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Bio 322 > Unit 1 > Flashcards

Unit 1 Flashcards

1
Q

when was earth formed?

A

4.5 BYA

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2
Q

why was earth inhospitable?

A

hot
no oxygen
water only as vapur

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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 is the surface origin theory?

A

spontaneous arise of membrane-enclosed strucutre from primordial organic-inorganic soup

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5
Q

what is the subsurface origin theory?

A

interaction between alkaline hot water beneath ocean and cold acidic water

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6
Q

what was the energy supply beneath the ocean?

A

H2S and H2

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7
Q

what was the energy supply on the surface?

A

iron

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8
Q

how did metal precipitates form?

A

interaction between sulfides and iron

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9
Q

how did the first macromolecules form?

A

metal precipitates catalyzed formation of amino acids. sugars and bases

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10
Q

what is the RNA world theory?

A

first molecule entrapped in self-replicating system were RNAs

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11
Q

how was the first semipermeable membrane formed?

A

RNA catalyzed formation of first simple peptides that coated mineral

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12
Q

what is the order of events according to RNA world theory?

A
  1. formation of amino acids, nucleotides and sugars
  2. RNA catalytic world and self-replicating RNA
  3. synthesis of complex proteins via catalysis
  4. DNA replaced RNA
  5. lipid arise and entrapped proteins, RNA and DNA
  6. LUCA appeared
  7. divergence of LUCA to Bacteria and Archaea
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13
Q

what evidence was there than B and A branched from LUCA?

A

structure of lipids in B have ester bond and ether bond in A

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14
Q

how was the first self-replicating organism formed?

A

after lipoprotein structure entrapped DNA and RNA

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15
Q

when did first methanogenesis develop?

A

Archaea
3.9 BYA

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16
Q

what developed after methanogenesis?

A

anoxygenic photosynthesis

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17
Q

who did anoxygenic photosynthesis?

A

purple and green bacteria
consumed H2S

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18
Q

what developed with anoxygenic bacteria?

A

H2 oxidizing organisms

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19
Q

who developed after anoxygenic photosynthesis?

A

cyanobacteria at the end of Archaean

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20
Q

what did Archaean end with?

A

big oxygenation event led by cyanobacteria

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21
Q

who developed in Proterozoic?

A

first eukaryote

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22
Q

who developed in phanerozoic?

A

multicellular eukaryote and early animals

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23
Q

how was banded iron formed?

A

oxygen and available iron

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24
Q

what kind of iron is in banded iron formations?

A

ferric

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25
Q

how did earth become oxic?

A

when all iron exhausted then o2 increased

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26
Q

what did o2 accumulation lead to?

A

formation of UV shield zone and evolution expanded

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27
Q

how did eukaryotic cell appear?

A

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

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28
Q

what commonality does eukaryotes and bacteria have?

A

types of lipids

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29
Q

what commonality does eukaryotes and archaea have?

A

transcription and translation

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30
Q

endosymbiosis

A

chemoorganotrophic bacterium host ingested O2-consuming and ATP producing bacteria
- facultative aerobic organism ingested chloroplast where O2 was made

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31
Q

what did early autotrophy discover?

A

Aquifex: hyperthermophile bacteria

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32
Q

what was the first cell?

A

anaerobic and autotrophic
obtained CO2 and electrons to reduce CO2 and get H2

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33
Q

what is phototrophy?

A

evolved in B
used solar radiation

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34
Q

what is the common ancestor for all bacteria?

A

chloroflexus (anaerobic phototrophs) except Aquifex and Thermotoga

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35
Q

what are the 4 evidences to support endosymbiosis?

A
  1. both mito and chloroplasts contain ribosomes that are prokaryotic 70S and have 16S r RNA same as prokaryotes
  2. same antibiotics that affect ribosomal function in Bacteria inhibit ribosomal function in mito and chloroplasts
  3. mito and chloroplasts have own DNA arranged in covalently closed circular form like B
  4. many signs of B are in eukaryotic organelles
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36
Q

what is the earliest evidence of microbial life?

A

stromatolites

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37
Q

how were ancient stromatolites formed?

A

phototropic filamentous bacteria

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38
Q

how were modern stromatolites formed?

A

phototrophic O2-evolving cyanobacteria

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39
Q

how do we use DNA to determine evolutionary history?

A
  1. DNA record of past evolutionary events
  2. determine phylogeny
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40
Q

what is phylogeny?

A

evolutionary history of organisms

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41
Q

what are eukaryotic cells made of?

A

B and A cells
- chimera

42
Q

what helped develop the evolution of microorganisms?

A

nucleic acids used to determine phylogeny

43
Q

what molecule revolutionized understanding of microbial evolution?

A

r RNA

44
Q

what did rRNA help to build?

A

first universal tree of life

45
Q

what did Haeckel do?

A

Monera bottom of tree
- ancestor of all life forms that branched to protists. plants and animals

46
Q

what did Whittaker do?

A

Monera bottom of tree and ancestor of protists
- Protists branched to Fungi, Plants and Animals

47
Q

what did Woese do?

A

r RNA and genes used to define evolutionary relationships between organisms

48
Q

why use rRNA for phylogeny?

A
  • universally distributed
  • functionally constant
  • highly conserved
  • adequate length to provide deep evolutionary relationships explanations
49
Q

what is the modern tree of life based on?

A

16S rRNA genes

50
Q

what does the modern tree of life show?

A
  • 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)
51
Q

what do phylogenetic trees contain?

A

nodes and branches

52
Q

nodes

A

stage of evolution where ancestors diverged in 2 new lineages

53
Q

branch length

A

number of changes occurring over time

54
Q

tips of branches

A

species existing

55
Q

types of trees?

A

rooted and unrooted

56
Q

rooted trees

A

position of ancestor for all analyzed organisms

57
Q

unrooted trees

A

relative relationships between analyzed organisms. no evidence of most recent ancestor

58
Q

how to use DNA sequences in phylogenetic analysis of microbial life?

A

extract DNA directly or amplify specific gene using PCR

59
Q

what happens to PCR products?

A
  • visualized by agarose gel electrophoresis
  • extracted from gel and sequences using same primers
60
Q

how is evolution defined?

A

change in frequencies of alleles in set of organisms over time

61
Q

alleles

A

alternative versions of given gene

62
Q

how do new alleles arise?

A

mutation and recombination

63
Q

what are the largest sources of genetic diversity?

A

mutation
recombination
- new alleles created

64
Q

mutations

A
  • 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
65
Q

recombination

A

DNA segments broken and rejoined to create new combo of genetic material

66
Q

homologous recombination

A

requires short segments of highly similar DNA sequences that flank regions of DNA transferred

67
Q

nonhomologous recombination

A

mediated by several mechanisms that have one fact common

68
Q

mechanisms of evolution

A

selection
genetic drift

69
Q

selection

A

ability of organism to produce progeny and contribute to genetic makeup of future generation based on fitness

70
Q

genetic drift

A

random process that cause changes in gene frequencies
(stronger in smaller pop- survive by chance)

71
Q

what do evolutionary changes in microorganisms caused by?

A

change in enviro or introductions of new cells

72
Q

2 examples of rapid evolution in bacteria?

A

Rhodobacter- rapid loss of trait
E. coli- gain of new trait

73
Q

orthologs

A

originate from single ancestral gene in common ancestor

74
Q

paralogs

A

result of gene duplication

75
Q

convergent evolution

A

homoplasy
- type of evolution when organisms share trait not inherited from common ancestor

76
Q

do we assume genes are inherited vertically when using gene sequence to conclude about phylogeny?

A

YES

77
Q

bottleneck events

A

severe reduction in size followed by overgrowth of cells
- important for evolution of pathogens

78
Q

Rhodobacter

A
  • 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
79
Q

E. coli

A
  • 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
80
Q

core genome

A

genes shared by all members of species

81
Q

pan genome

A

core genome plus genes not shared between species and usually acquired through HGT

82
Q

systematic

A

study in diversity of organism and relationship

83
Q

taxonomy

A

science that studies classification of organisms

84
Q

what does systematic link?

A

taxonomy and phylogeny
- classification and evolutionary history of organisms

85
Q

phenotypic analysis

A

identification of morphological, metabolic, physiological and chemical characteristics

86
Q

genotypic analysis

A

identification of genome characteristics

87
Q

phylogenetic analysis

A

placing organisms in evolutionary framework using molecular sequence data

88
Q

what are the fundamental units of bio diverstiy?

A

species

89
Q

species

A

groups of strains that share high degree of similarity in many traits and share recent common ancestor for their 16S rRNA genes

90
Q

DNA-DNA hybridization experiment

A
  • 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
91
Q

how do you know there are 2 different species?

A

value of less than 70% hybridization and difference in 16S rRNA is 3% or more

92
Q

what are the 4 phylas where 90% of bacteria belong?

A
  1. Actinobacteria
  2. Firmicutes
  3. Proteobacteria
  4. Bacteroidetes
93
Q

what is the best illustrator of microbial diversity?

A

phyla Proteobacteria
- diversity of physiological traits

94
Q

how many major phyla in Archeal

A

7

95
Q

how many Archaeal phyla based on lab?

A

5

96
Q

what 2 phyla do most Archaeal species belong to?

A
  • Crenarchaeota
  • Euyarchaeota
97
Q

which 3 phyla do minority of Archaeal species belong to?

A
  • Nanoarchaeota
  • Korarchaeota
  • Thaumarachaeota
98
Q

what is the eukaryotic analog to SSU r RNA?

A

18 S r RNA

99
Q

how are major eukaryotic organelles derived?

A

endosymbiosis with Bacteria

100
Q

where is the mitochondrial ancestor from?

A

Proteobacteria

101
Q

where is chloroplasts ancestor from?

A

cyanobacteria

Bio 322 (11 decks)

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