Classification of organisms

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Classification of organisms

• Kingdoms Eubacteria, Archaebacteria, Protist and
  Fungi

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classification

• Grouping objects or organisms based on a set of
  conditions.
• For biologists, doing this with all of the
  organisms there are on the earth, it makes it
  easier to study them!
• There are many different ways to group organisms.

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Early systems of classification

• Aristotle plant or animal
• Then animals were further classified based on
  habitat and physical characteristics.
• Plants were further classified by size and
  structure, trees, shrubs
• This system did NOT take into account the changes
  and evolutionary history of the organisms.

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New systems of classification

• In the 18th century
• Carolus Linnaeus developed
• Taxonomy
• A branch of biology concerned with naming,
  identifying and classifying species based on
  morphological and behavioral similarities and
  differences.
• Linnaeus gave each organism 2 names
• A genus and a species name and called this
  binomial nomenclature.

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Taxonomy

•   A systematic method of classifying plants and
  animals.
• Classification of organisms based on degrees of
  similarity representing evolutionary
  (phylogenetic) relatedness.

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Scientific Names

• Binomial nomenclature (Linnaeus)
• A 2 name system so that not two organisms will
  ever have the same name.
• The genus name is combined with a second name to
  make the species name unique.
• For example humans
• Genus Homo
• Species Homo sapiens

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Why 2 names?

• The name are Latin ( the language of science)
• The first is the genus
• The second is the epithet or specific identifying
  name. They are both needed to identify the
  organism.
• Common names can vary but scientific are
  universal.
• First names are capitalized, second are not.
• In books, names are italicized, if hand written
  they are underlined.
• The genus can be abbreviated with the first letter

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Human classification

• Kingdom Animalia
• Phylum (Division for plants) Chordata
• Class Mammalia
• Order Primates
• Family Hominidae
• Genus Homo
• Species Homo sapiens

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Levels of classification

• King Philip came over from Germany swimming

CLASS
KINGDOM
ORDER
PHYLUM
FAMILY
GENUS
SPECIES
SMALLEST
LARGEST
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Domains

• The largest groups
• Eukarya
• Archaea/ Archaebacteria
• Bacteria/Eubacteria

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• Each level has more and more similarities!

Domain Kingdom Phylum (Division for plants)
Class Order Family Genus Species
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6 Kingdoms
heterotroph
autotroph
heterotroph
autotroph
heterotroph
heterotroph
autotroph
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How has classification changed?

• Today classification looks at the evolutionary
  relationships and DNA similarities.
• Many organisms have been reclassified from where
  they were originally classified as new
  information is learned.

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genus

• A groups of organisms that are closely related
  and share a common ancestor.

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family

• A group of genera that have similar
  characteristics

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species

• Organisms so closely related that they can mate
  and produce fertile offspring in a natural
  setting.
• The biological species concept
• There are exceptions to this definition but it
  works for most organisms.
• Phylogenetic species goes with biologic and says
  the organisms have evolved independently from an
  ancestral population.

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phylogeny

• The evolutionary history of a species.
• Where did it come from?
• When organisms become isolated they become
  different, this can lead to new species

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characters

• Inherited features that vary among species
• Used by scientists to help put together the
  evolutionary history of a species its phylogeny.
• The more shared characters/the more closely
  related.
• Homologous structures show relationships
• Analogous structures dont

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Understanding phylogenetic trees

• http//www.youtube.com/watch?vxwuhmMIIspofeature
  youtube_gdata_player

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Dinosaurs and birds

• Oviraptor and sparrow
• Feathers, hollow spaces in bones similar bone
  structures to birds show more similarities to
  dinosaurs with birds then to reptiles.

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DNA sequences

• The more similar the sequences, the closer the
  relationship between the organisms.

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Molecular clocks

• Mutations occur randomly and can be used to
  determine how long the DNA has been mutating or
  changing from its original form.
• A major problem with this includes the fact that
  the genes dont mutate at a constant rate!
• These are used to try to determine when a
  divergence from a common ancestor occurred.

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cladistics

• A way to study evolutionary relationships.
• It rebuilds phylogenies and hypothesizes
  evolutionary relationships using shared
  characters.
• Cladograms show branching diagrams where each
  species may have originated.
• Kind of like a pedigree!

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• http//biology.unm.edu/ccouncil/Biology_203/Summar
  ies/Phylogeny.htm

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• Clades show hypothesized phylogeny based on DNA
  sequences, morphology all of the current
  information.
• Branches are called nodes.
• The closer to the end like species b and c, the
  more closely related..

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Construction a cladogram video

•  
• http//www.youtube.com/watch?v46L_2RI1k3kfeature
  youtube_gdata_player

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Cladograms
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Domains

• For now there are 3!

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Kingdoms/DomainsArchaea (Archaebacteria) and
Bacteria (Eubacteria)
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Archaea /Archaebacteria

• Prokaryotic
• Unicellular
• No nucleus
• No peptidoglycan on the cell walls
• Some similarities to eukaryotes in the cytoplasm
• Some Autotroph/ most heterotroph

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Archaebacteria

• The most primitive group, the archaebacteria, are
  today restricted to marginal habitats such as hot
  springs or areas of low oxygen concentration.

Three types of Archaebacteria methanogens,
halophiles, and thermacidophiles. They live in
extreme habitats like very salty water!
prokaryotes
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Domain and KingdomBacteria/Eubacteriaprokaryote
sunicellularno nucleuscell walls contain
peptidoglycansome autotrophs/most heterotrophs
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• Organisms in this group lack membrane-bound
  organelles associated with higher forms of life.
  Such organisms are known as prokaryotes.
• Their small size, ability to rapidly reproduce
  (E. coli can reproduce by binary fission every 15
  minutes), and diverse habitats/modes of existence
  make bacteria the most abundant and diversified
  kingdom on Earth.

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• Bacteria occur in almost every environment on
  Earth, from the bottom of the ocean floor, deep
  inside solid rock, to the cooling jackets of
  nuclear reactors.

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Rod-Shaped ( Bacillus) Bacterium, hemorrhagic E.
coli, strain 0157H7
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Scanning electron micrographs illustrating
external features of the rod-shaped bacterium E.
coli.
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Coccus round-shaped Bacterium (causes skin
infections), Enterococcus faecium
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Spiral shape bacteria (spirochete)
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Left, a cross-section of a cell illustrating the
location of a flagella inside the cell Center,
Borrelia burgdorferi, the organism that causes
Lyme disease and Right, Treponema pallidum, the
spirochete that causes the venereal disease
syphilis. The image above is from
http//www.bact.wisc.edu/Bact303/MajorGroupsOfProk
aryotes.
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binary fission
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Endospores

• are a method of survival, not one of
  reproduction. Certain bacteria will form a spore
  within their cell membrane (an endospore) that
  allows them to wait out deteriorating
  environmental conditions.
• Certain disease causing bacteria (such as the one
  that causes the disease Anthrax) can be virulent
  (capable of causing an infection) 1300 years
  after forming their endospores

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All other Kingdoms are made up of Eukaryotic
cellsDomain EUKARYAHAVE ORGANELLESA NUCLEUS
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Evolution of Eukaryotes

• The endosymbiosis hypothesis

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PROTISTS ??eukaryoticunicellular/ some
multiheterotrophic and autotrophic
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• New classification??
• Some plant like some animal like.
• This is a great example of how the system is
  constantly changing based on new information!!!

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Classification of Protists

• The protists include heterotrophs, autotrophs,
  and some organisms that can vary their
  nutritional mode depending on environmental
  conditions.
• Protists occur in freshwater, saltwater, soil,
  and as symbionts within other organisms.
• Due to this tremendous diversity, classification
  of the Protista is difficult.

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Protozoa Single-Celled, Motile Organisms
animal-like

• This group of protists are single-celled, motile,
  heterotrophs.
• Most digest their food by vacuoles formed by
  phagocytosing other organisms (bacteria or other
  single-celled creatures).
• Reproduction varies greatly, from a binary
  fission-like process to true meiosis.
• The main distinguishing feature is the method of
  locomotion flagella, cilia, or pseudopodia.

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Amoeboid Protozoa Use Pseudopods for Movement

• Amoeba and Pelomyxa move by extensions of their
  cytoplasm known as pseudopodia.

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Foraminifera

• live in the oceans and secrete a shell (also
  known as a test) composed of silica or calcium
  carbonate.
• Thus, the fossil record of forams is quite good.
  Oxygen isotope data from forams has been used to
  calculate ocean temperature fluctuations over the
  past 100,000 years.

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Sporozoans

• Members of this group cause malaria and
  toxoplasmosis.
• Toxoplasmosis is transmitted from cats to humans,
  with between 7 and 72 of the population
  infected, depending on the geographic area.

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Malaria

• infects an estimated 300 million people, and is
  spread by mosquitoes, transfusions, and shared
  hypodermic needles.
• Infected individuals can be treated with a
  variety of medicines. However, some of the
  sporazoans that cause malaria have developed
  immunity to some of the more commonly employed
  medicines.

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Ciliates

• Ciliates are complex, heterotrophic protozoans
  that lack cell walls and use multiple small cilia
  for locomotion.
• To increase strength of the cell boundary,
  ciliates have a pellicle, a sort of tougher
  membrane that still allows them to change shape.
• Most of the 8000 species are freshwater. Most
  ciliates have two nuclei a macronucleus that
  contains hundreds of copies of the genome and
  controls metabolisms, and a single small
  micronucleus that contains a single copy of the
  genome and functions in sexual reproduction.

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Paramecium is a common ciliate
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Paramecium Showing cillia
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Plant like ProtistsALGAE

• Photosynthetic Autotrophs
• Single and multicellular
• Phytoplankton are single cell basis of food
  chain
• diatoms, dinoflagellates,

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Rhodophyta, the Red Algae

• . Carrageenan is an additive to puddings and ice
  creams dried sheets of red algae are used in
  some Japanese dishes.

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Phaeophyta, the Brown Algae
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Chlorophyta, the Green Algae
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diatoms
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Red tides

• are caused by population explosions of certain
  dinoflagellates that release a neurotoxin into
  the environment.
• Shellfish concentrate this toxin and it can kill
  people who eat the contaminated shellfish.

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Fungus-like Protists

• Slime molds and mildews

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Slime Molds
Slime molds are often classified as fungi
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Euglenoidsboth plant and animal like

• Usually grouped with the plant like because they
  have the chloroplasts.

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Euglena
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FUNGIeukaryoticunicellular and
multicellularheterotrophicchitin in cell
wallscant move!Live in many environments
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Fungi

• Fungi are almost entirely multicellular (with
  yeast, Saccharomyces cerviseae, being a prominent
  unicellular fungus), Bread yeast

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• heterotrophic (deriving their energy from another
  organism, whether alive or dead), and usually
  having some cells with two nuclei (multinucleate,
  as opposed to the more common one, or
  uninucleate) per cell.

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• Ecologically this kingdom is important (along
  with certain bacteria) as decomposers and
  recyclers of nutrients.
• Economically, the Fungi provide us with food
  (mushrooms Bleu cheese/Roquefort cheese baking
  and brewing), antibiotics (the first of the
  wonder drugs, penicillin, was isolated from the
  fungus Penicillium), and crop parasites (doing
  several million dollars per year of damage).

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Structures in the bodies of fungi

• Hyphae filaments
• Fruiting bodies reproductive structures
• Cell walls made up of chitin
• Mycelium net like mass of hyphae

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• Beer and wine are produced through the action of
  fungi known as yeasts, such as Saccharomyces
  cerviseae.
• Many antibiotics are produced by fungi.

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• Fungi are important both as a source of food and
  in the preparation of food. Edible fungi include
  mushrooms, truffles, and morels. Cheeses such as
  Gorgonzola, Roquefort, Stilton, and bleu have
  fungal colonies that give theses cheeses their
  distinctive flavors.

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Reproduction of Fungi

• Budding
• Fragmentation
• spores

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Classification of Fungi

• Over 60,000 species of fungi are known. Fungi are
  classified by their method of reproduction (both
  sexual and asexual).
• Historically they have been divided into four
  taxonomic divisions Chytridiomycota (chytirids),
  Zygomycota (mold), Ascomycota (Yeast or sac
  fungi), Basidiomycota (club mushrooms), and
  Deuteromycota (imperfect).

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Mutualistic symbiotic fungal relationships

• Lichens fungus and algae
• Mycorrhizae fungus and plant roots

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• Genus Candida Disease(s) CandidiasisImage
  Legend Skin scraping from superficial
  candidiasis showing clusters of budding yeast
  cells and branching pseudohyphae.

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• Club fungi are important as commercial crops.
  They also cause many diseases that result in loss
  or reduction of grain yields.
• Agaricus campestris is the common mushroom found
  in grocery stores
• Lentinus edodes is the less commonly bought
  shitake mushroom more than 14 billion per year
  of these products are sold.

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• Amanita phalloides is the most poisonous of all
  mushrooms. Other mushrooms have hallucinogenic
  properties (such as the drug psilocybin)
  important in native religious rituals in Central
  and South America.

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Athlete's foot
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• Genus Epidermophyton Species
  floccosumDisease(s) Athlete's footTitle Tinea
  pedisImage Legend The disease is unusual
  because the nails are also involved.

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Genus Trichophyton Species verrucosumDisease(s
) Dermatophytosis, Tinea barbaeTitle
Dermatophytosis of the beard areaImage Legend
Severe tinea barbae caused when the patient
rubbed against cattle.
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Genus Microsporum Species gypseumDisease(s)
RingwormImage Type Microscopic
MorphologyTitle Macro- and microconidiaImage
Legend Macro- and microconidia. Lactophenol
cotton blue, phase contrast microscopy, 630X.
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Genus Microsporum Species canisDisease
TineaTitle Ringworm lesionsImage Legend
Ringworm lesions developed after an exposure to a
cat having ringworm.
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Genus Saccharomyces Species cerevisiaeDisease
(s) Disseminated infection VulvovaginitisImage
Type Microscopic MorphologyTitle Acid fast
stainImage Legend Asci, containing broadly
elliptical ascosporesColor enhanced.
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Bread mold
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plantae

• Multicellular
• Eukaryotic
• Cell walls with cellulose
• Autotrophic photosynthetic
• Some are heterotrophs
• Live in water and on the land
• Cant move

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Animals/Animalia

• Multicellular
• Eukaryotic
• Without cell walls
• Heterotrophs
• Live in water and on land
• Most can move / at least at some point in their
  life

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Viruses
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adenovirus
The Adenovirus is a DNA virus that causes colds
and "pink eye".                                
                                                  
                              
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The Papillomavirus is a DNA virus that causes
warts.
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The Influenza virus causes the flu. It has RNA as
its genetic material instead of DNA.
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• Bacteriophages invade the host cell, take over
  the cell, and begin replicating viruses,
  eventually lysing or bursting the host cell,
  releasing the new viruses to infect additional
  cells.

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Lysogenic cycle
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Lytic Cycle
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Retroviruses

• Retroviruses have RNA and the enzyme reverse
  transcriptase instead of DNA as their nucleic
  acid core.
• Once inside the host cell, reverse transcription
  (making DNA from RNA) is accomplished by the
  reverse transcriptase, turning the
  single-stranded RNA into DNA. This new DNA is
  incorporated into the host DNA, where it
  transcribes new viral RNA genomes, as well as the
  RNA to synthesize new reverse transcriptase and
  protein capsules.

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• Viruses are usually quite specific as to their
  hosts and even to the types of cells they infect
  in a multicellular host.
• Viruses can NOT be treated with antibiotics
  because antibiotics are designed to attack the
  cell wall or membrane and viruses do not have
  these!

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Viroids and Prions

• Viruses would appear to be the simplest form of
  infectious particle.
• The discovery of viroids, nucleic acid without a
  protein capsule and prions, infectious proteins,
  subtracts another level of complexity.
• Both viroids and prions can cause diseases.

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Review sheet

• 1. What is taxonomy?
• It is a systematic method of classifying plants
  and animals.
• 2. What is binomial nomenclature?
• It is a 2 name system so that no two organisms
  will ever have the same name.
• 3. Who is the person who came up with the 2 name
  system?
• (Linnaeus)

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• 4. What are the levels of classification from
  least to most specific?
• Kingdom , Phylum (Division for plants) , Class,
  Order , Family , Genus , Species
• 5. Name the 6 kingdoms
• Archaebacteria, Eubacteria, protist, fungi,
  plant, animal

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• 6. Are viruses alive? Why or why not?
• Viruses are NOT one of the 6 kingdoms and are
  not considered alive because they are not made
  up of cells, do not metabolize, can only
  reproduce inside another living cell and do not
  grow.
• 7. What is a virus?
• A virus is a submicroscopic infectious particle
  composed of a protein coat and a nucleic acid
  core.
• 8. Can viruses be treated with antibiotics?
• Viruses can NOT be treated with antibiotics
  because antibiotics are designed to attack the
  cell wall or membrane and viruses do not have
  these!

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• 9. What are the characteristics of the kingdom
  Archaebacteria?
• Prokaryotic, Unicellular, Autotroph/ heterotroph
• 10. What are examples of A bacteria? Where do
  you often find them?
• Three types of Archaebacteria methanogens,
  halophiles, and thermacidophiles.
• They live in extreme habitats like very salty
  water!
• 11. Describe Eubacteria
• Prokaryotes, unicellular, autotroph/heterotroph
  

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• 12. What are the three main shapes of bacteria?
• Round, cocci, Rod, bacilli, Spiral, spirilli
• 13. What is binary fission? Cell division
• Why do bacteria use this? Bacteria can
  reproduce by binary fission
• 14. Describe the Protist kingdom.
• Eukaryotic, unicellular/ some multi,
  heterotrophic and autotrophic

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• 15. List some examples of protists
• Euglena, amoeba, red algae
• 16. Describe the FUNGI kingdom eukaryotic,
  multicellular, heterotrophic, chitin in cell
  walls
• 17. List some examples of fungi.
• Mold, athletes foot, mushrooms