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BIOL 322: Diversity and Evolution of Microbial Life > Week 1 Unit 1 Main concepts > Flashcards

Week 1 Unit 1 Main concepts Flashcards

1
Q

Earth was formed how long ago? Was it hospitable at this time? Why/ why not

A

4.5 billion years ago
Inhospitable
- very hot, no oxygen, and water was only available as vapor

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2
Q

When did the first cellular life appear?

A

4 billion years ago (the end of the Hadean)

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3
Q

What are the 3 theories on how the first cell arose? Just list them

A
  1. Surface origin
  2. subsurface origin
  3. RNA world
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4
Q

Describe the surface origin theory on how the first cell arose

A

spontaneous arise of membrane-enclosed structure from primordial inorganic soup

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5
Q

Describe the sub-surface origin theory on how the first cell arose

A

interaction b/w alkaline hot water beneath the ocean and cold acidic ocean water
- beneath the ocean, H2S & H2 were present as a constant energy source. @ sfc: iron present
- interactions b/w iron and sulfides lead to formation of metal precipitates
- metal precipitates catalyzed formation of amino acids & sugars = basis for formation of 1st macromolecules

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6
Q

Describe the RNA world theory on how the first cell arose

A

the first molecule that was entrapped in self-replicating systems were RNAs
- RNA catalyzed the formation of first simple peptides that coated minerals (1st semipermeable membrane)

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7
Q

Put the following events in order according to the RNA world theory.
- Synthesis of complex proteins via RNA catalysis
- Formation of amino acids, nucleotides and sugars
- RNA catalytic world and self-replicating RNA
- LUCA appeared
- DNA replaced RNA
- Divergence of LUCA to Bacteria and Archaea
- Lipid arise and entrapped proteins, RNA and DNA

A

1)Formation of amino acids, nucleotides and sugars
2) RNA catalytic world and self-replicating RNA
3) Synthesis of complex proteins via RNA 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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8
Q

Explain evidence that bacteria and archaea branched from LUCA early

A

Evidence in the structure of their lipids

  • lipids in bacteria have ester bonds
  • lipids in archaea have ether bonds
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9
Q

When did cyanobacteria develop?

A

2.8 billion years ago: the end of Archaean

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10
Q

At the beginning of the Archaean, LUCA split into ______ and _____

A

bacteria and archaea

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11
Q

The Archean ended with the big _____ event that was led by cyanobacteria

A

oxygenation

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12
Q

After LUCA split into Bacteria & Archaea, both lineages evolved specific metabolisms to fit into the existing early-earth conditions.

Explain the timeline of when each strategy developed

A
  • First, methanogenesis developed in Archaea (3.9bya)
  • Next, anoxygenic photosynthetic organisms developed (purple & green bacteria- consumed H2S): 3.2bya
  • H2-oxidizing organisms developed along with the anoxygenic photosynthetic organisms
  • cyanobacteria developed 2.8bya
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13
Q

Cyanobacteria produced ___ which reacted with ____, making it insoluble in the ___ ____ formation

A

oxygen
iron
iron band formation

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14
Q

What kind of iron is present in the iron band formation?

A

ferric (Fe3+) (insoluble)
O2 was trapped

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15
Q

What happened when all the iron was exhausted in early earth?

A

oxygen could no longer react with it, so atmospheric [O2] increased. Earth became oxic

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16
Q

At what point did evolution expand to the earth surface?

A

When an ozone layer formed (O3 UV shield). This was caused by O2 accumulation
- UV was too damaging for life outside the water up until this point

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17
Q

Oxic earth was the base for the development of the _____ cell. Approx when was this?

A

eukaryotic
2bya

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18
Q

Describe the 2 theories on how eukaryotic cells appeared

A
  1. DNA accumulation led to the formation of nucleus and the 1st eukaryotic cell has a nucleus initially. Then the nuclear containing cell ingested chloroplasts & mitochondria
  2. Early cell was archaeal & consumed O2. To ensure an energy source, the host ingested H2-producing bacteria
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19
Q

We know that eukaryotic cells is a chimera between bacterial & archaeal cell. What does this mean? Give 2 pieces of evidence

A

chimera= parts taken from multiple sources (it’s a mix of bacteria & archaea)

  • eukaryotes have types of lipids found in bacteria
  • eukaryotes have transcription and translational apparatuses more like archaea
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20
Q

Describe the theory of endosymbiosis

A

Chemoorganotrophic bacterium host ingested O2- consuming and ATP producing mitochondria
- eventually, this host (facultative aerobic organism- chemoorganotroph) ingested chloroplast where O2 was made

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21
Q

Give 4 pieces of evidence supporting the endosymbiotic theory

A
  1. both mitochondria and chloroplasts contain ribosomes that are prokaryotic type 70S and they have 16S r RNA (same as prokaryotes)
  2. same antibiotics that affect ribosomal function in bacteria inhibit ribosomal fxn in mitochondria and chloroplasts
  3. mitochondria & chloroplasts contain their own DNA arranged in covalently closed circular form which is typical for bacteria
  4. many signs of bacteria are present in eukaryotic organelles
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22
Q

** copy table on slide 9

A
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23
Q

stromatolites are evidence of early microbial life. What formed ancient stromatolites vs modern ones?

A

ancient= formed by phototrophic filamentous bacteria

modern= formed by phototrophic O2- evolving cyanobacteria

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24
Q

To determine evolutionary history, we use DNA

T/F

  1. DNA is a record of future evolutionary events
  2. DNA is used to determine phylogeny
A
  1. false: past evolutionary events
  2. true
    - phylogeny= the evolutionary history of organisms
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25
Q

What discovery helped us a lot in determining the evolution of microorganisms?

A

discovering that nucleic acids can be used to determine phylogeny!
- ribosomal RNA (r RNA) is a molecule that revolutionized the understanding of microbial evolution

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26
Q

Which molecule was used to build the first universal tree of life?

A

r RNA

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27
Q

2 different ancient scientists proposed what the universal tree of life would be. Give the names of the scientists and each of their hypotheses

A
  1. Haeckel: hypothesized that Monera is on the bottom of the phylogenetic tree & it was the ancestor of all life forms that branched to the protists, animals, and plants
  2. Whittaker: hypothesized that Monera is on the bottom & it was the ancestor of protists. Protists then branched to fungo, plants, and animals
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28
Q

Why is Carl Woese significant in evolutionary biology?

A

He discovered the domain of archaea!

Used r RNA: determined r RNA and their genes can be used to define evolutionary relationships between organisms

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29
Q

Why do we use rRNA genes to determine phylogeny? Give 4 reasons

A
  1. they’re universally distributed
  2. they’re functionally constant
  3. they’re highly conserved (slowly changing)
  4. adequate length to provide deep evolutionary relationship explanations
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30
Q

The modern tree of life is based on what genes?

A

16S r RNA

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31
Q

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

A

LUCA: Last universal common ancestor

32
Q

T/F

Horizontal gene transfer (HGT) was extensive in early history, but eventually decreased as bacteria & archaea separated from LUCA and evolved independently

A

true

33
Q

When did eukaryotes separate from archaea?

A

2.8bya
after ozone layer developed

34
Q

What do nodes indicate in a phylogenetic tree?

A

a stage of evolution where ancestors diverged into two new lineages

35
Q

What does the branch length tell us in a phylogenetic tree?

A

The number of changes that occurred over time

36
Q

T/F

The only informative positions in phylogenetic trees are nodes and branch length

A

true

37
Q

What is at the tip of the branches in a phylogenetic tree?

A

species that currently exist

38
Q

There are 2 types of phylogenetic trees: rooted and unrooted. Explain the difference

A

Unrooted= relative relationship between analyzed organisms, but no evidence of the most recent ancestor

rooted= position of ancestor for all analyzed organisms

39
Q

Explain the process of using DNA sequences in phylogenetic analysis of microbial life

A
  1. obtain gene sequences of the organisms
  2. extract genomic DNA
    - directly OR
    - amplify specific gene using PCR

PCR products are then visualized by agarose gel electrophoresis & sequenced using the same primers

40
Q

Evolution is defined as:

A

the change in frequencies of alleles in the set of organisms over time

41
Q

alleles=

A

alternative versions of a given gene

42
Q

new alleles arise due to:

A

mutation and recombination

43
Q

_______ and ________ are the largest source of genetic diversity

A

mutations and recombination

44
Q

mutations=

A

random changes in DNA sequence that accumulate over time

  • fundamental source of the natural variations that drive evolutionary processes
45
Q

Mutations can have several forms. List 4.

Are these always beneficial?

A
  • substitution
  • insertion
  • deletions
  • duplications

No, they can be beneficial, detrimental, or neutral

46
Q

recombination=

A

a process by which DNA segments are broken and rejoined to create new combination of genetic material

Can be homologous or nonhomologous

47
Q

Homologous recombination=

A

this process required short segments of highly similar DNA sequences that flank regions of DNA that are getting transferred

48
Q

Nonhomologous recombination=

A

this process is mediated by several mechanisms that have one fact common

49
Q

Mutations and recombination cause variations in ____ sequence. This means new ___ are created

A

gene
alleles

50
Q

selection=

A

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

51
Q

genetic drift=

A

random process that can cause changes in gene frequencies
- stronger in small pops- individuals survive simply by chance

52
Q

Evolutionary changes in microorganisms are caused by what 2 things?

A

either changes in the environment or by introduction of new cells into the enviro

53
Q

T/F
microbes have a long generation time, so it’s hard to observe evolutionary changes in the lab

A

false

microbes have a short generation time

54
Q

New traits can evolve quickly in microorganisms. Explain how this happened in Rhodobacter

A

Rhodobacter produce bacteriochlorohylls & carotenoids that absorb light energy- in the dark these are useless
- the signal that stimulates the production of pigment in the dark is the lack of oxygen
- sometimes Rhodobacter mutates and loses the ability to make pigments

Even though photosynthesis is beneficial, the trait is lost due to mutation when there’s no selective pressure

Deleterious mutation in natural conditions provides a selective advantage in controlled lab conditions

55
Q

New traits can evolve quickly in microorganisms. Explain how this happened in E. coli

A

E. coli was grown on a minimal media with glucose (parental strain= rich media)

Mutations accumulated over time: fitness increased for mutated strain that grew in glucose. After many generations, they evolved the ability to use citrate as a C source

The accumulation of random mutations modified existing genes, & allowed genetic diversity + evolution of new adaptive trait

56
Q

The microbial genome can be places in two classes:

A
  1. the core genome: genes shared by all members of a species
  2. The pan genome: core genome plus genes not shared b/w species (usually acquired through HGT)
57
Q

Systematics=

A

the study of the diversity of the organism and their relationships

58
Q

What is the science that studies classification of organisms?

A

taxonomy

59
Q

T/F

Systematics links taxonomy and phylogeny

A

true

classification & evolutionary history of the organisms

60
Q

Name the 3 methods used for identification of bacteria & description of new species

A
  1. phenotypic analysis
  2. genotypic analysis
  3. phylogenetic analysis
61
Q

phenotypic analysis=

A

ID of morphological, metabolic, physiological & chemical characteristics to ID bacteria & describe new species

62
Q

Genotypic analysis=

A

ID of genome characteristics to ID bacteria & describe new species

63
Q

Phylogenetic analysis=

A

placing the organisms in evolutionary framework using molecular sequence data to ID bacteria & describe new species

64
Q

What are the fundamental units of biological diversity?

A

species

65
Q

Species=

A

a group of strains that share a high degree of similarity in many traits & share a recent common ancestor for their 16S rRNA genes

66
Q

What kind of experiment can we do to determine if 2 organisms are the same or different species?

A

DNA-DNA Hybridization experiment

67
Q

Explain the process of a DNA-DNA Hybridization experiment and what it accomplishes

A

purpose: the degree of DNA-DNA hybridization b/w the genomes of two organisms= measure of their genomic similarity
Steps:
1. probe DNA is obtained from organism 1 & labelled w/ fluorescent/ radioactive label
2. This is sheared into small pieces & heated to generate ss DNA
3. this is added to sheared ss DNA from organism 2
4. mixture of DNAs is mixed and cooled (allows re-annealing)

If the value of hybridization is less than 70%, & 16S rRNA is 3% or more different, then they are two different species

68
Q

how many bacterial lineages are discovered?

A

84

69
Q

The best illustrator of microbial diversity is which phyla of bacteria?

A

proteobacteria

shows lots of diversity of physiological traits

70
Q

There are __ major phyla in Archaea. How many of them were described based on cultivation data (growing in the lab)

A

7
5

71
Q

Most Archaeal species belong to which 2 phylums?

A

Crenarchaeota & Euryarchaeota

72
Q

What is the Eukaryotic analog to 16S rRNA?

A

18S rRNA

73
Q

Major eukaryotic organelles are derived from what?

A

endosymbiosis with domain bacteria

74
Q

The mitochondrial ancestor of Eukaryotes is ____ and chloroplasts are from ____

A

proteobacteria

cyanobacteria

75
Q
A

BIOL 322: Diversity and Evolution of Microbial Life (16 decks)

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