Week 1 Unit 1 Main concepts Flashcards
Earth was formed how long ago? Was it hospitable at this time? Why/ why not
4.5 billion years ago
Inhospitable
- very hot, no oxygen, and water was only available as vapor
When did the first cellular life appear?
4 billion years ago (the end of the Hadean)
What are the 3 theories on how the first cell arose? Just list them
- Surface origin
- subsurface origin
- RNA world
Describe the surface origin theory on how the first cell arose
spontaneous arise of membrane-enclosed structure from primordial inorganic soup
Describe the sub-surface origin theory on how the first cell arose
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
Describe the RNA world theory on how the first cell arose
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)
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
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
Explain evidence that bacteria and archaea branched from LUCA early
Evidence in the structure of their lipids
- lipids in bacteria have ester bonds
- lipids in archaea have ether bonds
When did cyanobacteria develop?
2.8 billion years ago: the end of Archaean
At the beginning of the Archaean, LUCA split into ______ and _____
bacteria and archaea
The Archean ended with the big _____ event that was led by cyanobacteria
oxygenation
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
- 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
Cyanobacteria produced ___ which reacted with ____, making it insoluble in the ___ ____ formation
oxygen
iron
iron band formation
What kind of iron is present in the iron band formation?
ferric (Fe3+) (insoluble)
O2 was trapped
What happened when all the iron was exhausted in early earth?
oxygen could no longer react with it, so atmospheric [O2] increased. Earth became oxic
At what point did evolution expand to the earth surface?
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
Oxic earth was the base for the development of the _____ cell. Approx when was this?
eukaryotic
2bya
Describe the 2 theories on how eukaryotic cells appeared
- 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
- Early cell was archaeal & consumed O2. To ensure an energy source, the host ingested H2-producing bacteria
We know that eukaryotic cells is a chimera between bacterial & archaeal cell. What does this mean? Give 2 pieces of evidence
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
Describe the theory of endosymbiosis
Chemoorganotrophic bacterium host ingested O2- consuming and ATP producing mitochondria
- eventually, this host (facultative aerobic organism- chemoorganotroph) ingested chloroplast where O2 was made
Give 4 pieces of evidence supporting the endosymbiotic theory
- both mitochondria and chloroplasts contain ribosomes that are prokaryotic type 70S and they have 16S r RNA (same as prokaryotes)
- same antibiotics that affect ribosomal function in bacteria inhibit ribosomal fxn in mitochondria and chloroplasts
- mitochondria & chloroplasts contain their own DNA arranged in covalently closed circular form which is typical for bacteria
- many signs of bacteria are present in eukaryotic organelles
** copy table on slide 9
stromatolites are evidence of early microbial life. What formed ancient stromatolites vs modern ones?
ancient= formed by phototrophic filamentous bacteria
modern= formed by phototrophic O2- evolving cyanobacteria
To determine evolutionary history, we use DNA
T/F
- DNA is a record of future evolutionary events
- DNA is used to determine phylogeny
- false: past evolutionary events
- true
- phylogeny= the evolutionary history of organisms
What discovery helped us a lot in determining the evolution of microorganisms?
discovering that nucleic acids can be used to determine phylogeny!
- ribosomal RNA (r RNA) is a molecule that revolutionized the understanding of microbial evolution
Which molecule was used to build the first universal tree of life?
r RNA
2 different ancient scientists proposed what the universal tree of life would be. Give the names of the scientists and each of their hypotheses
- 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
- Whittaker: hypothesized that Monera is on the bottom & it was the ancestor of protists. Protists then branched to fungo, plants, and animals
Why is Carl Woese significant in evolutionary biology?
He discovered the domain of archaea!
Used r RNA: determined r RNA and their genes can be used to define evolutionary relationships between organisms
Why do we use rRNA genes to determine phylogeny? Give 4 reasons
- they’re universally distributed
- they’re functionally constant
- they’re highly conserved (slowly changing)
- adequate length to provide deep evolutionary relationship explanations
The modern tree of life is based on what genes?
16S r RNA
What is at the bottom of our modern tree of life?
LUCA: Last universal common ancestor
T/F
Horizontal gene transfer (HGT) was extensive in early history, but eventually decreased as bacteria & archaea separated from LUCA and evolved independently
true
When did eukaryotes separate from archaea?
2.8bya
after ozone layer developed
What do nodes indicate in a phylogenetic tree?
a stage of evolution where ancestors diverged into two new lineages
What does the branch length tell us in a phylogenetic tree?
The number of changes that occurred over time
T/F
The only informative positions in phylogenetic trees are nodes and branch length
true
What is at the tip of the branches in a phylogenetic tree?
species that currently exist
There are 2 types of phylogenetic trees: rooted and unrooted. Explain the difference
Unrooted= relative relationship between analyzed organisms, but no evidence of the most recent ancestor
rooted= position of ancestor for all analyzed organisms
Explain the process of using DNA sequences in phylogenetic analysis of microbial life
- obtain gene sequences of the organisms
- extract genomic DNA
- directly OR
- amplify specific gene using PCR
PCR products are then visualized by agarose gel electrophoresis & sequenced using the same primers
Evolution is defined as:
the change in frequencies of alleles in the set of organisms over time
alleles=
alternative versions of a given gene
new alleles arise due to:
mutation and recombination
_______ and ________ are the largest source of genetic diversity
mutations and recombination
mutations=
random changes in DNA sequence that accumulate over time
- fundamental source of the natural variations that drive evolutionary processes
Mutations can have several forms. List 4.
Are these always beneficial?
- substitution
- insertion
- deletions
- duplications
No, they can be beneficial, detrimental, or neutral
recombination=
a process by which DNA segments are broken and rejoined to create new combination of genetic material
Can be homologous or nonhomologous
Homologous recombination=
this process required short segments of highly similar DNA sequences that flank regions of DNA that are getting transferred
Nonhomologous recombination=
this process is mediated by several mechanisms that have one fact common
Mutations and recombination cause variations in ____ sequence. This means new ___ are created
gene
alleles
selection=
the ability of an organism to produce progeny and contribute to the genetic makeup of the future generation based on fitness
genetic drift=
random process that can cause changes in gene frequencies
- stronger in small pops- individuals survive simply by chance
Evolutionary changes in microorganisms are caused by what 2 things?
either changes in the environment or by introduction of new cells into the enviro
T/F
microbes have a long generation time, so it’s hard to observe evolutionary changes in the lab
false
microbes have a short generation time
New traits can evolve quickly in microorganisms. Explain how this happened in Rhodobacter
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
New traits can evolve quickly in microorganisms. Explain how this happened in E. coli
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
The microbial genome can be places in two classes:
- the core genome: genes shared by all members of a species
- The pan genome: core genome plus genes not shared b/w species (usually acquired through HGT)
Systematics=
the study of the diversity of the organism and their relationships
What is the science that studies classification of organisms?
taxonomy
T/F
Systematics links taxonomy and phylogeny
true
classification & evolutionary history of the organisms
Name the 3 methods used for identification of bacteria & description of new species
- phenotypic analysis
- genotypic analysis
- phylogenetic analysis
phenotypic analysis=
ID of morphological, metabolic, physiological & chemical characteristics to ID bacteria & describe new species
Genotypic analysis=
ID of genome characteristics to ID bacteria & describe new species
Phylogenetic analysis=
placing the organisms in evolutionary framework using molecular sequence data to ID bacteria & describe new species
What are the fundamental units of biological diversity?
species
Species=
a group of strains that share a high degree of similarity in many traits & share a recent common ancestor for their 16S rRNA genes
What kind of experiment can we do to determine if 2 organisms are the same or different species?
DNA-DNA Hybridization experiment
Explain the process of a DNA-DNA Hybridization experiment and what it accomplishes
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
how many bacterial lineages are discovered?
84
The best illustrator of microbial diversity is which phyla of bacteria?
proteobacteria
shows lots of diversity of physiological traits
There are __ major phyla in Archaea. How many of them were described based on cultivation data (growing in the lab)
7
5
Most Archaeal species belong to which 2 phylums?
Crenarchaeota & Euryarchaeota
What is the Eukaryotic analog to 16S rRNA?
18S rRNA
Major eukaryotic organelles are derived from what?
endosymbiosis with domain bacteria
The mitochondrial ancestor of Eukaryotes is ____ and chloroplasts are from ____
proteobacteria
cyanobacteria
