Chapter 20: Classification of Living Things Nature of Systematics - Systematics includes 3 tasks o Characterization: listing characteristics of new organisms

o Classification: determining similarities between new and existing organisms May be found that organisms characteristics match those of a known species May be found that organisms characteristics match no known species but are similar to other species in the same genus. Would be classified as a new species within that genus o Naming No 2 species have the same name There are detailed and specific rules to nomenclature History of Systematics - Prehistory o Primitive man recognized and communicated knowledge of plant and animal differences o Knowledge of culinary and healing properties of plants and animals handed down by oral tradition. - Ancient history o First written records of systemics come from ancient orient and Mediterranean o Aristotle used broad classification system o Important western herbalists and their works include Theophrastus (371-287 BC) De historia plantarum Dioscorides (40-90 AD) De material medica Pliny (61-113 AD) Naturalis historia Galen (129-210 AD) De simplicium medicamentorum o Theophrastus was student of Aristotle The Lyceum had greatest success under his direction Work with plants so important is was still used after 1500 years - Middle Ages o Little scientific progress o Texts copied by hand in monasteries o Preserved when translated by Arabic cultures in their zenith o Text later recovered and translated once Europe came out of Dark Ages - The Renaissance o One of greatest contributions to advancement of science was the printing press o One of first types of books produced was the Herbal Herbals illustrated and described plants that could be used as food and medicines

o Important herbalists and herbals of the Renaissance Reinhard Beck (1517) Ortus Sanitatis Pietro Andrea Mattioli (1565) De material medica Rembert Dodoens (1578) A nieuue herball John Gerard (1633) The Herball 17th Century Academies and Botanists o Prominent academies Rome Italian Academy of the Lynx Florence The Academy of Experiments Rostock Germany Oxford The Royal Academy Paris Academie Francaise o New plants from western hemisphere demanded a better naming and classification system was required o Attempts were made by: Gaspard Bauhin 1623, Pinax theatri botanici Mediterranean travels Made comparative table of plants that accounted for 6000 species John Ray 1682, Methodus Pllantarum Nova Classification based on flowers, seeds, fruits, & rootts His system persisted in England for a little while after Linnaeus Joseph Pitton de Tournefort 1700, Institutiones rei herbariae Classification based on form of petals Distinguished between species and genera o These were predecessors to Linnaeus and had an impact on his methods 18th Century Botanists o Prior to Linnaeus, polynomials were used to refer to species Constructed by combining a noun as the proper name (genus) and then an adjective or adjectival phrase Linnaeus used trivial names epithets in margins of his writings next to the polynomial This epithet combined with the genus becomes the binomial i.e. Solidago sempervirens o Linnaeus system of classification was based on the number of reproductive parts of a flower This produced some mistakes because of strict adherence to sexual parts classification Often grouped plants unnaturally Natural classification groups species that are actually related to each other o Other taxonomists to propose classification systems Bernard de Jussieu (1699-1777)

System contained 3 main groups o Monocotyledon o Dicotyledon o Coniferae Antoine-Laurent de Jussieu (1748-1836) Nephew of Bernard. Gave theoretical basis to his uncles classification system Exposition dun nouvel Ordre des Plantes, adopte dans les demonstrations du Jardin royal Distinguished essential characteristics to classifying plants 3 main groups: Acotyledon, Monocotyledon, and Dicoteyledon o These divided into 15 classes Divided into 100 families He clearly defined the characteristics of each of the families Augustin-Pyramus de Candolle (1778-1841) Replaced artificial classification of Linnaeus with a natural system Theorie elementaire de la botanique, ou exposition des principes de la classification naturelle et de lart de decrire et detudier les vegetaux - 19th Century Botanists o Adolf Engler and Karl Pranti Further revised natural classification systems of de Jussieu and Candolle Wrote Das Pflanzenreich Became system that remained the standard well into the 20th century o Writings of Darwin and Alfred Wallace also affected science of classification th - 20 Century Botanists o Charles E Bessey (1845-1915) Challenged Engler and Prantis idea that amentiferae were the most primitive flowering plants Thought that flowers evolved from cones Found flowers similar to cones in the Magnolia Family. His list of primitive and advanced character states is known as Besseys Dicta. Classification Categories - Current classification scheme is a nested hierarchy - Plants o Kingdom -> Division -> Class -> Order -> Family -> Genus -> Species

Animals o Kingdom -> Phylum -> Class -> Order -> Family -> Genus -> Species Phylogenetic Trees - Phylogeny: traces the evolutionary history of a species or group of species - A product of the phylogenetic analysis is a phylogenetic tree: a family tree of sorts Sources of phylogenetic characteristics - Fossil record o Correct interpretation of their characteristics may permit us to determine relationships with living organisms o Often lack sufficient detail because they only durable structures are preserved - Homologous structures o Homology: similarity of characteristics between organisms that is due to presumed common ancestors o Sometimes, homologous structures do not indicate common ancestry o Convergent evolution: development of similar structures due to selection forces in effect in similar environments This process produces analogous structures o Parallel evolution: similar characteristics in related organisms developed independently of each other. Common ancestor wont have these shared characteristics - Molecular data o Comparison of DNA, RNA, and proteins in organisms o Cytochrome-c: protein in cell membranes and is important in cell metabolism Cytochrome-c amino acid sequence is different in all organisms Thus, similarities in sequence can provide clues to which organisms are related o Sequence of DNA and RNA nucleotides can be compared in different organisms to determine relationship Development of Modern Systematics - Modern systematics has passed from the traditional phase, through the phenetic phase, into the cladistic phase. - Traditional phase o Before 1950s o Used morphological and anatomical data to make taxonomic decisions Had to produce descriptions, diagnoses, and identification keys to use this classification system o Presented some biased results - Phenetic phase o Digital computers allowed for the computation of large amounts of data o Generated methodology emphasizing gathering a lot of data (at least 50 characteristics) o Product of phenetic analysis is a phenogram

Closeness of relationship is determined by closeness on horizontal line of phenogram - Cladistic phase o Based on work of entomologist Willi Hennig Uses shared derived characteristics as basis for relationship Organisms are related if they share advanced (or derived) characteristics More shared derived characteristicscloser relationship o Product of cladistic analysis is a branching tree called a cladogram o Represents what are thought to be realistic evolutionary relationships Classification Systems - Aristotle o 2 Kingdoms: Plants and Animals - 1600s o 2 kingdoms but single celled organisms divided between plant and animal - 1880 Ernst Haeckel o 3 Kingdoms: Protists, Plants, and Animals - 1969 R.H. Whitaker o Recognition that bacteria and fungi are fundamentally different from other organisms o 5 Kingdoms: Monera, Protists, Fungi, Plants, Animals - Current system o New molecular data has found some bacteria to be different than all other organisms New taxonomic category created above Kingdom Domain o Three Domains Domain Bacteria, Domain Archaea, Domain Eukarya Five Kingdom Classification System - Monera (bacteria) o Bacteria & blue-green algae o Prokaryotic o Asexual - Protista o Microscopic plants & animals o i.e. (Autotrophic) Volvox, green algae and (Animals) paramecium, amoeba o Eukaryotic o Single celled - Mycota o Macroscopic fungi o Mushrooms, molds, etc o Eukaryotic o Both sexual and asexual o Multicellular

Plantae o Macroscopic plants o Eukaryotic o Both sexual and asexual o Autotrophic and some heterotrophic - Animalia o Macroscopic animals o Eukaryotic o Sexual and some asexual o Heterotrophic Three Domain Classification System - Domain Bacteria o Contains most of the bacterial species in normal earth environments - Domain Archaea o Contains bacterial species that live in harsh environments, such as thermophilic and methanogenic (methane-producing) bacteria o Kind of bacteria that probably lived in early earth environments - Domain Eukarya o All other organisms: plants, animals, fungi, etc Chapter 21: Viruses, Bacteria, and Archaea The Viruses - Not considered living orgainisms o No internal metabolism o Cant reproduce independently o They are not included in any domains or kingdoms - Kinds of viral particles (4 kinds distinguished by shape) o Polyhedral viruses like Adenoviruses o Bacteriophage viruses like T-4 o Helical viruses like the tobacco mosaic virus o Spherical viruses like influenza Structure of viruses - All have an outer covering of proteins called a capsid o Capsid coat proteins cause allergic response in host o These proteins are recognized by immune system as foreign - Inner core contains DNA or RNA and proteins o Nucleic acid is injected into host cells and virus is able to reproduce Reproduction of viruses - Reproduction in bacteria involves 2 cycles o Lytic Cycle (5 stages) reproduction in and destruction of host cell Attachment: particles attach to outer surface of host cell Penetration: nucleic acids injected into cell. Capsid coats remain on surface of cell

Biosynthesis: nucleic acids take over metabolism of cell and reproduce new nucleic acids and proteins for capsid coats. Maturation: viruses assembled by packaging nucleic acids into capsid coats Release: host cell disintegrates and viruses released and can now infect other host cells o Lyosgenic Cycle virus remains dormant in host cell and then destroys it Integration stage Inserted between penetration and biosynthesis of lyctic cycle Viral nucleic acid joins with host nucleic acid This dormant nucleic acid called a prophage When conditions right, nucleic acid activates and lytic cycle continues The Prokaryotes: Bacteria and Archaea - Simplest and oldest life forms - Found in air, water, soil, and on objects - Louis Pasteur demonstrated presence of bacteria Structure of prokaryotes - Nucleoid: region that contains DNA - Thylakoids: specialized internal membranes that function in photosynthesis and cellular respiration - Plasma membrane inside cell wall that surrounds cytoplasm - Capsule: outer cell wall o Made of peptidoglycan: molecule of amino acids and carbohydrates - Cytoplasm contains ribosomes that function in protein synthesis - External surface by have flagella or sexual pili Reproduction of prokaryotes - Reproduce by binary fission o DNA duplicates and new plasma membrane and cell wall form between the 2 nuclear areas o Can still undergo changes in genetic materials which often changes cell function o 3 forms of genetic recombination Conjugation: donor cell passes DNA to recipient cell through sex pilus Transformation: cell incorporates DNA fragment from its environment Transduction: DNA fragments can be incorporated by vectors such as viruses and plasmids - When adverse conditions are present, prokaryotes can undergo dormant period by forming thick walled resting spore or endospore. Classification of Bacteria

One of earliest methods was developed by Hans Christian Gram o Stain bacteria with iodine and stain mixture Purple bacteria = Gram-positive No stain = Gram-negative - Another method uses shape of bacteria o Bacillus cells are elongated or rod-shaped o Coccus cells are round/spherical o Spirillum cells are spiral or helical Cyanobacteria - Also called blue-green algae - They have special form of chlorophyll to produce own food - Thought to be algae but they are more closely related to bacteria - Can turn nitrogen and oxygen into nitrates which fertilize plants - Abundance of nitrates and phosphorus in water can cause algal bloom o These large amounts of cyanobacteria steal the available oxygen and kill fish The Archaea - These prokaryotes were once classified with those in the Domain Bacteria o However, their rRNA differed from bacteria and more resembles Domain Eukarya, but not in structure - Live in extreme habitats o Hot springs, oceanic thermal vents, and salt basins - Some are methanogens: have the ability to produce methane - Their plasma membrane contains glycerol molecules linked with hydrocarbons instead of fatty acids like in bacteria and eukaryotes o This allows them to survive extreme environments - Three types of Archaea based on their habitat o Methanogens Live in anaerobic environments like swamps or intestinal tracts Like intestines of grazing animals where they break down cellulose of plant matter o Halophytes Live in high salt environments (Great Salt Lake, Dead sea, etc) o Thermoacidophiles Live in extreme heat and acid environments like hot springs, around volcanoes, and oceanic thermal vents Chapter 22: The Protists General Biology of the Protists - Nutrition of protests o Autotrophs Manufacture own food through photosynthesis

i.e. Algae and euglenoids o Heterotrophs Must ingest their food Parasites & predators Reproduction and life cycles in protests o Sexual reproduction o Asexual reproduction Fragmentation: Breaking off of a portion of the organisms body that establishes itself as an individual Spores: specialized cells that function in forming a new individual Level of body organization o Most protists are unicellular This can happen thanks to specialization of organelles o Some protists are colonial Body of organism consists of a number of cells arranged in a pattern Most of these cells are similar in structure and function o Some protists are multicellular Specialized cells or organs that have specific structures and functions. Ecological role of protists o Some are primary producers Can manufacture own food Food source of other protists and higher animal species o Some are consumers Function as predators, scavengers, decomposers, and/or parasites o Some are free-living and float in upper layers of bodies of water Plankton Diversity in life cycle o Most spend majority of life in haploid condition Single set of chromosomes Produce sex cells by mitosis These sex cells join to form a diploid fertilized egg cell (zygote) After fertilization, organism under goes meiosis to produce haploid cells Continue to grow and develop by mitosis through majority of life Life cycle known as zygotic (or haploid) life cycle o Some protists (red algae) have portion of their life with 4 sets of chromosomes Known as tetraploid

Origin of Eukaryotic Cell - Endosymbiotic theory o States that the chloroplats and mitochondria of todays cells originated as

free-living prokaryotic organisms that were at some time engulfed by heterotrophic cells o The mitochondria and chloroplasts remained in these cells and performed their functions of producing high-energy molecules for themselves and for their host cell o Cells thus equipped had an advantage over other cells and they rapidly increased in numbers Classification of Protists - Divided into 15 subcategories (phyla) o Phylum Chlorophyta - The Green Algae o Phylum Rhodophyta - The Red Algae o Phylum Phaeophyta - The Brown Algae o Phylum Bacillariophyta - The Golden-brown Algae o Phylum Pyrrophyta - The Dinoflagellates o Phylum Euglenophyta - The Euglenoids o Phylum Zoomastigophora - The Zooflagellates o Phylum Rhizopoda - The Ameoboids o Phylum Foraminifera - The Foraminiferans o Phylum Actinopoda - The Radiolarians o Phylum Ciliophora - The Ciliates o Phylum Apicomplexa - The Sporozoans o Phylum Myxomycota - The Plasmodial Slime Molds o Phylum Acrasiomycota - The Cellular Slime Molds o Phylum Oomycota - The Water Molds - These 15 can be grouped based on their mode of nutrition and locomotion o Algae green algae, red algae, brown algae o Diatoms golden-brown algae o Flagellates dinoflagellates, euglenoids, zooflagelates o Sarcodines amoeboids, foraminiferans, radiolarians o Ciliates ciliates o Sporozoans sporozoans o Slime Molds plasmodial slime molds, cellular slime molds o Water Molds water molds The Algae - Photosynthetic and have cell walls made of cellulose - Can be divided into three groups based on types of chlorophyll, structures, and stages of life cycles o Green Algae Habitat: aquatic and terrestrial Motile (flagellated) spores and gametes Many different body forms Flagellated Filamentous

o Red Algae Habitat: warmer seawater Photosynthetic: chlorophyll a and phycobilin Store nutrients such as floridean starch Body form as filaments or ribbons o Brown Algae Habitat: seawater Photosynthetic: chlorophyll a and c and fucoxanthin Store laminarin starch Motile spores and gametes Body form as filaments, ribbons, large blades (sea kelp) Diatoms - Habitat: aquatic major component of phytoplankton - Store lipid - Motile adults and gametes - Body with base and lid of silica with striations - Flagellate characteristics Flagellates - Have whip-like structure used for propulsion o Some have anterior flagella, others have posterior flagella - Divided into 3 phyla o Dinoflagellates Habitat: Marine, major component in plankton Motile adults (2 flagella) and gametes Body with cellulose plates o Euglenoids Habitat: freshwater Photosynthetic or heterotrophic Store paramylon starch Life cycle stages haploid Asexual Motile adults (2 flagella), eyespot Body with protein strips (pellicle) o Zooflagellates Habitat: freshwater Mostly parasitic Motile adults: undulating membrane and flagellum Body with protein strips with underlying microtubules Sarcodines - Habitat: aquatic major component of zooplankton - Heterotrophic (phagocytosis), some parasitic - Store nutrients in vesicles

Multicellular Colonial

- Asexual - Motile adults (pseudopodia) - Body naked or with shell of calcium carbonate Cilliates - Habitat: aquatic major component of zoo plankton - Heterotrophic (holozoic: gullet) - Store nutrients in vesicles - Asexual and sexual (conjugation) reproduction - Body covered with cilia Sporozoans - Habitat: all obligate parasites - Primary and secondary hosts - Absorb nutrients from host - Nonmotile (cyst) or motile (infective) - Body with specialized apical organelles Slime molds - Characterized by ability to secrete digestive enzymes to outside of body as they crawl over food source - Major decomposers of plant materials - 2 phyla o Plasmodial slime molds Habitat: all obligate decomposers Secrete digestive enzymes Absorb nutrients Asexual (spores) and sexual (zygote) Motile feeding stage (plasmodium), motile reproductive stage (amoeboid cells) o Cellular slime molds Habitat: all obligate decomposers Secrete digestive enzymes Asexual (spores) and sexual (zygote) Motile feeding stage (amoeboid cells), nonmotile reproductive stage (sporangia and spores) Water molds - Habitat: decomposers or parasites (land or water) - Secrete digestive enzymes - Asexual (zoospores) and sexual (gametes, zygospores) - Nonmotile except for reproductive stages Chapter 23: The Fungi Modes of nutrition - Most fungi are decomposers o Play role as major recycler of organic matter

o Grow on surface of intended food materials and then produce digestive enzymes that get secreted on food Some are adapted to be parasites o In post cases the host is harmed o Can cause diseases like ringworm, athletes foot, jock itch, valley fever, histoplasmosis and aspergillosis (lung infections), and cryptococcosis (yeast infection in the lung) o Plant diseases caused by fungi include club root, damping off of seedlings, downy mildew, leaf and stem rusts, loose smut, leaf blotch, ergot of grains, scab, and sooty molds Some form symbiotic relationships with other organisms called mutualism o Lichens o Mycorrhizae Specialized fungus that grows near plant roots Roots provide nutrients for fungus and fungus provides nutrients to the plant by breaking down organic matter in soil

Generalized Basic Structure of a Fungus - Difference of fungus from plants, animals and bacteria o Different from bacteria in that fungi have nuclei o Different from plants in that they are heterotrophic o Cell was is made of chitin and not cellulose Chitin is a polymer of glucose that contains and amino group o Fungal cells store nutrients in the form of glycogen (like animals), plants store energy as starch and lipids o Fungi are stationary, never motile o Major portion of fungal life cycle is haploid. Most plants and animals are diploid most of their lives - Body form o Some are unicellular but most are multicellular with body in form of network of filaments called a mycelium Hypha: individual filament o This body form is beneficial for its high surface-to-volume ratio Beneficial because fungus relies on surfaces for excretion of digestive enzymes and absorption of food materials o Some fungi have septa that divide hypha into individual cells Fungus is said to be septate Fungi without septa are called nonseptate - Fungal Growth o New cytoplasm, organelles, and cell wall grow at the tip of the hyphae o Hyphae extend over food material as long as there is material o Under favorable conditions, growth rate is rapid - Fungal reproduction o Either sexual or asexual

o In both cases, mycelium become modified for reproduction o Reproductive structures separated from body by septa o Species of fungi are placed into groups based on the morphology of their reproductive structures Asexual reproduction in the fungi - Can be accomplished by 2 processes o Portion of mycelium broken off and transported away Called fragmentation o Some species produce haploid spores called conidiospores These can be released from parent mycelium and carried in wind or water and germinate Sexual reproduction in the fungi - Involves joining of 2 haploid nuclei to form diploid nucleus and then the formation of haploid spores - This cycle follows the zygotic life cycle which consists of the following steps o Feeding stage mycelium consists of haploid cells o Cells in mycelium of 2 different mating types (+, -) can fuse Cytoplasm joins, not nuclei Produces dikaryotic stage 1 cell contains 2 nuclei Mycelium produces reproductive structures Dikaryotic nuclei fuse forming diploid nucleus This cell develops into a specific structure that varies depending on division Diploid nucleus undergoes meiosis and produces haploid meiospores Meiospores released and germinate Classification of the Fungi - Four major divisions Division Zygomycota (bread molds) - Haploid mycelium of isomorphic mating types (+, -) - Hyphae of 2 mating types grow in proximaty by chemical attraction - Hyphae form specialized branches (gametangia) that touch - Gametangial walls dissolve and haploid nuclei fuse - This wall develops around fused gametangia froming a zygospore - Diploid nucleus undergoes meiosis and produces haploid meiospores - Meiospores released and germinate - Examples: o Rhizopus stolonifer black bread mold o Sordaria macrospora used in genetic research o Neurospora crassa used in genetic research Division Ascomycota (sac fungi) - haploid mycelium of isomorphic mating types

Hyphae of two mating types grow near each other Hyphae form gametangia that touch each other Gametangial walls dissolve but haploid nuclei do not fuse o Produces dikaryotic hyphae - Cells of dikaryotic hyphae form a hymenial layer of the fruiting body (ascocarp) - 2 haploid nuclei in hymenial layer fuse to form diploid nucleus - Diploid nucleus undergoes meiosis followed by mitosis to produce eight haploid nuclei - Hymenial layer enlarges to form the ascus - Haploid nuclei are surrounded by portion of cytoplasm and cell wall o Now called ascospores - Ascospores released through pore in top of ascus - Ascospores germinate - Examples o Peziza vesiculosa crimson cup fungus o Morchella esculenta the edible morel o Uncinula necator powdery mildew of grape o Sphaerotheca panosa powdery mildew of rose o Saccharomyces cervevisiae brewers yeast Division Basidiomycota (club fungi) - Haploid mycelium of isomorphic mating types - Hyphae of two mating types grow near each other - Hyphae form gametangia that touch each other - Gametangial walls dissolve but haploid nuclei do not fuse o Produces dikaryotic hyphae - Cells of dikaryotic hyphae form hymenial layer of the fruiting body (basidiocarp) - Diploid nucleus undergoes meiosis to produce four haploid nuclei - Hymenial layer cell enlarges to form basidium - Haploid nuclei move to tip of basidium, packaged with cytoplasm, and walled off from the basidium o Now called basidiospores - Basidiospores released by breaking off from basidium - Basidiospores germinate - Examples o Agaricus bisporus edible mushroom o Boletus spp. pore mushrooms o Lycoperdon spp. - puffballs o Geaster spp. earth stars o Ustilago zeae corn smut o Puccinia graminis wheat rust o Amanita phalloides poisonous mushroom o Claviceps purpurea ergot on rye, ergotism, source of LSD Division Deuteromycota (imperfect fungi) - Sexual reproduction stages unknown

Can sometimes be stimulated to undergo sexual reproduction when subjected to adverse environmental conditions Those that have shown sexual stages have been placed in Division Ascomycota Examples o Penicillium spp. source of penicillin o Aspergillus oryzae used in making soy sauce o Aspergillus niger makes blue cheese o Aspergillus flavus produces poisonous aflatoxin o Candida albicans vaginal infections

Symbiotic Fungi - Lichens o Symbiotic relationship between fungus and a cyanobacterium or a green alga o Fungus provides a substrate in which alga grows o Alga provides nutrients by photosynthesis o Body types Crustose close to rock surfaces Foliose leaf-like on tree trunks Fruticose highly branched on trees o Lichen importance Soil stabilization in tundra and deserts Air pollution indicators Soil formation through rock breakdown - Mycorrhizae o Symbiotic relationship between a fungus and a plant root o Fungus grows on or in outer layer of roots but doesnt invade cytoplasm o Fungus decomposes old root material releasing nutrients to plant o Fungus increases root absorptive area