1.
What is a ribozyme, and why, in general, was the discovery of this type of RNA so important to hypotheses about the origin of life? Explain the statement that RNA can simultaneously possess both a genotype and a phenotype, and why DNA and proteins cannot.
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2.
Describe the basic "RNA World hypothesis" and discuss the evidence that RNA is ancient, as predicted by this hypothesis.
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3.
Describe Spiegelman et al.'s and Beaudry and Joyce's experimental evidence that RNA can evolve. List and briefly discuss the kinds of reactions ribozymes are now known to be able to catalyze, relating as many as possible to common cellular metabolic tasks. Defend the statement that a self-replicating population of RNA would have the essence of life even in the absence of cellular organization.
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4.
Why is the "RNA-dependent RNA autoreplicase" the "Holy Grail for origins-of-life research"? Describe Bartel et al.'s "selective breeding" experiments and Johnston et al.'s evolution of a catalytic RNA, and discuss their implications for the development of catalytic RNAs capable of self-replication. Give your own interpretation of what Gerald Joyce meant when he wrote that "Once an RNA enzyme with RNA replicase activity is in hand, the dreaming stops and the fun begins."
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5.
What four major issues must be addressed in order to reconstruct the advent of information-containing, self-replicating organic molecules? Discuss evidence from the Murchison meterorite and studies of the composition of the early atmosphere on Earth that simple organic molecules might have arrived on Earth from extraterrestrial sources. What are some of the critical arguments against this hypothesis?
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6.
Discuss the panspermia hypothesis for the origin of terrestrial life. What are some of the candidates for the extra-terrestrial birthplace of life? What evidence do we currently have that an extraterrestrial origin of life may have taken place? What are some of the problems with this hypothesis?
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7.
Describe the Oparin-Haldane model for prebiotic evolution. Discuss the relevance of Stanley Miller's experiments on the prebiotic synthesis of amino acids and Juan Oro's experiments on the prebiotic synthesis of nitrogenous bases to this model. What difficulties remain with the hypothesis that the earth possessed all the necessary ingredients and the appropriate conditions for the origins of life, and what precursors to the "RNA World" have been proposed?
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8.
Explain the "hydrolysis problem" with models of prebiotic biological polymerization. What solution have Ferris et al. proposed, and what evidence supports their hypothesis?
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9.
Discuss the evidence that life was established on Earth by 3.85 billion years ago. What evidence suggests that Earth would have been inhospitable to life much earlier than about 4 billion years ago? In what way would Earth have been more hospitable to the origins of life in the past than it is in the present? Use the diagram of the history of large impacts on the Earth and Moon to answer the question.
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10.
What advantages would cellular membranes have offered to early forms of life? What evidence does the fossil record provide about the origin of cellular life? Discuss the primary challenge in using nucleotide sequence data to address this question, being sure to include a description of the characteristics necessary for a given gene to be useful for this type of analysis. In what ways does the small-subunit rRNA meet the relevant criteria?
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11.
Describe the "universal phylogeny" developed by Woese and colleagues from rRNA sequences. How does the pattern represented by this phylogeny differ from that implied by the traditional "five kingdom" classification scheme? Discuss how the universal phylogeny (if correct) can be used to infer characteristics of the last common ancestor of modern life forms.
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12.
Describe the two trends that promise to improve both our understanding of the universal phylogeny and the biology of the most recent common ancestor. What is horizontal gene transfer, and what evidence suggests that it was rampant during the early stages of the evolution of cellular life? What are the earliest and most recent possible dates for the first branching in the universal phylogeny, and on what evidence are those dates based?
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13.
How do the Eucarya differ from Bacteria and Archaea? Discuss the endosymbiotic hypothesis for the origin of mitochondria and chloroplasts, including the evidence supporting it.
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14.
Compare and contrast nuclear DNA with the DNA found in chloroplasts and mitochondria. Compare and contrast the DNA found in chloroplasts with that found in mitochondria. How have the genomes of mitochondria and chloroplasts evolved since these symbionts took up residence inside eukaryotic cells?
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