Ch 10 Classifaction of Microbes

Taxonomy, taxa, or taxon

The science of classifying organisms. Provides universal names for organisms. Provide a reference for identifying organisms. Shows degrees of similarities among organisms

Systemic or Phylogeny

The study of the evolutionary history of organisms, and the hierarchy of taxa reflects their evolutionary or phylogenic, relationships

Domain

Higher than kingdom, Related kingdoms make up this

What are the three domains?

Archaea: Prokaryotes, Bacteria: Prokaryotes, Eukarya: Eukaryotes

Two domains of prokaryotes:

Bacteria and archaea

What are the three types of domains based on?

Ribotyping- Ribosomal RNA comparison. The Ribosome is found in all living organisms. Shared among all them

Ribosome

Is a complex of proteins and several RNA 16S RNA is analyzed in ribotyping. Found in all living organisms. Machinery to produce proteins. Protein synthesis `1

Three kingdoms of eukaryotes:

Fungi, plants, and animals

Bacteria

Includes all the pathogenic prokaryotes, as well as many of the nonpathogenic prokaryotes found in soil and water. The photoautotrophic prokaryotes are also found in the domain.

Archaea

Includes prokaryotes that do not have Peptidoglycan in their cell walls. They often live in extreme environments and carry out unusual Metabolic processes

What are the three major groups of Archaea?

Methanogens, Extreme halophiles, and hyperthermophiles

Methanogens

Strict anaerobes that produce methane (CH4) From carbon dioxide and hydrogen

Extreme halophiles

Require high concentrations of salt for survival

Hyperthermophiles

Normally grow in extremely hot environments

Endosymbiotic theory

Eukaryotic cells evolved from prokaryotic cells, living inside one another

Phylogenetic Hierarchy

Grouping organisms according to common properties, the organisms evolved from a common ancestor. Each species, retain some of the characteristics of the ancestor fossils are used to classify this. Found by using fossils, anatomy, rRNA, And molecular clock (Changes in DNA overtime)

Molecular clock

Changes in DNA overtime. For evolution is based on nucleotide sequences in the genomes of organisms. Based on differences in amino acids and hemoglobin among different animals.

Cladogram

Type of phylogenetic tree . Does not show evolutionary time nor exact distance from the common ancestor. Shows evolutionary relationships among organisms; Based on rRNA Sequences

Eukaryotic species

A group of closely related organisms that breed amongst themselves

Prokaryotic species

A population of cells with similar characteristics

Clone

Population of cells derived from a single cell

Strain

A population of cells that genetically differs from other members of the species (Identified by numbers, letters, or names after the specific epithet)

Culture

Grown in laboratory media

Viral species

Population of viruses with similar characteristics that occupies a Particular ecological niche

Classification

Placing organisms in groups of related species. List of characteristics of known organisms.

Identification

Matching characteristics of an “ Unknown “ Organism to list of known organisms.

Procedure for classification:

Determine the tax economic category of a newly isolated organism. Applies to newly discovered organism.

Procedure for identification:

Identify an isolated organism by comparing its characteristics. Applies to organisms already known and classified.

Morphology

Structures - bacillus, coccus, endospore

Differential staining:

Gram stain, Acid fast stain

Biochemical tests:

Presence of certain enzymes, production of metabolites

Immunological reaction:

Reaction between antigen and antibody

Phage-typing:

Test for determining which phages a bacterium is Susceptible too. Looks for similarities among bacteria. A plate covered with bacteria growing on agar. A drop of each different phage is Placed on the bacteria. Plaques appear wherever phages are able to infect and lyse the bacterial cells.

Polymerase chain reaction (PCR)

Technique used in molecular biology to amplify a segment of DNA. have billions and billions of copies of your DNA.

Ribosomal RNA sequencing:

rRNA are present in all cells

Base composition

Percentage of guanine plus cytosine (G+C). A single species is theoretically a fixed property. A comparison of the G +C content in different species can reveal the degree of species relatedness.

DNA fingerprinting:

Use of restriction enzyme to compare the sequence (Size and number of fragments). Restrictive fragment provides info about their genetic similarities and differences. More similar the patterns more closely related to organisms.

Nucleic acid hybridization

Form a double stranded molecule identical to the original double strand. If two species are similar, a major portion of their nucleic acid sequences will be similar. Measures the ability of DNA strands from one organism to hybridize with the DNA of another organism.

Hybridize

Buying through complementary base pairing

Protein profiling:

Sequence of amino acids compared

Genetic Homology:

When two genes in different species resemble each other because they were inherited from a common ancestor

Morphological characteristics are useful to identify what?

Useful for identifying eukaryotes

What do differential staining identify?

Gram, Acid fast. Useful for both ID and classification.

What do biochemical test identify?

Determines presence of bacterial enzymes

Nucleic acid hybridization

Measures the ability of DNA strands from one organism to hybridize with DNA strands of another organism. Greater degree of this, greater degree of relatedness. >70% Indicate same species

Southern blotting

Uses nucleic acid hybridization to identify unknown microorganisms using DNA probes. To detect a specific DNA sequence in a sample.

DNA probes

A short single stranded piece of DNA or RNA that is labeled in someway and used to detect the presence of a complementary DNA or RNA sequence in any sample

Northern blotting

A laboratory technique used to detect and study specific RNA molecules within a sample

Microarray (DNA chip)

Contains DNA probes and detect pathogens by hybridization between the probe and DNA in the sample. Detected by Fluorescence

DNA sequencing/DNA base composition

Draw conclusions about relatedness and is expressed as the percentage of guanine plus cytosine. GC + AT = 100%. Two organisms that are Closely related and have many identical or similar genes will have similar amount of the various bases in their DNA

DNA fingerprinting

Use restriction enzymes to compare the basic sequences of different organisms. Compare the number and sizes of restriction fragments that are produced from different organisms provides info about their genetic similarities and differences. The more similar the patterns the more closely related to organisms are.

Dichotomous keys

Use for identification. Based on the successive questions in each question has two possible answers. After answering one question the investigator is directed to another question until an organism is identified.

Restriction enzyme

Enable researchers to compare the basic sequences of different organisms. Cut a molecule of DNA wherever a specific base sequence occurs producing restriction fragments

Serology

The science that studies, serum and immune responses that are evident in Serum. Testing can differentiate between species and strands within species. Slide Agglutination test.

Enzyme-linked immunosorbent assay ELISA

A laboratory test to detect and measure the presence of antigens or antibodies in a sample. It relies on the specific binding between an antigen and an antibody and uses an enzyme linked reaction to produce a detectable signal (Usually color change)

Selective media

Contain ingredients that suppress the growth of competing organisms and encourage the growth of desired ones

Differential media

Allow the desired organism to form a colony that is somehow distinctive

Slide agglutination test

Rapid serological test used to detect the presence of specific antigen’s or antibodies by mixing them on a glass slide and observing visible clumping. Drop of antigen on glass slide, then add drop of specific anti-serum positive test → clumping. Negative test → no clumping

Enzyme linked immunosorbit assay

Known antibodies are placed in well of a microplate and unknown type of bacterium is added to each well. Reaction → Provides identification of bacteria