1. Chapter 26 The Tree of Life

2. 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.

3. 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.

4. 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.

6. 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.

7. 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.

10. 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.

11. Other Experiments  There is some evidence that 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.

12. 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.

14. Deep Sea Hydrothermal ventsDeep Sea Hydrothermal vents

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. More on the Miller-Urey Experiment  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.

24. 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 “life” could have arisen.

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

26. 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.

27. More on 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.

28. More on 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.

29. Fossils  Most fossils are found in sedimentary rock in layers called strata. The deeper the strata, the older the fossils.  Fossils found in each stratum are often compared to other fossils found at other sites.  Similar fossils are called index fossils.

30. Fossils  The sequence of the strata tells us the order of the fossils being laid down, but nothing of the year they were deposited.  There are a number of ways in which fossils can be dated using naturally occurring phenomenon.

32. Radiometric Dating  This is based on the decay of radioactive isotopes which are found naturally in all organisms.  Radiocarbon dating can be used to accurately date specimens up to 40,000 years old.  Radiopotassium dating can be used to date nearly everything.

33. Radiocarbon Dating  The normal carbon isotope is C-12  The radioactive isotope is C-14, and has a half-life of 5730 years.  C-14 decays and becomes N-14. Comparing the ratio of C-14 to N-14 allows us to determine a fossil’s age so long as it’s 40,000 years old or younger.

35. Radiopotassium Dating  The normal isotope of potassium is K- 39  The radioactive isotope of potassium is K-40  K-40 decays into Ar-40  The current ratio of K-40 to Ar-40 gives us an estimate of when the layer was formed.

37. Radiopotassium Dating  When fossils die between 2 layers of volcanic rock, paleontologists can measure the amount of radioactive potassium in each of the layers to determine the age.

38. Radiopotassium Dating  K-40 decays into Ar-40. When the rock gets heated during a volcanic eruption, all argon is driven off and the potassium remains. This process resets the K-40 decay to zero.  Comparing this ratio to the current K-40 to Ar-40 ratio gives us an estimate as to the age of the layers and thus the fossil.

40. Magnetism  The magnetism within rocks can also reveal clues of the past.  When volcanic or sedimentary rock forms, the particles within it that contains iron align themselves with the Earth’s magnetic field.  The Earth’s magnetic field occasionally shifts and the poles reverse.

41. Magnetism  By measuring the magnetism of the rock, and correlating the data from patterns obtained in other locations scientists can date material when other methods are not available.

42. Mass Extinctions  The boundaries of the major timeframes of the geologic record correspond to mass extinctions.  These extinctions are clearly seen in the fossil record.  A drastic decline of the number of hard bodied animals that once lived in the shallow seas illustrates this point.

44. Mass Extinctions  Mass extinctions are caused by a number of different things:  1. Habitat destruction  2. Rise or fall in ocean temperature  3. Cosmic events

45. Mass Extinctions  The Permian and Cretaceous mass extinctions are the most widely studied.  Permian-251 mya  96% of all marine animal species died.  8 of the 27 orders of insects were wiped out.  Cretaceous-65.5 mya  50% of all marine species were wiped out  Many families of plants and animals died, including the dinosaurs.

47. The Permian Mass Extinction  Occurred at a period of extreme volcanism in what is now known as Siberia.  It was the most active period of volcanism in the past 1/2 billion years.  The ash and CO 2 altered the global climate.  Slowed the ocean currents  Reduced the amount of O 2 available for marine organisms.

48. The Cretaceous Mass Extinction  May have been caused by a meteor impact.  The evidence in support of this is revealed by the fact that there is a thin layer of iridium enriched clay that separates the Cenozoic and Mesozoic eras.

49. The Cretaceous Mass Extinction  Walter and Luis Alvarez and their colleagues hypothesized that the iridium rich clay layer is result of the impact of the asteroid or comet.  Researchers located the impact crater off the coast of Mexico near the Yucatan peninsula.  It’s called the Chicxulub crater.

52. Mass Extinctions  The mass extinctions have provided great chances for adaptive radiation as ecological niches opened when species died.

53. Organized Life  The oldest known fossils are about 3.5 bya.  They are fossilized stromatolites. Which are rock-like layers of bacteria and sediment.  Present-day stromatolites are found in warm, shallow, salty bays.

57. Early On  Early on in prokaryotic history, 2 main branches occurred:  Bacteria and Archea  They diverged and still thrive today.

58. 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.

59. 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.

60. 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.

62. 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 descendents survive today as obligate anaerobes.

63. 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.

64. Eukaryotic Cells and Their Origin  The oldest fossils of eukaryotic cells are about 2.1-2.2 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.

65. 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.

66. The Theory of Endosymbiosis  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.

67. 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.

68. The Theory of Endosymbiosis  Evidence in support of endosymbiosis:  The inner membranes of plastids and mitochondria have enzymes that transport proteins that 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.

70. 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.

71. 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.

72. The Cambrian Explosion  This refers to the first 20 million years of the Cambrian period where the major phyla of animals appeared (540-520 mya).

73. 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

74. 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