Taxonomy
-orderly arrangement
-science of classifying organisms
-provides universal names for organisms
-provides a reference for identifying organisms
Phylogeny
evolutionary history of a group of organisms
Stanier defined prokaryote as
a cell in which nucleoplasm is not surrounded by a nuclear membrane
Whittaker
-proposed 5 kingdom system
-believed prokaryotes were ancestors of eukaryotes
-prokaryotes were placed in kingdom Monera
-Eukaryotes were placed in the other 4 kingdoms
What did scientists determine the difference between eukaryotes and prokaryotes was in?
ribosome and rRNA nucleotide sequences
how many types of prokaryotic cells vs eukaryotic cells?
two types of prokaryotic cells and one type of eukaryotic cell
What are the three domains?
-established by Carl Woese
1. Eukarya
2. Bacteria
3. Archaea
How many kingdoms does eukarya have?
4 kingdoms
1. fungi
2. protista
3. plantae
4. animalia
How many kingdoms does archaea have?
3 kingdoms (no peptidoglycan)
1. Methanogens
--> strict anaerobe
--> generates methane
2. Halophiles
--> need high salt
3. Hyperthermophiles
--> grow in hot, acidic environment
Archaea characteristics:
Cell type: prokaryotic
Cell wall: varies in composition - no peptidoglycan
Membrane lipids: branched carbon chains attached to glycerol by ether linkage
First AA in protein synthesis: Methionine
Antibiotic sensitivity: No
rRNA loop: lacking
Common arm of
Bacteria characteristics:
Cell type: prokaryotic
Cell wall: peptidoglycan
Membrane lipids: straight carbon chains attached to glycerol by ester linkage
First AA in protein synthesis: Formylmethionine
Antibiotic sensitivity: Yes
rRNA loop: present
Common arm of tRNA: present
Eukarya characteristics:
Cell type: eukaryotic
Cell wall: varies - contains carbohydrates
Membrane lipids:
First AA in protein synthesis: straight carbon chains attached to glycerol by ester linkage
Antibiotic sensitivity: no
rRNA loop: lacking
Common arm of tRNA: present
Endosymbiotic theory
theory that eukaryotic cells formed from a symbiosis among several different prokaryotic organisms
Evidence of a common ancestor comes from:
-anatomy
-fossils --> not available for prokaryotes
-rRNA
Paul Cano
isolated a Bacillus (25-40 million years old) embedded in amber
--> viable
Binomial nomenclature:
each organism is assigned two names
-genus
-specific epithet (species)
should be written in italic or be underlined
Genus is always capitalized
Only genus can be abbreviated
Taxonomic hierarchy
Domain
Kingdom
Division/Phylum
Class
Order
Family
Genus
Species
Prokaryotic species
not based on interbreeding but on similar characteristics
(clone, strain, viral species)
Clone
Population (colony) of cells derived from a single cell
considered a pure culture
Strain
Pure cultures of same bacteria are not always genetically identical
Viral Species
population of viruses with similar characteristics that occupies a particular ecological niche
-NOT classified in any of 3 domains
-NOT composed of cells
-obligatory intracellular parasites
Eukaryotic species
A group of closely related organisms that breed among themselves
Animalia kingdom
Multicellular
no cell walls
chemoheterotrophic
Plantae kingdom
Multicellular
fern, some algae, cellulose cell walls
Have chlorophylls
Usually photoautotrophic
Fungi kingdom
Chemoheterotrophic
unicellular or multicellular
cell walls of chitin
developed from spores of hyphal fragments, mushrooms
Protista kingdom
A kingdom for mostly unicellular eukaryotic organisms
-divided into two clades based on homologous features of a common ancestor
Methods of identifying bacteria
Morphological characteristics, differential staining, biochemical tests
Morphological characteristics identification
microbes can look very similar
cocci, bacillus
differential staining identification
gram staining, acid-fast staining
first step
biochemical tests identification
1. enzymatic activity (ability to ferment sugars)
2. Selective media: contains ingredients that suppresses growth of undesirable organisms
3. Differential media: bacteria generate a distinct morphology
4. Rapid system: used for medically important organis
Dichotomous Key
population is divided into two
Numerical Identification
1. One tube containing media for 15 biochemical tests is inoculated with an unknown enteric bacterium
2. After incubation, the tube is observed for results
3. The value for each positive test is circled, and the numbers from each group of tests are added
Serology
Combine known antiserum plus unknown bacterium
Slide agglutination test
ELISA
an example of a serological test
-Enzyme-linked immunosorbent assay
-known antibodies
-unknown type of bacterium
-antibodies linked to enzyme
-enzyme substrate
Positive direct ELISA
-detects antigens
-enzyme's substrate is added, and reaction produces a product that causes a visible color change
Positive indirect ELISA
-detects antibodies
-Enzyme's substrate is added, and reaction produces a product that causes a visible color change
Western Blot steps
1. electrophoresis is used to separate proteins in the serum --> proteins move at different rates based on their charge and size when the gel is exposed to an electric current
2. bands are transferred to a nitrocellulose filter by blotting --> each band c
What charge is DNA
negatively charged
Bacteriophage
a virus that infects bacteria --> viruses are host specific
Flow Cytometry
-no need to culture bacteria
-fluorescence of some species
-cells selectively stained with antibody plus fluorescent dye
-detects Listeria in milk
What is DNA fingerprinting?
Electrophoresis of restriction enzyme digests
Nucleic Acid hybridization steps
1. Take two organism's DNA
2. Heat to separate strands
3. combine single strands of opposite DNA's
4. Cool to allow renaturation of double-stranded DNA
5. Determine degree of hybridization
Complete hybridization
Organisms are identical
Partial hybridization
organisms are related
no hybridization
organisms are unrelated
DNA Chip Technology
1. A DNA chip can be manufactured to contain hundreds of thousands of synthetic single-stranded DNA sequences --> Assume that each DNA sequence was unique to a different gene
2.Unknown DNA from a patient is separated into single strands, enzymatically cut
FISH
Fluorescent In Situ Hybridization
-Add DNA probe for S. aureus
Cladogram
shows evolutionary relationship
How to build a cladogram
1. Determine the sequence of bases in an rRNA molecule for each organism
2. Calculate the percentage of similarity in the nucleotide bases between pairs of species
3. Construct a cladogram --> lengths of horizontal lines corresponds to the percent similar