Transcript The Origins of Life

Chapter 16
The Origin of Life and
Precambrian Evolution
3 Main Questions are being
pursued about the origin of the
Earth
1. What was the first living or primordial form?
2. Where did it come from?
3. What was the last common ancestor
(cenancestor) of today's organisms and
when did it live?
What was the first living
thing?
What was the first living thing?
• The origin of life has been under
investigation (observational studies as well
as experimentation) for almost 80 years.
• The main problem lies in the question
“which did life acquire first, proteins or
nucleic acid?”
What was first , RNA, DNA or
Protein?
• PROTEIN – can do complicated biological tasks
but cannot propagate themselves
• DNA – can propagate but cannot do any kind of
biological work.
Ribozymes
• Ribozymes discovered in 1982 by Sidney Altman
and Thomas Cech
• Enzymes that could break and reform bonds that
link nucleic acids into chains
– Enzymes were not made of protein, but nucleic acid
(RNA)
• Dozens of naturally occurring ribozymes have
now been discovered.
Structure of Rybozymes
• 30 to 1000 ribonucleotides long
• Single stranded
• Molecule folds back on itself many times to form
a three dimensional structure.
• This structure provides and active site that
enables it to have catalytic activity.
An RNA World?
• RNA used to be thought of as DNA’s poor
cousin.
• With the discovery of Rybozymes many
researches envision a time when life was based
entirely on RNA – An RNA world.
• RNA shows all of the following characteristics:
– Catalytic ( biological work)
– Information storage
– Information transmission
An RNA World ?
• RNA simultaneously possesses a
– Genotype – its primary sequence
– Phenotype – its biological reactivity . ( by
virtue of its ability to fold back on itself and
form an active site.)
Does RNA represent the first
molecules of life?
• Supportive evidence
– RNA is an ancient molecule
– Found in the most highly conserved
information processing machinery – the
ribosome.
– It is the RNA in ribosomes that catalyze the
formation of peptide bonds in translation.
– Ribonucleoside triphosphates are the major
component of energy molecules in cells –
ATP, NAD, FAD
Defining Life
• One of the defining characteristics of life is
the ability to evolve
– Descent with modification requires
• the ability to record and make alterations in
heritable information (genotype).
• The ability to distinguish valuable changes from
detrimental ones (variation in phenotype).
Shown to evolve in test tube
experiments
• Populations of catalytic RNA exhibit
variation in nucleotide sequence.
• This variation is heritable
• Researchers have devised experiments in
which sequence variation results in
differences in survival
• Exmple: Qb bacteriophage with replicase
One important problem remains
with RNA as first molecule of life
• RNA cannot copy itself without the
help of proteins.
– Some research is being done to find RNA
Ribozymes capable of synthesizing RNA.
Some success so far.
– RNA autoreplicase remains a Holy Grail for
origins of life research.
The question still remains
• Where did the first RNAs
come from?
What was the early atmosphere
like?
• Quite a debate
• Was it oxidizing, made up of mostly O2 and CO2
or
• Reducing made of H2 , CH4 and NH3
• Or maybe intermediate. …or…..
• Maybe the earliest organic molecules came
from outer space via meteorites.
– Murchison meteorite provide direct evidence that
some organic molecules have survived the trip to
earth from outer space (dozens of amino acids.)
Miller and Urey 1953
• Miller and Urey used
a highly reducing
atmosphere and
electric sparks to
produce a mixture of
organic molecules
(including some
amino acids) in just
one week.
But ancient atmosphere now
believed to be more oxidizing
• We now believe that the atmosphere was
not so reducing being mostly CO2 instead
of methane.
• A CO2 dominating atmosphere has been
shown to be able to produce aldehydes
(needed to make ribose) from carbon
dioxide
The Oparin-Haldane Model
A null model to be used to test hypotheses
for the formation of the first molecules of life.
1. Simple building block molecules such as
Cyanide, methane, carbon dioxide, ammonia
need to be assembled into organic molecules
such as amino acids and nucleotides.
2. Organic molecules need to be
assembled into biological polymers
3. A combination of biological polymers is
assembled into a self-replicating organism
that feeds off of existing organic molecules
How do we get from
inorganics to the building
blocks of life?
• Juan Oro and others have showed
adenine could be made form ammonia
and cyanide.
• Pyrimidines harder to synthesize
• Ribose sugars can be made from
formaldehyde
• Problem is in the handedness that
biological systems use is not faithfully
produced by these reactions
• Lots of questions remain
Next problem is the assembly of
biological molecules into polymers
• James Ferris – showed that polymers could be
formed from nucleotides and amino acids in a
prebiotic soup.
• Used a clay material on which the polymers
were allowed to form.
– Otherwise, hydrolysis in water would immediately
destroy polymers as they were formed.
• Clay also acts as a catalyst to join subunits
together
Early on the earth was not conducive to
formation of stable organic molecules or
“life”
 The extreme heat of the earth along with
regular meteor impacts prevented life from
forming earlier than about 4.4 to 3.8 bya
 The hot earth, volcanic activity, plate
tectonics, and erosion have destroyed
most evidence of the earliest life.
• The first evidence that life existed dates
back to 3.85 billion years ago. Evidence
that life arose shortly after the
environment allowed
Formation of Cellular Life
• Finding the Most Recent common
Ancestor of all living things – the
cenancestor
• Use principle of parsimony (the
simplest explanation with the fewest
steps that can explain all of the
evidence)
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Shared features of all living
things
DNA – heritable info
Proteins- how DNA is expressed
Same 20 amino acids
Use the same genetic code
Cell is basic unit of life
– Needed for compartmentalization so
chemicals can be concentrated in the cell
– Needed to link a genotype to a phenotype so
traits can be passed on
Long way from self-replicating
RNA to cells
• Sidney Fox found that mixtures of
polyamino acids in water or salt
solutions spontaneously form
microspheres
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The geological record
provides signs of when life formed
• Oldest fossils come from Apex chert in Western
Australia
• Simple cells growing in short filaments
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believed to be cyanobacteria
• Probably already fairly high up on the evolutionary
tree
Due to incomplete fossil record, no way to know if these
are ancestors of all living things or if they died out
Need other methods to determine ancestral cell lineages
Searching for a universal
phylogeny
• First tried to construct a phylogeny
based on morphology but
• Prokaryotes lack sufficient structural
diversity to allow morphological
comparisons for a phylogeny ·
• Also not enough detail in the fossil
record
The END
Latest techniques read
sequences in proteins or DNA
structure
• Use relative similarity of sequences to
infer their relationships
• More similar sequences go on neighboring
branches, less similar on more distant
branches
Goal is to make an evolutionary
tree for all living things
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Need a gene that is
present in all organisms
subject to strong stabilizing section
function has remained the same in all
organisms
• Example gene which codes for the RNA in
small ribosomal subunit studied by Carl Woese
• Today used as a resource for building whole-life
Basis for proposed changes in
the classification system
• 5 kingdom system of Whittaker bears little
resemblance to actual evolutionary
relationships
• Prokaryotes on 2 of 3 main branches
• Bacteria
– includes most of the well-known prokaryotes
• Archea
Archea
• First named archaebacteria
• but shown to be more closely related to the
eukaryotes than to the bacteria so now
called Archea
• live in physically harsh environments
– hyperthermophiles
– anaerobic methane producers
• halophiles Very difficult to grow in lab
cultures
Now have 3 domains above the
kingdom level
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Bacteria
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Archea
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Eucarya
• Animalia. Plantae and Fungi kingdoms
are still in pretty good shape, requiring
only minor revision
 Protista needs to be closely looked at
and broken up.
The Earliest Life
• Evidence indicates that the most recent
common ancestor of all living things was
highly evolved and biologically
sophisticated
A fly in the ointment
Horizontal Gene Transfer
• Using
genes to
estimate
phylogeny
gives
different
results.
Lateral gene transfer
• Scientists working on a universal
phylogeny ....
– Are finding examples of lateral gene transfer
at a rapid pace
– Believe that early in life’s history lateral
transfer of genes was rampant
– Think that phylogenies being built do not
reflect the organisms phylogeny but only the
phylogeny of the genes being used to
construct those phylogenies
For example phylogenies like this one in figure 6.18 on page 641
These scientists believe that this is more representative
of what early history looked like.
Recent studies have shown
that...
• Bacteria are showing lateral gene transfer at an
astonishing rate.
• Two strains of E. coli believed to be closely
related strains show one strain, O157:H7, which
causes food poisoning has 1,387 genes not
found in the non-virulent K-12 strain.
• On the other hand K-12 has 528 genes not
found in O157:H7.
• Another study showed that 18% of E. coli genes
were acquired by lateral gene transfer.
How do we root the estimated
phylogeny of all living things
• Look for the cenancestor or Most recent
common ancestor by using parsimony
• Need to make inferences about certain
fundamental cellular traits
• Map character state changes onto
phylogenies
• If a trait occurs in all three
domains it belonged to the
cenancestor . …. or ….
• If it occurs in two of the
domains but not the 3rd , we
can infer that the trait
occurred in the most recent
common ancestor and was
lost in one of the lineages.
• Otherwise the trait would have
had to arise 2 or 3 different
times which is much less likely
because it would require more
evolutionary transitions.
More evidence is being
gathered all the time on the
Archea
• Increased information is expected from comparing
whole genome sequences. This will allow the
comparison of a great number of genes.
Much of the new information seems to indicate that
there may not have been just one single common
ancestor
Evidence shows that there has been lateral transfer of
genes between organisms, perhaps at a very high
rate early on in evolution of life Figure 14.14
Phylogenies like those shown in the text may actually
only reflect the evolution of genes being looked at
When did life begin
• The earliest possible date is between 4.4
and 3.85 billion years ago
• Based in estimated universal phylogeny
• geological data
• paleontological data
From prokaryote to
Eukaryote, Origin of
organelles
• Evolution from common ancestors to the
Bacteria and Archea appears to have
occurred slowly and by a process of gradual
refinement
• Eucarya differ from Bacteria and Archea in
much more dramatic ways
• More complicated genomes
• introns ( noncoding DNA regions)
• organelles
• multicellularity
– tissues
Evolution of organelles
• All evidence points to evidence that
mitochondria and chloroplasts at least arose as
endosymbionts
– superficially resemble simple bacteria
– contain DNA
– The Genes in their DNA fits with the phylogeny of
the bacteria rather than the eukarya
– mitochondria are closely related to the purple
bacteria
– Chloroplasts are closely related to the
Organelle genomes
• Chloroplast and mitochondrial DNA is much more
highly conserved than nuclear DNA
• Mitochondrial DNA is very different in fungi ,
plants, and animals
• Chloroplasts and mitochondria contain only a
fraction of the DNA in a bacterial cell.
• Abundant evidence exists that chloroplasts and
mitochondria transferred genes to the nucleus
early on in their evolution
A few interesting facts about
organelle DNA
• RuBPCase (used in the Calvin cycle of
photosynthesis) has two subunits; one is coded
for by chloroplast DNA, the other in the nuclear
DNA
• A gene which codes for a translation factor is
found in chloroplast DNA in green algae but in
the nucleus in flowering plants
• The cox 2 gene (used in aerobic respiration) is
found in mitochondria of most plants but in
mung beans it is found only in the nucleus and
in legumes it is in both nucleus and
mitochondria.
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