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Microbio Midterm II > Lecture 10: Taxonomy of Bacteria & Archaea > Flashcards

Lecture 10: Taxonomy of Bacteria & Archaea Flashcards

1
Q

What are the two ways to classify bacteria?

A
  • Overall similarity (phenetic)

- Evolutionary relationships (Phylogenetics)

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2
Q

How long ago was the first evidence of microbial life?

A

3.5 by ago. (Earth is 4.5byo)

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3
Q

What is the best evidence we have of early life?

A

Stromatolites

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4
Q

What are stromatolites?

A

Microbial mats, layers of filamentous prokaryotes, sediments, and extracellular matrix.

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5
Q

True or false? Early earth was anoxic and hot.

A

True

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6
Q

What are ancient stromatolites?

A

Anoxygenic phototrophic filamentous bacteria.

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7
Q

What are moderm stromatolites?

A

Oxygenic phototrophic cyanobacteria

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8
Q

True or false? The 18s ribosomal subunit is found in prokaryotes.

A

False. Eukaryotes

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9
Q

What is the surface origin hypothesis?

A

1st membrane enclosed self repilcating cells arose out of primondial soup rich in organic/inorganic compounds on earths surface

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10
Q

What is the problem with the surface origin hypothesis?

A

Earth’s surface was not hospitable. Dramatic temp fluctuations (day/night), meteor impacts, dust clouds, UV, storms

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11
Q

What is the subsurface origin hypothesis?

A
  • life originated in hydrothermal vents on ocean floor
  • more stable conditions
  • steady and abundant supply of energy
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12
Q

True or false. Archaea are often extremophiles.

A

True

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13
Q

What role did hydrothermal vents play in the origin of life?

A
  • Nutrients in hot hydrothermal H20 flow up through mound
  • mineral pores form compartments=first cells=RNA
  • Compartments allow for coupling of energetic rxns to molecular replication
  • eventually lipid bilayers took place of mineral compartments
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14
Q

What is the RNA world theory?

A
  • First self-replication system may have been RNA based
  • RNA can bind small molecules (ATP)
  • RNA has catalytic activity, may have catalyzed it’s own synthesis (can be copied like DNA)
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15
Q

How did the great oxidation event occur?

A

In Archaen eon-origin of cyanobacteria creates so much O2 that it created possibility for eukaryotic life

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16
Q

What is phylogenetic classification?

A

Evolutionary relationships.

-Mutations, gene duplication, gene loss, HGT

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17
Q

What is an adaptive mutation?

A

Improve fitness of organism, increases survival

18
Q

what is an deleterious mutation?

A

Decrease fitness of organism, decreases survival

19
Q

What did Carl Woese do?

A
  • RNA sequencing if SSU RNA (16s in prokaryotes, 18s in eukaryotes)
  • Established presence of 3 domains of life
  • Provided unified phylogenetic framework for bacteria
  • Came up with RNA world theory
  • Comparative rRNA sequencing
20
Q

What is comparative rRNA sequencing?

A
  1. Amplification of gene encoding SSU rRNA
  2. Sequencing of amplified gene
  3. Analysis of sequence in reference to other sequences
21
Q

What is SSU rRNA?

A

Conserved and highly variable region, accumulates neutral mutations over time (genetic drift)
-Few ssu rRNA differences=closely related

22
Q

How do you sequence rRNA?

A
  1. Sequence 16s rRNA (Isolate DNA, amplify by PCR)
  2. Align sequences (take into acct. insertion/deletion)
  3. Look for similarities, count up base changes
  4. 5.
23
Q

True or false. Eukaryotic cells are chimeric.

A

True (formed from various parts)

24
Q

How do you sequence rRNA?

A
  1. Sequence 16s rRNA (Isolate DNA, amplify by PCR)
  2. Align sequences (take into acct. insertion/deletion)
  3. Look for similarities, count up base changes
  4. Construct phylogenetic tree
25
Q

How do you construct a phylogenetic tree?

A 
(Branch length represents # of changes)
(Nodes = common ancestor)
1. Align sequences
2. calculate difference graph from # of sequence differences
3. Construct forked tree
26
Q

What is the hypothesis of the endosybiotic origin of eukaryotes?

A

Mitochondria and chloroplasts arose from symbiotic association of prokaryotes within another type of cell=primitive eukaryote

27
Q

What are the two different hypotheses on how eukaryotes gained mitochondria and chloroplasts?

A
  1. Eukaryotes began as a nucleus bearing lineage that later acquired mitochondria & chloroplasts by endosymbiosis
  2. Eukaryotic cells arose from intracellular association between a H2 producing bacterium (symbiot) and that later became a mitochondria. Host later developed nucleus
28
Q

What are filamentous actinobacteria? (Streptomyces)

A
  • Filaments elongate from their ends and form branching hyphae
  • Cytoplasm separated by cross walls
  • produce desiccation resistant spores @ tip of sporophore when nutrients depleted
29
Q

What are predatory bacteria? (Bdellovibrio)

A
  • Infect other bacterial cells, acquire nutrients from host

- doesn’t grow on agar, gram + bact. not affected

30
Q

What are stalked bacteria? (Caulobacter)

A
  • Found in aquatic environments
  • chemoorganotroph
  • undergoes unequal binary fission
  • sedentary stalked mother cell and motile flagellated daughter cell (swarmer cell)
31
Q

What are obligate intracellular bacteria? (Chlamydia)

A
  • Parasites, grow only inside host cells
  • start as elementary body (infectious)
  • Host takes in elementary body thru phagocytosis
  • inside Host=reticulate body, non infectious
  • Reticulate body converts to elementary=lysis
32
Q

What is the polyphasic approach to taxonomy?

A

Phylogenetic analysis+phenotypic analysis+genotypic analysis

33
Q

What is multilocus sequence typing?

A
  • Type of phylogenetic analysis
  • looks at housekeeping genes
  • sequence and align different housekeeping genes from same species
  • sufficient resolving power to distinguish between closely related strains
  • identify new strains this way
34
Q

How do you identify an unknown organism?

A 
Look at: 
Morphology
Biochemical properties
16s gene
MLST
35
Q

What is a dichotomous key?

A

Graph that you can follow to see what characteristics an organism has:

  1. Gram stain
  2. glucose fermentation/morphology
  3. Motile @ 37C?
  4. Urea hydrolyzed?
  5. Indole produced/citrate utilized
36
Q

What are 2 differential and selective methods to identify organisms?

A

Glucose fermentation and API strips

37
Q

How can glucose fermentation be used to identify an organism?

A

If organism can ferment glucose, media will change from red to yellow

38
Q

How can API strips be used to identify an organism?

A

Analytical profile index, fast identification through a series of small reaction tubes with indicators.

39
Q

What is serotyping?

A

Based on binding of specific antibody to surface structure

Antibodies recognize and bind to molc on surface of microorganism/secreted proteins

40
Q

What is a serotype?

A

Separate groups within a species that share similar characteristics (ie Same # of antigens on surface)

  • LPS: O serotypes
  • Capsule: K serotypes
  • Flagella: H serotypes

Microbio Midterm II (7 decks)

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