Phys 214. Planets and Life

Transcription

1 Phys 214. Planets and Life Dr. Cristina Buzea Department of Physics Room (Please use PHYS214 in subject) Lecture 22. Origin and evolution of life. Part II March 7th, 2008

2 Contents Textbook pages , 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

3 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 (CH 4 ) and ammonia (NH 3 ). 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 (CO 2 ) and nitrogen (N 2 ). Prebiotic molecules are NOT be manufactured in Miller Urey experiments if oxygen (O 2 ) is present in the flask. Oxygen (even when bound in CO 2 ) 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 NASA- Ames Research Center's Chemical Evolution Branch.

4 All sources of organic molecules Credit: A. Marston (ESTEC/ESA) et al., JPL, Caltech, NASA 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.

5 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.

6 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!

7 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?

8 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.)

9 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.

10 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.

11 Bottom-up strategy - Self-assembled membranes

12 Chemistry Biology transition scenario 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

13 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)

14 The evolution of life on Earth The earliest organism must have been: - chemoautotrophs (obtained C from CO 2 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 (H 2 S) rather than water in photosynthesis, and therefore did not produce oxygen CO 2 + H 2 S + light -> (CH 2 O) + H 2 O + 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. CO 2 + H 2 O + light -> (CH 2 O) + O 2 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!

15 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.

16 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 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.

17 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 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 Cells resembling prokaryotes appear

18 Evolution of life Archean eon ( 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

19 Evolution of life Proterozoic eon (2.5 Ga Ga years ago) By 2.1 Ga eukaryotic cells appear. 1.2 Ga Simple multicellular organisms - cell colonies 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 O 2 Eukaryotes colonize the land surface -> weathering of silicates to access rock-bound nutrients -> decrease atmospheric CO 2 and cooled the planet. Weathering of phosphorus -> increased global productivity and contributed to oxygen rise.

20 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.

21 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.

22 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

23 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

24 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.

25 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.

26 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.

27 The K-T extinction 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.

28 Next lecture Origin and evolution of life. Part III