Phys 214. Planets and Life

Dr. Cristina Buzea

Department of Physics

Room 259

E-mail: cristi@physics.queensu.ca

(Please use PHYS214 in e-mail subject)

Lecture 22. Origin and evolution of life. Part II

March 7th, 2008

Contents

• Textbook pages 198-203, 206-217

• 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 fromchemical reactions on Earth.

Miller-Urey experiment tried to reproduce the conditions of earlyEarth: water vapors (representing the oceans), gaseous methaneand ammonia (the atmosphere), and electric sparks (the energy).The oxygen was not present in Earth; early atmosphere, being theresult of photosynthesis.

In the original Miller–Urey experiment it was assumed that carbon andnitrogen in the early atmosphere were present as methane (CH4)and ammonia (NH3). They obtained many amino acids and organicmolecules – the organic soup necessary for life.

In modern Miller–Urey experiments it is assumed that carbon andnitrogen in the early atmosphere were present as carbon dioxide(CO2) and nitrogen (N2).

Prebiotic molecules are NOT be manufactured in Miller–Ureyexperiments if oxygen (O2) is present in the flask. Oxygen (evenwhen bound in CO2) tends to suppress the formation of organiccompounds, while hydrogen is the key ingredient for theirformation.

It seems possible that hydrogen made as much as 30% of Earth`s earlyatmosphere, and did not escape at the same rate it escapes today.

Courtesy of NASA-

Ames 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 andextrapolates back towards the simplest living entities.

- aims to create artificial cells by simplifying and geneticallyreprogramming existing cells with simple genomes.

2. A bottom-up strategy - collection of inanimate elements,molecules and minerals - trying to figure out how they cameto create a living organism

- assemble artificial cells from scratch using nonliving organicand inorganic materials.

- to house informational polymers (DNA and RNA) and ametabolic system that chemically regulates and regeneratescellular components within a physical container (such as alipid vesicle).

Definition of life -> molecular assembly is alive if it continuallyregenerates 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?

Kaolinite crystal -Kugler, R.L. and Pashin, J.C., 1994,

Geological Survey of Alabama Circular 159, 91 p.

Bottom-up strategy - Template hypothesis

Experiments show that several types of inorganic minerals can facilitate the self-assembly ofcomplex 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 proximitymakes them interact, forming longer chains. Experiments - produced RNA chains more than100 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 freelyin the ocean it can speed up the replication of a competitor RNA, but if it is enclosed within acell it gives the cell RNA an advantage over other cells.)

Bottom-up strategy – Pre-cells

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.

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.

Bottom-up strategy - Membranes

Membranes form1) If we cool a warm-water solution of amino acids, they can form bonds

among themselves to make an enclosed spherical structure. They are notalive, but have many lifelike properties: grow in size by absorbing moreshort 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

• Based on current scientific evidence, it is very likely that life on Earth formed spontaneouslyfrom increasingly complex chemical reactions.

• A combination of atmospheric chemistry, chemistry near deep sea vents, and molecules fromspace made areas with abundant complex organic molecules

• More complex molecules (short strands RNA) grew with the aid of clay minerals. Some RNAmolecules became capable of self-replication

• Membranes formed spontaneously, probably with the aid of clay minerals and enclosed someof the complex molecules, facilitating their interaction

• Natural selection changed the pre-cells increasing their complexity - becoming livingorganisms

• DNA became the favoured hereditary molecule

Top-down strategy

1. A top- down strategy - looks at the presentbiology and extrapolates back towards thesimplest living entities

The synthesis of the largest DNA molecule ever tobe constructed synthetically!

Science vol. 319, 1215 (2008)

>500-kb genome of Mycoplasma genitalium.

M. genitalium has the smallest genome of any free-living cell.

Its circular genome was partitioned into 101overlapping sections, these cassettes weresynthesized, sequenced and then joined by invitro recombination to generate increasinglylarger intermediate stretches. The sections werepropagated in bacteria and yeast.

The resulting genome is identical to that of native M.genitalium in almost every way: except one genewhich would allow the organism to attach tomammalian cells and has been disrupted forsafety 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 fromchemical reactions involving inorganic chemicals) if life originated near deep sea vents

- very simple - with few enzymes and a rudimentary metabolism - resembling modernprokaryotes (without cell nuclei and organelles), experienced more errors copying DNA,and therefore a higher mutation rate -> they diversified fast, evolving many metabolicprocesses. Probably the major branches in the tree of life evolved quite fast.Stromatolites suggest rapid diversification – photosynthesis as long as 3.5 billion yearsago – a complex metabolic process.

Early photosynthetic microbes - (similar to modern purple sulfur bacteria and green sulfurbacteria) use hydrogen sulfide (H2S) rather than water in photosynthesis, and thereforedid not produce oxygen

CO2 + H2S + light -> (CH2O) + H2O + 2 S

Photosynthesis using water came later, and produced oxygen as a by-product – caused thebuild-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, somesurvived by being underground.

Because the content of oxygen arose gradually, some organisms evolved and adapted andthrived in the presence of oxygen. Our metabolism is the result of the oxygen crisis facesby 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 moreadvanced 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 majoradaptations

1) early species may have developed specialized infoldings of their membranes thatcompartmentalized 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 makingATP) – and chloroplasts (structure in plant cells that produce energy by photosynthesis)

- Mitochondria and chloroplast have their own DNA and reproduce themselves withintheir eukaryotic homes.

- Their DNA sequence indicate they originate from Bacteria. Therefore, initiallymitochondria 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 thebacteria and the common ancestor of archaea and eukarya.

Bacteria develop primitive forms of photosynthesis (which do notproduce oxygen).

3 Ga Photosynthesizing cyanobacteria evolve - they use water andthereby produce oxygen as waste product that initially oxidizesdissolved iron in the oceans, creating banded iron layers.

Life remained energetically limited until the origin of oxygenicphotosynthesis, sometime before 2.7 Gyr (breakthrough inmetabolic evolution - increased the free energy supply).

The oxygen concentration in the atmosphere subsequently rises,acting as a poison for many bacteria. The extinction of olderanaerobic life as oxygen builds up in the atmosphere is usuallycalled “The Oxygen Crisis” in relation to the evolution of life onEarth. 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 andtrace-making organisms.

It is subdivided into three eras, the Paleozoic, Mesozoic and Cenozoic, which are divided by majormass extinctions.

The Cambrian explosion = rapid appearance of most major groups of complex animals in thefossil record, around 530 million years ago. An explosion of genetic diversity, leading to theappearance of the first animals

Prior to the Cambrian Period, life consisted of single-celled organisms. occasionally organized intocolonies. In the following 70 million to 80 million years, the rate of evolution accelerated byan order of magnitude, and the diversity of life began to resemble today’s.

Cambrian explosion

• 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.Dickinsonia costata, an Ediacaran organism

Fossil of Spriggina, one of the Ediacaran biota Fossil of Kimberella, a triploblastic bilaterian

Cambrian explosion - Burgess Shale

Reconstruction of Opabinia, one of the

strangest animals from the Burgess Shale

The first complete Anomalocaris fossil found

Marella, the most abundant Burgess

Shale organism.

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 intorocks.

Larger animals remained confined to the oceans.

Plants and fungi were the first to colonize the land about 475 million years ago. Plantsevolved from a type of alga that survived in salty shallow ponds, evolving thick cellwalls that allowed it to survived dry periods. On land they had the advantage of no landanimals to eat them, and therefore thrived. Large plants gradually developed complexbodies, 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 thefastest ever. Humanity's destruction of the biosphere could cause the extinction of one-half of all species in the next 100 years.

6) K/T or Cretaceous–Tertiary extinction; 65 million years ago; about 50% of all speciesbecame extinct. It ended the reign of dinosaurs and opened the way for mammals tobecome 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

• 65 millions yeas ago, between Cretaceous and Tertiary periods dinosaurs went extinct, afterdominating 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 butcommon in meteorites), rich in osmium, gold and platinum, containing grains of shockedquartz, and ash - hypothesis that dinosaurs went extinct after an impact with an asteroid orcomet (10-15 km diameter).

• Geological record shows that 75% of all plant and animal species went extinct (99% of allliving plants and animals at that time) .

• A crater matches the age – is 200 km across in Mexico – Yucatan peninsula – the Chicxulubcrater

• The mammals survived because they were living in underground burrows, they had storedfood. Over the next 65 million years the mammals evolved into larger mammals, including us.

Next lecture

Origin and evolution of life. Part III