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Genes, Ecology, and Evolution Exam 3

Terms in this set (66)

common ancestor
Common Ancestor Descendance: universal ancestry
-horizontal gene transfer supports this; the universal common ancestor was not present at the beginning of life, but occurred millions of years later ----> all living organisms descended from this common ancestor and all living organisms utilizing genetic transfer to produce the next generation
-it is inevitable that there will be a "winner"--every other lineage was defeated by the extreme advantage for 1 single common ancestor
LUCA
Can we use the consensus "organismal tree" to learn more about LUCA? LUCA arose during LOW O2 on Earth ~3.8-4.2 billion years ago
-all original tree branches extended from thermophilic organisms
-the Deep Hot Hypothesis supports that LUCA originated in hydrothermal vents--community = same species of organisms, ecosystem = geology + organisms (is isolated from all other ecosystems), biome = all vent ecosystems combined (crusts, spreading centers, subduction zones, core-mantle hot spots)--similar organisms will be present in the Antarctic and Galapagos Islands b/c they contain the same biome
alkali
Alkali Thermal Vents (LUCA could have lived in these)--water interacts with serpentine and induces HIGH pH inside and forms heat and H2 gas as by-products
-CO2 forms calcium carbonate
universal
355 "core" genes were recently identified as the last universal common ancestor:
-its mode of H2O production is similar to photosynthesis and also contains nitrogen-fixing mechanisms (both poisoned by O2)--these prove that the last common ancestor lived in an atmosphere with NO oxygen present and lots of free hydrogen
-also found ATP Synthase which makes ATP from a H+ proton gradient
-also found H+ symporter for transporting organic molecules using an H+ proton gradient--within thermal vents, H+ gradient is present in which the common ancestor used this to generate energy
-also found Reverse DNA gyrase which overwinds DNA, making it harder to separate; found in thermophiles which compensates for their extreme hot environment which would otherwise denature their DNA
-also found H+-Na+ symporter in which Na+ is pumped out of a cell against its gradient--this suggests the common ancestor originated in seawater
-also lacked genes for ion-pumping transfers
stromatolites
There is no fossil evidence for the Deep Hot Hypothesis, but molecular fossils in DNA evidence!
Ex: By 3.8 billion years, life forms were for sure present--fossil stromatolites: living fossils and have outlived all mass extinctions
-they form on top of rocks and such rocks can be dated using zircon crystals
-the stromatolites are living because modern communities exhibit features of them--microbial mats
-photosynthetic bacteria also live in stromatolites and grow slowly by layers--stromatolite layers are of biological origin due to similar structures of modern cyanobacteria in 3.6 billion year old rocks...this evidence is not convincing enough b/c just because it looks like cyanobacteria does not mean it is
-Carbon is in stromatolites called kerogen, but this also does not prove they are living--looking at the 13C:14C isotope ratio could be a method of proving stromatolites are living
stromatolites
Cyanobacteria follow oxygenic photosynthesis--one can tell if formed in an oxygen rich environment based on oxide or sulfide present in the layers ----> red bands in the rock will show mass oxygen presence within the layers
Ex: Iron-silicate biomineralization forms a "sunscreen" layer on stromatolites
-around the time of stromatolite formation, oxygenic photosynthesis is beginning to make an appearance on Earth--a product of evolution is now changing the environment during this time!
DNA sequencing
How would you determine it was actually cyanobacteria in stromatolites? You can't, but DNA sequencing would be the 1st step.
de novo
Where do new genes come from?
1.) old genes: by descent or from horizontal gene transfer--comparing amino acid sequences shows relation to infer that 2 modern genes came from ancestral genes
2.) From scratch (de novo): Sulfide chemosynthesis--used Fe, Mn, Mg, and S as cofactors that were rich in hydrothermal vents
-very similar to photosynthesis, but uses enzymes and cofactors in a chemical pathway
-both photosynthesis and sulfide chemosynthesis contain very similar genes
-PAR = photosynthetic active radiation that measures the photosynthetic rate at different light wavelengths
GSB1
GSB1 = an anoxygenic photo-chemosynthetic bacteria in the oceanic aphotic zone--it requires infrared light and sulfide chemosynthesis to grow
-it contains chlorophyll-like pigments shown by the absorbance spectrum
-the source of IR light at this depth comes from the hydrothermal vents themselves that produce IR light and heat
-it can be hypothesized that something like GSB1 could have been an intermediate that used hydrothermal vent IR light and over time, developed to be able to function without it
-GSB1 is within the realm of evolutionary space in which organisms evolved to need chemical and light energy
eukarya
Eukarya--the best supported phylogenetic trees indicate a more recent common ancestor occurs between Eukarya and Archaea
Ex: Loki's Castle: a new group of archaeabacteria that are more closely related to Eukaryotes--this species suggests a branch between Eukarya and Archaea occurred from organisms in ancient thermal vents...BUT there are no true thermophilic eukaryotes!
-rapid division occurs between archaea and Loki's Castle ----> this produces a long gap before eukaryotic organisms evolved and a lot more changes in nucleotides
-Molecular Clock = more time equals more mutations
-ALL eukaryotic early branching lineages are single-celled heterotrophs
Ex: Naegleria--brain eating amoeba
mitochondrial
Human Mitochondrial Genome--1 singular circular DNA
-1 gene encodes 16S ribosomal RNA
-mitochondria lineage stems from the Bacteria domain and made its way into the Eukaryotic domain
-heterotrophic single-celled eukaryotes engulfed mitochondria-containing bacteria!
Ex: Rickettsia--obligate intra-cellular parasite; contains an 834 gene genome
-our eukaryotic ancestor became a host to this obligate parasite that ended up never leaving and coevolved over time
endosymbiotic hypothesis
Endosymbiotic Hypothesis--not widely accepted because it is primarily based on morphological evidence
-an intracellular pathogen was very well adapted at using the left overs from glycolysis--occurred when oxygen levels were increasing on Earth...so pyruvate oxidation evolved from this so the pathogen could squeeze out 38 ATPs/glucose for the host = mutualistic
-this pathogen evolved into the modern mitochondria
endosymbiotic hypothesis
Endosymbiotic Hypothesis
-Advantage to having genes in the nucleus rather than the mitochondrial genome: genes in the mitochondrial genome are inherited maternally and by only 1 parent--both mitochondrial genome and nuclear genome encode cellular products
-Advantage to nuclear encoding: because the mitochondrial genome is inherited from 1 parent (females for humans), but nuclear DNA is inherited from ALL of one's ancestors, making it more advantageous
Ex: Suppose a gene gains a favorable function...this gene can be passed down by an ancestor because of the nuclear genome, rather than the favorable function being bred out if passed down by the mitochondrial genome
Many multicellular organisms (e.g. plants and animals) set aside a germ cell lineage early in development. What is the possible evolutionary advantage of this phenomenon?
Multicellular organisms often reproduce through a unicellular propagule cell aided by cell differentiation.
-only certain cells from the unicellular propagule will be transmitted to the next generation ----> through the germ line
-somatic cells are NOT inherited, but germ cells are inherited and produce an evolutionary significant mutation
Only a few rounds of cell division occur during germ line formation--this occurs because of mutations that can be attributed just to DNA and would easily be passed on to the next generation. This is why organisms set aside specific cells for germ line formation to avoid several mutations.
Which germline cells are likely to be exposed to more UV light over the reproductive lifetime of an individual, plant germline cells or human germline cells?
Plant germlines cells.
-these are contained within their apical meristem which gives rise to all above-ground parts and reproductive organs
-UV light acts as a mutagen for plants--the apical meristem is constantly exposed to UV light--plant pigments and specific enzymes are available for repairing UV damage and protecting the plant germ line
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