chapter 10 notes
chapter 10 notes 2330
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GEOL 1313 - 002
Diana Hernandez Vega
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This 4 page Class Notes was uploaded by Marissa Reyes-Hernandez on Monday April 11, 2016. The Class Notes belongs to 2330 at University of Texas at El Paso taught by Roshanak Jafari in Spring 2016. Since its upload, it has received 15 views. For similar materials see Microorganisms and Disease - 18884 in Science at University of Texas at El Paso.
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Date Created: 04/11/16
Chapter 10 Review • Living organisms are divided into groups to better understand relationships among species • Taxonomy has three separate but interrelated areas: • Identification :Process of characterizing in order to group • Classification: Arranging organisms into similar or related groups • Nomenclature: System of assigning name • Strategies Used to Identify Prokaryotes • Wide assortment of technologies used to identify organisms including • Microscopic examination • Culture characteristics • Biochemical test • Nucleic acid analysis • Strategies Used to Classify Prokaryotes • Understanding organisms’ phylogeny assists in classification • Allows for organized classification of newly recognized organisms • Development of molecular techniques for classification and identification make genetic relatedness possible • Taxonomic Classification categories arranged in hierarchical order with the species being the basic unit. Categories include Species, Genus, Family, Order, Class, Phylum (Division) , Kingdom , and Domain. Individual strains within a species vary in minor properties. • Three-domain system ,(Bacteria, Archaea, and Eucarya), is based on evolutionary relatedness 1 Using Phenotypic Characteristics to Identify Prokaryotes: • Phenotype can be used in the process of identification of bacteria. Methods used include: • Microscopic morphology : The size, shape, and staining characteristics of a microorganism yield important clues as to its identity. Examples: • Gram-positive encapsulated diplococci found in sputum is indicative of Streptococcus pneumoniae. • Intracellular Gram-negative diplococci found in a urethral sample from a male is indicative of Nisseria gonorrhoeae • Mycobacterium tuberculosis is one of the few species of bacteria that are acid fast. • Culture characteristics: Colony morphology can give clues to the identity of the organism. • Streptococci: fairly small colonies • Serratia marcescens:red colonies at 22°C • Pseudomonas aeruginosa: green pigment & fruity odor • Selective and differential media used in the isolation process can provide information that helps identify an organism: • Streptococcus pyogenes (strep throat) yields B-hemolytic colonies on blood agar • E. coli (urinary tract infection) ferments lactose, forms pink colonies on MacConkey agar • Metabolic capabilities: Most biochemical tests rely on a pH indicator or chemical reaction that shows a color change when a compound is degraded. The basic strategy for identification using biochemical tests relies on the use of a dichotomous key. • Serology: Proteins & polysaccharides of prokaryotic cell’s surface are sometimes characteristic enough to be able to serve as identifying markers. Serological tests use antibodies to detect these markers. • Fatty Acid Analysis (FAME): Cellar fatty acid composition can be used as an identifying marker. 2 Using Genotypic Characteristics to Identify Prokaryotes: – Detecting Specific Nucleotide Sequences: • Tests can identify sequences unique to a given species or group – Nucleic acid probes: locate nucleotide sequence characteristic of species or group. DNA probes are very useful in identifying organisms in pure cultures – Nucleic acid amplification tests (NAATs): used to increase number of copies of specific DNA sequences » Allows detection of small numbers of organisms » Detection of organisms that cannot be cultured » Polymerase chain reaction (PCR) common technique – Sequencing Ribosomal RNA Genes • The sequence of ribosomal RNA (rRNAs) or encoding DNA (rDNAs) can be used to identify prokaryotes – the16S rRNA most useful – Can identify organisms that cannot be grown in culture Characterizing Strain Differences: • Biochemical Typing: Biochemical tests can be used to identify strains. • A group of strains with characteristic biochemical pattern: biovar, or biotype • Serological Typing: Identification made based on differences in serological molecules • A Group of strains with characteristic antigens which differs serologically from other strains: serovar, or serotype • Molecular Typing: Two isolates that have different restriction fragment length polymorphism (RFLPs) are considered different strains. Multilocus sequence typing determines the nucleotide sequence of representative segment. • Phage Typing: Identifies organisms by phage that infect them • Relies on differences in susceptibility to bacteriophages • Antibiograms: Antibiotic susceptibility patterns can be used to distinguish strains 3 Classifying Prokaryotes: DNA sequences can be used to construct a Phylogenetic Tree. Horizontal gene transfer can complicate insights provided by some types of DNA sequence comparison. • 16S rDNA Sequence Analysis: Analyzing and comparing the sequence of 16S rRNA, and its encoding gene, rDNA revolutionized classification. • DNA hybridization: The extent of nucleotide similarity between two organisms can be determined by measuring how completely single strands of their DNA will anneal to one another. • 70% similarity often considered same species • DNA Base Ratio (G + C Content): The G+C content can be measured by determining the temperature at which double stranded DNA melts. • If ratio(GC content) of two organisms deviates by more than a few percent, organisms not related, but Similarity does not mean relatedness. • Phenotypic Methods: Classification schemes that group organism by phenotype have been largely replaced by 16S ribosomal nucleic acid sequence methods. 4
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