Tuesday, September 6, 2016

Hello? Earth Calling . . . PART 4

For Hello? Earth Calling . . . PART 1 CLICK HERE
For Hello? Earth Calling . . . PART 2 CLICK HERE
For Hello? Earth Calling . . . PART 3 CLICK HERE

How did Life Arise On Earth?

No one knows exactly how life arose from non-living matter on Earth, but many researchers focus on the kinds of chemical reactions that could have given rise to the first living system. This is the field of abiogenesis. It is a multidisciplinary study that relies heavily on geology, chemistry and biology.

It is now well known that the starting material for life on Earth consisted of complex organic molecules. These are molecules that contain carbon, and they are not just found on Earth. They are present throughout our solar system and even in interstellar space. There, many complex molecules are formed on the surfaces and inside the water ice mantles of dust grains in the star-forming cores of giant gas clouds. Simple molecules like hydrogen and carbon monoxide are excited under gravitational pressure as they are bombarded with ultraviolet (UV) radiation. In this environment they break apart into reactive radicals. These charged molecular fragments reform over and over, gradually building new increasingly complex molecules. A tantalizing recent discovery was the detection of iso-propyl cyanide in a star-forming cloud 27,000 light years from Earth. Iso-propyl cyanide (C4H7N; shown below left as a simplified molecular diagram) is a fairly complex organic molecule composed of nitrogen, carbon and hydrogen and, like proteins, it has a branched carbon backbone.

Perhaps most intriguing is its carbon-nitrogen triple bond (triple lines, left), one of the most abundant bonds in biochemistry. This high-energy chemical bond participates in amino acid synthesis (amino acids bond together to form proteins). Its presence along with various other organics already detected in interstellar space suggests that life's potential building blocks are widespread in our galaxy. Computer models suggest that complex organic molecules also formed in our Sun's protoplanetary disc, a dense cloud of cosmic dust that would later form the Sun, Earth and all the other planets, moons and asteriods.

European Space Agency;Wikipedia
Like other star-forming clouds, UV photons from the forming Sun would have broken down molecular bonds in the protoplanetary dust and allowed those short simple fragments to recombine into more complex molecules. Earth, however, formed as a molten ball of material so hot that most of the chemical bonds in those complex organic molecules would have been destroyed, leaving behind much simpler molecules like hydrogen, water and carbon monoxide once again.

Tim Bertelink;Wikipedia
Once Earth cooled even slightly, in the presence of energy and water, the processes of increasingly complex organic chemistry would once again be underway. At the same time, as much as 40,000 tons of cosmic dust (which consists of both solar and interstellar molecules) rained down on the surface of Earth every year, offering its supply of complex organic building blocks.

Besides active complex organic prebiotic chemistry on Earth, other prerequisites scientists think are essential to life were present as well, including abundant water, terrestrial life's solvent. When Earth was just 500 million years old, it already contained oceans. Where the water originated remains somewhat mysterious but the picture is becoming clearer. Some researchers believed that comet impacts were a major contributor, but isotope analysis argues against this. Newer data suggests that the protoplanetary material itself, full of water-rich carbonaceous chondrites that aggregated to form Earth, contained sufficient water to form oceans. When the young Earth collided with another body and gave rise to the Moon, according to the giant impact hypothesis, the impact would have resulted in a primordial rock-water vapour atmosphere that would quickly condense into oceans.

Artist's rendering of the collision between Earth and a Mars-sized planet that formed our Moon approximately 4.5 billion years ago. Credit to NASA
There is evidence as well that those oceans could have been as hot as 230°C at first. The water condensed instead of evaporating away to be eventually lost to space because the pressure of the, then dense carbon-rich, atmosphere would have been too high to allow the water to boil.

Earth at this time would also have been constantly bombarded with asteroids, creating significant geological stress on the thin young crust and giving rise to intense volcanic activity. This violent period gave Earth all the conditions required to form life. The dense volcanic atmosphere itself also supplied abundant organic raw material, a chemical makeup that is thought to resemble gases released by volcanoes today, such as water vapour, carbon dioxide, sulphur, methane, nitrogen and hydrogen gas. With energy supplied by intense volcanic lightning and UV radiation from the Sun, chemically active organic compounds such as hydrogen cyanide, formaldehyde, acetylene and ammonia were created. These conditions have been recreated by the famous Miller-Urey experiment, which established that even many highly complex amino acids, the building blocks of proteins, can be created from simple inorganic compounds under those conditions.

General set-up of the Miller-Urey experiment. Credit to YassineMrabet;Wikipedia
These conditions were present for just 500 million years before signatures of life appeared in the (chemical) fossil record, suggesting that when conditions are right, the evolution from abiotic organic chemistry to biochemistry happens very rapidly from a geological standpoint.

As life arose, the environment on Earth would be deadly to most organisms today, including us. There was no oxygen in the atmosphere. There may have been very little or no land above water and the water itself was probably still around 100°C (boiling hot) when cellular life made its appearance. The young Sun's radiation output was also different than it is today. Even though the Sun was fainter in the visual spectrum, young Earth would have been subjected to more intense UV and X-ray radiation. Earth did not have a protective ozone layer until approximately 600 million years ago when plant life began to colonize land and release significant oxygen into the atmosphere (ozone is created when UV radiation splits oxygen (O2) molecules high up in the atmosphere, which then reform into ozone (O3)).

Life that managed to arise under these harsh conditions was also regularly bombarded by asteroid impacts. This was likely the result of gravitational instability caused by giant planets such as Jupiter and Saturn moving outward to their present orbits. A large meteor would strike the young Earth and cause all the surface water to vapourize. Computer models suggest that it would take up to 3000 years for the cloud deck to settle and rain back down into oceans. At first, life would not have a chance to develop but eventually, as asteroid impacts became fewer and less severe, large mats of unicellular extremophile-like microbes formed. Eventually, cyanobacteria colonized much of young Earth, oxygenating the oceans and atmosphere.

Microscopic colonial filaments of
cyanobacteria; Mathewjparker;Wikipedia
Until last year, the first life on Earth was thought to be cyanobacteria. Australian microfossils of strands of these unicellular organisms date back to about 3.5 billion years ago, although there is now some dispute about the identity of these fossils. 3.7 billion year old rock in Greenland more recently revealed 1-4 cm tall humps in the rock, later confirmed as fossilized communities of stromatolites. These structures are a bit like tiny apartment complexes for bacteria, especially cyanobacteria. Though which kind of microbe the stromatolites housed is unknown, they are proof that unicellular life lived as long ago as 3.7 billion years.

In even more ancient Australian rock, chemical fossils containing a specific mix of carbon isotopes unique to life were found. These chemical traces of life are dated even further back to 4.1 billion years, a period when hot pressurized oceans were still forming and Earth was decidedly violent. Because it is a chemical fossil rather than a physical fossil, the type of organism that lived then is unknown. It might be the chemical footprint of an organism similar to bacteria, archaea or even of early eukaryotic life. It could be of an ancestral life form common to all three domains before they diverged evolutionarily.

Life on Earth is divided up into three domains: Bacteria, Archaea and Eukaryota. All three may have diverged from a common ancestor, LUCA (bottom vertical line). Image credit to Eric Gaba;Wikipedia.
It could be the signature of carbon-based life that once existed and then was wiped out in the violence of a young unstable planet, to be replaced by our ancient microbial ancestors. The first Earth organisms to leave behind sufficient fossil evidence might be just one variation on a much larger theme. Several unique biochemistries could have evolved on Earth but only the ones that could adapt best to the rapidly changing conditions on early Earth survived and colonized. The general biochemistry that survives today might simply have been lucky enough to evolve in a relatively calm period between devastations or in a place that was sufficiently protected. Somehow, we know, life made its first appearance. At what point did a collection of chemical reactions become the biochemistry of a living organism?

Did Non-life Become Life In a Hydrothermal Vent?

When did the tipping point occur where non-life organic chemistry became life's biochemistry? In 1967, molecular biologist John Bernal suggested that life forms in three stages. First, biological monomers (such as amino acids) are created. This stage seems to have been achieved throughout the universe in interstellar space as well as on solid planets, moons and even on asteroids. The second stage is the origin of biological polymers, such as proteins, which consist of several amino acids linked together.

Diagram of the chemical structure of the peptide bond (in the box) between two amino acids, creating a peptide chain, which is a protein. Credit to Chemistry-grad-student;Wikipedia.
The achievement of this stage is less well understood. One big problem is that many organic chemicals produced under Miller-Urey conditions would react with amino acids that form as well, preventing them from bonding into peptide chains. Some work suggests that networks of reactions that begin with hydrogen cyanide and hydrogen sulfide (two molecules that should have been abundant on young Earth) found in shallow water irradiated by UV light could produce amino acids, as well as nucleic acids and lipids, while producing few molecules that would inhibit protein synthesis.

Another theory suggests that intense UV radiation from our young Sun may not have been responsible for kick-starting life. In fact, the earliest organisms might have required protection from it instead. Many asteroid strikes during The Late Heavy Bombardment would have involved giant asteroids far larger than the one that caused the extinction of the dinosaurs and these strikes would repeatedly sterilize Earth down to a depth of at least tens of metres, dooming any bourgeoning life forms on the surface. Meanwhile, life could have emerged around deep-sea hydrothermal vents where conditions would be much more stable.

White smokers around Champagne Vent deep in the Marianna Trench. Credit:NOAA
Deep under water, under intense pressure and heat and no sunlight, the laws of thermodynamics might have driven the synthesis of increasingly complex organic molecules and eventually lead to the first living cells. Computer simulations of geothermally heated ocean crust yield an even greater variety of amino acids and other organic molecules than any version of the Miler-Urey experiment has. The diagram below of a typical hydrothermal vent offers an idea of just how complex that chemistry can be.

This diagram of the biogeochemical cycle of a typical hydrothermal vent created by the U.S. government offers an idea of the complex chemistry at work.
Everett Shock and Mitchell Schulte suggest that there is significant thermodynamic drive to create these organic compounds as chemically unstable hydrothermal fluids are spontaneously driven toward a state of chemical equilibrium.

A similar thermodynamic disequilibrium drives the elegant process of photosynthesis, explored in a previous article. In that case, the photosynthetic production of energy-rich sugars in plants occurs down an electrochemical gradient across disc-like membranes that are located within cellular organelles called chloroplasts. A recent study done by Russell et al (2014) suggests that a similar membrane-spanning electrochemical gradient may have been a kind of prebiotic nano-engine, a precursor to the molecular motors across cell membranes and inside organelles today, which are driven by energy gradients moving toward chemical equilibrium. Examples of these very efficient motors are myosins that contract our muscles, the cilia that move mucus and dust out of our nasal passages, the tiny propeller-like flagella that propel some bacteria, protists and sperm, the proteins that condense long double strands of DNA into chromosomes, and even RNA polymerase, which transcribes new RNA from a DNA template, is a molecular motor.

Russell et al's modeling shows that the synthesis of various organic molecules (alkanes, alcohols, ketones, carboxylic acids, aldehydes, etc.) is favourable (and exothermic, which means it releases energy) when 2°C seawater containing bicarbonate is mixed into 350°C fluid water (water under enough pressure to stay liquid) containing dissolved carbon dioxide and hydrogen gas. This scenario is much like the conditions around a hydrothermal vent. The initial hydrothermal fluid becomes increasingly chemically reduced. In chemistry, reduction means the acceptance of electrons. For example, when iron and oxygen react to make rust, the iron is oxidized and the oxygen is reduced – it accepts electrons from the iron atom. As the fluid becomes more and more reduced, the rate of synthesis of organic compounds increases because the reaction becomes increasingly thermodynamically driven by the increasing differences in oxidation state (as an example, Fe, Fe2+ and Fe3+ represent three increasing states of oxidation for iron as it rusts in the presence of water or moist air). They also note that Earth's oceanic crust is mostly basalt. This is the rock through which hydrothermal vent fluid travels upward. Early Earth's basalt would have had a mineral composition much different from modern basalt because it had not yet gone through billions of years of recycling through continental plate subduction. In the beginning basalt was more highly reducing because it contained more magnesium and iron, two elements with multiple oxidation states. All of this suggests that conditions around 4 billion years ago were ripe for maximizing complex organic molecule syntheses, with nearly complete conversion of inorganic carbon (in bicarbonate in the water) into a wide variety of complex organic compounds.

Additional evidence from microbiology supports the hydrotherrmal vent life origin hypothesis. The last universal common ancestor of all living organisms on Earth may have been a unicellular thermophilic (heat-loving) organism, the kind of simple unicellular life that could have evolved around hydrothermal vents. Akanuma et al., (2013), make the argument that a universally conserved enzyme in current (extant) archaea and bacteria species, called nucleoside diphosphate kinase (NDK), must be an indispensible part of modern cell metabolism. This enzyme is not only found in all simple unicellular organisms, it is also found in a very similar form inside the mitochondria and in the cytoplasm of every living cell on Earth. It is the source of both RNA and DNA (ribonucleic acid and deoxyribonucleic acid; genetic material) precursors, and every cell on Earth uses RNA, DNA or a combination of the two (like our cells do) to reproduce. Knowing this, the researchers surmised that NDK must have been inherited from a common ancestor. It is thought to be a highly conserved protein, meaning its amino acid sequence hasn't changed much over billions of years, but it has evolved somewhat. They attempted to reconstruct its ancestral protein sequence by inferring it from NDK sequences of organisms along a reverse phylogenetic tree. They did this by obtaining the gene sequence for the proteins in NDK in extant life. Then, using reliable established methods from population genetics and probability theory, they came up with a series of possible ancestral sequences for the enzyme. After this step, they spliced those genes into very serviceable E. Coli bacteria, which then accurately translated the genetic code into the ancestral proteins. Finally, they exposed these proteins to various temperatures. They discovered that these enzyme proteins are extremely stable at very high (hydrothermal vent) temperatures, and they function optimally at around a hot 85°C. Compare this temperature to our human upper limit. Wet-bulb temperatures above 35°C for six hours or longer are fatal to humans and most other mammals because our cell membranes become unstable and most of our enzymes (essential for life's functions) become denatured. We certainly die at 85°C, but the NDK in our cells, with its ancient lineage, likely keeps on working just fine. This research suggests that the ancient enzyme and therefore the organism itself that housed it, life's universal common ancestor (LUCA), was likely a thermophile. It was probably a simple bacteria-like or archaea-like microbe and it may have gotten its start in a hydrothermal vent, meaning some of our cell machinery did too.

The Possible Co-Evolution of RNA and Proteins

Benal's third stage is the evolution from molecules to cells. The drive-to-equilibrium theory and the NDK research we explored provide a possible chemical scenario where inorganic molecules evolve into increasingly complex organic molecules such as nucleotides, lipids and amino acids, paving the way toward proteins, and toward RNA and DNA synthesis. Before we get to stage 3, however, we need to examine protein synthesis a bit further. We still don't have a possible scenario for their synthesis from amino acids, even though we have established ways in which it is possible. We know that eventually proteins evolved. As shown in an earlier diagram, proteins are composed of amino acids held together by peptide bonds. The big stumbling point here is that peptide bonds do not form spontaneously. It takes a lot of energy to make that reaction favourable enough to proceed. Inside cells, this energy is supplied by an energy-storage molecule called adenosine triphosphate (ATP)  and cellular enzymes are used to lower the activation energy (kind of like an energy hurdle that must be jumped over) of the synthesis reaction. Therefore, it is unlikely that proteins such as NDK arose unless there was a lot of free energy (perhaps in the form of heat) and a catalyst of some kind came on the scene. That catalyst could have been a simpler precursor to a modern RNA molecule and it suggests a possible scenario where RNA and proteins co-evolved. RNA is a fascinating molecule. It is self-replicating and it is an enzyme. Enzymes act as catalysts for biochemical reactions. They lower the activation energy and, by doing so, they allow reactions to proceed and they increase the reaction rate. According to the RNA world theory, spontaneously self-replicating ribonucleic acid (RNA) molecules may have been the ultimate precursor to all life on Earth. Modern RNA is a cellular master of all trades. Not only does it function as genetic material (which acts as an information storage molecule for cellular reproduction), it is also an essential non-protein enzyme. In cells, it catalyzes the formation of peptide bonds between amino acids to create protein polymers. In our bodies this happens inside the ribosomes in our cells. Inside the ribosome organelle, a complex composed of several RNA molecules and proteins carry out protein synthesis. If the first simple strands of protein polymerized thanks to the enzymatic boost from simple RNA-like molecules, we need to get to the synthesis of a simple RNA-like molecule. To evolutionarily get to the first RNA, we need to propose an abiotic (non-living) RNA synthesis pathway. The catch now is that the RNA molecule itself is very complex molecule.


A hairpin loop of RNA is shown left. A single strand is folding back on itself. It can be extremely long, composed of up to hundreds of nucleobases along a ribose-phosphate backbone. Nucleobases are green and the ribose-phosphate backbone of the molecule is blue. Image credit to Vossman;Wikipedia.

Most researchers consider it unlikely that the ribonucleotides within this molecule would form non-enzymatically.  A nucleotide is a basic building block of RNA and DNA. Each nucleotide follows the same basic plan. It is composed of a nitrogenous base (a nucleobase as in above) plus a 5-carbon sugar that is either ribose (for RNA) or deoxyribose (for DNA) and at least one phosphate group (HPO42-).

The general structure of a ribonucleotide consists of a phosphate group (the left part of the diagram shown right), a ribose sugar group (the bottom right pentagonal ring) and a nucleobase (top right). The base, or nucleobase, can be adenine, guanine, cytosine or uracil in RNA. (A, G, C or U). Image credit to Binhtroung;Wikipedia.

Ribonucleotides, as you can see, are highly complex organic molecules. The biggest problem when faced with the question of how nucleotides were formed non-biologically is the sugar unit. Sugars are biological molecules common and essential to plants, animals and many unicellular organisms but the 5-carbon sugars present in genetic material are found only in very trace amounts on meteors and geologically on Earth as sugar acids. Sugars are geologically rare and they also tend to be unstable. They decompose when exposed to heat (for example, making caramel, a partial decomposition of sucrose, requires less than 160°C) so if they were synthesized non-biologically they would not survive early Earth's violent conditions for long. However in 2011, British chemist John Sutherland discovered a non-biological pathway to create pyrimidine nucleosides that bypasses free sugars altogether. These exciting results were confirmed and explored further in a subsequent series of papers. Instead of sugars, 2 and 3-carbon molecules (glycolaldehyde, glyceraldehyde cyanamide, etc.) could be used and these are all molecules that would have been much more commonly available on and in our young planet.

There is also evidence that RNA didn't need to start out as the long complex chain of ribonucleotides that most modern forms tend to be. Even quite short sequences of RNA can still be enzymatically active. Much shorter simpler RNA-like polymers have even been shown to catalyze the formation of peptide bonds. Rajamani et al (2013) showed that these polymers could be created non-biologically (abiotically) in a lipid-rich environment. Lipids are naturally occurring molecules such as waxes, fats, phospholipids and sterols.

Once short RNA-like polymers arrive on the scene, what processes would abiotically drive them toward achieving the complexity of modern RNA? This part of our story gets quite interesting. Tracey Lincoln and Gerald Joyce (2009) suggest a form of chemical evolution might be responsible. The genetic code in RNA is built as a chain of four different ribonucleotides. Each one – G, U, A and C – has a different nucleobase that makes it unique. The chemical bonds that hold these ribonucleotides together have a fairly low potential energy. This means that (unlike peptide bonds) these bonds would have formed and broken apart regularly. While this took place, some particular combinations would have catalytic properties that can lower the activation energy required for their particular sequence to be created. This means those sequences would stay together for longer periods than other random sequences. They could also grow longer and form faster before breaking down again. RNA is a self-replicating molecule and these sequences would be able to replicate more frequently, giving them a competitive edge. Some biologists consider this point to be where life started. There are no living cells yet, but evolving RNA, by using chemical bond energy to replicate its strands, fits some definitions of life. Eventually, sequences that catalyze peptide bonding would randomly be built and some of the proteins that formed as a result would be active enzymes, which in turn would assist in RNA synthesis. A positive feedback system would be set up. Even short 5-ribonucleotide strands have been shown to catalyze protein synthesis. This RNA-protein co-evolution scenario provides us with a way in which we can start to visualize how the cellular machinery of life got its start billions of years ago. Eventually that machinery became housed in a protective envelope to form the first simple cells.

Next we will explore what may have been the first living cells on Earth.

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