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Module 3: Archaea (Structure) Flashcards

1
Q

Archaea

A

A domain of life lacking a nucleus characterized by features similar to BOTH eukarya and bacteria

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2
Q

Historically, what did archaea used to be lumped together with? Why?

A

Bacteria

–> Due to their superficial similarities; they “looked like” bacteria

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3
Q

What are superficial similarities between bacteria and archaea?

A

1) Similar size
2) Similar organization + size of chromosome
3) Lack of a nucleus

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4
Q

Why is 16s rRNA used in phylogenetic analysis?

A

Because it is a molecule found in ALL living organisms and fulfills the SAME function in all life BUT there is quite a bit of diversity in its specific sequence!

–> Makes it a good tool to compare across organisms

“To determine relationships covering the entire spectrum of extant living systems, one optimally needs a molecule of appropriately broad distribution” -Woese (1977)

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5
Q

What were the findings of rRNA analysis of Carl Woese and George Fox?

A

1) ALL eukaryal cells are related (very similar 16s rRNA)
2) Prokaryotes formed 2 distinct groups based on rRNA similarity

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6
Q

What were the organisms the preliminary categories of prokaryotes were based upon?

A

Bacteria category= based upon E.coli and S.aureus

Archael category = based upon methanogens (or what were thought of as “methane producing bacteria” at the time!)

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7
Q

Extremophiles

A

Archaea living in atypical, “extreme” environments

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8
Q

What is the optimal condition for Halobacterium spinosum?

A

3.0-5.0M NaCl
–> Halophile

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9
Q

What is the optimal condition for Pyrococcus furiosus?

A

100C
–> Hyperthermophile

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10
Q

What is the optimal condition for Picrophilus oshimae?

A

0.7pH
–>Acidophile

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11
Q

What is the optimal condition for Methanogenium frigidium?

A

15C
–> Psychrophile

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12
Q

What did individuals initially assume archaea were (based upon their extreme living conditions)?

A

Ancient organisms

–> Because early Earth was a very extreme environ, so it was thought that they live in such extreme environs. today because they adapted to life on early Earth

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13
Q

What did SSU rRNA analysis show about the evolutionary history/relationships between bacteria, eukarya, and archaea?

A

That archaea and eukarya share a MORE RECENT common ancestor than any common ancestor with bacteria

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14
Q

LUCA

A

Last Universal Common Ancestor

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15
Q

What did the LUCA give rise to?

A

The LUCA gave rise to ** bacteria** and some PRECURSOR that eventually gave rise to archaea and eukarya

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16
Q

What has been hypothesized that the archaea/eukarya precursor had that the LUCA/bacteria did not?

A

HISTONES

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17
Q

Histones

A

Proteins found in eukarya + archaea that protect and compact DNA

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18
Q

Appearance of histones may have led to…

A

a rapid evolutionary burst –> Giving rise to eukarya and archaea

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19
Q

Histones are able to…

(factors that possibly made it possible for eukarya and archaeal development)

A

1) Protect DNA in high-temp/extreme environs ==> Might have been able to allow for the evolution of extremophiles

2) Allow a larger genome to fit into a cell ==> Allows for more complex cells (eukarya)

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20
Q

What is the most common morphology of archaea?

A

1) Rod-shaped
2) Cocci

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21
Q

What is the morphology of the Sulfolobus genus?

A

Irregular shape

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22
Q

What is the morphology of the Thermoproteus + Pyrobaculum genuses?

A

Rectangular

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23
Q

What is the morphology of Haloquadratum walsbyi?

A

Flat, thin squares

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24
Q

What is the typical size of archaea?

A

0.5-5um
(same size as bacteria)

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25
What percentage of a eukaryal cell size is an archaeal cell?
1/10th the size of a typical eukaryal cell
26
What is the size of *Nanoarchaeum equitans*? (What is its volume?)
~0.4um --> Ranked as one of the smallest living organisms -->Internal volume is roughly 1% of E.coli cell volume
27
Where is N. equitans found?
Found in marine hydrothermal vents (grow with I. hospitalis)
28
What is the size of *Thermofilum pandens*?
Can have cells up to 100um in length
29
What archaeal genuses are abnormally large?
1) Thermofilum 2) Thermoproteus
30
What are examples of abnormally sized archaea? (2) small+big
1) Nanoarchaeum equitans (0.4um) 2) Thermofilum + Thermoproteus (100um) (genuses)
31
What archaeal cytoplasmic features are similar to bacteria?
1) Nucleoid 2) ONE circular chromosome 3) RNA + DNA polymerases found in the cytoplasm 4) Ribosomes in the cytoplasm 5) Complex structures (Ex: gas vesicles) in the cytoplasm
32
**Generally speaking**, what is similar between bacteria and archaea? What is different?
TYPES of molecules and their BASIC functions --> What's different is the biochemical nature of these components!
33
What feature do archaea share with eukarya?
Histones
34
Which eukarya have histones?
ALL of them
35
What is the composition/structure of eukaryal histones?
1) Octamer made up of 2 repeats of 4 histone proteins 2) H1 histone that interfaces with histone and DNA 3) ~160BPs of DNA wrapped around the octamer
36
What are the core histone proteins of eukarya?
H3, H4, H2A, H2B
37
What is the composition/structure of archaeal histones?
1) Tetrameric complex 2) No H1 histone 3) ~60 BPs wrapped around the tetramer
38
What are the core histone proteins of archaea?
Histone proteins similar to eukaryal H4 + H3
39
Eukaryal vs Archaeal Histones
Eukarya = Octamer, 160 BPs , Histone proteins H1, H2A/B, H3, H4 Archaea = Tetramer, 60 BPs, histone proteins like H3 +H4
40
The presence of histones in archaea but NOT bacteria suggests...
That histones evolved AFTER the split between bacteria and archaea but BEFORE eukarya evolved
41
What are the two cytoskeletal elements found in certain archaea?
1) Ta0583 (actin homolog) 2) MreB homologs
42
In what archaea has Ta0583 been found?
Thermophilic archaea: 1) Archaeologous fudigus 2) Ferroplasma acidarmanus Euryarchaeota: 1) **Thermoplasma acidophilum**
43
In what archaea have MreB homologs been found?
In SOME methanogens: 1) Methanopyrus kandleri 2) Methanobacterium thermoautotrophicum
44
The ______ of the archaeal PM is the same as bacteria and eukarya BUT the _________ is not
1) FUNCTION (=selectively permeable barrier that hosts proteins which control movement in and out of cell and other key processes) 2) STRUCTURE
45
What is the structure of eukaryal and bacterial PM?
A phospholipid bilayer!
46
What is the structure of phospholipids?
Fatty acids (hydrocarbon chains) linked to glycerol-3-phosphate (G3P) by an ESTER linkage
47
What components react to make up the ester linkage between G3P and fatty acid?
OH from glycerol and OH from the carboxy acid end of fatty acid chains
48
What is the structure of the archaeal PM?
Bilayer or monolayer of ISOPRENOIDS
49
Isoprenoids
Hydrocarbons built of 5-carbon isoprene subunits that are linked to glycerol-1-phosphate (G1P)
50
What is the structure of isoprenoids?
Isoprene polymers linked to G1P molecules via an ETHER linkage
51
What is the most common isoprene polymer found in isoprenoids of archaea?
Phytanyl
52
Isoprenoid bilayer vs monolayer
Bilayer = two layers of 20C phytanyl isoprenoids Monolayer = ONE layer of BIPHYTANYL isoprenoids
53
What is biphytanyl?
Two phytanyl chains linked to TWO G1P molecules that "cap" both ends of the biphytanyl
54
What is the advantage of an isoprenoid monolayer?
More RIGID = thought to provide greater stability at higher temperatures (good for thermophilic archaea)
55
Why use isoprenoids instead of phospholipids for the PM?
The ETHER linkages are more stable than ESTER linkages! **Ether linkages are more inert** and therefore more resistant to: 1) High temp 2) Oxidation 3) Alkaline degradation
56
What evidence did scientists find suggesting that monolayer membranes are more stable than bilayers?
By studing monolayer and bilayer liposomes --> Found the monolayer liposomes to be more stable at higher temperatures!
57
Liposomes and Archaeosomes
Liposomes = vesicles made of cell membrane materials Archaeosomes = Liposomes made from archaeal PM components
58
How are G1P and G3P related?
They are stereoisomers (just flipped spatial configuration)
59
What is unique about the cell envelope of Ignococcus genus?
Have an outer membrane and a plasma membrane with a LARGE periplasmic space (~20-400nm)
60
How big is the periplasmic space of Ignococci?
~20-400nm (E.coli for comparison have periplasm ~20-25nm wide)
61
What special function does the outer membrane of ignococci serve?
ATP synthase and proton pumps are in the OUTER membrane --> ATP is produced in the periplasm and the proton gradient is made between the periplasm and ECF
62
What is the function of archaeal cell wall?
1) Provides shape to cells 2) Provides protection (from osmotic pressure and mechanical stress)
63
What is the archaeal cell wall made of?
Pseudopeptidoglycan (AKA Pseudomurein)
64
What is the structure of pseudopeptidoglycan?
Polymer of alternating subunits of NAT and NAG that are linked together via B-1,3-linkages These polymers are cross linked via peptide chains on NAT subunits NAT = N-acetyltelosaminuronic acid NAG = N-acetylglucosamine
65
What are the main differences between peptidoglycan and pseudopeptidoglycan?
Peptidoglycan: 1) NAM + NAG polymer 2) Sugars linked via B-1,4-glycosidic linkages 3) NAM peptide chain made of D-AAs Pseudopeptidoglcyan: 1) NAT + NAG polymer 2) Sugars linked via B-1,3-glycosidic linkages 3) NAT peptide chain made of L-AAs
66
In what archaea is pseudopeptidoglycan mainly found?
Methanobacterium
67
In what archaea is pseudopeptidoglycan NOT found? (What have they been found to possibly have instead?)
Thermoplasma acidophilum (May have a cytoskeleton instead to maintain their non-spherical shape)
68
Cell surface features of archaea SIMILAR to bacteria
Extremely varied across archaeal species but **overall similar to bacteria** Similarities: 1) Some MAY have an **S-Layer** 2) **Functions**: Adhesion, motility, sensing, acquiring nutrients
69
Cell surface features of archaea DIFFERENT from bacteria
1) Cannulae 2) Flagellum structure
70
What are cannulae?
Hollow glycoprotein tubes that connect individual archaeal cells together to form a network --> Function is currently unknown!
71
What genus of archaea are cannulae mostly found in?
Pyrodictium genus
72
Structural features of archaeal flagellum:
1) Thin filament (10-14nm diameter) 2) Solid filament 3) Filament made of different types of flagellin (not uniform) 4) Rotation of motor powered by ATP 5) Grows from Base --> UP
73
What is the source of power for archaeal flagellum motor?
ATP hydrolysis
74
What is different about the flagellin variants in archaea vs bacteria?
Archaea = Some flagellin variants have N-glycosylation (sugar group added to N-terminus) Bacteria = Flagellin has O-glycosylation (sugar group added to oxygen of serine or threonine)
75
How do growth processes of flagellum differ beetween archaea and bacteria?
Archaea = Grow from the base by adding flagellin subunits to the base Bacteria = Grow from the TIP; Flagellin monomers travel up through the hollow developing filament and add to the tip of it
76
Main differences between archaeal and bacterial flagellum (5):
**Archaea**: 1) Thin SOLID filament (10-14nm wide) 2) Rotation powered by ATP 3) Filament is varied in composition (different types of flagellin) 4) Grows from base 5) Flagella rotate as ONE bundle **Bacteria**: 1) Thicker HOLLOW filament (20-24nm wide) 2) Rotation powered by PMF 3) Filament is uniform in composition (one type of flagellin) 4) Grows from tip 5) Flagella rotate individually
77
What does the construction process of archaeal flagellum mirror?
The construction of bacterial pilli!
78
How is archaeal flagellin related to pillin?
The AA sequence of archaeal flagellin is similar to bacterial pillin!

BIO 315 (25 decks)

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