Chapter 17: The Origins of Life and Precambrian Evolution
Primordial form (IDA) initial
Darwinian ancestor; first living things
Cenancestor (LUCA) among IDAs last
descendants; last universal common
ancestor of all extant organisms
What was the first living thing?
Ribozymes RNA enzymes
Which came first proteins or DNA?
Answer RNA
The RNA World Hypothesis proposes
that catalytic RNA molecules were a
transitional form between nonliving
matter and the earliest cell
RNA can possess a genotype
and a phenotype
One way to define life: If it forms
populations capable of evolving by
natural selection, then it is alive
The Case for RNA as an Early life-
form
DNA can better withstand high
temperatures and acid/base
degradation
RNA is ancient
(1) involved in early life forms
(2) basic currency for biological
energy: ribonucleoside
triphosphate
One way researchers have tested
the RNA World Hypothesis is to
check whether populations of RNA
molecules can evolve by natural
selection
Populations of catalytic RNA
molecules exhibit variation in
nucleotide sequence. This variation
is heritable when RNA is replicated.
And researchers have devised
experimental conditions which
sequence variation results in
differences in survival
Population will evolve if it exhibits
(1) variation having genotype
(2) inheritance having genotype
(3) excess reproduction self
replicating
(4) variation in survival or
reproductive success having a
phenotype that makes a
difference
Although populations of catalytic
RNa molecules have most of the
properties required for evolution by
natural selection, they cannot
evolve on their own without
considerable help from human
researchers. This is because
catalytic RNA molecules cannot yet
copy themselves
Researchers are performing
selective breeding experiments
with populations of catalytic RNAs
in an effort to develop catalytic
RNAs that can replicate
themselves. If the researchers
succeed, then by the definition we
proposed earlier, they will have
created life.
The proposition that catalytic RNAs
were a transitional form between
nonliving matter and cellular life
leaves many gaps. We must still
explain where the first RNA
molecules came from, and how a
population of self-replicating RNA
molecules evolved into DNA- and
protein-based cells.
Properties of Self-replication
Four issues:
1. Information-containing biomolecules
need to be made from simple
inorganic compounds.
Where did these compounds come
from?
2. The chemical reactions that
construct larger molecules from simple
inorganics must be favorable and have
a source of energy. What were these
reactions? (Simple inorganics to larger
molecules)
3. The building blocks must be able to
self-assemble into polymers such as
RNA and polypeptides.
How did this happen?
4. Larger biomolecules must be
protected from harsh environmental
conditions.
How was this accomplished?
Panspermia hypothesis suggests that
life may have arisen elsewhere and
traveled to Earth through space
Murchison meterorites biomolecules
of life all require carbon, hydrogen,
oxygen, nitrogen, sulfur, phosphorous
in large amounts plus trace quantities
of Mg, Ca, K
The simple organic molecules from
which life was built may have formed
in space and then fallen in Earth.
Researchers have tested this idea by
looking for amino acids and other
organic molecules inside meteorites.
One note: Crashing of meteorites and
comets generated heat that can
destroy these organic molecules
Early atmosphere may have dense
carbon dioxide soft landing
some organics survive
Oparin-Haldane Model
Stanford Miller in Harold Ureys
laboratory
1. Apparatus boiled water and
circulate hot vapor through
atmosphere of methane,
ammonia, hydrogen and electric
spark the through a cooling
flask that condensed the vapor
and directed it back to boiling
flask
2. Let it stay for one week water
turned red and cloudy
3. Paper chromatography to
identify cause of red color
mixture of organic molecules
amino acids glycine, alpha-
alanine and beta-alanine
Millers atmosphere ammonia,
hydrogen and methane
Implication of results lightning or UV
radiation played role then young
Earths ocean would be quickly rich in
biological building blocks
Aldehydes necessary in construction
of ribose sugars
Synopsis of Oparin-Haldane Model
1. formation of building blocks
from existing inorganics
2. polymerization of these building
blocks to macromolecules
3. Add membranes and energy
source living organism
Darwins warm little pond or prebiotic
soup aqueous environment
brimming with biological building
blocks
From simple inorganics to building
blocks of life (first step to Oparin-
Haldane model)
Rock of faith: Ammonia and hydrogen
cyanide (HCN) + heat Nitrogenous
base adenine (purine)
Problems
1. Sugar formation ( challenging to
understand how building blocks
became activated in RNA world)
Solution: Make sugar and base
in separate solutions to make
activated nucleotides
Add phosphate form different
intermediate products
activated pyrimidine nucleotide
(final product)
2. Origin of chirality or
handedness
living systems today use only one
stereoisomer
living systems before create both
mirror images in same quantities
Assembly of Biological polymers
(Second step)
The building blocks of life may have
been assembled into polymers on the
surface of clay crystals
(montmorillonite). Adhering to clay
helps a growing polymer avoid being
broken apart by hydrolysis
Protecting life from the environment
Challenges: (1) plate tectonics and
volcanic eruptions (2) large meteor
crashing on earth
What was the Last Common Ancestor
of all Extant Organisms and What is
the Shape of the Tree of Life?
(1) Fossil records
(2) The phylogeny of all living
things
Another way to learn about the
earliest cell is to estimate the
phylogeny of all living things, then
infer the characteristics of the
common ancestors
Three domains: Bacteria, Archaea,
Eukarya
Two fundamental branches of Archaea:
Crenarchaeota and Euryarchaeota
3 kingdoms in traditional classification:
Animals, Plants, Fungi
The Archaea and Eukarya are most
closely related to each then Bacteria
LUCA had DNA dependent RNA
polymerase DNA DNA
polymerase
- like a modern bacterium
Horizontal gene transfer explain the
discordance among whole life
phylogenies estimated from different
genes
Oldest known fossil of eukaryotes:
Grypania spiralis alga

How did LUCAs descendants
evolve into todays organisms?
The Universal Gene-Exchange Pool
Hypothesis
Major Points:
Lateral gene transfer rampant
and overshadowed vertical
inheritance
This model is not conducive to:
A non-Darwinian mechanism of
communal evolution
Proteins gradually became more
interdependent so that the
modularity (i.e., independent
functioning) of genomes became
more integrated and stable
Organismal self-replication became
more prominent, this is the point at
which populations have reached
the Darwinian threshold and began
to evolve via natural selection
Three stable lineages emerged
independently (i.e., crossed the
Darwinian threshold)
The Ring-of-Life Hypothesis
In general, eukaryotic genes involved
in storage and use of genetic
information tend to be more similar to
archaean genes
Eukaryotic genes involved in
metabolic processes tend to be more
similar to bacterial genes
Eukarya arose from the fusion of a
bacterium with an archaean
- Informational genes from
archaean and metabolic rates
from bacterium
Criticisms:
Bacterial and archaeal genes
present in eukaryotic genome
arose at different times from
different lineages
Provides no explanation as to
where hundreds of Eukarya
proteins came from
Archaea and bacteria lack
cytoskeleton that enables
phagocytosis (difficult to see how
they fuse)
The Chronocyte Hypothesis
Offers solution to phagocytosis
problem
Chronocyte
deepest fork of bacteria and
archaea that will become
eukarya
evolved cytoskeleton and
phagocytosis (eat other
microbes)
Chronocyte ate an archaean
that resisted digestion and
became an endosymbiont
evolved to organelle: nucleus
Criticism: A beast that has a
cytoskeleton and feeds on other cells
with no nucleus and mitochondria has
not been found yet
The Three Viruses, Three Domains
Hypothesis
Missing from the Bacteria and
Archaea is RNA-dependent RNA
polymerase replicate iRNA
Virus: remnants of earliest eras of
life on Earth including RNA world
and Early DNA world
Switch from RNA to DNA first
happened in viruses that made
their living parasitizing cells with
RNA-based genomes
o DNA is chemically more
stable
o DNA can repair mutations
converting cytosine to uracil
but not in RNA
Race with RNA-based host: cells
parasitized by virus evolve
defenses (enzymes to recognize
viral genomes) virus evolve with
counter defenses (prevent hosts
enzymes to recognize viral
genome)
Viruses infecting RNA-based cells first
evolved DNA as a defensive counter-
measure
DNA was then transferred to
cellular life when DNA-based
viruses became endosymbionts
The three domains first diverged
while still carrying their genetic
information in RNA
Each ancestor was converted to
DNA by a separate virus
This explains why the machinery
used by bacteria for DNA
replication appears to be unrelated
to the machinery used by
archaeans and eukaryotes and that
these three lineages outcompeted
and eliminated all other lineages of
RNA-based cells
Criticisms:
 No known cellular organisms with
RNA genomes
Must test this hypothesis using
only inferred gene phylogeny
estimates
Among the five kingdoms of the life,
there are three domains Archaea,
Bacteria, Eukarya. The first phylogeny
suggests that Archaea and Eukarya
are the closest relatives