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microbiology > taxonomy- bacteria > Flashcards

taxonomy- bacteria Flashcards

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Biology 101 flashcards
1
Q

name the 3 different aspects of taxonomy

A

1) nomenclature
2) identification
3) classification

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2
Q

binomial system developed by —– is used to name all cellular organisms, including microorganisms.

A

carl linnaeus

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3
Q

each organism is given 2 names, explain:

A

1) a generic name (genus) - homo

2) a specific name (species) - sapiens

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4
Q

—– were original classified in the class of chaos

A

animalcules

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5
Q

name the taxonomic categories

A 
domain 
kingdom
phylum 
class
order 
family
genus 
species
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6
Q

classification is based on:

A

1) overall similarity (phenetic)

2) evolutionary relationships (phylogenic)

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7
Q

a species is:

A

a group of organisms that can interbreed

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8
Q

most microorganisms reproduce —-

A

asexually

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9
Q

the evolutionary history of micro-organism is —–

A

very incomplete

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10
Q

the earth is about —– yo

first evidence of microbial life can be found in rocks —- yo

A
  1. 5

3. 5

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11
Q

what are stromatolites

A

these are microbial mats consisting of layers of filamentous prokaryotes, sediments and extracellular matrix. they fossilize very well

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12
Q

compare ancient and modern age stromatolites

A

ancient: anoxygenic phototrophic filamentous bacteria
modern: oxygenic phototrophic cyanobacteria

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13
Q

early earth was — and much —- than present day

A

anoxic, hotter

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14
Q

surface origin hypothesis:

A

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

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15
Q

what factors argue against surface origin hypothesis

A

temperature fluctuations, mixing from meter impacts, dust clouds and storms

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16
Q

subsurface origin hypothesis

A

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

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17
Q

first replicating system may have been — based

A

RNA

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18
Q

RNA can bind —- molecules

A

small e.g. ATP, other nucleotides

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19
Q

RNA has —- activity. may have catalyzed its own synthesis

A

catalytic

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20
Q

DNA/ RNA is a more stable molecules. THUS, —–

A

DNA, becoming the genetic repository

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21
Q

3 part systems evolved and became universal among cells

A

protein, DNA, RNA

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22
Q

Name other important steps in the emergence of cellular life (besides dan,rna and protein )

A

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

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23
Q

LUCA

A

last universal common ancestor – population of early cells from which cellular life may have diverged into ancestors of modern day bacteria and archaea

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24
Q

as early earth was anoxic, nrg generating metabolism of primitive cells was:
carbon source:
hydrogen source:

A

anaerobic and likely chemoautotrophic
co2, nrg and electron source
H2S reacting with FeS –> present in hydrothermal mounds
use atpase

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25
Q

early form of —– and —– support the production of large amounts of organic compounds

A

chemoautotrophic, photoautotrophic metabolism

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26
Q

organic material provide an abundant, diverse and continually renewed source of —– —- —- , stimulating evolution of various ——— metabolisms

A

reduced organic carbon, chemoheterotrophic

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27
Q

numerical taxonomy

A

traditional method for the classification of prokaryotes introduced by Michael Adanson

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28
Q

conditions for numerical taxonomy

A

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

29
Q

similarity coefficient or the jacquard coefficient

A

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

30
Q

dendrogram

A

a type of graph constructed to illustrate the relationship between species

31
Q

phenol

A

group of organisms that have characters in common

32
Q

S formula

A

shared / tot # tested

33
Q

Sj formula

A

shared/tot # tested # neg for both

34
Q

What is a mutation

A

a change in the genome of an organism (nucleotide change, insertion,deletion)

35
Q

what mutations include acquisition of a whole new gene from another organism

A

duplication, gene loss, horizontal gene transfer

36
Q

which functions include addition or substation of an activity/new fxn

A

silent, deleterious or beneficial

37
Q

—– selects or discards a mutation

A

evolutionary pressure

38
Q

—- mutations improve — of an organism, increasing survival in its env

A

adaptive, fitness

39
Q

silent mutations allow the microorganism’s to —- new —-

A

colonize, niches

40
Q

—- mutations are usually lost

A

deleterious

41
Q

accumulation of mutations may lead to:

A

speciation - rise of new species

42
Q

carl woese

A

sequencing go the small subunit rRNA

  • established the presence of 3 domains: eukarya, archaea, bacteria
  • provided a unified phylogenetic framework for bacteria
43
Q

sequencing of SSUrRNA for eukarya is —– and prokarya is —-

A

18S, 16S

44
Q

how does one sequence rRNA

A

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

45
Q

what is SSUrRNA

A
  • conserved region and variable region

- accumulation of neutral mutation through time

46
Q

the evolutionary relationship between 2 organisms is directly correlated to:

A

the number of mutations that have accumulated in each one

47
Q

fill in the blanks with either “a few” or “a lot of”
e.coli and salmonella have —– differences
bacteria and archaea have —– differences

A

1) a few

2) a lot of

48
Q

phylogenetic tree

A

graphic illustration of the relationships among sequences

49
Q

the branch length in a phylogenic tree represent:

A

number of changes that have occurred along that branch

50
Q

nodes

A

putative common ancestor

51
Q

how does one make a phylogenetic tree

A

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

52
Q

—– is a well supported hypothesis fro the origin of eukaryotic cells

A

endosymbiosis

53
Q

endosymbiosis

A

mitochondria and chloroplasts arose from symbiotic association of prokaryotes with another type of cell (primitive eukaryotes)

54
Q

what does it mean that a eukaryotic cell is chimeric:

A
  • eukaryotes have similar lipids and nrg metabolisms to bacteria
  • eukaryotes have transcription and translational machinery most similar to archaea
  • phylogenetically closer to archaea
55
Q

explain the 2 hypothesis for the formation of the eukaryotic cell

A

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

56
Q

we use —- to classify bacteria.

A

genotypes

57
Q

streptomyces

A
  • 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
58
Q

bdellovibrio

A
  • 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
59
Q

caulobacteria

A
  • 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
60
Q

chlamyda

A
  • 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
61
Q

archaea

A
  • extermophiles
  • diverse
  • evolutionary history is not very well known
62
Q

the polyphasic approach taxonomy uses these methods:

A

1) phylogenetic analysis - 16S,rRNA, MLST
2) phenotypic analysis - motility, capsule, virulence
3) genotypic analysis - present/ absence of specific genes …

63
Q

MLST

A

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
64
Q

identification

A

involves the comparison of a microorganism’s properties with those of organisms that have already been classified and named

65
Q

what are identifications based on:

A

1) morphology
2) biochemical properties
3) 16S rRNA sequencing
4) MLST

66
Q

Dichotomous key

A
  • useful for the clinical world
  • morphology and phenotype
  • page 40
  • specified order
67
Q

API strips

A

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

68
Q

serotyping

A
  • 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)

microbiology (9 decks)

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