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Classification of Organisms
1st system of Classification was designed by Aristotle, all organisms were categorized as
walks on land, swims in water, or fly in the sky.
Carolus Linneaus’ system replaced Aristotle’s using a series of categories.
Common features were used to place them in categories.
The more categories organisms share the more closely related they are.
Binomial Nomenclature- system of assigning 2 names to every species
Scientific Name- genus and species, ex Homo sapien (human), Canis lupus (wolf)
Traditional Classification system: What Linnaeus also did was systematically
categorize all known organisms. Linnaeus came up with a hierachy of ways to classify
plants and animals. The different levels are called taxa (plural of taxon). The different
taxa are:
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Kingdom
Phylum
Class
Order
Family
Genus -part of the scientific name
Species -part of the scientific name
Domain and Kingdom are the broadest of the taxa, all animals are in Kingdom
Animalia, all plants are in the Kingdom Plantae. The taxa Domain is the newest
addition, and was created to differentiate the two very different groups of bacteria.
Phyla are slightly less broad. There are usually a few phyla in each kingdom. Species
is the most restricted.
Taxonomist classify new organisms. Historically classification was based on easily
observable structures, and gradually this was extended to microscopic and electronmicroscopic detail. The recent advances in embryology and molecular biology have given
new tools such as patterns of life cycle, larval development, and gene sequences. These
have often led to radically different phylogenies (e.g. humans should really be the "third
chimpanzee"). After they assign each new organism a scientific name, taxonomist work
closely with Evolutionary Biologist to develop the organism’s phylogeny (evolutionary
history this is part of the science of systematics, the study of biodiversity and its
classification. Using comparative anatomy, embryology, fossil record, and molecular
biology, scientist can search for common ancestors and develop a cladistic analysis or
phylogenetic tree.
The cladogram depicts patterns of shared characteristics among taxa and forms the basis
of a phylogentic tree. A clade, within a tree, is defined as a group of species that includes
an ancestral species and all its descendants.
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Molecular Clocks help track evolutionary time, this method is used to measure the
absolute time of evolutionary change based on the observation that some genes and other
regions of the genome appear to evolve at constant rates. The rate of evolution of DNA
sequences varies from one part of the genome to another. Comparing these sequences and
analyzing the number of differences given scientist and idea of when they had a common
ancestor and when they diverged.
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DNA that codes for ribosomal RNA changes relatively slowly and is used to
investigate relationships in taxa that diverged hundreds of millions of years ago.
 DNA that codes for mitochondrial DNA evolves rapidly and is used to investigate
more recent evolutionary events, for instance the evolution and migration of man.
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Helpful resource: http://evolution.berkeley.edu/evolibrary/article/phylogenetics_01
Dichotomous key, is a tool used to identify an unknown species. It is written using two
questions at a time with a directive. The end result is the user can give the scientific name
of the species after looking at specific characteristics and narrowing down the choices.
The Evolution of Complexity: single cell prokaryote to multicelluar eukaryotes
Earth is approximately 4.5 billion years young
The first living things, prokaryotic bacteria cells, are found in 3.5 billion year old strata/
fossil record
The oldest fossils of Eukaryotic cells appear in 2.1 billion year old strata
Between 635- 530 million years ago the fossil record shows the diversity of algae and
small
Biogenesis: theory that life comes from life
How did life begin? The hypothesis of Oparin and Haldane were tested by Stanley Miller
in 1953, Miller was able to recreate anaerobic conditions similar to those hypothesized by
Oparin and synthesize organic molecules from inorganic using an apparatus he built.
Research on prebiotic origin of organic compounds continues.
Virus: Not a living cell, but rather a protein coat surrounding genetic material either
DNA or RNA.(retroviruses contain RNA and reverse transcriptase to transcribe RNA into
DNA ex. HIV)
Two types of viruses: 1. reproduce using Lytic cycle, the virus DNA takes over the host
cell to produce copies of the virus and ends in the lysis or death of the host cell. 2.
Lysogenic cycle, the DNA is incorporated into the genome of the cell..
Modern Classification system:
Domain, Kingdom, Phylum, Class, Order, Family, Genus, species
Domain was added when it was discovered that bacteria (Monera) were not that closely
related to each other, in fact some bacteria have more in common with eukaryotes than
other bacteria.
3 Domains: Archea, Bacteria, Eukarya
6 Kingdoms: Archeabacteria, Eubacteria, Protista, Fungi, Plantae, Animalia
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Common Characteristics of each Kingdom:
Kingdom
Archeabacteria
Eubacteria
Protista
Fungi
Plant
Animal
Characteristics
Prokaryotes, extreme environments: deep ocean, volcanic
ridges, geysers, hot springs, salt lakes, heterotrophic or
autochemotrophs, no peptidoglycan in cell membrane, has
histones and introns associated with DNA/chromosome
Prokaryotes, 3 common shapes rod, sphere, spiral, may be
autotrophic or heterotrophic, has peptidoglycan which is how
they are classified (Gram + or Gram -) no histones or introns
associated with their DNA/chromosome
ex. E.coli, Streptococcus
Eukaryotic cells (with nucleus) typically single celled but may
form colonies, Autotrophic- Algae, Heterotrophic Protozoa and
fungus-like
Eukaryotic multicelled, Heterotrophs, cell wall of chitin,
reproduce with spores, can not move
Eukaryotic multicelled, Autotrophs, cell wall of cellulose,
reporoduce with spores or seeds, can not move
Eukaryotic multicelled, Heterotrophs, can move, no cell wall,
can be invertebrate or vertebrates
Domain: the broadest taxa
Characteristic
Nucleus
Membrane bound organelles
Introns
Histone proteins associated
with DNA
Circular chromosome
Peptidoglycan in cell wall
Hydrocarbon content
Bacteria
No
No
No
No
Archaea
No
No
Yes
Yes
Eukarya
yes
yes
yes
yes
Yes
yes
Un-branched
hydrocarbons
Yes
no
branched
hydrocarbons
no
no
Un-branched
hydrocarbons
6 Kingdoms:
1. Archeabacteria- prokaryotes, most ancient and extreme, living in the harshest
environments, include methanogens (anaerobic/no oxygen), thermoacidophiles (hot), and
extreme halophiles (salty). No Peptidoglycan in cell wall
2. Eubacteria- prokaryotes, true bacteria, have peptidoglycan, classified by their shape
and response to gram staining (gram positive high level of peptidoglycan, gram negative
less peptidoglycan)
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Eubacteria Shapes:
Sphere- Cocci, can occur in chains Streptococcus pneumoniae which can cause Strep
throat or Scarlet Fever, or grapelike clusters Staphylococcus aureus causes Toxic Shock
Syndrome
Rod- Bacillus ex. Escherichia coli (E.Coli), Lactobacilli causes tooth decay, botulism,
typhoid fever, anthrax
Spiral- Spirilla ex Vibro (curved) ex Cholera, Spirillum (thick spiral), Spirochete (thin
spiral) ex Treponema pallidum causes Syphilis and Lyme disease
Cyanobacteria- photosynthetic bacteria, contain pigments- yellow, red, brown, green,
and even black, some are blue-green. Like plants they thrive on Phosphates and Nitrates
and can have a Population Bloom if water ways become loaded with fertilizer (process
called Eutrophication)
Nitrogen-Fixing Bacteria- grow symbiotically in the roots of plants, fixing atmospheric
nitrogen into ammonia so plants can utilize it.
Asexually reproducing – bacteria still have a tremendous amount of diversity. They have
Rapid reproduction, rapid mutation rates, and genetic recombination due to the following:
Transformation: taking up DNA fragments from the environment
Conjugation: exchanging DNA plasmids with another bacteria via a cytoplasmic bridge
Transduction: a virus delivers genetic material to the bacteria, which gets incorporated
into the genome of the bacteria
All Prokayotes:
Reproduce asexually
By binary fission
Single Celled organisms
Cell Wall
Single Strand of DNA
Some:
Autotrophic or Heterotrophic
some produce toxins
Some movement using flagella, slime, spiral motions
Some produce Endospores and go dormant during
extreme/hostile conditions
Bacteria can be helpful: fermentation process, digestion, biotechnology like
bioremediation where bacteria help digest petroleum products or
heavy metals in water or soil, nitrogen-fixing a symbiotic
relationship some bacteria have with plants, photosynthetic
bacteria fill water ways and oceans and act as CO2 sponges and
release oxygen also.
Bacteria can be killed using antibiotics which destroy the cell wall, Gram Negative
bacteria have and extra lipid layer that stops antibiotics from
entering the bacteria
Eukaryotes
evolved about 1.2 billion years ago.
Endosymbiosis: theory that bacteria gave rise to eukaryotic cells by engulfing bacteria
capable of photosynthesis and cellular respiration. This is the
origin of the organelles mitochondria and chloroplast
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3. Protistia
Kingdom of Mostly single celled organisms
Categorized by their likeness to 3 other kingdoms
All Eukaryotic some Autotrophic and some Heterotrophic
3 classifications:
Algae or Plant-like, Autotrophic, classified by pigment, cell wall, can join to form
elaborate colonies and multi-cellular structures (kelp and seaweed)
gave rise to land plants.
Chrysophyta- Golden Algae ex diatoms
Pyrrophyta- bioluminescent ex. Dinoflagellates - cause red tide
Euglenaphyta- ex Euglena
Rhodophyta- red
Phaeophyta- brown, seaweed and kelp
Chlorophyta- green, ex Volvox, Spirogyra
Protozoa or Animal-like, classified by mode of movement
Sarcodina ex. Amoeba- move by pseudopodia “false foot”
Ciliophora ex Paramecium- move by cilia, tiny hairs
Zoomastigina ex Trypanosoma (African Sleeping Sickness) moves
by flagella
Sporozoa, are the parasitic animal like protista, include
Plasmodium which causes Malaria
Fungus-like are all Heterotrophic with no cell wall, absorbing nutrients directly through
cell membrane
Include Slime Molds and Downy Mildews
Multicelled Eukaryotes-The colonization of land
occurred about 500 million years ago
when plants, fungi, and animals began to
appear on Earth
4. Fungi
All Eukaryotic, multicellular, heterotrophs (saprotrophs or detrivores living off
dead and decaying organisms or decomposers), cell wall made of chitin (type of
protein), and classified by reproductive structures.
Mycoses is the term for Fungal Infection, Fungus destroys the cells around the
infection site, to fight fungal infection you have to destroy the cell wall
Fungi are important part of an ecosystem because they recycle nutrients
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Club Fungi – Basidiomycota , Basidia, ex Mushrooms
Sac Fungi- Ascomycota, Asci, ex. Yeast, and Athletes Foot Fungus
Zygote Fungi – Zygomycota, Sporangia, ex. Bread molds
Imperfect- Deuteromycota, reproduce asexually, ex Penicillian
Lichen- Mycophycophyta, symbiotic relationship between fungus and photosynthetic
cells of cyanobacteria or algae.
5. Plantae
Multicellular, Eukaryotic, Cell wall made of cellulose, Autotrophs, not capable of
movement, reproduce sexually some produce spores and others seeds.
Most have vascular tissues which include roots, stems, and leaves, and specialized
tissues called xylem and phloem.
9 divisions of Plant Kingdom:
Spore producers
 Bryophyta only nonvascular plants, ex moss and liverwort (gametophyte
dominant stage of life cycle know as alternation of generations)
 Lycopodophyta ex. 1,000 species of Club and Spike moss
 Sphenophyta ex. 10 species of Horsetails
 Filicinophyta ex 11,000 species of Ferns (sporophyte dominant stage)
Seed producers
Gymnosperms: reproductive structure is the cone , “naked seed”
o Cycadophyta 200 species of these tropical plants
o Ginkgophyta 1 species remains the Gingko tree
o Coniferophyta 600 species of conifers, pine, spruce, cypress, juniper,
fir
o Gnetophyta 70 species of these arid/semi-desert dwelling plants
Angiosperms: reproductive structure is the flower, seeds are surrounded by
fleshy or dry fruit that ripen to encourage animals to disperse the seeds.
30,000 or more identified species
maple, hickory, oak, aloe, roses, tulips, dogwood, magnolia, corn, beans, tobacco,
apple tree, pecan tree
Monocots – corn, with one seed leaf or cotyledon and parallel veins on the leaf,
Dicots- beans, with two seed leafs and branched veins on the leaf
Symbiotic relations ships:
Plants and Bacteria
Flower patterns and scent attract pollinators
Fruits promote seed dispersal by offering a sweet reward to animals.
Plant Adaptations include hormones that control, phototropism, geotropism, and
thigmotropism, specialized leaves (needles, spines, fuzzy, waxy), specialized seed
capsules (wind, float, food, wings, burrs, sticky)
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6. Animalia
multicellular, eukaryotic, no cell wall, heterotrophs, capable of movement, reproduce
sexually, body symmetry (radial or bilateral)
Invertebrates: 8 phyla
 Porifera- two cell layers, collar cells w/flagella, filter feeders, ex. sponges
 Cnidarians- Stinging cells, radial symmetry, simple nervous system only
stimulus and response, central cavity only one body opening, ex. jellyfish,
coral, hydra, sea anemone
 Plathyhelmenthes, flat worms, only one body opening, three cell layers, but no
true body cavity (acoelomates)
ex. Tapeworm, Fluke, Planarian, Marine
worms
 Nematode, round worms, first with two body openings, 3 cell layers,
(pseudocoelomates) many parasitic, Heartworm, Roundworm, Vinegar Eel
 Annelid, segmented worms, two body openings, 3 cell layers, (coelomates
true body cavity) beginning of circulatory system, and digestive system
(crop), ex. Earthworm and Leech
 Mollusk, soft body, more complex body systems developing, eyes and
nervous system, levels of communication beyond stimulus and response, 3
classes include Gastropod (snails and slugs), Cephalopod (squid octopus
cuttlefish and chambered nautilus), Bivalve (oyster, clam, mussel, scallop)
 Arthropod, jointed legs, exoskeleton, body segments (head, thorax, and
abdomen), metamorphosis (complete or incomplete) 4 classes include Insect 6
legs (ant, grasshopper, beetle, bee, wasp) Arachnid 8 legs (spider, tick,
horseshoe crab), Crustacean 10 legs (shrimp, lobster, barnacles, crayfish), and
Myrapods many legs, centipede and millipedes
 Echinoderm, spiny skin that covers and endoskeleton, complex regeneration
capacity, found only in marine environments, radial symmetry, ex Sea urchin,
Sand dollar, Starfish, Sea cucumber
o Echinoderms and Chordates share a developmental characteristic: they
are deuterosomes which means during the gastrula stage and the
formation of the coelom or body cavity the anus is formed first, the
other bilateral inverts are protostomes and they develop their mouth
first.
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Chordata, notachord, complex body systems, sexual reproduction (internal
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or external fertilization)
Two invertebrate subphyla- tunicates and lancelets separated from the other
Chordata 550 million years ago during Precambrian
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 Subphyla vertebrates with 5 classes:
o Fish, moist skin covered in scales, gills to breathe, 2 chambered heart, cold
blooded, 3 types: 1.jawless, ex. Lamprey
2. Bony (Osteichthyes) ex Trout, Salmon, Bass, Catfish, Grouper, Tarpon.
and
3. Cartilaginous (Chondrichthyes) ex. Sharks and Rays
o Amphibian, cold blooded, 3 chambered heart, born in water, develop lungs,
smooth moist skin, ex. salamander, newts, skinks, frogs, and toads (only dry
skin)
o Reptile, dry leathery skin with scales, cold blooded, 3 chambered heart except
for crocodile and alligator which have 4, amniote/terrestrial eggs, ex. Lizards,
snakes, turtles, alligator, crocodile
o Bird, (Aves) warm blooded, 4 chambered heart, hollow bones, body with
feathers
o Mammalia, warm blooded, 4 chambered heart, milk producers, body with
hair/fur
o Placental (live birth), Marsupial (pouch) ex. Kangaroo, and Monotremes
(egg) ex Platypus
o Humans belong to the order Primates along with monkeys and gorillas.
Common characteristics include: opposable thumbs, large brains and short
jaws, forward looking eyes, flat nails, well-developed parental care, and
complex social behavior.
o Human alone have evolved increades brain volume, shortening of the jaw,
bipedal posture, reduced size difference between sexes, and certain important
changes in family structure.
Animal Behaviors and Adaptations:
Innate Behaviors and Learned Behaviors
Innate:
1. Instincts- complex pattern of innate behaviors, reflexes, fight or flight,
courtships, species recognition (language, song, flashes of pattern/light)
2. Territory- physical space needed for breeding, feeding, and shelter, organisms
can expend a lot of energy defending territory some will fight to the death.
3. Migration- instinctive seasonal movement, response to a changing environment,
includes hibernation (cold) and estivation (dry and hot)
Learned:
1. Habituation- animal repeats a successful behavior, and does not repeat an
unsuccessful behavior, birds learn which moths are poisonous by color and avoid
eating them after becoming ill or getting a bad taste. Deer return to the same
grazing field when successful.
2. Imprinting – salmon and turtles return to same stream or beach to lay eggs in
which they hatched, the environment left an imprint or memory
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Adaptations for Defense:
1. Mechanical- physical structures
2. Chemical- stinging sensations, poisons, bad taste, paralysis
3. Camouflage- color or pattern that blend into environment
o Disruptive- ex zebra
o Cryptic- ex chameleon and squid
o Countershading- ex Fish have light belly and dark back
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