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bacterio & viro > taxonomy & phylogeny > Flashcards

taxonomy & phylogeny Flashcards

1
Q

three domains

A

-bacteria
-archaea
-eukarya

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2
Q

membrane enclosed nucleus

A

-bacteria: no
-archaea: no
-eukarya: yes

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3
Q

DNA complexed with histones

A

-bacteria: no
-archaea: some
-eukarya: yes

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4
Q

chromosomes

A

-bacteria:
=usually one circular chromosome
=chromosomes have single origin
of replication
=some are polyploid
-archaea:
=one circular chromosome
=some have chromosomes w/
multiple origins of replication
=some are polyploid
-eukaryotes:
=multiple
=linear chromosomes w/ multiple
origins of replication

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5
Q

plasmids

A

-bacteria: very common
-archaea: very common
-eukarya: rare

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6
Q

introns in genes

A

-bacteria: rare
-archaea: rare
-eukaryotes: yes

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7
Q

nucleolus

A

-bacteria: no
-archaea: no
-eukarya: yes

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8
Q

mitochondria, chloroplasts, ER, golgi body & lysozymes observed

A

-bacteria: no
-archaea: no
-eukarya: yes

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9
Q

plasma membrane lipids

A

-bacteria:
=ester-linked phospholipids
=some have sterols
-archaea:
=glycerol diethers
=diglycerol teraethers
-eukarya:
=ester-linked phospholipids
=sterols

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10
Q

flagella

A

-bacteria:
=sub-microscopic in size
=filament composed of single type
of flagellin protein
-archaea:
=sub-microscopic in size
=some filaments composed of
more than one type of archaellin
protein
-eukarya:
=microscopic in size
=membrane bound
=usually 20 microtubules in 9+2
pattern

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11
Q

peptidoglycan in cell walls

A

-bacteria: yes
-archaea: no
-eukarya: no

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12
Q

ribosome size and structure

A

-bacteria:
=70S
=3 rRNAs
=~55 ribosomal proteins
-archaea:
=70S
=most have 3rRNAs
=~68 ribosomal proteins
-eukarya:
=80S
=4rRNAs
=~80 ribosomal proteins

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13
Q

cytoskeleton

A

-bacteria: rudimentary
-archaea: rudimentary
-eukarya: yes

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14
Q

gas vesicles

A

-bacteria: yes
-archaea: yes
-eukarya: no

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15
Q

bacterial taxonomy

A

DOMAIN: Bacteria
PHYLUM: Proteobacteria
KINGDOM: none
CLASS: γ-Proteobacteria
ORDER: Pseudomonadales
FAMILY: Psuedomonadaceae
GENUS: Pseudomonas
SPECIES: aeruginosa

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16
Q

microbial species

A

a collection of strains that share many stable properties and differ significantly from other groups
-collection of strains w/ similar G+C composition and >70% similarity using DNA-DNA hybridisation experiments

17
Q

concept of microbial species

A

may get divisions within species if a group of strains exhibit some distinct difference to other strains within that species

18
Q

strain

A

descendants of a single, pure microbial culture
-biovars: biochemical /
physiological variants
-morphovars: morphological
variants
-serovars: serogenic / antigenic
(immunologically
reactive) variants
-pathovars: pathogenic variants

19
Q

core genome

A

-set of genes found in all members of a species
-minimal set of genes required by microbe to survive
-‘house-keeping genes’ (e.g. replication, transcription, translation, core metabolism)

20
Q

accessory genome

A

-more recently acquired, non-essential genes
-enable colonisation of new niches (inc. hosts)
-not possessed by all members of a species
-often acquired via HGT (mobile genetic elements)

21
Q

pan genome

A

-combination of all genes found within a species

22
Q

horizontal gene transfer (HGT)

A

-prokaryotes are able to exchange genetic material via HGT
-make phylogenetic analyses more complicated

23
Q

mechanisms of HGT

A

-bacterial transformation
-bacterial transduction
-bacterial conjugation

24
Q

polyphasic taxonomy

A

multiple classifications systems used in identifications of a novel microbe
-phenetic classification:
-genotypic classification:

25
Q

phenetic classification

A

-compares phenotypic similarities between organisms
-classification based on phenotype
-traits: morphology/physiology
-microbial example:
=Clostridium spp. (anaerobic,
endospore-forming, gram +ve
rod)
-compared to
=Bacillus spp. (aerobic, endospore-
forming, gram +ve rod)

26
Q

genotypic classification

A

-compares genetic similarity between organisms
-classification based on genes and genomes
-traits: avg. nucleotide identity rRNA genes
-microbial example:
=E.coli
-compared to:
=Salmonella enterica

27
Q

phenetic classification

A

-morphological
-physiological & metabolic
-biochemical
-ecological

28
Q

morphological

A

-colony morphology and colour
-microscopic features (e.g. cell shape, size, ultrastructural features)
-cellular inclusions
-staining behaviour (e.g. Gram stain)
-spore morphology and location

29
Q

physiological & metabolic

A

-cell wall components
-motility (e.g. pili, flagella, surfactants)
-nutritional requirements + energy sources
-fermentation products
-secondary metabolites produced
-photosynthetic pigments
-oxygen requirements
-pH optima
-temperature optima
-osmotic tolerance
-luminescence
-sensitivity to antibiotics / inhibitors

30
Q

biochemical

A

-fatty acid methyl ester (FAME) analysis reveals diff. in chain length, degree of saturation, branching + hydroxyl groups
-matrix-laser desorption/ionisation-time of flight (MALDI-ToF) analysis reveals the masses of many highly abundant proteins
-neither technique is used to classify a novel species

31
Q

ecological

A

-colonisation of specific niches, typically linked w/ physiological characteristics (e.g. O2 req., temp. range, pH range + osmotic tolerance)
=pathogenesis / host specificity
=symbiotic relationships

32
Q

genotypic classification

A

-nucleic acid base composition
-nucleic acid hybridisation
-genetic fingerprinting
-nucleic acid sequencing

33
Q

nucleic acid base composition

A

-mol% G+C content = G+C / (G+C+A+T) x 100
-determined either by genome sequencing or from melting temp. of DNA (G+C=3 bonds harder to separate than A+T=2 bonds)
-difference of 10% in G+C content suggests different groups

34
Q

nucleic acid hybridisation

A

-outdated technique
-DNA-DNA hybridisation of genomes from two diff. organisms
-heat -> ssDNA then cool to 25°C below temp allows complementary strands to reassociate to dsDNA
-heat -> ssDNA then cool to 30-40°C below temp allows similar, but non-identical strands to form less stable dsDNA hybrids
-probe genome ssDNA bound to membrane w/ radioactively labelled ssDNA at appropriate temp, wash + then measure amount of radioactivity
=(compared to control of
radioactively labelled homologous
DNA)

35
Q

genomic fingerprinting

A

restriction fragment length polymorphism (RFLP)
-PCR amplify rRNA gene + digests
w/ restriction endonucleases,
agarose gel electrophoresis
=if nucleotide seq. differs the
band pattern will differ
ribotyping
-entire genome digested w/ one or
more restriction enzymes, agarose
gel electrophoresis, transfer to
nylon filter, probe w/ labelled rRNA
probe(s)

36
Q
A

bacterio & viro (1 decks)

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