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University of Toronto Mississauga
Christoph Richter

27.1: Phylogenetic Trees January-16-12 3:56 PM • Phylogeny: evolutionaryhistory of a group of orgs • Phylogenetictree: shows the ancestor-descendantrelationships among pops or species, clarifies who is related to whom • Branch: reps pop through time • Node/fork: pt where 2 branches diverge ; reps pt in time when an ancestral group slit into 2 or more descendant groups • Tip/terminal node: endpt of a branch ; reps group (species of larger taxon) living today or one that ended in extinction • ESTIMATING PHYLOGENIES • Phenetic Approach ○ Based on computing a statistic that summarizes overall similarity among pops, based on data ○ i.e. using gene sequences to compute an overall genetic distance  Genetic distance summarizes avg percentage of vases in a DNA sequence that differ bt 2 pops  Computer program build a tree that clusters mostsimilar pops and places more divergent pops on distant branches • Cladistic Approach ○ Based on realization that relationships among species can be reconstructedby identifying shared derived characteristics ○ Synapomorphies: shared, derived trait found in 2 or more taxa that is present in their most recent commonancestor but is missing in more distant ancestors  Useful for inferring evolutionaryrelationships  Allow biologists to recognize monophyleticgroups/clades/lineages  i.e. fur and lactation = synapomorphythat identify mammalsas monophyletic group ○ Monophyletic: evolutionaryunit that includes an ancestral pop and all of its descendants but no others  ○ Paraphyletic: evolutionaryunit that includes an ancestral pop and some but not all of its descendants • Issue w. phenetic and cladistic approach: traits can be similar in 2 species not bc those traits were present in a commonancestor, but bc similar traits evolved independently in 2 distantly related groups HOMOLOGYAND HOMOPLASY • Homology: occurs when traits are due to shared ancestry (same source) • Homoplasy: occurs when traits are similar for reasons other than commonancestry (same form) • i.e. ichthyosaurs (aquatic reptiles) are very similar to modern dolphins ○ Large marine animals, streamlined bodies, large dorsal fins, dagger like teeth ○ BUT icythyosaurs= reptiles, dolphins = mammals • Similarities result from convergent evolution • Convergent evolution: occurs when natural selection favours similar solutions to probs posed by similar way of making a living • Convergent traits done occur in commonancestor of similar species • Convergent evolution= commoncause of homoplasy ○ Results in analogous traits • If similar traits found in distantly related lineages are similar due to commonancestry, then similar traits should be found in intervening lineages on tree of life • Parsimony: logical principle that the most likely explanation of a phenomenon is the most economical/simplest; tree requiring the fewest evolutionarychanges is mostlikely to be correct • Homoplasyshould be rare compared w. similarity due to shared descent, so tree that implies fewest overall evolutionarychanges should be one that reflects what really happened during evolution 27.2: Fossil Record January-16-12 4:35 PM • Fossil record: total collection of fossils that have been found throughout world ○ Providesdirect evidence about what orgs that lived in the past looked like, where they lived, when they existed • Fossils: pc of physical evidence from an org that lived in the past FORMATION OF FOSSILS • Buried in ash, sand, mud, other type of sediment • decompositiondoesn’t occur - organic remains can be preserved intact • sediments accumulate on top of material and become cementedinto rocks - weight can compressorganic material into thin carbonaceous film • Remains decomposeafter buried - hole that remains can fill w. dissolved minerals and create cast of remains • Remains rot - dissolved minerals can infiltrate interior of cells and harden into stone, forming permineralized fossil LIMITATIONS OF FOSSIL RECORD • Habitat bias - orgs that live in areas where sediments are actively being deposited, burrowing orgs , morelikely to fossilize • Taxonomicbias - orgs w. hard parts and parts that are decay resistant (teeth, bones, shells) more likely to fossilize • Temporal bias - recent fossils are more commonthen ancient fossils (older a fossil is, more likely it is to be demolished by erosion etc) • Abundance bias - weighted towards commonspecies (orgs that are abundant, widespread, on earth for long time) LIFE'S TIMELINE • Precambrian - Hadean, Archaean, Proterozoic,eon ○ Life was unicellular ○ Oxygen was absent from oceans and atmosphere ○ Origin of life • Phanerozoic eon • Paleozoic 28.1: Why Do Biologists Study Bacteria and Archaea? January-16-12 5:19 PM • Bacteria - peptidoglycan in cell walls • Archaea - unique phospholipids (compounds containing HC called isoprenes in their tails) in plasma membrane • RNA polymerasesand ribosomes differ in archaea and bacteria • Microbe: any microscopicorg • Understanding diversityis key to bio • Ability to compare characteristicsin an array of diverse orgs is fundamental to increased understanding SOME BACTERIA CAUSE DISEASE • No archaea are known to cause disease in humans • Bacteria that cause disease = pathogenic • Robert Koch - first to establish link bt bacteria and disease ○ Studied anthrax (disease of cattle and other grazing mammals; results in fatal blood poisoning) ○ Proposed4 criteria had to be met in order to establish link ○ Koch's Postulates: 1) Microbe must be present in individuals suffering from disease and absent form health individuals 2) Org must be isolated and grown in a pure culture away from host org 3) If orgs from pure culture are injected into healthy experimental animal, disease symptomsshould appear 4) Org should be isolated from diseased experimentalanimal, again grown in pure culture, and be the same as original org • Germ Theory of Disease ○ Infectious diseases are caused by bacteria and viruses ○ Viruses = acellular particles that parasitize cells • Improvementsin sanitation and nutrition caused reductions in mortality rates due to infectious disease • Antibiotics discoveredin 1928 • Antibiotics: moleculesthat kill bacteria ○ Combat bacterial infections BACTERIA CAN CLEAN UP POLLUTION • Bioremediation: use of bac and archaea to degrade pollutants • Based on complementarystrategies: ○ Fertilizing contaminatedsites - to encourage growth of existing bac and archaea that degrade toxic compounds  i.e adding N to use as a fertilizer - N is used to synthesize enzymes and other compounds during cellular respiration ○ Seeding/adding specific species of bac and archaea - to contaminated sites shows promise of alleviating pollution in some situations  i.e somebac can render certain chlorinated, ring containing compounds harmless (instead of being poisoned by pollutants) and use them as e- acceptors EXTREMOPHILES • Extremophiles: bac or archaea that live in high-salt, high temp, low temp, or high pressure habitats ○ "extremelovers" • Live in conditions that are similar to early Earth's history ○ Therefore,extremophilesmay have been first forms of life on earth • Understanding them may explaining how life began • Understanding them may explaining how life began • Used as model orgs in search for extraterrestriallife • Useful in industrial processes HOW DO SMALL CELLS AFFECT GLOBAL CHANGE? • Bac that live in extremeenviro use toxic compounds as food bc they produce sophisticated enzymes • Potent forces for global change • Altered compositionof oceans, atmosphere,terrestrial enviros • Oxygen Revolution ○ No free molecular O existed for the first 2.3 bill yrs of earths existence ○ Based on 2 observations: 1) No plausible source of O at the time the planet formed 2) Oldest earth rocks indicate that any O that formed reacted w. iron atoms to produce iron oxides ○ Cyanobacteria: lineage of photosyntheticbac ○ First orgs to perform oxygenic photosynthesis  Produced oxygen ○ Oxygenic photosynth depends on proteins and pigments in photosystemII  Includes enzymescapable of stripping e- from water molecules ○ O is a waste product ○ Production of O allowed for aerobic respiration ○ Evolution of aerobic respiration = crucial event in history of life  O = extremelyEN and an efficient e- acceptor  Results in moreE release ○ Aerobic respiration makes large cell size and multicellularity possible • Nitrogen Cycle ○ Orgs must have N to synthesize proteins and nucleic acids ○ Most orgs can only obtain N in the form of ammoniaor nitrate ○ Only orgs that can convertN to ammonia = bacteria ○ Nitrogen fixation: complexand highly endergonic LEO-GER rxns ○ Enzymes required for N fixation found only in select bac lineages ○ Some N fixing bac live in assocation w. plants  Roots nodules form protectivestructure for bac that fix N ○ If bac couldn’t fix N, only tiny fraction of life would exist today • Nitrate Pollution ○ Addition of N is used to increase crop yields ○ When ammonia is added, most is used as food by bac that release nitrate or nitrite as waste products ○ Nitrate is highly soluble and pollute water bodies ○ Build up of N causes increase in pop of cyanobac and algae  May cause bodies of water to becomeO free bc it is used as e- acceptor 28.2: How Do Biologists Study Bacteria and Archaea January-19-12 6:54 PM USING ENRICHMENT CULTURES • Isolation of bac • Enrichment culture: method of obtaining cells w. specific characteristics by placing a sample, containing many types of cells, under a specific set of condns (i.e. temp, lighting, substrate, available nutrients) and isolating those cells that grow rapidly in response • Thermophiles - "heat lovers" • Way of isolating and characterizing new species of bac and archaea USING DIRECT SEQUENCING • Direct sequencing: strategy for documenting presence of bac and archaea that cannot be grown in culture • Based on identifying phylogenetic species ○ Pops that have enough distinctive characteristics to rep an independent twig on evolutionarytree • Allows biologists to identify and characterize orgs that have never been seen • Revealed new branches on tree of life • Steps in Direct Sequencing 1) Collect water of soil sample containing bac and archaea, lyse cells and purify DNA 2) Use universal primers to amplify specific genes in sample by PCR 3) Purify amplified genes, insert genes in to plasmids (one gene/plasmid) 4) Insert plasmid in E. coli , each culture contains gene from diff species in original sample 5) Purify genes from plasmids 6) Sequence genes and compare w. known sequences • Halophiles - salt lovers • Sulphate reducers - species that produce hydrogen sulphide as by product of cellular respiration • Methanogens - produce methane as by product of cellular respiration EVALUATING MOLECULARPHYLOGENIES • Tree is based on SSU RNA studies • Carl Woese - 3 groups = bacteria, archaea, eukarya • Bac = first of the 3 lineages to diverge from commonancestor of all living orgs • Archaea and eukarya are more closelyrelated that they are to bac 28.3: What Themes Occur in the Diversification of Bacteria and Archaea? January-19-12 7:45 PM MORPHOLOGICALDIVERSITY • Variety of shapes - filaments, spheres, rods, chains, spirals • Many cells are motile - w. swimming movements powered by flagella, gliding movements (mechanism is unknown) • Gram +ve: plasma membrane surrounded by cell wall w. lots of peptidoglycan ○ Gram stain = purple ○ • Gram -ve: plasma membrane surrounded by cell well w. 2 components - thin gelatinous layer containing peptidoglycan and outer phospholipid bilayer ○ Gram stain = pink ○ • Peptidoglycan = complex substance made of cross linked carb strands METABOLIC DIVERSITY • Produce ATP in 3 ways 1) Phototrophs: use light E to promote e- to top of e- transport chains  ATP is produced by photophosphorylation 2) Chemoorganotrophs: oxidize organic molecules w. high potential E, such as sugars  ATP may be produced by cellular respiration w. sugars serving as e- donor OR fermentation pathways 3) Chemolithotrophs: oxidize inorganic molecules w. high potential E, such as ammonia or methane  ATP is produced by cellular respiration w. inorganic compounds serving as e- donor ○ donor ○ • Bacteria and archaea obtain Carbon by: 1) Synthesizing their own from simple starting materials (carbon dioxide or methane) = autotrophs 2) Absorbing ready-to-use organic compounds from enviro = heterotrophs • ATP via Photosynthesis ○ Phototrophs use E in light to raise e- to high E states ○ As e- stepped down to lower E states by e- transport chain, E released it used to generate ATP ○ Species that use water as a source of e- for photosynth = OXYGENICphotosynthesis ○ e- donor is also often hydrogen sulphide or ferrous ion, where O is not a by product  Called ANOXYGENIC photosynthesis  Live in habitats where O is rare ○ Bacterial chlorophylls are also very diverse  Hypothesis is that diversity allows photosynthetic species w. diff absorption spectra to live together w.o competing for light • ATP via Cellular Respiration ○ Variation in e- donor and acceptor ○ Oxidize organic compounds to make ATP  i.e. sugar, starch, fatty acids ○ Cellular enzymes strip e- from organic molecules that have high potential E and transfer them to e- carriers (NADH, FADH 2 ○ Compounds feed e- to ETC where step down from high E to low E state ○ E released allows components of ETC to generate p+ gradient across plasma membrane ○ ATP by chemiosmosis ○ Cellular respiration - molecule w. high potential E serves as original e- donor and is oxidized ; molecule w. low potential E serves as final e- acceptor and gets reduced • Metabolic diversity explain ecological diversity, why they are capable of cleaning up pollution, role in global change, role in cycling of nutrients • ATP via Fermentation ○ ATP production w.o use of ETC ○ No outside e- acceptor used ○ Redox rxns are internally balanced ○ Less efficient compared to cellular respiration ○ Variation in substrates • Obtaining Building-Block Compounds ○ Variation in pathways for fixing C ○ Some use Calvin Cycle to make building-block molecules  Enzymes transform CO2 to organic molecules ○ Some proteobacteria called methanotrophs use methane as C source  Process methane into complex organic compounds via enzymatic pathways ○ Some bacteria use CO or methanol as starting material • 28.4: Key Lineages of Bacteria and Archaea January-19-12 9:47 PM BACTERIA • 16 major lineages/phyla domain Bacteria Morphology Metabolism Human + EcologicalImpacts Firmicutes -Rod/spherical -Can fix N -Cause anthrax, botulism, -Spherical species -Performnon-oxygenic tetanus, walking form chains/tetras photosynth pneumonia, boils, -Few form spores -ATP via fermentation gangrene, strep throat (durable resting -Cellular respiration -Produces toxin used as stage) using H as e- donor insecticide -Subgroup may lack -Important componentsof cell wall, or soil (speed up decomp) synthesize cell wall made of cellulose Spirochaetes -Unique corkscrew -ATP via fermentation -Syphilis, Lime disease (Spirochetes) shape and unusual -Can fix N -Commonin freshwater flagella and marine habitats -Flagella contained -Live only under anaerobic structure called condns outer sheath (surrounds cell) -When flagella beat, cell lashes back and forth and swims forward Actinobacteria -Varies from rod to -Heterotrophsthat use -Creation of antibiotics by filaments array or organic isolated genus -Soil-dwelling compounds as e- Streptomyces species are found as donors, O as e- -Tuberculosis, leprosy chains of cell that acceptor -Manufactures swiss form mycelia -Some are parasitic cheese -Abundant in soil -Some live in associationw. plant roots and fix N Cyanobacteria -Independent cells, -Oxygenic photosynth -Can release molecules chains that form -Can fix N toxic to plants and animals filaments, loose -Responsible for origin of O aggregations of -Some live in associationw. individual cells fungi - forming lichens (colonies) Chlamydiales -Spherical -Live as parasites inside -Chlamydia trachomatis -Extremelysmall host cells infection = most common -Endosymbionts cause of blindness in -Contain few enzymes, humans get almost all nutrition -STD from host Proteobacteria -Rods, spheres, -Non perform oxygenic -Pathogenic proteobac= (5 major spirals photosynth Legionnaire's disease, groups: alpha, -Some form stalks -Cellular respiration by cholera, food poisoning, beta, gamma, -Some are motile using organic dysentry, gonorrhea, rocky delta, epsilon) -May form colonies compounds as e- mtn spotted fever, typhus, delta, epsilon) -May form colonies compounds as e- mtn spotted fever, typhus, which can donors ulcers, diarrhea aggregate and make -Use Agrobacterium cells to fruiting bodies transfer new genes into crop plants -Some used in production of vinegars -Critical in cycling of N atoms through terrestrial and aquatic ecosystems ARCHAEA • Live everywhere • No parasitic archaea • At least 2 major phyla = Crenarchaeota and Euryarchaeota Archaea Morphology Metabolism Human + EcologicalImpacts Crenarchaeota -Filaments, rods, discs, -Cellular respiration -In certain extremelyhot, high spheres can involve organic pressure, cold, acidic enviro - -On species has tough compounds may be only life form present cell wall made of -ATP by glycoprotein fermentation Euryarchaeota -Spheres, filaments, -Methane -Produce acids that drain into rods, discs, spiral producing streams and pollute them, -Some have several -Cellular respiration add methane to atmosphere flagella can be based on H -Some lack cell wall ; gas or Fe2+ some have cell walls -Can use molecule made of glycoprotein retinal to perform photosynth 29.1: Why Do Biologists Study Protists January-19-12 10:30 PM EUKARYA • Largest and most morphologicallycomplex orgs = eukaryotes • Eukaryotesare defined by presence of nuclear envelope • Contain many more organelles and cytoskeleton • Undergo cell division via mitosis • Have chromoswhere DNA is complexedw. histones • Protist: all eukaryotesthat are not green plants, fungi, or animals • Protists don’t make up a monophyleticgroup ○ They are paraphyletic • No synapomorphiesdefine protists IMPACTS ON HUMAN HEALTH AND WELFARE • Irish potato famine - due to Phytophthorainfestans ○ 1 mill ppl died of starvation • Malaria ○ Caused by Apicomplexa ○ Worlds mostchronic public health problem ○ Over 1 mill die from disease annually ○ Four species of protist Plasmodium = capable of parasitizing humans and causing malaria ○ Plasmodium enters bloodstream during mosquito bite ○ Affect liver and RBC ○ Evolvedresistance to most drugs used to control its growth in infected ppl • Harmful Algal Blooms ○ Unicellular species experiences rapid pop growth and reaches high densities in an aquatic enviro ○ Due to photosyntheticprotist dinoflagellates ○ Synthesize toxins to protect themselvesfrom predation by copepods ○ Red Tides - toxin producing dinoflagellates have high conc. of red accessorypigments calle xanthophylls ○ During bloom,high levels of toxin can build up in shellfish which can harm humans when consumed ○ Paralytic shellfish poisoning ○ No antidote exists to poisons secreted by protists during harmful blooms ECOLOGICAL IMPORTANCEOF PROTISTS • Play key role in aquatic food chains ○ • Phytoplankton(photosyntheticplankton) are the basis of food chains in freshwater and marine enviros • w.o protists - most food chains would collapse • Global carbon cycle: movementof C atoms form CO2 moleculesin atmosphere to orgs in soil/oceanand back to atmosphere • May reduce CO2 levels in atmosphere 29.2: How Do Biologists Study Protists? January-19-12 11:04 PM MICROSCOPY: STUDYING CELL STRUCTURE • Light microscopy • Transmission e- microscopesallowed for detailed studies of cell structure • Protists can be grouped by overall form, organelles w. distinct features or both • Flagella: organelles that project from cell and whip back and forth to produce swimming movements ○ i.e. potato famine protists = 2 flagella that are tiny, hollow, hairlike • Eight major groups of eukaryotes Lineage Synapomorphy Excavata -Cells have pronounced "feeding groove"where prey/organicdebris is ingested -No functioning mitochondria,genes derived from mitochondriafound in nucleus Discicristata -Cells have mitochondriaw. distinctive disc-shaped cristae Alveolate -Cells have sac like structures called alveoli that form cts layer under plasma membrane -Alveoli thought to provide support Stramenopila -If flagella present: cells usually have 2 - one of which is covered w. hairlike projections Rhizaria -Cell lack cell walls, although some produce elaborate shell-like covering -when portions of cell extend outward to movecell, they are slender in shape Plantae -Cells have chloroplasts w. double membrane Amoebozoa -Cell lack cell walls -When portions of cell extend outward to movecell, form large lobes Opisthokonta -Reproductivecells have single flagellum at base -Cristae inside mitochondria are flat, not tube shaped ○ EVALUATING MOLECULARPHYLOGENIES • Most studies based on genes that code for RNA molecule in small subunit of ribosomes • Amoebozoaand Opisthokontaform monophyleticgroup = Unikonta • Alveolata and Stramenopila form monophyleticgroup = Chromalveolata DISCOVERING NEW LINEAGES VIS DIRECT SEQUENCING • Direct sequencing: based on collecting orgs from habitat and analyzing DNA sequence of specific genes w.o growing larger pops of individuals in laboratory culture • Approach is based on using PCR to amplify certain genes in orgs • Allowed investigators to recognize large numbers of previouslyundescribed eukaryotes(some which are really small) 29.3: What Themes Occur in the Diversification of Protists? January-22-12 3:53 PM • Protists = paraphyletic • Diversity in size, morphologyand ecology WHAT MORPHOLOGICALINNOVATIONSEVOLVEDPROTISTS? • earliesteukaryote = single celledorg, nucleus,endomembrane system, mitochondria,cytoskeleton,no cell wall • Commonancestorof eukaryote lackedcell wall • Eukaryoticflagella= made of microtubules,dynein,undulatingmotion occur ○ Bacteria+archaea= madeof proteinflagellin,rotatingmotion • NuclearEnvelope ○ Hypothesis - derivedfrom infoldingsof plasmamembrane  May have given rise to ER too ○ Evidence- infoldings of plasmamembraneoccur in some bac today ; nuclearenvelopeof ER is cts ○ Nuclearenvelopeseparated translationand transcription ○ RNA transcripts = insidenucleus; translation= outside ○ Allowedfor alternative splicingand other forms of RNA processing  Controlgene expression ○ New way to manageand processgenetic info • Mitochondrion ○ Organellesthat generate ATP usingpyruvate as e- donorand O as e- acceptor ○ 1981: Lynn Margulis - EndosymbiosisTheory   Proposedmitochondriaoriginatedwhen bacterialcell took up residenceinsideeukaryote  Eukaryoticcellsstarted to use cytoskeletal elementsto surroundand engulfsmaller prey  Instead of beingdigested/engulfed,bac lived insidehost  Engulfedcell survivedby absorbingC w. high potentialE from its host and oxidizedthem  Host = anaerobicfermentation(cant use O as e- acceptor)  Mutualadv existed = host suppliedbac w. protectionand C compounds; bac producedmore ATP than host couldmake on its own ○ Symbiosis: individuals of 2 diff specieslive in physicalcontact ○ Endosymbiosis: org of one species lives insideorg of anotherspecies ○ Evidencefor EndosymbiosisTheory  size of avg bac and replicate by fission- duplicationof mitochondriatakes placeindependentlyof divisionof host cell  Have their own ribosomesand manufacturetheir own proteins- mitochondrialribosomesresemble bacterialribosomes, poisonedby antibiotics that inhibit bacterialbut not eukaryoticribosomes  Doublemembrane  Have their own genomewhich are organizedas circularmolecules- genes code for enzymes needed to replicatedand transcribemitochondrialgenome • Structures for Supportand Protection ○ Microfilaments, intermediate filaments,microtubulesform extensive and dynamicinternalskeleton ○ Diatoms= surroundedby glass-likesilicon-oxideshell  Shell is made up of 2 pcs that fit together in a box and lid arrangement Dinoflagellates= cell wallmade of celluloseplates Dinoflagellates= cell wallmade of celluloseplates ○ ○ Foraminifera= some lineagessecrete intricate chamberedtest/shell of calciumcarbonate  Other lineagesand some amoebae= cover themselves w. tiny pebbles ○ Parabasalids= distinctiveinternalsupportrod,consistingof cross-linkedmicrotubules that run the length of the cell ○ Euglenids= collectionof proteinstrips locatedunderplasmamembrane  Strips supportedby microtubulesand stiffen cell ○ Alveolates = distinctsac like structure (alveoli)underplasmamembrane that helpstiffen cell • Multicellularity ○ Multicellular= more than one cell ○ Cells have be specializedfor difffunctions ○ Not all cellsexpresssame genes ○ Synapomorphysharedby all brownalgaeand all plasmodialand cellularslime moulds,some red algae lineages ○ Bac that can aggregate and form fruitingbodies= multicellular  Most other multicell= eukarya HOW DO PROTISTS FIND FOOD? • Photosynthesisor absorbfood from enviro • Ingestive feeding- individualtakes in packetsof food much largerthan individualmolecules • Ingestive Feeding ○ Engulfingprocess = possible in protistsw.o cell wall ○ Requireflexiblemembrane anddynamiccytoskeleton ○ Surroundand swallow prey usingpseudopodia ○ Can also attach themselves to surfaceand sweep pray into gullets w. water currents set up by beatingcilia • Absorptive Feeding ○ Nutrientstaken up directlyfrom enviroacrossplasmamembrane ○ Most can onlyfermentsugars ○ Decomposer: org that feeds on deadorganicmatter/detritus ○ Many protiststhat absorptively feed live insideother orgs ○ Parasite - damagehost • Photosynthesis ○ Endosymbiosistheory - applicableto chloroplasts ○ Photosystemsdid not evolve in protists  Stolen via endosymbiosis ○ Evidencefor Chloroplastsvia Endosymbiosis  Chloroplastshave same list of bac-likecharacteristics(mitochondria)  Photosyntheticorganelleof one groupof protists(glaucophyte algae) hasan outer layer containing peptidoglycanfound in cyanobacteria  Cyanobacteriumcontainschlorophylla andb found in chloroplasts  And system of internalmembraneswhere photosyntheticpigmentsand enzymes are found ○ Primaryendosymbiosis= acquisitionof chloroplast/mitchondria  Traitsis a synapomorphy ○ Secondaryendosymbiosis: when an org engulfsphotosyntheticeukaryoticcell and retainsits chloroplasts as intracellularsymbionts   Organelles w. 4 membranes  Organelles w. 4 membranes ○ Evolutionof unique combosof pigments allowedeukaryotes to harvestlightw.o competition • All 3 feedingmethodscan a clade HOW DO PROTISTS MOVE? • Amoeboidmotion: slidingmovement ○ Pseudopodiastream forwardover substrate w. rest following ○ Requires ATP and involvesinteractionsbt actin and myosin insidecytoplasm ○ Related to muscle movementin animals • Movementby flagellaor cilia ○ Nine sets of pairedmicrotubulesarrangedaround2 centralsinglemicrotubules ○ Flagella - long and usuallyfound aloneor in pairs ○ Cilia - shortand usuallyoccur in largenumberson any one cell • Variationin movement amonglineages • Some can floatpassivelyin water currents HOW DO PROTISTS REPRODUCE? • sexualreproductionevolved in protists • Meiosisand fusionof gametes • Most significantevolutionaryinnovationobservedin eukaryotes • Sexualvs Asexual ○ Meiosis= geneticallydiff offspring ○ Meiosismay have evolved bc variable offspringmay be ableto thrive if enviro changes ○ i.e. parasitic attacks ○ Adaptationto fightdisease • Variationin Life Cycles ○ Life cycle describes sequence of events that occur as individualsgrow,mature,reproduce ○ Diploidor haploiddominatedlife cycles  ○ Alternationof generations   Multicellularhaploidform = gametophyte (specializedcellsproducegametes by mitosis)  Multicellulardiploidform = sporophyte (specializedcellsthat undergo meiosisto make haploidcells calledspores)  Spore: single cell that developsinto adult org but isnt productof fusionby gametes  Spore dividesby mitosisto form gametophyte  Haploidgametes fuse to form diploidzygote which grows into sporophyte  Brown algae,red algae,other groups  Brown algae,red algae,other groups 29.4: Key Lineages of Protists January-22-12 7:31 PM EXCAVATA • Excavated feeding groove found on one side of cell • Lack mitochondria ○ But have nuclear genomes containing genes that are normally found in mitochondria OR organelles vestigial mitochondria Exacavata Morphology Feeding and Reproduction Human and Ecological Impacts Locomotion Diplomonadida -2 nuclei -Some parasitic -Asexual -Intestinal parasites, cause -Each nucleus = 4 flagella (total of -Most ingest bac beaver fever 8) whole -Agricultural pests in turkey -Some lack peroxisomes and -Swim using farms lysosomes flagella -Lack cell wall Parabasalida -Lack cell wall and mitochondria -Engulf bacteria, -Asexual -Reproductive tract problems -Single nucleus archaea, organic -Sexual -Live in gut or mouth of -Distinctive rod of cross-linked matter observed in humans microtubules run length of cell -Swim using a few -Live in guts of termites - -Rod = attached to basal bodies flagella symbiosis where cluster of flagella arise -Help break down wood -4/5 flagella DISCICRISTATA • Unicellular • Distinctive disc shape of cristae mitochondria Discicristata Morphology Feeding and Reproduction Human and Ecological Impacts Locomotion Euglenida -Lack external wall -Chloroplasts -Asexual -Important component of freshwater -Unique system of -Ingest bac and plankton and food chains interlocking protein other small -common in ponds and lakes molecules lying under cells/particles plasma membrane (support cell) ALVEOLATA • Small sacs = alveoli ; located under plasma membrane Unicellular Alveolata Morphology Feeding and Reproduction Human and Locomotion Ecological Impacts Apicomplexa -System of -Absorb nutrition -Sexual -Parasites organelles at from host -Asexual -Cause malaria one end called -Lack cilia/flagella -Some involve 2 -Can be used to apical complex -Some can move host cells control pests -Allows for by amoeboid penetration of motion the hosts plasma membrane -Chloroplast- derived, non- photosynthetic organelle w. 4 membranes Ciliata -2 nuclei: large -Filter feeders, -Produce daughter -Abundant in - - - - Ciliata 2 nuclei: large Filter feeders, Produce daughter Abundant in macronucleus predators, or cells asexually marine and small parasites -Conjugation plankton micronucleus -Swim by cilia -Micronuclei -Digestive tract -Macro = -Mouth area exchange of grazers - polyploid and where food is help animal actively ingested digest plant transcribed matter -Micro = diploid, involved in reproduction Dinoflagellata -Unicellular, -Half are -Asexual -Important some live in photosynthetic -Sexual - may form primary aggregations -Most are tough cysts producers in called colonies planktonic -Cyst: resistant marine -Distinct shape -Others are structure that can ecosystems maintained by predatory or remain dormant -Harmful algae plates of parasitic until enviro blooms cellulose inside -2 flagella - one condns improve -Red tide cell projects out from -Chromos cell, other runs attached to across cell in a nuclear groove envelope at all -Flagella are time, no perpendicular histones -Swim in spinning motion using flagella STRAMENOPILA (HETEROKONTA) • Different hairs • At some pt in life cycle - flagella covered w. hollow hairs Stramenopila Morphology Feeding and Reproduction Human and Ecological Locomotion Impacts Diatoms -Supported by -Photosynthetic -Divide by mitosis -Found in all aquatic external, Si rich -Only sperm cells (Asexual) habitats glassy shells have flagellaand -Meiosis to form -Most important (box-lid) capable of gametes producer of C movement -Produce spores compounds in fresh and -Float dormant during salt water -Some can glide unfavourable -Accumulation of their via microtubules growing condns shells are mined and sold as diatomaceous earth (filtering apps, paint, cosmetics etc) Oomycota -Some form long Decaying organic -Diploid -Decomposers in aquatic (water branching matter -Spores ecosystems moulds) filaments called -Few parasitic -Asexual/sexual -Irish potato famine hyphae -Mature -Unicellular/mul individualsare ti sessile -Walls containing cellulose Phaeophyta -Cellulose and -Photosynthetic -Sexual -Form habitats in costal (Brown Algae) complex and sessile -Alternation of areas polymers in cell (permanently generations -Form rafts that harbour walls fixed to abundance of animal -Multi substrate) species - Multi substrate) species -Leaflike blades, -Reproductive -Align - purified from kep stalk called a cells may have and used in manufacture stipe, rootlike flagellaand of cosmetics and paint holdfast motile RHIZARIA • Single-celled amoebae that lack cell wall • Amoeboid motion • Produce long, slender pseudopodia Rhizaria Morphology Feeding and Locomotion Reproduction Human and Ecological Impacts Foraminifera -Multiple -Extend pseudopodia and -Mitosis -Tests of dead nuceli use them to capture and -Meiosis - forams form -Shells = engulf gametes sediment calcium bac/archaea/organic released into deposits carbonate dbris open water -Date rocks by -Digested in food vacuole presence of -Float in water some foram species PLANTAE • Red algae, green algae, land plants, glaucophyte algae • Descendants of common ancestor that engulfed cyanobacterium • Chloroplast = distinct feature Plantae Morphology Feeding and Reproduction Human and Locomotion Ecological Impacts Rhodophyt -Cell walls made - Photosynthetic -Asexual -Contribute to reef a (Red of cellulose and - Few parasites -Spores by mitosis building and help Algae) other polymers - Lack flagella -Alternation of gens stabilizeentire -Most are multi is common reef structure -Filamentous or -Variable life cycles grown thin hard crusts on rocks or coral -Thalli -Many nuclei AMOEBOZOA • Lack cell walls • Engulf food • Amoeboid motion and produce large lobe-like pseudopodia Amoebozoa Morphology Feeding and Reproduction Human and Locomotion Ecological Impacts Myxogastrida -Huge - Amoeboid -Food is scarce: form stalk - Decomposer (Plasmodial supercell motion topped by ball like structure in s in forests Slime Moulds) form -Feed on which nuclei undergoes -Many decaying meiosis nuclei in vegetation -Forms spores single cell 30.1: Why Study Green Plants February-21-12 10:01 PM • Green plants = green algae and land plants • Green algae: photosyntheticorgs in aquatics, closest living relative to land plants (form monophyleticgroup), transition from aquatic to terrestrial (land plants evolved from algae) • Land plants: first orgs w. tissues exposed to air, colonized land in conjunction w. fungi (mutualism) ○ Fungi = below ground and provided nutrients ○ Land plants = sugars and products of photosynth ECOSYSTEM SERVICES • Add to qual of atmosphere,surface water, soil, physical components • Alter landscape in ways that benefit orgs • Produce oxygen • Build soil ○ Improvewater holding capacity • Hold soil ○ Prevent wind and water erosion • Hold water ○ Tissues retain water ○ Soften physical impact of rainfall • Moderatelocal climate ○ Shade = reduction in temp ○ Reduce wind impact ○ Increase relative humidity • Provisionof food ○ Dom primary producers, base of food chain • C cycle ○ Reduce CO2 to make sugars • FOOD ○ Agriculture began w. domesticationof crop plants ○ Artificial selection • FUEL ○ Wood burning ○ Coal - forms form partially decayed plant matter • FIBRES ○ Cotton, plant fibres in clothing and household articles ○ Raw materials • BUILDING MATERIALS ○ Lumber • MEDICINE ○ Drugs ○ Plants synthesize compounds to repel predators  i.e. morphine, cocaine, nicotine, caffeine 30.2: How Green Plants are Studied February-21-12 10:26 PM ANALYZING MORPHOLOGICALTRAITS • Similarities bt green algae and land plants ○ Chloroplasts w. chlorophyll a and b, beta carotene ○ Arrangement of thylakoids ○ Composition - starch, sperm, peroxisomes  Peroxisomes= organelles in which specialized oxidation rxns take place • Algae similar to land plants = Coleochaetophyceae(coleochaetes)and Charaphyceae (stoneworts) • Major lineages a. Nonvascular Plants  Hepaticophyta (liverworts),Anthocerophyta (hornworts),Bryophyta (mosses)  Liverwortsand hornwortslack vascular tissue  Mosses have specialize tissues that conduct water but not true vascular tissue  Small, grow close to ground b. Seedless Vascular Plants  Seed: consists of embryo,store of nutritive tissue, surrounded by tough protectivelayer  i.e. lycophyta,psiolphyta, sphenophyta, pteridophtya  Relativelysmall in stature c. Seed Plants  6 lineages: Ginkophyta, Cycadophyta,Gnetophyta, Pinophyta, Conifers, Anthophyta □ First 5 = 5 gymnosperms  Angiosperms - seeds develop inside carpel (protectivestructure) FOSSIL RECORD • First green plants = green algae ; fossils form 700-725mill yrs ago • Land plants = 475 mill yrs old ○ Supports hypoth. that land plants derived from green algae • Appearance of green algae = appearance of O rich atmosphereand oceans • Earliest record = of spores and cuticles ○ Fossils came from land green plants ○ Sporopollenin: encases spores and pollen from modern land plants and helps resist drying ○ Sporangia: spore producing structures • Silurian-Devonian explosion ○ Most major morphologicalinnovations ○ Stomata,vascular tissue, roots, leaves • Carboniferous: Lycophytesand horsetail (abundant) ○ Extensive coal-formingswamps • Gymnospermabundant ○ Wet and dry enviros contained green plants • Angiosperms abundant ○ Diversificationof flowering plants • Orgs that appear late in fossil record = less dependent on moist habitats EVALUATING MOLECULARPHYLOGENIES • Most basal branches led to green algae (similar to land plants) ○ Supports that land plants evolvedfrom green algae • Caraphyceae is the sister group to land plants ○ Closest living relative ○ Multicell ○ Live in freshwater ○ Supports that land plants evolvedform multicell ancestor in aquatic habitat • Land plants are monophyletic ○ Supports that transition from water to land occurred once • Nonvascular plants = earliest among land plants ○ Unclear whether it is para or mono • Some mosseshave simple water conducting tissues, liverwortsand hornworts have none ○ Suggest earliest land plants lacked water conducting cells and vascular tissue ○ Evolvedin gradual fashion (simple preceding complex) • Lycophytes= sister group to seedless vascular plants ○ Whiskferns, horsetails ferns = mono ○ WHOLE = grade: sequence of lineages that arent mono • Vascular plants = mono ○ Vascular tissue evolvedonce • Morphologicalsimplicity of whisk ferns is a derived traits • Seed plants = mono • Gymnosperms= mono • Evoln = nonvascular plants - seedless vascular - seed plants 30.3: Themes February-22-12 11:53 PM DRY CONDITIONS • Cuticle and Stomata ○ Prevent water loss and regulate gas exchange ○ Cuticle = waxy, watertight sealant that covers aboveground parts of plants ○ Stomata = opening surrounded by guard cells ○ Opening = pore ; opens/closes as guard cells change shape  Soft = close stomata (limit water loss)  Taut = open stomata (diffusion of CO2 in, O2 out) ○ No stomata in liverworts ○ • Vascular Tissue and Uptight Growth ○ Transporting water ○ "Defying gravity" ○ Escape competition (mosses, low growing plants) by growing erect ○ Evolution of lignin rings gave stem tissues strength to remain erect ○ Lignin: complex polymer built from 6 C rings  Effecting in resisting compressing Fs ○ Vascular tissue = lignin in cell walls of water conducting cells ○ Allowed for support of erect stems and transport water from roots to aboveground rissues ○ Tracheids: long, thin, tapering cells w. thickened lignin containing secondary cell wall and cellulose based primary cell wall AND gaps in secondary cell wall where water can flow efficiently from one tracheid to next  Secondary cell wall allows tracheids to provide better support ○ Vessel elements: short and wider than tracheids, upper and lower ends have gaps in primary and secondary wall, makes water movement efficient  Lined up to form cts pipelike structure ○ Tracheids and vessels can form wood ○ Dead when they mature= lacking cytoplasm  Allows water to move more efficiently • Cuticle, pores, stomata, vascular tissue, tracheids evolved once • Vessels evolved independently in gnetophytes and angiosperms REPRODUCTION • Land Plants as Embryophytes ○ Retaining and nourishing offspring 1) Evolution of gametangium = important bc protected gametes from drying and from mechanicaldamage  Antheridia: sperm producing structure  Archegonia: egg producing structure 2) Eggs formed inside archegonia instead of being shed into water  Fertilization occurs - sperm swims to egg  Zygotes begin to develop on parent plant, forming multicell embryo that is attached to parent and nourished  Retention of embryo = embryophytes  Transfer cells: make physical contact w. parental cells and facilitate transfer of nutrients (similar to placenta) • Alternation of Generations ○ Multicell haploid and diploid phase  Multicell haploid = gametophyte  Multicell diploid = sporophyte Phases connected by distinct types of reproductive cells - gametes and spores ○ Phases connected by distinct types of reproductive cells - gametes and spores ○  Evolution of alternation of gens occurred independently Spore Zygote Single cells Single cells Mitosis Mitosis ○ Fusion of 2 cells Form Gametophytes Form sporophytes Produced in sporangia Produced in gametangia • Gametophyte Dom vs Sporophyte Dom ○ i.e. mosses - gametophyte is large and long lived ; sporophyte depends on gametophyte for nutrition i.e. ferns - sporophyte is large and long lived, but when young, depends on gametophyte for nutrition ○ Transition to sporophyte dom in land plant evolution ○ Hypothesis: advantageous bc diploid cells can respond to varying enviro conditions more efficiently than haploid cells • Heterospory ○ Heterospory: production of 2 distinct types of spore producing structures (and spores) ○ Homosporous: produce single type of spore ○ • Pollen ○ Doesn’t require water, carried by wind/animals ○ Microspore germinates to form tiny M gametophtye surrounded by sough desiccation resistant coat of sporopollenin = pollen grain • Seeds ○ Seed: structure that includes embryo and food supply surrounded by tough coat ○ Allows embryos to be dispersed to new habitat away form parent ○ Dispersed by wind, water, animal • Flowers ○ Reproductive organ, contains:  Stamen: includes anther, where microsporangiadevelop □ Forms microspores which make pollen grain  Carpel: containes ovary where ovules are found ○ Angiosperm - fertilization reqs to 2 sperm cells  One fuses with egg to form zygote  Second fuses w. 2 nuclei in F gametophyte to form triploid endosperm (nutritive  Second fuses w. 2 nuclei in F gametophyte to form triploid endosperm (nutritive tissue) ○ 2 sperm nuclei = double fertilization ○ Elaboration of heterospory  Evolution of ovary, which helps protect F gametophytes from predators ○ Sepals and petals enclose stamens and carpels ○ Increase probability that animal will perform pollination ○ Mutual beneficial - nectar and fertilization • Fruits ○ Fruit: structure derived from ovary and encloses one or more seeds ○ Made pollination efficient ○ Efficient seed dispersal • ANGIOSPERM RADIATION • Adaptive radiation • 3 key adaptations: vessels, flowers, fruits ○ Transport water, pollen, seeds efficiently • Monocotyledons (monocots) - grasses, orchids, palms, lilies MONO ○ Visible inside seed ○ Vasculartissue scattered throughout stem ○ Parallel veins in leaves (bundles of vascular tissue) ○ Flower petals in multiples of 3 • Dicotyledons (dicots) - roses, oaks, maples PARA ○ Visible in newly germinated plants ○ Vasculartissue in circular arrangement in stem ○ Branching veins in leaves ○ Flower petals in multiples of 4/5 • Cotyledon: first leaf formed in an embryonic plant • Eudicots - true dicots ○ i.e. roses, daisies, maples 30.4: Key Lineages February-28-12 12:18 AM GREEN ALGAE • Para • Chloroplast w. double membraneand chlorophyll and b, few accessorypigments • Synthesize starch in chloroplast as storage product of photosynth • Cell wall made up cellulose • Primary producers in aquatic habitats • Lichens ○ Stable associations bt green algae and fungi/cyanobac and fungi ○ Found in terrestrial enviro that lack soil (tree bark/bare rock) ○ Protectingfrom drying by fungus ○ Provide fungus w. sugars ○ Algae = unicell or grow long filaments • Unicell green algae commonendosymbiontsin planktonic protists in lakes and ponds ○ Mutually beneficisal ○ Algae supplies food ○ Protist provided protection NONVASCULAR (BRYOPHYTES) • Unclear if mono or para • Most basal lineages of land plants • Liver
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