Taxonomy bacteria Flashcards
Who developed binomial system of naming organisms and in what century
Cark Linnaeus , 18 th century
Each organism is given too names ___
A generic name (genus) and a specific name (species)
Most names for the microorganism are derived from
- Latin or Greek- descriptive ( Staphyloccoccus aureus: cluster-grain/berry-golden)
- The name of the discoverer (Salmonella typhi :salmon discovered)
Taxonomy categories
Dear (domain) King (kingdom) Phillip (phylum) Came (class) Over (order) For (family) Good (genus) Spaghetti (species)
Two characteristics on the basis of which organisms can be classified
Phenetic (overall similarity)
Phylogenetic (evolutionary similarity)
What is a species
A group of organisms that can interbreed: give a sexual productive outsprings
How old is the Earth?
Around 4.5 billion years
First evidence of microbial life can be found
In rocks ( around 3.5 billion years_
What are stromatolites?
Microbial mats consisting of layers of filamentous prokaryotes, sediments and extracellular matrix
When were the first stromatolites found
In rocks 3.5 billion years ago or younger
What is the difference between ancient and modern stromatolites?
Ancient- anocygenic phototrophic filamentous bacteria
Modern-oxygenic phototrophic cyanobacteria
What were the conditions on early Earth?
It was anoxic and much hotter
Two hypotheses of origin of life
Surface origin
Subsurface origin
Explain surface origin hypothesis and why it is not the best
- 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
Explain substance origin hypothesis
-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.
Explain the timeline of evolution
- 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
What do we know about LUCA
Nothing except it existed
First self-replicating systems may have been ___ and why
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
Why RNA got replaced by DNA
Because it is more stable
Other important steps in the emergence of cellular life
- Buildup of lipids
- Synthesis of phospholipid membrane vesicles
- Assembly of vesicles catalyzed by the clay of the mound, produce cytoplasmic membrane
Who is Last Universal Common Ancestor
Population of early cells from which cellular life may have diverged into ancestors of modern-day Bacteria and Archea
As early Earth was anoxic, energy-generating metabolism of primitive cells was exclusively
anaerobic and likely chemoautotrophic
Carbon ,electron and energy sources for early life on earth
Carbon: CO2
Energy and electron source :H2 , which was likely generated by H2S reacting with FeS (2 compounds present in hydrothermal mounds)
Explain how chemically we got energy on early earth
Formation of pyrite (FeS2) leads to H2 production and S0 reduction, which fuels a
primitive ATPase.
How we got organic compounds on Earth
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.
How oxygen content increased on Earth? And when
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
When did the Great Oxidation event started
2.5 bya
Three characteristics for phenetic similarity
Morphology
Physiology
Biochemistry
Who and when invented the traditional method for the classification of prokaryotes
Michael Adanson- 200 years ago
What are some features of this traditional method of organism classification
- 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
What is numerical taxonomy
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
What is the other name for similarity coefficient
The Jaccard coefficient
What is done to illustrate the relationship between the species
Construction of dendogram
What is phenon
A group of organisms that have characters in common
How similarity coefficient is counted
Number shared/ total number tested
How the Jaccard coefficient is counted
Number shared/ total number tested- number negative for both
At what value of similarity coefficient species and genus similarity start
Species:0.85
Genus:0.65
What are characteristics of phylogenetic relationship?
Fossil record
Ribosomal RNA sequence
Multi-locus sequence typing
Whole genome sequencing
What is a mutation?
A change in the genome of an organism ( nucleotide insertion, deletion,etc.)
What can happen with the gene in the organism? (not nucleotide)
Gene duplication, gene loss and horizontal gene transfer from another organism
Genetic change can be ____
Silent, deleterious or beneficial (new function or change in activity)
What does evolutionary pressure and stress do
Selects or discards mutation
Adaptative mutations improve
Fitness of an organism, increasing survival in its environment
Why silent mutations can be beneficial
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
What does deleterious mutation mean
Harmful
What is usually done with deleterious mutation
They are usually lost, because they decrease the fitness and the survival ability of the organism
Accumulation of mutations can lead to
Specification- rise of a new species
What did Carl Woese do in 1970s
- 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
What for sequencing of SSU rRNA is done
To infer the phylogeny of prokaryotes and other microorganisms (find the relatives and make the tree)
How rRNA sequencing is done
- Amplification of the gene encoding SSU rRNA
- Sequencing of the amplified gene
- Analysis of sequence in reference to other sequences
Why SSU of rRNA is used for finding relationship between organisms?
SSU rRNA genes are highly conserved, present in all
cellular organisms, and easily sequenced and analyzed
There are two types of regions in rRNA
Conserved and variable
What is the genetic drift
Accumulation of neutral mutation through time
The evolutionary relationship between two organisms is directly correlated to
The number of mutations that have accumulated in each organism
What are the steps in constructing phylogenetic tree
- Sequence 16s rRNa
- Align sequences ( to take into account insertion/deletion)
- Calculate distance matrix
- The tree is constructed
What does the nodes and numbers mean in the phylogenenetic tree
Nodes: purative common ancestor
Number: how many differences between the organisms
What is endosymbiosis
A well-supported hypothesis for the origin of eukaryotic cells
What does endosymbioses theory imply
Mitochondria and chloroplasts arose from symbyotic association of prokaryotes within another primitive eukaryote
Why eukaryotic cells are chimeric( have parts from different organisms )
- They have similar lipids and energy metabolism to Bacteria
- Eukaryotes have transcription and translational machinery most similar to Arhea
- Phylogenetically closer to Archea
What are two hypothesis to explain the formation of the eukaryotic cells
- 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
The representative of filamentous actinobacteria
Streptomyces
What kind of growth does streptomyces have
Hyphal growth ( filament of cytoplasm usually not separated by cross-walks)
Where do streptomyces produce endospores
At the tip of an elevated structure called sporophore
The name of predatory bacteria
Bdellovibrio
What are characteristics of bdellovibrio
- Infect other bacterial cells
- Acquire nutrients from host cells
- Does not grow on agar plates
- Gram-positive bacteria are not infected
What are the steps in bdellovibrio penetration
- Attachement
- Formation of prey periplasm space inside the bdelloplast
- Lysis
What is the name of the stalked bacteria
Caulobacter
Where does caulobacter live
In aquatic bacteria
What is the unique characteristics of caulobacter
Unique cell cycle that includes cell differentiation: sedentary stalked mother cell and a motile flagelled daughter cell
What does the tip do in caulobacter
The tip of the stalk secrete the stickiest substance known
What are the steps in caulobacter cell cycle
- 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
the name of obligate intracellular bacteria
- Chlamydia trachomatis
- Chlamydia pneumoniae
Why Chlamydia trachomatis and Chlamydia are obligate pneumoniae are obligate intracellular
Grow only inside host cells
Two types of states of intracellualr bacteria
Elementary bodies: infectious, release from host cells
Reticulate body: intracellular, active growth
Bacterial taxonomy incorporates ____
Multiple methods for classification of old and new species
The polyphasic approach to taxonomy uses these methods:
- Phylogenetic analaysis (16 s rRNA, MLST)
- Phenotypic analysis (motility, capsule, virulence, etc.)
- Genotypic analysis ( presence/absence of specific genes)
What is MLST
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
What are the steps in MLST
- Isolate DNA
- Amplify 6-7 target genes
- sequence
- Allele analysis and compare with other strains and generate tree
Identification of an unknown microorganism will depend on ____
The comparison of its properties with those of organisms that have already been classified and named ( Type strains)
What properties are compared for identification of the organism
- Morphology
- Biochemical properties
- 16S rRNA gene sequencing
- MLST
What is dichototomous key
a tool created to help scientists and identify objects and organisms by a tree.
Serotyping what is it
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
What are API strips
Sets of differential methods and biochemical tests. ( glucose fermentation, etc.)
What are antibodies
Molecules of the immune system that recognize and bind to molecule on the surface of a microorganism or to secreted proteins
What is positive reaction for serotyping
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.
