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Organismal Biology
Organism-of-the-week: Pantherophis guttatus
 Common names: corn snake, red rat snake, chicken snake, etc.
 Arboreal=tree dwelling
 Species= Pantherophis guttatus
o Common name: corn snake
o Rules for species:
 Binomen= two name
 First name= Genus
 Always capitalized
 Always underlined OR italicized
 Plural: Genera
 Second name= Specific Epithet
 Not capitalized
 Always underlined OR italicized
 Genus= Pantherophis
o Common name: rate snake
o Plural: Genera
 Family= Colubridae
o Non-venomous snakes
o Family usually ends in –idae or –aceae
 Order= Squamata
o All snakes and lizards
o Suborder= serpentes
 Just snakes
 Suborders usually start with: Sub-, super-, Infra Class=Reptilia
o Common name: reptiles
 Phlyum= Chordata
o Common name: vertebrates and other chordates
o Plural: Phyla
 Kingdom= Animalia
o Common name: animals
Biology= Study of life
 Bi= two
o Plants and animals
 -ology= the study of
Biodiversity= study of how organisms are different
 Survey
Cladistics= common ancestry is the primary criterion used to classify organisms
 Clades= groups that contain an ancestral species and all of its descendents
o Equal to a monophyletic group
 Monophyletic= single ancestor
o Holophyletic= all descendents of the single ancestor
o Paraphyletic= some but not all of descendents of the single ancestor
o Monophylogeny is what we strive for
 Polyphyletic= more than one ancestor
o (Not good)
 Plesiomorphic= around for a long time
o Ancestral
 Apomorphic= newly evolved characteristic
o Derived
 Symplesiomorphic= shared ancestral characteristic
 Synapomorphic= shared derived characteristics
o This is what scientists want to avoid polyphyletic groups
 Autapomorphic= single unshared characteristic
Systematics
 Taxonomy= the naming and classification of organisms
o Taxon: the named taxonomic unit at any level of the hierarchy
 Example= snake
 Plural: taxa
o Taxonomic revisions—why?
 (1) New information
 Molecular vs morphological
 Similarities among organisms
o Analogous= common environment
 having characteristics that are similar because of
convergent evolution
 Not ancestral traits
 Not used for classification
o Homologous= come from same ancestors
 Similar in characteristics resulting from a shared
ancestry
 Used for classification
 Ancestral traits
 What scientists want!
 (2)Different philosophy
 Dendogram (phylogram): family tree
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 (3)Change: just because someone feels like changing it
Phlogeny= evolutional history (natural selection)
Classification= way of categorizing organisms
Survey:
3 Domains, 6 Kingdoms, 35-40 Phyla
Domains:
 Eukarya- True nucleus
 Archae- no nucleus or other membrane organelles
 Bacteria- no nucleus or other membrane organelles
Eukarya:
 Kingdoms
o Animalia
 Movement
 Cell membrane
o Plantae
 Cell wall
 Autotrophic
o
o
Fungi
 Cell wall
 Almost no movement
 Heterotrophs
Protista
 Difficult to explain
 Variety
Prokaryotes= Bacteria and Archae
 Not an official taxon
 The grouping of bacteria and archae as prokaryotes is incorrect because archaea is more related
to eukarya than it is to bacteria
 Diversity
o 2 domains
o 2+ kingdoms
 Size
o Small
o Most are 1-5 m (micrometer)
 Shape
o ⃝ –coccus
 Plural: cocci
 Spherical in shape
o Oval shaped –bacillus
 Plural: bacilli
o
~~-- Spirilla
 Plural: spirillae
Solitary vs colonial
 Solitary= found alone
 Colonial= found in groups
 Streptoo OOOOOOO
o One line
 Staphyloo Clusters
 Cell Wall
o Present in most
o Has a different chemistry than the one animals have
o Variable
 Example: Gram Stain
 A staining method that distinguishes between two different kinds of
bacterial cell wall
o
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o
Used to look at cell wall
Positive/negative
o Gram negative= describing the group of bacteria that have a cell
wall that is structurally MORE complex and contains LESS
peptidoglycan than the cell wall of a gram-positive bacteria.
Gram negative bacteria are often more toxic than gram positive
bacteria.
o Gram positive= describing the group of bacteria that have a cell
wall that is structurally LESS complex and contains MORE
peptidoglycan than the cell wall of a gram-negative bacteria.
Less toxic than gram-negative
o Peptidoglycan is a type of polymer in bacterial cell walls
consisting of modified sugars cross-linked by short polypeptides
Capsule
 Fimbria
 Plural: fimbriae
 A short, hairlike appendage of a prokaryotic cell that helps it adhere to
the substrate or to other cells
o a substrate is the surface on which a plant or animal live
 Thinner and shorter than flagellum
 Pilus
 Plural: pili
 In bacteria, a structure that links one cell to another at the start of
conjugation, also called a sex pilus or conjugation pilus
o Conjugation is the direct transfer of DNA from one bacterial cell
to another bacterial cell
 AKA “sex” pilus
 Motility
o Flagellum
 A long cellular appendage specialized for locomotion
 There are different types
 Plural: flagella
o Taxis= an oriented movement toward or away from a stimulus
 Phototaxis- move toward or away from light
 Chemotaxis- move toward or away from a chemical
 Genome
o Nucleoid= a non-membrane enclosed region in a prokaryotic cell where its chromosome
is located
o Ring shaped DNA
o
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Plasmids= a small circular double-stranded DNA molecule that carries accessory genes
separate from those of a bacterial chromosome.
Reproduction
o Asexual reproduction
 No meiosis
 The generation of offspring from a single parent that occurs without the fusion
of gametes. In most cases, the offspring are genetically identical to the parent
o Binary fission
 Splits two ways
 A method of asexual reproduction by “division in half”.
 In prokaryotes binary fission does not involve mitosis (but it does in
eukaryotes)
 Usually pretty rapid, but time varies
o Budding
o Endospores= a thick-coated, resistant cell produced by some bacterial cells when they
are exposed to harsh conditions
 Very resistant
 Dormancy and dispersal
Nutritional Mode
o Heterotrophic= heterotrophs are organisms that obtain organic food molecules by
eating other organisms or substances derived from them
 Decomposers= an organism that absorbs nutrients from nonliving organic
material such as corpses, fallen plant material, and the wastes of living
organisms and converts them to inorganic forms; aka a detritivore
 Pathogenic- causes disease
o Autotrophic= autotrophs are organisms that obtain organic food molecules without
eating other organisms or substances derived from other organisms. They use energy
from the sun or from oxidation of inorganic substances to make organic molecules from
inorganic ones.
 Photoautotrophic= capable of synthesizing their own food from inorganic
substances (carbon dioxide) using light as an energy source
 Chemoautotrophic= an organism, typically a bacterium, that derives energy
from the oxidation of inorganic compounds
o Photoheterotrophs= organisms that use light for energy (ATP), but cannot use carbon
dioxide as their sole carbon source. They must obtain carbon in organic form.
Oxygen Relationships
o Aerobic= with oxygen
o Anaerobic= without oxygen
o Facultative= can use oxygen, but can survive without it
o Strict= obligate= cannot survive with oxygen OR cannot survive without oxygen
Ecological Relationships
o Free-living= do not depend on another organism for survival
o
o
o
o
Pathogen= depends on another organism for survival
 An organism or virus that causes disease
Symbiont= provides a benefit for the organism
 The smaller participant in the symbiotic relationship, living in or on the host
Free-living heterotrophs= decomposers
Biofilms= surface coating colony of one or more species of prokaryotes that engage in
metabolic cooperation
 Lives on surfaces of water, etc.
 Community
 Combination of species
 Waste products used by the community
Organism-of-the-week:
 Species: Nostoc commune
o Common name: star jelly, mare’s eggs, witch’s butter, monster boogers
 Genus: Nostoc
 Family: Nostocaceae
 Order: Nostocales
 Class: Cyanophyceae
 Phylum: Cyanobacteria
 Kingdom: Eubacteria
 Domain: Bacteria
 Characteristics:
o Cosmopolitan= worldwide
o N-fixation= the conversion of atmospheric nitrogen (N2) to ammonia (NH3)
 N2NH3
o Desiccation resistant
 Dormancy
o Photosynthesis
o colonial
Domain Archae
 1-4+ Kingdoms
 Kingdom Archaebacteria
o Gram negative
 Lack peptidoglycans
 Extremophiles
o Love extreme conditions
o Thermophiles= love extreme temperatures
o Halophiles= love salty conditions
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Methanogens
o Produces methane (CH4) as a waste productfossil fuel
o Anaerobic
Non-extreme archaea
Domain Bacteria
 1-200+ kingdoms
 Kingdom Eubacteria
o Contains most of the familiar bacteria
o Phylum Cyanobacteria
 Performs photosynthesis
 Internal membrane
 Looks like chloroplasts
 Serial endosymbiotic hypothesis of Eukaryotic organelle origin
 A hypothesis for the origin of eukaryotes consisting of a sequence of
endosymbiotic events in which mitochondria, chloroplasts, and perhaps
other cellular structures were derived from small prokaryotes that had
been engulfed by larger cells.
 Endosymbiosis= a relationship between two species in which one
organism lives inside the cell or cells of another organism
o Proteobacteria
 Gram negative largest group
 Escherischia Coli
 E. Coli
 Coliformin colon
 Gut flora
 Pathogenic strains
o Alphaproteobacteria
 Purple-green
 Inner membrane looks like mitochondria (ring-shaped DNA)
o Spirochaetes
 Spirilla shape many pathogens
o Gram Positive Groups:
 Chlamydias all are animal diseases
 Mycoplasmas
 Smallest of all bacteria
 No cell wall
 Ex: walking pneumonia
Domain Eukarya
 4 kingdoms
 True nucleus
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Sexual reproduction
o Usually in addition to asexual
 Why?
 Because of environmental factors
 variety in offspring meiosis (mitosis)
3 basic life cycle patterns
Meiosis
o Replication + 2 divisions
o 2nn (1 of each type)
o Vocabulary:
 Reduction division
 Haploid (half)
 23 for humans
 (n)
 Diploid
 46 for humans
 (2n)
 Homologous pair
 Maternal
 Paternal
Mitosis
o 1 replication + 1 division
o 2n2n or nn
o Gamete
 Haploid
 Will fuse= fertilization=syngamy
 Produced by mitosis or meiosis
o Syngamy
 Fusion of gametes
 Plasmogamy
 n+n  n+n
 Karyogamy
 n+n  2n
o zygote
 diploid
o spores
 dormancy and dispersal
 n or 2n
 asexual or sexual
 mitosis or meiosis
 do not fuse
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3 patterns:
o Zygotic Meiosis
 Fungi and some protista
 “Zygote undergoes meiosis”
 Life cycle:
o
Gametic Meiosis
 Animalia and some protista
 “Gametes produced by meiosis”
 Life cycle:
o
Sporic Meiosis
 Plantae and some protista
 “spores produced by meiosis”
 “alternation of generations”
 A life cycle in which there is both a multicellular diploid form, a
sporophyte, and a multicellular haploid form, the gametophyte
 Life cycle:

Evolutionary Trends:
o (ancestral)(derived)
o Asexual reproductionsexual reproduction
o Zygotic meiosisgametic and sporic meiosis
o Unicellularmulticellular
o Isomorphicheteromorphic
 Isomorphic= referring to alternating generations in plants and some algae in
which the sporophytes and gametophytes look alike, although they differ in
chromosome number
 Heteromorphic= referring to a condition in the life cycle of plants and some
algae in which the sporophyte and gametophyte generations differ in
morphology.
o Isogamyanisogamy (oogamy)
o Dominant gametophytesporophyte dominant
o Homosporyheterospory
 Homosporous= a plant species that has a single kind of spore, which typically
develops into a bisexual gametophyte
 Heterosporous= a plant species that has two kinds of spores: microspores,
which develop into male gametophytes, and megaspores, which develop into
female gametophytes.
Kingdom Protista
 “protozoa and algae”
o Protozoa=first animal
 Autotrophs/heterotrophs or mixotrophic
 Motile/sessile
o Sessile= immobile
 All 3 sexual life cycles
o Zygotic, gametic, and sporic meiosis
 Polyphyletic
o 4 or 5 monophyletic clades
 Most are unicellular
 Not plants, animals, or fungi
 Membrane bound nucleus and other organelles
 An almost abandoned taxon
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Phylum diplomonadida
o Synapamorphic
o Double nuclei in equal sizes
o Multiple flagella
 8 or more
o Giardia intestinalis
 Intestinal parasite in humans
Phylum Parabasala
o Connected to basal body of flagella
 Basal body similar to golgi body in humans
o Trichomonas vaginalis
 STD
 Mostly parasitic
Phylum Kinetoplastida
o Kinetoplast large mass of DNA in a mitochondrion
o Bodo
o Trypanosoma brucei
 Causes African sleeping sickness
 Transmitted by Tsetse fly
 Causes anemia
Phylum Euglenozoa
o Has flagella and chloroplasts
o Animal and plant like
o Many are photosynthetic
o Euglena
 Nominate genus
 Nominate=names after
 Two flagella
 Stigma
 Eye like
 Absorbs light
 Spot of pigment
 Alters movement of flagella
 Light changes the shape of it
 Positive phototaxis
 Means moves toward light
 Inside flagella: 9+2 flagellar and ciliary axoneme
 doubles
 Inside basal body: 9+0
 Triplets
 Undulation
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Movement of flagella
Tip-to-base
Anterior flagellum
o Moves with flagella in front
 Chloroplast in Euglena
 3 membranes
o Peranema
 Undulates flagellum at the tip
Phylum Dinoflagellata
o Whirly
o 2 flagella
 1 is longitudinal
 1 is circumferential
o Gymnodinium
 Red pigment
 In gulf water
 Autotrophic
 Toxins
 Bloom
 Bloom=photosynthetic population
 Causes red tide
o Noctiluca
 Sea sparkle
 Bioluminescent
 In sea water
Phylum Apicomplexa
o Apical complex
 At the tip
 Allows penetration of host cells
o Spore forming parasites
o Plasmodium
 Causes malaria
 Stages of malaria (zygotic meiosis)
 Sporozite: n, infective stage
 Trophozoite: feeding cells in RBC
 Merozoites: product of schizogony (synchrony)
 Gametocytes: (micro-, macro-), picked up by mosquito
 Gametes: (in mosquito now): n, fuse by syngamy
 Oocyst: zygote(2n)
 Then undergoes meiosis and starts over at sporozoite
o Anopheles
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 Vector= an organism that transmits pathogens from one host to another
Phylum Ciliophora
o Ciliates= type of protist that moves by cilia
o Possesses cilia
o Paramecium multimicronucleatum
 Several micro nuclei
o Complex structure:
 Organelles
 Pellicle= cell membrane + alveoli
 Oral groove
 Where feeding begins
 Cytostome
 Cell mouth
 Cytopharynx
 Leads food particle
 Food vacuole
 Cytoproct
 Cell anus
 Exocytosis
 WEV= water expulsion vesicle
 Contractile vacuole
o Osmoregulatory adaptation
 Parasites in isotonic fluids do not perform osmosis so there is no need
for contractile vacuole
 Membranelle
 Example: Vorticella
 Cirrus
 Examples: Euplotes
Phylum Bacillariophyta
o Photosynthetic
o Common name: diatoms
 Photosynthetic protist in the stramenopile clade; diatoms have a unique glass
like wall made of silicon dioxide embedded in an organic matrix
o Cell wall= frustule
 Silicious (SiO2)
 Glass like
 2 valves
o Centric or pennate
o Bloom
o Diatomaceous earth
 Used for water filtering
o
o
o
o
 Sandpaper
 Toothpaste
Asexual and sexual reproduction
2ngametic meiosis
Mitosis1 valve conserved in each cell
Valve picture:
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Gets as small as 1/3 in size then sexual reproduction occurs and a zygote is
formed
Phylum Phaeophyta
o Brown algae
o Macroalgae
o Simple multicellularity
o Kelp
o Sargassum
 Air filled bladders that help them float
o Sporic meiosis
o Thallus= a plant body that is not differentiated into stem and leaves and lacks true roots
and a vascular system
o Picture:
Phylum Rhodophyta
o Red algae
o Agar
o Carageenan in ice cream
o
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Ameboid protozoa
 Amoebozoan= a protist in a clade that includes many species with lobe-shaped
or tube-shaped pseudopodia
 Amebas= with or without tests
 Test= in foram protists, a porous shell that consists of a single piece of
organic material hardened with calcium carbonate.
o Shell like exterior structure
 Pseudopods used for movement and phagocytosis
 Picture:
Phylum Gymnamoeba
o Naked- Without tests
Phylum Radiolaria
o With tests
 Silicious
o Axopodia
 Needle-like pseudopods
o Lobopodia
 Opposite of axopodia
 Not found in radiolaria
 Most common
Phylum Foraminifera
o Test is full of chambers
o –fera: to bear
o Calcareous tests (CaCO2)
 Chalky appearance
o Mermaid’s pennies
o Reticulopodia= another type of pseudopod
o Forms white cliffs, chalk, pink sand in Bermuda
o Ooze amoeba parasitic population
Types of Pseudopods
 Reticulopodia – net like
 Axopodia
 Lobopodia
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Phylum Myxomycota (Mycetoza)
o Plasmodial slime molds
o Myxo = fungus
o Characteristics
 Plasmodium- growth form
 Multinucleate
 mass of protoplasm
 Detritivores= feed on dead stuff
 Sporic meiosis
 Complex life cycle
Phylum Chlorophyta
o Chloro: green
o Common name: green algae
o In common with plants
o Independent solitary cells: Chlamydomonas
o Volvox
 Colonial
o Some thallus
o Look the same and shaped the same regardless of haploid or diploid=isomorphic
o Example: sea grass
Zygotic Meiosis
Haploid organisms form gametes by mitosis
Isogamy – all the gametes are the same
Syngamy results in zygote
Zygospores undergoes meiosis in spring
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Phylum Choanoflagellata: common ancestor with animals
o structure and DNA most related to animals
 Sister group of all multicellular organisms
 Collar – extensions of cell membrane with microvilli that are finger- like foldings
 Food vacule = filter feeding
Organism-of-the-week:
 Species: Braseni schreberi
o Common name: water shield
 Genus: Braseni
 Family: Cabombaceae
 Order: Nymphaeales
 Class: Eudicot
 Phylum: Mognoliophyta
 Kingdom: Plantae
 Domain: Eukarya
 Characteristics:
o Hydrophilic
o Hydrophobic
o Mucilage
o Anti-herbivore
 Prevents getting eaten
Kingdom Plantae
 “the land plants”
 Sporic meiosis
o Kingdom plantae has the most complicated of life cycles
 Most photosynthesis
 Cell walls
o Cellulose- primary structural component
 Movement by growth
 Multicellular
o Characteristic that distinguishes plants between protists
 Bryophytes—Super phylum – the oldest group of plants
o 3 phyla
o Not far from water
o Non-vascular
 Lack vascular tissue
 Cannot have true plant organs
 Lack ability to pump water from source
 Prevents them from getting big because taller means farther from water
o Small
o No true organs
o Require Moist environment
o Flagellated sperm
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 Must have water to swim so hence moist environments
o Dominant gametophyte generation
 Asexual
o “amphibians” of plant world
Phylum Bryophyta
o A phyla of bryophytes
o Bry- means moss
o –phyta means plant
o True mosses and relatives
o Sporophytes attached to and are dependent on gametophyte
o The sporophyte does not perform photosynthesis
o Gametophyte undergoes asexual reproduction
o Anisogomy= gametes are not the same
 Egg and sperm
o Sperm gets to the egg by splashing out and swimming from antheridium to archegonium
o Water is require for sperm dispersal
o Zygote (2n) forms in archegonium
 Gametophyte  sporophyte
 1st zygote formation
o Gametangium= House the cells that become the gamete
o Peristome with teeth like structures
o Seta = thread like structure
o Bryophyta life cycle:
Phylum Hepatophyta
o Another phyla of the bryophytes
o Same life cycle as Bryophyta except:
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Antheridiophore
 Structures that bear antheridia (male)
 Archegoniophore
 Structures that bear archegonia(female)
 Sporangium
 Spore container
 Same thing as a capsule in Bryophyta
 Sporophyte is upside down
 Elatershygroscopic
o Aids in spore dispersal
o Change based on humidity
o Common name: liverworts
 Doctrine of signatures: idea that God put his signature in organisms so they
would look like what they are used for
o Lobed thallus
 With rhizoids
 Sheet-like structures
 Dichotomous branching= how the lobes grow
 Gemmae in gemma cups = for asexual reproduction
Phylum Anthocerophyta
o Hornwortsthallus gametophyte
 Horn-like sporophyte
o Plants that look like horns
o Meiospores dispersed by dehiscence
 Dehiscence= splitting open to release contents