BSC 116 BSC 116
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This 11 page Class Notes was uploaded by Ashley Bartolomeo on Sunday January 31, 2016. The Class Notes belongs to BSC 116 at University of Alabama - Tuscaloosa taught by Professor Harris in Spring 2016. Since its upload, it has received 17 views. For similar materials see Principles Biology II in Biological Sciences at University of Alabama - Tuscaloosa.
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Date Created: 01/31/16
Lecture 4: Prokaryotes Bacteria & Archaea Overview 5 kingdoms vs. 3 domains Biology and diversity of prokaryotes o Cellular organization o Reproduction o Metabolic Adaptations o Evolutionary diversity o Ecological relationships Testing Traditional Hypotheses with DNA Molecular characters allow us to assess relationships when there is little morphology to go on o Molecular phylogenetics, molecular clocks Traditional view of organismal diversity: 5 kingdoms o Kingdom Monera (prokaryotes) o Kingdom Protista (singlecelled eukaryotes) o Kingdom Fungi (multicelled eukaryotes) o Kingdom Plantae (multicelled eukaryotes) o Kingdom Animalia (multicelled eukaryotes) This classification is a hypothesis about evolutionary relationships and character change 5 Kingdoms Phylogeny Each kingdom monophyletic o Ancestor & all its descendants o Diagnosed by shared derived characters Prokaryotes vs. eukaryotes Singlecelled vs. multicelled 3 Domains Phylogeny 3 distinct clades (monophyletic): domains o Prokaryotes: bacteria & archaea o Eukaryotes: eukarya Other interesting observations o Protists not monophyletic: paraphyletic (ancestor & some descendants) o Multicellular not monophyletic: polyphyletic (independent origins) Prokaryotes: 2 Clades Sharing Ancestral Characters Two clades of prokaryotes o Bacteria & archaea o Know most about bacteria Modern prokaryotes give info about original forms of life Characteristics tell us about the evolutionary transition to eukaryotes Prokaryotes only life on earth 3.62.1 Gy Prokaryotes “Body Plan” Very small: usually < 5 um Very numerous: most abundant organisms o Total mass = 10x total eukaryotic mass Difficult to know how many species there are o Only really know the ones we can grow in the lab Three basic shapes: cocci, bacilli, & spiral Surrounded by cell wall to keep shape o Composed of peptidoglycan: sugars linked together by proteins Gram stain: standard test, provides information about cell wall structure; stains purple or pink o Gram positive: simple, with a lot of peptidoglycan o Gram negative: complex, outer membrane, with less peptidoglycan Tend to be more toxic Prokaryote Locomotion Have structures to maintain position o Capsule: sticky coat of polysaccharide or protein o Fimbriae (attachment pili): proteinaceous spines Many species capable of moving around o Flagella: in the front to pull, in the back to push, or both o Taxis: actively moving toward or away from stimulus Example, positive phototaxis: moving toward light Example, negative chemotaxis: moving away from a particular chemical (toxin, etc.) Cellular Organization “Simpler” than eukaryotes, but must carry out all the same functions o Lack compartmentalization and membrane bound organelles o Perform same functions on folded membrane surfaces Single circular chromosome in cytoplasm o No nucleus; nucleoid region May have accessory DNA: plasmids o Replicate independent of chromosome Asexual Reproduction: Binary Fission Rapid genome duplication & cell fission o Many generations over short periods of time Optimal conditions: 13 hours (generation), some as fast as 20 minutes (from 1 to 1 billion in 10 hours) More typical: 1224 hours o Large populations, large opportunity for mutations If mutation occurs once each 10 million divisions If there are 20 billion new E. coli in your gut per day Then, there will be 2000 mutant bacteria each day If there are 4300 E. coli genes, then there will be 9 million new mutations per day per human host In bacterial populations, even very rare mutations are generally present, and natural selection can act on them “Accidental” Recombination Can Spread Variation Recombination = sex o Creates new genotypes Transformation: can pick up DNA from environment Transduction: viruses (phages) carry bacterial DNA Conjugation is “Intentional” Recombination Conjugation: one way transfer of DNA o Donor & receiver connected by sex pilus (“mating bridge”) Donation and pilus formation requires F factor(fertility) F plasmids: plasmid passed o F+ passes plasmid to F via pilus o Carries plasmid genes & F factor Hfr cell: F factor on chromosome o High frequency recombination o Chromosome passed & recombined Prokaryotes Can Use Various Energy & Carbon Sources Phototrophs vs. chemotrophs o Energy from light vs. chemical bonds Autotrophs vs. heterotrophs o Inorganic C sources vs. organic C sources Some Require Oxygen, Some Don’t Prokaryotes function under various oxygen levels o Obligate aerobes: require aerobic respiration (like us) o Obligate anaerobes: poisoned by oxygen Fermentation/ glycolysis: non Krebs cycle Anaerobic respiration: final electrons accepted by other than O2 (e.g., NO3, SO4) o Facultative anaerobes: use either method Diversity of Bacteria Better know of two clades: cause diseases 5 major clades Most lineages Gram positive Diversity of Archaea 4 major clades Extremophiles o Halophiles: require high salt concentrations Example, species living in Great Salt Lake o Thermophiles: require high temperatures Example, species living in hot springs Methanogens: use CO2 and H2; create methane o Obligate anaerobes o Example, species in anaerobic marshes Prokaryotes Have Important Roles in Nutrient Cycling Ecosystems depend upon cycling of nutrients: living and nonliving Decomposers o Release C & N to environment Photosynthesis o Fix C, produce O2 Nitrogen fixation: can convert atmospheric N2, into NH3 o Can then be used by other organisms Decrease availability of some chemicals by holding them Other Important Ecological Interactions Often have symbiotic associations with larger organisms o Mutualism: example, gut has 5001000 species; help with digestion o Commensalism: 150+ species on skim Parasitism: pathogens o Bacteria only (not archaea) o Half of all human diseases o Examples of bacterial diseases Cholera (exotoxic) Tuberculosis Botulism Food poisoning (e.g., gram negative, endotoxic) Lyme disease Prokaryote Differences Targeted by Antibiotics 1 big step in controlling bacterial pathogens: washing (germ theory) nd 2 big step: antibiotics, drugs that target prokaryote traits wont harm us o Cell wall: peptidoglycan not found in eukaryotes Targeted by penicillin o Ribosomes: use different proteins than eukaryotes Targeted by tetracycline Use of antibiotics strong selection for resistance o Mutations can reduce effectiveness: change target of antibiotic o R plasmids (resistance plasmids): have genes for enzymes that destroy antibiotics Some Beneficial Uses of Bacteria Culture for food: cheese & yogurt Bioremediation: using bacteria to breakdown sewage, chemical spills, etc. Genetic engineering: use cellular machinery to make chemicals we can use (vitamins, antibiotics, etc.) Lecture 5: SingleCelled Eukaryotes The Protists Overview Protists are (mostly) singlecelled eukaryotes Primary & secondary endosymbiosis Diversity of major protest groups Protist ecology, including pathogens 3 Domains Phylogeny Eukarya: all eukaryotes, single and multicellular o Monophyletic: ancestral eukaryotic species and all descendants form a clade “Kingdom Protista”: single celled eukaryotes o Paraphyletic: does not include all descendants of their common ancestor (excludes multicellular clades) Fungi, plants and animals represent independent origins of multicellularity (polyphyletic) Paraphyletic groups like protists are recognized by what they are not Protists are a “Grade” Rather than a Clade “Kingdom Protista” diagnosed by being (mostly) singlecelled eukaryotes That is a shared ancestral character o Provides no information about evolutionary relationships within Eukarya Protists represent a grade: a level of complexity o More complex than prokaryotes o Trending toward multicellularity Eukaryotes arose ca. 2.1 Gy o Multicellularity not until ca. 1.4 Gy o Major animal, plant, etc. lineages much later Protists are More Complex than Prokaryotes, More Diverse Ecologically Than Other Multicellular Life Most singlecelled o Also colonial and multicellular lineages Eukaryotic cells with organelles o Typical organelles like nucleus, mitochondria, ER Found in single and multicelled eukaryotes o Also have contractile vacuoles to expel water Only in singlecelled forms Diverse metabolic adaptations: use various carbon and energy sources o Autotrophs: photosynthetic Use light energy to fix inorganic CO2 o Heterotrophs: feed on other organisms, absorb dissolved molecules Get C and energy from organic C (sugars, proteins, fats) o Mixotrophs: same individual capable of both Photosynthesis in light, heterotrophs in dark Eukaryotes Arose Through Endosymbiosis Can reconstruct evolution of eukaryote organization using cladistics method o Use distribution of characters among species to determines order of events Evolution of nucleus, ER Mitochondria is acquired via endosymbiosis o “tamed” heterotrophic prokaryote Chloroplasts acquired via endosymbiosis o “tamed” photosynthetic prokaryote Evidence for endosymbiosis o Retain portions of circular ancestral chromosome o Surrounded by double membranes: 1 from prokaryote, 1 from engulfing vacuole Secondary Endosymbiosis There has been at least three instances of secondary endosymbiosis o Plastid: acquired by engulfing photosynthetic eukaryote Evidence: o Chloroplast (2 membranes) surrounded by two more membranes: 1 from engulfed eukaryote, 1 from vacuole rd o Nucleomorph: remnant of eukaryote genome within 3 membrane There are 4 Main Protist Lineages Molecular phylogenetic analyses identify 4 major groups o Excavata o Stramenopiles + Alveolates + Rhiziaria = SAR o Archeaplastida o Unikonts Groups often composed of heterogeneous taxa o Same traits appear repeatedly in different groups o Difficult to generalize about Groupings summarize trends and variety Excavates are Mostly Parasitic Many excavates are flagellated parasites; two main groups Diplomonads + Parabasalids o Have reduced mitochondria o Obligate or facultative anaerobes o Generally parasites Euglenozoans o Have flagella with unique morphology o Euglenids: mostly free living mixotrophs, like Euglena o Kinetoplastids: free living predators and parasites, like Trypanosoma (causes sleeping sickness) Stramenopiles Have Characteristic Flagella Stramenopiles “hairy Flagella” o Have 2 endosymbiotic plastids: autotrophs. Heterotrophs & mixotrophs o Four major lineages Diatoms: photosynthetic algae, with silica (glass) wall around cell) Golden algae: unicellular or colonial mixotrophs o Many species form protective cysts that can survive for decades Brown algae: multiceulluar “seaweeds” & kelp Alveolates Share Similar Cytoskeletons Alveolates grouped together based upon shared presence of alveoli beneath the cell membrane; three distinct lineages Ciliates: cell covered in many short cilia rather than few long flagella; two types of nuclei o Generally freeliving, like Paramecium Apicomplexans: parasites with complex life cycles o Like Plasmodium, causes malaria Dinoflagellates: cellulose plates, with two flagella in grooves o Can cause neurotoxic shellfish poisoning o Can cause a crimson tide Rhizarians are one Group of Amoebas Rhizarians: amoeboid pseudopodia cytoplasmic streaming for locomotion, prey capture, etc. o 3 groups, two with hard shells Foraminiferans: shell (test) of calcium carbonate Planktonic When they settle to bottom, form limestone/ chalk Radiolarians: shell of silica (glass); planktonic Chlorarachniophytes are a third mixotrophic group; secondary endosymbiosis with green alga Archaeplastida Includes the Plants and Related Algae Photosynthetic; primary endosymbiosis event Red algae: multicellular, with accessory photopigmentthat makes them red Green algae o Chlorophytes: unicellular colonial and multicellular green algae o Charophyceans & land plants Unikonts Represent Disparate Taxa, Including Fungi and Animals Unikonts composed of two major groups, based upon general DNA and myosin protein similarity o Amoebozoans: slime molds and other amoebas; locomotion via pseudopodia Generally unicellular, but slime molds form large aggregations (sometimes acellular) o Opisthokonts: unicellular and multicellular flagellate heterotrophs Including fungi and animals Various Trends Repeated During Protist Evolution Some traits have arisen only a single time o Example, chloroplast (primary endosymbiosis) Some traits have arisen multiple times (convergent evolution) o Secondary endosymbiosis (photosynthesis) o Multicellularity o Significant parasites Complex Life Cycles & Multicellularity Complex life cycles: alternation of generation o Asexual & sexual phases o Mitosis (2n), meiosis (n) & fertilization Found in groups that have evolved multicellularity o Stramenopiles (brown algae) o Archaeplastida o Unikonts Complex life cycles provide organization needed for multicellularity o Development of organism from single cell o Differentiation of cells into tissues Ecological Roles of Protists Photosynthetic protists are producers o 25% of Earth’s photosynthesis by protists o Especially in aquatic environments Example, diatoms Protists are part of important mutualisms, examples: o Photosynthetic Dinoflagellates: live in tissues of organisms in coral reefs, including coral and giant clams o Parabasalids: symbionts in termite guts to break down cellulose There are Important Protist Pathogens Many different protists cause disease in humans, examples: o Giardia (Diplomonad): causes giardiasis Why you filter your drinking water on the Appalachian Trail o Trypanosoma (Euglenozoan): causes African Sleeping Sickness Spread by tsetse flies Lives in blood and other fluids Interesting adaptation to avoid immune system o Plasmodium (apricomplexa): causes malaria Spread by mosquitoes Live in blood cells Complex life cycles Lecture 6: Multicellular Eukaryotes Fungi Parakaryon Myojinensis An apparent intermediate between prokaryotes and eukaryotes o 10 um long, 3 um in diameter, >100 times the volume of E. coli o Large nucleoid consisting of naked DNA fibers o Single nucleoid membrane o Endosymbionts that resemble bacteria o No mitochondria Overview Fungi and plants (both multicellular) arose independently from different eukaryotic clades Fungi are heterotrophs with complex life cycles o Sexual/ asexual reproduction Fungi have ancient ecological associations with plants Multicellularity Has Arisen More Than Once Multicellular organisms occur in several clades Not the same as colonials o Example, slime molds (singlecell and colonial stages) Fungi are (Generally) Multicellular heterotrophs that Represent Diverse Ecological Roles Heterotrophs: absorb nutrients without ingestion (unlike animals) Qsecrete enzymes that breakdown many compounds: good decomposers Can be parasitic and pathogenic Can be mutualistic Fungi Body Structure Single vs. multicelled o Singlecelled: yeast o Multicelled filaments: hyphae o Filaments form masses: mycelia, increase surface area uptake Cell structure o Cell wall chitin (POLYSACCHARIDE) o Hyphae may be 1. Divided by septa or 2. Undivided, coenocytic fungi Fungi Have Complex Life Cycles Reproduce by producing spores o Haploid hyphae and spores N vs. 2n o Sexual (meiosis) and asexual (mitosis) Sexual reproduction o Plasmogamy: fusion of cytoplasm of 2 different mating types o Heterokaryon/ dikaryon: 2 parental nuclei in 1 cyotplasm (n + n) o Karyogamy: fusion of nuclei (2n) o Spores (n) produced by meiosis Asexual reproduction (molds) o Spores (n) produced by mitosis Fungi Evolved from SingleCelled Protists Unikonts divided into two main groups o Amoebozoans Slime molds, other amoeba o Opisthokonts Animals plus choanoflagellates Fungi plus Nucleariids amoeba that feed on algae and bacteria Unclear when first fungi appeared o Oldest fossil fungi: 460 My, terrestrial o DNA evidence suggests animals and fungi evolved independently from different protest ancestors Even though fungi are often taught with plants, they have much more in common with animals Fungi Have Important Associations with Plants Parasitic/ mutualistic relationships between fungi and plant roots use haustoria o Perforate plant cell wall but not plasma membrane Mycorrhizal fungi mutualism with roots o Fungi provides phosphorus, other nutrients o Plant provides carbohydrtaes o Two kinds: Arbuscular mycorrhizae: haustoria Extomycorrhizae: form sheaths around roots Extremely important to plants o Almost all vascular plants have mycorrhizae o Fossil plants show association important for colonization of terrestrial habitats There are about 100,000 Fungal Species in Five Clades Chytrids 1000 species o Earliest branch; flagellated zoospores o Decomposers, parasites & some mutualists Zygomycetes 1000 species o Form sexual spores in zygosporangium o Decomposers (like Rhizopus, black bread mold) Also parasites/ commensals on animals Glomeromycetes 160 species o Similar to zygomycetes, but most have arbuscular mycorrhizal associations with plants (90% of plants species) Ascomycetes 65,000 species: sac fungi o Sexual spores formed in asci, with ascocarps (fruiting bodies) Basidiomycetes 30,000 species: club fungi o Sexual spores formed in basidia, with basidiocarps (fruiting bodies) Ascomycetes 65,000 species; yeast and multicellular Some ycorrhizae 40% of species lichens with green algae or cyanobacteria Neurospora: example life cycle o Conidia: asexual spores Form at hyphal tips (conidiophores) o Conidia also involved in sexual reproduction Plasmogamy with different mating type Dikaryotic cells develop into asci Karyogamy (2n), then meiosis (4 x n) then mitosis (8 x n) Ascospores form in asci arranged into ascocarps Basidiomycetes Decomposers, especially of wood (lignin) o Example, shelf mushrooms Life cycle has prominent dikaryotic mycelium o Plasmogamy of haploid (n) mycelia o Dikaryotic (n + n) mycelium grows quickly May produce basidiocarp (“mushroom”) o Gills of basidiocarp lined with basidia: dikaryotic cells at the end of hypae o Karyogamy of basidia (2n(, meiosis (4 x n) produces basidiospores (100s of millions) Harmful Fungi About 1/3 of fungi parasites/ pathogens o Especially on plants (80% of plant diseases) Plant parasites o Cryphonectria parasitica & American chestnuts o Parasites on crops Decrease yields (1050% per year for fruit) Sometimes toxic to humans Claviceps purpurea, rya & ergotism Animal parasites o Skin (external) mycosis: athlete’s foot, yeast infection, etc o Systematic (internal) mycosis: can be caused by inhaled spores Helpful Fungi Mycorrhizae & lichens o Phototroph and heterotroph exchanging products Ascomycete endophytes between leaf cells o Release compounds that protect plant from insects Food: mushrooms, truffles, cheeses, bread, beer Medicine: antibiotics and other drugs Bioengineering: fungi can make eukaryotic products that bacteria cant
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