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BIOL 322 > LEC. 1/2 - Formation and early history of earth/Living fossils and DNA records > Flashcards

LEC. 1/2 - Formation and early history of earth/Living fossils and DNA records Flashcards

1
Q

When was earth formed?

A

4.5 BYA

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2
Q

Describe the environment of Earth 4.5 BYA?

A

inhospitable bc there was no O2, water was a vapour and it was hot

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3
Q

When did the first cellular life appear?

A

4 BYA - end of Hadean

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4
Q

What are the 3 theories on how the first cell arose?

A
  1. surface origin
  2. subsurface origin
  3. RNA world
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5
Q

What is the surface origin theory?

A

spontaneous membrane-enclosed structure from primordial organic-inorganic soup

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6
Q

What is the subsurface origin hypothesis?

A

interaction between ocean water (cold and acidic) and hot water beneath ocean (alkaline)

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7
Q

What are the 3 key aspects of the subsurface origin hypothesis?

A
  1. H2S + H2 are beneath ocean and are a constant energy supply, but on surface there’s only iron
  2. sulfides + iron interact to produce metal precipitates
  3. metal precipitates catalyze formation of amino acids, sugars (basis for formation of macromolecules)
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8
Q

What is the RNA world hypothesis?

A
  • in the self-replicating system, the first molecule was RNA (entrapped)
  • RNA catalyzed first simple peptides that coated minerals (first semipermeable membrane)
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9
Q

What is the correct order of events according to the RNA world theory?

A
  1. amino acids, nucleotides, and sugars form
  2. RNA catalytic world + self-replicating RNA
  3. RNA catalysis makes makes complex proteins
  4. DNA replaces RNA
  5. lipid appears, and entrapped proteins (DNA and RNA)
  6. LUCA appeared
  7. LUCA diverges into bacteria and archaea
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10
Q

How do we know that Bacteria and Archaea branched from LUCA?

A

structure of their lipids
- bacteria lipids are ester bond
- archaea lipids are ether bond

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11
Q

What is the key event that happened at the beginning of the Archaean era?

A

LUCA splits to Bacteria and Archaea

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12
Q

When was the first methanogenesis developed?

A

3.9 BYA

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13
Q

After methanogenesis was developed, which type of organisms developed?

A

anoxygenic photosynthetic (purple and green bacteria)

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14
Q

At 3.2 BYA, what did purple and green bacteria primarily consume?

A

H2S

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15
Q

What other type of organism formed alongside anoxygenic photosynthetic organisms?

A

H2 oxidizing organisms

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16
Q

At the end of the Archaean era (2.8 BYA), what key organism developed?

A

cyanobacteria

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17
Q

What was the name of the key event that signified the end of the Archaean event?

A

oxygenic event led by cyanobacteria

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18
Q

What did cyanobacteria react with and what happened to cyanobacteria itself when this event happened?

A

when cyanobacteria produced O2, it reacted with iron which made it insoluble in banded iron formation

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19
Q

What is the term that describes iron in banded iron formations?

A

Ferric (FE3+) - O2 is trapped

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20
Q

During the banded iron formations, when all the iron was exhausted, what happened to the level of oxygen?

A

increased, Earth becomes oxic

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21
Q

What did the O2 accumulation lead to, 2 BYA? (2 things)

A
  1. basis for eukaryotic organisms
  2. ozone layer forms
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22
Q

What are the 2 theories for how the eukaryotic cell appeared?

A
  1. DNA accumulation => nucleus forming; nucleus containing cell ingested chloroplasts and mitochondria
  2. archaeal was early cell and consumed O2. to make sure it had enough energy, host ingests H2 producing bacteria
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23
Q

How are eukaryotes similar to bacteria?

A

same type of lipids

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24
Q

How are eukaryotes similar to archaea?

A

same transcriptional and translational apparatus

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25
Q

What is endosymbiosis?

A
  1. chemoorganotrophic bacterium ingest O2 consuming + ATP producing mitochondria
  2. facultative aerobic organism (host - chemoorganotrophs) ingest chloroplast (O2 is made here)
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26
Q

What are some key pieces of evidence that support the endosymbiotic theory?

A
  1. mitochondria and chloroplasts have ribosomes that are prokaryotic type 70S (16S r RNA also same as prokaryotes
  2. antiobiotics that affect ribosomal function in bacteria inhibit it in mitochondria and chloroplasts
  3. mitochondria and chloroplasts have DNA in covalently arranged closed circular form (typical for bacteria)
  4. signs of bacteria also in eukaryotic organelles
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27
Q

What is the main evidence for early microbial life?

A

stromatolites

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28
Q

What were ancient stromatilites formed by?

A

phototropic filamentous bacteria

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29
Q

What are modern stromatolites formed by?

A

phototropic O2 - evolving cyanobacteria

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30
Q

Why do we use DNA to determine evolutionary history?

A
  1. record of past evolutionary events
  2. determines phylogeny
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31
Q

What is phylogeny?

A

evolutionary history of organisms

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32
Q

What is the significance of r RNA?

A
  • used to build first universal tree of life
  • revolutionized understanding of microbial evolution
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33
Q

What did the universal tree of life look like for Haeckel’s hypothesis?

A

monera on bottom (ancestor to all life forms) and branched out to protists, plants, and animals

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34
Q

What did the universal tree of life look like for Whittaker’s hypothesis?

A
  • monera on bottom (ancestor of protists)
  • protists branch out to Fungi, Plants, and Animals
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35
Q

What did the tree of life look like for Woese’s hypothesis?

A

r RNA + their genes define evolutionary relationships between organisms

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36
Q

Why do we use rRNA to determine phylogeny?

A
  1. universally distributed
  2. functionally constant
  3. highly conserved (slowly changing)
  4. good length for explaining deep evolutionary hypotheses
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37
Q

What is the modern tree of life based on?

A

16S rRNA genes

38
Q

What is at the bottom of the modern tree of life?

39
Q

What is the dynamic of horizontal gene transfer now?

A

decreased when Bacteria and Archaea separated from LUCA and evolve independently

40
Q

2.8 BYA, what developed that made eukaryotes separate from archaea?

A

ozone shield

41
Q

In a phylogenetic tree, what do the nodes signify?

A

stage of evolution when ancestors diverge into 2 new lineages

42
Q

In a phylogenetic tree, what does the branch length signify?

A

changes over time

43
Q

What do the tips of the branches signify in a phylogenetic tree?

A

species existing today

44
Q

What are the only 2 parts of a phylogenetic tree that are informative?

A
  1. nodes
  2. branch length
45
Q

What are the 2 types of phylogenetic trees?

A
  1. unrooted tree
  2. rooted tree
46
Q

What is a unrooted tree?

A

relationships between organisms; no recent ancestor

47
Q

What is a rooted tree?

A

position of ancestor for all analyzed organisms

48
Q

How do we use DNA sequences in phylogenetic analysis of
microbial life?

A

get gene sequence of organism

49
Q

What are the 2 options of extracting genomic DNA?

A
  1. sequence genome directly
  2. amplify specific gene using PCR
50
Q

When genes are amplified using PCR, what is done after?

A
  1. PCR products visualized by agarose gel electrophoresis
  2. extracted from gel/cleaned up
  3. sequenced using same primers
51
Q

What is evolution?

A

change in frequencies in alleles in set of organisms over time

52
Q

What are alleles?

A

alternative versions of gene

53
Q

How do new alleles arise?

A

mutation and recombination

54
Q

Which 2 methods (from the production of new alleles) is the largest source of genetic diversity?

A

mutations and recombinations

55
Q

Microbial evolution is driven by?…

A

mutations and recombinations

56
Q

What is the term for random changes in DNA sequences that accumulate over time?

57
Q

What are the 4 different forms that mutations can take?

A
  1. substitutions
  2. deletions
  3. insertions
  4. duplications
58
Q

Which type of mutation correctly identifies the following description? => DNA segments are broken down and rejoined to create new combination of genetic material

A

recombination

59
Q

What are the 2 different ways that recombination can occur?

A
  1. homologous
  2. nonhomologous
60
Q

What is homologous recombination?

A

short segments of similar DNA sequences flanking regions of DNA that is getting transferred

61
Q

What is nonhomologous recombination?

A

mediated by many mechanisms that have 1 common fact

62
Q

What is selection?

A

ability to produce progeny and add to genetic makeup of future generations based on fitness

62
Q

What is genetic drift?

A

random processes => changes in gene frequencies

63
Q

Which type of population is genetic drift most powerful in?

A

smaller populations
- individuals survive “by chance”

64
Q

Do microbes have a short or long generation time?

65
Q

What are 2 examples of rapid evolution in bacteria?

A
  1. Rhodobacter (rapid loss of trait)
  2. E. coli (acquisition of new trait)
66
Q

How do Rhodobacter lose its trait?

A
  • produces bacteriochlorophylls and carotenoids = absorb light energy
  • lack of O2 signals production of pigment in dark
  • occasionally mutates and cant make pigments
  • no selective pressure = lost trait
67
Q

How is an adaptive trait able to be built in E. coli?

A
  • E.coli grown in CM and MM with glucose (cells adapt to MM)
  • parental strain for CM and mutated strain for MM
  • mutations accumulate over time
  • improved over 500 generations
  • after 315000 gens, evolved strains use citrate as C source
  • evolution (modification of preexisting gene)
68
Q

in the Rhodobacter case, what provides selective advantage in controlled lab conditions?

A

deleterious mutations in natural conditions

69
Q

What are the 2 classes that microbial genomes can be placed into?

A
  1. core genome
  2. pan genome
70
Q

What is a core genome?

A

genes shared by all members of a species

71
Q

What is a pan genome?

A

core genome + genes not shared between species and acquired through HGT

72
Q

How is evolution dynamic maintained?

A

through selection and genetic drift

73
Q

What is systematic?

A

study of diversity of organism and their relationships

74
Q

What is taxonomy?

A

science studying classification of organisms

75
Q

What type of analysis describes the following? => identifying morphological, metabolic, physiological, and chemical characteristics

A

phenotypic analysis

76
Q

What is genotypic analysis?

A

identifying genome characteristics

77
Q

What is phylogenetic analysis?

A

organisms in evolutionary framework using molecular sequence data

78
Q

What are species?

A

group of strains sharing high degree of similarity and share recent common ancestor for their 16S rRNA genes

79
Q

How can we tell if a group of species is the same or different?

A

DNA-DNA hybridization experiment

80
Q

How does the DNA-DNA hybridization experiment work?

A
  1. probe DNA taken from organism 1 (labelled with fluorescent/radioactive label)
  2. DNA sheared + heated = ss DNA
  3. probe added to sheared ss DNA from organ. 2
  4. mixture cooled for re annealing
  5. if less than 70% in hybridization = difference in 16S r RNA is 3% or more = 2 different species
81
Q

How many lineages of bacterial diversity were discovered?

82
Q

Bacterial diversity:
How many were described based on cultivation data (grown in lab)?

A

third = 32

83
Q

For bacterial diversity, 90% belonged to which phyla’s?

A
  1. Actinobacteria
  2. Firmicutes
  3. Proteobacteria
  4. Bacteroidetes
84
Q

Which phyla is the best illustrator of microbial diversity?

A

phyla Proteobacteria (diversity of physiological traits)

85
Q

How many major phylas are in archaeal diversity?

86
Q

How many phyla’s are described based on cultivation data?

87
Q

Which phyla’s do most species belong to in archaeal diversity?

A

Crenarchaeota and Euryarchaeota

88
Q

What do the minority of species belong to, in archaeal diversity?

A

phyla:
1. Nanoarchaeota
2. Korarchaeota
3. Thaumarchaeota

89
Q

What is the eukaryotic analog to 16 S r RNA (SSU r RNA)?

A

18 S r RNA

90
Q

How are major eukaryotic organelles derived from?

A

endosymbiosis with domain Bacteria

91
Q

For Eukaryotes, what is the mitochondrial ancestor and the chloroplasts ancestor form?

A

Proteobacteria and Cyanobacteria

BIOL 322 (3 decks)

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