taxonomy & phylogeny

Question 1

three domains

Answer 1

-bacteria
-archaea
-eukarya

Question 2

membrane enclosed nucleus

Answer 2

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

Question 3

DNA complexed with histones

Answer 3

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

Question 4

chromosomes

Answer 4

-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

Question 5

plasmids

Answer 5

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

Question 6

introns in genes

Answer 6

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

Question 7

nucleolus

Answer 7

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

Question 8

mitochondria, chloroplasts, ER, golgi body & lysozymes observed

Answer 8

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

Question 9

plasma membrane lipids

Answer 9

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

Question 10

flagella

Answer 10

-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

Question 11

peptidoglycan in cell walls

Answer 11

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

Question 12

ribosome size and structure

Answer 12

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

Question 13

cytoskeleton

Answer 13

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

Question 14

gas vesicles

Answer 14

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

Question 15

bacterial taxonomy

Answer 15

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

Question 16

microbial species

Answer 16

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

Question 17

concept of microbial species

Answer 17

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

Question 18

strain

Answer 18

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

Question 19

core genome

Answer 19

-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)

Question 20

accessory genome

Answer 20

-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)

Question 21

pan genome

Answer 21

-combination of all genes found within a species

Question 22

horizontal gene transfer (HGT)

Answer 22

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

Question 23

mechanisms of HGT

Answer 23

-bacterial transformation
-bacterial transduction
-bacterial conjugation

Question 24

polyphasic taxonomy

Answer 24

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

Question 25

phenetic classification

Answer 25

-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)

Question 26

genotypic classification

Answer 26

-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

Question 27

phenetic classification

Answer 27

-morphological -physiological & metabolic -biochemical -ecological

Question 28

morphological

Answer 28

-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

Question 29

physiological & metabolic

Answer 29

-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

Question 30

biochemical

Answer 30

-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

Question 31

ecological

Answer 31

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

Question 32

genotypic classification

Answer 32

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

Question 33

nucleic acid base composition

Answer 33

-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

Question 34

nucleic acid hybridisation

Answer 34

-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)

Question 35

genomic fingerprinting

Answer 35

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)