1. BIOE 109 Summer 2009 Lecture 12-Part I The origin of life

2. There is grandeur in this view of life, having been breathed into a few forms or into one; …….from so simple a beginning endless forms most beautiful and most wonderful have been, and are being, evolved.” Charles Darwin, 1859

3. Did life originate on earth once or many times? What was the first living thing? When did the last common ancestor of all living things come into existence? What is the shape of tree of life? questions, questions and questions………

4. Some problems in addressing the origin of life on earth

5. Some problems in addressing the origin of life on earth 1. Narrow time window

6. Some problems in addressing the origin of life on earth 1. Narrow time window the age of the earth is 4.55 billion years old.

7. Some problems in addressing the origin of life on earth 1. Narrow time window the age of the earth is 4.55 billion years old. life first appeared about 3.8 billion years ago.

8. Some problems in addressing the origin of life on earth 1. Narrow time window the age of the earth is 4.55 billion years old. life first appeared about 3.8 billion years ago. the planet could not have sustained life for its first 500 million years!

9. Some problems in addressing the origin of life on earth 1. Narrow time window planet could not have sustained life for its first 500 million years!

10. Early large impact strikes on the earth and moon Moon formed!

11. Some problems in addressing the origin of life on earth 2. Most “simple” cells are extremely complex Staphylococcus epidermidis

12. Some problems in addressing the origin of life on earth 2. Most “simple” cells are extremely complex “simple” bacteria possess about 1,600 genes. Haemophilus influenzae 1,743 genes

13. Some problems in addressing the origin of life on earth 2. Most “simple” cells are extremely complex “simple” bacteria possess about 1,600 genes. how did primitive cells evolve without enzyme- catalyzed metabolism?

14. Some problems in addressing the origin of life on earth 2. Most “simple” cells are extremely complex “simple” bacteria possess about 1,600 genes. how did primitive cells evolve without enzyme- catalyzed metabolism? Hammerhead ribozyme!

15. Some problems in addressing the origin of life on earth 2. Most “simple” cells are extremely complex “simple” bacteria possess about 1,600 genes. how did primitive cells evolve without enzyme- catalyzed metabolism? 3. Life evolved under very different conditions

16. Some problems in addressing the origin of life on earth 2. Most “simple” cells are extremely complex “simple” bacteria possess about 1,600 genes. how did primitive cells evolve without enzyme- catalyzed metabolism? 3. Life evolved under very different conditions atmosphere dominated by methane, hydrogen sulfide, ammonia, carbon monoxide, water vapor.

17. How do we define life?

18. 1. Must be capable of reproducing.

19. How do we define life? 1. Must be capable of reproducing. 2. Must possess a genotype and a phenotype.

20. How do we define life? 1. Must be capable of reproducing. 2. Must possess a genotype and a phenotype. 3. Must possess a metabolism.

21. How do we define life? 1. Must be capable of reproducing. 2. Must possess a genotype and a phenotype. 3. Must possess a metabolism. 4. Must be capable of evolving.

22. Theories for the evolution of life

23. Theories for the evolution of life 1. Extraterrestrial theories in 1907, Arrhenius proposed the theory of “Panspermia”.

24. Theories for the evolution of life 1. Extraterrestrial theories in 1907, Arrhenius proposed the theory of “Panspermia”. panspermia means “germs everywhere”.

25. Theories for the evolution of life 1. Extraterrestrial theories in 1907, Arrhenius proposed the theory of “Panspermia”. panspermia means “germs everywhere”. life originated elsewhere in the universe and drifted from planet to planet by pressure of starlight.

26. Sir Francis Crick was an advocate for “directed panspermia”

27. Theories for the evolution of life 2. The chemical theory (Oparin-Haldane theory)

28. Theories for the evolution of life 2. The chemical theory (Oparin-Haldane theory) life originated on earth following a period of “chemical evolution”. both scientists were strongly influenced by a letter written by Darwin in 1871.

29. The chemical theory

30. inorganic molecules  organic molecules  biological polymers  replicating systems  protobionts  true cells

31. Step 1. Inorganic molecules  organic molecules

32. Step 1. Inorganic molecules  organic molecules 1. Extraterrestrial evidence

33. Step 1. Inorganic molecules  organic molecules 1. Extraterrestrial evidence the Murchison meteorite contained over 70 amino acids!

34. Step 1. Inorganic molecules  organic molecules 1. Extraterrestrial evidence the Murchison meteorite contained over 70 amino acids! equal mixture of D and L isomers present.

35. Step 1. Inorganic molecules  organic molecules 1. Extraterrestrial evidence the Murchison meteorite contained over 70 amino acids! equal mixture of D and L isomers present. urea, various amides, ketones and aldehydes were also found.

36. 2. Laboratory experiments successful in producing amino acids, sugars, and nucleic acids. “Miller-Urey” experiment Stanley Miller (1930-2007) Volcanic spark discharge experiment

37. Step 2. Organic molecules  biological polymers

38. Step 2. Organic molecules  biological polymers polynucleotides (n = 40) have been synthesized on the clay mineral montmorillonite. polypeptides (n = 55) have been synthesized on a mixture of two minerals - illite and hydroxylapatite

39. Step 3. Biological polymers  replicating systems

40. Step 3. Biological polymers  replicating systems early replicating systems may have been RNA-based.

41. Step 3. Biological polymers  replicating systems early replicating systems may have been RNA-based. catalytic RNAs called ribozymes may have preceded enzymes (proteins). Hairpin ribozyme Hammerhead ribozyme

42. Ribozyme from Tetrahymena thermophila

43. Step 3. Biological polymers  replicating systems early replicating systems may have been RNA-based. catalytic RNAs called ribozymes may have preceded enzymes (proteins). RNAs may have replicated by “base-pairing rules”.

45. Step 3. Biological polymers  replicating systems early replicating systems may have been RNA-based. catalytic RNAs called ribozymes may have preceded enzymes (proteins). RNAs may have replicated by “base-pairing rules”. if “mistakes” made in copying, natural selection can occur!

46. Evidence for an early role for RNA “The RNA World”

47. Evidence for an early role for RNA (“The RNA world”) RNA is involved in: 1. DNA replication. 2. Protein synthesis. 3. Ribonucleoside triphosphates (ATP, GTP) are the energy currency of cells. 4. Deoxyribonucleotides are synthesized from RNA precursors.

48. Step 4. Replicating systems  protobionts

49. Step 4. Replicating systems  protobionts heating and cooling mixtures of amino acids can form spherical proteinoids.

50. Step 4. Replicating systems  protobionts heating and cooling mixtures of amino acids can form spherical proteinoids. mixtures of lipids and proteins can form liposomes.

51. Step 4. Replicating systems  protobionts heating and cooling mixtures of amino acids can form spherical proteinoids. mixtures of lipids and proteins can form liposomes. liposomes can “reproduce” by budding off smaller units.

52. Step 4. Replicating systems  protobionts heating and cooling mixtures of amino acids can form spherical proteinoids. mixtures of lipids and proteins can form liposomes. liposomes can “reproduce” by budding off smaller units. if an RNA-protein based metabolism evolved, natural selection can again occur.

53. Step 5. Protobionts  true cells

54. Step 5. Protobionts  true cells natural selection would have acted to biochemical sophistication of protobionts.

55. Step 5. Protobionts  true cells natural selection would have acted to biochemical sophistication of protobionts. DNA became the “repository” of the genetic information.

56. Step 5. Protobionts  true cells natural selection would have acted to biochemical sophistication of protobionts. DNA became the “repository” of the genetic information. Why?

57. Step 5. Protobionts  true cells natural selection would have acted to biochemical sophistication of protobionts. DNA became the “repository” of the genetic information. Why? 1. DNA is more stable than RNA.

58. Step 5. Protobionts  true cells natural selection would have acted to biochemical sophistication of protobionts. DNA became the “repository” of the genetic information. Why? 1. DNA is more stable than RNA. 2. RNA freed to act only in one arena (catalysis).

59. DNA takes control of information storage

60. What is the evidence for prokaryotic life 3.5 to 4.0 BYA?

61. What is the evidence for prokaryotic life 3.5 to 4.0 BYA? 1. Stromatolites

62. What is the evidence for prokaryotic life 3.5 to 4.0 BYA? 1. Stromatolites are bun-shaped structures made by cyanobacteria. fossil stromatolites are abundant 3.5 bya.

63. What is the evidence for prokaryotic life 3.5 to 4.0 BYA? 1. Stromatolites are bun-shaped structures made by cyanobacteria. fossil stromatolites are abundant 3.5 bya. recently “re-discovered” in shallow, hypersaline environments (e.g., Hamelin pool in Shark Bay, western Australia).

64. What is the evidence for prokaryotic life 3.5 to 4.0 BYA? 2. C isotope ratios suggest early photosynthesis

65. What is the evidence for prokaryotic life 3.5 to 4.0 BYA? 2. C isotope ratios suggest early photosynthesis 12 CO 2 is preferentially fixed in photosynthesis than the heavier 13 CO 2.

66. What is the evidence for prokaryotic life 3.5 to 4.0 BYA? 2. C isotope ratios suggest early photosynthesis 12 CO 2 is preferentially fixed in photosynthesis than the heavier 13 CO 2. isotopic ratios of 13 C to 12 C indicate that autotrophic bacteria fixing carbon via the Calvin cycle by 3.5 bya.

67. What is the evidence for prokaryotic life 3.5 to 4.0 BYA? 2. C isotope ratios suggest early photosynthesis 12 CO 2 is preferentially fixed in photosynthesis than the heavier 13 CO 2. isotopic ratios of 13 C to 12 C indicate that autotrophic bacteria fixing carbon via the Calvin cycle by 3.5 bya. where did the O 2 go? Into the oceans to form banded ironstone sediments.

68. The origin and early evolution of the eukaryotes

69. The origin and early evolution of the eukaryotes 1.The universal gene-exchange pool hypothesis -Proposed by Carl Woese (the discoverer of Archaea) -Based on the fact that significant conflict exists between branching patterns of Archaea, Bacteria and Eucarya -Downplays importance of natural selection -Is extremely controversial

70. The origin and early evolution of the eukaryotes 1. The universal gene-exchange pool hypothesis Archaea, Bacteria, and Eucarya evolved only after extensive lateral gene transfer ceased. Lot of gene swapping at the base of the tree

71. The origin and early evolution of the eukaryotes 1. The universal gene-exchange pool hypothesis Archaea, Bacteria, and Eucarya evolved only after extensive lateral gene transfer ceased. 2. The ring of life hypothesis

72. The origin and early evolution of the eukaryotes 1. The universal gene-exchange pool hypothesis Archaea, Bacteria, and Eucarya evolved only after extensive lateral gene transfer ceased. 2. The ring of life hypothesis Eucarya evolved from a fusion of a bacterium and an archean.

73. The ring of life hypothesis

74. The origin and early evolution of the eukaryotes 3. The chronocyte hypothesis

75. The chronocyte hypothesis

76. The origin and early evolution of the eukaryotes 3. The chronocyte hypothesis a chronocyte lineage evolves cytoskeleton and phagocytosis. chronocyte engulfs an archaean that became an endosymbiont the endosymbiont eventually becomes the nucleus.

77. The origin and early evolution of the eukaryotes 4. The three viruses, three domains hypothesis

78. The origin and early evolution of the eukaryotes 4. The three viruses, three domains hypothesis DNA-based viruses evolved to counter host’s defenses (that were RNA-based).

79. The origin and early evolution of the eukaryotes 4. The three viruses, three domains hypothesis DNA-based viruses evolved to counter host’s defenses (that were RNA-based). DNA-based viruses invaded RNA-based lineages.

80. The origin and early evolution of the eukaryotes 4. The three viruses, three domains hypothesis DNA-based viruses evolved to counter hosts defenses. DNA-based viruses invaded RNA-based lineages. the RNA genes were reverse-transcribed into DNA and incorporated into new lineages.

81. The three viruses, three domains hypothesis