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Section 22_1: Origin of Life of Earth

Page history last edited by Aditya Aiyer 9 years, 10 months ago

 

A. Learning Objectives:

• Outline the four overlapping stages that are hypothesized to result in cellular life as we currently understand it. 

 

B. Section Summary:

     The origin of life has been a bewildering subject that scientists have long since debated, and several studies have been conducted to theorize the origin of life. How did life begin? One scientifically accepted explanation of the origin of life is that the Earth was formed 13.7 billion years ago by growing planetesimals, or objects composed of dust, rock, and other materials, and had a extremely hot temperature . After 4.6 billion years from the formation of the Earth, the solar system started to form. About 50 million years later, the Earth's tremendous temperature cooled down, eventually forming oceans, and giving rise to a range of temperatures suitable for life to exist. Thus, with the fossil record and this above explanation, scientists have defined four overlapping stages of the potential origin of life. 

 

      In the first portion of section 22.1, four stages are ordered as follows: Stage 1: Organic molecules, like amino acids and nucleotides, were formed first and the precursors to all life, Stage 2: Simple organic molecules were synthesized into complex molecules such as nucleic acids and proteins, Stage 3: Complex molecules are enclosed by membranous structures that lead to the cell-like structure formation, and Stage 4: Cell characteristics became more defined as the membranous structures became more chemically selective and developed unique properties.

 

     Stage 1 discusses how two scientists, Oparin and Haldane, theorized the formation, or "prebiotic/abiotic synthesis", of organic molecules occurred due to conducive conditions in early Earth development. Haldane and Oparin called the newly synthesized organic molecules a "primordial soup" that gave rise to living cells. Recent hypotheses suggest that due to little free oxygen gas to oxidize the complex molecules or no living organisms to metabolize complex molecules, the gradual accumulation of complex molecules gave rise to a "prebiotic soup" that caused life to emerge. Among widely debated experiments with supporting hypotheses were conducted to understand how organic molecules formed, there are some hypotheses still frequently debated.

     One such hypothesis discussed was the Reducing Atmosphere hypothesis, which states high atmospheric levels of water vapor, methane, hydrogen, and ammonia gases caused redox reactions where low oxygen levels mean more methane and ammonia molecules can reduce other inorganic molecules, lead to the formation of organic molecules. The scientists Stanley Miller and Harold Urey devised an experiment to support this hypothesis in which he produced hydrogen cyanide and formaldehyde, organic molecules, from water vapor, methane, and hydrogen gases in vitro. In doing so, Miller and Urey proved the prebiotic formation of molecules existed. However, scientists still debate on whether Miller and Urey's experiments supporting the reducing atmosphere is accurate because recent experiments support the idea that prebiotic synthesis could have occurred in environments besides a reducing atmosphere. 

     Another widely debated hypothesis is the Extraterrestrial hypothesis, which states that the carbon needed for organic molecule formation came from asteroids and comets to the Earth's surface, and the organic monomers like amino acids came from meteorites. Due to inconclusive evidence, this hypothesis still remains debatable as to its validity.

     Finally, a third widely debated hypothesis is the Deep Sea Vent hypothesis, which states that organic molecules may have came from deep sea vents, or cracks in the Earth's surface, where superheated water containing metal ions and hydrogen sulfide and cold seawater mix. This hypothesis is expanded to state that biologically important organic molecules are synthesized from a temperature gradient between the hot and cold waters that surround the deep sea vent. Although this hypothesis is scientifically enticing, this hypothesis is still subject to debate because there is still doubt among scientists on truly how organic molecules prebiotically came about. 

 

     Stage 2 discusses scientists hypothesize that because hydrolysis is complemented with dehydration synthesis, complex molecule formation may have occurred on a solid surface or evaporating tidal pools, not in a watery prebiotic soup. Particularly, scientist John Bernal stated that complex organic molecule synthesis has taken place on clay as many clay minerals have been noted to bind to amino acids and nucleotides. Some experiments have proven organic molecule-clay interactions, but work of Luke Leman suggests otherwise that complex molecules are made from aqueous solutions, which supports the hypothesis that prebiotic organic molecules were made in the "prebiotic soup".  

 

     Stage 3 discusses how scientists characterize the formation of a boundary or membrane composed of macromolecules that isolates the inner nucleic acid contents and chemical properties from the outer environment as nonliving structures called "protobionts". The complex organic molecules also possessed information, developed enzymatic functions, and eventually developed an nonspecific cell replication capability. Researchers believe that protobionts may have exhibited structures like liposomes and coacervates. Russian scientist Oparin theorized that living cells are descendants of coacervates, or clusters of charged polymers surrounded by water that are chemically selective. Liposomes are another type of protobiont structure, differing from coacervate in that a liposomes are vesicles surrounded by lipid bilayers. In a recent experiment, scientists Hanczyc, Fujikawa, and Szotak showed that clay can break down liposomes, and found that RNA was contained in the liposomes and the liposomes had the ability to replicate, and provided a reasonable explanation for the emergence of the first cell-like structures.

 

     Stage 4 discusses how scientists believe that RNA was the first complex organic molecule found in protobionts because RNA could store information within its sequence, self-replicate, and perform several enzymatic functions as ribozymes, which are characteristics DNA and proteins do not share. Scientists noted that the prebiotic RNA molecules acquired properties and characteristics that aided cellular survival and reproduction. Scientists proposed that populations of normal RNA were changed through mutations gradually to become a mutant RNA population with different nucleotide sequence composition, a concept known as chemical selection. The process of chemical selection was believed to occur in two steps: first, a mutation causes an RNA molecule to enzymatically synthesize an RNA molecule from a preexisting template, thus increasing the amount of RNA can perform enzymatic function. Second, another mutation causes causes an RNA molecule to synthesize ribonucleotides, and through replication, the resulting population acquired the property of synthesizing ribonucleotides. Thus, protobionts consisting of RNA contents were able to evolve into the living cells that resulted in the emergence of life.

 

C. Useful Materials:

 

 


This video is very informative. It is a lecture by Professor David Deamer at UC Santa Cruz. This lecture discusses about self-assembly, polymerization, and replication. This lecture thoroughly explains how Stage 3, the self-assembly of liposomes,  Stage 2, organic molecule polymerization, occurs and why these stages are essential to the existence of living cells. Skip to 1:00 to start the discussion of the Origin of Life and stop at 22:14.

 

It also highlights and explains why experiments like Stanley Miller's experiment supporting the prebiotic synthesis of organic molecules are important to the origin of life. This lecture is really interesting even in later parts as the professor gives real examples of his work dealing with the origin of cellular life. Hope this helps. 

 
 

This short 6 minute video is pretty awesome. When I finished reading on the four overlapping stages, I did not exactly understand the purpose of the extraterrestrial hypothesis and Stage 3. After watching this mini-lecture given by Professor Deamer, I got a better sense of how the extraterrestrial hypothesis and Stage 3 are relevant to the origin of life. Professor Deamer goes into some detail about his work on self-assembly of molecules. 

 

A cool part about this video is that Deamer actually explains his different findings across the globe and how those findings relate to a bigger picture: his team believes that without membranes, cellular life cannot exist. I thought Professor Deamer goes a great job in giving a perspective about how science is able to approach the origin of life more objectively than does religion. Like it helped me understand some confusing concepts, I think you may gain helpful perspective on how the different pieces fit together. 

http://www.mcb.ucdavis.edu/faculty-labs/scholey/journal%20papers/Ricardo-Szostak-SA2009.pdf 

I would prefer informative videos with diagrams to papers as solid learning, but this paper gave me a clear understanding of Stage 4 of the origin of life. It explained the reason why RNA could have come before DNA. It discussed about how Stage 3, which is dealing with protobionts, were formed. The paper also includes information about the RNA world (which is covered in this portion of section 22.1). If you are interested, feel free to read further into the paper to gather extra information to get ready for the next portion of section 22.1.

 

Stage 4 is a major portion of this portion in section 22.1 and is essential to understand the remaining portion of section 22.1 covered later. So, this article expands on the central reasons as to why RNA was the inner contents of protobionts, and how it shaped the evolution of protobionts into the living cells that carry many interconnected functions with specialized organelles. Just as I enhanced my understanding of Stage 4 from reading this article, I believe this may help clarify some doubts you have about why Stage 4 is as important stage in the origin of life.  

 
http://www.mansfield.ohio-state.edu/~sabedon/campbl26.htm 

This link provides a great overview of the Reducing Atmosphere hypothesis, and other useful information as well. It explains that the lack of fossils from the earliest existing organism has left left several hypotheses regarding the origin of life. In addition, it expands on some concepts in Stage 2 such as the Clay theory.

 

This link is a helpful review of the Reducing Atmosphere hypothesis and Clay theory with the purpose of enhancing understanding of these concepts. I found that this link provides information about the RNA World as well, which may be of help to read for the next portion of section 22.1. As I found this link to be worth referring to, it may be of help to you to read the relevant material found in this link, which pertains to the focus of this portion of section 22.1.  


 

D. Primary Literature:

 

http://www.im.microbios.org/0801/0801023.pdf 

 

    On the concept of the origin of life, many scientists have debated on the heterotrophic mechanism of the origin of life based on the formation of simple microanaerobic organisms. These organisms were produced from abiotic materials that arose from conditions in early Earth. However, some scientists believe that the origin of life started with an autotrophic mechanism originating from inorganic molecules. There have been several arguments on the self-replication process of the first gene versus the first simple metabolic enzymatic network as a starting point. The formation of a cell and its boundary, the cell membrane, and intracellular organelles has been another important topic of debate among several researchers trying to validate their work. Autonomy and open ended evolution concepts were introduced to explain life as an autonomous system with evolutionary capacities. In this article, the author analyzes systematically the work of several researchers and proposes that origin of life was primarily based on organic molecules prebiotically synthesized to form complex macromolecules as a primitive metabolism network inside cell-like structures. The flow of matter and energy within this early metabolic system has allowed the formation of more complex molecules like nucleic acids, which led to the formation genes, and then more highly developed genomes. At this point, scientists acknowledged that the origin of life was an intricate process involving an interaction between ecological/environmental systems and complex organic molecules with a boundary of autonomous capabilities, eventually evolving into living cells with hereditary and Darwinian evolutionary capabilities.

 

      In an effort to understand the first steps of life evolution, there were two strategies taken. One was called the “Top-down” strategy in which all organisms were compared in order to reconstruct an accurate genetic and metabolic makeup of an universal ancestor. However, in this methodology, the tools are limited to a retrospective study of such ancestral structures. The other strategy is called the “bottom-up” strategy in which the interaction of cosmochemical, planetelogical, geological, and other sources of information were used to construct an ambient and chemical inventory for the origin of life. This strategy was also supported by computer modeling and scientific theorizing of early Earth’s atmosphere and primitive geochemical conditions. Some experiments trying to explain the prebiotic origin of organic molecule include Oparin's 1920 experiment involved chemically implementing simple artificial life forms, and the Urey-Miller experiment investigated the prebiotic chemistry and formation of amino acids from hydrogen cyanide and formaldehyde, which proved the abiotic synthesis of organic matter. Additionally, both terrestrial and extraterrestrial mechanisms were proposed such as the widely debated Extraterrestrial hypothesis, although no substantial evidence regarding early Earth’s atmosphere existed other than the experiments featuring the Reducing Atmosphere hypothesis. Another hypothesis, called Deep Sea Vent hypothesis, proposed by organic chemist Gunter Wachtershauser, states tha geothermal vents were a mechanism through which organic molecules were prebiotically synthesized where the superheated water containing hydrogen sulfide and metal ions mixed with the cold seawater, ultimately created a temperature gradient that allowed prebiotic synthesis and release of organic molecules. Chemical evolution has produced a primitive self-maintaining chemical system with metabolism capabilities for a primitive cell called a “protocell”. As seen in stage 4 of the origin of life, RNA had acquired chemical properties and constituted the inner information of a "protocell", and as highlighted in the summary above, provides a basic metabolic function as a ribozyme for synthesis of proteins, and has the ability to self-replicate and store information. Eventually DNA replaces the RNA and begins a process called open-ended evolution that will be covered in the later portion of section 22.1. 

 

     In essence, an organized mechanism was needed to explain a theory of the origin of life in which precursors that existed prebiotically were converted gradually into chemical or biochemical entities that could support life under ambient environmental conditions. In addition. future studies are needed to enhance scientific understanding of the origin of true heredity, and the flow of matter through the emerging system. As this article helped me further my understanding of the origin of life, particularly shedding light to the way the four stages of the origin of life applies to a broader picture, I believe this article may give you insight on why the origin of life is a widely debated, yet fascinating concept to research and interpret.  

 

 

E. Virtual Lectures:

 

 

F. PowerPoint Slides:

 

Section 22.1 Overlapping Stages AA.ppt

                             or

Section 22.1 Lecture Slides

 

G. Final Exam Questions:

Submitted via Lion's Mail

H. Grading Sheet:

Grading Sheet (Aditya)

 


Chemical Selection and the RNA World 

 

A. Summary:

     

     As the previous section briefly discussed, many scientists believe that the current world (DNA, RNA, protein) evolved from a world where living cells contained only RNA. The driving force behind this theory is that through chemical selection, RNA with special properties was passed on through many generations.

 

     First, let's discuss the process of chemical selection. Chemical selection, in simplest terms, happens when a chemical has special abilities that allow it to increase in number as opposed to other chemicals that don't have these abilities. What better example than RNA? RNA has three special properties that no other molecule has. RNA can: store information using nucleotides, self-replicate (base pairs can be added to a complementary strand of RNA and then separate), and act as an enzyme (ribozymes). The pertinent question is: how did this RNA ever come to exist? Scientists have used their knowledge of chemical selection to piece together a scenario. First, a mutation has to occur. We can theorize that a mutation that caused RNA to self-replicate occurred first. Now that this mutant RNA has the enzymatic ability to attach nucleotides, the amount of RNA with this mutation increases. Now, we can theorize that a second mutation occurred. This second mutation would have given RNA the property of synthesizing nucleotides. Since nucleotides are the building blocks of RNA, more RNA could be synthesized at a faster rate. Now, RNA with both mutations would be favored over RNA with one or no mutation. This led to the introduction of the RNA world hypothesis, which is a proposed scenario where genetic information and enzymatic abilities all lied in RNA at one point before current life. We might ask ourselves, why RNA and not DNA or proteins? RNA can act as both an enzyme and source of genetic information, the two functions of proteins and DNA, respectively. In other words, it is more versatile. Now that there is a scenario, how can one support it? This is what scientists David Bartel and Jack Szostak set out to do.

 

    Bartel and Szostak hypothesized that out of a large amount of RNA molecules, a few might have the ability to catalyze a covalent bond between nucleotides and that these molecules could be used in the laboratory. The experiment consisted of two types of RNA, termed long and short RNA. The scientists synthesized about 10^15 long RNA molecules. Each long RNA had two regions: one identical to all RNA molecules (a stem-loop structure), and a 220 nucleotide long region that varied among each RNA molecule. Different variants of the 220 nucleotide structure may have had the ability to catalyze covalent bond formation. The short RNA also had two regions. The first region contained a 3' end and was complementary to the 5' end of the long RNA. The second region contained a sequence (tag sequence) that had the ability to bind to a packing material (referred to as "beads"). First, the two RNA's were mixed together to allow for covalent bonds to form between them. Next, this mixture was passed through the beads. The purpose of this step was to separate the covalently bonded RNA from the non-bonded RNA. The long RNA that bonded to short RNA (which binded to the beads) stayed behind, and the long RNA that didn't bind was flushed out and discarded. Then, a low pH solution was run over the beads to separate the RNA from them to make a pool. Using PCR, the long RNA in the pool (Pool #1) was used to make more long RNA. Since the new long RNA was derived from RNA that was shown to have the ability to form covalent bonds, it was expected that the new batch of long RNA would have a greater ability to bond than the first batch. This process was repeated until 10 pools were made. These pools plus the original sample were tested for covalent bond formation, and the data showed that after each repetition of the experiment, covalent bond formation increased substantially! The final pool had a ratio of bonded molecules to non-bonded molecules that was about 3 million times that of the original batch! Bartel and Szostak concluded that chemical selection can occur because of the increase in covalent bond formation shown in the data.

 

      Eventually, the RNA world was taken over by a world with DNA and proteins. In this hypothesized RNA world, RNA would have had the duty of both storing genetic information and catalyzing chemical reactions. If DNA instead took over storing genetic information, RNA would have been able to perform more functions; DNA could code for RNA molecules with more catalytic functions. Also, another proposed reason for the DNA takeover is that DNA is more stable than RNA. However, this fails to explain how DNA came into existence. A hypothesis is that a mutated RNA molecule had the ability to reverse transcript, turning RNA into DNA. Now, we have to ponder how proteins came into the picture. Since amino acids have great variation among themselves, they would allow for more chemical reactions than RNA. It has been shown experimentally that RNA can form peptide bonds, which form proteins. This is a possible way the first proteins were formed. Also, we have to remember that RNA still has a role in protein formation currently through transcription and translation. These examples show how the RNA world possibly shaped the DNA, RNA, protein world of today.

 

B. Useful Materials

 

This video is a short presentation on the RNA world hypothesis. The lecture provides a good summary of the RNA world hypothesis and the role RNA played in the past life and current life.

 

The lecture brings up excellent examples such as how structure is directly related to function, and how RNA can act as both a carrier of genetic information and as an enzyme. These facts both contribute to the possibility of the existence of an RNA world.

 

 

This much longer, more detailed lecture is extremely insightful. The professor, Sidney Altman, details RNA itself and how the RNA world hypothesis was thought of. He also meticulously explains the possibility of an RNA world and how it would have happened.

 

This lecture is more of an explanation of RNA; it's structure and function. Although the lecture goes into great detail, his explanation of RNA helps the viewer to understand how it is possible that an RNA world existed, such as his explanation of how RNA can catalyze chemical reactions.

 

Note: Professor Altman begins speaking at about 5:00, and his explanation of RNA starts at about 23:00.

http://exploringorigins.org/nucleicacids.html  

If watching 58 minute lectures aren't your thing, then this website is. It contains good summaries and quick, informative, eye-catching videos about RNA and the RNA world hypothesis. It goes into detail about how ribozymes play a part in the RNA world hypothesis and how ribosomes themselves are ribozymes, supporting the RNA world hypothesis.

 

The simple layout, short videos, diagrams, and extra links make this website a great reference for anyone trying to understand RNA and the RNA world. In addition, there are more sections about different aspects of the beginnings of life that reference RNA, such as protocells. 

http://www.science20.com/news_articles/rna_world_hypothesis_gets_challenge-90437

This article challenges the RNA world hypothesis and explains why it may not have been possible. The main argument is that the ribosome is more complex than assumed, and RNA itself would not have the capabilities to synthesize proteins.

 

The article is beneficial because it raises the question: what if the RNA world hypothesis is wrong? Although there is much evidence for it, we also have to consider the evidence against it. This is crucial for scientists to understand. Regardless of how much you can support an idea such as the RNA world hypothesis, there is always a chance that it is incorrect.  

This separate, extra, humorous video shows what happens when evolution goes wrong. 

 

C. Primary Literature (click to read article)

 

   This article mainly discusses how RNA came to be a molecule that uses 4 nucleotides (adenine, uracil, guanine, and cytosine). It raises three good questions. First, are two sets of nucleotides optimal? Next, is a four-nucleotide system better than a two-nucleotide system? Finally, are there better systems than a four letter alphabet (six and eight nucleotides)? The article begins with discussing how most scientists, when given the situation of the beginnings of modern life, generally use an RNA world to explain it. The purpose of the article is to find the optimal scenario for an RNA world, where the alphabet must be able to fold into secondary structures without the use of chaperones, which is a core concept of the RNA world hypothesis.

 

     Two experiments were done to find which scenario would be the best for RNA: 2, 4, 6, or 8 nucleotides. The first experiment uses a program, RNAfold, to determine possible secondary structures of different RNA molecules.  It determines two values, Q and P. Q is the certainty that the secondary structure is well-defined, or in other words, how many possible secondary structures there are. A low Q value is characteristic of a favored molecule. A high Q value indicates that it is uncertain which secondary structure will form. P is the amount of paired bases within the secondary structure. The higher the ratio of P, the more favored the molecule is. From this experiment we found that the more nucleotides, the higher the Q value, or, the higher the uncertainty. We also found that with more nucleotides, the P value decreases. This happens because with more nucleotides, there is less of a chance that a base matches with its complement. However, we also learn that a two-letter alphabet does not have the capability to form functional secondary structures. We also learn from the graphs that some certain two-letter systems would have a high Q value despite the general rule being that less nucleotides means less uncertainty. This data can rule out that the optimal scenario is a two-nucleotide molecule. 

 

     The second experiment consisted of a pool of random RNA sequences. These RNA sequences are replicated and purposefully mutated. The molecules that "evolve" or are mutated are the ones that are favored. The data showed that the AUGC system is favored over other four-nucleotide molecules, six-nucleotide molecules, and eight-nucleotide molecules. This happened because four-nucleotide molecules can conformationally change easier than six or eight-nucleotide molecules. We know that the AUGC system is favored because for another system to be favored, a mutation would have had to occur in the RNA world, and the possibility of this was low (due to how favored RNA was, as shown in the lesson).

 

     This paper concludes that two sets of nucleotides and that a four-nucleotide RNA molecule is favored over an RNA molecule with two, six, or eight nucleotides. Also, the authors conclude that the most favored system is the AUGC system. This paper explains another prime example of chemical selection. It also helps the reader understand why RNA is still vital today and why it hasn't mutated to become a different molecule. 

 

 

D. Virtual Lectures

 

Part 1


 

Part 2

 

E. Lecture Slides

 

F. Practice Quiz


 

Grading Sheet (Daniel)

 

Comments (2)

Aditya Aiyer said

at 5:33 am on Mar 28, 2013

Note on the 3/27 class discussion on RNA's catalytic function being replaced by proteins.
The reason for proteins replacing the primitive catalytic function of RNA as highlighted in Stage 4 of the origin of life is the twenty amino acids of proteins can account for a variety of different proteins that can perform different forms of catalysis specific to the needs of the cell, whereas the four ribonucleotides of RNA can be arranged in only so many ways to encompass a diverse array of catalytic needs for a cell to properly function.

Aditya Aiyer said

at 5:43 am on Mar 28, 2013

Since proteins have a vastly greater catalytic ability than do RNA molecules, cells containing both RNA and proteins had a major advantage.

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