II. Taxonomy

Key focus of this chapter: domains and kingdoms

This chapter focuses on domain and kingdom and gives concise summaries of the important things about 3 domains 5 kingdoms in more detail.

A. Chronological order of pre-biotic chemicals

* Early earth consisted of reducing atmosphere of CH₄, NH₃, H₂, H₂O, and H₂S

B. Hierarchy

Domain – Eukarya, Bacteria, Archea

Kingdom – Monera, Protista, Fungi, Plantae, Animalia

Phylum – Chordata

Class – Mammalia

Order – Carnivora, Primates

Family – Hominidae

Genus – Homo

Species – Homo Sapiens

** Classification of human indicated in bold

C. Three domains and five kingdoms

3 Domains	5 Kingdoms	Characteristics
Bacteria	Monera (Prokarya)	• Unicellular microorganism • Reproduction by asexual binary fission • Movement by flagella, taxis (motility by stimulus) • Containing Nucleic acids as a plasmids • Transferring information by conjugation • Eg/ cyanobacteria (blue-green algae)
Archaea	Monera (Prokarya)
Eukarya	Protista	• Sexual or asexual reproduction • Photoautotrophs, heterotrophs, or mixotrophs • Endosymbiosis • Eg/ protozoa, slime molds, multicellular algae	Most unicellular
	Fungi	• Sexual or asexual reproduction • Heterotrophs and parasites • Mutualists and decomposers (Saprobes) • Eg/ Mold, yeast, mushroom	Most multicellular
	Plantae	• Photosynthetic organisms • Cell wall with cellulose • Alternation of generations	Most multicellular
	Animalia	• Heterotrophs • High mobility	Multicellular

1. Domain Bacteria

Most diverse and widespread microorganism.
Shapes with spiral, rod-shaped, and spherical.
Getting energy from glycolysis and electron transport chain.
Eg/ Proteobacteria, Gram-positive and gram-negative bacteria, Blue-green algae (cyanobacteria), Spirochete, Chlamydias

2. Domain Archaea

Living in extreme environments.
Eg/ Crenarchaeotes, euryarchaeotes, korarchaeotes, nanoarchaeotes, sulfolobus

D. Diversity of metabolic adaptations

Classification	Energy source	Carbon source	Organisms
Photoautotroph	Light		Cyanobacteria, Plant, algae
Photoheterotroph	Light	Organic compound	Chloroflexus, Rhodobacter
Chemoautotroph	Chemical inorganic		Sulfolobus
Chemoheterotroph	Chemical organic	Organic compound	Many prokaryotes and protists, fungi, animals

E. Kingdom Protista

Main Clade	Classification	Characteristics & Examples
Diplomonadida • Two nuclei • Lack plastids • Multiple flagella • Reduced mitochondria		• Eg/ Giardia
Parabasalids • Mutuality and parasites • Lack plastids • Reduced mitochondria		• Trichomonads – moving flagella and undulation plasma membrane • Found in gut of termites • Eg/ Trichomonas
Euglenozoa • Predatory heterotrophs and photosynthetic autotrophs	Euglenids	• Most living in water • Flageller pocket and eyespot • Plant like (having chloroplast) and animal like (motile, lack cell wall) • Eg/ Euglena
	Kinetoplastids	• Kinetoplast – containing DNA in mitochondria • Eg/ Trypanosoma
Alveolates • Alveoli membrane bound sacs	Apicomplexans	• Apical complex organelles • Sporozoites in plasmodium • Intricate life cycle • Eg/ Plasmodium (causing malaria)
	Ciliates	• Many ciliates to move and feed • Micronuclei and macronuclei • Eg/ paramecium, stentor
	Dinoflagellates	• Phytoplankton and red tide • Symbiosis with coral or clam • Eg/ Ceratium, pfiesteria
Stramenopiles • Hairy flagella • Photosynthetic or hetero trophic	Oomycetes	• Cell walls made of cellulose • Having hyphae to absorb nutrients • Resembling fungi • Irish potato blight • Eg/ Water mold, downy mildews
	Diatoms	• Two shells made of silica • Eg/ Marine phytoplankton
	Golden algae	• Eg/ Dinobryon
	Brown algae	• Multicellular • Eg/ Seaweed, laminaria, macrocystis
Amoebozoans • Moving by pseudopodia	Gymnamoebas	• Living soil, fresh or marine water • Eg/ Amoeba
	Entamoebas	• Parasites • Eg/ Entamoeba
	Myxogastrida	• Plasmodial slime molds • Multinucleate plasmodium • Acellular slime molds • Eg/ Physarum
	Dictyostelida	• Cellular slime molds • Fruiting bodies with asexual reproduction • Living independently as haploids • Dictyostelium
Rhodophyta	Red algae	• Multicellular • Photosynthetic accessory pigment (phycoerythrin) • Alternation generation with diverse life cycles • No flagellated stages • Eg/ Bonnemaisonia, palmaria
Chlorophyta	Green algae	• Plant ancestors and having plant-type chloroplasts • Lichens (algae + fungi) • Eg/ Chlamydomonas, spirogyra, ulva, volvox, caulerpa

F. Kingdom Fungi

: heterotroph organisms that break down molecules and absorb nutrients

Important roles on ecosystems and human welfare

– decomposer to recycle chemical elements

– symbionts (mycorrhizae, lichens)

– yeast, food source, antibiotic producer

Cell walls with chitin
Absent chloroplasts
Both asexual and sexual reproduction
Pathogens to human

1. Structure

Cell wall made of chitin
Mycelium: Interwoven mass of hyphae
Hyphae: Network of filaments composed of tubular cells

– septate hypha: Dividing cells by crossing walls in hyphae

– conecytic hypha: a continuous cytoplasmic cell of hyphae

Mycorrhizae: Symbiotic mutual relationship with plants

– plants supply to fungi organic nutrients

– fungi supply to plants minerals that plants cannot acquire

2. Classification

Phylum	Characteristics
Basidiomycota	• Club fungi • Fruiting bodies called basidiocarps in sexual reproduction • Eg/ Mushrooms, rusts, toadstools
Ascomycota	• Sac fungi • Production of sexual spores in sacs called asci • Fruiting bodies called ascocarps in production of sexual spores • Production of asexual spores called conidia • Lichen of symbiotic relation • Eg/ Yeast, truffles, morels
Chytridiomycota	• Freshwater and terrestrial habitats • Saprobic or parasitic • Motile flagellated spores (zoospores) • Eg/ Allomyces
Glomeromycota	• Arbuscular mycorrhizal fungi • Symbiotic relationship with plants • Eg/ Arbuscular mycorrhizae
Zygomycota	• Resistant zygosporangium in sexual reproduction • Life cycle with black bread mold • Eg/ Rhizopus (black bread mold)

** Lichens (pioneer and symbiosis organism between algae and fungi)

G. Kingdom Plantae

1. Classification of plantae

Land plants	Classification		Characteristics & Examples
Bryophytes • Nonvascular plants • Gametophyte dominant	Liverworts		• Liver shaped gametophytes of Marchantia • Single-celled rhizoids
	Hornworts		• Gametophytes grow horizontally • Multicellular sporophyte
	Mosses		• Gametophytes grow vertically • Complex leaves
Vascular plants • Tracheophytes	Seedless Vascular Plants	Lycophytes	• Most primitive group in vascular plants • Eg/ Club mosses, spike mosses, quillworts
		Pterophytes	• Eg/ Ferns, horsetails
	Seed Plants	Gymnosperms	• Naked seeds • Eg/ Pines, ginkgo, cycads, conifers
		Angiosperms	• Monocots & dicots • Flowering plants • Product fruit • Eg/ Maple, banana, lily, apple

2. Plant of Angiosperms

a. Monocot and dicot

Monocot	Dicot
• One cotyledon • Three flower parts • Parallel leaf veins • Scattered vascular bundles • Fibrous root system • Absent of secondary growth (Such as bark and wood)	• Two cotyledons • Four or five flower parts • Reticulated leaf veins • Circular oriented vascular bundles • Main root with fibrous root • Secondary growth usually present

b. Structures and functions of flower

Structures	Classification	Functions
Female part (Carpel)	Stigma	• Receiving the pollen during the fertilization
	Style	• Connecting pollen tube between ovary and stigma
	Ovary	• Female reproductive organ
Male part (Stamen)	Anther	• Male reproductive organ (cell) – producing pollen
Male part (Stamen)	Filament	• Holding the anther
Other parts	Petal	• Attracting insects into the flower
	Receptacle	• Flower’s attachment to the stalk which sometimes becomes part of the fruit after fertilization
	Sepal	• Small leaves under the flower -protecting flower during budding

c. Plant tissues

Plant tissues	Functions and features
Parenchyma cells	• Thin and flexible primary cell wall • Metabolic functions, photosynthesis, and storing organic molecules • Eg/ Mesophyll
Collenchyma cells	• Thicker and flexible primary cell walls • Supporting young tissue of primary cell wall • Living cells
Sclerenchyma cells	• Thicker and rigid secondary cell wall • Containing lignin • Supporting elements of plant • Dead cells

d. Anatomy of leaf

Structures	Functions
Guard cell	• Controlling the size of opening
Stoma	• A pore for exchanging gas
Cuticle	• Wax layer for protecting epidermal cells
Epidermis	• Producing wax to cuticle • Secreting metabolic materials
Mesophyll	• Parenchyma and chlorenchyma tissues • Primary site for photosynthesis
Bundle sheath	• Containing Xylem and phloem • Transfer system for water and nutrients

** Transpiration

– evaporation of water by temperature, wind, and light at the surface of leaves

– this creates water tension and moves water upward in xylem.

e. Anatomy of stem

Structures	Functions
Periderm	• Covering cork cambium and dermal tissue
Cork cambium	• Responsible for growing secondary dermal tissue • Undifferentiated and actively dividing cell
Phloem	• Transporting nutrients and sugars through out sieve tubes (both up and down direction) • Main force of transporting - diffusion and active transport • Composed of living cells (companion cells and sieve tubes) • Sieve plate and plasmoderma
Vascular cambium	• Responsible for growing xylem and phloem • Undifferentiated and actively dividing cell
Xylem	• Transporting water and minerals (upward only) • Composed of dead cells (vessel elements and tracheids) • Main force of transporting – surface tension and negative pressure • Pit pairs
Pith	• Sponge parenchyma cells • Located in the center of vascular tissues (ground tissues)

f. Modified stems

Modified stems	Features
Buls	• Short and vertical underground stem • Storage food in the enlarged leaves • Eg/ onions
Stolons	• Horizontal stem along the surface of the ground • Producing rooted plantlets at the end of their nodes • Eg/ strawberry and spider plant
Tubers	• Underground storage stem • Enlarged ends of rhizomes • Eg/ potatoes
Rhizomes	• Horizontal stem along or below the surface of ground • Eg/ ginger

g. Plant hormones

Hormones	Functions
Auxin	• Phototropism – shoot growing toward light • Gravitropism (geotropism) - root growing downward in response to gravity (negative gravitropism) - stem growing upward against gravity (positive gravitropism) • Hydrotropism – growing toward water
Cytokinins	• Stimulate cell division and growth
Gibberellins	• Stem elongation • Stimulate flowering
Abscisic acid	• Inhibits growth • Blocks cell division
Ethylene	• Promotes fruit ripening
Kinins	• Promote cell division

h. Life cycle of angiosperm

H. Kingdom Animalia

1. Pedigree and summary

Phylum	Class	Animals and Distinctive features
Porifera - no true tissues or organs - respiration and excretion by diffusion		Sponge • Choanocytes – creating a water current through water channels to get food particles
Cnidarian - most radial symmetry - tentacles - gastrovascular cavity - two body types (polyps and medusa) - nerve system begins		Hydra • Cnidocyte – containing nematocyst (stinging capsule or cell) • Polyp – produced by asexual budding • Medusa – swimming off and reproducing sexually
Platyhelminithes - body flattened dorsoventrally - incomplete digestive system - pair of anterior ganglia with longitudinal nervous system	Turbellaria	Planaria • Protonephridia- containing flame bulbs, excretory system
	Cestoda	Tapeworm • Scolex – hooks and sucker
Mollusca - mantle cavity	Gastropoda	Snail • Open circulation system • Breathing with gills by chambered heart • Embryonic torsion • Radula
	Bivalvia	Clams, muscles, oysters • Open circulation system • Two valves • Adductor muscles • Breathing with gills and mantle • Siphons
	Cephalopoda	Octopus & Squid • Cephalization - the highly advanced sensory equipment and the central nervous system on the head of body. • Closed circulatory system • Tentacles for grasping or movement
Annelida - complete digestive system (one way) - closed circulatory system - double ventral nerve cord		Earthworm • Metanephridium – excretory system through the skin • Septurm – dividing coelom cavities
Arthropods - jointed appendages - exoskeleton of cuticle - well developed sensory structures - open circulatory system - metamorphosis	Insecta	Grasshopper • Malpighian tubules – excretion waste from hemolymph to gut • Breathing by tracheal tubes • Three body divisions (head, thorax, abdomen) • 3 pairs of legs and 2 pairs of wings
	Diplopoda	Millipedes, centipedes • Mandible – jaw like structure for eating food
	Arachnida	Spider • Compound eyes (8 simple eyes) • 4 pairs legs • Respiration by book lungs (modified gills)
Echinodermata - radial symmetry - water vascular system - endoskeleton of dermal calcareous ossicles - nervous system with a circular ring and radial nerves		Sea star • Tube feet – water vascular system • Madreporite • Ampulla
Chordata	Agnatha	Jawless fishes (lampreys, hagfishes) • Naked skin • Two chambered hearts and one circuit begin • No paired appendages
	Chondrichthyes	Cartilaginous fishes (sharks, skates, rays) • Jaws present • Ventral mouth and two olfactory sacs • Skin with scales or naked • No swim bladder of lung • Lateral line system begins
	Osteichthyes	Bony fishes • Common operculum • Swim bladder
	Amphibia	Frog, toads, salamanders • Three chambered heart and two circuits begin • Usually four limbs • Combinational respiration by lungs, skin, and gills • Metamorphosis
	Reptilia	Snakes, lizards, turtles, alligators, crocodiles • Body covered with an exoskeleton of horny epidermal scales
	Aves	Birds • Four chambered hearts and two circuits begin • Epidermal covering of feathers and leg scales • Beak, no teeth
	Mammalia	• Brain highly developed • Female has estrus cycle

2. Diagram of pedigree

I. Animal Reproduction

1. Asexual reproduction

Budding: new individual arises from parent body
Fission: the separation of a parent body into two parts
Fragmentation: the breaking of the parent body into several pieces and growing into complete adults.
Regeneration: Growing of lost body part
Parthenogenesis: Developing an egg without fertilization

2. Sexual reproduction

Reproduction of vertebrates	Descriptions
Oviparity	• Fertilized eggs are laid and hatched outside mother’s body. • Eg/ All birds
Ovoviviparity	• Fertilized eggs are laid within the mother’s body • Young obtain nourishment from egg yolk • Eg/ Many reptiles
Viviparity	• Fertilized eggs develop within the mother’s body • Young obtain nourishment from mother’s blood • Eg/ Almost all mammals

** Duck-billed platypus: a mammal but ovoviviparity

3. Sexual and asexual reproduction

Hermaphroditism: Each individual organism has both male and female reproductive systems

J. Life cycle of animals, plants, and fungi

Protists and fungi: Haploid life cycle dominates
Plant: Alternation of generation
Animal: Diploid life cycle dominates