Lecture 12 - Classification and Identification Flashcards
what is the definition of taxonomy?
the study of organisms to arrange them into groups for purposes of classification or identification
what are the two components of taxonomy?
Classification and Identification
what component of taxonomy is emphasized in medicine?
identification
what is the classification of organisms? what is phylogeny?
Classification is the universal way of organizing organisms based on their evolutionary relationships, which is phylogeny
What is the identification of organisms used for?
it is important in medicine
what is the purpose of taxonomic hierarchy?
The purpose of the taxonomic hierarchy is to help scientists understand and organize the diversity of life on our planet.
Hierarchical classification basically means that we classify groups within larger groups
what are the selected components in the levels of taxonomic hierarchy?
- Domain
- Genus
- Species (some may or may not have strains)
what is an example of the domain level of taxonomic hierarchy?
Bacteria
what is an example of the genus level of the taxonomic hierarchy?
Escherichia
what is an example of the species level with a strain of the taxonomic hierarchy?
coli with the strain 0157:H7
what exactly are strains within species?
they are different subtypes or forms within a species
in the following Bacteria, what is the domain, genus, species, and strain?
E. coli 0157:H7
Domain: bacteria
E - genus
coli - species
0157:H7 - strain
what naming system do we use for taxonomic hierarchy?
binomial nomenclature
what is a prokaryotic species?
A group of genetically related cells that are identified on the basis of their DNA sequence similarity or genotype
how do we name a species?
based on the DNA sequence AKA genotype
in a phylogeny chart, what does it mean when the bacteria are closer together?
the closer the bacteria, the more similar they are
what does phylogeny mean?
evolution
what is the three-domain classification system?
It is derived from the 16s rRNA gene sequencing - it classifies the 3 domains: Bacteria, Archaea, and Eukarya
what are the two parts of ribosomes?
rRNA and proteins
when performing 16s rRNA gene sequencing, why is rRNA preferred?
Because this rRNA gene is present in all organisms. It makes rRNA, which makes up the small subunit of ribosomes. Ribosomes perform an essential function for the cell (protein synthesis) and less mutations/changes are tolerated in the rRNA gene, so it is well-conserved in closely related organisms.
organisms are divided into the 3 Domains based on the sequence of what gene?
of the rRNA gene
T/F: the more similar the DNA sequences of organisms, the more closely related they are
True
what are the 4 ways to identify prokaryotes?
- Phenotype (how it looks)
- Biotype (it’s metabolic properties)
- Serotype (proteins on the surface of the cell for immunology)
- Genotype (DNA)
what is a phenotype and 2 ways to help identify the phenotype of an organism?
It is the physical features of an organism.
Two ways to identify it:
1. Microscopic morphology: The size, shape, and arrangement. Included Gram and special stains.
2. Colony morphology: The unique appearance and pigments. May require differential media (EMB). Example: Pseudomonas aeruginosa will be green on an agar plate.
what is the biotyping of a prokaryote?
The metabolic testing.
It tests for enzymes, groups of enzymes (a pathway), and uses dichotomous key.
what is serotyping?
Performing immunological tests. It is based on different antigens/proteins located on the cell’s surface. It has Antigen (Ag)-Antibody (Ab) reactions.
what is the genotype identification for prokaryotes? what are three different ways to do so?
It detects the genetic composition of an organism using:
- DNA fingerprinting
- DNA probes
- Sequencing DNA/rRNA (can be used in diagnosis and is used to classify different organisms)
in traditional clinical microbiology, what does genotyping a sample look like?
-Collect the sample
-Transfer
-Delivery to laboratory
-Wait for the cultures
-Interpretation by laboratory personnel
-Individual reports by culture
in 16s rRNA sequencing, what does genotyping a sample look like?
-Collect the sample
-Transfer
-Deliver to laboratory
-DNA extraction
-Sequencing and bioinformatics identification
-Comprehensive microbiome report
when genotyping what are the important steps/buzzwords?
- DNA isolation
- PCR amplification (with 16s rRNA gene primers?)
- DNA sequencing
which steps will you use to identify unknown microbes in a soil sample?
- DNA isolation
- PCR
- DNA sequencing
in the 3 domains, compare the following:
-Cell type
-Cell wall
-Membrane lipids
-First amino acid in protein
Bacteria:
-Cell type: prokaryotic
-Cell wall: usually PG
-Membrane lipids: straight fatty acid chains attached to glycerol by ester linkage
-First amino acid in protein: Formyl methionine
Archaea:
-Cell type: prokaryotic
-Cell wall: varies; no PG
-Membrane lipids: branched fatty acid chains attached to glycerol by either linkage
-First amino acid in protein: Methionine
Eukarya:
-Cell type: Eukaryotic
-Cell wall: varies; no PG
-Membrane lipids: straight fatty acid chains attached to glycerol by ester linkage
-First amino acid in protein: Methionine
In the scientific name, Enterobacter aerogenes, Enterobacter is the:
Genus
Which of the following is not true in the three-domain classification system?
1. Bacteria and Archaea are prokaryotes.
2. Bacteria, Archaea and Eukarya arose from a common prokaryotic ancestor.
3. Bacteria and Archaea contain the same membrane lipids.
4. Bacteria and Archaea have a significantly different 16srRNA sequences.
5. Eukarya have a membrane-bound nucleus.
- Bacteria and Archaea contain the same membrane lipids.
You discover an organism that is single-celled but with no nucleus or peptidoglycan. What might this be?
An archaea
Which of the following can be used to identify the genotype of an unknown organism?
1. Gram stain
2. Metabolic tests
3. PCR
4. Colony morphology
5. Serology
- PCR
study dichotomous key and from practice q’s
*
Why is a pure culture necessary for metabolic tests, but not for DNA probes?
Answer: A pure culture is necessary for metabolic tests because mixed bacteria can create confusing results. For example, in a specific medium, different bacteria will use the medium differently; some will have a negative reaction and others will have a positive reaction. In addition, there may be a medium, such as glucose, where two results are possible (acid and gas), and one bacterium may produce acid while another produces gas. In contrast, a pure culture is not necessary for DNA probes because the DNA probe is highly specific and will only bind to its specific counterpart in a mixed culture. This reflects the specificity of complementary base pairing.
What is the most inclusive and most exclusive level in the taxonomic organization?
The most inclusive level in the taxonomic organization is: Domain
The most exclusive level in the taxonomic organization is: Species
Identify the domain, genus, species, and strain in the archaeon Methanosarcina barkeri Fusaro.
Domain: Archaea
Genus: Methanosarcina
Species: barkeri
Strain: Fusaro
Which gene sequence is used to build the phylogenetic tree of life and why?
The gene sequence that is used to build the phylogenetic tree of life is the 16s rRNA gene since this rRNA gene is present in all organisms. It makes rRNA, which makes up the small subunit of ribosomes. Ribosomes perform an essential function for the cell (protein synthesis) and less mutations/changes are tolerated in the rRNA gene, so it is well-conserved in closely related organisms.
What are the four ways used to identify microbes?
Phenotype
Biotype
Serotype
Genotype
List the steps used to identify microbial species on your skin.
- DNA isolation from the specimin
- PCR amplification of the bacterial 16s rRNA gene
- DNA sequencing
