Flashcards
Lecture 23 PMB
Cards in this deck (34)
- 1Layers of living stromatolitessedimentary layers of limestone accreted by centuries of microbial growth
Oxygenic phototrophs on top --> red light-induced H2S photolysis to sulfate -->
sulfate reducers on bottom - 2microfossilsto 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 - 3Biosignaturesspecific organic molecules (that can only be made by microbes!!) found within the rocks
Ex: hopanoids - 4problems with biosignatures1) 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 - 5isotope ratios as evidence for lifeenzymes 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 - 6problems with using isotope ratios as evidence for life1) 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 - 7Hadeon era"hell" era, all a vocanic soupy mess
- 8Archaean erafirst period with liquid water forming stable oceans, oldest stromatolites from here
cyanobacterial hopanoids found at the END --> molecular oxygen waste product changes everything - 9Paleoproterozoicenough atmospheric oxygen to support a little aerobic respiration --> colonial cyanobacteria, eukaryotic microbes, ozone layer!
- 10Neoproterozoic eraO2 reaches present day levels, early multicellular life
- 11Possible energy sources for earliest life1) Light driven ion pumps AKA bacteriorhodopsins
2) Redox reactions involving available substrates
3) Methanogenesis
4) Primitive hydrogenase that splits H2 across membrane - 12earliest conditions for living things on earthno atmospheric protection from UV light, so everything had to live underwater
really cold or really hot? - 13redox reactions involving available substrates during the Archaean eraoxidized 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 - 14Oxygenic Photosynthesis of Cyanobacteriaafter 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
- 15Evolutionary relationshipsdescribed by phylogenetic trees:
- a monophyletic group shares a common ancestor not shared by anyone else - 16Possible phenotypic characteristics (not DNA) that were used to determine evolutionary relatednessshape, gram stain, oxygen use, carbon use (autotroph or heterotroph), temperature, living conditions
- 17problems 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 - 18Assumptions of using DNA as molecular clocks1) 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!!! - 19what 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 - 20Why 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 - 21Methods of comparing two 16S rRNA sequences1) 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 - 22correlation factorconsiders 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 - 23endosymbiosishypothesis 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 - 24evidence for endosymbiosismitochondria and chloroplasts resemble bacteria; have own circular genomes, ribosomes, and tRNAs; make own proteins
- 25discovery of three domains16S rRNA sequencing led to discovery of three distinct groups (Bacteria, Archaea, Eukaryotes) all equidistant in sequence differences
- 26evolutionary tree LUCAsLBCA = last bacterial common ancestor
LACA = last archaeal common ancestor
LECA = last eukaryal common ancestor
FME = first eukaryotic ancestor with a mitochondrion - 27relationship between archaea and eukaryotespreviously thought up to be sister domains, but new sequences has led to conclusions that eukaryotes emerged from WITHIN archaea (*Korarchaeota, Agiarchaeota,
and Thaumarchaeota*) - 28Major groups of Archaea1) Euryarchaeota
2) Crenarchaeota
3) Thaumarchaeota - 29EuryarchaeotaMethanogens: 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 - 30CrenarchaeotaExtreme 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 - 31ThaumoarchaeotaAmmonia 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!! - 32memorize key differences between domains!!!
- 33When 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 - 34Limitations of using phylogenetic trees1) 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)