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| Frage | Antworten |
| what is the main point behind the tree of life? | all organisms are related and share a common ancestry |
| what is the size of the mrca of all turtles? how do we know this? explain the evolution of gigantism | small medium, by the most parsimonious method we know turtle converged to have larger size on islands that select for that body type |
| list the non-monophyletic groups in the tree of life | archaea + bacteria- exclude eukaryotes, so they're paraphyletic |
| list the monophyletic groups in the tree of life | plant animals and fungi |
| list the functions of a phylogenetic tree | 1. allow us to trace history of evolutionary changes in orgs 2. common ancestors of morphologically similar orgs 3. help us predict similarities, differences |
| what does a tree tell us about lineage? | The lineage has diverged separating completely |
| define taxon (taxa) | any org or group at an unspecified level that we designate with a name. Can be species, domain, phyla. |
| speciation | one homologous group diverges into differing groups due to reproductive isolation |
| what are phlyo trees unable to show us? | -time it took for each taxa to speciate - exact time at which they diverged - sequence of divergence of sister taxa |
| why are the internal nodes of a tree not counted as taxa? | once the group diverges, that homologous group at the int. node no longer exists- speciated. |
| monophyletic groups | include MRCA and all descendant taxa |
| paraphyletic groups | include MRCA, exclude some of the descendant taxa |
| polyphyletic groups | include descendant taxa, but exclude their MRCA |
| how was it determined that the L. bicolor were separate species? | ancestral character state reconstruction or trait mapping determined these new relationships and taxanomic categories- they were fooled b/c they converged at the same time |
| bifurcating vs polytomic trees | 2 species diverge from one internal node vs 3+ species from one node |
| what do polytomies indicate about the tree? | there is uncertainty in the phylo relationships of those taxa- results from equally parsimonious trees |
| what do the # of internal nodes tell us about a tree? | the # of monophyletic groups in the tree - minus those mono groups made up by the terminal taxa |
| why were reptiles ever paraphyletic? | they excluded a group of desc.- birds |
| why are reptiles considered to be monophyletic now? | they include all the desc. groups including birds |
| why are bacteria and archaea non monophyletic? | exclude euks |
| what type of group are bacteria and archaea? | paraphyletic |
| what do clades have that other group types do not | synamorphies shared within group from common ancestor not shared with other groups |
| synapomorphies vs homologous traits | * synapomorphies are not present in the ancestral group. shared derived traits that distinguish one group from another vs same characteristics from the same common ancestor |
| when a trait evolves independently in 2+ separate groups or taxa | convergence or conv. evol. |
| is the 4 chamber heart of birds homologous or analogous with mammals? | it is analogous, this is because the trait independently evolved in birds and not seen in the mrca of the birds that it shares with the other taxa in its group |
| explain how a trait by looking at a tree would be homologous or homoplasious/ analogous | homo if present in the common ancestor of the two groups or taxa, if not then it is analogous/ homoplasious |
| homology vs homoplasy/ analogy | 1. similar characteristics, share common ancestor 2. similar characteristics, DO NOT share common ancestor |
| the main points in using phylo trees in conservation | identify hidden diversity, reveal major lienages and emphasize the older ancestral groups- overall you must conserve the greatest diversity of the lineage |
| how you can discern species name from names of higher groups | species names are binomial and all groups above species are unomial |
| why can't non-monophyletic groups be characterized? | they are historically artificial groups that cannot be characterized by synamorphies that arose in a common ancestor |
| how do you identify a sister group? | the group that diverged from a lineage at the same time as the other |
| what is the importance of sister groups | they're used to contrast between taxa with different traits |
| at what point does a derived trait appear on a tree? | when you start splitting up into the in groups |
| what kind of traits do the out groups share with the ancestor? | ancestral traits |
| what does a cladogram tell us | branching order: which taxa came along first |
| importance of a phylogram | branch length= amount of character change |
| importance of chronogram | branch length= how long taxa took to speciating |
| what must be true about traits to build a phylogenic tree | there must be variation= discrete traits |
| steps to estimating phylogeny | 1. look for varying traits and similar ones among organisms 2. then you assign codes to the character states 3. form a data matrix with these codes 4. look for similarities 5. find most parsimonious tree |
| what does an unrooted tree tell us | sequence of branching events and relationships but no temporal sequences |
| how many unrooted trees are possible for 4 taxa | 3 (3 different taxa can be adjacent to reference taxa) |
| how many different rooted trees are possible for a 4 taxa unrooted tree? | 5= the # of segments |
| which characters are the parsimony uninformative ones? | the traits that don't change or only change once which get scores 0 and 1 |
| which characters in a matrix are parsimony informative? | the ones that involve 2 possible changes or more |
| name a type of parsimony uninformative character | invariant characters |
| what type of group are unicellular eukaryotes? | non- monophyletic, paraphyletic |
| describe character state changes at the molecular level. How long does this take? | nucleotide substitution at different dna sites that occur over generations at the population level |
| what are the three things we can look at to build a phylo tree? | morphology, ecology and behavior or orgs |
| list the possible causes of changes in character states in a phylo tree | dna substitutions, LGT, convergent evolution, mutations |
| why are many flowers self incompatible? | genetic variation would increase the fitness of the flower |
| in the example of the Linanthus phlox flowers, which trait evolved? how many times | self-compatibility, can self fertilize. evolved 3 times. |
| what is character conflict on a tree? | when there are different characters that only experience 1 change on diff trees : char. 1&3 on one tree and 2 on another- the same characters on 2 diff trees have diff #s of changes |
| what is a model based approach for tree building | taking into account the probability of rates of change for diff nucleotide subs |
| what types of nucleotide subs can occur | transitions: C<->T, A<->G and transversions: A<->C, G<->T, C<->G, A<-> T |
| which is more likely between transitions and transversions? | transitions- therefore they hold less weight when they differ slightly |
| how do trees with close to the same # of transitions compare | they are approximately as likely since it is common- transversions are taken into account more |
| T or F: a tree with a transversion may have a higher likelihood. | yes b/c they are rare-- but why though?! |
| how can we use models to find the ML tree? | relative frequencies of transition rates vs transversion rates |
| list several ways to find likelihood of trees in a model based approach | 1. freq of transitions vs transversion rates 2. synonymous and non syn 3. subs at different codons |
| synonymous vs non synonymous | nuc sub causes no change in AA nuc sub causes a change in the AA it codes for |
| list applications of phylogeny | 1. method/rate of character changes 2. coevolution: how when clades evolve 3. biogeography- org distribution 4. community- ecology 5. conservation priorities |
| how phylogeny is used in conservation | *save the older lineage and maintain diversity- identify unsuspected diversity, reveals major lineages of a clade, emphasizes conservation of the older lineages |
| the african cichlid fish study | by looking at the phylo tree, we can better understand how to conserve greater diversity of the lineage b/c we see what other pops of cichlids we should conserve in order to promote diversity and include the mrca |
| what is the purpose behind using phylo trees for conservation? | preserving the sets of species that best capture the evol history of the group from mrca |
| steps to finding where an event occurred on the phylo tree | 1. use characters like DNA to build the tree 2. see how other traits evolved on this tree by looking at morph, behav, ecological |
| 3 ways to look at the evo of traits on a phylo tree | 1. most parsimony 2. outgroup method 3. probability of state changes |
| which is more likely: a plant becomes self compatible or incompatible? | self incompatible- increases the genetic diversity of the flower in most cases |
| in the case of the linanthus phlox flowers, which trait evolved by convergent evolution? | self compatibility converged |
| how many times did tortoises evolve gigantism | twice: convergent evolution- b/c these separate taxa both got that same trait and evolved at the same time |
| why were the L. bicolor flowers of the phlox family thought to be the same species? | they had similar morphology but through a phylo tree they realized they are different- by reduced petal size |
| is large size in tortoises analogous or homologous? | analogous- arose from convergence |
| are the L. bicolor traits analogous or homologous? | analogous |
| why do we compare sister taxa to find why one group has more species than another? | we use time as a control b/c we know they speciated at the same time from the same lineage so we can look at other factors such as ecology and behavioral |
| what is net diversification? | the # of extant taxa, used in contrasting sister species |
| what 2 things determine net diversification? | speciation and extinction rates |
| conclusion of the study about clade diversification rates - plants with canals (rubber or resin) | the clades with the canals were more diverse than those without. these evolved by convergence. |
| conclusion of case study of biogeography in horses | used an area phylogeny (locations replaced names on the tree) + fossils, horses originated in North America |
| what type of tree is used for biogeography in phylogenetics? ex in horse study | chronogram: tells us how long ago taxa have bee speciated |
| how do we find out when an event occured on a tree? | use dna and use # of mutations as indicator of time (mutation rate) as a molecular clock, and calibrate that clock with other data like a fossil |
| to say that 2 sister taxa are 10% divergent is to say that ... | they are each 5% diveregent, so with mutation rate we can date back to when it split from the mrca |
| how long ago did humans start wearing clothes? | 100,000 |
| how lice tells us how long ago human started wearing clothes | speciate when the new ecological niche for lice arose when human started wearing clothes (became body lice), so use that as a basis |
| how was the tree in the body lice study calibrated | out group method by a head louse in a chimp b/c we know that branch point in time |
| function of gene annotation in phylogenomics | what does a gene do |
| steps in gene annotation | 1. identify homologs in sequence 2. align them 3. add additional sequences- this allows you to see what resulted from mere substitutions and deletions |
| what does sequence similarity indicate in gene annotation? | which gene is closest to the one in question by which sequence would undergo the fewest changes to be like our one in question |
| how we find gene function with gene annotation and parsimony | most parsimonious function for our gene would be the one with the fewest # changes to get the that function |
| why are microbes difficult to sort into a phylogenic tree? | lacks informative traits, many homologies- morph, ambiguous evo relationships leading to polytomies, lack nucleus, unculturable, |
| why is RNA used to infer phylogeny? | all cellular organisms have them in common, they infer homologies and are phylogenetically informative |
| prokaryotes vs eukaryotes | proks: lack nucleus and cytoskeleton, do not divide by mitosis but binary fission, lack membrane bound organelles, and has circular chromosomes |
| if it has a peptidoglycan cell wall, it must be... | bacteria |
| what groups are nitrogen fixators? | bacteria and archaea |
| in the eocyte tree, are the archaea mono or non mono? 3 domains tree? | in the eocyte tree, the archaea are a paraphyletic group because they exclude euks, 3 domains tree they are mono |
| brief overview of the history of antibiotics | used in the 40s, Golden Age in the 50s, focus on resistance after that |
| how mutations quickly spread in a bacterial pop | since they are haploid and have a short speciation/extinction rate, mutation moves quickly |
| vertical transmission of genes in bacteria | genes are cloned by binary fission as mother and daughter cells are formed |
| conjugation | dna exchange between bacteria via pilus , can occur intra or interspecies, only some or parts of genome passed along |
| bacterial plasmid | not needed for growth or reproduction, that is why it can be removed to lose pathogenicity |
| LGT vs sexual reproduction | LGT can occur across different species and domains, does not involve the transfer of the entire genome, has multiple mechanisms, not linked to reproduction (swap and go like conjugation) |
| functions of plasmids | metabolic: allow them to find niche, fertility: controls formation of fertility factors, resistance to antibiotics and toxins, virulence: presence determines pathogenicity |
| what establishes new pops in microbes? | lateral gene transfer followed by vertical gene transfer (bunnies) |
| transformation: | the dna of lysed, foreign bacterial cell is taken in by another cell and added by recombination |
| transformation vs transduction | 1. genotype of cell is altered by the uptake of foreign dna from its environment 2. viruses carry prok. genes from one cell to another |
| case study of a. tumefaciens | bacteria that causes tumor in plants via transformation, used in biotech to grow plants by LGT |
| list the bacterial traits introduced by LGT | virulence, antibiotic resistance, metabolism |
| how do we know if it is convergent evolution occurring rather than lgt? | distantly related taxa have adaptations that require a change in not just one gene but the whole genome, like thermophily, then its conv. |
| how can you tell if it is lgt or maybe convergence? | distantly related orgs have the same genes needed to alter metabolic process (more simple) like antibiotic resistance |
| list the possible sources of antibiotic resistant bacteria | 1. free living soil bacteria with resistance, 2. non pathogenic human bacteria with antib resistance 3. antibiotic producing bacteria 4. other pathogens that produce resistance and are found in animals/ humans |
| what is xanthan gum and its uses? | bacteria used as a thickener in many foods due to its polysach capsule it forms around each bacterium |
| the roles of microbes | -food industry - plant symbionts -enzymes -bioproducts -medicine -probiotic -pathogen -global cycle -biodiversity -bioremediation |
| ways that prokaryotes differ | 1. form/morph: shape, gram + or - 2.functional: 3. phylogenetic diversity |
| key features of biofilms | polysach matrix, heterogeneic structure, adhere to liquid air interfaces, soft tissues and solid surfaces, has genetic diversity |
| stages in biofilm production | attachment/aggregation matrix production communication heterogeneity |
| quorum sensing is a system of communication between ... | intra and interspecies bacteria |
| virus group type | polyphyletic |
| structure shared by all viruses | capsid, nucleic acid |
| virus hosts are mostly | bacteria |
| where many viruses are found | ocean-water |
| what type of life cycles can plants have? | alternation of generations |
| list the types of eukaryotic life cycles | alternation of generations, haplontic and diplontic |
| do all land plants form a monophyletic group? | yes |
| mosses, liverworts and hornworts make what type of group? | non-monophyletic group- they are paraphyletic |
| which hypothesis is correct for turtle gigantism? | gigantism evolved separately on the galapagos and aldabra islands by the most parsimonious method |
| the case studies showing how to find where an event occured on a phylo tree | the phlox bicolor flowers and the gigantism in tortoises |
| how we compare clade diversification rates | we look at the net diversification of many different sister taxa with different # of extant species to control for time |
| case study of clade diversification rates | plant defense by use of canals- which ended up having higher net diversification (higher speciation rates) due to it aiding in defense against herbivores |
| give an example of tree applications in biogeography | horses: tells geo history and the dispersal pattern of the horses: used an area phylo tree |
| where the ancestral horses originated | 1. przelwaski's horses from central asia then they dispersed to Africa then Europe and N Americ: East to west |
| where did horses speciate? | as they moved from central asia to africa |
| where did the speciation of zebras take place? which species has lead to the modern horses? | only in africa przewalski's horse |
| how do we find out "when" an event occured on a phylo tree? | # of mutations of dna on the tree and use mutation rates as molecular clocks to say how many years ago something happened- model approach + phylogram = cladogram;must calibrate with fossil or ancient thing |
| to say 2 sister taxa are n% divergent, it means they are .5n% divergent from common ancestor | use this value of time to find when the 2 speciated by the molecular clock method= called a DIVERGENCE TIME ESTIMATE |
| molecular clock assumptions and caveats | -rates of dna changes are constant - the generation times are the same - the dna sites are assumed neutral and not like sex linked or some other |
| molecular clock case study | when did humans start wearing clothes |
| human clothing case study | body lice speciation time conforms to the est time in which humans started wearing clothes because they evolve as their niches do ~100,000 years ago |
| what was used to calibrate the tree in the molecular clock study? | head lice sequence dna from a chimp b/c they diverged 5.5 mya like we did - we use this as an outgroup to date the emergence of the body lice we have |
| genome sequencing case study | phylogenetics: dna sequence to annotate genes in a genome |
| steps in the gene annotation | you get a known gene and align the gene sequnces so you can see the homologs and insertion and deletions between them, add more sequences to find more alignments, most parsimonious is the one w/ fewest steps back to original sequence in question |
| microbes are what type of group? | monophyletic? |
| in which major branches in the tree of life are the microbes found? | all 3: euks, proks, archaea |
| the problems with classifying microbes | - morphology varies - many cannot be cultured - homologous and analogous traits indistinguishable -no phylo informative traits to infer a phylo tree |
| universal homologies shared by yeast, humans bacteria and archaea | dna, protiens, codons |
| the importance of the rRNA in systematics | they are perfect for building trees because they all have them but * * rRNA is PHYLOGENETICALLY INFORMATIVE. they vary in protein synthesis allowing us to classify and place on the tree |
| How do prokaryotic cells divide | not by mitosis (differentiation)- lack cytoskeleton and nucleus- binary fission |
| do archaea divide by mitosis? | no they lack a cytoskeleton and nucleus |
| differences of prokaryotes vs euks | proks: binary fission or schizogeny, nucleiod, no membrane bound organelles or cytoskeleton, circular dna plasmids, 1 chromosome. euks opposite |
| how archaea are unique to the euks and bacteria | ether linked cell walls, some are methanogens and none conduct chlorophyll based photosynthesis |
| unique characteristics of bacteria to euks and arch | peptidoglycan in cell wall, ribosomes denatured by streptomycin and not effected by diptheria toxin |
| how does the eocyte tree differ from the 3 domains tree of life? | archaea are a paraphyletic group vs 3 domains where they are monophyletic |
| when did antibiotic resistance arise? | pharmacologic era 1960s |
| steps in binary fission | elongation of plasma membrane, doubling of the chromosome, cleaving of the cell then cytokinesis producing clones |
| vertical transmission of genes | parents pass directly to offspring |
| an example of vertical gene transmission | binary fission |
| what is the ploidy of bacterial cells? | haploid |
| how does genetic recombination occur in LGT? | crossing over with dna fragments of new cell and plasmid of recipient cell followed by cell division |
| how bacteria exchange plasmids | via conjugation tube where the plasmids of one flows to the other then the tube is retracted |
| convergence or LGT? how you can tell | LGT can't transfer entire genomes so if a distance relative gets thermophilic traits, it convergence |
| how to tell traits arise via LGT or convergence | simple transfer not requiring the entire genome: virulence, metabolism, resistance- can be LGT or convergence |
| explain which type of bacteria would be most affected by penecillin | gram positive- penicillin binds to peptidoglycan layer- + has more peptido. |
| effects of penicillin on bacteria- how it kills it | binds to enzymes holding peptid. layer, cell wall weakens, leads to cell death can't divide |
| biofilm: who can make it? | all domains: archaea bacteria protists fungi algae |
| characteristics of a mature biofilm | has more than one species of bacteria- intraspecies communication |
| bacteria: uni or multicellular? | uni cellular until they are part of a mature biofilm colony which then becomes multicellular |
| positive types of biofilms | bioremediation, protect against pathogens, nutrient cycling and part of food chain |
| negative biofilm examples | pathogenicity, dental plaque, corrosion of pipes on boats |
| metabolic diversity in bacteria | aerobes and anaerobes |
| is oxygen toxic to all anaerobes? | only the obligate anaerobes. Facultative switches between oxygen and none, and the aerotolerant don't use it but aren't hurt by it |
| photoautotrophs: where they're found, energy and C source | all domains, light energy, CO2 |
| photoheterotrophs | some bacteria: light energy, organic compounds |
| chemolithotrophs | some bacteria and most archaea: inorganic compounds, CO2 |
| chemoheterotrophs | all domains, organic compounds and organic compounds |
| metabolic types found in all domains | chemoheterotrophs and photoautotrophs |
| metabolic types with same carbon sources | photoautotrophs with chemolithotrophs, photoheterotrophs with chemohetertrophs |
| metabolic types with same energy sources | photoautotroph and photoheterotroph |
| list functional diversity in prokaryotes | interactions with other orgs, global nutrient cycles, industrial and agricultural uses and shaping earth's history |
| global cycles microbes aid | C, N, P, S and cations |
| # of bacteria in the soil, mL of water, and in the world | 40million, 1 million, and 5x10^30 (5 nonillion) |
| extremophiles | anaerobes, thermophiles, psychrophiles, halophiles, barophiles, xerophiles, alkaphiles, acidophiles, radiophiles |
| example of a mesophile | e.coli |
| heat adaptations of thermophiles | decrease fluidity/fluid content of membranes; make proteins more stable prevent denaturing with different amino acids and salt bridges; slow down enzyme rate since heat increases it |
| relationships between thermophilic species | closely related by lineage not thermophilic capabilities |
| how we study microbes | uptake of CO2, decomposition rates, |
| why it's hard to study microbes | convergence leads to similarities not from homology, few character traits to refer to, rapid divergence, difficult to culture |
| benefits of culturing samples | determine process and properties of single org, rRNA sequence analysis, morph, produce large volumes, genetics and genomics |
| what is the result of the great plate culture anomaly | more can be observed via microscope than cultured |
| metagenomics | *you don't culture the sample, this is what makes it different from other analyses. dna sample of the entire microbial community in the environment and you sequence them to infer functions and compare to other communities |
| blood falls | red due to Fe cycling microbes underneath surface |
| culturable bacteria | proteobacteria, cyanobacteria and firmicutes |
| cyanobacteria: | photosynthetic w/ chlorophyll A, membrane system for photosyn, developed from endosymbiosis, some toxic, nitrogen fixation in heterocysts |
| what is the largest group of bacteria | proteobacteria |
| proteobacteria | gram negative, N fixing rhizobium, largest group, most diversity, e. coli- human pathogen, cholera, plague and gi issues, formed from endosym with mitochondria |
| firmicutes | low gc/ta ratios, gram +, produce endospores to endure harsh env, agents of disease like staph strep tetanus; include small mycoplasmas |
| bacteria vs archaea | archaea have no peptidoglycan cell wall, have etherlinked membrane, are the only methanogens, do not conduct photosynthesis, and none are pathogenic. |
| what group holds the only know methanogens? | euryarcheota |
| 2 clades of archaea | crenacrchaota and euryarcheota |
| crenarchaota | thermophilic and acidophilic- some are mesophiles, not all are extremophiles |
| euryarchaeota | methanogens that use chemautotrophy to reduce co2 and make ch4, found in animal guts, |
| methanogen habitat | deep sea thermal vents and guts of grazers |
| pink euryarcheaota in basic alkaline environment | halophiles |
| bacteriosrodohpsin | uses light to make atp- not photosynthetic though? |
| extreme halophiles | monophyletic group of euryarcheoata that have square cells only |
| methanogen group type | paraphyletic/non mono |
| halotolerant, halophilic and non halophilic growth rate comparison to ion concentration | non- e.coli: lower conc., halotolerant like staph: mid range, halophile like vibrio fischeri: high |
| most archaea have what metabolic type | chemolithotroph |
| steps to pcr for phylo analysis | dna extraction -- pcr - rna sequence - |
| fourth domain hypothesis | rna polymerase II mapped and showed 4th domain of viruses |
| T or F: Archaea perform photosynthesis | yes- but not chlorophyll based! |
| which prokaryotes perform nitrogen fixation | some in bacteria and archaea |
| define virus | NONCELLULAR infectious agents that replicate only in host cell and makes cell syn virions to tranfer infection and make more bacteriophages |
| virus definition | intracellular parasites with nucleic acids capable of replication and lacking own cells |
| are viruses alive? | argue for: replicate mutate experience natural selection evolve against: noncellular don't replicate by division and have no metabolism |
| components of virion | nucleic acid capsid sometimes an envelope |
| capsid function | contains dna needed to inject into the host cell for replication |
| genomic diversity in viruses | dna and rna, shape, strandedness, + and - sense |
| describe the central dogma of molecular biology | replication transcription and translation by dna rna and proteins- viruses don't follow this path! |
| viruse genomes location | rna, not dna |
| virus types with most diverse host cell types | double stranded +/- retroid |
| features of tobacco mosaic virus | helical virions codes for 4 genes |
| what is the largest virus? | mimivirus codes for 1000 genes larger than mycoplasmas- largest bacteria |
| viruses be like... | 1. Viruses to survive they must be able to do 3 things o Get into a susceptible host. Attachment to host cell membrane. Not in plant, fungal and bacterial viruses. Penetration of host cell membrane: endocytosis, mechanical penetration with plant and fungal viruses. Inject genome with some bacterial viruses o Must be able to replicate and make more virus. Uncoating. Replication. Self-assembly of virus particles o Most have some mechanism to move the newly made viruses to new susceptible host. |
| virus replication cycle | 1. attachment to host cell membrane - 2. penetration of host cell membrane by: endocytosis, mechanical penetration, inject genome 3. uncoating 4. replication and assembly 5. find new cell host |
| 2 stages of virus replication cycle | lytic: cell lyses releasing viruses and lysogenic: the prophage is apart of the bacterial chromosome as the cell replicates and is noninfective |
| how viruses hijack host cells | mRNA proteins block transcription of host cell, uses host rna polymerase to transcribe its own cells |
| what type of phylo group are viruses? | polyphyletic |
| are there more microbes or viruses on earth? | viruses- 1x10^31 |
| viruses effecting plants- | stunt growth, discolored and reduced biomass: cassava mosaic, citrus tristeza, |
| biomass and abundance in proks euks and viruses | proks= most biomass virus= most abundant 94 |
| are viruses only parasitic? | yes |
| are all parasites pathogenic? | some may be, some not |
| define parasite | live in or on another org getting nutrients from it and may or not be pathogenic |
| define pathogen | biological agent causing disease to host; can be bacteria or virus. can be harmful or not. |
| infectious diseases are caused by... | pathogens |
| non infectious diseases are caused by ... | environmental or host factors |
| indicator for disease | symptoms |
| examples of infectious and non infectious diseases | inf: rabies noninf: heart disease |
| which are there more of in rich countries: infectious or non diseases? | non infectious - 93% |
| more infectious disease deaths in rich or poor? | poor countries- 64% deaths |
| what are the sources for human disease? | animal diseases became human diseases |
| zoonotic disease: define and examples | animal disease goes to humans or vice versa like rabies lyme plague- complete life cycle in the host |
| zoonotic disease stages | stage 5: comes from humans only- HIV stage 4: human mostly and animals- dengue stage 3: some human and animals- ebola stage 2: only from animals-rabies stage 1: only in animals- |
| a human only disease is what zoonotic stage? | 5 |
| factors driving zoonotic disease emergence | human wildlife interactions |
| nipah virus | high fatal rate: bats-fruit-pigs-humans |
| symbiotic relationships effects on host | parasitism: - or +, commensalism: 0 mutualism: + |
| # of bacterial species on the stomach | 40,000 |
| most abundant cell type in human body | microbial, fewer human cells |
| human microbe key points | varies person to person, but person's own microbiome is constant, microbiomes are similar among body parts of others, microbiomes classification of species differ greatly between people, microbiomes similar if classified by function |
| gut microbe functions | digestions, vitamin synthesis, drug metabolism, pathogen resistance, immune response, gut epo cells, odor appearance, cardiac size and behavior |
| changes in human ecology effecting microbes | population density, weather/climate, technology |
| diseases caused by microbial changes | asthma, crohns disease, allergies autism obesity |
| group type for mrca of all eukaryotes | polytomy |
| microbial eukaryotes phyly type | paraphyletic |
| how euk microbes differ | reproduction morphology symbioses ecological importance metabolism locomotion morph: unicellular/cellular reprod: sexual/asexual; many groups, strictly or both; diploid vs haploid loco: flagella, cilia, pseudopods metab: auto;/heterotrophs, an/aerobic symb: endosymbiosis, parasites |
| are euk microbes uni or multicellular? | they can be either |
| what is the cellular ancestral state for euk microbes? | unicellular, then later became multi by convergence |
| asexual repro types in euk microbes | binary fission schizogeny budding spores |
| sexual reprod in euk microbes | alternation of generations |
| locomotion in euk microbes | due to pseudopods, cilia and flagella |
| land plant metabolism can be... | photosynthetic pathogenic parasitic |
| metabolic types in microbial euks | auto/heterotrophs an/aerobes |
| likelihood of LGT in euks vs proks | more likely in proks- not as common in euks but happens |
| where euks lack ability to acquire new metabolic processes... | they are awesome at symbiosis with other domains of life |
| mutualist symbioses in euks | digestive defensive behavioral autotrophic and nutritional |
| an example of defensive symbiosis | biofilms |
| sister taxa of brown algae | diatoms! |
| brown algae and diatoms found in which clade | chromoalveolates |
| how chromoalveolates were made | secondary symbiosis with red algae in a flagellate |
| plastid loss | cilliates and oomycites |
| photosynthetic chromoalveolate | dinoflagellates |
| apicomplexans | all parasites of animals- like malaria. organelles at tip for transfer. |
| function of apicoplast | no photosynthesis but involved in lipid protein syn for malaria transfer |
| apicomplexans life cycle | completed in 2 different hosts |
| toxoplasma life cycle | can only reproduce in the host cell- cat. virus must find way back |
| photosynthetic sister taxa to apicomplexans | dinoflagellates |
| dinoflagellates | primary producers in marine env- endosymb with coral- when they die cloral bleaching occurs |
| alveolate clade | ciliates dinoflags and apicomplexans |
| straminopile clade | oomycetes diatoms brown algae slime nets: all have synapomorphy- hairs on longer of 2 flagella |
| straminopile synapomorphy | hairs on longer of the 2 flagella |
| diatom features | photosynthetic producers in marine and fresh h2o unicellular and filamentous store oil in vacuole- so oil source |
| brown algae and oomycetes | brown algae multicellular marine exclusive oomycetes multcellular non photsynth, absorptive heterotrophs |
| irish potato famine and sudden oak death | oomycetes did it |
| feature of unikont clade | single flagella |
| amoebozoan groups locomotion/ feeding | loboseans, slime molds pseudopods phagocytosis or parastism |
| plasmodial slime modes | mitosis and no cytokinesis: single cells form multinucleate plasmodium feeds by phago forms fruiting bodys to repro |
| cellular slime molds | indiv. cells eat by phago and form multicellular fruiting bodies |
| slime mold life cycles | sexual: single. aggregate, fruiting body, spores released, start over sexual: zygote from agreggation, karygamy, zygote -meiosis - amoeba born |
| hypothesis for virus origins? | ? |
| sexual reproduction | 2 steps: haploid gametes fuse to form diploid zygote and diploid zygote undergoes meiosis making haploid gametes |
| sexual reproduction steps | diploid zygote- meiosis- haploid gametes- syngamy- fusion of gametes- forms zygote |
| multicellular orgs repro cycles: which is multicellular? | haploid stage diploid or both |
| 3 variations of reprod cycle: | diplontic haplontic and alt of generations |
| diplontic life cycle | expansion of diploid phase, gametes are the only haploid cells |
| haplontic life cycle | expanded haploid phase only diploid cell is zygote |
| alternation of generations | A diploid spore-forming organism gives rise to a haploid gamete-forming organism ! When haploid gametes fuse a diploid zygote is formed. ! Both stages multicellular and undergo mitosis, meiosis forms spores H |
| evidence of endosymb in mitochondria and chloroplasts | membrane components more like that of bacteria than of other euks morph resembles bacteria contain own genomes components resemble bacterias |
| do all euks have mitochondria? | most- not all, diplomonads |
| how we know mitochondria came from endosymbiosis | pcr and phylogenetic analysis of dna in mitochondria linked it single endosym event with a proteobacterium |
| conclusions of mitochondria phylo analysis | 1 endosym with proteobacterium, mitochondria presence is a homologous trait in euks, derived trait- not present before endosymb |
| ancestral and derived features of euks | ancestral: cell wall membrane dna derived: cytoskeleton cell wall lost membrane bound dna phagocytosis |
| mitochondria endosymbiosis type | primary endosymbiosis - proteobacteria in cell |
| method to find origin of chloroplasts | phylo analysis of dna plastids in genomes traced plastids that derived from endosymb event with cyanobacterium |
| primary symbiosis of chloroplasts | three genomes in one cells: host mitochon and chlroplast phagocytosis then double membrane |
| why chloroplasts are scattered about | endosymb of chloroplasts happened in the plantae ancestor only- those who formed endosymbiotic relationship with this group got it |
| secondary symbiosis gave rise to | euk host cells with plant symbionts with chloroplasts |
| which plantae was the endosymbiont leading to chloroplasts | euglenid |
| primary vs secondary endosymbiosis | 1. bacteria engulfed for mitochondria or chloroplasts 2. a eukaryotic symbiont is engulfed and already contains chloroplast/ mito |
| results of secondary endosymbiosis | diatoms-red algae apicomplexans, dinoflag and amoebozoans |
| # of nuclei present in tertiary endosymbiosis | 3 (host, symbiont w/ own nuc + that of cyanobacterium)- photosynth euk symbiont engulfed by nucleus having host |
| tertiary endosymbiosis resulted in... | photosynthetic properties of dinoflaggs and brown algae |
| transitions vs transversions: which requires the fewest steps? | transitions are generally more common than transversions B. if the character in the tree undergoes the minimum amount of change it will involve a transversion C. if the character in the tree undergoes multiple changes it could involve both transitions and transversions E. the character exhibits homoplasy on this tree |
| cladogram relationships | closer within immediate clade than with outgroup |
| Viruses to survive they must be able to do 3 things o Get into a susceptible host. Attachment to host cell membrane. Not in plant, fungal and bacterial viruses. Penetration of host cell membrane: endocytosis, mechanical penetration with plant and fungal viruses. Inject genome with some bacterial viruses o Must be able to replicate and make more virus. Uncoating. Replication. Self-assembly of virus particles o Most have some mechanism to move the newly made viruses to new susceptible host. | Viruses to survive they must be able to do 3 things o Get into a susceptible host. Attachment to host cell membrane. Not in plant, fungal and bacterial viruses. Penetration of host cell membrane: endocytosis, mechanical penetration with plant and fungal viruses. Inject genome with some bacterial viruses o Must be able to replicate and make more virus. Uncoating. Replication. Self-assembly of virus particles o Most have some mechanism to move the newly made viruses to new susceptible host. |
| Primary: symbiosis between a cell that engulfed either a mitochondria or a chloroplast. Should have 3 genomes, if you count organelles (1) and nuclear DNA separately (2), in the end (one nuclear genome, one mitochondrial genome, one chloroplast genome) * Secondary: engulfing one cell/organism that has a chloroplast/mitochondria from primary endosymbiosis. Should have 5 genomes, if you count organelles and nuclear DNA separately, in the end (3 from primary + 1 nuclear genome + 1 mitochondrial genome) * Tertiary: engulfing an organism that is already secondary endosymbiont. Thus, acquiring their mitochondria and/or chloroplasts. Should have 7 genomes, if you count organelles and nuclear DNA separately, in the end (5 from secondary + 1 mitochondrial and 1 nuclear genome) | Primary: symbiosis between a cell that engulfed either a mitochondria or a chloroplast. Should have 3 genomes, if you count organelles and nuclear DNA separately, in the end (one nuclear genome, one mitochondrial genome, one chloroplast genome) * Secondary: engulfing one cell/organism that has a chloroplast/mitochondria from primary endosymbiosis. Should have 5 genomes, if you count organelles and nuclear DNA separately, in the end (3 from primary + 1 nuclear genome + 1 mitochondrial genome) * Tertiary: engulfing an organism that is already secondary endosymbiont. Thus, acquiring their mitochondria and/or chloroplasts. Should have 7 genomes, if you count organelles and nuclear DNA separately, in the end (5 from secondary + 1 mitochondrial and 1 nuclear genome) * |
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