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General Microbiology > Microbial Taxonomy and Systematics > Flashcards

Microbial Taxonomy and Systematics Flashcards

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1
Q

involves not just naming organisms but grouping them with other organisms that share common properties

A

Taxonomy

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2
Q

is involved in the classification and naming of organisms

A

taxonomy

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3
Q

is involved in the determination of evolutionary relationships of organisms.

A

systematics

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4
Q

ascertain the sharing of the common ancestry by different organisms

A

systematics

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5
Q

different organisms are scientifically named and grouped in different taxonomic levels

taxonomy or systematics?

A

taxonomy

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6
Q

organisms are grouped based on their evolutionary relationships.

systematics or taxonomy

A

systematics

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7
Q

can be considered as a branch of systematics

A

taxonomy

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8
Q

assigns every organism a kingdom, phylum, class, order, family, genus, and species, which, among other possibilities,

A

Linnean system of classification

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9
Q

mnemonic of Linnean system of classification

A

Kingdom
Phylum
Class
Order
Family
Genus
Species

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10
Q

. It was in 1735 when the two-kingdom system, Plantae and Animalia was formally introduced by Swedish botanist

A

Carolus Linnaeus

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11
Q

proposed to include bacteria and fungi in the plant kingdom

A

Carl von Nägeli

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12
Q

proposed the Kingdom Protista, to include bacteria, protozoa, algae, and fungi.

A

Ernst Haeckel

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13
Q

. The term prokaryote was then introduced in 1937 by

A

Edouard Chatton

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14
Q

what term is introduced to distinguish cells having no nucleus from the nucleated cells of plants and animals

A

prokaryote

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15
Q

cells in which the nuclear material (nucleoplasm) is not surrounded by a nuclear membrane

who defined prokarytoes this way

A

Roger Stanier

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16
Q

proposed the Kingdom Prokaryotae

A

Robert G.E. Murray

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17
Q

founded the five-kingdom system in which prokaryotes were placed in the Kingdom Prokaryotae, or Monera, and eukaryotes comprised the other four kingdoms.

A

Robert H. Whittaker

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18
Q

names only clades — groups of organisms that descended from a common ancestor.

A

phylogenetic classification system

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19
Q

DNA sequence-based phylogenetic analysis has revealed that the five kingdoms do not represent five primary evolutionary lines. Instead, cellular life on Earth has evolved along three primary lineages called

A

domains

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20
Q

contains the eukaryotes including the plants, animals, fungi, and protists.

what domain

A

Eukarya

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21
Q

Molecular studies in the 1970s revealed that the Archaea differed from all other bacteria in their what sequence and what structures

A

16s rRNA sequence
cell wall
membrane lipids
aspects of protein snythesis

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22
Q

are excellent tools for discerning evolutionary relationships because all cells contain ribosomes

A

rRNA (ribosomal RNAs)

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23
Q

an American microbiologist, pioneered the use of comparative rRNA sequence analysis as a measure of microbial phylogeny and, in so doing, revolutionized our understanding of cellular evolution.

A

Carl Woese

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24
Q

the greater the sequence variation between any two organisms, the greater/lesser their evolutionary divergence.

A

greater

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25
Q

The phylogenetic tree of life reveals two very important evolutionary facts:

A

(1) all prokaryotes are not phylogenetically closely related

(2) Archaea are actually more closely related to Eukarya than to Bacteria

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26
Q

The universal tree of life shows that LUCA resides very early within the ___ domain

A

Bacteria

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27
Q

largest group of bacteria

A

Proteobacteria

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28
Q

the most phylogenetically ancient phylum contains the genus

A

Aquifex

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29
Q

which are hyperthermophilic H2 (Hydrogen) – oxidizing chemolitotrop

A

Aquifex

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30
Q

green non-sulfur bacteria

A

Chloroflexus

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31
Q

follows Aquifex as the most phylogenetically acient phylum (3)

A

Thermodesulfobacterium
Thermotoga
Chloroflexus

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32
Q

the phototrophic green sulfur bacteria

A

Spirochetes

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33
Q

chemoorganotrophic bacteria (2)

A

Flavobacterium
Cytophaga

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34
Q

budding bacteria

A

Plantomyces

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35
Q

Verrucomicrobium group

A

Chlamydia

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36
Q

gram positive bacteria (2)

A

actinobacteria
firmicutes
mollicutes

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37
Q

along with his colleagues, constructed the phylogenetic trees for the prokaryotes, which showed evolutionary relatedness

A

Carl Woese

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38
Q

which differ from bacteria by its cell wall and plasma membrane chemistry, as well as the sequences of its 16S rRNA

A

Archaea

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39
Q

does Archaea and Bacteria have the same genetic material?

A

Yes

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40
Q

which domains have histones

A

Archaea
Eukarya

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41
Q

gene strucuture for three domains of life

introns absent/present

A

A = absent
B = absent
E = present

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42
Q

plasmids for three domains of life

common/rare

A

A = common
B = common
E = rare

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43
Q

polycistronic mRNA presence in three domains of life

present/absent

A

A = present
B = present
E = absent

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44
Q

ribosomes in three domains of life

70s/80s

A

A = 70s
B = 70s
E = 80s

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45
Q

which three domains of life are sensitive to streptomycin, chloramphenicol

A

Bacteria

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46
Q

initiator tRNA for each domain of life

A

A = Methionine
B = N-formyl methionine
C = Methionine

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47
Q

membrane fatty acids in three domains of life

ether linked, branched/ ester-linked, straight

A

A = ether-linked, branched
B = ester-linked, straight
E = ester-linked, straight

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48
Q

internal organelles presence in three domains of life

A

A = absent
B = absent
E = present

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49
Q

site of energy generation in three domains of life

A

A = cytoplasmic membrane
B = cytoplasmic membrane
E = mitochondira

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50
Q

presence of muramic in the cell wall in three domains of life

A

A = muramic acid absent
B = muramic acid present
E = muramic acid absent

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51
Q

have flattened square or triangular cells in domain Archaea

A

Haloarcula

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52
Q

which is composed of different substituted L-amino acids and polysaccharides

A

pseudomurein

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53
Q

have cell walls composed of a layer of proteinaceous subunits known as an ___, which is directly associated with the cell membrane

A

S-layer

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54
Q

This difference actually makes the Archaean members not susceptible to antibiotics such as penicillin and lysozyme, whose antibacterial action is specifically directed to peptidoglycan.

A

S-layer in Archaea

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55
Q

membranes, in which the lipid component of the part contains branched isoprenes instead of fatty acids

what domains

A

Archaea

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56
Q

found in extreme environments

A

Archaea

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57
Q

can live well at over 100 C what kind of Archaea

A

thermophilic

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58
Q

forms of Archaea can thrive in very cold environments, like in the Antarctic

A

psychropilic

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59
Q

The reason that this lay undetected for so long is that these organisms cannot as yet be cultured in the laboratory, and their presence can only be inferred by the use of modern DNA-based analysis

A

Archaea

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60
Q

The oldest known fossils are the remains of ____ that lived more than 3.5 billion years ago.

A

prokarytoes

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61
Q

cells evolved more recently, about 2.5 billion years ago

A

Eukaryotic cells

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62
Q

according to this theory, eukaryotic cells evolved from prokaryotic cells living inside one another, as endosymbionts

A

endosymbiotic theory

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63
Q

The original nucleoplasmic cell was prokaryotic. However, infoldings in its plasma membrane may have surrounded the nuclear region to produce a true

A

nucleus

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64
Q

endosymbiotic prokaryotes give rise to what organelles

A

mitochondria
chloroplast

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65
Q

organism in which the eukaryotic host and bacterium require each other for survival

A

Cyanophora paradoxa

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66
Q

Phylogenetic trees of species in the domain Eukarya have been constructed from comparative sequence analysis of what rRNA gene

A

18s

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67
Q

appears to give a skewed view of eukaryotic microbial evolution, it still clearly sorts the eukaryotes out as a distinct domain of life with evolutionary roots more closely tied to the Archaea than to the Bacteria.

A

18s rRNA sequencing

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68
Q

is the actual naming of organisms and follows the binomial system of nomenclature

A

Nomenclature

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69
Q

Nomenclature is the actual naming of organisms and follows the binomial system of nomenclature devised by the Swedish medical doctor and botanist

A

Carl Linnaeus

70
Q

The creation of new names of Bacteria must follow the rules described in

A

The International Code of Nomenclature of Bacteria

71
Q

Because taxonomy is largely a matter of scientific judgment, there is no “official” classification of Bacteria and Archaea. Presently, the classification system most widely accepted by microbiologists is that of

A

Bergey’s Manual of Systematic Bacteriology

72
Q

, a reference that provides detailed information on the enrichment, isolation, and culture of Bacteria and Archaea

A

The Prokaryotes

73
Q

. A major vehicle for the description of new taxa is the

A

International Journal of Systematic and Evolutionary Microbiology (IJSEM)

74
Q

the official publication of record for the taxonomy and classification of Bacteria and Archaea.

A

IJSEM

75
Q

is the study of the diversity of organisms and their relationships

A

systematics

76
Q

traditionally has focused on practical aspects of identification and description, activities that have relied heavily on phenotypic comparisons

A

bacterial taxonomy

77
Q

This polyphasic approach to taxonomy uses three kinds of methods (3)

A

phenotypic
genotypic
phylogenetic

78
Q

analysis examines the morphological, metabolic, physiological, and chemical characteristics of the cell

what analysis

A

phenotypic

79
Q

analysis considers characteristics of the genome

what analysis

A

Genotypic

80
Q

Colony morphology; Gram reaction; cell size and shape; pattern of flagellation; presence of spores, inclusion bodies (e.g., PHB,a glycogen, or polyphosphate granules, gas vesicles, magnetosomes); capsules, S-layers or slime layers; stalks or appendages; fruiting-body formation

what category

A

morphology

81
Q

Motility Nonmotile; gliding motility; swimming (flagellar) motility; swarming; motile by gas vesicles

what category

A

motility

82
Q

Mechanism of energy conservation (phototroph, chemoorganotroph, chemolithotroph); utilization of individual carbon, nitrogen, or sulfur compounds; fermentation of sugars; nitrogen fixation; growth factor requirements

what category

A

metabolism

83
Q

Physiology Temperature, pH, and salt ranges for growth; response to oxygen (aerobic, facultative, anaerobic); presence of catalase or oxidase; production of extracellular enzymes

what category

A

physiology

84
Q

Cell lipid chemistry Fatty acids; polar lipids; respiratory quinones

what category

A

cell lipid chemistry

85
Q

Cell wall chemistry Presence or absence of peptidoglycan; amino acid composition of cross-links; presence or absence of cross-link interbridge

what category

A

cell wall chemistry

86
Q

other traits for phenotypic characteristics

A

Cell wall chemistry Presence or absence of peptidoglycan; amino acid composition of cross-links; presence or absence of cross-link interbridge

87
Q

genotypic method that Genome-wide comparison of sequence similarity. Useful for distinguishing species within a genus

A

DNA-DNA hybridization

88
Q

Ribotyping (Section 16.9), AFLP, rep-PCR (Figure 16.21). Rapid method to distinguish between species and strains within a species

genotypic method

A

DNA profiling

89
Q

strain typing using DNA sequences of multiple genes (Figure 16.22). High resolution, useful for distinguishing even very closely related strains within a species

what genotypic methods

A

Multilocus sequence typing

90
Q

Percentage of guanine–cytosine base pairs in the genome. If the GC ratio of two organisms differs by more than about 5%, they cannot be closely related, but organisms with similar or even identical GC ratios may be unrelated. Not much used now in taxonomy because of poor resolution

what genotypic method

A

GC ratio

91
Q

The evolutionary history of a group of organisms is called its

A

phylogeny

92
Q

___ is inferred indirectly from nucleotide sequence data. Our premises are that (1) all organisms are related by descent, and (2) that the sequence of DNA in a cell’s genome is a record of the organism’s ancestry.

A

phylogeny

93
Q

is a process of inherited nucleotide sequence change, comparative analyses of DNA sequences allow us to reconstruct phylogenetic histories

A

evolution

94
Q

The most widely used and useful for defining relationships in prokaryotes is the gene encoding

A

16s rRNA (prokaryotes)
18s rRNA (eukaryotes)

95
Q

sequences of shared evolutionary ancestry that encode functionally equivalent molecules.

A

homologous sequences

96
Q

If sequences do change at a constant rate, such pairs would serve as an approximate

A

molecular clock

97
Q

relies heavily on the polymerase chain reaction (PCR) to obtain sufficient copies of a gene for reliable sequencing

A

DNA sequence

98
Q

analysis of DNA sequences that are related by common ancestry

A

homology

99
Q

Once the DNA sequence of a gene is obtained, the next step in phylogenetic analysis is to align that sequence with homologous sequences from other organisms. By doing this, nucleotide mismatches and insertions and deletions, some of which may be phylogenetically informative, can be pinpointed.

what analysis

A

sequence alignment

100
Q

which is a graphic depiction of the relationships among sequences of the organisms under study, much like a family tree.

A

phylogenetic tree

101
Q

branches represent species that exist now and from which the sequence data were obtained.

what part of phylogenetic tree

A

tips

102
Q

are points in evolution where an ancestor diverged into two new organisms, each of which then began to evolve along its separate pathway.

what part of phylogenetic tree

A

nodes

103
Q

define both the order of descent and the ancestry of the nodes,

what part of phylogenetic tree

A

branches

104
Q

represents the number of changes that have occurred along that branch.

A

branch length

105
Q

combines phenotypic, genotypic, and sequence-based phylogenetic data within a framework of standards and guidelines for describing and identifying prokaryotes, but the issue of what actually constitutes a prokaryotic species remains controversial

A

microbial systematics

106
Q

is defined operationally as a group of strains sharing a high degree of similarity in several independent traits.

A

prokaryotic species

107
Q

Traits currently considered most important for grouping strains together as a species include ___% or greater genomic DNA–DNA hybridization

A

70 percent

108
Q

percent or grater identity in 16s rRNA sequence to group strains together as a species

A

98%

109
Q

How do new prokaryotic species arise? A likely possibility is by the process of

A

periodic purges and selection

110
Q

If cells in this population share a particular resource (for example, a key nutrient), the population is considered an

A

ecotype

111
Q

Biological systematics encompasses three distinct activities:

A

taxonomy
classification
nomeclature

112
Q
A
113
Q

commonly used outside the biological
systematic community as almost any animate or inanimate object, place, concept or event can be
classified according to some criteria or scheme.

A

classification

114
Q

e act of assigning individuals to a class or
classes based on some common relations or affinities.

A

classification

115
Q

classifications may be represented by assignment of ‘taxonomic’ rank (species, genera, families,
superfamilies, orders etc.) or by evolutionary scenarios.

what systematics

A

evolutionary systematics

116
Q

interacts with both taxonomy and nomenclature

A

classification

117
Q

view natural groups as those taxa linked by the greatest similarity to one another

A

phenetists

118
Q

s consider natural groups to be monophyletic, and natural classifications to reflect
organismal history.

A

cladist

119
Q

e is defined as referring to
the most recent Common ancestor of two designated taxa and its descendants

A

node

120
Q

defined as referring to all organisms sharing a more recent common
ancestor with one designated taxon than with a second such taxon (

A

stem

121
Q

defined as referring to the first ancestor to evolve a designated character (bar) and its
descendants (

A

apomorphy

122
Q

Science of classification,
Objective: classify, establish
relationship and differences
The theory and practice…
Reference for newer microorganisms
A universal language for scientist

A

Taxonomy

123
Q

determination of the evolutionary
relationship/common ancestry
consists of both taxonomy and evolution.
Involves cladistics, and phylogenetics.

A

Systematics

124
Q

refers to the classification of
organisms based on the branching of
different lineages from a common
ancestor.

A

Cladistics

125
Q

refers to the study of the
history of evolution and the relationship
among groups of organisms.

A

Phylogenetics

126
Q

§ assigns every organism a kingdom, phylum, class, order,
family, genus, and species, which, among other possibilities,
has the handy

A

Linnean System

127
Q

§ Two-kingdom System

A

Linnean System

128
Q

created long before scientists understood that organisms
evolved.

§ not based on evolution; most biologists are switching to a
classification system that reflects the organisms’ evolutionary
history.

A

Linnean system

129
Q

inclusion of bacteria and
fungi in plant kingdom

who included

A

Carl von Nageli

130
Q

who defined - definition
of prokaryote

A

Edouard Chatton
Roger Stanier

131
Q

proposed the Kingdom
Prokaryotae.

A

Robert G.E Murray

131
Q

addition of
Kingdom Protista to
include bacteria, protozoa,
algae, and fungi

who

A

Ernst Haeckel

132
Q

§ A phylogenetic tree based on 16s rRNA gene data, showing the
separation of bacteria, archaea, and eukaryotes by

A

Carl Woese

133
Q

also differ in their cell wall structure, membrane lipids and
aspects of protein synthesis from bacteria.

A

Archaea

134
Q

major taxonomic treatment
of Bacteria and Archaea.

A

Bergey’s Manual of Systematic Bacteriology

135
Q
  • a
    reference that provides
    detailed information on the
    enrichment, isolation, and
    culture of Bacteria and
    Archaea
A

The Prokaryotes

136
Q

gramnegative cell walls, thinskinned i.e E. coli

A

Proteobacteria

137
Q

– gram-positive
cell walls, thick skinned i.e.
bacilli

A

Firmicutes

138
Q

– lack a cell
wall & are soft i.e
Mycoplasma

A

Tenericutes

139
Q

– i.e
actinomycetes

A

Actinobacteria

140
Q

group of microorganisms (5)

A

bacteria (archeans, eubacteria)
protists (algae, protozans, slime molds)
fungi (yeast and molds)
helminths
viruses, viroids, prions (acellular)

141
Q

not classified as part of
any of the three domains.

A

virus

142
Q

population of
viruses with similar characteristics
(including morphology, genes, and
enzymes) that occupies a particular
ecological niche ~ International
Committee on Taxonomy of Viruses

A

viral species

143
Q

Closely related organisms that can interbreed

A

eukaryotic species

144
Q

population of cells with similar characteristics.

A

prokaryotic species

145
Q

– pure cultures of one species which are
not 100% identical

A

strain

146
Q

Traits currently considered most important for
grouping strains together as a species
* __% or greater genomic DNA–DNA
hybridization

A

70

147
Q

Traits currently considered most important for
grouping strains together as a species

___% or greater identity (3% difference) in
16S rRNA gene sequence

A

97

148
Q

Which among can be used to classify/identify microorganisms? (Select all that applies)

using 16s rRNA
DNA fingerprinting
interbreeding behaviors
ecological characteristics
morphologic characteristics

A

morphologic characteristics
using 16S rRNA
DNA fingerprinting

149
Q

During the second golden age of microbiology, __ was established as the __ material

A

DNA
genetic

150
Q

Which field of microbiology studies bacterial taxonomy and systematics

A

Evolutionary microbiology

151
Q

cell membrane with lipid monolayer

A

Archaea

152
Q

includes the mitochondria and chloroplast

A

bacteria

153
Q

with multiple linear chromosomes

A

eukarya

154
Q

Koch established the postulate for the __ theory

A

germ

155
Q

Whose discovery paved the way to unraveling the microscopic world of bacteria?

A

Leeuwenhoek

156
Q

Microbiology became established during the times when spontaneous generation theory was being promoted.

T/F

A

False

157
Q

Who among the following disproved the theory of abiogenesis? (Select all that applies)

Pasteur
Spallanzani
Rediehrlich
needham
Leeuwenhoek

A

Pasteur
Spallanzani
Redi

158
Q

first man (Y chromosome) is what race

A

African

159
Q

LUCA means

A

Last Universal Common Ancestor

160
Q

similar to bacteria (compared to eukarya)

A

mitochondrial gene

161
Q

one gene > one mRNA > 1 protein (___)
one gene > one mRNA > 3 protein (___)

A

traditionally
polycystronic

162
Q

plasmids is only present in what eukaryotic organism

A

yeast

163
Q

ribosomes in eukarya

A

80s
70s (mitochondrion)

164
Q

(additional properties, characteristics of a species

A

strain

165
Q

smell during the rainy season
- look like fungi when grown in culture bacteria

A

actinobacteria

166
Q

are not included in the domain because they do not have ribosomes

A

viruses

167
Q

species can be determined based on
___

A

reproducibility

168
Q

n cooked rice, spores germinate causing sliminess or ice

A

bacillus cereus

169
Q

causes anthrax

A

Bacillus anthracis

General Microbiology (8 decks)

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