chapter 10 microbio: classifying organisms

define taxonomy

the science of classifying organisms by showing relationships by showing relationships among different organisms (way to identify organisms)

during Aristotle era

recognized the world as being divided into 2 groups

the world was divided into what two groups

plants vs animals

in 1735 Linnaeus proposed

dividing things into kingdoms

what kingdoms did linnaeus propose

plantae and animalia

in 1800 Nageli proposed

that bacteria and fungi should be classified under the kingdom plantae

in 1937 prokaryotes were recognized as

cells with nuclei

in 1959 what kingdom was created

Fungi

in 1968 what kingdom was created

prokaryata

describe phylogeny

evolutionary history ; goes further than taxonomy

characteristics of taxonomic hierarchy

physical and phylogenic

describe phylogenic tree

group taxa according to phylogenic relationships based on a common ancestor

how is the information for phylogenic trees obtained

through fossil record and rRNA sequencing

describe rRNA sequencing

molecular clock; where mutations are observed based on their rate and can work backward to find common ancestry and group via phylogeny

who proposed a 3 domain system in 1978

Carl Woease

the 3 domain system is based on

rRNA, membrane lipids, tRNA, sensitivity to antibiotics

what are the 3 domains

bacteria, archaea, and eukarya

what are the kingdoms of eukarya

plantae, animalia, fungi

what are the kingdoms of bacteria

prokaryotes with peptidoglycan cell walls

what are the kingdoms of archaea

prokaryotes with unusual cell walls

the taxonomic hierarchy divides organisms into

species

describe species

particular with who they bred with; species are able to bred with other but not with individuals of another species

describe genus

includes a group of species

hierarchy of organisms

domain

kingdom

phylum

class

order

family

mnemonic from most to least inclusive

Dear Kingdom Phillip Came Over For Good Soup

Dear corresponds to

Domain

King corresponds to

Kingdom

Phillip corresponds to

Phylum

Came corresponds to

Class

Over corresponds to

Order

For corresponds to

Family

Good corresponds to

Genus

Soup corresponds to

Species

domain of eukaryotes

eukarya

kingdoms of eukaryotes

fungi plantae, animalia, protista*

what is not considered a true kingdom

protista

describe fungi

absorptive chemoheterotrophs, develop spores, associated with hyphae

describe hypahe

yeast, mold, and mushrooms

yeast have what type of cell

unicellular

mold and mushrooms are what types of cells

multicellular

describe animalia

multicellular ingestive heterotrophs

types of animalia

worms (helminths), insects, vertebrates

describe phototrophs

mosses, ferns, conifers, and flowering plants

describe protista

mostly unicellular eukaryotes

how are protista divided

into claves (based on genetically related groups)

why are protista not a true kingdom

theyre a catch all group, organisms that dont fit anywhere else were placed here

describe polyphyletic

no common ancestor, organisms can be assigned to different kingdoms, no based on normal phylogeny but physical characteristics

what are the domains of prokaryotes

bacteria and archaea

bacteria have what type of ribosomes

70S

archaea have what type of ribosomes

80S

80S is associated with eukarya so which domain is closely related to it

archaea (seen as the middle ground)

what is used to classify bacteria

Bergey’s model of systemic bacteriology

describe bergey’s model

identifies bacteria and observes closely related bacterial strains

describe strains

group if bacteria that are derived from a single cell, genetically identical to that single cell

describe pure culture

gives a lot of clones (genetically identical)

describe impure culture

multiple strains in culture (not genetically identical)

bergey’s model is based on similar characteristics and not inbred because

bacteria reproduce through binary fission

viruses cannot be placed in any kingdom because

acellular and not an organism at all (acellular obligatory parasites)

describe viral species

similar characteristics that occupies particular ecological niche

characteristics of viral species

morphology, genome/nucleic acid, enzymes

viral species are characterized by

the international taxonomy of viruses

describe the morphological characteristics method

staining techniques

bacteria involve gram staining and acid fast staining

presence of various enzymes method

biochemical tests

describe biochemical tests

identifies nitrogen fixation

sulfur oxidation

lactose fermentation

describe serological tests

interaction with antibodies

serological tests function

look for ability of organism to interact with particular antibodies

serological tests identifies

specific strains and species

types of serological tests

ELISA (enzyme-linked immunosorbent assay) and western blotting

susceptibility to bacteriophages describe

phage typing

function of phage typing

identifies bacterial species to see if a phage will infect it

describe fatty acid profiles

testing to see what fatty acids are produced

describe flow cytometry

Measure physical and chemical characteristics 

• Does not require culturing 

how does flow cytometry work

Bacteria-containing fluid passes through small opening in machine 

• Machine measures the difference in electrical conductivity (physical and chemical characteristics are observed)

describe GC % base pairs

used to analyze, manipulate, or replicate DNA regions with high GC content. Because GC pairs share three hydrogen bonds (compared to two in AT pairs), they require higher temperatures and specialized conditions to separate.

Nucleic acid amplification Tests (NAATS) describe

looks for presence or identification 

highly sensitive diagnostic tools that detect specific genetic material from viruses or bacteria 

PCR is used for

DNA

RT-PCR is used for

RNA