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biol 6250 > exam 2 > Flashcards

exam 2 Flashcards

1
Q

Name of Archaea before they were recognized as a separate domain

A

Archaeabacteria

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2
Q

Habitats where Archaea were first identified and studied

A

Hot springs of Yellowstone National Park

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3
Q

3 characteristics that distinguished Archaea from bacteria that were the basis for their recognition as a domain of life

A
  1. Archaeal lipids
  2. Archaeal cell walls
  3. Archaeal genome
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4
Q

Advantages that Dr. Carl Woese suggested that would come from having a 3 domain organization of the tree of life

A
  1. Provide a more natural system of classification
  2. Take out the assumption that plants and animals are more important evolutionarily
  3. Foster the understanding of diversity of ancient microbial lineages
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5
Q

Similarity between Bacterial and Archaeal chromosomes and plasmids

A

Both are circular

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6
Q

Similarity between Bacterial and Archaeal DNA

A

DNA not contained within a membrane

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7
Q

Similarity between Bacterial and Archaeal infrastructure

A

No organelles

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8
Q

How lipids in Archaea are different from lipids in Bacteria

A

Archaeal lipids use L-glycerol, not D-glycerol like Bacteria, and therefore have ether linkages, not ester linkages; More branched

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9
Q

Selective advantage Archaeal lipids provide them

A

Allows them to be more resistant to harsher conditions

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10
Q

Why the Archaeal cell wall is resistant to lysozyme that can degrade Bacterial cell walls

A

Archaeal cell wall is made of pseudopeptidoglycans with a different beta-linkage than the one found in peptidoglycan that lysozyme attacks

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11
Q

3 similarities between Archaea and Eukaryotes?

A
  1. Presence of introns
  2. RNA polymerase
  3. Presence of histone homologues
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12
Q

5 phyla within the domain Archaea

A
  1. Halobacterium
  2. Haloferax
  3. Archaeoglobus
  4. Methanococcus
  5. Pyrococcus
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13
Q

Metabolism of Archaea within “Thaumarchaeota” or “Wonder Archaea” that is important in environmental nutrient cycling

A

Ammonia-oxidizers, the first step of nitrification

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14
Q

Phylum within the domain Archaea that is the most closely related to the branch that evolved to become the domain Eukarya

A

Lokiarchaeota

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15
Q

Habitat where you would be likely to find members of the Crenarchaeota

A

Hot springs

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16
Q

Tetraether produced by Crenarchaeota members that helps them survive extremely high temperatures

A

Crenarchaeol

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17
Q

Example of a temperature and pH at which you might find a Crenarchaeota in a hot spring

A

70-100C, pH 5-9

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18
Q

Oxidized by Delsulforococcus

A

Organic molecules

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19
Q

Reduced by Desulforococcus

A

Elemental sulfur

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20
Q

End product of redox reaction by Desulforococcus

A

Hydrogen sulfide gas

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21
Q

Found in association with Ignicoccus islandicus in deep thermal vents

A

Nanarchaeon symbiont

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22
Q

Oxidized by Ignicoccus islandicus

A

H2

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23
Q

Reduced by Ignicoccus islandicus

A

Elemental sulfur

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24
Q

End product of redox reaction by Ignicoccus islandicus

A

Hydrogen sulfide gas

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25
Q

Pyrodictium species metabolism

A

Heterotrophs or lithotrophs

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26
Q

Pyrodictium species live in deep sea vent ecosystems within this protease-resistant structure where there are extreme temperature gradients

A

Hyperthermal biofilms

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27
Q

Produced by Pyrodictium species

A

Network of hollow cannulae

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28
Q

Hollow cannulae network of Pyrodictium spp. is used to connect what part of cells?

A

Periplasm

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29
Q

Sulfolobus solfataricus metabolism

A

Heterotroph and lithotroph

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30
Q

Similar to Eukaryotes, Sulfolobus solfataricus has 2 of these

A

Origins of replication

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31
Q

Technique used to identify psychrophilic Thaumarchaeota as being abundant in the deep ocean

A

Fluorescent In-Situ Hybridization (FISH)

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32
Q

3 examples of environments in which Thaumarchaeota have been discovered

A
  1. Deep sea depths off Hawaii
  2. Roots of tomato plants
  3. With sponges
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33
Q

Metabolism of Thaumarchaeota that helps them contribute to the N cycle

A

Lithotrophic/ammonia oxidizers

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34
Q

Thaumarchaeota fix this from the atmosphere

A

CO2

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35
Q

Environmental consequence of methane emissions

A

Greenhouse gas

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36
Q

Sources of methane emissions

A
  1. Enteric fermentation
  2. Rice cultivation
  3. Wastewater
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37
Q

What inhibits metabolism of methanogens?

A

Oxygen/aerobic environments

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38
Q

Phylum of the domain Archaea where you find methanogens

A

Euryarchaeota

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39
Q

Prefix for each genera of methanogenic Archaea

A

Methano-

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40
Q

Morphology of methanogens

A

Diverse morphology –spiral, cocci, and rods

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41
Q

2 components that can comprise the Archaeal cell wall

A
  1. No cell wall, only an S layer

2. Pseudopeptidoglycan

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42
Q

Substrates required for the metabolism of methanogens

A

CO2 (terminal electron acceptor), H2 (electron donor), and Na+

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43
Q

Unique component of methanogenic Archaea that transfer hydrogen and reduced carbon to each enzyme in the pathway

A

Cofactors

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44
Q

Gradient required for methanogens to import H2

A

Sodium (Na+)

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45
Q

2 microorganisms that are metabolically dependent on each other

A

Syntrophic consortium

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46
Q

Waste product produced by acetogens that is used as an electron donor by methanogens

A

H2

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47
Q

Habitats where you would find methanogens

A
  1. Anaerobic soils of wetlands
  2. Digestive tracts
  3. Landfills
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48
Q

Compound produced by combining water and methane under very low temperatures and high pressure

A

Methane hydrate

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49
Q

Potential benefit and concern associated with the formation of methane hydrate

A

There is a lot of energy locked up in the compound, but even if a small amount is released into Earth’s atmosphere, it would have serious effects

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50
Q

Term that means “salt loving”

A

Halophilic

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51
Q

Phylum of Archaea where you would find salt-loving species

A

Euryarchaeota

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52
Q

2 pigments made by salt-loving archaea

A
  1. Bacterioruberin

2. Bacteriorhodopsin

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53
Q

Function of bacterioruberin

A

Protects halophiles from light

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54
Q

Function of bacteriorhodopsin

A

Absorbs light of a certain wavelength to generate a proton gradient to power ATP synthesis

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55
Q

Strategy used by salt-loving Archaea that enables them to survive and grow at high salt concentrations

A

Maintain high intracellular KCl concentration, have DNA with a higher G-C content, and have proteins with more acidic amino acids

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56
Q

Unique Archaeal morphology discovered by Professor Walsby

A

Square cells

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57
Q

Internal structure observed by Professor Walsby

A

Gas vesicles

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58
Q

pH range observed for salt-loving Archaea

A

7-10

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59
Q

3 examples of habitats where you can find salt-loving Archaea

A
  1. Thalassic lakes
  2. Athalassic lakes
  3. Solar salterns
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60
Q

Relationship between sensory rhodopsins, bacteriorhodopsins, and halorhodopsins

A

Paralogs

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61
Q

Relationship between bacteriorhodopsins and proteorhodopsins

A

Orthologs

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62
Q

How were proteorhodopsins discovered?

A

Metagenomic study of DNA from SAR11 with an rRNA operon

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63
Q

Metabolism of Thermococcales

A

Heterotrophs that use sulfur as a terminal electron acceptor to reduce sulfur

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64
Q

Where you would find Pyrococcus furiosus from Thermococcales

A

Deep sea vent

65
Q

Characteristic of Pyrococcus furiosus

A

Monopolar polytrichous archaella

66
Q

Where Ferroplasma get their energy

A

Oxidizing ferrous iron

67
Q

Extreme environment where Ferroplasma can grow

A

Low pH

68
Q

Method used to assemble Ferroplasma genome from biofilm samples collected from Iron Mountain mine

A

Shotgun sequencing?

69
Q

The 2 major phyla of Gram-positive bacteria

A

Phylum Firmicutes and Phylum Actinobacteria

70
Q

G-C content of Firmicutes

A

Low

71
Q

G-C content of Actinobacteria

A

High

72
Q

In what bacterial superphylum would you find Firmicutes and Actinobacteria

A

Superphylum Terrabacteria

73
Q

Characteristics of a Gram-positive bacterial membrane and cell wall

A
  1. Have thick cell walls that retain crystal violet stain
  2. Cell walls reinforced by teichoic acids
  3. No outer membrane, but have a cytoplasmic membrane
74
Q

Environment where you are most likely to encounter a high abundance of Gram-positive bacteria

A

Soil and sediment environments

75
Q

Best known genus of aerobic endospore formers

A

Bacillales

76
Q

Best known genus of anaerobic endospore formers

A

Clostridiales

77
Q

Environmental extremes that endospores are resistant to

A

Hostile physical and chemical conditions

78
Q

Cascade of these molecules drives a developmental process responsible for endospore formation

A

Sigma factors

79
Q

Induces the sigma factor cascade

A

Starvation

80
Q

Model bacterial species for the study of endospore formation

A

Bacillus subtilis

81
Q

Toxin involved in Botox

A

Botulinum

82
Q

Species that produces the toxin used in Botox

A

Clostridium botulinum

83
Q

Introduces the genes responsible for the production of Botulinum toxin

A

Phage

84
Q

How phage carrying botulinum toxin has been incorporated into bacteria

A

Lysogenic conversion

85
Q

How Epulopiscium fishelsioni produces its offspring

A

Live birth

86
Q

Genus containing one of the most primitive photosystems

A

Heliobacterium

87
Q

Very dangerous food borne pathogen that does not produce a spore but is highly motile and is invasive in people

A

Listeria monocytogenes

88
Q

System used by Listeria monocytogenes that makes it highly motile

A

Actin propulsion system

89
Q

Genus of bacteria used for producing sauerkraut

A

Lactobacillus

90
Q

Facultative anaerobic bacterium that forms clusters of cells and can result in life-threatening skin and heart infections in people

A

Methicillin-resistant Staphylococcus aureus (MRSA)

91
Q

Unique features of bacteria within the phylum Tenericutes

A
  1. Lack a cell wall
  2. Have sterols that make the membrane more rigid
  3. Obligate intracellular pathogens
92
Q

2 other species that are genetically similar enough to Bacillus cereus to be considered the same species, but have unique phenotypes

A

Bacillus anthracis and Bacillus thuringiensis

93
Q

Famous German scientist that determined the causative agent for the disease Anthrax

A

Robert Koch

94
Q

Required by the bacterium responsible for Anthrax to be fully virulent

A

2 plasmids, pxO2 and pxO1

95
Q

Encodes for an antiphagocytic capsule

A

pxO2

96
Q

Encodes for 3 exotoxin components

A

pxO1

97
Q

3 exotoxin components of pxO1

A
  1. Protective antigen
  2. Edema factor
  3. Lethal factor
98
Q

Occupations that put humans at greater risk for being exposed to the bacterium that causes Anthrax

A

Exposure to livestock, wool and hides, and laboratory settings

99
Q

The most deadly form of Anthrax

A

Inhalation

100
Q

Why the use of antibiotics is not usually effective at preventing mortality from Anthrax

A

Production of spores and delayed germination after antibiotic suppression

101
Q

Type of disease caused by Bacillus cereus

A

Foodborne illness

102
Q

Toxin produced by emetic strains of B. cereus

A

Cereulide

103
Q

Genetic element that carries the genes responsible for the toxin produced by emetic strains of B. cereus

A

Peptide produced by non-ribosomal peptide synthesis (NRPS)

104
Q

Where Bt toxin binds in an insect or other host

A

Specific receptors in the gut

105
Q

Bacterial species from which a Bt toxin is produced

A

B. thuringiensis

106
Q

Also responsible for the Bt toxin to have insecticidal activity

A

Other gut bacteria sometimes required for Bt binding

107
Q

How the Bt toxin has been used in modern agriculture

A

Used to create genetically modified plants like corn, soybeans, and cotton to protect them from insects

108
Q

Environments or hosts in which you would look for B. cereus, B. anthracis, and B. thuringiensis

A

Silkworms or flour moths?

109
Q

Environment that would be predicted to include diverse Actinobacteria species

A

Soil

110
Q

What many Actinobacteria use as a source of energy

A

Decomposing organic matter (i.e. cellulose, chitin)

111
Q

Unusual characteristics of Streptomyces species that make them highly complex with large genomes

A
  1. Produce many antibiotics
  2. Have telomeres
  3. Genome has a high G-C content
112
Q

Streptomyces life cycle

A
  1. Spore
  2. Germinating spore
  3. Vegetative mycelium
  4. Aerial hyphae
  5. Spore chains
113
Q

A compound produced in the stationary phase of life

A

Secondary metabolite

114
Q

Example of a secondary metabolite

A

Antibiotics

115
Q

Why some bacteria like Streptomyces devote considerable energy to produce secondary metabolites

A

They can help the organism compete for limited resources

116
Q

Why members of Actinobacteria were confused with fungi in the past

A

Because of convergent evolution they resemble filamentous fungi and also produce a spore

117
Q

Example of a symbiotic association between a eukaryotic host and a species of Actinobacteria

A

Leaf-cutter ants and Actinobacteria

118
Q

Select pressures that led to the convergent evolution of Actinobacteria and some fungi

A

Similar pressures form the same lifestyle of penetrating and consuming complex organic matter in terrestrial habitats

119
Q

What leaf-cutter ants gain from symbiotic association with Actinobacteria

A

Nutrients from leaves they normally wouldn’t be able to break down

120
Q

What Actinobacteria gain from their symbiotic association with leaf-cutter ants

A

Protection from fungi and place to live and nutrients

121
Q

Interactions between a Frankia species and alder plants

A

Frankia infect alder plant root cells and form nodules where biologically available nitrogen is produced while the plant provides the Frankia with sugars and food

122
Q

Why infections due to Mycobacterium species are hard to treat

A

Slow-growing and difficult to culture (antibiotics are rarely used against fast-growing bacteria and slow-growers are less affected by slowing down cell wall synthesis)

123
Q

How the Mycobacterium membrane is distinct from other bacteria

A

Form a waxy layer with mycolic acid

124
Q

A gene sequence that doesn’t produce a protein

A

Pseudogene

125
Q

What a high% of pseudogenes in a genome indicates

A

Indicates host dependence for nutrients and different processes

126
Q

Propionibacterium species metabolism

A

Ferment lactic acid (produced by lactic acid bacteria) into propionic acid (primary metabolite) and CO2

127
Q

Process responsible for the introduction of the diphtheriae toxin into Corynebacterium diphtheria

A

Lysogenic conversion due to laterial transfer of the toxin gene by the phage

128
Q

Diphtheriae toxin effect on host cell

A

Blocks protein synthesis and has degenerative effects on many organs

129
Q

Morphology of Arthrobacter cell

A

Pleomorphic

130
Q

Responsible for the “snapping division” observed when Arthrobacter cells divide

A

Bent-rod morphology causes rupture on only one side of the cell as the cell grows

131
Q

Habitat where you would expect to find Cytophaga species

A

Soil and decaying plant matter, freshwater, and sewage treatment plants

132
Q

Energy sources used by Cytophaga for metabolism

A

Degrade macromolecules like DNA, RNA, proteins, cellulose, chitin, and agar

133
Q

Motility associated with Cytophaga and Flavobacterium species and the surface involved

A

Gliding motility on solid surface

134
Q

Habitat where Rhodothermus species may be found

A

Thermophilic environments like hot springs in marine or freshwater habitats

135
Q

Habitat of Salinibacter species

A

High salt environments

136
Q

Unusual colony morphology of Flavobacterium

A

Rhizoid/plant-root like

137
Q

Pigmentation associated with Cytophaga or Flavobacterium

A

Yellow or orange

138
Q

Infected by Flavobacterium columnare

A

Fish

139
Q

Where Flavobacterium columnare colonize that eventually results in asphyxia

A

Fish gills

140
Q

What some marine Flavobacterium use as their energy source

A

Organic matter produced by algal blooms

141
Q

When organic matter isn’t available, Flavobacterium use this

A

Proteorhodopsin

142
Q

Ortholog to Proteorhodopsin

A

Bacteriorhodopsin?

143
Q

Degraded by Bacteroides in the human gut

A

Plant sugar polymers like cellulose

144
Q

Environment required by Bacteroides

A

Obligate anaerobes

145
Q

2 major contributions of Bacteroides species to humans

A

Part of a healthy gut microbiome – Catabolize plant material that could be toxic and fermentation products of plant materials can provide up to 15% of the caloric value from food

146
Q

Causes an increase in the relative abundance of Bacteroides species in the human gut

A

Eating more plant matter

147
Q

This phylum decreases in response to increased Bacteroides

A

Firmicutes

148
Q

Metabolism and habitat for members of the phylum Chlorobi

A

Photosynthetic obligate anaerobes that use hydrogen sulfide as a source of electrons; Live below cyanobacteria

149
Q

Unit that make up the branched archaeal lipids

A

Isoprenoid

150
Q

The 2 best described phyla of Archaea

A
  1. Crenarchaeota

2. Euryarchaeota

151
Q

Example of a barophilic hyperthermophile

A

Pyrodictium abyssi

152
Q

Example of a double extremophile that grows at 80C and pH 3

A

Sulfolobus solfataricus

153
Q

Carbon dioxide and hydrogen gas methanogen reaction

A

CO2 + 4H2 -> CH4 + 2H2O

154
Q

Example of syntrophic consortium

A

An acetogen + a methanogen

155
Q

Halorhodopsin function

A

Pumps in Cl-

156
Q

Detects and moves toward red light

A

Sensory rhodopsin I

157
Q

Activated by blue light and initiates a reverse motor

A

Sensory rhodopsin II

158
Q

Model Streptomyces species

A

Streptomyces coelicolor

159
Q

How lactic acid bacteria make ATP

A

Substrate-level phosphorylation

biol 6250 (1 decks)

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