taxonomy- bacteria Flashcards
name the 3 different aspects of taxonomy
1) nomenclature
2) identification
3) classification
binomial system developed by —– is used to name all cellular organisms, including microorganisms.
carl linnaeus
each organism is given 2 names, explain:
1) a generic name (genus) - homo
2) a specific name (species) - sapiens
—– were original classified in the class of chaos
animalcules
name the taxonomic categories
domain kingdom phylum class order family genus species
classification is based on:
1) overall similarity (phenetic)
2) evolutionary relationships (phylogenic)
a species is:
a group of organisms that can interbreed
most microorganisms reproduce —-
asexually
the evolutionary history of micro-organism is —–
very incomplete
the earth is about —– yo
first evidence of microbial life can be found in rocks —- yo
- 5
3. 5
what are stromatolites
these are microbial mats consisting of layers of filamentous prokaryotes, sediments and extracellular matrix. they fossilize very well
compare ancient and modern age stromatolites
ancient: anoxygenic phototrophic filamentous bacteria
modern: oxygenic phototrophic cyanobacteria
early earth was — and much —- than present day
anoxic, hotter
surface origin hypothesis:
the first membrane enclosed, self replicating cells arose out of primordial soup rich in organic and inorganic compounds in ponds on earth’s surface.
in other words organic molecules assembled into something bigger
*** you need organic molecules
what factors argue against surface origin hypothesis
temperature fluctuations, mixing from meter impacts, dust clouds and storms
subsurface origin hypothesis
life originated in hypothermal springs on the ocean floor because it is warmer and more nutrients are available.
- steady and abundant supply of org (H2 and H2S) was likely available at these sites
first replicating system may have been — based
RNA
RNA can bind —- molecules
small e.g. ATP, other nucleotides
RNA has —- activity. may have catalyzed its own synthesis
catalytic
DNA/ RNA is a more stable molecules. THUS, —–
DNA, becoming the genetic repository
3 part systems evolved and became universal among cells
protein, DNA, RNA
Name other important steps in the emergence of cellular life (besides dan,rna and protein )
1) build up of lipids
2) synthesis of phospholipid membrane vesicles
3) assembly of vesicles catalyzed by the clay of the mound, produce cytoplasmic membrane
LUCA
last universal common ancestor – population of early cells from which cellular life may have diverged into ancestors of modern day bacteria and archaea
as early earth was anoxic, nrg generating metabolism of primitive cells was:
carbon source:
hydrogen source:
anaerobic and likely chemoautotrophic
co2, nrg and electron source
H2S reacting with FeS –> present in hydrothermal mounds
use atpase
early form of —– and —– support the production of large amounts of organic compounds
chemoautotrophic, photoautotrophic metabolism
organic material provide an abundant, diverse and continually renewed source of —– —- —- , stimulating evolution of various ——— metabolisms
reduced organic carbon, chemoheterotrophic
numerical taxonomy
traditional method for the classification of prokaryotes introduced by Michael Adanson
conditions for numerical taxonomy
1) all characteristics should be considered of equal importance (unbiased)
2) classification should be grouped based on overall similarity
3) classification should be based on as many features as possible
similarity coefficient or the jacquard coefficient
a large number of characteristics are determined for each organism and the similarities between pairs of microorganisms are then calculated and expressed as the S or the Sj coefficient
dendrogram
a type of graph constructed to illustrate the relationship between species
phenol
group of organisms that have characters in common
S formula
shared / tot # tested
Sj formula
shared/tot # tested # neg for both
What is a mutation
a change in the genome of an organism (nucleotide change, insertion,deletion)
what mutations include acquisition of a whole new gene from another organism
duplication, gene loss, horizontal gene transfer
which functions include addition or substation of an activity/new fxn
silent, deleterious or beneficial
—– selects or discards a mutation
evolutionary pressure
—- mutations improve — of an organism, increasing survival in its env
adaptive, fitness
silent mutations allow the microorganism’s to —- new —-
colonize, niches
—- mutations are usually lost
deleterious
accumulation of mutations may lead to:
speciation - rise of new species
carl woese
sequencing go the small subunit rRNA
- established the presence of 3 domains: eukarya, archaea, bacteria
- provided a unified phylogenetic framework for bacteria
sequencing of SSUrRNA for eukarya is —– and prokarya is —-
18S, 16S
how does one sequence rRNA
1) amplification of the gene encoding SSUrRNA
2) sequencing of the amplified gene
3) analysis of the sequence by aligning them and observing their characteristics
what is SSUrRNA
- conserved region and variable region
- accumulation of neutral mutation through time
the evolutionary relationship between 2 organisms is directly correlated to:
the number of mutations that have accumulated in each one
fill in the blanks with either “a few” or “a lot of”
e.coli and salmonella have —– differences
bacteria and archaea have —– differences
1) a few
2) a lot of
phylogenetic tree
graphic illustration of the relationships among sequences
the branch length in a phylogenic tree represent:
number of changes that have occurred along that branch
nodes
putative common ancestor
how does one make a phylogenetic tree
1) align sequence
2) a distance matrix is calculated from the number of sequence differences
3) the tree is constructed by adding nodes to join lineages that have the fewest differences
—– is a well supported hypothesis fro the origin of eukaryotic cells
endosymbiosis
endosymbiosis
mitochondria and chloroplasts arose from symbiotic association of prokaryotes with another type of cell (primitive eukaryotes)
what does it mean that a eukaryotic cell is chimeric:
- eukaryotes have similar lipids and nrg metabolisms to bacteria
- eukaryotes have transcription and translational machinery most similar to archaea
- phylogenetically closer to archaea
explain the 2 hypothesis for the formation of the eukaryotic cell
1) eukaryotes began as a nucleus bearing lineage that later acquired mitochondria and chloroplasts by endosymbiosis
2) eukaryotic cells arose from intracellular association between a H2 consuming archaea host. the archaea host later developed nucleus
we use —- to classify bacteria.
genotypes
streptomyces
- filamentous actinobacteria
- their like mushrooms
- hyphal growth –> filament of cytoplasm usually not separated by cross walls
- produce desiccation in resistant spores at the tip of an elevated structure called sporophore –> elevates from the surface of the plate
- produce secondary metabolites including antibiotics
bdellovibrio
- predatory bacteria
- infect other bacterial cells
- acquire nutrients from the host cell
- doesn’t grow on agar plates
- doesn’t infect gram positive
- penetrate through the outer membrane, placed between the inner and outer
- they grow within the prey –> prey lysis
caulobacteria
- stalked bacteria
- found in aqueous env
- unique cell cycle that includes cell differentiation
swarmer cell (swim and move) –> solid surface –> loses it flagellum and produces a stalk –> becomes longer –> glue like sol’n produced that attaches the cll to the solid surface –> mother cell –> elongates and divides producing other cells –> swarmer cell –> and the cycle continues
chlamyda
- obligate intracellular
- grows only inside the host
- reticulate body: intracellular, active growth
- elementary body: infectious, release from host cell, outside - doesn’t grow just tries to infect
- like: chlamydia trachoma’s, chlamydia pneumoniae
archaea
- extermophiles
- diverse
- evolutionary history is not very well known
the polyphasic approach taxonomy uses these methods:
1) phylogenetic analysis - 16S,rRNA, MLST
2) phenotypic analysis - motility, capsule, virulence
3) genotypic analysis - present/ absence of specific genes …
MLST
housekeeping agents from a species are sequenced and aligned to the respective sequences of other individuals of the same species
- sufficient resolving power
- you use multiple locus (genes) for this
identification
involves the comparison of a microorganism’s properties with those of organisms that have already been classified and named
what are identifications based on:
1) morphology
2) biochemical properties
3) 16S rRNA sequencing
4) MLST
Dichotomous key
- useful for the clinical world
- morphology and phenotype
- page 40
- specified order
API strips
in strips you fill each with a solution and you can take the results and make data
- old and not used anymore – MLST is used more often
serotyping
- based on the binding of specific antibody to surface structure:
1) LPS: O serotypes ( e.g. E.coli)
2) capsule: K serotypes
3) flagella: H serotypes
positive run indicated by agglutination (makes a flux)
