Unit 1 Flashcards
when was earth formed?
4.5 BYA
why was earth inhospitable?
hot
no oxygen
water only as vapur
when did the first cellular life appear?
4 bya (end of Hadean)
what is the surface origin theory?
spontaneous arise of membrane-enclosed strucutre from primordial organic-inorganic soup
what is the subsurface origin theory?
interaction between alkaline hot water beneath ocean and cold acidic water
what was the energy supply beneath the ocean?
H2S and H2
what was the energy supply on the surface?
iron
how did metal precipitates form?
interaction between sulfides and iron
how did the first macromolecules form?
metal precipitates catalyzed formation of amino acids. sugars and bases
what is the RNA world theory?
first molecule entrapped in self-replicating system were RNAs
how was the first semipermeable membrane formed?
RNA catalyzed formation of first simple peptides that coated mineral
what is the order of events according to RNA world theory?
- formation of amino acids, nucleotides and sugars
- RNA catalytic world and self-replicating RNA
- synthesis of complex proteins via catalysis
- DNA replaced RNA
- lipid arise and entrapped proteins, RNA and DNA
- LUCA appeared
- divergence of LUCA to Bacteria and Archaea
what evidence was there than B and A branched from LUCA?
structure of lipids in B have ester bond and ether bond in A
how was the first self-replicating organism formed?
after lipoprotein structure entrapped DNA and RNA
when did first methanogenesis develop?
Archaea
3.9 BYA
what developed after methanogenesis?
anoxygenic photosynthesis
who did anoxygenic photosynthesis?
purple and green bacteria
consumed H2S
what developed with anoxygenic bacteria?
H2 oxidizing organisms
who developed after anoxygenic photosynthesis?
cyanobacteria at the end of Archaean
what did Archaean end with?
big oxygenation event led by cyanobacteria
who developed in Proterozoic?
first eukaryote
who developed in phanerozoic?
multicellular eukaryote and early animals
how was banded iron formed?
oxygen and available iron
what kind of iron is in banded iron formations?
ferric
how did earth become oxic?
when all iron exhausted then o2 increased
what did o2 accumulation lead to?
formation of UV shield zone and evolution expanded
how did eukaryotic cell appear?
1) DNA accumulation led to nucleus formation then nucleus containing cell ingested chloroplasts and mitochondria
2) early cell was archaeal and consumed O2. host ingested H2-producing bacteria
what commonality does eukaryotes and bacteria have?
types of lipids
what commonality does eukaryotes and archaea have?
transcription and translation
endosymbiosis
chemoorganotrophic bacterium host ingested O2-consuming and ATP producing bacteria
- facultative aerobic organism ingested chloroplast where O2 was made
what did early autotrophy discover?
Aquifex: hyperthermophile bacteria
what was the first cell?
anaerobic and autotrophic
obtained CO2 and electrons to reduce CO2 and get H2
what is phototrophy?
evolved in B
used solar radiation
what is the common ancestor for all bacteria?
chloroflexus (anaerobic phototrophs) except Aquifex and Thermotoga
what are the 4 evidences to support endosymbiosis?
- both mito and chloroplasts contain ribosomes that are prokaryotic 70S and have 16S r RNA same as prokaryotes
- same antibiotics that affect ribosomal function in Bacteria inhibit ribosomal function in mito and chloroplasts
- mito and chloroplasts have own DNA arranged in covalently closed circular form like B
- many signs of B are in eukaryotic organelles
what is the earliest evidence of microbial life?
stromatolites
how were ancient stromatolites formed?
phototropic filamentous bacteria
how were modern stromatolites formed?
phototrophic O2-evolving cyanobacteria
how do we use DNA to determine evolutionary history?
- DNA record of past evolutionary events
- determine phylogeny
what is phylogeny?
evolutionary history of organisms
what are eukaryotic cells made of?
B and A cells
- chimera
what helped develop the evolution of microorganisms?
nucleic acids used to determine phylogeny
what molecule revolutionized understanding of microbial evolution?
r RNA
what did rRNA help to build?
first universal tree of life
what did Haeckel do?
Monera bottom of tree
- ancestor of all life forms that branched to protists. plants and animals
what did Whittaker do?
Monera bottom of tree and ancestor of protists
- Protists branched to Fungi, Plants and Animals
what did Woese do?
r RNA and genes used to define evolutionary relationships between organisms
why use rRNA for phylogeny?
- universally distributed
- functionally constant
- highly conserved
- adequate length to provide deep evolutionary relationships explanations
what is the modern tree of life based on?
16S rRNA genes
what does the modern tree of life show?
- LUCA is at the bottom
- HGT extensive in early history but decreased as 2 lineages B and A separated from LUCA and evolved independently
- eukaryotes separated from Archaea (after ozone developed)
what do phylogenetic trees contain?
nodes and branches
nodes
stage of evolution where ancestors diverged in 2 new lineages
branch length
number of changes occurring over time
tips of branches
species existing
types of trees?
rooted and unrooted
rooted trees
position of ancestor for all analyzed organisms
unrooted trees
relative relationships between analyzed organisms. no evidence of most recent ancestor
how to use DNA sequences in phylogenetic analysis of microbial life?
extract DNA directly or amplify specific gene using PCR
what happens to PCR products?
- visualized by agarose gel electrophoresis
- extracted from gel and sequences using same primers
how is evolution defined?
change in frequencies of alleles in set of organisms over time
alleles
alternative versions of given gene
how do new alleles arise?
mutation and recombination
what are the largest sources of genetic diversity?
mutation
recombination
- new alleles created
mutations
- random changes in DNA sequences that accumulate over time
- fundamental source of natural variations that drive evolutionary process
- +,- or neutral
- several forms: sub, delete, insert, duplicate
recombination
DNA segments broken and rejoined to create new combo of genetic material
homologous recombination
requires short segments of highly similar DNA sequences that flank regions of DNA transferred
nonhomologous recombination
mediated by several mechanisms that have one fact common
mechanisms of evolution
selection
genetic drift
selection
ability of organism to produce progeny and contribute to genetic makeup of future generation based on fitness
genetic drift
random process that cause changes in gene frequencies
(stronger in smaller pop- survive by chance)
what do evolutionary changes in microorganisms caused by?
change in enviro or introductions of new cells
2 examples of rapid evolution in bacteria?
Rhodobacter- rapid loss of trait
E. coli- gain of new trait
orthologs
originate from single ancestral gene in common ancestor
paralogs
result of gene duplication
convergent evolution
homoplasy
- type of evolution when organisms share trait not inherited from common ancestor
do we assume genes are inherited vertically when using gene sequence to conclude about phylogeny?
YES
bottleneck events
severe reduction in size followed by overgrowth of cells
- important for evolution of pathogens
Rhodobacter
- produces bacteriochlorophylls
- carotenoids absorb light energy
- dark = pigments useless
- signal stimulates production of pigment in dark is lack of oxygen
- sometimes mutates and loses ability to make pigments
- when no selective pressure the trait is lost due to mutation
E. coli
- after sequencing mutations accumulated
- evolved strain fitness improved dramatically over first 500 gen
- after 31500 gen then evolved strains evolved ability to use citrate as carbon source
- random accumulation of mutation modified preexisting genes, allowed evolution of new adaptive trait
core genome
genes shared by all members of species
pan genome
core genome plus genes not shared between species and usually acquired through HGT
systematic
study in diversity of organism and relationship
taxonomy
science that studies classification of organisms
what does systematic link?
taxonomy and phylogeny
- classification and evolutionary history of organisms
phenotypic analysis
identification of morphological, metabolic, physiological and chemical characteristics
genotypic analysis
identification of genome characteristics
phylogenetic analysis
placing organisms in evolutionary framework using molecular sequence data
what are the fundamental units of bio diverstiy?
species
species
groups of strains that share high degree of similarity in many traits and share recent common ancestor for their 16S rRNA genes
DNA-DNA hybridization experiment
- degree between genomes of 2 organisms is measure of genomic similarity
- probe DNA obtained from organism 1 and labeled with fluorescent or radioactive label
- DNA from 1 sheared into small pieces and heated to generate ss DNA
- probe added to sheared ss DNA from 2
- mixture from 1 and 2 mixed and cooled for re annealing
how do you know there are 2 different species?
value of less than 70% hybridization and difference in 16S rRNA is 3% or more
what are the 4 phylas where 90% of bacteria belong?
- Actinobacteria
- Firmicutes
- Proteobacteria
- Bacteroidetes
what is the best illustrator of microbial diversity?
phyla Proteobacteria
- diversity of physiological traits
how many major phyla in Archeal
7
how many Archaeal phyla based on lab?
5
what 2 phyla do most Archaeal species belong to?
- Crenarchaeota
- Euyarchaeota
which 3 phyla do minority of Archaeal species belong to?
- Nanoarchaeota
- Korarchaeota
- Thaumarachaeota
what is the eukaryotic analog to SSU r RNA?
18 S r RNA
how are major eukaryotic organelles derived?
endosymbiosis with Bacteria
where is the mitochondrial ancestor from?
Proteobacteria
where is chloroplasts ancestor from?
cyanobacteria
