11649870
Description
| Question | Answer |
| Layers of living stromatolites | sedimentary layers of limestone accreted by centuries of microbial growth Oxygenic phototrophs on top --> red light-induced H2S photolysis to sulfate --> sulfate reducers on bottom |
| microfossils | to form these, minerals precipitate & fill in forms of ancient microbial cells Must show regular 3D patterns that cannot be explained by abiotic processes --> this is subjective and can be wrong |
| Biosignatures | specific organic molecules (that can only be made by microbes!!) found within the rocks Ex: hopanoids |
| problems with biosignatures | 1) biosignatures may not actually be as specific to an organism as we believe 2) hard to rule out abiotic sources of the biosignature 3) the oldest biosignatures probably have already been destroyed |
| isotope ratios as evidence for life | enzymes favor metabolizing substrates containing C12, while abiotic processes use C13 and C12 equally CO2 converted to CaCO3 in sedimentary rock, will contain less C13/C12 ratio in biologically derived CaCO3 these ratios depend on WHERE you are |
| problems with using isotope ratios as evidence for life | 1) tells us nothing about the actual early FORMS of life 2) can't necessarily prove that abiotic processes uses the isotopes equally 3) a false positive could form if enzymes depleted isotopes the other way around |
| Hadeon era | "hell" era, all a vocanic soupy mess |
| Archaean era | first period with liquid water forming stable oceans, oldest stromatolites from here cyanobacterial hopanoids found at the END --> molecular oxygen waste product changes everything |
| Paleoproterozoic | enough atmospheric oxygen to support a little aerobic respiration --> colonial cyanobacteria, eukaryotic microbes, ozone layer! |
| Neoproterozoic era | O2 reaches present day levels, early multicellular life |
| Possible energy sources for earliest life | 1) Light driven ion pumps AKA bacteriorhodopsins 2) Redox reactions involving available substrates 3) Methanogenesis 4) Primitive hydrogenase that splits H2 across membrane |
| earliest conditions for living things on earth | no atmospheric protection from UV light, so everything had to live underwater really cold or really hot? |
| redox reactions involving available substrates during the Archaean era | oxidized substances diffuse down into water from atmosphere, reduced substances diffuse up from ocean floor --> redox reactions at interface include cyanobacteria, anoxygenic photosynthesizers, methanotrophs and fermenters, FeS bacteria, methanogens |
| Oxygenic Photosynthesis of Cyanobacteria | after a lot of Fe2+ oxidized to Fe3+, metabolism began to accumulate oxygen in atmosphere --> evolution of aerobic respirators, ozone layer created to shield life from UV light |
| Evolutionary relationships | described by phylogenetic trees: - a monophyletic group shares a common ancestor not shared by anyone else |
| Possible phenotypic characteristics (not DNA) that were used to determine evolutionary relatedness | shape, gram stain, oxygen use, carbon use (autotroph or heterotroph), temperature, living conditions |
| problems of using phenotypic similarities to determine evolutionary relatedness | -can't really determine which phenotypic difference is important --> conflicting trees -little fossil record -lack of complex structures -metabolic characteristics may change according to how a strain is cultured -can’t define species as a group capable of interbreeding/having fertile offspring |
| Assumptions of using DNA as molecular clocks | 1) Mutations in DNA accumulate randomly due to errors in replication 2) Mutations can cause phenotypic changes subject to natural selection 3) Random mutations with neutral effects accumulate at a steady rate 4) More sequence differences between two organisms means that they diverged from each other further in the past!!! |
| what type of DNA can we look at? | can't use "junk DNA" that doesn't contain a known gene/function can't pick DNA with no selective constraints, since these will lose their coherent identity throughout recent brancings |
| Why is 16S rRNA a good choice of DNA to study evolutionary relatedness? | 1) does not face different selective pressures in different organisms 2) has highly conserved regions that make it easier to align and amplify 2 sequences 3) has less conserved regions where sequence variability occurs 4) didn't evolve twice through convergent evolution, present in ALL organisms |
| Methods of comparing two 16S rRNA sequences | 1) Isolate genomic DNA from organisms to be compared 2) PCR 16S rRNA genes using universal primers based on conserved nucleotides 3) Obtain & align sequences 4) Compute number of differences 5) Repeat for all other sequence pairs --> create a distance matrix 6) Use these distances to make a tree that reflects evolutionary relationships |
| correlation factor | considers that whatever sequence changes we see are considered to be the minimum, because a sequence could have mutated forward and backward, or forward twice depends on mutation rate at time of divergence |
| endosymbiosis | hypothesis that mitochondria/chloroplasts originated as proteobacteria/cyanobacteria that were engulfed by a protist and came to live as permanent symbionts believed eukaryotes evolved FROM prokaryotes, rather than alongside them |
| evidence for endosymbiosis | mitochondria and chloroplasts resemble bacteria; have own circular genomes, ribosomes, and tRNAs; make own proteins |
| discovery of three domains | 16S rRNA sequencing led to discovery of three distinct groups (Bacteria, Archaea, Eukaryotes) all equidistant in sequence differences |
| evolutionary tree LUCAs | LBCA = last bacterial common ancestor LACA = last archaeal common ancestor LECA = last eukaryal common ancestor FME = first eukaryotic ancestor with a mitochondrion |
| relationship between archaea and eukaryotes | previously thought up to be sister domains, but new sequences has led to conclusions that eukaryotes emerged from WITHIN archaea (*Korarchaeota, Agiarchaeota, and Thaumarchaeota*) |
| Major groups of Archaea | 1) Euryarchaeota 2) Crenarchaeota 3) Thaumarchaeota |
| Euryarchaeota | Methanogens: synthesize methane, are autotrophic obligate aerobes, found in stagnant water, sewage treatment plants, intestinal tracts, ocean bottom, hot springs Extreme halophiles: optimal growth in water much more salty than the sea (ocean borders/etc), are aerobic heterotrophs, use bacteriorhodopsin in low O2 environments, pump K+ into cell as a compatible solute to maintain water balance |
| Crenarchaeota | Extreme thermophiles: some have temperature optima above 80C, ALL are obligate/facultative anaerobes and chemolithotrophs/chemoorganotrophs use diverse electron acceptors and donors, can either be autotrophs or heterotrophs |
| Thaumoarchaeota | Ammonia oxidizers: really abundant and widespread, NH3 = donor, O2 = acceptor can grow in really low concentrations of NH3/in acidic soils where only archaea can grow --> key part of biological N cycle!! |
| memorize key differences between domains!!! | |
| When are evolutionary trees a good model of relationships? | When: 1) DNA you have used for the tree is passed from “parents” 2) Genes change by accumulation of point mutations |
| Limitations of using phylogenetic trees | 1) More than one tree can sometimes be drawn using the same data! 2) Similar sequences result from convergent evolution at the sequence level (homoplasmy), rather than inheritance of the same allele 3) DNA not always passed down by parents (horizontal gene transfer) |
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