The Origin of Life
The RNA World
The Last Universal Common Ancestor (LUCA)
The History of the Three-Domain System

(http://www.britannica.com/blogs/wp-content/uploads/2009/05/earth.jpg?a14544)
(http://www.britannica.com/blogs/wp-content/uploads/2009/05/earth.jpg?a14544)

Michael Roytman

Contents.
  • The Origin of Life
    • Introduction
    • A Brief Overview
    • Reconciling the Conflict between Spontaneous Generation and Biogenesis
      .
  • The RNA World
    • The RNA World
    • Natural Selection and RNA
      .
  • The Last Universal Common Ancestor (LUCA)
    • An Overview of the Last Universal Common Ancestor

  • The History of the Three-Domain System

  • Works Cited

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The Origin of Life.
Introduction
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The Earth is believed to have been formed approximately 4.5 billion years ago, and evidence of life exists that is 3.5 billion years old, although it is certainly possible that life began as early as 3.9 billion years ago, as some biologists may postulate. The scientific explanations for the origin of life are not, by any means, absolute and are still open to fervent discussion and revision. However, most biologists have come to accept the theory that life on Earth originates from nonliving materials. These nonliving substances are believed to have become ordered into molecular aggregates, referred to as protobionts, which later became able to self-replicate and perform metabolism, leading to the “genesis of prokaryotes” (Campbell 516).
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A Brief Overview
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Life on Earth as we recognize it is believed to have its origins in simple, prokaryotic cells, created, through a number of steps, by means of primordial chemical and physical processes. There is no scientific consensus regarding the character of these biological phases, but there are a number of leading hypotheses. The hypothesis explained in the text suggests the following chronology:
  1. small organic molecules ,or monomers, such as nucleotides or amino acids, are created through the synthesis of nonliving or abiotic molecules or substances
  2. larger molecules, called polymers, , such as nucleic acids and proteins are formed through the fusion of monomers
  3. the emergence of self-replicating molecules
  4. the emergence of protobionts, small membrane-bound droplets that created an internal environment separate from the surrounding external chemistry
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Reconciling the Conflict between Spontaneous Generation and Biogenesis
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Spontaneous generation was an idea that stated that life could come from nonliving or inanimate material; it persisted from the time of Ancient Greece to the 19th century until it was finally defeated by Louis Pasteur’s broth experiment in 1862 in favor of the principle of life referred to as biogenesis, which states that modern life emerges only through the reproduction of existing life. However, this advance in the understanding of the beginning of life raises the question: How, if living substances can only come from other living substances, did living substances come into existence in the first place? This ideological conflict is frequently called the biogenesis paradox. Scientists resolve this obstacle through the use of the Oparin-Haldane hypothesis, which is the notion that because the conditions of early Earth were very different billions of years ago, organic molecules were able to be created from inorganic “precursors”: there was little atmospheric oxygen (and thus a much less severe threat of oxidation) and much more intense energy sources like “lightning, volcanic activity, and ultraviolet sunlight” (516). Therefore, it is believed that these conditions fostered the formation of organic molecules from inorganic molecules; this hypothesis, called the Oparin-Haldane hypothesis, has been experimentally proven multiple times, particularly by the Miller-Urey model.
The Miller-Urey experiment put molecules representing the major components of the Earth's atmosphere into a closed system with gases such as methane, ammonia, hydrogen, and water with a continuous electric current to simulate lightning storms that were thought to be common for early earth. Analyzed by chromotography at the end of one week, Miller found that about 10 to 15% of the carbon had formed organic compounds. 2% had formed some amino acids that are used to make proteins. Therefore, Miller was able to show that under conditions believed to be similar to early earth, amino acids that are essential to cellular life can be made. (IL)
The origin of these organic molecules remains a question surrounded by much debate. Difference hypotheses about early life suggest that the environment played a large role in the formation of these early organic molecules, while others suspect that volcanoes and deep-sea hydrothermal vents were the source of essential abiotic resources or that organic molecules like nucleic acids came to Earth from space on asteroids or even further that life is much more simple than biologists have imagined. Regardless, it is generally accepted that life originated from abiotic sources, although how is still contested.
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The RNA World
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The Role of RNA
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Today’s modern life generally uses a mixture of DNA, RNA, and proteins to carry out life’s essential functions. However, many researchers believe that Earth’s first hereditary material was actually RNA, which is stated in the RNA world hypothesis. This hypothesis helps in part to answer the question of which originated first, nucleic acids or proteins: since nucleic acids are essential in protein-building, and proteins are needed to create nucleic acids, which came first? When researchers discovered that some types of RNA have catalytic properties and/or abilities – these RNA catalysts are called ribozymes -, they were able to better answer this “chicken or the egg” question. That is, since some types of RNA in the prebiotic world were able to catalyze reactions before the existence of enzymes or proteins and DNA, these types of self-replicator RNA were able to both store genetic information and perform ribozyme-catalyzed replication (519). Thus, it is believed that RNA was the first to be used by early organisms for basic cellular processes and requirements.
26-11-AbioticRNAReplicat-L.gif
The autocatalytic replication of RNA
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Natural Selection and RNA

When organisms or molecules are able to self-replicate, they are also able to undergo the process of inheritance, meaning that evolution is able to operate even among early RNA molecules. Indeed, natural selection functioned as a mechanism of evolution among RNA molecules, favoring RNA that was more stable, replicated faster, was better suited to the environment, etc until different forms of life evolved.

It has also been studied through In Vitro experiments (experiments which are performed within a closed environment such as a glass tube) that the early form of RNA was able to self replicate within an hour. It was determined to have been produced through molecular competition for the stability with other competing enzymes. Scientists have now approximated the initial version of the RNA. (RK)

Natural Selection (CM)
Natural Selection (CM)

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Protobionts
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Protobionts are defined as “aggregates of abiotically produced molecules” (Campbell 520). Because life comes from the steady organization of molecules into higher levels of order, the importance of protobionts is in the idea that they preceded living cells. Indeed, protobionts differ greatly from living cells in their capacities – they were not able to reproduce, for example -, but they were, nonetheless, the first instance of membrane-bound structures that had an internal environment that favored evolution due to the microscopic vicinity of necessary and valuable components and that possessed some life-like abilities like metabolism and excitability.
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(JP)
(JP)



Protobionts and RNA
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The revolutionary and critical point in the evolution of early cells would have been the “packaging of primitive RNA genes and their polypeptide products within a membrane” (Campbell 520). Following this incorporation of RNA, protobionts would, due to the ability to self-replicate, have the capacity for evolution and molecular cooperation. Naturally, evolution would take its gradual course, refining and sophisticating the processes of natural selection and metabolism within these protobionts, eventually leading to the development of DNA as the dominant genetic material. As the book so states, this early, microscopic “RNA world” would soon give way to a more familiar “DNA world”.

26-13-MolecCoopHypoth-L.gif
A graph displaying two hypotheses of the start of molecular cooperation

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The Last Universal Common Ancestor
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An Overview of the Last Universal Common Ancestor
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The name is self-explanatory. The Last Universal Common Ancestor, of LUCA for short, is the most recent ancestor of all life on Earth, although to say that it is “recent” is a bit of a misnomer, considering that it is estimated to have been alive around 3.5 to 3.8 billion years ago. Speaking to Discovery News, author of a paper published in the journal Biology Direct, Manfredo Seufferheld described LUCA as “a single celled organism because the extracellular machinery needed for multicellularity was developed in eukaryotes (organisms whose cells contain microstructures) very late in evolution.” Researchers hypothesize that LUCA resembled very closely an archaeum; achaea is a domain of microscopic life somewhat similar but simultaneously quite distinct from bacteria. Characteristic of LUCA is a region of the cell with a relatively high concentration of polyphosphate, which is actually believed to be the very first known universal organelle. Through the use of analytical devices such as phylogenetic trees, researchers have suggested that these polyphosphate storage units date back to LUCA.
Some scientists debate if LUCA was even a cell. It’s been hypothesized to be a “crude assemblage of molecular parts” (Science Daily). Cell researchers, however, have zeroed in on polyphosphate, a type of energy. There are storage units for the polyphosphate all three domains share. This was probably the first organelle, and has led to a breakthrough hypothesizing LUCA may be more complex than previously believed! (LPE)
The LUCA is believed to have lived between 3.6 and 4.1 billion years ago.Although fossils from the period are scant and highly degraded, we can extrapolate characteristics of the LUCA by seeing what features all of life has in common today. This includes a genetic code based on double-stranded DNA, including four nucleotides, making up 64 possible three-nucleotide codons. This selection of nucleotides is arbitrary but universal to all earthly life (RW)

cellzoom.jpg
Bacteria were studied in order to gain a better understanding of LUCA (http://news.discovery.com/animals/zooms/luca-ancestor-complex-111005.html)
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The History of the Three-Domain System
Carolus Linneas, a Swedish scientist, first thought of taxonomy, the idea of classify organisms based on the characteristics of the organisms. Carl Woese discovered the three domain system after coming to the conclusion that archea and bacteria were drastically different. The RNA continues to prove the three domain system correct. (RJ)
The Three-Domain System uses differences in ribosomal RNA to classify species into five kingdoms. Ribosomal RNA, as apparent from the name, determines the structure and purpose of the ribosomes. Genetic sequencing has provided more accuracy in classification and taxonomy. (JS)

external image 450px-Phylogenetic_tree.svg.png(AP)
Review Questions:
1) What is the main purpose, or main role of RNA? (MM)
2) What are Protobionts and what are their relationship to RNA? (CP)
3) How is biogenesis different than the theory of Spontaneous Generation? (AR)
4) What are some characteristics of RNA that lead Scientists to believe that it was Earth's first hereditary material? (AR)
5) What were the 4 biological phases that lead up to simple, prokaryotic cells? (VN)
6) What is the RNA world hypothesis and what has it helped scientists to determine? (ZJ)
7) Define and explain Protobionts in detail, and why they are important in the world of science. (MB)
8) At what point in the history of life did evolution begin, and how did natural selection work at that point in time? (PS)
9) How did RNA evolve into DNA and what is its present function in modern organism? (MS)







Works Cited.
Campbell, Neil A., James B. Reece, Evelyn Dahlgren, Donna Kalal, and Karl Miyajima. Biology, Campbell, Reece, Sixth Edition. San Francisco, CA: B. Cummings, 2002. Print.

"From Soup to Cells—the Origin of Life." Understanding Evolution. U of California Museum of Paleontology, 2006. Web. 23 Oct. 2011. http://evolution.berkeley.edu/evosite/evo101/IIE2aOriginoflife.shtml.

Hamilton, Garry. "Mother superior: she's the ancestor of every living thing on the planet, yet we know so little about her. Time for a bit of extreme genealogy." New Scientist 187.2515 (2005): 26+. Gale Science In Context. Web. 23 Oct. 2011.

How did life originate?" Understanding Evolution. U of California Museum of Paleontology, 2006. Web. 23 Oct. 2011. < http://evolution.berkeley.edu/evosite/evo101/IIE2bDetailsoforigin.shtml>.

"Origin of Life." Biology. Ed. Richard Robinson. New York: Macmillan Reference USA, 2009. Gale Science In Context. Web. 23 Oct. 2011.

"Origin of Life." World of Earth Science. Ed. K. Lee Lerner and Brenda Wilmoth Lerner. Detroit: Gale, 2007. Gale Science In Context. Web. 23 Oct. 2011.

"Studying the origin of life." Understanding Evolution. U of California Museum of Paleontology, 2006. Web. 23 Oct. 2011. http://evolution.berkeley.edu/evosite/evo101/IIE2bStudyorigins.shtml.

Viegas, Jennifer. "Meet LUCA: Our Complex Ancestor." Discovery News. Discovery Communications, 2011. Web. 23 Oct. 2011. <http://news.discovery.com/animals/luca-ancestor-complex-111005.html>.

Wade, Nicholas. "Chemist shows how RNA can be the starting point for life." New York Times 14 May 2009: na(L). Gale Science In Context. Web. 23 Oct. 2011.


http://www.sciencedaily.com/releases/2011/10/111005112145.htm (LPE)


'What is the Three Domain System?' innovatus.com.2006. Oct.30,2011.http://www.innovateus.net/science/what-three-domain-system

http://biology.about.com/od/evolution/a/aa041708a.htm (JS)

http://www.biocab.org/files/PROBABLE_APPEARANCE_OF_AN_EARLY_PROTOBIONT.jpg (JP- picture)


Lincoln, Tracey A.; Joyce, Gerald F. (January 8, 2009). "Self-Sustained Replication of an RNA Enzyme". Science (New York: American Association for the Advancement of Science) 323 (5918): 1229–32. doi:10.1126/science.1167856. PMC 2652413.PMID 19131595. Retrieved 2009-01-13. Lay summaryMedical News Today(January 12, 2009). (RK)

"The Miller/Urey Experiment." Cruising Chemistry. Duke University. Web. 14 Nov. 2011. <http://www.chem.duke.edu/~jds/cruise_chem/Exobiology/miller.html>. (IL)
http://www.wisegeek.com/what-is-the-last-universal-common-ancestor-luca.htm (RW)