Biology 2
Dr. Tim Revell
Welcome to Bio 2!
•  Plant and Animal Interactions
•  Second Semester Majors Course
•  A course on Taxonomy, Biodiversity,
Ecology, Conservation, Comparative
Anatomy and Physiology
•  What have you heard???
•  Powerpoint
– Notes
– Coming to class
– Camera!
– Everything in the powerpoints is fair
8/30/16
game for lecture quizzes/exams!
2
Class Expectations
•  No Cell Phones (talking or texting)!
•  No Cheating, stealing, or other
behaviors deemed unethical
•  Be On Time; Be Awake; Be
present!
•  Participate
•  Grades/Letters of Rec
•  Questions?
8/30/16
3
SI/Coaching
•  1 point each session – Max 30
(You can still go but can’t earn more
than 30)
8/30/16
4
Carl Linneaus
q Father of “_________”
q Swedish botanist,
physician, and zoologist
q Wrote Systema Naturae in
1735
q The science concerned
with naming and
classifying the diverse
forms of life
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Domain Bacteria:
Group: Proteobacteria
ex: Salmonella, E. Coli
Group: Gram (+) Bacteria
ex: Clostridium, Bacillus Anthracis,
Streptococcus, Staphylococcus
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Group: Cyanobacteria
ex: Oscillatoria
Group: Spirochetes
ex: Treponema pallidum,
Borrelia burgdorferi
Group: Chlamydias
ex: Chlamydia
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Domain Eukarya, Kingdom Protista
Supergroup: Excavata
Clade: Diplomonads
Clade: Parabasalids
Clade: Euglenozoans
Group:
Group:
Supergroup: Chromalveolatas
Clade: Alveolatas
Group:
Group:
Group:
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Kingdom Plantae
Division: Hepatophyta (liverworts)
Division: Anthocerophyta (hornworts)
Division: Bryophyta (Mosses)
Division: Lycophyta (Club Mosses)
Division: Pterophyta
* Psilophyta (Whisk Ferns)
* Sphenophyta (Horse Tails)
Division: Pterophyta (Ferns)
Division: Ginkgophyta
Division: Cycadophyta
Division: Gnetophyta
Division: Coniferophyta
Division: Anthophyta
Domain Archaea:
Group: Methanogens
Group: Halophiles
Group: Thermophiles
Euglenids
Kinetoplastids
Dinoflagellates
Apicomplexans
Ciliates
Clade: Stramenopila
Group:
Group:
Group:
Group:
Kingdom Fungi:
Division: Chytridiomycota
Division: Zygomycota (Zygomycetes)
Division: Glomeromycota
Division: Ascomycota
Division: Basidiomycota
Division: Deuteromycota
Bacillariophyta
Phaeophyta
Chrysophyta
Oomycota
Supergroup: Rhizaria
Group: Foraminiferans
Group: Radiolarians
Supergroup: Archaeplastida
Group: Rhodophyta
Group: Chlorophyta
Supergroup: Unikonta
Clade: Amoebozoans
Group: Slime molds
Group: Gymnamoebas
Group: Entamoebas
Clade: Opisthokonts
Group: Nucleariids
Group: Choanoflagellate
Kingdom Animalia
(Lophophorate Phyla)
Phylum: Bryozoa
Phylum: Phoronida
Phylum: Brachiopoda
Phylum Porifera
Class: Calcarea
Class: Hexactinellidae
Class: Demospongiae
Phylum Cnidaria
Class: Hydrozoa
Class: Scyphozoa (Jellies)
Class: Anthozoa
Class: Cubozoa (Box Jellies)
Phylum Ctenophora (Comb Jellies)
Phylum Platyhelminthes (Flatworms)
Class: Tubellaria
Class: Monogenea
Class: Trematoda
Class: Cestoidea
Phylum Rotifera
Phylum Nemertea (Ribbon Worms)
Phylum Nematoda (Round Worms)
Phylum Mollusca
Class: Monoplacophora
Class: Polyplacophora
Class: Gastropoda
Class: Scaphopoda
Class: Bivalvia
Class: Cephalopoda
Phylum Annedlida
Class: Oligochaeta
Class: Polychaeta
Class: Hirudinea
Phylum Onychophora
Phylum Arthropoda
Subphylum: Trilobita
Subphylum: Chelicerata
Class: Merostomata
Class: Pycogonida
Class: Arachnida
Subphylum: Crustacea
Class: Crustacea
Subphylum: Uniramia/Myriapoda
Class: Chilopoda
Class: Diplopoda
Subphylum: Hexapoda
Class: Insecta
Phylum Echinodermata
Class: Asteroidea
Class: Ophiuroidea
Class: Echinodea
Class: Holothuroidea
Class: Cnnoidea
Phylum Chordata
Subphylum: Urochordata (tunicates)
Subphylum: Cephalochordata (lancelets)
Subphylum: Vertebrata
Superclass: Agnatha (lampreys/hagfish)
Superclass: Gnathostomata
Class: Chondrichthyes
Class: Osteichthyes
Superorder: Ostariophysi
Superorder: Procantheropterygii
Superorder: Acantheropterygii
Class: Amphibians
Order: Urodela (Salamanders)
Order: Anurans (Frogs/Toads)
Order: Apodans (Caecillians)
Reptiles
Class: Testudines (Turtles/Tortoises)
Class: Sphenodontia (Tuataras)
Class: Squamata (Lizards/Snakes)
Class: Crocodilia
Class: Dinosauria
Order: Omithiscians
Order: Sauriscians
Class: Aves
Order: Passeriformes
Order: Anseriformes
Order: Columbiformes
Class: Mammalia
Order: Monotremata
Order: Marsupialia
Superorder: Eutheria
Order: Artiodactyla
Order: Perissodactyla
Order: Rodentia
Order: Carnivora
Order: Sirenia
Order: Cetaceans
Order: Insectivora
Order: Lagomorpha
Order: Probocidea
Order: Chiroptera
Order: Edentata
8/30/16
9
Bacteria - Prokaryotes
Bacteria Characteristics
•  Nucleoid Region
–  single circular
chromosome
–  plasmids
•  No membranebound
organelles
•  Ribosomes
(70S)
•  Plasma
membrane
•  Cell wall
_____________
•  Capsule
– glycocalyx
•  Flagella
•  Pilli
•  Fimbrae
Classification
•  Shape (Cocci or Rod)
•  Staining
– Gram
– Spore
– Acid-fast
•  Oxygen requirements
•  Feeding strategies
Shapes
•  Sperical (Cocci)
•  Rod-Shaped
(Bacillus)
•  Spiral
(Spirochetes)
8/30/16
15
Shapes and Groups
Cocci:
Spherical
_____ –
in lines
_____ –
in grape
like
clusters
Shape
Helical:
Spiralshaped
(Spirillium)
Shape
Filamentous
Gram Stain
•  Bacteria are stained with a violet
dye and iodine
•  Rinsed in Alcohol (Gram + retain
violet dye, Gram - decolorize)
•  Stained again with a red dye
•  Results
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– 
= gram positive
= gram negative
Know these steps!
Lab
Acid-fast Stain
–  Mycobacterium leprae, M.
tuberculosis (Acid-Fast + Red,
Negative Blue)
8/30/16
24
Spore Stain
Oxygen Requirements
•  Obligate aerobes – require oxygen
•  Obligate anaerobes – require no
oxygen
•  ____________________– can grow
with or without oxygen
•  Aerotolerant Anaerobes – only
anaerobic growth but oxygen does not
harm.
•  _________________– aerobic growth
in low oxygen concentrations.
Feeding Strategies
•  Based on energy and carbon
sources
– Photoautotrophs
– Chemoautotrophs
– Photoheterotrophs
– Chemoheterotrophs
Feeding Strategies
Good essay Question!
Nitrogen Metabolism
Which tree is most parsimonious?
Phylogeny of Prokaryotes
5 Groups of
Bacteria
Domain: Bacteria
•  Group:Proteobacteria
–  Salmonella
•  bacillus shape, gram
negative, facultative
anaerobe
•  Diarrhea, nausea –
(chicken and reptiles)
• 
– caused by
cell wall
Domain: Bacteria
•  Group: Proteobacteria
–  E. coli
•  bacillus shape, gram
negative, facultative
anaerobe
•  Diarrhea
• 
– releases
proteins that cause illness
Domain: Bacteria
•  Group: Gram-positive
bacteria
–  Clostridium
•  Bacillus shape
•  endospore
•  Obligate anaerobes exotoxins
•  Causes gangrene,
__________ (strongest
poison in the world! – 1
gram can kill 1 million
people!)
Domain:
Bacteria
•  Group: Grampositive bacteria
–  Bacillus anthracis
•  Bacillus shape
(endospore)
•  Aerobic
•  Causes pustules,
pneumonia
Domain:
Bacteria
•  Group: Grampositive bacteria
–  Streptococcus
•  Coccus shape &
gram positive,
anaerobic but are air
tolerant
•  necrotizing fasciitis,
strep throat, scarlet
fever
Domain:
Bacteria
•  Group: Gram-positive
bacteria
–  Staphylococcus, MRSA
•  coccus shape & gram
positive, facultative
anaerobe
•  Most common type of
food poisoning, toxic
shock syndrome
•  Dangerous in
hospitals (________
infections)
•  Iatrogenic
•  Group:
Cyanobacteria
–  Contains
Chlorophyll A
and
phycocyanin
•  Only organism
on planet that
can fix
nitrogen and
release
oxygen
•  pools
Domain:
Bacteria
Domain: Bacteria
•  Group: Spirochetes
–  __________________
• Syphilis
• anaerobic
–  __________________
• Lyme Disease
• Microaerophile
• 
Domain: Bacteria
•  Group: Chlamydias
–  Chlamydia
•  coccus shape &
gram negative
•  Causes blindness
and is one of the
most common
STD’s in U.S.
•  Oxygen requirement
uncertain
Origins of Eukaryotic
Diversity – Protists Diversity
Water Molds
(Oomycota)
For
Lecture,
Make
sure
you
know
the
names
and
charact
eristics
Characteristics
Four Supergroups:
•  Excavata
•  SAR
(Stramenopiles,
Alveolata, Rhizaria)
•  Archaeplastida
(includes land plants)
•  Unikonta (includes
animals and fungi)
Supergroup: Excavata ex. Giardia
Clade: Diplomonads “excavated”
groove on one
side of the body
(lack plastids,
lack DNA in
mitochondria,
two _______
nuclei, flagella,
simple
cytoskeleton)
Supergroup: Excavata
Clade: Parabaslids
ex.
Trichimonas
(Causes Trichomoniasis)
“excavated” groove
on one side of the
body
(lack plastids,
lack DNA in
mitochondria,
___________
__________)
Supergroup: Excavata
Clade: Euglenozoa
“excavated” groove on one side of
the body
•  Move by flagella with spiral or
crystalline rod
•  2 Groups:
– Euglenids
– Kinetoplastids
Supergroup: Excavata
Clade: Euglenozoa
Group: Euglenids
Supergroup: Excavata
Clade: Euglenozoa
Group: Kinetoplastids
ex.
___________
(single large
mitochondria
with kinetoplast
- organized
mass of DNA)
Supergroup: SAR
Clade: Alveolata
•  Supergroup Char: DNA
•  Clade characteristics: Contain
Alveoli (membrane-bounded sacs)
beneath their cell surface
•  3 Groups:
– Dinoflagellates
– Apicomplexans
– Ciliates
Supergroup: SAR
Clade: Alveolata
Group:
_____________
(2 flagella
located within a
groove,
xanthophyll)
Supergroup: SAR
Clade: Alveolata
group:
Apicomplexans
ex. __________
(parasitic, apical
structure)
Supergroup: SAR
Clade: Alveolata
Group: Ciliates (have Cilia used for
movement)
Supergroup: SAR
Clade: _____________
•  Supergroup Char: DNA
•  Clade characteristics: Have hairlike projections on flagella
•  Four Groups:
– Diatoms (Bacillariophyta)
– Golden Algae (Chrysophyta)
– Brown Algae (Phaeophyta)
– Water Mold (Oomycetes)
Supergroup: SAR
Clade: Stramenopiles
Groups: Diatoms
Supergroup: SAR
Clade: Stramenopiles
Groups: Golden Algae
(Chrysophyta)
cell wall: ________
pigments: carotene,
xanthophyll
Supergroup: SAR
Clade: Stramenopiles
Groups: Brown Algae
Supergroup: SAR
Clade: Stramenopiles
Groups: Water Molds
(Oomycota)
pigments:none
cell wall:
cellulose,
coenocytic
(aseptate)
hyphae
Irish Potato Famine, French Wine Crisis
(1800’s)
SAR (Rhizaria)
•  Thin pseudopodia Used
for movement and
feeding
•  Groups:
– Cercozoans
– Foraminiferans
– Radiolarians
Supergroup: SAR
Group: Cercozoans
Plastids surrounded by
four membranes
(secondary
endosymbiosis).
2 from cyanobacterium
3rd from alga’s plasma
membrane
4th from heterotrophic
food vacuole.
Supergroup: SAR (Rhizaria)
Group: Foraminiferans (Forams)
porous shells –
made of
____________
Supergroup: SAR (Rhizaria)
Group: Radiolarians
Supergroup: Archaeplastida
•  Ancient protists that
engulfed a
cyanobacterium
•  Three Groups:
–  Red Algae
(Rodophyta)
–  Green Algae
(Chlorophyta)
–  Land Plants
Supergroup:
Archaeplastida
Group: Rhodophyta
(Red)
•  Red Algae
•  Phycoerythrin
Supergroup:
Archaeplastida
Group: Chlorophyta
(& Charophytes)
Supergroup: Unikonta
•  Very Diverse Group
•  Molecular Systematics links groups
(but highly debatable)
– Two Clades:
• Amoebozoans
• Opisthokonts
Supergroup: Unikonta
Clade: Amoebozoans
Group:Slime Molds
Group:Gymnamoebas
Group:Entamoebas
• Many With Lobe
or tube shaped
_____________
Supergroup: Unikonta
Clade: Amoebozoans
Group:Slime Molds
Group:Gymnamoebas
Group:Entamoebas
•  Produce fruiting body
that aids in spore
dispersal
•  Plasmoidial – NOT
________________
•  From a plasmodium
(feeding stage) single
mass of cytoplasm
with many nuclei
–  diploid
Supergroup: Unikonta
Clade: Amoebozoans
Group:Slime Molds
Group:Gymnamoebas
Group:Entamoebas
•  Produce fruiting body
that aids in spore
dispersal
•  ___________
•  (feed like individual
amoebas)
–  aggregate to breed
or during stress
Haploid Organisms
Supergroup: Unikonta
Clade: Amoebozoans
Group:Slime Molds
Group:Gymnamoebas
Group:Entamoebas
Supergroup: Unikonta
Clade: Amoebozoans
Group:Slime Molds
Group:Gymnamoebas
Group:Entamoebas
Most are parastic
amoebas
Entamoeba histolytica 3rd eukaryotic after
Malaria and Schistosomiasis
Supergroup: Unikonta
Clade: Opisthokonts
Group:Nucleariids
Group:Choanoflagellates
Very Diverse Group:
Nucleariids = most closely
related to Fungi
Choanoflagellates = most closely
related to animals
Supergroup: Unikonta
Clade: Opisthokonts
Group:Nucleariids
Supergroup: Unikonta
Clade: Opisthokonts
Group:Choanoflagellates
•  Similar in
morphology
and DNA to
animals