Phys 214. Planets and Life
Dr. Cristina Buzea
Department of Physics
Room 259
E-mail: [email protected]
(Please use PHYS214 in e-mail subject)
Lecture 22. Origin and evolution of life. Part II
March 7th, 2008
Contents
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Textbook pages 198-203, 206-217
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Origin and evolution of life
Sources of organic molecules on Earth
RNA world hypothesis
Self-assembled membranes
Template hypothesis
The evolution of Eukarya
Cambrian explosion
Mass extinction events
Origin of life - Sources of organic molecules
Miller - Urey experiment
Try to demonstyrate that organic molecules were produced from
chemical reactions on Earth.
Miller-Urey experiment tried to reproduce the conditions of early
Earth: water vapors (representing the oceans), gaseous methane
and ammonia (the atmosphere), and electric sparks (the energy).
The oxygen was not present in Earth; early atmosphere, being the
result of photosynthesis.
In the original Miller–Urey experiment it was assumed that carbon and
nitrogen in the early atmosphere were present as methane (CH4)
and ammonia (NH3). They obtained many amino acids and organic
molecules – the organic soup necessary for life.
In modern Miller–Urey experiments it is assumed that carbon and
nitrogen in the early atmosphere were present as carbon dioxide
(CO2) and nitrogen (N2).
Prebiotic molecules are NOT be manufactured in Miller–Urey
experiments if oxygen (O2) is present in the flask. Oxygen (even
when bound in CO2) tends to suppress the formation of organic
compounds, while hydrogen is the key ingredient for their
formation.
It seems possible that hydrogen made as much as 30% of Earth`s early
atmosphere, and did not escape at the same rate it escapes today.
Courtesy of NASAAmes Research Center's
Chemical Evolution
Branch.
All sources of organic molecules
1) Chemical reactions in the atmosphere
2) Chemical reactions near deep-sea
vents
3) Material from space
Meteorites contain organic molecules –
during the heavy bombardment; the
heat and pressure generated by
impacts may have facilitated the
production of organic molecules as
well
Comets contain organic molecules.
Organic molecules created in the solar
nebula as UV light from the young
Sun caused chemical reactions on
dust grains. This dust rained down on
the young Earth.
Credit: A. Marston (ESTEC/ESA) et al., JPL,
Caltech, NASA
Two approaches to the origin of life
1. A top- down strategy - looks at the present biology and
extrapolates back towards the simplest living entities.
- aims to create artificial cells by simplifying and genetically
reprogramming existing cells with simple genomes.
2. A bottom-up strategy - collection of inanimate elements,
molecules and minerals - trying to figure out how they came
to create a living organism
- assemble artificial cells from scratch using nonliving organic
and inorganic materials.
- to house informational polymers (DNA and RNA) and a
metabolic system that chemically regulates and regenerates
cellular components within a physical container (such as a
lipid vesicle).
Definition of life -> molecular assembly is alive if it continually
regenerates itself, replicates itself, and is capable of evolving.
What was the transition from chemistry to biology?
Life needs a self-replicating molecule.
The initial self-replicating molecule
was not DNA because DNA is too
complex and its replications is too
complex requiring RNA and proteins
“Chicken-and-egg” dilemma - which
came first? proteins or nucleic acids?
nucleic acids cannot replicate without
proteins, and proteins cannot be made
without nucleic acids
• Recently it was discovered the RNA
can catalyze biochemical reactions
(much like enzymes) and can at least
partially catalyze their own
replication. Dilemma solved!
• RNA was probably the initial self
replicating molecule!
RNA world hypothesis
RNA world hypothesis
RNA is able to store information (similar to DNA)
and catalyze reactions (similar to enzymes),
may have supported cellular or pre-cellular
life.
The first step in the evolution of cellular life
was RNA-based catalysis and information
storage.
Later on, the RNA world evolved into the DNA
and protein world of today.
DNA (due to its greater chemical stability) took
over the role of data storage.
Proteins (more flexible in catalysis) became the
specialized catalytic molecules.
How did the RNA world got started?
How can RNA replicate itself spontaneously?
Bottom-up strategy - Template hypothesis
Kaolinite crystal -Kugler, R.L. and Pashin, J.C., 1994,
Geological Survey of Alabama Circular 159, 91 p.
Experiments show that several types of inorganic minerals can facilitate the self-assembly of
complex organic molecules.
The first molecules of RNA were probably made on the surfaces of clays or other minerals.
Clays –contain layers of molecules to which organic molecules can adhere, and the proximity
makes them interact, forming longer chains. Experiments - produced RNA chains more than
100 bases in length.
The molecular evolution would have been much faster if confined in a closed environment –
similar to living cells. – keep the molecules concentrated to increase the rate of reactions
The isolation from the outside would have facilitated natural selection among RNA molecules (e.g.
a RNA assembles a protein that is able to speed up its replication. If the enzyme floats freely
in the ocean it can speed up the replication of a competitor RNA, but if it is enclosed within a
cell it gives the cell RNA an advantage over other cells.)
Bottom-up strategy – Pre-cells
Lipid pre-cells can form on
the surface of clay minerals
that help assembly RNA
molecules, sometimes with
RNA inside them.
RNA world might have been
born on early Earth with the
catalytic assistance of clay
minerals.
The dehydration and incorporation of
molecules, and rehydration of membranes.
Advances in the development of artificial
cells. Short RNA (red) is adsorbed to
a particle of clay and encapsulated
within a fatty acid vesicle (green).
The assembly of RNA within the
vesicle is coordinated by the clay
particle. Rasmussen et al, Science 303
(2004) 963.
Bottom-up strategy - Membranes
Membranes form
1) If we cool a warm-water solution of amino acids, they can form bonds
among themselves to make an enclosed spherical structure. They are not
alive, but have many lifelike properties: grow in size by absorbing more
short chains of amino acids, until they reach an unstable size and split;
they allow some molecules to cross in or out.
2) The second type of membrane forms when we mix lipids with water.
Bottom-up strategy - Self-assembled membranes
Chemistry – Biology transition scenario
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Based on current scientific evidence, it is very likely that life on Earth formed spontaneously
from increasingly complex chemical reactions.
A combination of atmospheric chemistry, chemistry near deep sea vents, and molecules from
space made areas with abundant complex organic molecules
More complex molecules (short strands RNA) grew with the aid of clay minerals. Some RNA
molecules became capable of self-replication
Membranes formed spontaneously, probably with the aid of clay minerals and enclosed some
of the complex molecules, facilitating their interaction
Natural selection changed the pre-cells increasing their complexity - becoming living
organisms
DNA became the favoured hereditary molecule
Top-down strategy
1.
A top- down strategy - looks at the present
biology and extrapolates back towards the
simplest living entities
The synthesis of the largest DNA molecule ever to
be constructed synthetically!
Science vol. 319, 1215 (2008)
>500-kb genome of Mycoplasma genitalium.
M. genitalium has the smallest genome of any freeliving cell.
Its circular genome was partitioned into 101
overlapping sections, these cassettes were
synthesized, sequenced and then joined by in
vitro recombination to generate increasingly
larger intermediate stretches. The sections were
propagated in bacteria and yeast.
The resulting genome is identical to that of native M.
genitalium in almost every way: except one gene
which would allow the organism to attach to
mammalian cells and has been disrupted for
safety reasons.
Science 309 (2005)
The evolution of life on Earth
The earliest organism must have been:
- chemoautotrophs (obtained C from CO2 dissolved in the oceans and the energy from
chemical reactions involving inorganic chemicals) if life originated near deep sea vents
- very simple - with few enzymes and a rudimentary metabolism - resembling modern
prokaryotes (without cell nuclei and organelles), experienced more errors copying DNA,
and therefore a higher mutation rate -> they diversified fast, evolving many metabolic
processes. Probably the major branches in the tree of life evolved quite fast.
Stromatolites suggest rapid diversification – photosynthesis as long as 3.5 billion years
ago – a complex metabolic process.
Early photosynthetic microbes - (similar to modern purple sulfur bacteria and green sulfur
bacteria) use hydrogen sulfide (H2S) rather than water in photosynthesis, and therefore
did not produce oxygen
CO2 + H2S + light -> (CH2O) + H2O + 2 S
Photosynthesis using water came later, and produced oxygen as a by-product – caused the
build-up of oxygen in Earth’s atmosphere about 2.4 billions years ago.
CO2 + H2O + light -> (CH2O) + O2
The rise of oxygen created a crisis for life, many species probably went extinct, some
survived by being underground.
Because the content of oxygen arose gradually, some organisms evolved and adapted and
thrived in the presence of oxygen. Our metabolism is the result of the oxygen crisis faces
by organisms some 2.4 billion years ago!
The evolution of Eukarya - complexity
The complexity of eukaryote cells – allowed the
selection of many more adaptations than in prokaryotic cells and the evolution of more
advanced organisms.
• The oldest fossils that show cell nuclei date about 2.1 billions years ago.
• Complex eukarya probably evolved through a combination of at least two major
adaptations
1) early species may have developed specialized infoldings of their membranes that
compartmentalized cell function – leading to the creation of cell nucleus.
2) Some large ancestral host absorbed smaller prokaryotes – living a symbiotic relationship
– leading to modern mitochondria (cellular organs that helps produce energy by making
ATP) – and chloroplasts (structure in plant cells that produce energy by photosynthesis)
- Mitochondria and chloroplast have their own DNA and reproduce themselves within
their eukaryotic homes.
- Their DNA sequence indicate they originate from Bacteria. Therefore, initially
mitochondria and chloroplasts were free living bacteria.
Co-evolution ladder - Earth environment and life
Life emerged soon after Earth’s surface conditions became
habitable (formation of oceans and cessation of sterilizing
asteroid impacts).
Closed recycling loops developed (one life form’s waste
became another’s food)!
Oxygenic photosynthesis facilitated the great oxidation of the
atmosphere ~ 2.2 Gyr.
The extreme Neoproterozoic glaciations of 0.8–0.6 Gyr were
accompanied by a second rise in oxygen.
The oxygen rise -> opened the door for the diversification of
larger, hard-shelled, animal life in the Cambrian
explosion.
Vascular land plants caused a further rise in oxygen and fall in
carbon dioxide,played its part in creating the
environmental conditions in which we evolved.
Weathering = decomposition of rocks, soils and their minerals through
direct contact with the Earth's atmosphere.
Lenton et al, Nature 431 (2004) 913.
Evolution of life
Hadean eon (Ga - billion years ago)
4.5 Ga - planet Earth and Moon forms. The gravitational pull of the
Moon stabilizes the Earth's fluctuating axis of rotation.
4.1 Ga - Earth’s surface cools and crust solidifies. The atmosphere and
the oceans form.
3.85 Ga - the earliest life appears, possibly derived from self-reproducing
RNA molecules within proto-cells. DNA molecules then take over as
the main replicators.
3.9 Ga - late Heavy Bombardment - probably obliterated any life that had
already evolved, as the oceans boiled away completely; life may have
been transported to Earth by a meteor.
3.9 -2.5 - Cells resembling prokaryotes appear
Evolution of life
Archean eon (3.8 -2.5 Ga)
3.5 Ga - Lifetime of the last universal ancestor; the split between the
bacteria and the common ancestor of archaea and eukarya.
Bacteria develop primitive forms of photosynthesis (which do not
produce oxygen).
3 Ga Photosynthesizing cyanobacteria evolve - they use water and
thereby produce oxygen as waste product that initially oxidizes
dissolved iron in the oceans, creating banded iron layers.
Life remained energetically limited until the origin of oxygenic
photosynthesis, sometime before 2.7 Gyr (breakthrough in
metabolic evolution - increased the free energy supply).
The oxygen concentration in the atmosphere subsequently rises,
acting as a poison for many bacteria. The extinction of older
anaerobic life as oxygen builds up in the atmosphere is usually
called “The Oxygen Crisis” in relation to the evolution of life on
Earth.
2.1 billion year old rock
with black-band ironstone
Evolution of life
Proterozoic eon (2.5 Ga - 0.54 Ga years ago)
By 2.1 Ga eukaryotic cells appear.
1.2 Ga Simple multicellular organisms - cell
colonies.
0.8–0.6 Ga - global glaciation - Neoproterozoic
glaciations - reduced the diversity of life.
Eukaryotes may be implicated in the worst crisis of
past co-evolution: Neoproterozoic glaciations accompanied by a second rise O2
Eukaryotes colonize the land surface -> weathering
of silicates to access rock-bound nutrients ->
decrease atmospheric CO2 and cooled the
planet. Weathering of phosphorus -> increased
global productivity and contributed to oxygen
rise.
Evolution of life
Phanerozoic eon (0.542 G - present)
Period of well-displayed life - the appearance in the fossil record of abundant, shell-forming and
trace-making organisms.
It is subdivided into three eras, the Paleozoic, Mesozoic and Cenozoic, which are divided by major
mass extinctions.
The Cambrian explosion = rapid appearance of most major groups of complex animals in the
fossil record, around 530 million years ago. An explosion of genetic diversity, leading to the
appearance of the first animals
Prior to the Cambrian Period, life consisted of single-celled organisms. occasionally organized into
colonies. In the following 70 million to 80 million years, the rate of evolution accelerated by
an order of magnitude, and the diversity of life began to resemble today’s.
Cambrian explosion
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We are interested in animal and plants evolution, because the animal branch is our branch.
Animals are classified according to their “body plans” into about 30 phyla. Reptiles and
mammals - belong to phylum Chordata (animals with internal skeletons) - are
fundamentally different from insects that belong to phylum Arthropoda (jointed legs,
external skeleton, segmented body parts).
Cambrian explosion marks the only major diversification of body plans, probably because:
1) oxygen levels were too low before the Cambrian explosion for the survival of larger and
more energy-intensive life forms
2) the evolution of genetic complexity achieved a threshold, organisms having enough variation
in their DNA, allowing for further variation
3) climate change – the snowball Earth ended around the beginning of Cambrian explosion
evolutionary pressure
4) the absence of efficient predators; many animals
had a large window of opportunity to evolve.
Once predators were efficient and widespread
it was more difficult for new body plan animals
to evolve.
Cambrian explosion
Trilobite fossil: Redlichia chinensis. Cambrian.
measures 7.5 cm in length. Hunan Province, China.
Fossil of Spriggina, one of the Ediacaran biota
Dickinsonia costata, an Ediacaran organism
Fossil of Kimberella, a triploblastic bilaterian
Cambrian explosion - Burgess Shale
Reconstruction of Opabinia, one of the
strangest animals from the Burgess Shale
Marella, the most abundant Burgess
Shale organism.
The first complete Anomalocaris fossil found
Evolution of life
The colonization of land
The colonization of life onto land was closely tied to the development of the ozone layer.
Microbes probably colonized the land before, being very small and able to find shelter into
rocks.
Larger animals remained confined to the oceans.
Plants and fungi were the first to colonize the land about 475 million years ago. Plants
evolved from a type of alga that survived in salty shallow ponds, evolving thick cell
walls that allowed it to survived dry periods. On land they had the advantage of no land
animals to eat them, and therefore thrived. Large plants gradually developed complex
bodies, with parts for energy collection above grounds (leaves) and underground parts
(roots) for nutrients from the soil.
Soon after plants colonized the land, animals followed, within 75 million years.
Evolution of life
During the Carboniferous Period, land was covered with
dense forests with the appearance of the first insects and
amphibians.
The Carboniferous Period began about 360 million years ago.
Carboniferous forests – important in our modern economy; much of the land was flooded by
shallow seas, hindering the decay of dead plants – over time the heat and pressure
converted them onto coal. The fossil fuel deposits we use today are the remains of
organisms from the Carboniferous Period.
If the conditions required for substantial amounts of oxygen to build up in a planetary
atmosphere are quite rare, then life on other worlds may still be common but may never
be able to evolve past microscopic forms.
Early dinosaurs and mammals evolved about 245 millions years ago.
Mass extinctions events
7) Holocene extinction - The present Holocene era (11,550-present); possibly one of the
fastest ever. Humanity's destruction of the biosphere could cause the extinction of onehalf of all species in the next 100 years.
6) K/T or Cretaceous–Tertiary extinction; 65 million years ago; about 50% of all species
became extinct. It ended the reign of dinosaurs and opened the way for mammals to
become the dominant land vertebrates.
5) 200 MY ago — the Triassic-Jurassic extinction; about 20% of all marine families,
and the last of the large amphibians were eliminated.
4) P/Tr or Permian-Triassic extinction 251 MY ago — Earth's largest extinction ;
Killed about 96% of all marine species and an estimated 70% of land species
3) Late Devonian extinction; 360 MY ago;
not a sudden event - lasted 20 million years
- eliminated about 70% of all species.
2) two Ordovician-Silurian extinction
444 MY ago occurred, ranked as the second
largest of the five major extinctions in
Earth's history
1) Cambrian-Ordovician extinction;
488 MY ago — series of events eliminated
many brachiopods and severely reduced
the number of trilobite species.
The K-T extinction
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65 millions yeas ago, between Cretaceous and Tertiary periods dinosaurs went extinct, after
dominating the earth for 180 million years, allowing mammals to evolve.
The discovery of a layer - the K-T layer, rich in iridium (element rare on Earth surface but
common in meteorites), rich in osmium, gold and platinum, containing grains of shocked
quartz, and ash - hypothesis that dinosaurs went extinct after an impact with an asteroid or
comet (10-15 km diameter).
Geological record shows that 75% of all plant and animal species went extinct (99% of all
living plants and animals at that time) .
A crater matches the age – is 200 km across in Mexico – Yucatan peninsula – the Chicxulub
crater
The mammals survived because they were living in underground burrows, they had stored
food. Over the next 65 million years the mammals evolved into larger mammals, including us.
Next lecture
Origin and evolution of life. Part III