Module 3 - Archaea Flashcards
How were archaea first characterized?
As bacteria (Archaebacteria)
How come archaea were first characterized as bacteria?
Because they look very similar
True or false: classification of archaea is simple
False: it is very difficult
How come classification of archaea is difficult?
A majority of them have not been isolated in the lab
How are archaea discovered if most of them are not easy to culture?
Detection of nucleic acids from samples of their environment
What are archaea?
Single celled prokaryotes that have distinct characteristics from bacteria (and eukarya)
True or false: many archaea can survive in the most inhospitable environments
True: many archaea are extremophiles
Where were the first archeons found?
In extreme environments (high saline, acidic, alkaline, temperature, etc.)
Where are a large amount of archaea found?
In the plankton community
What are plankton?
Small, microscopic organisms that live in large bodies of water
How many of the microbial cells in the ocean are archaea?
1/5 (20%)
True or false: all archaea live in extreme environments
False: some live in very mild environments
Why are rRNA genes used to establish evolutionary relationships?
Ribosomes are needed in all organisms to produce polypeptides
What is the structure of a ribosome?
A large subunit and a small subunit
What does the large subunit of the ribosome do?
Acts as a ribozyme to catalyze peptide bond formation
What rRNA gene is used for phylogeny?
16S
Where is the 16S rRNA found?
In the small subunit of the ribosome
What was the first group of archeons discovered?
The methanogens
What are methanogens?
A group of microbes that can produce methane as a byproduct in anoxic conditions
True or false: all methanogens are archaea
True: there are no methanogens in bacteria or eukarya
Where are methanogens usually found?
In the GI track of mammals
How do methanogens help mammals?
By digesting food
How much does methane impact the environment?
Methane is the 2nd highest greenhouse gas emitted from humans in the US
How does methane impact climate change compared to carbon dioxide?
It is more efficient at trapping radiation, and it has a bigger impact on climate change than carbon dioxide
True or false: only animals release methane
False: industries also release methane
How come methane released from animals is considered human related?
Because humans raise animals for food
What are the largest sources of methane from industry?
Natural gas and petroleum systems
What are extremophiles?
Organisms that live in extreme environments (salt, temperature, acidity, etc.)
True or false: if two archeons have similar 16S sequences, they have similar growth requirements
False: the growth requirements can vary drastically, even if the 16S sequences are similar
What type of environment do Halobacterium salinarum grow in?
High salt concentrations
What type of environment do Pyrococcus furiosus grow in?
High temperature
What type of environment do Picrophilus oshimae grow in?
Acidic conditions
What type of environment do Methanogenium frigidum grow in?
Low temperature
How did all cells start on Earth?
From a universal cell
What does sequencing data suggest about how bacteria, eukarya, and archaea evolved?
Archaea and eukarya branched off from bacteria
What was a branching point for when archaea became different from bacteria?
The presence of histones
How does the plasma membrane of archaea compare to bacteria and eukarya?
It is significantly different
What is a possible function of the unique plasma membrane of archaea?
It may provide thermal stability
What are some issues with the function of the unique plasma membrane being for thermal stability?
- Not all archaea thrive in high temperatures
2. Some bacteria can grow in high temperatures without this plasma membrane
What is the general size of archaea?
0.5 - 5 um
What is the smallest archeon?
Nanoarchaeum equitans (0.4 um)
How big is Nanoarchaeum equitans?
0.4 um
What is the largest archeon?
Those in the Thermoproteus species
How big is Thermoproteus?
100 um
What is special about Ignicoccus?
It grows together with Nanoarchaeum
How does Nanoarchaeum grow?
Connected to Ignicoccus
What shape are most archaeons?
Coccus or rod shaped
What are some other less common shapes of archaeons?
Unusual thin, flat, square, or irregular shapes
What is the shape of Sulfolobus species?
Irregular
Which archaeons are irregularly shaped?
Sulfolobus species
What is the shape of Thermoproteus species?
Rectangular
Which archaeons are rectangularly shaped?
Thermoproteus species
What is the purpose of the special shapes of archeons?
It is not clear currently
What is the cytoplasm of archeons composed of?
Several molecules, such as the nucleoid
What is the structure of the nucleoid in archaeal cells?
A singular, circular chromosome
What do the archaeal DNA replication enzymes resemble?
The eukaryal versions
True or false: gas vesicles have been found in archaeal cells
True: some complex structures have been found in archaeal cells
True or false: archaea have plasmids
True: they may be able to pass them in a process similar to conjugation
In general, what is similar between archaea and bacteria?
The types of molecules and the overall functions
In general, what is different between archaea and bacteria?
The biochemical nature of the molecules
True or false: archaeons have histones
True: some can have histones
What are histones and what do they do?
Proteins that compact DNA to fit more in the nucleoid area
What is the structure of a histone in eukaryotic cells?
An octomeric complex, with 2 each of H1A, H2B, H3 and H4
How many bp of DNA wraps each histone octomer (in eukaryotic cells)?
160 bp
What does histone H1 do (in eukaryotes)?
Interacts with the DNA and the histone complex
What is the structure of a histone in archaeal cells?
A tetrameric complex, with 2 each of H3 and H4
How many bp of DNA wraps each histone tetramer (in archaeal cells)?
60 bp
What does the presence of histones in archaeons suggest?
Histones evolved early in the history of life
What would having histones be a prerequisite for (in terms of evolution)?
Increase genome size (as seen in eukaryotic cells)
What is Ta0583?
An actin homolog found in archaea
What is an actin homolog found in archaea?
Ta0583
In what species is Ta0583 found?
In Thermoplasma acidophilum
What is Ta0583 closer to: eukaryotic actin or bacterial ParM/MreB?
Eukaryotic actin
What is the actin found in Methanogenic bacteria closer to (eukaryotic or bacterial actin)?
Bacterial actin (MreB/ParM)
True or false: all archaeons have a plasma membrane
True: it is required for life, although it is structured differently
True or false: all archaeons have a cell wall
False: most, but not all, archaeons have a cell wall
What is the structure of a bacterial/eukaryal plasma membrane?
A phospholipid bilayer
What is the structure of a phospholipid?
Fatty acids connected to a glycerol-3-phosphate
What molecule do the fatty acids bind to in a phospholipid?
Glycerol-3-phosphate
What type of bond is found between a fatty acid and the glycerol-3-phosphate in a phospholipid?
Ester linkages (O-C==O)
What is the structure of an archaeal plasma membrane?
Isoprenoids attached to glycerol-1-phosphate in a monolayer or bilayer
What molecule do the isoprenoids bind in an archaeal plasma membrane?
Glycerol-1-phosphate
What type of bound is found between an isoprenoid and the glycerol-1-phosphate?
Ether linkages (O-C)
What is the subunit of an isoprenoid?
Isoprene units
What is the most common isoprene unit in archaeal plasma membranes?
Phytanyl
What is phytanyl?
A 20-carbon hydrocarbon used to make up isoprenoids in the archaeal plasma membrane
True or false: all archaeons have a plasma membrane monolayer
False: some have a bilayer, while others have a monolayer
What is the structure of a bilayer plasma membrane in archaeons?
Two isoprenoids attach to the glycerol-1-phosphate, and two of these complexes forms a bilayer
What is the structure of a monolayer plasma membrane in archaeons?
Each isoprenoid has a glycerol-1-phosphate on both ends, and one of these complexes forms a monolayer
Which archaeons typically have a monolayer?
Those that live in high temperatures
How come archaeons that live in high temperatures typically have a monolayer?
A monolayer is more stable than a bilayer at high temperatures
True or false: some archaeons look like Gram-negative bacteria
True: some, like Ignicoccus, have an outer membrane and a periplasm
What archaeon has an outer membrane and a periplasm?
Ignicoccus
In archaeons with an outer membrane, how are protons transported?
From the periplasm to the extracellular space (then back to the cell through ATP synthase)
Where is ATP synthase found in an archaeal cell with an outer membrane?
In the outer membrane
Where is ATP synthase found in a bacterial cell with an outer membrane?
In the inner membrane
What is the significance of the outer membrane in archaea?
It can be exploited for drug delivery and vaccine effectiveness
What is the purpose of the cell wall?
To provide physical and osmotic protection
What is the cell wall in archaea composed of?
Pseudopeptidoglycan (pseudomurein)
What is the structure of pseudomurein?
NAG and NAT linked to a small peptide chain
Where is NAG found?
In both bacterial and archaeal cell walls
Where is NAM found?
Only in bacterial cell walls
Where is NAT found?
Only in archaeal cell walls
What does NAT stand for?
N-acetyltalosaminuronic acid
What type of linkage is found between NAG and NAT?
Beta 1-3 linkage
Where is the peptide found in the archaeal cell wall?
Attached to the NAT subunit only
What types of amino acids are found in the short peptide attached to NAT?
L amino acids
True or false: lysozyme is effective against archaeal cell walls
False: it cannot break the linkages
How come lysozymes are not effective against archaeal cell walls?
They can only break down the beta 1-4 linkages in bacterial cell walls, not the beta 1-3 linkages in archaeal cell walls
True or false: penicillins are effective against archaea
False: they are not effective
True or false: all archaea have a cell wall
False: some archaea do not have a cell wall
What is the appearance of an archaeon without a cell wall?
Non-spherical
True or false: all archaea have flagella
False: some, not all, have flagella
What is the function of flagella in archaea?
To provide movement
In terms of size, how does archaeal flagella compare to bacterial flagella?
Archaeal flagella is usually thinner than bacterial flagella
What is the composition of bacterial flagella?
A long filament composed of one type of flagellin protein
What is the composition of archaeal flagella?
A variety of different flagellin protein species
How do multiple bacterial flagella move?
They rotate independently
How do multiple archaeal flagella move?
Together as a single assembly
How are bacterial flagella motorized?
Through a proton (or sodium) gradient
How are archaeal flagella motorized?
Through ATP hydrolysis
True or false: the archaeal motor has been identified
False: it has not been identified yet
How are bacterial flagella assembled?
By adding subunits to the tip
How are archaeal flagella assembled?
By adding subunits to the base
What is the overall summary of bacterial and archaeal flagella?
While the functions may be similar, the overall composition is very different
What are archaeonics?
Antibiotics produced by archaea
True or false: archaea produce antibiotics
True: they are called archaeonics
Which species are thought to contain many archaeonics?
Haloarchaea and Sulfolobus
What enzyme is needed for PCR?
DNA polymerase
What DNA polymerase is commonly used for PCR?
Taq polymerase
Where is Taq polymerase from?
The DNA polymerase of Thermus aquaticus
Where is Pfu polymerase from?
The DNA polymerase of Pyrococcus furiosis
What is the advantage of Pfu polymerase over Taq polymerase?
More thermostability, and has 3’ to 5’ exonuclease proofreading activity
What is the significance of PCR?
Allowed for a simple and rapid technique for cloning DNA
What does 3’ to 5’ exonuclease proofreading activity mean?
It can remove mismatched nucleotides from the growing DNA strand
Are there pathogenic archaea?
There are no clear examples, but some may cause infections in the mouth
What are the two main phyla of archaea?
Euryarchaeota and Crenarchaeota
How have other phyla for archaea been proposed?
Through sequencing of the 16S rRNA gene
What are some other phyla that have been proposed for archaea?
Nanoarchaeota and Korarchaeota
What archeon has its own phylum?
Nanoarchaeum equitans (part of Nanoarchaeota)
What types of species are part of Korarchaeota?
Unusual thermophilic species
What is Korarchaeota more closely related to?
Crenarchaeota
What does ARMAN stand for?
Archeal Richmond Mine Acidophilic Nanoorganisms
What is ARMAN?
A new species of archaeons comprising microarchaeota and parvarchaeota (some of the smallest organisms known)
What is special about ARMAN?
They are some of the smallest organisms known
What were Crenarchaeota originally thought to be?
Sulfur extremophiles
What has recent results concluded about Crenarchaeota (in terms of their members)?
They are the most abundant archaea in the marine environment
What type of extremophiles are a majority of Crenarchaeota?
Thermophiles or hyperthermophiles
What is a thermophile?
An organism that grows optimally in conditions greater than 55 C
What is a hyperthermophile?
An organism that grows optimally in conditions greater than 80 C
What is one of the most well studied Crenarchaeota?
Sulfolobus solfataricus
Which organism is a model organism for studying hyperthermophiles?
Sulfolobus solfataricus
In Crenarchaeota, what type of organism are many hyperthermophiles as well?
Acidophiles
What is an acidophile?
An organism that grows optimally in a low pH environment
What major phylum is majorly thermophiles and hyperthermophiles?
Crenarchaeota
What major phylum contains acidophiles?
Crenarchaeota
What is an example of an acidophile?
Sulfolobus solfataricus
What are barophiles?
An organism that grows optimally under high pressure
What type of organisms are found in deep sea thermal vents?
Organisms that are both thermophiles and barophiles
What are some examples of adaptations that help Crenarchaeota survive in high temperature environments?
Tetraether lipids/lipid monolayers, more alpha-helixes in proteins, more salt bridges/side chain interactions, more arginine/tyrosine, less cysteine/serine, strong protein chaperones, thermostable DNA binding proteins, and reverse DNA gyrase
What does high temperature lead to in most organisms?
Disruption of the plasma membrane
What can be done to the plasma membrane to make it extra stable at high temperatures?
Have tetraether lipids or lipid monolayers
What can be done to the proteins to make it extra stable at high temperatures?
More alpha helixes, salt bridges, side chain interactions, arginine, and tyrosine, and less cysteine and serine. Also having strong protein chaperones
What can be done to the DNA to make it extra stable at high temperatures?
Have thermostable DNA binding proteins, and reverse DNA gyrase
Why are alpha-helixes stable structures?
Interchain hydrogen bonds can help stabilize the structure
Why would a protein want more alpha-helixes in a high temperature environment?
The alpha-helix is a very stable structure
How would a protein maintain its shape at higher temperatures?
By promoting more amino acid interactions
How can a protein increase the amino acid interactions?
By having more arginine, tyrosine, salt bridges, and side chain interactions
How come a protein in a high temperature would not have a lot of cysteine?
Cysteine is a temperature sensitive amino-acid, so it would denature easily
What are chaperone proteins?
Proteins that help fold proteins or refold denatured proteins
What do archaeal chaperone proteins more closely represent?
Eukaryotic chaperone proteins
What do thermostable DNA binding proteins do?
Increase the melting temperature of DNA
True or false: all hyperthermophiles have reverse DNA gyrase
True: they all have this enzyme to increase supercoiling
What does reverse DNA gyrase do?
Increases supercoiling of the DNA
What is the advantage of increasing the supercoiling of DNA?
It increases the temperature that DNA unwinds and denatures
Besides supercoiling, what does reverse DNA gyrase do to the DNA?
Has heat protective DNA chaperone activity
Besides thermophiles, what types of organisms are found in Crenarchaeota?
Mesophiles and psychrophiles
What are mesophiles?
Organisms that grow in conditions between 15 C and 40 C
What are psychrophiles?
Organisms that grow in conditions less than 15 C
What is a possible role of the mesophiles and psychrophiles?
Important to biogeochemical cycling of carbon and nitogren in the ocean
How are the mesophiles and psychrophiles usually detected?
Often through rRNA sequencing (not by cultivation)
What is special about Cenarchaeum symbiosum?
It shares some genes with both Crenarchaeota and Euryarchaeotes, thus potenitally being part of a new phylum
What groups are primarily found in Euryarchaeota?
Methanogens and halophiles
Most methanogens are part of what phylum?
Euryarchaeota
Most halophiles are part of what phylum?
Euryarchaeota
How are Euryarchaeota similar and different within the phylum?
They are highly diverse based on morphology and biochemical properties, but they have similar 16S rRNA gene sequences
What are halophiles?
Organisms that can survive extreme concentrations of salt (1.5 M)
True or false: all methanogens are anarobes
True: they all live in anoxic environments
What is an example of a methanogen?
Methanobrevibacter smithii
Where is M. smithii found?
In the human gut
What does M. smithii do?
Aids in the digestion of polysaccharides by consuming the end products of bacterial fermentation
How does M. smithii aid in digestion?
By consuming the end products of bacterial fermentation
What reaction do methanogens perform?
CO2 + 4H2 –> CH4 + 2H2O
What is important about the methanogen reaction?
Enough energy is released to fix carbon
What are the most well known high salt environments?
The Great Salt Lake in Utah, and the Dead Sea between Israel and Jordan
What is the salt concentration in areas with high salinity?
Between 5-34%
How much salinity does the ocean have?
3.5% (0.6 M)
What happens if a cell is placed in an isotonic solution?
No net movement of water
What happens if a cell is placed in a hypotonic solution?
The cell swells due to water influx
What happens if a cell is placed in a hypertonic solution?
The cell shrinks due to water efflux
What is a hypertonic solution?
The solution has more solute (salt) than the cell
What is a hypotonic solution?
The solution has less solute (salt) than the cell
What is an isotonic solution?
The solution has equal solute (salt) to the cell
What is a model organism for studying halophiles?
Halobacterium salinarum
How does H. salinarum offset the osmotic shock of high extracellular salt environments?
By maintaining high intracellular potassium levels
What are the potential problems of having high intracellular potassium levels?
It can denature proteins and split dsDNA
How does Halobacterium overcome the problem of splitting dsDNA?
By having a high GC content
How does having high GC content protect the dsDNA from splitting in high salt conditions?
GC are stronger bonds (3 H bonds) compared to AT (2 H bonds)
How does Halobacterium overcome the problem of denaturing proteins?
By having highly acidic proteins
Which amino acids are acidic?
Aspartic acid and glutamic acid
How does having acidic proteins protect it from denaturing in high salt conditions?
The negatively charged acids are more stable in a high (positive) salt (potassium) environment
True or false: Halobacterium gets energy from sunlight
True: while it does not use photosynthesis, it can get energy from sunlight
True or false: Halobacterium uses photosynthesis
False: while they can get energy from sunlight, they do not use photosynthesis
What does Halobacterium not use for producing energy from sunlight?
Chlorophyll or an ETC
How does Halobacterium harvest energy from sunlight?
Through bacteriorhodopsin
What is bacteriorhodopsin?
An integral protein that can harvest energy from sunlight
How much of the surface area of Halobacterium is bacteriorhodopsin?
~50%
What light is bacteriorhodopsin best at absorbing?
Green light
What is the appearance of bacteriorhodopsin?
Reddish/purplish hue
How does bacteriorhodopsin work?
It acts as a proton pump, using the light energy to pump protons across the cell membrane out of the cell
What happens once the proton gradient is established by bacteriorhodopsin?
They flow back into the cell through ATP synthase to generate ATP
True or false: methanogens and halophiles are the only members of Euryarchaeota
False: while those two groups are the most well studied, other types of organisms exist
What are the other species of Euryarchaeota (besides methanogens and halophiles)?
Thermophiles, hyperthermophiles, and acidophiles
What is an example of an archeon from Euryarchaeota that is a theromphile and acidophile?
Picrophilus species
What happens to Picrophilus species when pH increases?
The plasma membrane becomes destabilized
What species are part of Nanoarchaeota?
Nanoarchaeum equitans
How was N. equitans decided to be its own phylum?
Based on the differences in 16S rRNA sequences from both Crenarchaeota and Euryarchaeota
How big is N. equitans?
One of the smallest organisms on Earth
How does N. equitans survive?
Through symbiosis with other organisms
How was archaea first distinguished from bacteria?
Through 16S rRNA sequencing by Carl Woese of the methanogens
True or false: the plasma membrane of archaea is required to live in high temperature environments
False: some bacteria can also live in high temperature environments without this membrane
What shape is Sulfolobus?
Irregular
What shape is Thermoproteus and Pyrobaculum?
Rectangular
What shape is Haloquadratum walsbyi?
Thin and flat squares
When did histones evolve?
After bacteria but before eukarya (during archaea)
What is the importance of histones?
It allows for larger genome size through DNA packaging
How many carbons are in an isoprene?
5
What is the relationship between glycerol-3-phosphate and glycerol-1-phosphate?
They are stereoisomers
What is biphytanyl?
A 40 carbon hydrocarbon found in archaeal monolayers
Where is biphytanyl found?
In archaeal monolayers
True or false: monolayer liposomes are more stable than bilayer liposomes
True: this is seen in archaea that live in high temperature environments
What is the advantage of an ether linkage over an ester linkage?
They are more resistant to high temperatures, oxidation, and alkaline degradation
Since T. acidophilum does not have a cell wall, how does it maintain its shape?
Likely through a cytoskeleton
How come archaeosomes may be useful clinically?
They are more stable, so they may be more effective in vaccine delivery
True or false: archaea can have an S-layer
True: this may help to protect the cell
What is special about Pyrodictium?
They have cannulae
What species features cannulae?
Pyrodictium?
What are cannulae, and what do they do?
Hollow glycoprotein tubes that connect individual cells together
Where are cannulae located?
In the periplasm, but not cytoplasm, of cells
What is the archaellum?
The archaeal flagella
How thick are archaeal flagella?
10-14 nm
How thick are bacterial flagella?
20-24 nm
What type of glycosylation is found in archaeal flagella?
N-linked glycosylation
What type of glycosylation is found in bacterial flagella?
O-linked glycosylation
Through what pathway are bacterial flagella assembled?
Through the type III secretory pathway
How do flagellin monomers reach the tip of the filament (in bacteria)?
By traveling through the developing filament
What is the assembly of archaeal flagella similar to?
The assembly of bacterial pili
What are the links between bacterial pili and archaeal flagella?
- They exhibit some amino acid similarity
2. Homologous assembly proteins have been identified
True or false: homologous assembly proteins have been found for bacterial flagella in archaea
False: no such proteins have been found
True or false: homologous assembly proteins have been found for archaeal flagella in bacteria
False: no such proteins have been found
True or false: bacterial and archaeal flagella may have similar chemotaxis pathways
True: similar genes have been found for this in both bacteria and archaea
What proteins are involved in chemotaxis?
CheA, CheB, and CheY
What three other phyla have been proposed alongside Crenarchaeota and Euryarchaeota?
Thaumarchaeota, Korarchaeota, and Nanoarchaeota
What is a thermosome?
A complex of protein chaperons found in hyperthermophiles
What is the importance of proteins that function under high temperatures?
They could have important industrial uses
What phyla were Thaumarchaeota thought to be a part of?
Crenarchaeota
What types of organisms are part of Thaumarchaeota?
Mesophiles and psychrophiles
Where are Thaumarchaeota commonly found?
In marine environments, such as near hydrothermal vents
What is the importance of organisms in Thaumarchaeota?
They may function in carbon cycling and biogeochemical cycles in the oceans
What does AOA stand for?
Ammonia-oxidizing archaea
What does AOB stand for?
Ammonia-oxidizing bacteria
What is the signifance of AOAs?
They function in the first step of the nitrification process
True or false: methanogens are autotrophs
True: they can incorporate inorganic carbon into organic molecules
True or false: all methanogens are thermophiles
False: they can also be mesophiles or psychrophiles
If an environment has high sodium carbonate, what environment is created?
An alkaline environment
What is phototrophy?
The acquisition of energy from sunlight
Which organism undergoes an unusual method of phototrophy?
Halobacterium salinarum
What molecule in bacteriorhodopsin captures the light energy?
Retinal
True or false: Korarchaeota has been cultured
False: no archaea in this phylum have been cultured
If no Korarchaeota has been cultured, how has its genome been sequenced?
Through enrichment culture
How come Korarchaeota has been proposed as a separate phylum?
It has genes similar to both Crenarchaeota and Euryarchaeota
Why does N. equitans grow with Ignicoccus?
It depends on the host for survival
What evidence shows that N. equitans needs a host for survival?
- All attempts to grow N. equitans independently have failed
- Its genome lacks genes to synthesize nucleotides, lipids, cofactors, and amino acids
