Transcript (Part 1) Origin of life

BIOE 109
Summer 2009
Lecture 12-Part I
The origin of life
There is grandeur in this view of life, having been
breathed into a few forms or into one; …….from so
simple a beginning endless forms most beautiful and
most wonderful have been, and are being, evolved.”
Charles Darwin, 1859
• Did life originate on earth once or many times?
• What was the first living thing?
• When did the last common ancestor of all living things
come into existence?
• What is the shape of tree of life?
questions, questions and questions………
Some problems in addressing the origin of
life on earth
Some problems in addressing the origin of
life on earth
1. Narrow time window
Some problems in addressing the origin of
life on earth
1. Narrow time window
• the age of the earth is 4.55 billion years old.
Some problems in addressing the origin of
life on earth
1. Narrow time window
• the age of the earth is 4.55 billion years old.
• life first appeared about 3.8 billion years ago.
Some problems in addressing the origin of
life on earth
1. Narrow time window
• the age of the earth is 4.55 billion years old.
• life first appeared about 3.8 billion years ago.
• the planet could not have sustained life for its first 500
million years!
Some problems in addressing the origin of
life on earth
1. Narrow time window
• planet could not have sustained life for its first 500
million years!
Early large impact strikes on the earth and
moon
Moon formed!
Some problems in addressing the origin of
life on earth
2. Most “simple” cells are extremely complex
Staphylococcus
epidermidis
Some problems in addressing the origin of
life on earth
2. Most “simple” cells are extremely complex
• “simple” bacteria possess about 1,600 genes.
Haemophilus influenzae
1,743 genes
Some problems in addressing the origin of
life on earth
2. Most “simple” cells are extremely complex
• “simple” bacteria possess about 1,600 genes.
• how did primitive cells evolve without enzymecatalyzed metabolism?
Some problems in addressing the origin of
life on earth
2. Most “simple” cells are extremely complex
• “simple” bacteria possess about 1,600 genes.
• how did primitive cells evolve without enzymecatalyzed metabolism?
Hammerhead ribozyme!
Some problems in addressing the origin of
life on earth
2. Most “simple” cells are extremely complex
• “simple” bacteria possess about 1,600 genes.
• how did primitive cells evolve without enzymecatalyzed metabolism?
3. Life evolved under very different conditions
Some problems in addressing the origin of
life on earth
2. Most “simple” cells are extremely complex
• “simple” bacteria possess about 1,600 genes.
• how did primitive cells evolve without enzymecatalyzed metabolism?
3. Life evolved under very different conditions
• atmosphere dominated by methane, hydrogen sulfide,
ammonia, carbon monoxide, water vapor.
How do we define life?
How do we define life?
1. Must be capable of reproducing.
How do we define life?
1. Must be capable of reproducing.
2. Must possess a genotype and a phenotype.
How do we define life?
1. Must be capable of reproducing.
2. Must possess a genotype and a phenotype.
3. Must possess a metabolism.
How do we define life?
1. Must be capable of reproducing.
2. Must possess a genotype and a phenotype.
3. Must possess a metabolism.
4. Must be capable of evolving.
Theories for the evolution of life
Theories for the evolution of life
1. Extraterrestrial theories
• in 1907, Arrhenius proposed the theory of
“Panspermia”.
Theories for the evolution of life
1. Extraterrestrial theories
• in 1907, Arrhenius proposed the theory of
“Panspermia”.
• panspermia means “germs everywhere”.
Theories for the evolution of life
1. Extraterrestrial theories
• in 1907, Arrhenius proposed the theory of
“Panspermia”.
• panspermia means “germs everywhere”.
• life originated elsewhere in the universe and drifted
from planet to planet by pressure of starlight.
Sir Francis Crick was an advocate for “directed
panspermia”
Theories for the evolution of life
2. The chemical theory (Oparin-Haldane theory)
Theories for the evolution of life
2. The chemical theory (Oparin-Haldane theory)
• life originated on earth following a period of
“chemical evolution”.
• both scientists were strongly influenced by a letter
written by Darwin in 1871.
The chemical theory
The chemical theory
inorganic molecules

organic molecules

biological polymers

replicating systems

protobionts

true cells
Step 1. Inorganic molecules  organic
molecules
Step 1. Inorganic molecules  organic
molecules
1. Extraterrestrial evidence
Step 1. Inorganic molecules  organic
molecules
1. Extraterrestrial evidence
• the Murchison meteorite contained over 70 amino
acids!
Step 1. Inorganic molecules  organic
molecules
1. Extraterrestrial evidence
• the Murchison meteorite contained over 70 amino
acids!
• equal mixture of D and L isomers present.
Step 1. Inorganic molecules  organic
molecules
1. Extraterrestrial evidence
• the Murchison meteorite contained over 70 amino
acids!
• equal mixture of D and L isomers present.
• urea, various amides, ketones and aldehydes were
also found.
2. Laboratory experiments
• successful in producing amino acids, sugars, and
nucleic acids.
“Miller-Urey” experiment
Volcanic spark discharge experiment
Stanley Miller
(1930-2007)
Step 2. Organic molecules  biological
polymers
Step 2. Organic molecules  biological
polymers
• polynucleotides (n = 40) have been synthesized on the
clay mineral montmorillonite.
• polypeptides (n = 55) have been synthesized on a
mixture of two minerals - illite and hydroxylapatite
Step 3. Biological polymers  replicating
systems
Step 3. Biological polymers  replicating
systems
• early replicating systems may have been RNA-based.
Step 3. Biological polymers  replicating
systems
• early replicating systems may have been RNA-based.
• catalytic RNAs called ribozymes may have preceded
enzymes (proteins).
Hairpin ribozyme
Hammerhead ribozyme
Ribozyme from Tetrahymena thermophila
Step 3. Biological polymers  replicating
systems
• early replicating systems may have been RNA-based.
• catalytic RNAs called ribozymes may have preceded
enzymes (proteins).
• RNAs may have replicated by “base-pairing rules”.
Step 3. Biological polymers  replicating
systems
• early replicating systems may have been RNA-based.
• catalytic RNAs called ribozymes may have preceded
enzymes (proteins).
• RNAs may have replicated by “base-pairing rules”.
• if “mistakes” made in copying, natural selection can
occur!
Evidence for an early role for RNA
“The RNA World”
Evidence for an early role for RNA
(“The RNA world”)
RNA is involved in:
1. DNA replication.
2. Protein synthesis.
3. Ribonucleoside triphosphates (ATP, GTP) are the
energy currency of cells.
4. Deoxyribonucleotides are synthesized from RNA
precursors.
Step 4. Replicating systems  protobionts
Step 4. Replicating systems  protobionts
• heating and cooling mixtures of amino acids can form
spherical proteinoids.
Step 4. Replicating systems  protobionts
• heating and cooling mixtures of amino acids can form
spherical proteinoids.
• mixtures of lipids and proteins can form liposomes.
Step 4. Replicating systems  protobionts
• heating and cooling mixtures of amino acids can form
spherical proteinoids.
• mixtures of lipids and proteins can form liposomes.
• liposomes can “reproduce” by budding off smaller units.
Step 4. Replicating systems  protobionts
• heating and cooling mixtures of amino acids can form
spherical proteinoids.
• mixtures of lipids and proteins can form liposomes.
• liposomes can “reproduce” by budding off smaller units.
• if an RNA-protein based metabolism evolved, natural
selection can again occur.
Step 5. Protobionts  true cells
Step 5. Protobionts  true cells
• natural selection would have acted to biochemical
sophistication of protobionts.
Step 5. Protobionts  true cells
• natural selection would have acted to biochemical
sophistication of protobionts.
• DNA became the “repository” of the genetic
information.
Step 5. Protobionts  true cells
• natural selection would have acted to biochemical
sophistication of protobionts.
• DNA became the “repository” of the genetic
information.
Why?
Step 5. Protobionts  true cells
• natural selection would have acted to biochemical
sophistication of protobionts.
• DNA became the “repository” of the genetic
information.
Why?
1. DNA is more stable than RNA.
Step 5. Protobionts  true cells
• natural selection would have acted to biochemical
sophistication of protobionts.
• DNA became the “repository” of the genetic
information.
Why?
1. DNA is more stable than RNA.
2. RNA freed to act only in one arena (catalysis).
DNA takes control of information storage
What is the evidence for prokaryotic life
3.5 to 4.0 BYA?
What is the evidence for prokaryotic life
3.5 to 4.0 BYA?
1. Stromatolites
What is the evidence for prokaryotic life
3.5 to 4.0 BYA?
1. Stromatolites
• are bun-shaped structures made by cyanobacteria.
• fossil stromatolites are abundant 3.5 bya.
What is the evidence for prokaryotic life
3.5 to 4.0 BYA?
1. Stromatolites
• are bun-shaped structures made by cyanobacteria.
• fossil stromatolites are abundant 3.5 bya.
• recently “re-discovered” in shallow, hypersaline
environments (e.g., Hamelin pool in Shark Bay,
western Australia).
What is the evidence for prokaryotic life
3.5 to 4.0 BYA?
2. C isotope ratios suggest early
photosynthesis
What is the evidence for prokaryotic life
3.5 to 4.0 BYA?
2. C isotope ratios suggest early
photosynthesis
• 12CO2 is preferentially fixed in photosynthesis than
the heavier 13CO2.
What is the evidence for prokaryotic life
3.5 to 4.0 BYA?
2. C isotope ratios suggest early
photosynthesis
• 12CO2 is preferentially fixed in photosynthesis than
the heavier 13CO2.
• isotopic ratios of 13C to 12C indicate that autotrophic
bacteria fixing carbon via the Calvin cycle by 3.5 bya.
What is the evidence for prokaryotic life
3.5 to 4.0 BYA?
2. C isotope ratios suggest early
photosynthesis
• 12CO2 is preferentially fixed in photosynthesis than
the heavier 13CO2.
• isotopic ratios of 13C to 12C indicate that autotrophic
bacteria fixing carbon via the Calvin cycle by 3.5 bya.
• where did the O2 go? Into the oceans to form
banded ironstone sediments.
The origin and early evolution of the
eukaryotes
The origin and early evolution of the
eukaryotes
1. The universal gene-exchange pool hypothesis
-
Proposed by Carl Woese (the discoverer of Archaea)
-
Based on the fact that significant conflict exists between
branching patterns of Archaea, Bacteria and Eucarya
-
Downplays importance of natural selection
-
Is extremely controversial
The origin and early evolution of the
eukaryotes
1. The universal gene-exchange pool hypothesis
• Archaea, Bacteria, and Eucarya evolved only after
extensive lateral gene transfer ceased.
Lot of gene swapping
at the base of the tree
The origin and early evolution of the
eukaryotes
1. The universal gene-exchange pool hypothesis
• Archaea, Bacteria, and Eucarya evolved only after
extensive lateral gene transfer ceased.
2. The ring of life hypothesis
The origin and early evolution of the
eukaryotes
1. The universal gene-exchange pool hypothesis
• Archaea, Bacteria, and Eucarya evolved only after
extensive lateral gene transfer ceased.
2. The ring of life hypothesis
• Eucarya evolved from a fusion of a bacterium and an
archean.
The ring of life hypothesis
The origin and early evolution of the
eukaryotes
3. The chronocyte hypothesis
The chronocyte hypothesis
The origin and early evolution of the
eukaryotes
3. The chronocyte hypothesis
• a chronocyte lineage evolves cytoskeleton and
phagocytosis.
• chronocyte engulfs an archaean that became an
endosymbiont
• the endosymbiont eventually becomes the nucleus.
The origin and early evolution of the
eukaryotes
4. The three viruses, three domains hypothesis
The origin and early evolution of the
eukaryotes
4. The three viruses, three domains hypothesis
• DNA-based viruses evolved to counter host’s
defenses (that were RNA-based).
The origin and early evolution of the
eukaryotes
4. The three viruses, three domains hypothesis
• DNA-based viruses evolved to counter host’s
defenses (that were RNA-based).
• DNA-based viruses invaded RNA-based lineages.
The origin and early evolution of the
eukaryotes
4. The three viruses, three domains hypothesis
• DNA-based viruses evolved to counter hosts
defenses.
• DNA-based viruses invaded RNA-based lineages.
• the RNA genes were reverse-transcribed into DNA
and incorporated into new lineages.
The three viruses, three domains hypothesis