BIOL 112 1ST Edition Exam 2 Study Guide Lectures 12 22 Lecture 12 September 29 Taxonomy grouping species together subjective Linnaeus s nested hierarchical classification system All species in any taxon share certain features ex lions leopards and housecats Domain kingdom phylum class order family genus species Phylogeny evolutionary history and relationships to other species Branch point where lineage diverges Sister taxa share an immediate common ancestor Polytomy 3 or more branches from a common ancestor unresolved pattern of divergence Basal Taxon distant relative Systematics study of phylogenic relationships Monophyletic Taxa ancestor and all its descendants Paraphyletic Taxa leaves out a common descendant Cladistics a method of determining phylogeny Must identify characteristics in a group as ancestral or derived Create dichotomous trees based on synapomorphies Use maximum parsimony Homologous genes reveal relationships and Orthologous genes encode for similar proteins with the same function in both genes which are derived from ancestral groups More mutations in orthologous genes more distant relationship Interpreting cladistic trees Clade all the species on a branch All species in a clade share homologies More shared characteristics closer relationship Sequence of evolutionary events can be inferred from cladistic trees Trees may be scaled to geologic time Molecular clock assumes that DNA mutates at a constant rate Tree of life Old system monera Animalia plantae fungi Protista Current domain system bacteria archaea Eukarya Horizontal gene transfer exchanging DNA with other organisms ex endosymbiosis Lecture 13 October 1 Bacteria and Archaea Prokaryote structure Smallest of all cells 3 shapes cocci bacilli and spirilla or spirochetes Mostly unicellular can be in chains or clusters Most have a cell wall outside the membrane Prevents cell lysis Bacteria have peptidoglycan walls Archaea have walls of other polysaccharides Gram stain shows type of cell wall Gram thick peptidoglycan layer stains purple Gram thin peptidoglycan layer and outer lipid membrane stains pink usually toxic Capsule slime layer secreted out of the cell wall Acts like glue Resists immune attack Retains moisture Fimbriae protein hairs act like glue as well Pili allows conjugation DNA transfer Forms a mating bridge Many have motility Taxis movement towards or away from or stimulus Chemotaxis food Phototaxis sunlight Geotaxis up or down Slime gliding ejecting slime Rotating flagella fibers Spirochetes have internal flagella No membrane bound organelles DNA is in the nucleoid region Aerobic cellular respiration and photosynthetic bacteria have folded plasma membranes Lecture 14 October 3 Prokaryote genetic diversity 1 chromosome with circular DNA Plasmids Independent small DNA rings Non essential but add diversity Binary fission yields 2 genetically identical cells Growth limited by food moisture and crowding Endospores can form under stress Resists heat and drought for years ex tetanus anthrax DNA mutations during division can cause diversity High cell division rate leads to many mutations One mutation can change the phenotype Mutations are passed on in clones Therefore prokaryotes evolve rapidly Recombination by Transformation Griffith s experiment DNA bits from ruptured donor cell are directly absorbed by other bacteria and new homologous alleles are inserted into the chromosome new recombinant DNA Horizontal gene transfer Recombination by Transduction Bacteriophage carries DNA from donor to acceptor strain New chromosomal alleles inserted into recipient cell Recombination by Conjugation Donor must have the F factor F factor genes build sex pilus Mating bridge is a one way transfer of a complementary strand of the F plasmid F becomes F cell F factor can carry other genes Hfr cell combination F factor is part of the actual chromosome of the donor F recipient gets new bacterial DNA but it remains F Prokaryote nutritional metabolic diversity Need an energy and carbon source Photoautotrophs chemoautotrophs photoheterotrophs chemoheterotrophs Oxygen and metabolism Obligate aerobes need oxygen for cellular respiration Obligate anaerobes poisoned by oxygen Facultative anaerobes normally use oxygen but can be anaerobic Metabolic cooperation better growth occurs together Ex Cyanobacteria most cells are photosynthetic but heterocysts fix nitrogen Ex Biofilms cells recruit other cells not always of the same species Prokaryote ecological roles Food webs and nutrient cycling Primary producers Autotrophs fix CO2 into organic carbon Chemoautotrophs are the base of hydrothermal vent food webs Decomposers heterotrophs that break down dead material or wastes Releases CO2 and nutrients Most important decomposers on earth Oxygen cycle Cyanobacteria are photosynthetic and a major source of oxygen Nitrogen cycle Most cells need nitrogen as ammonia or and organic compound Nitrogen fixation atmospheric N2 is fixed into NH4 Ex Cyanobacteria heterocysts fix nitrogen Ex Symbiotic bacteria in alfalfa roots give off nitrogen Symbiosis 2 species in a close relationship Parasitism parasite benefits off the host Includes pathogenic bacteria Commensalism one species benefits from the host without affecting it Mutualism both species benefit from each other Ex Rhizobium in legume roots Ex Probiotics produce vitamin K in the colon Prokaryotes and humans Mutualistic bacteria mostly in digestive tract ward off pathogenic bacteria Produce vitamins Helps immune system Pathogenic bacteria produce bacterial toxins Exotoxins secreted proteins that attack cell receptors ex botox Endotoxins outer membrane of gram negative bacteria can be toxic ex salmonella Overuse of antibiotics causes antibiotic resistance in bacteria Beneficial uses of Prokaryotes Basic research on cells and DNA DNA technology Commercial chemical and drug production Bioremediation Food products yogurt cheese kombucha etc Lecture 15 October 6 Prokaryote Phylogeny Archaea are more closely related to eukaryotes than bacteria Bacteria Proteobacteria Gram highly diverse metabolism ex sulfur bacteria Includes gastrointestinal pathogens ex E coli salmonella cholera Chlamydias Endoparasites ex trachomatis Spirochetes Spiral shape flagella on the inside Mostly free living Includes pathogens ex syphilis Lyme disease Cyanobacteria Generates O2 in photosynthesis Some fix N Some blooms are toxic Gram bacteria Includes soil decomposers ex Streptomyces makes antibiotics Includes pathogens ex