Identification and classification of prokaryotes chapter 10

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Microbiology a human perspective

Taxonomy

The science that studies organisms in order to arrange them into groups (taxa);
involves three interrelated areas--identification,classification, and nomenclature.

Identification

The process of characterizing an isolate in order to determine the group (taxon) to which it belongs

Classification

The process of arranging organisms into similar or related groups (taxa), primarily to provide easy identification and study.

Nomenclature

The system of assigning names to organisms.

Explain why organisms are arranged in taxonomic groups

They are arranged in a hierarchical order, with the species being the basic unit. The species designation gives a formal taxonomic status to a group of related isolates or strains, which, in turn, permits their identification. Without classification, scientists and others would not be able to communicate about organisms with any degree of accuracy.

Give the order of taxonomic groups from the most general to the most specific.

Species
Genus
Family
Order
Class
Phylum or Division
Kingdom
Domain

Define Domain

A collection of similar kingdoms. The domain is a relatively new taxonomic category that reflects the characteristics of the cells that make up the organism.

Define Genus

A collection of similar species

Define Species

A group of closely related isolates or strains. Note that members of a species are not all identical; individual strains may vary in minor properties. The difficulty for the taxonomist is to decide how different two isolates must be in order to be classified as separate species rather than strains of the same species.

Define Strain

An isolate; subgroup within a species

Describe the basis for the identification of prokaryotes using:
Phenotypic characteristics

Pg. 237 table 10.4
Microscopic Morphology-determine its size & shape, and staining characteristics such as Gram stain can give suggestive information as to the identity of the organism. Further testing, however is needed to confirm the identification.
Metabolic capabilities-Culture characteristics can give suggestive information. A battery of biochemical tests can be used to confirm the identification.
Serology-Proteins and polysaccharides that make up a prokaryote are sometimes characteristic enough to be considered identifying markers. These can be detected using specific antibodies.
Fatty acid analysis-Cellular fatty acid composition can be used as an identifying marker and is analyzed by gas chromatography.

Describe the basis for the identification of prokaryotes using:
Genotypic characteristics

pg 237 table 10.4
Nucleic acid probes to detect specific nucleotide sequences-Probes can be used to identify prokaryotes grown in culture. IN some cases, the method is sensitive enough to detect the organism directly in a specimen.
Amplifying specific DNA sequences using PCR-Even an organism that occurs in very low numbers in a mixed culture can be identified.
Sequencing rRNA genes-This requires amplifying and then sequencing rRNA genes, but it can be used to identify organisms that have not yet been grown in culture.

Describe the information provided by:
Morphological studies

...

Describe the information provided by:
Staining reactions

...

Describe the information provided by:
biochemical reactions

...

Describe the information provided by:
serology

pg 244 table 10.6
Proteins and carbohydrates that vary among strains can be used to differentiate strains. A group of strains that have a characteristic serological type is called a serovar or a serotype.

Describe the information provided by:
Phage Typing

Pg 244 table 10.6
Strains of a given species sometimes differ in their susceptibility to various types of bacteriophage.

Describe the information provided by:
Sequencing rRNA genes

pg 242
The nucleotide sequence of ribosomal RNA (rRNA) can be used to identify prokaryotes, particularly those difficult or currently impossible to grow in culture. The prokaryote 70S ribosome, which plays an indispensable role in protein syntesis, is composed of protein and three different rRNAs (5S, 16S, and 23S). Because of their highly constrained and essential function, the nucleotide sequence changes that can occur in the rRNA's, ;yet still allow the ribosome to operate, are limited.

Describe the information provided by:
Genomic typing

pg 244 table 10.6
Molecular methods such as pulsed-field gel electrophoresis can be used to detect restriction fragment length polymorphisms (RFLPs)

Describe the information provided by:
DNA hybridization

pg 248 table 10.7
The extent of nucleotide sequence similarity between two isolates can be determined by measuring how completely single strands of their DNA hybridize to one another.

Describe the information provided by:
DNA base ratios

pg 248 table 10.7
Determining the G+C content offers a crude comparison of genomes. Organisms with identical G+C contents can be entirely unrelated, however.

Describe the information provided by:
Numerical taxonomy

Uses a quantitive approach to phenotypic classification, comparing a battery of characteristics.

Explain the basis of nucleic acid hybridization and the kind of information it provides.

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Explain how rRNA sequences can be used in identification and classification

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