIA AND ARCHAEA FROM EUKARYA
- microorganisms
A
BACTERIA: all
ARCHAEA: all
EUKARYA: many
14
Q
ARCHAEA:
adaptations to extreme environments
A
- Membrane lipids
- Cell walls
- Proteins
- Chromosomal structure
15
Q
archaea inhabit a..
A
wide range of extreme environments
- salt
- temperature
- pH
16
Q
ARCHAEAL CYTOPLASMIC MEMBRANE
- bilayer
A
- Glycerol diethers made from C20 phytanyl lipids
- Forms a lipid BILAYER
17
Q
ARCHAEAL CYTOPLASMIC MEMBRANE
- monolayer
A
- Diglycerol tetraether made from C40 Biphythanyl lipids
- Forms a lipid monolayer
18
Q
Hyperthermophiles
A
- Isolated from geothermal springs and soils
o Temperatures of 100 degrees or more - Sulphur rich springs (solfataras)
o pH ranges from mildly alkaline to pH 1
o low pH (H2SO4) - Hydrothermal vents (on the ocean floor)
o Under sea hot spring
o Water is under pressure
o Temperatures above 100 degrees (up to 500 degrees)
19
Q
Sulfolobales
A
- Sulfolobus acidocaldarius
o Grows in sulphur-rich acidic hot springs
o Aerobic chemolithotrophs that oxidise reduce sulphur or iron
Gain energy by doing this
Energy from organic compounds
o 90 degrees, pH 1-5
o Spherical/ lobed (slightly lumpy)
o Adheres to sulphur crystals
o Can use carbon dioxide as a carbon source
Can oxidise iron2+ to iron3+ - Used in biological leaching of metals from ores
20
Q
The S-layer (surface layer)
- what
A
- Key feature that allows them to live in extreme environments
o Protein layer outside of a microorganism - Regularly spaced array of protein subunits
- Self assemble into a structure which coats the entire cell creating a porous lattice
21
Q
The S-layer (surface layer)
- bacteria
A
o Covalently attached to the peptidoglycan in Gam positives
o Covalently attached to the O-polysaccharide chains of LPS in Gram negatives
22
Q
The S-layer (surface layer)
- archaea
A
o Anchored in CM or to pseudomurein
23
Q
Sulfolobales
A
- S layer
- Crystalline array of proteins
- Anchored in the cytoplasmic membrane
- Heat makes membranes more fluid
o Having a rigid protein structure around the outside is going to help combat this added fluidity
24
Q
Desulfurococcales
Pyrolobus fumarii
- optimum growth temp.
A
106 degrees
25
Desulfurococcales
Pyrolobus fumarii
- where?
- Lives in the walls of black smokers (at the bottom of the ocean)
26
Desulfurococcales
Pyrolobus fumarii
- S-layer
composed of diglycerol tetraethers
27
Desulfurococcales
Pyrolobus fumarii
- autotrophic
o Nothing at the bottom of the ocean (no light)
o Just black smokers
o So need to be autotrophic to use inorganic chemicals to produce everything they need to survive
28
Desulfurococcales
Pyrolobus fumarii
- aerobic, facultative aerobe, anaerobic
facultative aerobe
29
Desulfurococcales
Pyrolobus fumarii
- what
- Obligate H2 chemolithotroph
30
Desulfurococcales
Pyrolobus fumarii
- terminal acceptor
- NO3- is used as a terminal acceptor in strict anaerobic conditions
o NO3- + H2 --> NH4
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Desulfurococcales
Pyrolobus fumarii
- food chain
- These are at the base of the food chain
- E.g. fish and shrimp deep in ocean rely on these organisms to create stuff that they can survive on
32
ADAPTATIONS TO LIFE AT HIGH TEMPERATURES:
- problem
o Instability of biomolecules at high temperatures
o E.g. proteins unfold when you heat them
33
ADAPTATIONS TO LIFE AT HIGH TEMPERATURES:
- proteins
Molecular chaperons (heat shock proteins)
- Proteins which refold partially denatured proteins
- Termosome
- Produced in very high amounts at growth limiting temperature
Molecular chaperones provide an environment in which a misfolded protein can be unfolded and the refolded correctly
- Specific archaeal heat shock proteins
* Provide a cage that a protein can fit into
* Then it can be encouraged to unfold and refold
- This is a thermosome
Produces in very high amounts when organisms get to the high end of that range of temperatures that they can grow in
34
ADAPTATIONS TO LIFE AT HIGH TEMPERATURES:
- lipids
o Glycerol tetraethers in membranes
- Diglycerol tetraether monolayer membrane most resistant
35
ADAPTATIONS TO LIFE AT HIGH TEMPERATURES:
DNA (key adaptations)
- reverse DNA Gyrase (enzyme)
- DNA binding proteins
36
ADAPTATIONS TO LIFE AT HIGH TEMPERATURES:
DNA - Reverse DNA Gyrase
(enzyme)
Introduced positive supercoils
* Protects DNA
* More stable
* Less likely to denature / fall apart when heated up
* This has consequences for transcription (unwinding)
37
ADAPTATIONS TO LIFE AT HIGH TEMPERATURES:
DNA - DNA binding proteins
Sac7d in Sulfolobus, binds the minor groove, increases Tm by 40 degrees
* Not specific interactions with particular nucleotides
* Fits into minor groove
* Stabilises the DNA
o DNA has major and minor grooves
Archaeal histones, DNA wound and compacted
* Wound and compacted around histones
o More stable
o Again consequences for replication and transcription
38
Nonthermophilic Crenarchaeota
Important example that can survive in very low temperatures.
- Found in nutrient poor marine environments
- Can survive in very cold seawater and ice
o Get very small channels forming in ice because water cant escape
o So temps can be less than 0 degrees C
- Planktonic (floating)
- Identified by SSU rRNA sampling
o Very difficult to grow in the lab
- Can fix inorganic carbon
o Probably play a key role in the carbon cycle
- They make up 40% of the prokaryotes in the deep ocean
o Very important
39
ADAPTATIONS TO HIGH SALT:
problems
o Osmotic forces
o High solute levels inside cells
Compensating solutes are usually organic and made my the cell inside the cell
Raise the overall concentration inside the cell without having negative effects that having a high salt concentration do
Archaea don’t really do this!
o These problems make a single cells organism very vulnerable
Water moving out --> proteins not working as they should
40
ADAPTATIONS TO HIGH SALT:
key features:
- Maintain positive water balance by pumping K+ into cells
- Glycoprotein cell wall
- Cellular proteins composed of more acidic amino acids
41
ADAPTATIONS TO HIGH SALT:
- Maintain positive water balance by pumping K+ into cells
Higher K+ inside than Na+ outside
- Selectively taking potassium from their environment in increase K+ conc. Inside
- K+ inside higher than Na+ outside
- This compensates for the very high salt concentration
42
ADAPTATIONS TO HIGH SALT:
- Glycoprotein cell wall
o Cell wall stabalised by Na+
o S-layers (need to have these to start to fall apart
43
ADAPTATIONS TO HIGH SALT:
- Cellular proteins composed of more acidic amino acids
More soluble at high solute concentration
- Because more acidic amino acids are more soluble at high solute concentrations
- Don’t see as much as this as might expect
44
Halophilic archaea
Halobacterium salinarum
what
- Extreme halophile
- Have a requirement for high salt concentrations typically at leat 1.5 M (~9%) NaCl for growth
o Our blood is 0.9%
- Have a requirement for high salt because their cell walls (the s-layers) will fall apart if there isn't enough salt
o stabilised by sodium
- These organisms often have large plasmids
o Make up maybe 30% of genome
o Usually a sign of an organism that’s acquired lots of extra bits and pieces from other places
o In order to let it adapt to this environment?
45
where do we find high salt environments
- Lakes where water goes in but doesn’t go out (top pic)
- Sea salt evaporation ponds (bottom picture)
- Found is sea salt evaporation ponds, salt lakes, and artificial saline habitats (i.e. salted foods)
46
Methanogens
Not really an extremophile but a very unusual organisms
- Produce methane (CH4)
o Several carbon substrates can be used
Doing this in order to generate energy
o ATP is produced
- Unique to Archaea
o Important in degradation of organic matter
o Found in:
Sediments low in O2 (marsh swamp etc), Hydrothermal vents
- Obligate anaerobes
- Methanobacterium
o Pseudomurein in cell wall
o Named before understood they were archaea
47
Methanogens and climate change
- Methane is a greenhouse gas
- Farming has created new opportunities for methanogens
o Much more methane is being produced
48
Methanogens and climate change
Ruminants
Ruminants (cows, sheep, goats) harbour methanogens in their rumen
o Because these are organisms which use cellulose
o And cellulose is really hard to break down
o Don’t have enzymes that can break down cellulose
o Can only feed on grass because they have methanogens in their gut
Which can break down cellulose
49
Methanogens and climate change
rice production
- Rice production creates artificial wetlands that harbour methanogens
o Huge amounts of artificial wetlands
o Huge numbers of methanogens
50
ARCHAEA FEATURES IN COMMON WITH EUKARYA
- Histones
BACTERIA: no
ARCHAEA: yes (need for additional DNA protection)
EUKARYA: yes
51
ARCHAEA FEATURES IN COMMON WITH EUKARYA
- RNA polymerase
BACTERIA: One type of relatively simple RNA polymerase
ARCHAEA: One complex RNA polymerase similar to. RNA polymerase II
(because of how DNA is protected more complex machinery needed to unwind DNA)
EUKARYA: Complex RNA polymerases types I, II, III
52
ARCHAEA FEATURES IN COMMON WITH EUKARYA
- promotor structure
BACTERIA: -10, -35 sequences
ARCHAEA: TATA box (TTTATATA)
EUKARYA: TATA box
53
ARCHAEA FEATURES IN COMMON WITH EUKARYA
- initiator sequence
BACTERIA: fMet, formal methionine
ARCHAEA: Met
EUKARYA: Met
54
ADAPTATIONS TO EXTREME ENVIRONMENTS:
membrane lipids
o Glycerol tetraethers (Heat stable)
55
ADAPTATIONS TO EXTREME ENVIRONMENTS:
cell walls
o Glycoprotein cell wall (resistant to osmotic stress)
56
ADAPTATIONS TO EXTREME ENVIRONMENTS:
- proteins
o Chaperones (refold proteins denatured by heat)
o Proteins with acidic amino acids (soluble at high salt concentrations)
57
ADAPTATIONS TO EXTREME ENVIRONMENTS:
- chromosomal structure
o Histones and other DNA binding proteins maintain stability at high temperature
58
archaea live in...
all environments
not just extreme ones
59
EXAMPLES OF ARCHAEA:
Sulfolobus acidocaldarius
HABITAT
Sulphur rich environments (sulphur rich acidic hot springs)
60
EXAMPLES OF ARCHAEA:
Sulfolobus acidocaldarius
ADAPTATION
S layer
Heat shock proteins
Glycerol tetraethers in membranes
Reverse DNA Gyrase (enzyme)
DNA binding proteins
61
EXAMPLES OF ARCHAEA:
Pyrilobus fumarii
HABITAT
Walls of black smokers (bottom of ocean)
62
EXAMPLES OF ARCHAEA:
Pyrilobus fumarii
ADAPTATION
S layer
Heat shock proteins
Glycerol tetraethers in membranes
Reverse DNA Gyrase (enzyme)
DNA binding proteins
63
EXAMPLES OF ARCHAEA:
Nonthermophillic salinarum
HABITAT
Nutrient poor marine environments
Cold --> gaps in ice
64
EXAMPLES OF ARCHAEA:
Nonthermophillic salinarum
ADAPTATIONS
Glycerol tetraethers in membranes
65
EXAMPLES OF ARCHAEA:
Halobacterium salinarum
HABITAT
Evaporation ponds
- High conc of salt
Salt lakes
66
EXAMPLES OF ARCHAEA:
Halobacterium salinarum
ADAPTATIONS
S layer
Maintain positive water balance by pumping K+ into cells
Glycoprotein cell wall
Cellular proteins composed of more acidic amino acids
67
EXAMPLES OF ARCHAEA:
Methanobacterium
HABITAT
Ponds
Cows (grass feeding animals) animal digestive tracts
Rice (artificial wetlands)
Sediments low in O2
Hydrothermal vents
68
EXAMPLES OF ARCHAEA:
Methanobacterium
ADAPTATIONS
Several carbon substrates can be used
Obligate anaerobes pseudomurein in cell wall
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