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46 Cards in this Set

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what are the steps to compare a new prokaryote to an existing one phylogenetically?
1. Seq 16srna of new org, primers to conserved portion, isolate genomic dna, perform pcr, clone pcr product and sequence clone or pcr
2. compare 16srna in database to pcr sequence
3. phylogenic analyses to determine relatedness
Where does comparison of 16srna fit into assigning taxonomic units to a new prokaryote?
you can determine if they are in the same genus but comparing 16srna
Strains are considered to be in the same species if what criteria are met?
similiar mole percent g+c and 70% or greater dna dna reassociation
how do you determine mol% g+c?
SHT 1) Sequence entire genome and count g+c 2) hydralyze dna and count each base with hplc 3) thermal denaturation -heat and break h bonds strand seperate and increases ability to absorb light measure with spectrophotmeter
which bondings are stronger g-c or a-t?
what is the midpoint temperature directly related to?
mol % g+c
what is the range of mol%g+c in bacteria?
largest range 20-80%
what is the range of mol%g+c in archaea?
what is the range of mol%g+c in eukaryotes?
smallest for humans and animals
because mol%g+c doesn't provide info about linear arrangement - what does?
dna dna hybridization or reassociation
in dna dna hybridization - what is determined?
amount of reannealing not actual order of bases
what is dna dna reassociation protocol? control
place radioactive labeled single dna with unlabeled dna, heat and cool so that it reanneals. use nuclease to get rid of single stranded, collect double on a filter and count radiolabeled ones.
what is dna dna reassociation protocol? actual experiment
mix unlabeled from new strain with radiolabeled dna from control, heat, cool , anneal, nuclease, collect radiolabled dna if 70% or above than control =strains in same species
how many phyla do archea have?
how many phyla do bacteria have?
how can certain strains exist if no strains representative of them have yet been isolated?
dna can be extracted from natural env and genes amplified by pcr and gene sequences determined. 1 gram soil-extract dna-pcr-clone pcr seq-seq indiviual clones- compare to database
what are the 3 phyla of archeae?
which contains the most thermaphilic organisms known?and where are they found?
crenacheota , in ocean vents
what groups does eucaryarcheota contain and what do each do?
methanogens make methane out of C, halophiles live in saturated salt, hyperthermaphiles
where are koracheota been identified at and what group?
in hot springs, no strains isolated and thermophilic
what are the 23 phyla for bacteria?
proteobacteria firmicutes actinobacteria cholorflexi chlorobi cyanobacteria aquificae thermatogae thermamicrobia thermodesulfobacteria deinococcus bacteriodes planctomycetes chlamydiae veruccomicrobia spirochetes fibrobacteres acidobacteria fusobacteria dictyglomi nitrospiraa defurribacteres chrysiogenetes
large and diverse group , contains all 4 nutritional groups, enteric-ecoli symbiotic-agrobacterium prsthecate and myxobacteria sliding
which PS bacteria are included in proteobacteria?
purple sulfur and purple non sulfur
2 firmicutes
gram + (including mycoplasma which stains -), no cell wall just membrane , unicellular low mol%gc
which PS bacteria is in firmicutes?
3 actinobacteria
gram +, uni and multi cellular, soil bacteria like bacillus and streptomyces, high mol%gc
4 chloroflexi
green gliding bacteria, complex nutritional req, grow photosyn or chemoheterotrophs PS
5 chlorobi
green sulfur bacter PS
6 cyanobacteria
unicellular or multicellular PS
7 aquificae
hydrogen autotrophs - most thermophilic
8 thermotogae
fermentative, thermophiles and hyperthermophiles
9 thermomicrobia
thermphiles in hot springs
10 thermodesulfobacteria
thermo sulfur reducing bacteria
11 deinococcus
resistant to gamma radiation and uv light , thermophiles worldwide in tap water
12 bacteriodes
aerobes and anerobes, human colon
13 planctomycetes
budding unicellular or multicellular - lack peptidoglycan
14 chylmidia
obligate intracellular parasite - no peptidoglycan
chly tstacci
chly trachomatis
disease in birds
eye disease or venereal disease
15 veruccomicrobia
soil bacteria 3% of microbes in soil
16 spirocheates
helical with axial filament
17 fibrobacteres
anerobic live in GI track
18 acidobacteria
variety of soil env
19 fusobacteria
obligate anerobes found in oral and intestinal tracks
20 dictyglomi
thermophilic obligately anerobic fermentative bacteria
what are the last 3 bacteria phyla?
what tests are too time consuming?
phylogenetic tests and dna dna reassociation
what methods can be used to rapidly determine at least the genus and possible species?
do archaea produce fatty acid?
1- 10-20 phentypic tests
2-fatty acid profiles - extract from cells and analyze on gas chromotograph compare to database
3-nucleic acid probes - radioactive or flur single dna/rna probe hybridizes with a seq for a certain species