Classifications of Microorganisms Flashcards
What is Taxonomy?
Taxonomy: The science of classifying organisms according to how similar they are to other organisms
-These similarities are due to relatedness which reflects evolutionary relationships
What is Phylogeny? What does it comprise of?
Phylogeny (or systematics); is the study of the evolutionally history of organisms
Phylogeny uses the tools of taxonomy to clarify the evolution of organisms, as well as their interrelationships
-Grouping organisms according to common properties implies that they Evolved from a common ancestor; each species retaining some of the ancestor’s characteristics
Differentiate between Taxonomy and Phylogeny.
**Taxonomy proudces a HIERARCHY; while Phylogeny produces a PHYLOGENETIC TREE or Cladogram
Where does some information for phylogenetic relationships come from? Do Fossils of bacteria exist?
In higher organisms, some of the information used to determine phylogenetic relationships comes from FOSSILS
Yes, fossils of bacteria exist (they are Rare)
What are examples of Fossilized microorganisms?
Fossilized microorganims
-Their structures are NOT readily fossilized
Some exceptions (examples)
* A. Fossilized colonies of a marine protist from the White cliffs of Dover, England
B. Fossilized bacterial communities. Limestone buildups of cyanobacterial mats (and other microbes) that form in shallow water called stromatolites (as old as 3.5 billion years)
-since fossil evidence is Not available for most prokaryotes, their phylogeny must be based on other evidence
What Is a stromatolite?
Stromatolite: rock structures formed by layers of bacteria like, cyanobacteria and other microbes (algae?)
What is the Three-Domain System and how is it classified? What evidence supports this classification? Where did mitochondria and chloroplast originate from?
The Three-Domain system: composed of 3 domains, Bacteria, Archaea and Eukarya
** In 1990, Carl Woese Elevated the three cell types to a level ABOVE the kingdom
-There was no history of classification for domain. The domains were classified **Based on similarities on rRNA **
-Mitochondria and Chloroplasts originated from Bacteria
Why were Archaea initially thought to be the most primitive?
Archaea initially thought to be most primitive b/c they were EXTREMOPHILES
Which organisms are a part of each domain?
Bacteria Doman: Mitochondria, proteobacteria, cyanobacteria, chloroplasts, gram-positive bacteria, and Thermotoga
Archaea domain: methanogens, hyperthermophiles, extreme halophiles
Eukarya Domain: animals, fungi, amebae, slime molds, plants, ciliates, green algae, dinoflagellates, diatoms, euglenozoa, gird (protozoan parasites), mitosomes (mitochondria degenerates)
Which gene are transferred horizontally in phylogenetic tree of the Three domains ? what does analysis of genome show?
Genera near the origin or “root” of the evolutionary tree appear to have transferred genes horizontally.
-The analysis of completed genomes show that each domain showers genes with other domains
For example, the bacterium Thermatoga acquired 1/4 of its genes form an archaeon.
Discuss the cellular characteristics of the 3 domains; including cell type, cell wall, membrane lipids, first Amon acid in protein synthesis, antibiotic sensitive, tRNA loop, common arm of tRNA
Cellular characteristics of the 3 domains:
Archaea:
Cell type: Prokaryotic
Cell Wall: Varies in composition; contains NO Peptidoglycan
Membrane lipids: composed of Branched carbon chains attached to glycerol by Ether linkage
First amino acid in synthesis: Methionine
***Antibiotic Sensitivity: NO
**tRNA loop: Lacking
**Common Arm of tRNA: Lacking
ex: Sulfolobus sp.
Bacteria:
Cell Type: Prokaryotic
Cell wall: contains peptidoglycan
Membrane Lipids: composed of Straight carbon chains attached to glycerol by Ester linkage
First Amino Acid in Protein synthesis; Formylmethoinine
**Antibiotic Sensitivity: YES
**rRNA loop: PRESENT
**Common Arm of tRNA; PRESENT
ex: E.coli
Eukarya:
Cell type: Eukaryotic
Cell wall: Varies in composition; contains carbohydrates
Membrane Lipids: composed of Straight carbon chains attached to glycerol by Ester linkage
First Amino acid in protein synthesis: Methionine
Antibiotic sensitivity: NO
rRNA loop; Lacking
Common Arm of tRNA: PRESENT
ex. Amoeba sp
**the rRNA loop is only in Bacteria
Describe the features of the Hairpin loop seen in Bacteria? What structure does Bacteria and eukaryotes have in common
Compare and contrast the membrane lipids of bacteria, Archaea, and eukarya domains.
Hairpin loop
-seen in bacteria (ex; E. coli)
contains 16s rRNA
- Bacteria and Eukaryotes BOTH have common arm of TRNA
-that are sequences of bases in tRNA, guanine-thymine-pseudoridine-Cytoisne guanine
-Both Bacteria and Eukarya have membrane lipids that are composed of STRAIGHT carbon chains attached to Glycerol by ESTER linkages
-Meanwhile, Archaea have membrane lipids that are composed of BRANCHED carbon chains attached to glycerol by ETHER linkages
What are the different parts of tRNA structure
tRNA structure:
4 loops
Top loop is Acceptor arm (contains ester bond
left side is Common arm (Guanine-Thymine-pseudouridine-cytosine-guanine)
-Bottom: Anticodon arm
right side: D arm
Explain the endosymbiotic theory and recognize the features shared by prokaryotic cells and mitochondria/chloroplasts to support this theory.
The nuclear envelope and ER of eukaryotes may have formed by invagination of the plasma membrane
The Endosymbitoic theory: proposes that eukaryotic cells evolved from prokaryotic cells living inside a host prokaryote
(chloroplasts and mitochondria originated from Bacteria and were engulfed by Eukaryotes)
(according to theory, ancestral eukaryotes engulfed aerobic bacteria that eventually evolved into mitochondria; while the early eukaryotes engulfed cyanobacteria that evolved to become chloroplasts (photosynthetic bacteria)
Describe the similarities between prokaryotic cells and eukaryotic mitochondria and chloroplasts that support Endosymbiotic theory
The best comparison is between mitochondria and bacteria (since they are very SIMILAR )
- Prokaryotic Cell and Eukaryotic Organelles (mitochondria and chloroplasts) both have Circular DNA, have 70s Ribosomes and Grow by BINARY FISSION
-Prokaryotic cell Is unique in that it has Histones (in archaea), and the first amino acid in protein synthesis is formylmethionine (bacteria); Methionine (Archaea)
-They also can have one circular DNA; some two circular; some linear DNA
-Eukaryotic cell has LINEAR DNA, and has Histones. Their first Amino acid in protein synthesis is. Methionine and they have 80 s Ribosomes. They grow by Mitosis
-Eukaryotic organelles (mito and chroloplasts) share the same features as bacteria (prokaryotic cell), Except that mitochondria and chloroplasts have NO histones and have Formylmethionine as first amino acid in protein synthesis (like bacteria)
-hence this supports endosymbiotic theory (mito/chlorplasts evolved from bacteria)
Discuss the unique characteristics of present-day bacteria Gemmata obscuriglobus and Cyanophora paradoxa
organism that create present day evidence that plasma membrane infolding could produce a nuclear envelope
-Gemmata obscuriglobus: A bacterium (based on rRNA sequence) that has a nuclear envelope surrounding its nucleic
- Cyanophora paradoxa: a protist harboring a photosynthetic endosymbiont (cyanelle) resembling modern day cyanobacteria (Ex; peptidoglycan cell wall and genome organization)
(the cyanelle is closer to a cynaobacteria than a chloroplast)
Both host and endosymbiont require each other survive
Cells also contain mitochondria
Explain why scientific names are used, list and apply the naming rules, outline the process for naming newly discovered prokaryote, and renaming based on new information
Scientific Nomenclature is used since
Common Names:
-Vary with geography
2 different organisms are called Spanish Moss (neither actually moss)
-Buttercup (East Texas) name for Oenothera speciosa
whereas Buttercup (elsewhere) misnamed for 250 Ranunculus sp
-Vary with languages
-multiple names for the same organism
What are naming rules of organisms using Scientific nomenclature.
Scientific Nomenclature:
-Binomial Nomenclature (genus _ specific epithet)
-Used worldwide
-Names taken from Latin or Greek and may be descriptive or honor a scientist
-Genus name is capitalized and a noun
-Species name is lower case and usually an adjective
-Both names are underlined or italicized
ex: Homo sapiens (man/wise)
providing universal names for organism facilitates research, scholarship and communication
Give the scientific names, including their name, Source of genus name, and source of specific epithet for the bacteria: Klebsiella pneumonia, Pfiesteria piscida, Salmonella typhimurium, Streptococcus pyogenes, Penicillum chyrsogenum, and trypanosome Cruz
Scientific Binom Source of genus Source of Epithet
1. Klebsiella Honors Edwin Klebs The disease
pneumonia
2. Pfiesteria Honors Lois Pfiester Disease in fish
piscicida
3. Salmonella Honors Daniel Salmon Stupor (typh-)
typhimurium in mice
4.Streptococcus Chains of cells (strepto) Forms pus
pyogenes (pyo-)
5. Penicillium Tuftlike (penicilli-) produces yellow
chrysogenum (chryso) pigment
6. Trypanosoma Corkscrew-like Honors Oswaldo
cruzi (trypano-, borer; Cruz
soma- body)
Describe the process for naming an newly discovered prokaryote
Process for naming a newly discovered prokaryote:
International Committee on Systematics of Prokaryotes
1) **Establish a name based upon Bacteriological Code (rules for naming) **
2) Publish description and evidence of classification in the “International Journal of Systematic and Evolutionary Biology
3) Once published, name is incorporated into the reference book “Bergey’s Manual of Systematics of Archaea and Bacteria, First Edition”
What are the 3 common names for Saccharomyces cerevisiae?
Saccharomyces cerevisiae:
1. Baker’s Yeast
2. Brewer’s Yeast
3. Budding Yeast
Explain the purpose and distinguish between the two Bergey’s manuals. What are the major groups in Bergey’s 9th edition manual .
Bergey’s Manual and Systematics of Archaea and Bacteria
*First Edition: Published online since April 2015. This online manual replaces and expands upon the first two paper editions of Bergey’s Manual of Systematic Bacteriology (first two editions 1984-2012)
*It is organized by phylum, provides Phylogenetic information on bacteria and archaea, based on rRNA sequencing
Bergey’s Manual of Determinative Bacteriology. 9th Edition
-Book organization is STRICTLY PHENOTYPIC, with not attempt to offer a natural higher classification
-It is utilitarian and is **intended to aid in the identification of bacteria **
-Bacteria are divided into 35 easily recognized phenotypic groups most useful for diagnostic purposes
Group 1: The spirochetes .
Group 4: Gram-negative aerobic/microaerophillic rods and cocci
Group 8: Anaerobic gram-negative cocci
Group 11: Oxygenic photooptic bacteria
An explosion in the isolation and description of new taxa prokaryotes over past 5 years has resulted in description of more than one hundred new genera and six hundred new species each year (first edition)
List the major taxa and differentiate between eukaryotic and prokaryotic species. Define strain
Taxonomic Hierarchy:
Domain
Kingdom
Phylum
Class
Order
Family
Genus
Species
(Dear King Phillip Came Over For Good Soup)
Eukaryotic species: Group of closely related organisms that breed among themselves
Prokaryotic species
-A population of cells with similar characteristics
What is a strain?
Strain: A variant of a organism.
Strain can be identified by numbers, letters, or name following the species designation (ex: E.coli K12 or S. cerevisiae S288C)
Which of the Three Domains do NOT have a Kingdom?
Archaea and Bacteria do NOT have Kingdom in their taxonomy.
They start with Phylum
List the major characteristics used to differentiate the kingdoms of Eukarya
Kingdoms in the Domain of Eukarya:
-Animalia: Multicellular; no cell walls; chemoheterotrophic
- Plantae: Multicellular; cellulose cell walls; usually Photoautotrophic
- Fungi; chemoheterotrophic; unicellular or multicellular; cell walls of chitin; can develop from spores or hyphal fragments
-Protista: A catch-all kingdom for eukaryotic organism that do NOT fit other kingdoms
-Grwouped into CLADES based on rRNA
**There is NOT absolute agreement regrind the number of eukaryotic kingdoms
Explain how organisms can be renamed based on new information
In 1984, DNA hybridization studies indicated that Streptococcus faecalis and Streptococcus faecium were only distantly related to other streptococcal species. New genus called Enterococcus was formed and species renamed E. faecalis, and E. faecium
-In 2001, based on DNA hybridization and rRNA studies, some Chlamydia species were placed in a new genus Chlamodphila
To avoid confusion when an organism is renamed, the Old name is often written in parenthesis following the new name
ex: Burkholderia (pseudomonas) pseudomalleli
Compare and contrast classification and indentification
Classification: Placing organisms in groups of related species. Lists of characteristics known organisms
-estimated that only 1% of prokaryotes have been discovered
Identification: Matching characteristics of an “unknown” organism to lists of known organisms
-clinical lab identification.