CHAPTER 7. ARCHEAN AEON (3900 TO 2600 MYA): THE ORIGIN OF LIFE

This chapter explains the origin and development of life. The development of life occurred through the process of evolution. It has to be stressed, however, that evolution takes place within an ecological context. One cannot understand the development of life without referring to the interaction between the different species (both plant and animal) within a larger ecological setting. Indeed, explanations of the very origins of life refer to certain habitats, such as deep, stagnant ponds, because this is the particular ecology within which life first arose. In other words, evolution cannot be understood without reference to ecology.

In the chapter at hand the question of how life arose will be discussed in detail. This question has always fascinated man. Traditionally, humans ascribed this great mystery to divine intervention. However, it has already been shown, that the origin of the universe in general, and the earth in particular, can be explained in terms of natural "laws." The same can be said of life itself. Life is the result of the combination of special chemicals, called organic chemicals. This chapter presents some basics of organic chemistry. From these chemical beginnings, it then covers the origin of life itself. It shows that many of the organic chemicals that later came together to form actual life were already present in the primitive atmosphere of early earth.

There are several important ways in which biologists approach the study of living matter. Three of the most important ways are evolution, systematics, and ecology. The approach taken in the following chapters of this half of the book takes all three approaches. However, systematics will not be gone into in depth because of the brevity of space and the difficulty of the subject. Suffice it to say, however, that systematists primarily use the reproductive functions to classify species into kingdoms, phyla, orders, families, and genera.

Organic Chemistry

Early scientists discovered that carbon compounds behave differently than the compounds of other elements. Carbon forms particularly strong bonds that persist in the presence of water and oxygen. Carbon also forms very strong bonds with itself.

Since carbon compounds were originally obtained from living things or from the remains of living things, like coal, the early chemists called the study of these compounds "organic chemistry." Indeed, the key element present in all organic compounds is carbon. This makes carbon the "king" of organic chemistry.

Of course, carbon is not the only element found in organic compounds. The big four of the organic elements are hydrogen, oxygen, carbon, and nitrogen. These four elements make up 96 percent of all the elements in living matter. Hydrogen makes up 9.9, oxygen 63, carbon 20.2, and nitrogen 2.5 percent.

There are so many different carbon compounds that to make sense of them chemists have divided them into three major classes. The first group includes the hydrocarbons, which are compounds of carbon and hydrogen. These compounds are highly combustible substances, such as oil and gas, which burn when vigorously oxidized to form carbon dioxide and water. The second group of carbon compounds contains the oxidation products of hydrocarbons, including alcohols and ethers, aldehydes and ketones, and acids and esters (which include the fats). The third group encompasses the nitrogen compounds. There are some very important nitrogen compounds in organic chemistry. Especially important are the amines that form the amino acids. Amino acids in turn make up proteins, a basic component of life.

The Major Chemical Building Blocks

The major chemical building blocks of organic substances are carbohydrates, fats, proteins, and nucleic acids. Carbohydrates are compounds of carbon, hydrogen, and oxygen that usually have a hydrogen to oxygen atomic ratio of 2 to 1, the same as in water. The chief members of this family of compounds are cellulose, starches, and sugars. Through the process of photosynthesis, both cellulose and starch are formed in plants. Starches are subsequently converted into sugars.

Proteins are especially important as building blocks of animal tissues. Proteins consist of amino acids (i.e., hydrocarbon groups that contain oxygen or sulfur atoms). There are twenty "most common" amino acids.

A fat is an ester of glycerin (a sweet, syrupy liquid obtained as a by-product from the manufacture of soap) and an organic acid. Nucleic acids are a group of protein-combined polymers found in all living cells, both plant and animal. Important nucleic acid molecules are deoxyribonucleic acid (DNA) and its messenger, ribonucleic acid (RNA), which direct life itself. The nature of DNA and RNA will be treated more substantially because these compounds are the starting points for the creation of life.

A Chemical that Replicates Itself

Biochemistry is the organic chemistry of life. In fact, the Greek word bios means life, and life is a product of organic molecules. However, early earth contained only inorganic molecules. How did the organic molecules arise? Basically the simplest organic compounds arose through free combination. The atoms in organic chemistry are all highly reactive. Even in the atmosphere, carbon dioxide, ammonia, and methane exist in combined states.

So far, only simple organic compounds have been discussed. These certainly by themselves could not create life for they all lack the crucial ingredient of replication. But, natural forces actually created an organic compound that could duplicate itself. This compound is RNA.

Each RNA molecule contains four different nucleotides: Adenine, Cytosine, Guanine, and Uracil. A nucleotide consists of a ribonucleic sugar plus one of the four bases listed above, and a phosphate group. Each RNA nucleotide is able to form a bond with one, and one only, of the other bases. Thus Adenine can combine with Uracil and Cytosine with Guanine. This combination forms a double strand of RNA. The unique feature of RNA is that the two strands can separate and form two new double strands of RNA. This is possible because the bonds are relatively weak and easily broken. The two separate, single strands of RNA then go through a replicating process in which each base of each strand recombines with its complementary base and forms two double strands of RNA. These two new strands are exact duplicates of each other, as shown in Figure 5.1. This replication process made life possible.

Figure 5.1

Original Double

double strand Each strand The result is

strand of RNA of RNA two identical

of RNA splits recombines copies

------------------------------------------------------------

UA U A UA UA UA UA

CG C G CG CG CG CG

CG C G CG CG CG CG

AU A U AU AU AU AU

UA U A UA UA UA UA

Early Atmosphere of the Earth

As the earth squeezed together in the process of formation, ammonia and methane, plus a little hydrogen sulfide, squeezed out to form the atmosphere. Owing to the geologically young state of the earth, the atmosphere was subjected to violent electrical storms and, because of the lack of a protective ozone layer, to intense ultraviolet radiation from the sun. Added to all of this was the intense volcanic heat and the decay of radioactive

elements in the rocks forming the earth's surface. Along with this was water vapor. This atmosphere was soon replaced by another atmosphere.

Under the influence of ultraviolet light from the sun, water molecules broke up into hydrogen and oxygen. Gravity was not strong enough to hold the hydrogen so it leaked away, but the oxygen remained. Oxygen in turn pulled hydrogen atoms from the ammonia molecules, reforming water and freeing the nitrogen. Oxygen also pulled hydrogen atoms from methane, resulting in water and carbon dioxide. And lastly, oxygen pulled hydrogen atoms away from hydrogen sulfide, resulting in water and sulfur dioxide (SO2). The sulfur dioxide largely disappeared from the earth's atmosphere because it combined with the rocky material of the solid crust and dissolved in the ocean. The end result of all these chemical interactions was an atmosphere dominated by nitrogen, followed by carbon dioxide and water vapor. Also present were carbon monoxide and hydrogen sulfide, but, more importantly, there was no oxygen.

Preconditions for the Origin of Life

Before life formed, most of the planet was land, with only small, shallow seas or streams. Climactic conditions were much more uniform than today, without cold poles and a hot equator. As mentioned below, it is believed that the first atmosphere had very little free oxygen. Experiments with this type of atmosphere have created many different types of organic chemicals. Beginning with the successful experiments of Stanley Miller in 1953, chemists and biologists found that the first steps in chemical evolution occurred when inorganic chemicals combined to form organic molecules. Miller simulated the effects of violent electrical discharges on the hot gases of the primeval atmosphere, and found that a number of simple organic molecules, including amino acids, were produced. Other scientists have done similar experiments using as energy sources ultraviolet radiation, heat, and even the intense sonic shock wave created by thunder. In each case, the result was a mixture of organic molecules. For instance, Leslie Orgel has produced simple nucleic acids via these types of experiments. Through such processes, the earth became home to a number of organic molecules, such as proteins, lipids, nucleic acids, and carbohydrates.

The big mystery, however, is how these chemicals came together to form actual life. The probability of life spontaneously being created as a result of random interactions is extremely slight. However, the idea of collective order provides a possible explanation. Paul Davies (1983) notes that in physics there are a number of principles that explain how inanimate systems manage to achieve spontaneous self-organization. Thermodynamics is the branch of physics that studies the principles of heat energy. We know that energy can be neither created nor destroyed. So the energy of any system must balance out in the end. However, when fluids are forced away from thermodynamic equilibrium, the mixture becomes unstable and spontaneously organizes itself. For instance, if a horizontal layer of liquid is heated from below, a critical temperature is reached after which the liquid organizes itself into a regular pattern of cells wherein large numbers of molecules move coherently in a recognizable pattern of flow.

Certain chemical reactions also produce self-organization. In the Belousov-Zhabotinski reaction, a chemical mix in a test tube can striate into horizontal bands. If placed in a shallow dish, spiral forms appear in the chemical mix. These reactions illustrate how organized chemical behavior is frequently observed in organic (but non-living) substances.

The primeval soup of early earth could have been driven into a sequence of ever more complex self-organizing reactions by some external influence (such as the light of the sun) that upset thermodynamic equilibrium. This could have led to self-reinforcing "feedback" loops, thereby increasing the odds in favor of creating life.

Development of Protocells

In their book Five Kingdoms Lynn Margulis and Karlene V. Schwartz break all living things into five kingdoms. These kingdoms, based partly on their respective reproductive systems, are prokaryotae, protoctista, fungi, plantae, and animalae.

During this period the first protocells developed. Life itself began about 3.5 billion years ago. The earliest living cell may have resulted from waves stirring up the lipid membrane on the ocean's surface. This wave action or other disturbances of the surface could have created small compartments with an outer lipid layer surrounding a tiny drop of water containing nucleic acids (and other dissolved organic substances). Then these small cell-like structures (called micro-spheres) could have grown by simple chemical addition.

The formation of proteins could have occurred as the result of the development of primitive proto-enzymes. (An enzyme is a protein which catalyzes, or speeds up, and controls natural chemical reactions.) The enzyme catalysts could have quickened the combining of amino acids.

Patterns of spikes (called action potentials) indicate that there is electrical activity in the cell. Studying action potentials suggests that light stimulated primitive forms of cell metabolism. Metabolism is all of the chemical reactions that occur in a living cell, but more specifically refers to the breakdown of chemicals to form energy sources. Enzymes regulate metabolism. Each enzyme will catalyze only one type of chemical reaction involving one or a limited number of substrate molecules. This would then have provided the energy source for other chemical combinations within the cell.

The first steps toward life took place at the bottom of deep, stagnant pools. Here there was no danger from the sun's deadly ultraviolet radiation. The primitive forms of life that did exist fed on simple substances dissolved in the water, and obtained their energy by fermentation processes (which did not require free oxygen). The chemo-synthetic process of fermentation (Flint 1973:117-118) breaks down hydrocarbons, which are then reassembled into other compounds. A small amount of energy is released as heat. Carbon dioxide is released into the sea and this made possible the development of photosynthesis.

No one knows what the first life was actually like. It might have been a primitive form of a virus. The simpler viruses, like tobacco mosaic virus, contain only RNA. Very short, single-strand RNA molecules could have replicated themselves. Then, in association with proto-enzymes, it could have formed more complex, but still simple, protein molecules. Random splitting of larger cells into smaller ones then could have produced, at least some of the time, two cells, each containing identical nucleic acid molecules. In this scenario, RNA could have formed the more complex replicating substance known as DNA (which is found in all higher life forms). Other changes in the cell occurred and those that increased the chances of reproduction of a particular DNA molecule were more likely to survive the harsh conditions of early earth.

The oldest earth rocks extend back as far as 3800 million years ago. Life itself began around 3500 million years ago. The oldest fossil evidence for proto-bacteria goes back to 3400 million years ago.

It is a long time from 3.5 billion years ago to the beginning of the Proterophytic Aeon some 2.6 billion years ago. Life, however, had not stood still. From the primitive conditions of replicating RNA, life began to develop key processes necessary for the development of more complicated forms of life.

Developing billions of years ago, one of the most important events in evolutionary history is the development of photosynthesis, wherein a living organism uses the energy of the sun to take in carbon dioxide and water, along with various minerals, and turns these into carbohydrates and oxygen. Like fermentation, photosynthesis is an essentially anaerobic process. Life, obviously, is dependent on the capturing of energy. This energy source is primarily from the sun. Plants capture the sun's energy by taking advantage of the physical features of light and the structure of certain molecules. In short, the sun's energy (in the form of photons) is captured when the photons strike a molecule of chlorophyll, boosting electrons out of their orbit, thereby freeing them. At the same time that the electrons are freed, so are the protons associated with them. Plants use the energized electrons and the protons to produce energy sources (namely ATP and NADPH) useable by the plant to produce food (starches and sugars).

There are two phases of photosynthesis: the energy capturing phase (the light reactions of photosystems I and II) and the food production phases (the dark reactions) of photosynthesis. The light reactions are controlled by light, while the dark are controlled by enzymes. The general equation for photosynthesis is:

6CO(2) + 12H(2)O ----> C(6)H(12)O(6) + 6O(2) + 6H(2)O,

the oxygen being liberated coming from water.

Photosynthesis occurs within the chloroplast. The chloroplast is a specialized cytoplasmic body, containing chlorophyll. Chlorophyll is the green pigment found in the chloroplast, important in the absorption of light energy in photosynthesis.

Each photosynthetic reaction center is associated with a group of functional light-harvesting pigments. These are known as accessory pigments. There are two kinds of pigment systems. In Photosystem I, the reaction center has P(700) because it absorbs light with wavelengths of about 703 nm. It has a high proportion of chlorophyll a relative to chlorophyll b in its light-harvesting pigment system and is sensitive to longer wavelength light. In Photosystem II the reaction center contains P(680). It absorbs light with wavelengths of about 682 nm. It has a high proportion of chlorophyll b in its light-harvesting system.

The general nature of photosynthesis is that it is an oxidation-reduction (electron donation) process involving the transfer of large amounts of energy in relatively small energy steps. These energy transfers are brought about by the flow of electrons from reducing agents, electron donors, to oxidizing agents, electron acceptors.

The compounds involved in this process form a chain of molecules along which electrons flow. Just as electrons moving along a copper wire in an electrical circuit can cause work to be done, electrons moving along a chain of electron carriers in a membrane can drive chemical reactions.

The steps in the light reactions of photosynthesis are too complicated to go into in this volume. Let it be said, however, that photosystem II starts the process, which is continued by photosystem I. The electrons are transported via an electron transport chain to photosystem I. The processes produce ATP (i.e., adenosine triphosphate), which is a nucleotide that storesenergy in the bonds between its three phosphate groups. This energy is released by hydrolysis to drive synthetic reactions in the cell. Also produced is the energy-rich NADPH(2) molecules.

The second series of processes in photosynthesis involves the production of food. These processes are called the dark reactions of photosynthesis. We saw how ATP and NADPH(2) are produced by the light reactions of photosynthesis. These substances are subsequently used in the dark reactions, in which carbon dioxide is fixated into carbohydrates. In other words, the energy from ATP produced in the light reaction is used to drive the reactions of the dark reactions' reductive pentose pathway. In the pathway, CO(2) is fixed to give PGA (phosphoglyceric acid). NADPH(2) is then used to reduce PGA. The result is hexose sugar. The dark reactions take place in the stroma of the chloroplast. One of the crucial cycles involved is the Calvin Cycle. The end result of photosynthesis is the production of glucose from carbon dioxide and water.

Another crucial process worked out during the Archean aeon was respiration. Respiration is technically the breakdown of carbohydrates to release their energy and the transfer of this energy to ATP. The formula is:

C(6)H(12)O(6) + 6O(2) -----> 6CO(2) + 6H(2)O + energy.

There are three distinct stages of respiration. In glycolysis, the glucose molecule produced by photosynthesis is broken down to a pair of molecules of pyruvic acid (or pyruvate). The next cycle is the Krebs Cycle. This cycle takes place in the inner part of the mitochondria. In this cycle, some of the energy stored in the glucose molecules is used to convert ADP into ATP.

However, most of the energy from the glucose molecule remains in the electrons removed from the oxidized carbon atoms. The third process is the electron transport chain. During one rotation of the Krebs cycle NADH is produced. The hydrogen in NADH breaks up into electrons and protons. The protons are transported outside the inner mitochondrial space. This creates a situation where in the inner mitochondrial space there is a low proton concentration, while on the outside there is a high proton concentration. This difference in gradient drives the protons back into the inner sac. This occurs through diffusion channels in the stalked knobs. The result of this movement is that ATP is formed from ADP. The energy yield from respiration can now be used by various cells to perform various tasks. Key areas of high energy demands are in those areas where there is heavy growth.

 

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