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Slide 1 Prokaryotes 2 and viruses Scitechdaily.com 1 Today’s goals Bacteria and Archaea Classification and phylogeny Bacterial diversity Archaeal diversity Why are prokaryotes important? Viruses 2 prokaryote phylogeny: general issues... classifying “bacteria” and constructing phylogenies was historically difficult because... - tiny - can’t apply biological species concept - simple morphology - diverse physiology (e.g., nutrition, metabolic pathways)... but to learn about these traits, you need to grow them in culture, and <1% of known "species" can be grown in culture! so, until the 1970s or so, we weren't good at either classifying them (called “monera” under old 5 kingdom model), or understanding their phylogeny. prokaryote phylogeny: general issues... but then dna sequencing came along! - focus on genes coding for ribosomal rna (rrna), because: rrna genes are evolutionarily ancient all organisms have rrna genes, so they can be compared across the tree of life 3) rrna has evolved very slowly, so sequence similarities between very different taxa are easy to find 4) rrna has the same fundamental role in translation in all organisms; it's thought that lateral transfer of these genes is very unlikely diversity of bacteria - incredible diversity, mostly uncultured and undiscovered - we'll just talk about members of a few of the major known clades of bacteria... diversity of bacteria question: who is the sister taxa to the cyanobacteria? who is the sister group to the archaea? the relationship between the taxa of the domain bacteria is? diversity of bacteria: proteobacteria proteobacteria largest group of bacteria all gram-negative metabolically very diverse: photoautotrophs chemoheterotrophs chemoautotrophs includes rhizobium – n2-fixer escherichia coli – lab model salmonella – food poisoning diversity of bacteria: spirochetes, chlamydias spirochetes gram-negative move by rotating chemoheterotrophic many free-living some human parasites or pathogens syphilis lyme disease diversity of bacteria: spirochetes, chlamydias chlamydias gram-negative very small (0.2-1.5 µm in diameter) lack peptidoglycan parasites in eukaryotic cells some are human pathogens various chlamydias diversity of bacteria: cyanobacteria cyanobacteria photoautotrophs chlorophyll a found in the photosynthetic lamellae (internal membrane system) produce oxygen oxygenic photosynthesis caused increase in earth’s oxygen levels (oxygen revolution) diversity of bacteria: cyanobacteria multiple cells work together some form filaments, cells specialized for particular functions: vegetative cells - photosynthetic spores - dormant stages heterocysts - where n2 fixation takes place separated from other cells n2 fixation can't occur in the presence of oxygen diversity of bacteria: gram-positives high-gc gram positives (aka actinobacteria) - high proportion of nucleotides are gc - elaborately branched system of filaments - some are pathogens of humans (e.g., tuberculosis is caused by mycobacterium tuberculosis) - but many produce antibiotics that humans use! e.g., streptomyces produces streptomycin diversity of bacteria: gram-positives low-gc gram positives (aka firmicutes) - low proportion of nucleotides are gc - some can produce endospores (heat-resistant, dormant, thick peptidoglycan layer) - endospores of bacillus anthracis cause anthrax clostridium is the bacterium that produces botulinum toxin in improperly preserved food... diversity of bacteria: gram-positives low-gc gram positives (aka firmicutes) - staphylococci are important human pathogens; cause a variety of infections. they often form "clusters" of spherical cells - mycoplasmas = smallest cellular organisms known! -- no cell wall -- tiny genomes diversity of archaea first differentiated from bacteria based on rrna genes • notably some are “extremophiles”, but many live in more "normal" habitats • lots of differences from both bacteria and eukarya... extremophiles 15 diversity of archaea - differences from bacteria highlighted in red... • cell wall composition • membrane lipid composition • sensitivity to antibiotics diversity of archaea: crenarcheota - some are thermophiles (like hot places), some are acidophiles (like low ph places), and some are both! sulfolobus lives in hot sulfur springs, 70–75°c, ph 2 to 3 (like in yellowstone national park) - now characterized as crenarchaeota e.g. nitrosopumilus are very abundant nitrifiers in the deep ocean diversity of archaea: euryarcheota some are halophiles (salt-lovers) live in very salty, often very basic (up to ph 11.5) habitats contain pink carotenoid pigments, easy to see if growing at high density (e.g., salt evaporation ponds on san francisco bay) halophilic archaea have a completely different system than phototrophs for trapping light energy – bacteriorhodopsin diversity of archaea: euryarcheota some are methanogens • obligate anaerobes that convert co2 to ch4 • many live in the foreguts of grazing mammals (e.g. cows), but others live in sediments in lakes and oceans • methanogenic archaea produce ~2 billion tons of methane each year; important greenhouse gas today’s goals bacteria and archaea classification and phylogeny bacterial diversity archaeal diversity why are prokaryotes important? viruses 20 importance of prokaryotes... 1) key players in element cycling carbon cycling: help to decompose dead bodies, which are primarily composed of organic carbon, and return that carbon to the environment as co2 nutrient cycling (n, p, s, fe) decomposition release the n in proteins as ammonia, nitrate, nitrite (used by plants) affects crop production importance of prokaryotes... 2) important in many symbiotic relationships symbiosis: when members of two species (a host and a symbiont) live in close association. three varieties... commensalism: one species benefits, one species is neither helped nor harmed mutualism: both species benefit parasitism: one species benefits, one species is harmed (when these cause disease, they are called pathogens) commensalism +/0 mutualism +/+ parasitism +/- 22 importance of prokaryotes... 2) important in many symbiotic relationships a mutualism: flashlight fish host bacteria in organs beneath their eyes; the bacteria produce light (bioluminescence) that the fish uses to attract prey another mutualism: cows host anaerobic bacteria in their hindguts; these bacteria produce cellulase, which allows cows to digest their plant food importance of prokaryotes... 2) important in many symbiotic relationships - many prokaryotes are mutualists of humans! - e.g., many of the bacteria in our intestines are important to our health – protect us from invasion of pathogenic bacteria, make vitamins that we then absorb, and more! importance of prokaryotes... 2) important in many symbiotic relationships - some prokaryotes are pathogens of humans... - only a very small minority of bacteria are pathogenic (but those are important and are always in the news...) anthrax (bacillus anthracis) bubonic plague (yersinia pestis) tetanus (clostridium tetani) food poisoning (e. coli, salmonella) necrotizing fascitis (lots of bacteria) "flesh-eating" bacterial infection (necrotizing fascitis) discussion a clownfish and the sea anemone have a symbiotic relationship. the clownfish is able to hide within the stinging tentacles of a sea anemone without being killed. what kind of symbiosis is this? how would you change it to be the other two kinds of symbiosis? today’s goals bacteria and archaea classification and phylogeny bacterial diversity archaeal diversity why are prokaryotes important? viruses 27 viruses viruses are not cellular (no plasma membrane, no ribosomes) cannot replicate without living cells hijack the nucleic acid replication and protein manufacturing machinery of living cells in order to replicate themselves 2 main components: capsid – shell of protein on outside genome – a few genes (either encoded in dna or rna) inside the capsid viruses • viral genomes are made of either: double-stranded dnasingle-stranded dna double-stranded rnasingle-stranded rna (most viruses are rna viruses) • viral genomes can be tiny! the genomes of the smallest viruses known have genes for only two proteins! the largest virus known is pandoravirus; it has genes for 2000 proteins (remember the gram-positive mycoplasmas? they had only ~500 genes) pandoravirus viruses • viruses infect all cellular forms of life, and are the most abundant biotic entities on the planet! (estimates of virus density in seawater are ~10 million virus particles [mostly bacteriophage, aka phage, viruses that infect bacteria] per drop of seawater) • they replicate inside their host cell, using some of the host's dna replication and protein- making machinery, then burst out to reinfect new cells viruses • lytic and lysogenic cycles in temperate bacteriophages (phages that only do the lytic cycle are called virulent phages) viruses understanding their origins is very difficult, because... there are no known viral fossils their genomes are tiny, which restricts the kinds of genes that can be compared among taxa (e.g., most have no ribosomal rna genes...) they evolve very rapidly, so it's hard to identify homologous genes in e.g. prokaryotes three hypotheses... 1) viruses evolved from "mobile genetic elements" (like plasmids) that gained capsid protein genes 2) viruses evolved from prokaryotes that became obligate intracellular parasites 3) viruses arose before cellular life (some who argue this think that cells are just derived viruses!) protists 1 (eukaryotes that are not plants, animals, or fungi) chapter 28.4-.6 clockwise from top right volvox archaeplastida stentor giardia excavate unikont amoeba diatoms = sar 1 learning objectives distinguish eukaryotes from prokaryotes. observe phylogenetically how protists contribute to biodiversity. major clades of protists. describe the 3 protistan groups within the archyplastida red algae, green algae (chlorophytes, charophytes) describe 3 of the protistan groups within the unikonts slime molds, tubulinids, entamoebas directly from cyanobacterium. chlorarachniophytes 2-endosymbiosis, mixotrophic. 2 eukaryote origins • so, how did eukaryotic cells arise from a prokaryotic ancestor? 1) gain of a flexible cell surface • prokaryotic cell wall was lost • we infer this because though some eukaryotes have cell walls, they are relatively rare in the domain, and where they occur they are made of other materials than those of prokaryotes... so they were likely lost in the common ancestor of euks, and evolved independently in several euk lineages later on eukaryote origins 2) origin of a cytoskeleton • the flexible cell membrane requires some mechanical support; this was provided by a network of microfilaments and microtubules under the plasma membrane a cytoskeleton... supports the cell and allows it to change shape allows for the construction of motile extensions of cells (e.g., eukaryotic flagellae) aids in moving materials around the cell 4 eukaryote origins these two steps (loss of cell wall, gain of cytoskeleton) would have permitted: 3) origin of a nuclear envelope, and the ability to endocytose external materials into the cell • the nuclear envelope likely developed from infoldings of="" known="" "species"="" can="" be="" grown="" in="" culture!="" ="" so,="" until="" the="" 1970s="" or="" so,="" we="" weren't="" good="" at="" either="" classifying="" them="" (called="" “monera”="" under="" old="" 5="" kingdom="" model),="" or="" understanding="" their="" phylogeny.="" prokaryote="" phylogeny:="" general="" issues...="" but="" then="" dna="" sequencing="" came="" along!="" -="" focus="" on="" genes="" coding="" for="" ribosomal="" rna="" (rrna),="" because:="" rrna="" genes="" are="" evolutionarily="" ancient="" all="" organisms="" have="" rrna="" genes,="" so="" they="" can="" be="" compared="" across="" the="" tree="" of="" life="" 3)="" rrna="" has="" evolved="" very="" slowly,="" so="" sequence="" similarities="" between="" very="" different="" taxa="" are="" easy="" to="" find="" 4)="" rrna="" has="" the="" same="" fundamental="" role="" in="" translation="" in="" all="" organisms;="" it's="" thought="" that="" lateral="" transfer="" of="" these="" genes="" is="" very="" unlikely="" diversity="" of="" bacteria="" -="" incredible="" diversity,="" mostly="" uncultured="" and="" undiscovered="" -="" we'll="" just="" talk="" about="" members="" of="" a="" few="" of="" the="" major="" known="" clades="" of="" bacteria...="" diversity="" of="" bacteria="" question:="" who="" is="" the="" sister="" taxa="" to="" the="" cyanobacteria?="" who="" is="" the="" sister="" group="" to="" the="" archaea?="" the="" relationship="" between="" the="" taxa="" of="" the="" domain="" bacteria="" is?="" diversity="" of="" bacteria:="" proteobacteria="" proteobacteria="" largest="" group="" of="" bacteria="" all="" gram-negative="" metabolically="" very="" diverse:="" photoautotrophs="" chemoheterotrophs="" chemoautotrophs="" includes="" rhizobium="" –="" n2-fixer="" escherichia="" coli="" –="" lab="" model="" salmonella="" –="" food="" poisoning="" diversity="" of="" bacteria:="" spirochetes,="" chlamydias="" spirochetes="" gram-negative="" move="" by="" rotating="" chemoheterotrophic="" many="" free-living="" some="" human="" parasites="" or="" pathogens="" syphilis="" lyme="" disease="" diversity="" of="" bacteria:="" spirochetes,="" chlamydias="" chlamydias="" gram-negative="" very="" small="" (0.2-1.5="" µm="" in="" diameter)="" lack="" peptidoglycan="" parasites="" in="" eukaryotic="" cells="" some="" are="" human="" pathogens="" various="" chlamydias="" diversity="" of="" bacteria:="" cyanobacteria="" cyanobacteria="" photoautotrophs="" chlorophyll="" a="" found="" in="" the="" photosynthetic="" lamellae="" (internal="" membrane="" system)="" produce="" oxygen="" oxygenic="" photosynthesis="" caused="" increase="" in="" earth’s="" oxygen="" levels="" (oxygen="" revolution)="" diversity="" of="" bacteria:="" cyanobacteria="" multiple="" cells="" work="" together="" some="" form="" filaments,="" cells="" specialized="" for="" particular="" functions:="" vegetative="" cells="" -="" photosynthetic="" spores="" -="" dormant="" stages="" heterocysts="" -="" where="" n2="" fixation="" takes="" place="" separated="" from="" other="" cells="" n2="" fixation="" can't="" occur="" in="" the="" presence="" of="" oxygen="" diversity="" of="" bacteria:="" gram-positives="" high-gc="" gram="" positives="" (aka="" actinobacteria)="" -="" high="" proportion="" of="" nucleotides="" are="" gc="" -="" elaborately="" branched="" system="" of="" filaments="" -="" some="" are="" pathogens="" of="" humans="" (e.g.,="" tuberculosis="" is="" caused="" by="" mycobacterium="" tuberculosis)="" -="" but="" many="" produce="" antibiotics="" that="" humans="" use!="" e.g.,="" streptomyces="" produces="" streptomycin="" diversity="" of="" bacteria:="" gram-positives="" low-gc="" gram="" positives="" (aka="" firmicutes)="" -="" low="" proportion="" of="" nucleotides="" are="" gc="" -="" some="" can="" produce="" endospores="" (heat-resistant,="" dormant,="" thick="" peptidoglycan="" layer)="" -="" endospores="" of="" bacillus="" anthracis="" cause="" anthrax="" clostridium="" is="" the="" bacterium="" that="" produces="" botulinum="" toxin="" in="" improperly="" preserved="" food...="" diversity="" of="" bacteria:="" gram-positives="" low-gc="" gram="" positives="" (aka="" firmicutes)="" -="" staphylococci="" are="" important="" human="" pathogens;="" cause="" a="" variety="" of="" infections.="" they="" often="" form="" "clusters"="" of="" spherical="" cells="" -="" mycoplasmas="smallest" cellular="" organisms="" known!="" --="" no="" cell="" wall="" --="" tiny="" genomes="" diversity="" of="" archaea="" first="" differentiated="" from="" bacteria="" based="" on="" rrna="" genes="" •="" notably="" some="" are="" “extremophiles”,="" but="" many="" live="" in="" more="" "normal"="" habitats="" •="" lots="" of="" differences="" from="" both="" bacteria="" and="" eukarya...="" extremophiles="" 15="" diversity="" of="" archaea="" -="" differences="" from="" bacteria="" highlighted="" in="" red...="" •="" cell="" wall="" composition="" •="" membrane="" lipid="" composition="" •="" sensitivity="" to="" antibiotics="" diversity="" of="" archaea:="" crenarcheota="" -="" some="" are="" thermophiles="" (like="" hot="" places),="" some="" are="" acidophiles="" (like="" low="" ph="" places),="" and="" some="" are="" both!="" sulfolobus="" lives="" in="" hot="" sulfur="" springs,="" 70–75°c,="" ph="" 2="" to="" 3="" (like="" in="" yellowstone="" national="" park)="" -="" now="" characterized="" as="" crenarchaeota="" e.g.="" nitrosopumilus="" are="" very="" abundant="" nitrifiers="" in="" the="" deep="" ocean="" diversity="" of="" archaea:="" euryarcheota="" some="" are="" halophiles="" (salt-lovers)="" live="" in="" very="" salty,="" often="" very="" basic="" (up="" to="" ph="" 11.5)="" habitats="" contain="" pink="" carotenoid="" pigments,="" easy="" to="" see="" if="" growing="" at="" high="" density="" (e.g.,="" salt="" evaporation="" ponds="" on="" san="" francisco="" bay)="" ="" halophilic="" archaea="" have="" a="" completely="" different="" system="" than="" phototrophs="" for="" trapping="" light="" energy="" –="" bacteriorhodopsin="" diversity="" of="" archaea:="" euryarcheota="" some="" are="" methanogens="" •="" obligate="" anaerobes="" that="" convert="" co2="" to="" ch4="" •="" many="" live="" in="" the="" foreguts="" of="" grazing="" mammals="" (e.g.="" cows),="" but="" others="" live="" in="" sediments="" in="" lakes="" and="" oceans="" •="" methanogenic="" archaea="" produce="" ~2="" billion="" tons="" of="" methane="" each="" year;="" important="" greenhouse="" gas="" today’s="" goals="" bacteria="" and="" archaea="" classification="" and="" phylogeny="" bacterial="" diversity="" archaeal="" diversity="" why="" are="" prokaryotes="" important?="" viruses="" 20="" importance="" of="" prokaryotes...="" 1)="" key="" players="" in="" element="" cycling="" carbon="" cycling:="" help="" to="" decompose="" dead="" bodies,="" which="" are="" primarily="" composed="" of="" organic="" carbon,="" and="" return="" that="" carbon="" to="" the="" environment="" as="" co2="" nutrient="" cycling="" (n,="" p,="" s,="" fe)="" decomposition="" release="" the="" n="" in="" proteins="" as="" ammonia,="" nitrate,="" nitrite="" (used="" by="" plants)="" affects="" crop="" production="" importance="" of="" prokaryotes...="" 2)="" important="" in="" many="" symbiotic="" relationships="" symbiosis:="" when="" members="" of="" two="" species="" (a="" host="" and="" a="" symbiont)="" live="" in="" close="" association.="" three="" varieties...="" commensalism:="" one="" species="" benefits,="" one="" species="" is="" neither="" helped="" nor="" harmed="" mutualism:="" both="" species="" benefit="" parasitism:="" one="" species="" benefits,="" one="" species="" is="" harmed="" (when="" these="" cause="" disease,="" they="" are="" called="" pathogens)="" commensalism="" +/0="" mutualism="" +/+="" parasitism="" +/-="" 22="" importance="" of="" prokaryotes...="" 2)="" important="" in="" many="" symbiotic="" relationships="" a="" mutualism:="" flashlight="" fish="" host="" bacteria="" in="" organs="" beneath="" their="" eyes;="" the="" bacteria="" produce="" light="" (bioluminescence)="" that="" the="" fish="" uses="" to="" attract="" prey="" another="" mutualism:="" cows="" host="" anaerobic="" bacteria="" in="" their="" hindguts;="" these="" bacteria="" produce="" cellulase,="" which="" allows="" cows="" to="" digest="" their="" plant="" food="" importance="" of="" prokaryotes...="" 2)="" important="" in="" many="" symbiotic="" relationships="" -="" many="" prokaryotes="" are="" mutualists="" of="" humans!="" -="" e.g.,="" many="" of="" the="" bacteria="" in="" our="" intestines="" are="" important="" to="" our="" health="" –="" protect="" us="" from="" invasion="" of="" pathogenic="" bacteria,="" make="" vitamins="" that="" we="" then="" absorb,="" and="" more!="" importance="" of="" prokaryotes...="" 2)="" important="" in="" many="" symbiotic="" relationships="" -="" some="" prokaryotes="" are="" pathogens="" of="" humans...="" -="" only="" a="" very="" small="" minority="" of="" bacteria="" are="" pathogenic="" (but="" those="" are="" important="" and="" are="" always="" in="" the="" news...)="" anthrax="" (bacillus="" anthracis)="" bubonic="" plague="" (yersinia="" pestis)="" tetanus="" (clostridium="" tetani)="" food="" poisoning="" (e.="" coli,="" salmonella)="" necrotizing="" fascitis="" (lots="" of="" bacteria)="" "flesh-eating"="" bacterial="" infection="" (necrotizing="" fascitis)="" discussion="" a="" clownfish="" and="" the="" sea="" anemone="" have="" a="" symbiotic="" relationship.="" the="" clownfish="" is="" able="" to="" hide="" within="" the="" stinging="" tentacles="" of="" a="" sea="" anemone="" without="" being="" killed.="" what="" kind="" of="" symbiosis="" is="" this?="" how="" would="" you="" change="" it="" to="" be="" the="" other="" two="" kinds="" of="" symbiosis?="" today’s="" goals="" bacteria="" and="" archaea="" classification="" and="" phylogeny="" bacterial="" diversity="" archaeal="" diversity="" why="" are="" prokaryotes="" important?="" viruses="" 27="" viruses="" viruses="" are="" not="" cellular="" (no="" plasma="" membrane,="" no="" ribosomes)="" cannot="" replicate="" without="" living="" cells="" hijack="" the="" nucleic="" acid="" replication="" and="" protein="" manufacturing="" machinery="" of="" living="" cells="" in="" order="" to="" replicate="" themselves="" 2="" main="" components:="" capsid="" –="" shell="" of="" protein="" on="" outside="" genome="" –="" a="" few="" genes="" (either="" encoded="" in="" dna="" or="" rna)="" inside="" the="" capsid="" viruses="" •="" viral="" genomes="" are="" made="" of="" either:="" double-stranded="" dna="" single-stranded="" dna="" double-stranded="" rna="" single-stranded="" rna="" (most="" viruses="" are="" rna="" viruses)="" •="" viral="" genomes="" can="" be="" tiny!="" the="" genomes="" of="" the="" smallest="" viruses="" known="" have="" genes="" for="" only="" two="" proteins!="" the="" largest="" virus="" known="" is="" pandoravirus;="" it="" has="" genes="" for="" 2000="" proteins="" (remember="" the="" gram-positive="" mycoplasmas?="" they="" had="" only="" ~500="" genes)="" pandoravirus="" viruses="" •="" viruses="" infect="" all="" cellular="" forms="" of="" life,="" and="" are="" the="" most="" abundant="" biotic="" entities="" on="" the="" planet!="" (estimates="" of="" virus="" density="" in="" seawater="" are="" ~10="" million="" virus="" particles="" [mostly="" bacteriophage,="" aka="" phage,="" viruses="" that="" infect="" bacteria]="" per="" drop="" of="" seawater)="" •="" they="" replicate="" inside="" their="" host="" cell,="" using="" some="" of="" the="" host's="" dna="" replication="" and="" protein-="" making="" machinery,="" then="" burst="" out="" to="" reinfect="" new="" cells="" viruses="" •="" lytic="" and="" lysogenic="" cycles="" in="" temperate="" bacteriophages="" (phages="" that="" only="" do="" the="" lytic="" cycle="" are="" called="" virulent="" phages)="" viruses="" understanding="" their="" origins="" is="" very="" difficult,="" because...="" ="" there="" are="" no="" known="" viral="" fossils="" ="" their="" genomes="" are="" tiny,="" which="" restricts="" the="" kinds="" of="" genes="" that="" can="" be="" compared="" among="" taxa="" (e.g.,="" most="" have="" no="" ribosomal="" rna="" genes...)="" ="" they="" evolve="" very="" rapidly,="" so="" it's="" hard="" to="" identify="" homologous="" genes="" in="" e.g.="" prokaryotes="" three="" hypotheses...="" 1)="" viruses="" evolved="" from="" "mobile="" genetic="" elements"="" (like="" plasmids)="" that="" gained="" capsid="" protein="" genes="" 2)="" viruses="" evolved="" from="" prokaryotes="" that="" became="" obligate="" intracellular="" parasites="" 3)="" viruses="" arose="" before="" cellular="" life="" (some="" who="" argue="" this="" think="" that="" cells="" are="" just="" derived="" viruses!)="" protists="" 1="" (eukaryotes="" that="" are="" not="" plants,="" animals,="" or="" fungi)="" chapter="" 28.4-.6="" clockwise="" from="" top="" right="" volvox="" archaeplastida="" stentor="" giardia="" excavate="" unikont="" amoeba="" diatoms="SAR" 1="" learning="" objectives="" distinguish="" eukaryotes="" from="" prokaryotes.="" observe="" phylogenetically="" how="" protists="" contribute="" to="" biodiversity.="" major="" clades="" of="" protists.="" describe="" the="" 3="" protistan="" groups="" within="" the="" archyplastida="" red="" algae,="" green="" algae="" (chlorophytes,="" charophytes)="" describe="" 3="" of="" the="" protistan="" groups="" within="" the="" unikonts="" slime="" molds,="" tubulinids,="" entamoebas="" directly="" from="" cyanobacterium.="" chlorarachniophytes="" 2-endosymbiosis,="" mixotrophic.="" 2="" eukaryote="" origins="" •="" so,="" how="" did="" eukaryotic="" cells="" arise="" from="" a="" prokaryotic="" ancestor?="" 1)="" gain="" of="" a="" flexible="" cell="" surface="" •="" prokaryotic="" cell="" wall="" was="" lost="" •="" we="" infer="" this="" because="" though="" some="" eukaryotes="" have="" cell="" walls,="" they="" are="" relatively="" rare="" in="" the="" domain,="" and="" where="" they="" occur="" they="" are="" made="" of="" other="" materials="" than="" those="" of="" prokaryotes...="" so="" they="" were="" likely="" lost="" in="" the="" common="" ancestor="" of="" euks,="" and="" evolved="" independently="" in="" several="" euk="" lineages="" later="" on="" eukaryote="" origins="" 2)="" origin="" of="" a="" cytoskeleton="" •="" the="" flexible="" cell="" membrane="" requires="" some="" mechanical="" support;="" this="" was="" provided="" by="" a="" network="" of="" microfilaments="" and="" microtubules="" under="" the="" plasma="" membrane="" a="" cytoskeleton...="" ="" supports="" the="" cell="" and="" allows="" it="" to="" change="" shape="" ="" allows="" for="" the="" construction="" of="" motile="" extensions="" of="" cells="" (e.g.,="" eukaryotic="" flagellae)="" ="" aids="" in="" moving="" materials="" around="" the="" cell="" 4="" eukaryote="" origins="" these="" two="" steps="" (loss="" of="" cell="" wall,="" gain="" of="" cytoskeleton)="" would="" have="" permitted:="" 3)="" origin="" of="" a="" nuclear="" envelope,="" and="" the="" ability="" to="" endocytose="" external="" materials="" into="" the="" cell="" •="" the="" nuclear="" envelope="" likely="" developed="" from="">