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Bio 240 > Topic 3 > Flashcards

Topic 3 Flashcards

1
Q

Where do archaea live?

A

Live in most inhabitable places on earth, very extreme locations

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2
Q

Are there achaeal human pathogens?

A

NO, have never been proven to be the causation of disease

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3
Q

Are archaea extremophiles?

A

YES

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4
Q

Phylogenetic trees are established by what

A

Comparison of rRNA genes, Woese and fox began these studies

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5
Q

What were the first archaea discovered

A

Methanogens, all methane poducing things are methanogens

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6
Q

What is the size of Archaea

A

0.5-5um, but vary greatly

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7
Q

What is the shape of archaea

A

ROds, cocci, spirals, irregular shapes, rectangular, squares (halobacterium, flat squares so large surface area, so high nutrient intake, found in water capturing sunlight into atp)

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8
Q

What is in the cytoplasm of archaea

A

Similar to bacteria

-inclusion bodies observed (gas vacoules)
-single, circular chromosome
-DNA replication enzymes look like those of eukarya
-histones present (early branching point of eukarya and archaea fom bacteria
-histones form structures that wrap around DNA, different from eukarya though

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9
Q

How are histones wrapped around dna

A

tetramer of positively charged histones used for dna to wrap around rather than octomer like eukarya

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10
Q

What is an actin homolog found in this

A

Ta0583, found in thermoplasma acidophilum , resembles actin from eukarya

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11
Q

Cell Envelope consists of?

A

Cell wall, plasma membrane, and NO OUTER MEMBRANE

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12
Q

Plasma membrane consists of?

A

-G1P, instead of G3P in euk and bac
-Ether linkages, instead of ester linkages in bac: ether provide more stability
-phytanyl side chains (repeating isoprene units) instead of fatty acid chain

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13
Q

Monolayer of plasma membrane?

A

Phosphoglycerol head on both ends, since they are covalently linked in middle, creates by-phytanyl chains
-STABILITY so allows fo them to live in high temp environments

THIS AND ETHER LINKAGES ALLOW FOR STABILITY

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14
Q

What increases stability in plasma membrane

A

Ether linkages and biphyntanyl chains (two chains covalently link togethe to form to heads on both ends (think fatty acid but tails bonded together but for ARCHAEA so phytanyls are bonded together
-ring pentane structues are also added to tails for stability (isoprene of phyntanyl)

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15
Q

Ignicoccus is an exception for what?

A

-has outer membrane and periplasm similar to gram negative bacteria
-atp synthase enzymes are house in OUTER MEMBRANE
VERY UNUSUAL EVEN FOR ACHAEA

-This is why ignococcus is an exception for having an outer membrane that also has atp synthase enzymes on it. needs it bc nano need it, there are also lots of vesicles in the periplasm of ignococcus, it carries lipids, proteins, whatever that go to nanoarachaeum

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16
Q

What is the cell wall made up of

A

-Composed of pseudomurein, similar to bacteria peptidoglycan (pseudopeptidoglycan)
-NAM (n-acetylglucosamine AND NAT (n-acetylosaminuronic acid)
-Beta 1,3 linkages of nag and nat
-LYSOZYME insensitive
-has L amino acid 4 peptide chain instead of D amino acid

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17
Q

Cell Surface

A

1) S layer: protect against predation/ virsues and mediate adhesion
2) cannulae: hollow glycoprotein tubes that link cells together to form a complex network, use this to exchange stuff

18
Q

Archaellum

A

-used to move
-grows from the base rather than the tip (like hair)
-Uses ATP not Proton motor force to spin

not evolutionary related to flagellum

19
Q

Four major phyla

A

1) Euryarchaeota
2)Crenarchaeota
3)Thaumarchaetoa
4) Nanoarchaetoa

20
Q

Info about crenaechaeota

A

-Extreme lovers, high temp, high pressure, high acid

-thermophiles or hyperthermophiles
-Acidophiles (thrive in low pH) acid mine drains
-Barophiles (thrive in high pressure) bottom of ocean

21
Q

What are adaptations of crenarchaeota

A

Membrane:
-tetraether lipids/ lipid monolayer
PACK biphyntanyl layer as this keeps membrane stable and intact
Proteins:
MODIFIED PROTEINS
-more alpha helical regions, more hydrogen bonding so more tighter and stabilized
-more salt bridges and side chain interactions (pos and neg charges make it stronger)
-more arginine/tyrosine (have side chains that promote side and salt bridges)
-less cysteine/serine
STRONG CHAPERONE PROTEINS
-help keep proteins folded, ensure they dont unfold at high temps
Dna:
THERMOSTABLE DNA BINDING PROTEINS
keep dna stabke and not denatured like chaperone proteins
REVERSE DNA GYRASE ENZYME
type of topoisomerase that supercoils DNA to ensure it stays together at high temps

22
Q

Euryarchaeota

A

Halophiles! - salt lovers
ex: halobacterium
-require 1.5 molar salt to grow
-live in high salt environments with 5-35% salinity (ocean is usually 3.5 salinity) so it needs ALOT

23
Q

What are hypotonic, hypertonic and isotonic solution and their affect on cells

A

Hypotonic solution (low salt solution) net movement into cell
Hypertonic solution (high salt solution (net movement out of cell
Isotonic (equivalent salt solution) no net loss or gain

24
Q

How do halophiles deal with osmotic shock and loss of water?

A

-They create an isotonic like solution
-Have VERY HIGH INTRACELLULAR [K+] to offset high extracellular [Na+]
-Causes the ions to be balanced, so no h2o net loss or gain
-these cells pump in potassium from environment to make osmotic pressure the same,
-K+ not toxic to proteins and dna in cell like Na, it is a compatible solute

25
Q

What is the compatible solute halophiles use? EURYARCHAEOTA

A

K+

26
Q

What is the downside to using k+ as a compatible protein

A

High intracellular levels can cause denaturing of proteins and split dsDNA
-although it is compatible solute, high levels can be harmful

27
Q

How does halophiles counter the possible denaturing of intracellular K+?

A

1) increases GC content cause these have triple bonds so are stronger so prevent DNA denaturing
2) Create highly acidic proteins that remain more stable in high salt environments prevents protein denaturing, makes them more salt bridges so more stable bc have more interactions

28
Q

Why does halobacterium produce red hue?

A

-It is phototrophic, but doesnt have chlorophyll or electron transport chain
-has Bacteriorhodopsin that harnessess energy and produces a pmf
-this gives off a reddish hue due to retinal that fives off the red hue

how it works:
when light is captured by retinal, protons H+ are pumped out, when enough is pumped out, they come back in via atp synthase channel, creating ATP

29
Q

Methanogens

A

Another Euryarchaeota
-methane makers by reducing co2 with h2—> CH4 and H2O
-energy released can be used to fix C
-strict ANAEROBE, found only inplaces with no oxygen
-found in human gut (gas) and swamp sediment (forms combustible air)

30
Q

What is the only phyla that has methane production

A

Euryarchaeota

31
Q

What is the volta experiment

A

-ignites lake water in funnel, get the air and light it on fire

32
Q

Methanogen habitats

A

Anoxic sediments: marshes, lakes, rice paddies, moist landfill

Animal digestive tracts:
-ruminant animal rumen (cattle, sheep, elk, deer) not farts, their front (belches)
-cecal animals (cecum of horse, rabbits)
-large intestines of monogastrals (humans, swine, dogs)

Geothermal H2/Co2 sources
-hydrothermal vents

Artificial biodegradation facilities
-seweage slude digestors

Endosymbionts of anaerobic protozoa

Termite gut symbionts

33
Q

TACK superphylum

A

Thaum- , Aig-, cren-, kor-

34
Q

Thaumarchaeota

A

-Aka Nitrososphareota
-seperates phylum for many mesophillic (intermediate temp lovers) crenarchaeotes
-ammonium oxidizing - important in N cycle, to use it for energy
-mesophiles (15-40 degrees celsius)
or Psychrophiles (<15 degrees C)
-improtant for bicycling of C and N

other members:
Cenarchaeum symbiosum (marine sponge)
-shares genes with crenarchaeota and eukyarchaoests

35
Q

What is the A and K in TACK Phyla

A

Aigarchaeota
-no species cultivated yet
-one genome available: thermophile

Korarchaeota:
-distinct 16S rRNA sequences obtained from hydrothermal vents
-no species cultivated yet
-one genome available

36
Q

NanoArchaeota

A

Part of DPANN
GROWS ON BACK OF IGNOCOCCUS part of crenarchaeota (dont know if it is parasitic or mutualistic
-2 available genomes
-possibly one of the smallest living organisms on earth (0.4um)
-distinct 16s rRNA sequences
-0.59 mbp (no metabolic genes, only carries proteins for replication, transcription and translation)
-it gets everything else from ignococcus (amino acids, lipids for membrane)

-This is why ignococcus is an exception for having an outer membrane that also has atp synthase enzymes on it. needs it bc nano need it, there are also lots of vesicles in the periplasm of ignococcus, it carries lipids, proteins, whatever that go to nanoarachaeum

37
Q

what is the relationship between ignococcus and nanoarchaeum

A

hypothesized as being mutualistic since igno cannot make s layer and nano can,
nano cant do anything else but translation, transcription and replication machinery so igno gives it the rest of them

38
Q

Asgard Superphylum

A

Lokiarchaeota, thorarchaeorta

-both thermophiles
-closest ancestor to eukaryotes
genome shows eukaryotic like compartmnetalization

39
Q

How are archaea assigned to a phylum?

A

Based on DNA sequencing similarities

40
Q

HOW DO BACTERIA AND ARCHAEOTA DO TRANSCRIPTION AND TRANSLATION

A

BY COUPLING TRANSCRIPTION AND TRANSLATION. POLYMERASE AND RIBOSOMES WORK ON SAME TEMPLATE AT THE SAME TIME

Bio 240 (7 decks)

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