Biology 2 Dr. Tim Revell SI: Claire Suh TA: Bryan Quintero 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 2/17/14game 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? 2/17/14 3 Carl Linneaus q Father of “_________Taxonomy ” 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 • Domain Bacteria: • Group: Proteobacteria Kingdom Fungi: • ex: Salmonella, E. Coli Division: Chytridiomycota • Group: Gram (+) Bacteria Division: Zygomycota (Zygomycetes) • ex: Clostridium, Bacillus Anthracis, Division: Glomeromycota Streptococcus, Staphylococcus Division: Ascomycota • Group: Cyanobacteria Division: Basidiomycota • ex: Oscillatoria Division: Deuteromycota • Group: Spirochetes • ex: Treponema pallidum, Kingdom Plantae • Borrelia burgdorferi Division: Hepatophyta (liverworts) • Group: Chlamydias Division: Anthocerophyta (hornworts) • ex: Chlamydia Division: Bryophyta (Mosses) • Division: Lycophyta (Club Mosses) • Doman Archaea: Division: Pterophyta • Group: Methanogens * Psilophyta (Whisk Ferns) • Group: Halophiles * Sphenophyta (Horse Tails) • Group: ThermophilesDomain Eukarya, Kingdom Protista Division: Pterophyta (Ferns) Division: Ginkgophyta • Supergroup: Excavata Division: Cycadophyta • Clade: Diplomonads Division: Gnetophyta • Clade: Parabasalids Division: Coniferophyta • Clade: Euglenozoans Division: Anthophyta • Group: Euglenids • Group: Kinetoplastids Kingdom Animalia • Supergroup: Chromalveolatas (Lophophorate Phyla) • Clade: Alveolatas Phylum: Bryozoa • Group: Dinoflagellates Phylum: Phoronida • Group: Apicomplexans Phylum: Brachiopoda • Group: Ciliates Phylum Porifera • Clade: Stramenopila Class: Calcarea • Group: Bacillariophyta Class: Hexactinellidae • Group: Phaeophyta Class: Demospongiae • Group: Chrysophyta Phylum Cnidaria • Group: Oomycota Class: Hydrozoa • Supergroup: Rhizaria Class: Scyphozoa (Jellies) • Group: Foraminiferans Class: Anthozoa • Group: Radiolarians Class: Cubozoa (Box Jellies) • Supergroup: Archaeplastida Phylum Ctenophora (Comb Jellies) Phylum Platyhelminthes (Flatworms) • Group: Rhodophyta Class: Tubellaria • Group: Chlorophyta Class: Monogenea • Supergroup: Unikonta Class: Trematoda • Clade: Amoebozoans Class: Cestoidea • Group: Slime molds Phylum Rotifera • Group: Gymnamoebas Phylum Nemertea (Ribbon Worms) • Group: Entamoebas Phylum Nematoda (Round Worms) • Clade: Opisthokonts Phylum Mollusca • Group: Nucleariids Class: Monoplacophora • Group: Choanoflagellate Class: Polyplacophora Class: Gastropoda Class: Scaphopoda Class: Bivalvia Class: Cephalopoda Phylum Chordata Phylum Annedlida Subphylum: Urochordata (tunicates) Class: Oligochaeta Subphylum: Cephalochordata (lancelets) Subphylum: Vertebrata Class: Polychaeta Superclass: Agnatha (lampreys/hagfish) Class: Hirudinea Superclass: Gnathostomata Phylum Onychophora Class: Chondrichthyes Phylum Arthropoda Class: Osteichthyes Subphylum: Trilobita Superorder: Ostariophysi Superorder: Procantheropterygii Subphylum: Chelicerata Superorder: Acantheropterygii Class: Merostomata Class: Amphibians Class: Pycogonida Order: Urodela (Salamanders) Class: Arachnida Order: Anurans (Frogs/Toads) Subphylum: Crustacea Order: Apodans (Caecillians) Reptiles Class: Crustacea Class: Testudines (Turtles/Tortoises) Subphylum: Uniramia/Myriapoda Class: Sphenodontia (Tuataras) Class: Chilopoda Class: Squamata (Lizards/Snakes) Class: Diplopoda Class: Crocodilia Subphylum: Hexapoda Class: Dinosauria Order: Omithiscians Class: Insecta Order: Sauriscians Phylum Echinodermata Class: Aves Class: Asteroidea Order: Passeriformes Class: Ophiuroidea Order: Anseriformes Class: Echinodea Order: Columbiformes Class: Holothuroidea Class: Mammalia Order: Monotremata Class: Cnnoidea 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 Many different “systems” or “styles” for classifying life…. 8 Cladistics • ___________Cladogram – A type of chart showing the relationship of the different groups to one another. • Clade – Any grouping on a cladogram that includes all of the descendents and a common ancestor. • Sister Taxa Cladistics • Shared ancestral characters – ____________Plesiomorphies • Shared derived characters – ____________Synapomorphies Cladistics • Outgroups – a clade (species) closely related to the ingroup but less closely related than any of the ingroup members. • Ingroups – The group we are trying to determine the relationships for. • The Law of Parisimony (Occam’s Razor) Cladistics Groupings • Monophyletic___________ – Clade that includes ancestor and all of its descendants. • ____________Paraphyletic – Clade that includes ancestor and some, but not all, of it’s descendants. • ____________Polyphyletic – Grouping that lacks a most recent common ancestor. 2/17/14 13 Domain: Bacteria Domain: Archeae Domain: Eukaryote Bacteria - Prokaryotes Bacteria Characteristics • Nucleoid Region • Plasma – single circular membrane chromosome • Cell wall – plasmids _____________– peptidoglycan • No membrane- • Capsule bound – glycocalyx organelles • Flagella • Ribosomes • Pilli (70S) • Fimbrae Classification • Shape (Cocci or Rod) • Staining – Gram – Spore – Acid-fast • Oxygen requirements • Feeding strategies Shapes • Sperical (Cocci) • Rod-Shaped (Bacillus) • Spiral (Spirochetes) 2/17/14 19 Shapes and Groups Cocci: Spherical Strep_____ – in lines Staph_____ – in grape like clusters Shape Helical: Spiral- shaped (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 – Violet = gram positive – Red = gram negative Know these steps! Lab Acid-fast Stain – Mycobacterium leprae, M. tuberculosis (Acid-Fast + Red, Negative Blue) 2/17/14 28 Spore Stain Oxygen Requirements • Obligate aerobes – require oxygen • Obligate anaerobes – require no oxygen • ____________________–Facultative anaerobe can grow with or without oxygen • Aerotolerant Anaerobes – only anaerobic growth but oxygen does not harm. • _________________–Microaerophiles aerobic growth in low oxygen concentrations. Make sure you know this figure! Good Essay Question!!! Feeding Strategies • Based on energy and carbon sources – Photoautotrophs – Chemoautotrophs – Photoheterotrophs – Chemoheterotrophs Feeding Strategies Good essay Question! Nitrogen Metabolism • Nitrogen is needed proteins/ nucleic acids • Nitrogen fixation - convert atmospheric N into ammonia • Makes N available for other organisms 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) • Endotoxin – caused by cell wall Domain: Bacteria • Group: Proteobacteria – E. coli • bacillus shape, gram negative, facultative anaerobe • Diarrhea • Exotoxin – releases proteins that cause illness Domain: Bacteria • Group: Gram-positive bacteria – Clostridium • Bacillus shape • endospore • Obligate anaerobes - exotoxins • Causes gangrene, __________Botulism (strongest poison in the world! – 1 gram can kill 1 million people!) Domain: • Group: Gram- Bacteria positive bacteria – Bacillus anthracis • Bacillus shape (endospore) • Aerobic • Causes pustules, pneumonia Domain: Bacteria • Group: Gram- positive bacteria – Streptococcus • Coccus shape & gram positive, anaerobic but are air tolerant • necrotizing fasciitis, strep throat, scarlet fever • Group: Gram-positive Domain: bacteria Bacteria – Staphylococcus, MRSA • coccus shape & gram positive, facultative anaerobe • Most common type of food poisoning, toxic shock syndrome • Dangerous in hospitals (________Nosocimal infections) • Iatrogenic • Group: Cyanobacteria Domain: – Contains Chlorophyll A Bacteria and phycocyanin • Only organism on planet that can fix nitrogen and release oxygen • pools Domain: Bacteria • Group: Spirochetes – Treponema__________________ pallidum • Syphilis • anaerobic – Borrelia__________________ burgdorferi • Lyme Disease • Microaerophile • zoonosis 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 Data: The Fossil Record 2/17/14 48 Fossil Record • __________Sedimentary • Hard Parts – most Rocks – type of rock likely to be that usually makes preserved as fossils best fossils 2/17/14 49 Fossil Record • Organic Material • Minerals – when part of the replacing organic organism remains material 2/17/14 50 Fossil Record • Casts – • Trace Fossils – impressions made footprints, burrows, or by an organism other signs of activity 2/17/14 51 Fossil Record • Entire Organisms 2/17/14 52 Limitations of the Fossil Record • Habitat Bias – some habitat betters than others at making fossils • Slow Decay – Some organisms decompose too quickly or get destroyed before fossilizing • Temporal Bias –