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Microbiology > Chapter 10 > Flashcards

Chapter 10 Flashcards

1
Q

what is used to name all cellular organisms + who invented it

A

binominal system by Carl Linneaeus (1707-1778)

  • each given organism is given 2 names:
    1. a generic names (genus)
    2. a specific name (species)
    • most names derive from greek to latin or sometimes derived from the name of the discoverer
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2
Q

3 examples of name + where they came from

A
  • salmonella typhi: Daniel Salmon- typhoid fever (bacillus typhi)
  • saccharomise cerevisiae: sugar-fungus-beer
  • staphyloccocus aureus: cluster-grain/berry-golden
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3
Q

animalcules were originally classified in the class ___ with a mixture of other items: ___

A

Chaos

agents of fermentation, spermatozoa, the cause of syphilis…

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4
Q

8 taxonomic categories

A 
domain
kingdom
phylum
class
order
family
genus
species
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5
Q

2 ways of classification in taxonomy

A
  1. overall similarity (phenetic)
  2. evolutionary relationship (phylogenetic)
    • plants, animals and organisms that are capable of sexual reproduction: a species is a group of organism that can be interbreed
    • history of microorganisms is incomplete, some microorganisms are capable of sexual reproduction (combination of genetic material from two individuals) but most reproduce assexually, so it is a species?
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6
Q

time first evidence of microbial life

A

first evidence can be foud environ 3,5 billion years old (byo)

ex: microfossil bacteria (environ 3.45 byo)
* * earth is 4.5 byo

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7
Q

what are stromatolites + comparison between ancient and modern stromatolites

A

microbial mats consisting of layers of filamentous prokaryotes, sediments and extracellular matrix

    • similar structure found in rocks 3.5 byo or younger
  • anoxygenic phototrophic filamentous bacteria formed ancient stromatolites
  • oxygenic phototrophic cyanobacteria dominate modern stromatolites
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8
Q

early earth was ___ and much ___ than present day

+ first biochemical compunds were made by what

A

anoxic, hotter

** they were made by abiotic systems that set the stage for origin of life

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9
Q

what are surface and subsurface origin synthesis

A

surface:

  • the first membrane-enclosed, self-replicating cell arose out of primordial soup rich in organic and inorganic compunds in ponds on Earth’s surface
  • dramatic temperature fluctuations (day/night) and mixing from meteor impacts, dust clouds, UV radiation, and storms argue against this hypothesis

subsurface:

  • life originated in hydrothermal springs on the ocean floor
  • conditions would have been more stable
  • steady and aboundant supply of energy (H2S,H2) was likely available at these sites
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10
Q

5 steps of the origin of life

A
  1. prebiotic chemistry: biological building blocks (AA,nucleosides, sugars), it set the stage for self-replicating systems
  2. precellular life: (RNA world theory where RNA-base may have been the first self-replicating system), DNA (a more stable molecule, eventually became the genetic repository), and proteins
    * * so three-part systems (RNA, DNA and proteins) evolved and became universal among the cells
  3. early cellular life: early cells likely had high rates of HGT (horizontal gene transfer which is exchange of genetic material between cells)
    - building up lipids
    - synthesis of phospholipid membrane vesicles
    - assembly of vesicles catalyze by the clay of the mound, produce cytoplasmic membrane
    * * these 3 steps are between 4.3-3.8 byo***
  4. LUCA to diversity modification: population of early cells from which cellular life may have diverged into ancestors of modern-day Bacteria and Archaea
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11
Q

what was energy-generating metabolism of primitive cells

A

as Early Earth was anoxic, it was exclusively anaerobic and likely chemoautotroph

  • C source: CO2
  • energy and electron sources: H2 likely generated by H2S reacting with FeS (2 compunds present in hydrothermal mounds)
    • alternative source of H2: Fe+ H+ with UV = H2
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12
Q

early forms of _______ and ______ metabolism would have support production of large amounts of _______.
+ what organic material provided

A
  • chemoautotrophics and photoautotrophic
  • large amount of organic compunds

organic material provided an abundant, diverse and continually renewed source of reduced organic carbon, stimulation evolution of various chemoheterotrophic metabolisms

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13
Q

what is phenetic + 3 characteristics

A
  • traditional method for the classification of prokaryotes introduced 200 years ago by Michael Adanson
  • all characteristics should be considered to be equal of importance (unbiased)
  • classification should be based on as many features as possible
  • organisms should be grouped on the basis of overall similarity
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14
Q

calcul associate with phenetic + what is phenon

A
  • a large number of characteristics are determined for each organisms and the similarities between pairs of microorganisms are then calculated and expressed as the similarity coefficient (S) or the Jaccard coefficient (Sj)
    S= number shared/total number tested
    Sj= number shared/ total number tasted - number negative for both
  • construction of dendogram to illustrate the relationship between species
  • phenon: groups of organisms that have characteristics in common
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15
Q

3 terms associated with phenetic

4 terms associated with phylogenetic

A

phenetic: morphology, biochemistry, physiology
phylogenetic:
- fossil record
- ribosomal RNA sequences
- multi-locus sequences typing
- whole genome sequencing

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16
Q

4 aspects of phylogenetic: evolutionnary process

A
  • a mutation is a change in the genome of an organism (nucleotide change, insertion, deletion)
  • gene duplication, gene loss and horizontal gene transfer (acquisition of a whole new gene from another organism)
  • genetic change may be silent, deleterious or beneficial (new function or change in activity)
  • evolutionary pressure (stress) selects or discards mutation
17
Q

4 characteristics of mutation

A
  • adaptative mutations improve fitness of an organisation, increasing survival in its environment
  • silent mutations may be beneficial in other environments allowing the microorganisms to colonize new niches
  • deleterious mutations are usually lost
  • accumulation of mutations may lead to speciation (rise new species)
18
Q

3 things Carl Woese (1970s) did

A
  • sequencing of the small subunit rRNA (SSU rRNA): 16S rRNA in prokaryotes, 18S rRNA in eukaryotes
  • established the presence of 3 domains of life: Bacteria, Archaea, and Eukarya
  • provided a unified phylogenetic framework for bacteria
19
Q

comparative rRNA sequencing is a routine procedure that involves the following : (3)
+ rRNA sequencing is used for what

A
  1. amplification of the gene encoding SSU rRNA
  2. sequencing of the amplified gene
  3. analysis of sequence in reference to other sequences
    * * it is used to infer the phylogeny of prokaryotes and other microorganisms
20
Q

3 characteristics of SSU rRNA

A
  • conserved region and variable region
  • accumulation of neutral mutation through time (genetic drift)
  • the evolutionary relationship between 2 organisms is directly linked to the number of mutation that have accumulated in each one
    ex: few differences: closely related (ex: e.coli and salmonella)
    ex: many differences: diverse a long time ago (bacteria and archaea)
21
Q

3 steps to do the phylogenetic tree + its definition and 3 characteristics

A
  1. align the sequences
  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
  • def: graphic illustration of the relationships among sequences
  • branch lenght represent the numbers of changes that have occured along that branch (usually a scale is included)
  • branches define the order and of descent and ancestry of the nodes
  • note: putative common ancestor
22
Q

what is endosymbiosis + what is implied

A

def: it is a well-supported hypothesis for the origin of eukariotic cells
- it implies that mitochondria and chloroplasts arose from symbiotic association of prokaryotes within another type of cell (primitive eukaryote)

23
Q

eukaryotic cell are chimeric why? (3)

A
  • eukaryotes have similar lipids andenergy metabolism to bacteria
  • eukaryotes have transcription and translational machinery most similar to Archaea
  • phylogenetically closer to Archaea
24
Q

2 hypothesis to explain the formation of the eukaryotic cell

A
  1. eukaryotes begins as a nucleus-bearing lineage that later acquired mitochondria and chloroplasts by endosymbiosis
  2. eukaryotic cells arose from intracellular association between a H2-producing bacterium (the symbiont), which gave rise to mitochondria, and an H2-consuming archaeal host. The archaeal host later develop a nucleus
25
Q

2 characteristics of filamentous actinobacteria: streptomyces
+ 5 steps from growth phase to spore mature

A
  • hyphal growth (filament of cytoplasm usually not separated by cross-walls)
  • produce desiccation resistant spores at the tip of an elevated structure called sporophore
  1. growth phase
  2. tip curls
  3. partitioning of tip
  4. cell walls thicken and constrict
  5. spores mature
26
Q

4 characteristics of predatory bacteria: Bdellovibrio

+ 5 steps of the infection

A

infect other bacteria cells

  • acquired nutrients from host cells
  • does not grow on agar plates
  • gram positive bacteria are not infected
  1. attachment
  2. penetration
  3. elongation of bdellovibrio inside the bdelloplast
  4. prey lysis (2.5-4h postattachment)
  5. release of progeny
27
Q

3 characteristics of stalked bacteria : caulobacter

+ steps of cell division (5)

A
  • found in aquatic environment
  • unique cell cycle that include cell differentiation: sedentary stalked mother cell and amotile flagellated daughter cell
  • the tip of the stack secrete the stickiest substance known
  1. loss of flagellum (swarmer cell)
  2. initiation of DNA synthesis (stalked cell)
  3. synthesis of flagellin (elongated stalked cell)
  4. cross-band formation (predivisional cell)
  5. cell division (predivisional cell)
    environ 90 minutes
28
Q

4 characteristics of obligated intrac ellular cell: chlamydia + steps (6)

A
  • grow only inside host cell
  • elementary bodies: infectious, release from host cells
  • reticulate bodies: intracellular, active growth
  • chlamydia trachomatis, chlamydia pneumoniae
  1. elementary body attacks host cell
  2. phagocythosis of elementary bodies
  3. conversion to reticulate body
  4. multiplication of reticulate body
  5. conversion to elementary bodies
  6. release of elementary bodies
29
Q

Bacterial and Archaeal taxonomy: 2 characteristics + 3 methods of the polyphasic approach to taxonomy

A
  • bacterial taxonomy incroporates multiple methods for classification of old and new species
  • there is also a need to classify different strains of the same species
    1. phylogenetic analysis (16S rRNA,MLST)
    2. phenotypic analysis (motility, virulence, capsule..)
    3. genotypic analysis (presence/absence of specific genes..)
30
Q

what is MLST (multilocus sequence typing)

+ 4 steps

A
  • method in which several different housekeeping genes from a species are sequenced and aligned to the respective sequences of other individuals of the same species
  • has sufficient resolving power to distinguish between very closely related strains
  1. isolate DNA
  2. amplify 6-7 target genes
  3. sequence
  4. allele analysis, compare with other strains and generate tree
31
Q

how do we classify

A

identification of an unknown microorganism will depend on the comparison of its propoerties with those of organisms that has already been named and classified

  • morphology
  • biochemical properties
  • MLST
  • 16s rRNA gene sequencing
  • dichotomous key (morphology and phenotype)
  • serotyping
32
Q

different steps of dichotomous key

A
  1. gram + or -?
  2. if gram + = morphology ?
    if gram - = acide fermentation (acid or acid and gas)
  3. if acid and gas : motile at 37degree ? (yes or no)
  4. if no: urea hydrolyzed ? (yes or no)
  5. if no : indole produced?
    if yes: citrate utilized?
33
Q

serotyping is based on what + definition of antibody

A
  • it is based on the binding of specific antibody to surface structureL
  • LPS: O serotypes (E.Coli O157:H7)
  • capsule: k serotype (Klebsiella pneumoniae K1, higher virulence)
  • flagella: H serotypes (E.coli O157:H7)
def antibody: molecules of the immune system that recognize and bind to molecule on the surface of a microorganism or to secreted proteins.
- positive reaction: agglutination
34
Q

technique for phylogenetic analysis (classification of species)

A

16S rRNA, MLST

35
Q

classification of strains

A

MLST, phenotypic analysis, genotypic analysis (presence of specific genes) serotyping

36
Q

identification

A

MLST, 16S rRNA, serotyping, dichotomous key, FAME

Microbiology (25 decks)

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