The Cell
Part 2. Origins

by Ian Magrath

Model of the small, 30S subunit of the bacterial ribosome. Ribosomes are responsible for synthesizing the specific protein encoded in the nucleotide sequence of mRNA and hence, of translating information into structure and function. Modern ribosomes contain both RNA and protein, but it is the RNA that is primarily responsible for the catalytic activity (peptidyl transferase) that links amino acids together to form polypeptide chains. Therefore, ribosomes are classified as ribozymes (see text). Their existence would seem essential to the emergence of cells, and the critical role of catalytic RNA would support the existence of a prebiotic RNA world. Photo by V. Ramakrishnan.

Leeuwenhoek’s discovery of tiny animalcules visible only with the aid of his microscopes opened up entirely new vistas for scientific speculation and endeavor, although for long the extreme limitations in investigative techniques meant that little more could be done beyond naming those microscopic creatures that were easily recognizable and beginning to probe the microscopic structure of the plants and animals that inhabited the familiar world of the human senses. In the past, the vast lacunae in our understanding of nature had been filled by a host of confabulations implicating creation by design, spontaneous generation, and in the context of disease, evil spirits, internal humors and the like. Now, as suggested by Hook, better microscopes might well provide a means by which the instruments and contrivances used by nature to bring her designs and ends to pass might be discovered. And while microscopes of increasingly sophisticated design led to a corresponding increase of our understanding of the very small – including the fundamental particles of nature themselves - telescopes similarly extended the range of the human senses to the very distant and often very large.

Creation of the Chemical Elements

Remarkably, these two worlds, the very large and the very small, proved to be more closely integrated than ever suspected, for there is now ample evidence that the massive gravitational force generated by stars, is responsible for creating the atoms that comprise the chemical elements and, consequently, matter and Life. Starting with single protons (hydrogen), thermonuclear fusion, the details of which vary in stars of different masses, gives rise to all of the elements up to nickel (i.e., elements with up to 28 protons). The first step in this process, at least in stars larger than our sun, is the fusion of four hydrogen nuclei (each a single proton) to form helium, in which two of the protons have been converted to neutrons by the weak nuclear force (beta radioactive decay). Since the mass of the newly formed helium nucleus is less than the sum of its four constituent nucleons, the extra mass is converted into electromagnetic radiation and released as starlight (or sunlight). This radiation also creates the pressure that prevents the star from imploding as a result of its own gravitational field. Other elements can be made in a similar way, e.g., carbon via the combination of three helium nuclei, but nuclear fusion cannot give rise to all the elements. Since the nuclei of nickel-56, and iron-56, the latter derived from nickel-56 by radioactive decay, have the highest binding energy of all the elements, the addition of more protons requires energy, and cannot, therefore, be accomplished via nuclear fusion. The heavier elements are formed predominantly in supernovae – the spectacular stellar explosions that occur just once or twice a century in a galaxy the size of ours. Supernovae are of several types only one of which will be described. Type II supernovae occur when a massive star has used up all its hydrogen (which occurs after approximately 90% of its lifespan), and although still able to create energy through helium fusion into carbon, and the successive use of carbon, neon, oxygen and silica as fuel, each new fusion process releases progressively less energy and each new fuel is quickly used up. As iron-56 accumulates in the core, derived from the final phase of silica burning, the star is less and less able to create enough energy to maintain its structure and the core begins to shrink. When fusion abruptly ceases there is a sudden drop in the core pressure (occurring in less than a second), leading to implosion. The core then recoils in a tremendous outburst of energy which blows off the outer layers of the star and transiently emits as much light as an entire galaxy. High energy neutrons produced by the core collapse (as negatively charged electrons and positively charged protons are compressed together) collide with the elements previously made by nuclear fusion, creating the heavier elements by a process of neutron capture and conversion, again via the weak nuclear force, of some of the neutrons into protons. The core remnant may persist as a small neutron star several kilometers across, but in very large stars the end result is a black hole. The matter ejected from the supernova is dispersed, and often interacts with interstellar matter in the local region of the universe, creating nebulae of sufficient density that the gravitational forces generated can give rise to new stars. Sometimes, when there are high concentrations of the heavier elements, a spinning disc is formed in which the largest concentration of matter is in the center. If large enough, the central portion ignites and a new star is formed, surrounded by a protoplanetory disc. The dust and ice-grains (water, essential to life as we know it, is the commonest substance in such discs) orbiting the star may condense into various sized objects, including asteroids, meteorites and comets that, by accretion, can develop into protoplanets and thence dwarf planets or planets. Such is believed to be the process by which our own solar system formed some 4.5 billion years ago.

The Crucible of Life

The young solar system was a tempestuous place, and most of the events that resulted in the formation of the planet Earth took place in the course of tens of millions of years through accretion of smaller masses. During this period a major collision with a body believed to be approximately the size of Mars is believed to have occurred. It both provided additional mass to the Earth and resulted in the formation of the moon, whose gravitational pull causes tides in large bodies of water. It may also have resulted in Earth’s axial tilt, responsible for the seasons which, along with the tides, have greatly influenced the diversity of Life. Even after the formation of the solar system, various sized chunks of ice and rock, including meteorites and comets, continued to smash into the inner planets, particularly in a period 3.8 to 4.1 billion years ago referred to as the Late Heavy Bombardment. In the case of Earth, some of these objects, especially ice-containing comets, added water to the growing planet – a sine qua non for the emergence of carbon-based life. The kinetic energy of these numerous collisions was converted into heat and the hot molten planet evolved structure as the heavier metals, particularly iron, sank down to form the central core. This resulted in the creation of a magnetic field, a factor critical to the subsequent evolution of life on land since it blocks the harmful charged particles that radiate from the sun – the so-called solar wind – which had, until then, prevented the formation of a stable atmosphere. The outer layers of the planet (some of which may have come from a surrounding cloud of gaseous silica) solidified as the Earth cooled, but the molten rocks and gas in the deeper layers frequently force their way through weaker points in the Earth’s crust as volcanic eruptions that contributed a major part of the early atmosphere, much of it steam, which, as it cooled, rained down on the planet and formed vast seas. Today, 71% of the Earth’s surface is still covered by salt water. The composition of the primeval atmosphere remains a matter of controversy, but it is likely that it contained water vapor, ammonia, methane, nitrogen and carbon dioxide – sufficient to create a greenhouse effect and slow the gradual cooling of the planet. One molecule that was fortunately absent was oxygen, for this would certainly have oxidized organic material into carbon dioxide, thus preventing the emergence of Life, although later, oxygen was to play a crucial role in the development of complex life-forms.

It was this hot, watery and violent world that, as hostile as it may seem, provided the necessary conditions for life to evolve.

Carbon

Life, as we know it, is dependent upon the branch of carbon chemistry known as organic chemistry, i.e., the chemistry of molecules derived from carbon (C) and hydrogen (H), the simplest of which is methane (CH4). Carbon, the fourth most abundant molecule in the universe (after hydrogen, helium and oxygen) differs from all other elements in its ability to form long chains of atoms or ring structures that are stable in water, and which provide, as it were, the skeletons of a broad range of molecules that comprise the complex system we call Life. Silica can also form such structures, although only in non-aqueous solvents, such that silica-based life in the universe would seem unlikely. In addition to hydrogen, oxygen, nitrogen and phosphorus many other atoms participate in or project from the carbon skeletons, often in combinations referred to as groups, such as hydroxyl groups, amino groups, or phosphate groups, which are critical to the functional attributes of the organic molecules. Among the vast range of possibilities with respect to organic compounds, however, only a select few were to participate in the creation of Life, which evolved within a billion years of the Earth’s formation. Among the great many amino acids possible, for example, all known life-forms encode only 20 in their genes, and all are “left handed” alpha-amino acids, terms which relate to the particular enantiomer (mirror image version) and positioning of the amino group in the molecule. Similarly, Life uses only 5 and 6 carbon sugars, which, unlike the amino acids, are nearly always the “right handed” versions of the sugar molecules. The limitation to specific types of molecule may have a deep explanation, but it is also possible that these happened to be the molecules available when life emerged, and that life might well have been built with other molecules (e.g., with right handed amino acids and left handed sugars) had they been in the right place at the right time.

The Prebiotic Era

For most of human history, Life was believed to consist of some kind of “spirit” or “soul” that animated living creatures (plants and animals). Such a view persists in one form or another in various philosophies, primitive, religious or otherwise, but from a scientific perspective life is a complex, self-organizing, self-replicating and adaptive system that is dependent for its existence upon physico-chemical processes, many of which can be reproduced in the laboratory. On earth, modern molecular evidence strongly suggests that all existing life-forms evolved from a single cell, i.e., Life emerged only once. This is reminiscent of the singularity from which the Universe is believed to have originated.

Life’s Key Molecules

The molecular systems that comprise life, however, had to be in place before it was possible for cells to evolve. This occurred in the prebiotic era, biotic, referring to cellular Life. The key molecules are the nucleic acids, deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), which carry the information required for the production of proteins involved in cell structure and the molecular pathways vital to the life, replication and functions of the cell. Perhaps equally important are the molecules (proteins and small RNAs) that regulate the use of the stored information, specifying which genes (informational units), for example, will be expressed and when; and the 20 amino acids which, when bound together in chains, form proteins. Whether polypeptides initially evolved separately from nucleic acids is not known. In either event, molecules with catalytic action (enzymes) that evolved by chance (possibly only once) would have conferred advantages on evolving molecular systems and been retained. This is presumably why the molecules involved in Life’s basic processes (metabolism) are remarkably similar in all living organisms. A key molecule found in all cells is adenosine triphosphate, which can store energy and transfer it, as needed, to proteins engaged in specific molecular interactions.

Nucleic acids are comprised of long chains of ring-structured molecules called nucleotides, attached to pentose sugar molecules (deoxyribose or ribose). These sugar-nucleotide units (nucleosides) can be joined into long chains via phosphate molecules (Figure 1). The five different nucleotides – purines (guanine and adenine, or uracil, in RNA) and pyrimidines (thymine and cytosine) along with pentose sugars must have evolved in the prebiotic era, and polymerized into RNA and DNA.

Figure 1. Diagram showing, in simplified form, the structure of a short length of a single DNA strand comprised of nucleosides linked together via the pentose sugar, deoxyribose (DR) by phosphate groups (phosphodiester bonds) (PO4).

Replication and Translation of Genetic Information

Of profound significance to the existence of Life is the ability of nucleotides to pair with each other in a highly specific way - guanine binds to cytosine and thymine to adenine (or uracil in RNA) - which permits one chain to be used as a template on which to build a complementary chain, or for double stranded forms of DNA and RNA to exist (Figure 2). This is relevant to both the replication of DNA (and RNA) molecules today and to the emergence of self-replicating molecules in the prebiotic era. It also allows the translation of information encoded by genes into protein molecules – which, when organized appropriately, give rise to both the structure and function of cells.

Figure 2. Diagram showing how the nucleotides of DNA undergo “base pairing”. Adenine binds to thymine and guanine binds to cytosine via hydrogen bonding, in which a hydrogen atom is “attracted” to certain other atoms such as nitrogen and oxygen (dotted lines).

The fact that DNA and RNA use different sugars results in differences in their structure that enables RNA to take on a broader range of functional roles than DNA. For example, small non-coding RNA molecules have enzymatic functions that are involved in the regulation of the reading of genetic information (i.e., information encoded in genes, whereby specific nucleotide triplets code for individual amino acids) as well as its translation into proteins. Translation involves the building of a complementary messenger RNA (mRNA) on one of the DNA strands (cellular DNA is always double stranded). The information encoded in the mRNA nucleotide sequence is read by a ribosome containing non-coding ribosomal RNA, which moves along the mRNA molecule and catalyzes the sequential binding of transfer RNA molecules, via their contained RNA triplet anticodons complementary to a triplet in the mRNA chain. Each transfer RNA carries a specific amino acid, so that a polypeptide (a chain of amino acids, each joined to the next via a peptide bond) is built step by step as the ribosome progresses along the mRNA molecule.

An RNA World?

RNA’s versatility makes it possible that it provided an intermediate step to the use of proteins as enzymes in the prebiotic era and some postulate the existence of an RNA world prior to the evolution of DNA, proteins and cells. Recently, naturally occurring RNA molecules with catalytic activity (ribozymes) have been discovered, and ribozymes able to replicate each other in the laboratory have been synthesized. Even modern ribosomes are ribozymes – providing support for an RNA-world. Other small, non-coding RNAs such as interfering RNAs and micro RNAs have an important role in regulating the expression of genes in all living organisms, and could also be, along, perhaps, with RNA viruses (see below), the remnants of this era. The process whereby RNA might have transferred its contained information to DNA is not difficult to envisage, given the existence of reverse transcriptase, a protein used by modern retroviruses to create a DNA copy of their RNA genomes.

Replication Fidelity – Striking a Balance

Double stranded DNA and its contained genes defined by the nucleotide sequence, can be thought of as a kind of zipper. The DNA can be unzipped and a new chain synthesized by base pairing on each side of the zipper (Figure 3), creating a double chain identical to the parental double chain (assuming 100% accuracy). This process led to the accumulation of specific DNA molecules in the (late?) prebiotic era, and provides identical copies for each of the daughter cells during cell division in the biotic era. The process of replication is not, however, perfect, and would be a lot less perfect if the enzymes that catalyze DNA replication (DNA polymerases) were not, at least in cells, associated with a proof-reading element that detects copying errors. Repair enzymes then excise incorrectly placed nucleotides (i.e., that do not correspond to the template) and replace them with the correct nucleotide. Changes in the nucleotide sequence (mutations) can also occur as a result of interactions with environmental agents. Mutation, of course, is critical to change, i.e., to evolution, but too high a rate of mutation would hinder the accuracy of self replication, preventing the emergence of stable molecules with specific functions in the prebiotic era, and hence of Life. Similarly, high enough mutation rates in cellular DNA would lead to cell death. In practice, it seems that the accuracy of replication is similar in all cells (from bacteria to humans) at approximately 1 error per 109 to 1010 nucleotides. The absolute number of errors made during replication both depends upon and defines the size of the genome. In the prebiotic era the mutation rate, in the absence of proof-reading and repair enzymes, must have been much higher, until, by chance, proteins (or perhaps RNAs) arose that were capable of improving the accuracy of replication, resulting in an increase in the stability of molecules over multiple replication cycles. Mutations, including mutations in repair enzymes, are one of the several types of genetic lesions that contribute to the development of cancer.

Figure 3. Diagram showing, in simplified form, how DNA is replicated through the uncoiling of its two strands and the use of each as a template on which to build another strand. To the left, the original double strand, to the right, two new double strands. Nucleotides are indicated by long (purine) and short (pyrimidine) lines.

Artificial Cells

The emergence of cells left traces in the fossil record that date to 3.5 to 3.8 billion years ago (e.g., stromatolites containing microorganisms). The prior prebiotic era has left no such traces and therefore, no direct evidence of the nature of the first self-replicating molecules. However, the most basic aspects of cell replication and metabolism are common to all life-forms and probably to molecular systems of the later prebiotic era too. The translation of genes encoded in DNA into mRNA and proteins, for example, must surely have been a prerequisite for the emergence of living cells. If so, it is unlikely that the complex molecular interactions required could occur in a postulated “primeval soup” of dilute organic molecules in the oceans of the young planet. Even if this were the origin of some organic molecules, it would seem likely that the development of complex molecular systems would require close proximity of the component molecules, as might occur in an artificial cell in porous rocks or bubbles trapped in ice. Consistent with this is the discovery of microorganisms known as endoliths and hypoliths, which occupy microscopic spaces in rocks. Some of these organisms are able to live on traces of iron, potassium or sulphur – also a potential source of energy for prebiotic molecules - and may divide only once a century. Modern extremophiles (predominantly Archea and Eubacteria) able to tolerate superheated water or freezing temperatures may have evolved in locations essential to the emergence of Life’s key molecules because of the necessity either to prolong the half life of their component units in order that they have enough time to polymerize (cold), or to create complex molecules from simple precursors in the absence of enzymes (heat). Extreme conditions were, in fact, the rule on Earth during the prebiotic era and may have been essential to the synthesis of molecules essential to life.

The origin of such molecules has been intensively studied in the laboratory. In the now classical Miller-Urey experiment, for example, water under an atmosphere of ammonia, methane, hydrogen and water vapor was subjected to electrical discharges, which resulted in the production of a “soup” of organic compounds, including seven of the amino acids present in proteins. Interestingly, some of the key constituents of life have been synthesized from simple carbon structures such as glyceraldehydes and cyanamide or ammonium cyanide. Adenine, for example, which has a half-life of 17,000 years in freezing water, but just 19 days at 100°C) has been synthesized from hydrocyanic acid (HCN), ironically, a highly toxic molecule to modern organisms dependent upon oxygen to generate energy (ATP). It has also been shown that minerals, such as iron sulphide could catalyze the synthesis and polymerization of organic molecules in the very hot environment of volcanic ocean vents, using volcanic gases such as carbon monoxide, hydrogen sulphide and hydrogen cyanide as raw materials. These and other laboratory experiments demonstrating the synthesis of organic molecules, including nucleotides, sugars and amino acids, from non-organic compounds, do not demonstrate how such molecules evolved, but do provide sufficient information to understand how they might have evolved.

Modern Prebiotic Molecules?

In the 17th century some natural philosophers speculated that the animalcules discovered by Leeuwenhoek and others might be a link between the living and the dead. While at first sight, such a concept seems alien to our understanding of life and death, these words predate the modern era and were coined in the context of animals (including people) and plants, where alive and dead are distinct states. Leeuwenhoek’s animalcules proved not to differ in this regard, but the complex molecules that evolved in the prebiotic era can legitimately be considered intermediate between the mineral, or purely chemical, and living cells. Such molecules, like ancient microorganisms, may well have modern counterparts. The likeliest candidates are viruses, which are, in effect, nucleic acids enclosed in protein (and sometimes lipid) coats, which are entirely dependent upon cells to replicate. Similarly, the replication of prebiotic molecules must also have been subject to the availability of raw materials and energy, which was possibly provided by suitably located artificial cells (e.g., near volcanic ocean vents). And since RNA viral polymerases do not have proof-reading and repair enzymes as part of their replicating machinery, RNA viruses have a much higher rate of copying errors - some 10,000 to a million times higher than in bacteria and probably similar to that of prebiotic molecules prior to the evolution of proof-reading and repair enzymes. The mutation rate imposes an upper limit on the size of genomes since the risk of a copying error arising is in direct proportion to the size of the genome. Once copying became more accurate, larger molecules, perhaps created by combination with smaller molecules, would be stable. Indeed, prebiotic recombination could be reflected in modern mobile genetic elements (transposons, or jumping genes), which may have had a much more important role in the construction of genomes than previously believed. Some prebiotic molecules may have acted quite similarly to viruses, since RNA or DNA protected by adherent protein could have migrated to other locations where it could recombine with other stretches of nucleic acid. For example, among the several kinds of transposons are retrotransposons that are transcribed into mRNA then reinserted into the DNA genome with the aid of a reverse transcriptase (which also lacks proof-reading properties) that catalyzes the assembly of a DNA copy. Retroviruses are RNA viruses with the same capability and as such represent a class of transposons. Such viruses occasionally “pick up” a cellular gene adjacent to the insertion point and transfer it to another cell, which could have been a means of genetic recombination in the prebiotic era. Today, a similar process has been shown to lead to cancer in animals - it was the discovery of the Rous sarcoma (RSV) virus oncogene (SRC) in both normal chicken cells and in RSV that led eventually to a broad understanding of cancer at a molecular genetic level.

How molecular systems of nucleic acids and protein became enclosed in a cell membrane is entirely conjectural, but the propensity for phospholipids in water to form spherical lipid bilayers (the basic element of the cell membrane) when agitated, capable of enclosing admixed molecules, provides at least a crude model for how the formation of the first cell might have happened. While the chance of all necessary ingredients being present at a single location was doubtless extremely low, hence Life’s origin in a biotic singularity, the construction of trillions of prebiotic molecules and a time-frame of hundreds of millions of years may well have made the emergence of the cell almost inevitable.