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Introductory Microbiology > Taxonomy bacteria > Flashcards

Taxonomy bacteria Flashcards

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Biology 101 flashcards
1
Q

Who developed binomial system of naming organisms and in what century

A

Cark Linnaeus , 18 th century

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2
Q

Each organism is given too names ___

A

A generic name (genus) and a specific name (species)

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3
Q

Most names for the microorganism are derived from

A
  • Latin or Greek- descriptive ( Staphyloccoccus aureus: cluster-grain/berry-golden)
  • The name of the discoverer (Salmonella typhi :salmon discovered)
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4
Q

Taxonomy categories

A 
Dear (domain)
King (kingdom)
Phillip (phylum)
Came (class)
Over (order)
For (family)
Good (genus)
Spaghetti (species)
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5
Q

Two characteristics on the basis of which organisms can be classified

A

Phenetic (overall similarity)

Phylogenetic (evolutionary similarity)

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6
Q

What is a species

A

A group of organisms that can interbreed: give a sexual productive outsprings

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7
Q

How old is the Earth?

A

Around 4.5 billion years

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8
Q

First evidence of microbial life can be found

A

In rocks ( around 3.5 billion years_

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9
Q

What are stromatolites?

A

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

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10
Q

When were the first stromatolites found

A

In rocks 3.5 billion years ago or younger

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11
Q

What is the difference between ancient and modern stromatolites?

A

Ancient- anocygenic phototrophic filamentous bacteria

Modern-oxygenic phototrophic cyanobacteria

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12
Q

What were the conditions on early Earth?

A

It was anoxic and much hotter

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13
Q

Two hypotheses of origin of life

A

Surface origin

Subsurface origin

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14
Q

Explain surface origin hypothesis and why it is not the best

A
  • the first membrane-enclosed, self-replicating cells arouse out of primordial soup rich in organic and inorganic compounds 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
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15
Q

Explain substance origin hypothesis

A

-Life originated in hydrothermal springs on the ocean floor, where Conditions would have been more stable
-Steady and abundant supply of energy (e.g. H2 and H2S) was likely available at these sites
. Hot, mineral-rich hydrothermal fluid mixes with cooler, more oxidized ocean
water, forming precipitates of Fe and S compounds, clays, silicates, and carbonates.
Mineral precipitates form pores that could have served as energy-rich compartments that
facilitated the evolution of precellular forms of life. In this clay compartments( the preversion of cells) RNA molecules were formed, proteins, etc.

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16
Q

Explain the timeline of evolution

A
  • Prebiotic chemistry (Biological building blocks: AA,Sugars,Nucleotides)
  • 4.3-3.8 bya-> precellular life 1)RNA world: catalytic RNA,Self-replicating RNA 2)Protein Synthesis: RNA templated translation 3)DNA: replication, transcription
  • Early cellular organisms: Lipid bilayers->cellular compartments and Early cells likely had high rates of Horizontal Gene transfer(exchange of genetic material between cells)
  • 3.8-3.7 bya Divergence of Bacteria and Archea
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17
Q

What do we know about LUCA

A

Nothing except it existed

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18
Q

First self-replicating systems may have been ___ and why

A

RNA-based, because 1) RNA can bind small molecules (ATP, other nucleotides)

2) RNA has catalytic activity; may have catalyzed its own synthesis (Ribozymes)
3) RNA can be copied like DNA

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19
Q

Why RNA got replaced by DNA

A

Because it is more stable

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20
Q

Other important steps in the emergence of cellular life

A
  • Buildup of lipids
  • Synthesis of phospholipid membrane vesicles
  • Assembly of vesicles catalyzed by the clay of the mound, produce cytoplasmic membrane
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21
Q

Who is Last Universal Common Ancestor

A

Population of early cells from which cellular life may have diverged into ancestors of modern-day Bacteria and Archea

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22
Q

As early Earth was anoxic, energy-generating metabolism of primitive cells was exclusively

A

anaerobic and likely chemoautotrophic

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23
Q

Carbon ,electron and energy sources for early life on earth

A

Carbon: CO2
Energy and electron source :H2 , which was likely generated by H2S reacting with FeS (2 compounds present in hydrothermal mounds)

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24
Q

Explain how chemically we got energy on early earth

A

Formation of pyrite (FeS2) leads to H2 production and S0 reduction, which fuels a
primitive ATPase.

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25
Q

How we got organic compounds on Earth

A

early microorganisms may have used H2 and CO2 to produce
acetate or methane. These
early forms of chemolithotrophic metabolism driven by H2 would
likely have supported the production of large amounts of organic
compounds from autotrophic CO2 fixation.

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26
Q

How oxygen content increased on Earth? And when

A

The ability to use solar radiation
as an energy source allowed phototrophs to diversify extensively.
By 2.5–3.3 billion years ago, the cyanobacterial lineage evolved a
photosystem capable of oxygenic photosynthesis in which H2O supplanted H2S as the reductant for CO2, thereby
generating O2 as a waste product

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27
Q

When did the Great Oxidation event started

A

2.5 bya

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28
Q

Three characteristics for phenetic similarity

A

Morphology
Physiology
Biochemistry

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29
Q

Who and when invented the traditional method for the classification of prokaryotes

A

Michael Adanson- 200 years ago

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30
Q

What are some features of this traditional method of organism classification

A
  • All characteristics should be considered to be equal importance (unbiased)
  • Classification should be base on as many features as possible
  • Organisms should be grouped on the basis of overall similarity
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31
Q

What is numerical taxonomy

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 similarity coefficient

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32
Q

What is the other name for similarity coefficient

A

The Jaccard coefficient

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33
Q

What is done to illustrate the relationship between the species

A

Construction of dendogram

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34
Q

What is phenon

A

A group of organisms that have characters in common

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35
Q

How similarity coefficient is counted

A

Number shared/ total number tested

36
Q

How the Jaccard coefficient is counted

A

Number shared/ total number tested- number negative for both

37
Q

At what value of similarity coefficient species and genus similarity start

A

Species:0.85
Genus:0.65

38
Q

What are characteristics of phylogenetic relationship?

A

Fossil record
Ribosomal RNA sequence
Multi-locus sequence typing
Whole genome sequencing

39
Q

What is a mutation?

A

A change in the genome of an organism ( nucleotide insertion, deletion,etc.)

40
Q

What can happen with the gene in the organism? (not nucleotide)

A

Gene duplication, gene loss and horizontal gene transfer from another organism

41
Q

Genetic change can be ____

A

Silent, deleterious or beneficial (new function or change in activity)

42
Q

What does evolutionary pressure and stress do

A

Selects or discards mutation

43
Q

Adaptative mutations improve

A

Fitness of an organism, increasing survival in its environment

44
Q

Why silent mutations can be beneficial

A

Silent- a third base is changed, but the amino acid is not. In the environments not alike the ones that were before to colonize new niches

45
Q

What does deleterious mutation mean

A

Harmful

46
Q

What is usually done with deleterious mutation

A

They are usually lost, because they decrease the fitness and the survival ability of the organism

47
Q

Accumulation of mutations can lead to

A

Specification- rise of a new species

48
Q

What did Carl Woese do in 1970s

A
  • Sequencing of the small subunit rRNA: 16 SrRNA in prokaryotes and 18S rRNA in eukaryotes
  • Established the presence of three domains of life: Bacteria, Archea, and Eukarya
  • Provided a unified phylogenetic framework for Bacteria
49
Q

What for sequencing of SSU rRNA is done

A

To infer the phylogeny of prokaryotes and other microorganisms (find the relatives and make the tree)

50
Q

How rRNA sequencing is done

A
  • Amplification of the gene encoding SSU rRNA
  • Sequencing of the amplified gene
  • Analysis of sequence in reference to other sequences
51
Q

Why SSU of rRNA is used for finding relationship between organisms?

A

SSU rRNA genes are highly conserved, present in all

cellular organisms, and easily sequenced and analyzed

52
Q

There are two types of regions in rRNA

A

Conserved and variable

53
Q

What is the genetic drift

A

Accumulation of neutral mutation through time

54
Q

The evolutionary relationship between two organisms is directly correlated to

A

The number of mutations that have accumulated in each organism

55
Q

What are the steps in constructing phylogenetic tree

A
  1. Sequence 16s rRNa
  2. Align sequences ( to take into account insertion/deletion)
  3. Calculate distance matrix
  4. The tree is constructed
56
Q

What does the nodes and numbers mean in the phylogenenetic tree

A

Nodes: purative common ancestor
Number: how many differences between the organisms

57
Q

What is endosymbiosis

A

A well-supported hypothesis for the origin of eukaryotic cells

58
Q

What does endosymbioses theory imply

A

Mitochondria and chloroplasts arose from symbyotic association of prokaryotes within another primitive eukaryote

59
Q

Why eukaryotic cells are chimeric( have parts from different organisms )

A
  • They have similar lipids and energy metabolism to Bacteria
  • Eukaryotes have transcription and translational machinery most similar to Arhea
  • Phylogenetically closer to Archea
60
Q

What are two hypothesis to explain the formation of the eukaryotic cells

A
  • Eukaryotes began as a nucleus-bearing lineage that later acquired mitochondria and chloroplasts by endosymbioses
  • Eukaryotic cells arose from intracellular association between a H2-prodcuing bacterium (the symbiont), which gave rise to mitochondria , and an H2-consuming archeal host. the arheal host later developed a nucleus
61
Q

The representative of filamentous actinobacteria

A

Streptomyces

62
Q

What kind of growth does streptomyces have

A

Hyphal growth ( filament of cytoplasm usually not separated by cross-walks)

63
Q

Where do streptomyces produce endospores

A

At the tip of an elevated structure called sporophore

64
Q

The name of predatory bacteria

A

Bdellovibrio

65
Q

What are characteristics of bdellovibrio

A
  • Infect other bacterial cells
  • Acquire nutrients from host cells
  • Does not grow on agar plates
  • Gram-positive bacteria are not infected
66
Q

What are the steps in bdellovibrio penetration

A
  • Attachement
  • Formation of prey periplasm space inside the bdelloplast
  • Lysis
67
Q

What is the name of the stalked bacteria

A

Caulobacter

68
Q

Where does caulobacter live

A

In aquatic bacteria

69
Q

What is the unique characteristics of caulobacter

A

Unique cell cycle that includes cell differentiation: sedentary stalked mother cell and a motile flagelled daughter cell

70
Q

What does the tip do in caulobacter

A

The tip of the stalk secrete the stickiest substance known

71
Q

What are the steps in caulobacter cell cycle

A
  • Swarmer cell
  • Loss of flagellum
  • Initiation of DNA synthesis
  • Synthesis of flagellin-> elongation of stalked cell
  • Cross-band formation ( one form is stalk, another with flagellum)
  • Cell division
72
Q

the name of obligate intracellular bacteria

A
  • Chlamydia trachomatis

- Chlamydia pneumoniae

73
Q

Why Chlamydia trachomatis and Chlamydia are obligate pneumoniae are obligate intracellular

A

Grow only inside host cells

74
Q

Two types of states of intracellualr bacteria

A

Elementary bodies: infectious, release from host cells

Reticulate body: intracellular, active growth

75
Q

Bacterial taxonomy incorporates ____

A

Multiple methods for classification of old and new species

76
Q

The polyphasic approach to taxonomy uses these methods:

A
  • Phylogenetic analaysis (16 s rRNA, MLST)
  • Phenotypic analysis (motility, capsule, virulence, etc.)
  • Genotypic analysis ( presence/absence of specific genes)
77
Q

What is MLST

A

Multilocus sequence typing
Method in which several different “housekeeping genes” from a species are sequences and aligned to the respective sequences of other individuals of the same species

78
Q

What are the steps in MLST

A
  • Isolate DNA
  • Amplify 6-7 target genes
  • sequence
  • Allele analysis and compare with other strains and generate tree
79
Q

Identification of an unknown microorganism will depend on ____

A

The comparison of its properties with those of organisms that have already been classified and named ( Type strains)

80
Q

What properties are compared for identification of the organism

A
  • Morphology
  • Biochemical properties
  • 16S rRNA gene sequencing
  • MLST
81
Q

What is dichototomous key

A

a tool created to help scientists and identify objects and organisms by a tree.

82
Q

Serotyping what is it

A

These microorganisms, viruses, or cells are classified together based on their cell surface antigens, allowing the epidemiologic classification of organisms to the sub-species level

83
Q

What are API strips

A

Sets of differential methods and biochemical tests. ( glucose fermentation, etc.)

84
Q

What are antibodies

A

Molecules of the immune system that recognize and bind to molecule on the surface of a microorganism or to secreted proteins

85
Q

What is positive reaction for serotyping

A

The agglutination between the antigen and the antibody is made with a specific antisera, which reacts with the antigen to produce a mass. The antigen O is tested with a bacterial suspension from an agar plate, whereas the antigen H is tested with a bacterial suspension from a broth culture.

Introductory Microbiology (21 decks)

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