Chapter 10 Flashcards
What are taxa
Related groups
A collection of similar kingdoms
Domain
3 domains
Bacteria, archaea, eukaryotes
A collection of related species
Genus
The system of assigning names to organisms
Nomenclature
Evolutionary relatedness of organisms
Phylogeny
A group of closely related strains, the basic unit of taxonomy
Species
A pure culture isolate,, subgroup within species
Strain
Identification
Classification
Nomenclature
Are 3 interrelated areas of…
Taxonomy
Name a problem with trying to classify species of prokaryotoes
They do need breed like eukaryotes which is the primary way of defining an eukaryotic species
The domains are based on comparison of nucleotide sequences of (type of molecule)….
rRNA
Cytoplasmic membrane: Hydrocarbon linked to glycerol by ether linkage
Cytoplasmic membrane: fatty acid linked to glycerol by ether linkage
Archea: Hydrocarbon
Bacteria & Eukaryotic: Fatty acids
Do archaea or bacteria have introns?
Archaea sometimes do
2 types of biochemical test and what they are looking for
- An assay for enzyme catalase. Drop of hydrogen peroxide is added to sample. If it bubbles then there is catalyse
- Fermenting sugars. Add specimen to a broth with a ph indicator liquid. If it ferments the sugar acid will be produced changing the color
A series of alternative choices that lead to the ID of an organism or object
Dichotomous key
_____ testing uses antibodies to detect specific proteins and polysaccharides
Serological testing
MALDI-TOF MS is used to
Identify microorganisms protein profile
Protiens and polysaccharides are sometimes unique enough to be considered identifying markers
T or F
T
These characteristics nucleotide sequences in certain rRNA genes, or their products, that can be used to classify or ID certain organisms
Signature sequence
_____ prokarytoic molecule is the most useful in taxonomy because of its moderate size
What is the Eukaryotic equivalent
S16 & S 18
Whole gene sequencing is a feasible method for ID a given isolate. An advantage is that it can predict _____
WGS is also used to study disease outbreaks
Antibiotic resistance
Morphology
Cultue characteristics
Metabolic capabilities
Serological testing
Protein profile
Are all this type of characteristics
Phenotype
Detecting specific nucleotide sequences
Sequencing rRNA
Whole genome sequencing
Are all this type of characteristics
Genotype
Microorganism can be iD by using NAAT (PCR) and a probe to detect….
Nucleotide sequence
An advantage of using rRNA genes sequence to ID organisms
They don’t need to be grown in a culture
When using a probe to detect an organsim, why is it necessary to have some idea of the organisms identity
A probe will only stick to a complementary nucleotide unit
Why is 16S RNA referred to as SSU RNA
It is the smallest subunit of the ribosome
A group of strains that have a characteristics biochemical pattern different from other strains are called
Biovar / biotype
A group of strains that have a characteristics antigen structure that differs from other strains are called
Serovar / Serotype
Antibiotic susceptibility pattern, used to distinguish between different bacterial strains
Antibiogram
Biochemical tests are most commonly used to ID bacteria, but in some cases they can distinguish between different strains.
A group of strains that have a characteristics Biochemical pattern is called _____
Biovar / biotype
Proteins and carbohydrates that vary among strains can be used to differentiate strains. A group of strains that have a characteristics serological type is called ….
Serovar / serotype
Surveillance networks now use _____ to track outbreaks
Whole genome sequencing
Evolutionary relatedness
Phylogeny
A diagram that depicts the evolutionary heritage of organisms
Phylogenetic tree
What genes encode for rRNA
rDNA
rRNA is better at determining the phylogeny of (closely or distantly) related species
Distantly
In the whole genome sequence to assess the relatedness of two isolate shared genes are compared and a measure called _____ is then calculated
Average nucleotide identity
Differences in DNA sequences can be used to determine the point in time which two organisms diverged from a common ancestor.
What type of characteristics are they looking for?
Genotypic characteristics
The extent of nucleotide sequence similarly between two isolates can be determined by measuring how completely single strands of their DNA hybridize to one another
DNA-DNA hybridization
This type of classification of microorganisms involves
The nucleotide sequence of shared genes can be compared and the average nucleotide identity then calculated
Sequence analysis of genomes
The ______ can be measured by determining the temperature at which double-stranded DNA melts
G + C content
The “O157:H7” of E. coli O157:H7 refers to what
Biotype
Serotype
Phage type
Antibiogram
Serotype
Which is the newest taxonomic unit
Domain
Microscopic examination
Culture characteristics
Biochemical test
Nucleic Acid analysis
Symptoms of illness
Are used to _____ Prokaryotes
Identify
Phylogeny is used to _____ prokaryotes
Classify
E. Coli
Domain:
Phylum
Class
Family
Genus
Species
Strain
Domain Bacteria
Phylum Protobacteria
Class Gamma Protobacteria
Family Enterobacteria
Genus Escherichia
Species Coli
Strain 0157
Phenotypic characteristics
Staining properties (3)
Gram
Acidfast
Capsule
Phenotypic characteristics
Sugars utilized
End products produced
Size and color of colonies
Differential media & selective responses
Are of this type of differences
Metabolic difference
Bile salt select against certain bacteria
Is this specific type of differential and selective medium
MacConkey agar
What does McConky agar use to select for?
Lactose sugar & PH indicator
Identify Protein and Polysaccharide structure of an organism
Serology
Fatty acid analysis (FAME) uses…
To accomplish what?
Gas Chromatography
ID species
Catalase test is positive if _____ are seen after H²O² is added
O² bubbles
Serological test use _____ to detect specific molecules
Antibodies
Two test that can be done in conjunction to ID specific nucleotide sequences
Nucleic acid probes
Nucleic acid amplificación test
FISH probe for 16S rRNA to locate nucleotide sequence
Does it require an amplification step
No
What is the most useful ribosome size for sequencing nucleic acids
16S rRNA
Proteins and carbohydrates that vary among strains can be used to differentiate strains.
Is this type of typing
Serological
Gel electrophoresis can be used to detect restriction fragment length polymorphism.
Whole-genome sequencing is increasingly being used to detect differences
In this type of testing
Molecular typing
Antibiotic susceptibility patterns can be used to characterize strains in this procedure
Antibiograms
Molecular typing uses DNA sequences to distinguish _______
DNA cut with restriction enzymes.
Seperate via _________ ( this machine/ technique)
Patterns called _________
Strain length
Gel electrophoresis
Restriction fragment length polymorphism
______ makes it easier to use RFLP data to track food borne disease outbreaks
(System established by CDC)
PulseNet
Classification historically based on…
Phenotypes
DNA sequencing allows construction of …
Phylogenetic tree
Sequence analysis of _____ may not resolve at species level because closely related prokaryotes can have identical SSU
_____ is a better tool in these cases
rRNA
DNA Hybridization
The _____ is the entire set of DNA instructions found in a cell.
Genome
_______ consists of a base (one of four chemicals: adenine, thymine, guanine, and cytosine) plus a molecule of sugar and one of phosphoric acid.
Nucleotide
