1 TOK  Biology is the study of life, yet life is an emergent property. Under what circumstances is a systems approach productive in biology and under what circumstances is a reductionist approach more appropriate? How do scientists decide between competing approaches? 1

2 Chapter 25 The Tree of Life “All truths are easy to understand once they are discovered; the point is to discover them.” --Galileo Galilei

3 Essential Idea  There is an unbroken chain of life from the first cells on Earth to all cells in organisms today. 3

4 Early Earth and the Origin of Life  There is a lot of evidence accumulating that there were four sequences of events that led to the production of simple cells:  1. Abiotic synthesis of small organic molecules  Amino acids and nucleotides  2. The joining of these monomers into polymers  Proteins and nucleic acids  3. The packaging of these polymers into protobionts.  Small, membrane enclosed environments where the chemistry was different from that of the outside.  4. The origin of self-replicating molecules which eventually made self-replication possible.

5 Early Earth and the Origin of Life  Conditions were much different on early Earth.  It was constantly being bombarded with chunks of debris.  As the Earth cooled, conditions began to change and an atmosphere filled with water vapor and compounds from volcanic eruptions (CO 2, CH 4, NH 3, H 2, and H 2 S).  Further cooling led to the condensation of the water vapor and the filling of the oceans.

6 The Early Atmosphere  A.I. Oparin and J.B.S. Haldane independently proposed that the early atmosphere was reducing and organic compounds could have been formed from simple molecules.  The energy for such synthesis could have come from lightning and/or intense UV radiation.

8 The Origin of Life?  Haldane suggested that the oceans were a “primitive soup” containing a solution of organic molecules.  In 1953, Stanley Miller and Harold Urey tested the Oparin-Haldane hypothesis with an experiment.

9 The Miller-Urey Experiment  They created an apparatus that resembled the presumed atmosphere of early Earth.  It was a sealed, sterile, glass container containing only the substances believed to be in the primitive Earth.  2 electrodes supplied “energy,” and from this the found numerous compounds and amino acids.

12 Other Experiments  Many other such experiments have been performed using a wide variety of primitive environments and they always find the same thing: Organic compounds.

13 Other Experiments  Other evidence suggests the early atmosphere was neither oxidizing nor reducing and contained a lot of CO 2 and N 2.  Experiments similar to the one Miller and Urey performed have been run using the CO 2 and N 2, and haven’t produced any organic molecules.

14 Other Experiments  It is likely, however, that pockets of an “early” atmosphere existed and could have produced the same results as those obtained by Miller and Urey.  Example: Regions around volcanoes and deep-sea hydrothermal vents.  These regions are good sources of sulfur and iron compounds that are important to ATPsynthases of today’s organisms.

15 Other Experiments  Many other polymers have been synthesized abiotically.  Dripping aa solutions over hot rocks, clay, and/or sand have been found to produce polymers spontaneously.

16 Organic Compounds from Space  Outer space may have been a source of organic compounds. Meteors that have been found contain numerous amino acids in similar proportions to those produced in the Miller-Urey experiment.

17 Organic Compounds from Space  The aa’s are not contaminants because both L & D isomers are found in equal amounts. Living organisms only make L isomers.

18 2 Main Properties of Life  1. Accurate Replication  2. Metabolism  Neither can occur without the other. DNA requires enzymatic machinery and a lot of nucleotide bases to pass heritable material along. The enzymes and the energy which helps them comes from a cell’s metabolism.

19 The Miller-Urey Experiment & Self-Replicating Molecules  This experiment did produce some nitrogenous bases of DNA and RNA, but they did not produce anything like nucleotides.  The nucleic acid building blocks were not likely to be a part of the primitive soup.  So, how did self-replicating molecules and a metabolism-like source of building blocks appear together?

20 Protobionts  These are aggregates of abiotically produced molecules which are surrounded by a membrane or membrane-like structure.  They exhibit some properties associated with life:  1. Simple reproduction  2. Metabolism  3. Maintenance of an internal chemistry different from the surrounding environment.

22 Lab Experiments and Protobionts  Lab experiments have shown that protobionts could have arisen spontaneously.  When lipid and other molecules are added to water, liposomes form which are organized into a lipid bilayer with an internal environment.  The bilayer is selectively permeable and allows water and electric charge in and out.

23 An Interesting Thought to Ponder…  If early liposomes allowed random polymers into their membranes then allowed organic molecules to enter and exit the cell, you can see how it is possible that “life” could have arisen.

24 RNA  The first genetic material was probably RNA.  RNA is single-stranded, can take on a variety of different shapes, and can perform a variety of different functions.  RNA is involved in protein synthesis and can play a number of other roles.  Ribozymes are RNA molecules that have enzymatic properties.

25 Ribozymes  1. Can make complementary copies of short pieces of RNA if nucleotide building blocks are available.  2. Can remove segments of themselves (self- replicating introns).  3. Can act on different molecules such as tRNA, cutting out pieces and making them fully functional.

26 The Relation to Protobionts  A protobiont with self-replicating, catalytic RNA is different from its neighbors.  If it can grow and split, natural selection could act on it and the most successful protobionts would increase in number.  There were likely large numbers of protobionts like these available.  The timeframe for which natural selection was allowed to act on these protobionts was large as well.

27 Protobionts  As the protobionts grew and multiplied, they could have become more complex and given way to DNA.  The RNA could have then began performing more of the modern functions.  The stage was now set for the explosion of life forms driven by natural selection and the formation of early prokaryotes.

28 The First Prokaryotes  The first prokaryotes evolved from protobionts.  As the protobionts became more complex, they diversified into a wide variety of autotrophs.  Eventually, they had all of the “stuff” they needed to sustain themselves.  The autotrophs and heterotrophs lived symbiotically for about 1.5 billion years and transformed the biosphere.

29 A TOK Moment  The first cells must have arisen from non- living material, yet it has been shown that cells can only be formed by division of pre- existing cells. Pasteur provided experimental evidence that spontaneous generation of cells and organisms does not now occur on Earth.  To what extent is this true, and what reasons can you give for why spontaneous generation no longer occurs yet could have in the past? 29

30 The Origin of O 2  Most O 2 is of biological origin--a direct result of photosynthesis.  The atmosphere did not become filled with O 2 for quite some time.  Cyanobacteria began photosynthesizing about 3.5 bya, but the O 2 quickly dissolved into the surrounding water.

31 The Origin of O 2  As the O 2 levels in the seas increased, the O 2 started reacting with the iron forming vast layers of sediment containing iron oxide. This process took approximately 800 million years.  Eventually, the O 2 being produced began to accumulate in the atmosphere and had an enormous impact on life.

34 O 2 in the Atmosphere  For about 500 million years, O 2 levels in the atmosphere increased.  The gradual rise in O 2 was due to cyanobacteria.  The accelerated rise a few hundred million years later was due to eukaryotic cells which contained chloroplasts.  Many prokaryotes died out.  Others survived in anaerobic environments.  Many of their descendants survive today as obligate anaerobes.

35 O 2 in the Atmosphere  As a result of the changing atmosphere, cellular respiration evolved and O 2 began to be used to harvest energy stored in organic molecules.

36 Eukaryotic Cells and Their Origin  The oldest fossils of eukaryotic cells are about billion years old.  Prokaryotes lack internal structures.  They also lack the cytoskeleton which enables eukaryotes to engulf other cells.  It is likely that the first eukaryotic cells were predators of other cells.

37 Eukaryotic Cells and Their Origin  The process of endosymbiosis probably led to the complex organization of eukaryotic cells.  Mitochondria and plastids are examples of the result of endosymbiosis.

38 The Theory of Endosymbiosis  This theory proposes that mitochondria and plastids were formerly small prokaryotes living within larger cells.  Proposed ancestors of mitochondria: aerobic prokaryotic heterotrophs  Proposed ancestors of plastids: photosynthetic prokaryotes  These endosymbionts probably gained access to the interior of the cell as undigested prey.

39 The Theory of Endosymbiosis  The benefit to both organisms is easy to consider:  The heterotrophic host could use the nutrients produced by photosynthetic endosymbionts.  A cell that was anaerobic could benefit from a cell that takes advantage of O 2 -- which was increasing in the atmosphere at the time.

40 The Theory of Endosymbiosis  Some evidence in support of endosymbiosis:  The inner membranes of plastids and mitochondria have enzymes that transport proteins and are homologous to those found in living prokaryotes.  Mitochondria and plastids have a replication process similar to binary fission.  Each organelle has a single, circular DNA molecule like that of bacteria--and it isn’t associated with histones or other proteins.

42 Increasing Complexity  The first multicellular organisms were collections of self-replicating cells that became more specialized as time went on.  This specialization likely led to more complexity within a colony of cells that led to the evolution of tissues, organs, and organ systems.

43 Increasing Complexity  Just as the evolution of unicellular eukaryotes led to the increased structural complexity of cells, the evolution of multicellular eukaryotes broke the threshold barrier and led to the explosion of different eukaryotes.  Multicellularity evolved several times in eukaryotes giving rise to many different types of algae, plants, fungi, and animals.

44 The Cambrian Explosion  This refers to the first 20 million years of the Cambrian period where the major phyla of animals appeared ( mya).  This period is well documented in what is referred to as the Burgess Shale.

45 Revising the Tree of Life  In 1969, Robert Whittaker established five major kingdoms of life based on the two types of cells he distinguished: prokaryotes and eukaryotes.  1. Monerans  2. Plants  3. Protists  4. Animal  5. Fungi

46 The Revised Tree of Life  As time went on, scientists began to realize that the organisms did not easily fit into these categories.  This system has since given way to the classification scheme that recognizes 3 major domains:  1. Archea  2. Bacteria  3. Eukarya

47 Classification from the Domain  Two of the domains include bacteria.  For the eukaryotes, once the domain has been identified, it becomes more and more specific:  Kingdom  Phylum  Class  Order  Family  Genus  Species 47