Download Molecular Evolution

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Evolution of life
Molecular Evolution
Early Evolution: The Building Blocks of Life
Biogenesis - the development of life from preexisting life
Abiogenesis - emergence of life from inanimate
organic and inorganic molecules
Dr. Erica Bree Rosenblum
Life - an organismic state characterized by capacity for
organization, metabolism, growth, adaptation, reaction to
stimuli, and reproduction
Evolution of life
Evolution of life
4.5
3.6
b.y.a
b.y.a
“The duration was once considered too
short for the emergence of something
as complex as a living cell. Hence
suggestions were made that germs of
life may have come to earth from outer
space…even on a spaceship sent out by
some distant civilization”
Inorganic materials to
cellular life in a
few hundred million years!
4.5
3.6
b.y.a
b.y.a
X
Duve, Scientific American, 1995
There are now compelling explanations for how life originated
on earth within a relatively short timeframe.
today
Formation of earth
~4.6 BYA - formation of our solar system
Bombardment with interstellar debris for many million years
Heat of some impacts enough to sterilize entire planet
Take home message from first 1/2 billion years: Even if there
were very early steps in origin of life they were likely wiped out.
Probiotic chemistry
Cosmic spaces contain carbon, hydrogen, oxygen,
nitrogen, sulfur, silicon, etc.
These small molecules can interact to form stable
organic compounds. (Organic chemistry is just carbon
chemistry.)
Obviously not all organic compounds are alive.
But carbon chemistry is the basis for life on earth.
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Abiotic chemistry experiments
Probiotic chemistry experiments
Abiotic chemistry: aims to recreate in the lab the chemical
events that lead to the early building blocks of life.
Abiotic chemistry: aims to recreate in the lab the chemical
events that lead to the early building blocks of life.
1828: Friedrich Wohler synthesized urea.
1953: Miller-Urey experiment
Demonstration that organic compounds
could be synthesized from inorganic
materials without any “vital force”.
Water, methane, ammonia and hydrogen
sealed inside flasks - subject to heat and
electricity (to simulate lightning through
amtomspheric water vapor).
Probiotic chemistry experiments
Probiotic chemistry experiments
Abiotic chemistry: aims to recreate in the lab the chemical
events that lead to the early building blocks of life.
After one week, nearly 15% of carbon was in
organic compounds.
DNA and RNA were not formed but sugars,
lipids and some building blocks for nucleic
acids were formed.
2% of carbon formed amino acids!
What macromolecule came first?
Abiotic chemistry: aims to recreate in the lab the chemical
events that lead to the early building blocks of life.
There is debate over whether:
- experimental conditions were similar
enough to primitive atmospheric conditions
- experimental yields were too low to explain
prebiotic processes
But these and other more recent experiments
demonstrate the feasibility of generating
organic compounds from inorganic materials.
What macromolecule came first?
"At some point a particularly remarkable molecule was formed
by accident. We will call it the Replicator. It may not have been
the biggest or the most complex molecule around, but it had the
extraordinary property of being able to create copies of itself."
"At some point a particularly remarkable molecule was formed
by accident. We will call it the Replicator. It may not have been
the biggest or the most complex molecule around, but it had the
extraordinary property of being able to create copies of itself."
Richard Dawkins, The Selfish Gene
Richard Dawkins, The Selfish Gene
DNA
RNA
Proteins
DNA
Proteins
information
storage
DNA processing
protein production
cell structure
enzymatic activity
Needed for protein
construction
Needed for DNA
replication
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X
What macromolecule came first? Proteins?
Proteins do not self-replicate.
X
What macromolecule came first? DNA?
DNA is catalytically inert and does not
directly participate in protein synthesis
DNA
RNA
Proteins
DNA
RNA
Proteins
information
storage
DNA processing
protein production
cell structure
enzymatic activity
information
storage
DNA processing
protein production
cell structure
enzymatic activity
X
What macromolecule came first? RNA?
RNA can both STORE and PROCESS information
X
X
What macromolecule came first? RNA?
RNA solves the chicken and egg problem
DNA
RNA
Proteins
RNA
information
storage
DNA processing
protein production
cell structure
enzymatic activity
DNA processing
protein production
X
X
Experimental RNA Evolution
RNA can be selected for different catalytic activities in the
lab, including key steps toward self.
The RNA World
Have not been able to recreate all these steps
In 2006 Nobel Prize in both Chemistry and Medicine were
awarded for discoveries related to RNA
RNA “is swiftly emerging from the shadows of its betterknown cousin DNA” - Warren Leary
“RNA world”: The hypothesis that RNA predated DNAbased life and may have been the first step in the
evolution of cellular life
Term coined by Walter Gilbert in 1986:
hypothetical historical stage where:
“RNA molecules and cofactors [were] a
sufficient set of enzymes to carry out all
the chemical reactions necessary for the
first cellular structures”.
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2009 Nature
The pro-RNA World
Have not been able to recreate all these steps
2009 Science
Important distinction: “RNA Early” NOT necessarily
“RNA first”.
Take home message: There is strong evidence that RNA
came before DNA and proteins. However, there were
likely stages between the formation of the first organic
compounds and the origin of RNA.
More research needed to understand transition from
probiotic chemistry to pro-RNA world.
The pro-RNA World
The RNA World
Have not been able to recreate all these steps
Likely stages in the pro-RNA world:
-  development of pathway that turned raw organic
material into RNA
- development of RNA replication
With the origin of RNA replication, Darwinian evolution
was possible.
- inevitable replication mistakes generated variation.
-  variants which replicated faster or were more stable
had an advantage
- development of RNA-dependent protein synthesis
Take home message: A simple Darwinian process involving
variation, competition, selection, and differential survival
could explain early molecular evolution.
Evolution of molecular cooperation
Darwinian evolution continued to generate the other
macromolecules and to generate more complex enzymedependent metabolism
Evolution of molecular cooperation
RNA world implies existence of genetic code before DNA.
DNA most likely evolved from RNA.
All major macromolecules (RNA, DNA, proteins)
existed by ~ 3.5 bya
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Evolution of molecular cooperation
There is a possibility that DNA evolved from RNA
more than once!
Thymidylate synthases catalyze dTMPs (necessary for
DNA synthesis), and there are 2 unrelated thymidylate
synthases in prokaryotic lineages.
There are 2 unrelated sets of DNA replication
proteins in different prokaryotic lineages
Evolution of molecular cooperation
Nearly all extant organisms have DNA-based genomes.
Why did DNA-based (instead of RNA-based) genomes win?
-  DNA is mutationally less vulnerable than RNA.
[e.g., RNA doesn’t correct the very common
mutation from C->U]
-  This chemical advantage lead to more reliable
production of progeny genotypes.
Summary of early life
First unambiguous fossils of cellular life
Summary of early life:
By 3.2 B.Y.A. first unambiguous fossils
RNA based genomes
Origin of ribosome, proteins, genetic code
Filamentous organisms
around hydrothermal vents
Origin of DNA based genomes
Membranes before or after DNA?
Origin of cell membranes
Timing of early diversification?
Diversification of cellular life
Tree of life
Tree of life
First billion years of life
dominated by prokaryotes
First billion years of life
dominated by prokaryotes
Simple cells without membraneenclosed organelles.
Simple cells without membraneenclosed organelles.
Two prokaryotic domains evolved
independently from ancient
common ancestor:
- Bacteria
- Archaea
Two prokaryotic domains evolved
independently from ancient
common ancestor:
- Bacteria
- Archaea
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Tree of life
Tree of life
2.7 B.Y.A.
First evidence of Eukaryotes cells with membrane-enclosed
organelles and nucleus.
Phenomenal prokaryotic diversity.
Bacteria form much of earth’s biomass.
40 million bacterial cells in gram of soil.
10 times more bacterial cells than
human cells in human body!
Tree of life
Rooting the tree of life
“Three domain system”
- Bacteria
- Archaea
- Eukaryotes
For early evolution, there is
evidence for a “ring of life”
instead of a “tree of life”:
Eukaryotic genes involved in:
- information processing
(transcription and translation)
cluster with archaea
- housekeeping
(metabolism)
cluster with eubacteria
Eukaryote origin may be
Archaea-Bacteria chimera.
Ring of Life
Bacteria
Eukaryotes
Genomic re-patterning in Eukaryotes
Archea
Evolution of genome complexity
Due to a simple fusion or a more
gradual horizontal transfer?
This was a LONG time ago so
there are still debates about this.
-  Genome size expansion
-  Chromosome linearity
(from a circular ancestral genome)
- Transcript processing
- Intragenic spacers (introns)
- Mobile genetic elements
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Eukaryotic explosion
Tree of life
Land plants ~ 0.4 B.Y.A
Another billion years pass..
Flowering plants ~ 0.14 B.Y.A
By 0.55 M.Y.A
Multicellular animals appear
This is followed by the
Cambrian explosion
Mammals ~ 0.10 B.Y.A
Humans ~ 0.002 B.Y.A
Nearly ALL animal phyla
appear within about
10 million years!
A geological perspective on life on earth
4.5 bya
earth
3.6 bya
life
mammals
evolve
2.7 bya
eukaryotes
earth
forms
eukaryotes
arrive
Summary
0.02 bya
mammals
Humans have been
on earth for < 0.0001%
of its history!
life begins
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