BIOE 109 Summer 2009 Lecture 12-Part I The origin of life

BIOE 109Summer 2009

Lecture 12-Part IThe origin of life

There is grandeur in this view of life, having beenbreathed into a few forms or into one; …….from sosimple 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


1. Narrow time window


1. Narrow time window • the age of the earth is 4.55 billion years old.


1. Narrow time window • the age of the earth is 4.55 billion years old. • life first appeared about 3.8 billion years ago.


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!


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!


2. Most “simple” cells are extremely complex

Staphylococcusepidermidis


2. Most “simple” cells are extremely complex • “simple” bacteria possess about 1,600 genes.

Haemophilus influenzae1,743 genes


2. Most “simple” cells are extremely complex • “simple” bacteria possess about 1,600 genes. • how did primitive cells evolve without enzyme-catalyzed metabolism?


2. Most “simple” cells are extremely complex • “simple” bacteria possess about 1,600 genes. • how did primitive cells evolve without enzyme-catalyzed metabolism?

Hammerhead ribozyme!


2. Most “simple” cells are extremely complex • “simple” bacteria possess about 1,600 genes. • how did primitive cells evolve without enzyme-catalyzed metabolism? 3. Life evolved under very different conditions


2. Most “simple” cells are extremely complex • “simple” bacteria possess about 1,600 genes. • how did primitive cells evolve without enzyme-catalyzed metabolism? 3. Life evolved under very different conditions • atmosphere dominated by methane, hydrogen sulfide, ammonia, carbon monoxide, water vapor.

How do we define life?


1. Must be capable of reproducing.



2. Must possess a genotype and a phenotype.




3. Must possess a metabolism.




3. Must possess a metabolism.

4. Must be capable of evolving.

Theories for the evolution of life


1. Extraterrestrial theories • in 1907, Arrhenius proposed the theory of “Panspermia”.


1. Extraterrestrial theories • in 1907, Arrhenius proposed the theory of “Panspermia”. • panspermia means “germs everywhere”.


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


1. Extraterrestrial evidence


1. Extraterrestrial evidence • the Murchison meteorite contained over 70 amino acids!



• equal mixture of D and L isomers present.



• 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 Stanley Miller(1930-2007)Volcanic spark discharge experiment

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


• early replicating systems may have been RNA-based.


• 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


• 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”.


• 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


• heating and cooling mixtures of amino acids can form spherical proteinoids.


• heating and cooling mixtures of amino acids can form spherical proteinoids. • mixtures of lipids and proteins can form liposomes.


• 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.


• 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


• natural selection would have acted to biochemical sophistication of protobionts.


• natural selection would have acted to biochemical sophistication of protobionts. • DNA became the “repository” of the genetic information.



Why?



Why?

1. DNA is more stable than RNA.



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?


1. Stromatolites


1. Stromatolites

• are bun-shaped structures made by cyanobacteria.

• fossil stromatolites are abundant 3.5 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).


2. C isotope ratios suggest early photosynthesis



• 12CO2 is preferentially fixed in photosynthesis than

the heavier 13CO2.




the heavier 13CO2.

• isotopic ratios of 13C to 12C indicate that autotrophic bacteria fixing carbon via the Calvin cycle by 3.5 bya.




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


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



• Archaea, Bacteria, and Eucarya evolved only after extensive lateral gene transfer ceased.

Lot of gene swapping at the base of the tree




2. The ring of life hypothesis




2. The ring of life hypothesis

• Eucarya evolved from a fusion of a bacterium and an archean.

The ring of life hypothesis


3. The chronocyte hypothesis

The chronocyte hypothesis


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.


4. The three viruses, three domains hypothesis



• DNA-based viruses evolved to counter host’s defenses (that were RNA-based).



• DNA-based viruses evolved to counter host’s defenses (that were RNA-based).

• DNA-based viruses invaded RNA-based lineages.



• 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

BIOE 109 Summer 2009 Lecture 12-Part I The origin of life

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