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MICROBIOLOGY Y1 > week 10 - archaea > Flashcards

week 10 - archaea Flashcards

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1
Q

Archaea
overview

A
  • Single celled prokaryotic microorganisms
  • Form one of the three domains of life
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2
Q

Archaea
- found in…

A

a wide range of environments
o Oceans, soils, humans, foods
o Also found in extreme environments

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3
Q

archaea
pathogenic?

A
  • No pathogenic archaea have been identified
    o Some may be associated with conditions such as gum disease and diverticulosis
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4
Q

archaea
common ancestors

A
  • Common ancestor between archaea and euk much more recent than common ancestor with bacteria and archaea
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5
Q

KEY FEATURES DISTINGUISHING BACTERIA AND ARCHAEA FROM EUKARYA:
- membrane enclosed nucleus

A

BACTERIA: no

ARCHAEA: no

EUKARYA: yes

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6
Q

KEY FEATURES DISTINGUISHING BACTERIA AND ARCHAEA FROM EUKARYA
- membrane enclosed organelles

A

BACTERIA: rarely

ARCHAEA: no

EUKARYA: yes

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7
Q

KEY FEATURES DISTINGUISHING BACTERIA AND ARCHAEA FROM EUKARYA
- circular chromosomes

A

BACTERIA: almost always

ARCHAEA: yes

EUKARYA: no

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8
Q

KEY FEATURES DISTINGUISHING BACTERIA AND ARCHAEA FROM EUKARYA
- paired chromosomes

A

BACTERIA: no

ARCHAEA: no

EUKARYA: yes

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9
Q

KEY FEATURES DISTINGUISHING BACTERIA AND ARCHAEA FROM EUKARYA
- ribosomes size

A

BACTERIA: 70S

ARCHAEA: 70S

EUKARYA: 80S

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10
Q

KEY FEATURES DISTINGUISHING BACTERIA AND ARCHAEA FROM EUKARYA
- introns in genes

A

BACTERIA: not usually

ARCHAEA: no

EUKARYA: yes

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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)

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12
Q

KEY FEATURES DISTINGUISHING BACTERIA AND ARCHAEA FROM EUKARYA
- growth above 70 degrees

A

BACTERIA: yes

ARCHAEA: yes

EUKARYA: no

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13
Q

KEY FEATURES DISTINGUISHING BACTERIA AND ARCHAEA FROM EUKARYA
- microorganisms

A

BACTERIA: all

ARCHAEA: all

EUKARYA: many

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14
Q

ARCHAEA:
adaptations to extreme environments

A
  • Membrane lipids
  • Cell walls
  • Proteins
  • Chromosomal structure
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15
Q

archaea inhabit a..

A

wide range of extreme environments

  • salt
  • temperature
  • pH
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16
Q

ARCHAEAL CYTOPLASMIC MEMBRANE
- bilayer

A
  • Glycerol diethers made from C20 phytanyl lipids
  • Forms a lipid BILAYER
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17
Q

ARCHAEAL CYTOPLASMIC MEMBRANE
- monolayer

A
  • Diglycerol tetraether made from C40 Biphythanyl lipids
  • Forms a lipid monolayer
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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)
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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
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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
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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

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22
Q

The S-layer (surface layer)
- archaea

A

o Anchored in CM or to pseudomurein

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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
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24
Q

Desulfurococcales
Pyrolobus fumarii
- optimum growth temp.

A

106 degrees

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25
Q

Desulfurococcales
Pyrolobus fumarii
- where?

A
  • Lives in the walls of black smokers (at the bottom of the ocean)
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26
Q

Desulfurococcales
Pyrolobus fumarii
- S-layer

A

composed of diglycerol tetraethers

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27
Q

Desulfurococcales
Pyrolobus fumarii
- autotrophic

A

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

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28
Q

Desulfurococcales
Pyrolobus fumarii
- aerobic, facultative aerobe, anaerobic

A

facultative aerobe

29
Q

Desulfurococcales
Pyrolobus fumarii
- what

A
  • Obligate H2 chemolithotroph
30
Q

Desulfurococcales
Pyrolobus fumarii
- terminal acceptor

A
  • NO3- is used as a terminal acceptor in strict anaerobic conditions
    o NO3- + H2 –> NH4
31
Q

Desulfurococcales
Pyrolobus fumarii
- food chain

A
  • 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
Q

ADAPTATIONS TO LIFE AT HIGH TEMPERATURES:
- problem

A

o Instability of biomolecules at high temperatures
o E.g. proteins unfold when you heat them

33
Q

ADAPTATIONS TO LIFE AT HIGH TEMPERATURES:
- proteins

A

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
Q

ADAPTATIONS TO LIFE AT HIGH TEMPERATURES:
- lipids

A

o Glycerol tetraethers in membranes
- Diglycerol tetraether monolayer membrane most resistant

35
Q

ADAPTATIONS TO LIFE AT HIGH TEMPERATURES:
DNA (key adaptations)

A
  • reverse DNA Gyrase (enzyme)
  • DNA binding proteins
36
Q

ADAPTATIONS TO LIFE AT HIGH TEMPERATURES:
DNA - Reverse DNA Gyrase

A

(enzyme)
 Introduced positive supercoils
* Protects DNA
* More stable
* Less likely to denature / fall apart when heated up
* This has consequences for transcription (unwinding)

37
Q

ADAPTATIONS TO LIFE AT HIGH TEMPERATURES:
DNA - DNA binding proteins

A

 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
Q

Nonthermophilic Crenarchaeota

A

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
Q

ADAPTATIONS TO HIGH SALT:
problems

A

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
Q

ADAPTATIONS TO HIGH SALT:
key features:

A
  • Maintain positive water balance by pumping K+ into cells
  • Glycoprotein cell wall
  • Cellular proteins composed of more acidic amino acids
41
Q

ADAPTATIONS TO HIGH SALT:
- Maintain positive water balance by pumping K+ into cells

A

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
Q

ADAPTATIONS TO HIGH SALT:
- Glycoprotein cell wall

A

o Cell wall stabalised by Na+
o S-layers (need to have these to start to fall apart

43
Q

ADAPTATIONS TO HIGH SALT:
- Cellular proteins composed of more acidic amino acids

A

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
Q

Halophilic archaea
Halobacterium salinarum
what

A
  • 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
Q

where do we find high salt environments

A
  • 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
Q

Methanogens

A

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
Q

Methanogens and climate change

A
  • Methane is a greenhouse gas
  • Farming has created new opportunities for methanogens
    o Much more methane is being produced
48
Q

Methanogens and climate change
Ruminants

A

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
Q

Methanogens and climate change
rice production

A
  • Rice production creates artificial wetlands that harbour methanogens
    o Huge amounts of artificial wetlands
    o Huge numbers of methanogens
50
Q

ARCHAEA FEATURES IN COMMON WITH EUKARYA
- Histones

A

BACTERIA: no

ARCHAEA: yes (need for additional DNA protection)

EUKARYA: yes

51
Q

ARCHAEA FEATURES IN COMMON WITH EUKARYA
- RNA polymerase

A

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
Q

ARCHAEA FEATURES IN COMMON WITH EUKARYA
- promotor structure

A

BACTERIA: -10, -35 sequences

ARCHAEA: TATA box (TTTATATA)

EUKARYA: TATA box

53
Q

ARCHAEA FEATURES IN COMMON WITH EUKARYA
- initiator sequence

A

BACTERIA: fMet, formal methionine

ARCHAEA: Met

EUKARYA: Met

54
Q

ADAPTATIONS TO EXTREME ENVIRONMENTS:
membrane lipids

A

o Glycerol tetraethers (Heat stable)

55
Q

ADAPTATIONS TO EXTREME ENVIRONMENTS:
cell walls

A

o Glycoprotein cell wall (resistant to osmotic stress)

56
Q

ADAPTATIONS TO EXTREME ENVIRONMENTS:
- proteins

A

o Chaperones (refold proteins denatured by heat)
o Proteins with acidic amino acids (soluble at high salt concentrations)

57
Q

ADAPTATIONS TO EXTREME ENVIRONMENTS:
- chromosomal structure

A

o Histones and other DNA binding proteins maintain stability at high temperature

58
Q

archaea live in…

A

all environments

not just extreme ones

59
Q

EXAMPLES OF ARCHAEA:
Sulfolobus acidocaldarius
HABITAT

A

Sulphur rich environments (sulphur rich acidic hot springs)

60
Q

EXAMPLES OF ARCHAEA:
Sulfolobus acidocaldarius
ADAPTATION

A

S layer
Heat shock proteins
Glycerol tetraethers in membranes
Reverse DNA Gyrase (enzyme)
DNA binding proteins

61
Q

EXAMPLES OF ARCHAEA:
Pyrilobus fumarii
HABITAT

A

Walls of black smokers (bottom of ocean)

62
Q

EXAMPLES OF ARCHAEA:
Pyrilobus fumarii
ADAPTATION

A

S layer
Heat shock proteins
Glycerol tetraethers in membranes
Reverse DNA Gyrase (enzyme)
DNA binding proteins

63
Q

EXAMPLES OF ARCHAEA:
Nonthermophillic salinarum
HABITAT

A

Nutrient poor marine environments
Cold –> gaps in ice

64
Q

EXAMPLES OF ARCHAEA:
Nonthermophillic salinarum
ADAPTATIONS

A

Glycerol tetraethers in membranes

65
Q

EXAMPLES OF ARCHAEA:
Halobacterium salinarum
HABITAT

A

Evaporation ponds
- High conc of salt
Salt lakes

66
Q

EXAMPLES OF ARCHAEA:
Halobacterium salinarum
ADAPTATIONS

A

S layer
Maintain positive water balance by pumping K+ into cells
Glycoprotein cell wall
Cellular proteins composed of more acidic amino acids

67
Q

EXAMPLES OF ARCHAEA:
Methanobacterium
HABITAT

A

Ponds
Cows (grass feeding animals) animal digestive tracts
Rice (artificial wetlands)
Sediments low in O2
Hydrothermal vents

68
Q

EXAMPLES OF ARCHAEA:
Methanobacterium
ADAPTATIONS

A

Several carbon substrates can be used
Obligate anaerobes pseudomurein in cell wall

69
Q
A

MICROBIOLOGY Y1 (28 decks)

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