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35 Cards in this Set
- Front
- Back
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How do calculate Evolutionary Distance between organisms A and B?
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look at common ancestor to A and B.
Evo D = (sum of changes from common --> A) + (sum of changes from common --> B) |
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How to root an unrooted phylogenetic tree?
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1. select root at midpoint of unrooted tree.
2. select root at junction of outgroups 3. Ancient Duplicated Genes method |
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Ancient Duplicated Genes method of rooting a phylogenetic tree
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look at where branching occurred: each gene group counts as an outgroup
common ancestor has one gene = root of tree. |
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How does Lateral Gene Transfer impact phylogenetic trees?
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creates linkages that don't "make sense" in context of linear model of evolution.
connections between faraway branches |
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Taxonomy vs. Phylogeny
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Taxonomy: looks at physical characteristics (anatomy/physiology) to gague relatedness
Phylogeny: looks at sequences of conserved molecules (rRNA) |
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Hypothetical role of rhodopsin in establishing primitive PMF?
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Rhodopsin absorbs light energy and uses it to transport H+ across membrane --> PMF
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Iron-Sulfur World Hypothesis
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guesses that Fe/S proteins functioned as electron carriers in a self-amplifying CO2 fixation cycle
Lithotrophic, autotrophic cells H2 + S --> H2S |
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What is the rationale behind isotope fractionation?
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enzymes prefer certain isotopes so if enzymes are present we should start seeing certain isotopes more or less often in biologically related compounds.
ex. we start seeing less C-13 in 3.5 byo rocks after the advent of life because enzymes prefer to use C12. |
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What is accepted evidence for the advent of an oxygenic atmosphere?
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Bands of iron oxides start appearing in rocks ~2.9 bya
Hopanoids in 2.7 byo sediments: associated with oxygenic photosynthesis |
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How long ago was the origin of the universe?
Of Earth? |
Universe: 14 billion years ago
Earth: 4.6 billion years ago |
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Thermophile temperature range?
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45-80 degrees C
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Hyperthermophile temperature range?
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80-106 degrees C
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Pryridictium
morphology? metabolism? optimal growth T? |
ARCHAEA
disc shaped, connected by tubes H2-oxidizing Sulfur reducer H2 + S --> H2S 105 C optimal T (Hydrothermal vent) |
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Adaptations to thermophilic lifestyle?
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Phytanyl monolayer (tetra-ether lipid analog)
reverse gyrase to protect DNA from unwinding protein stabilization (disulfide bridges) |
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What are the two types of Methanogenic Archaea?
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1. hydrogenotrophs
2. methylotrophs |
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Photoautotrophs
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e- source: organic molecules
energy source: light energy carbon source: CO2 |
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Chemolithotrophs
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energy source: inorganic molecules
carbon source: CO2 = Chemoautotrophs |
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Metabolic classifications for energy sources?
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organo- (organic cpds)
litho- (inorganic cpds) photo- (sunlight energy) |
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Metabolic classifications for carbon sources?
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hetero- (organic carbon compounds)
auto- (CO2 fixation) |
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Chemoheterotroph
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e- source: organic molecules
energy source: organic molecules carbon source: organic molecules =Chemoorganotroph |
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Photoheterotroph
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energy source: light energy
carbon source: organic molecules Purple Sulfur Bacteria |
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Methanobacterium
shape? taxonomic class? habitat? |
CRENARCHAEOTA
irregular rod Hydrogen oxidizing Methanogen H2 + CO2 --> CH4 anaerobic pond sediment, GI tracts, geothermal vents |
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Desulfovibrio
shape? taxonomic class? habitat? |
delta PROTEOBACTERIA
vibrio shaped Sulfate reducer SO4-- + H2 --> H2S + acetate lives in marine sediments |
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What is evidence for early lateral gene transfer in the sulfite reductase phylogenetic tree?
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Archaeoglobus appears to reside on proteobacteria branch rather than archaeal branch
Lateral gene transfer must have occurred from Thermodesulfovibrio. |
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How to enrich for Sulfate reducers?
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agar shake tube: agar + sulfate + e- donor + minerals + iron + stinky mud
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Biological importance of methanogens?
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-make natural gas for energy/heating
-partially responsible for global warming -part of carbon cycle |
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Lithotrophic Heterotroph
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aka Mixotroph: uses inorganic energy to assimilate organic C
energy source: inroganic cpds carbon source: organic cpds |
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What is an easy diagnostic test for identifying an isolate as a methanogenic archaea?
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UV light: cells should fluoresce blue-green.
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What electron donors and acceptors are used by Methylotrophic Methanogens?
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H2 + CO2 --> CH4
CH3OH + CO2 --> CH4 2 CH3OH --> CH4 + CO2 methanol as acceptor + donor CH3COOH --> CO2 + CH4 |
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What is the first step carried out in reduction of CO2 by methanogens?
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Ferredoxin + H2 --> Fd(red)
CO2 + Ferredoxin(red) --(methanofuran)--> HCO-MF + Fd(ox) formate esterified to methanofuran |
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What is the second step carried out in reduction of CO2 by methanogens? (formic acid --> ?)
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MF-formate + MP --> MP-formate + MF
MP-formate + F420(red) - --> MP-methylene + F420(ox) methylene group attached to methanopterin. |
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What is the third step carried out in reduction of CO2 by methanogens?
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MP-methylene + F420(red) --> MP-CH3 + F420(ox)
F420 reduces methylene to methyl. |
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What is the fourth step carried out in reduction of CO2 by methanogens?
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MP-CH3 + CoM-SH --> CoM-S-CH3
methyl transferred from methanopterin to coenzyme M |
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What is the fifth step carried out in reduction of CO2 by methanogens?
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CoM-S-CH3 + F30 Methyl Reductase --> CH4!
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Why do Methylotrophic Methanogens have higher growth yields?
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primitive ETchain in PM generates additional PMF in reduction of Coenzyme M/Coenzyme B heterodisulfide
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