Chapter 17. The origins of life and Precambrian evolution

EVOLUTION/LECTURE1 

Evolution (PCB 4674). 

Chapter 17. The origins of life and Precambrian 

evolution 

Main topics of lecture: 

I: The RNA world: 

1.- Defining life 

2.- Ribozymes as evidence for the origin of life 

3.- The case for RNA as an early life form 

4.- Self-replication 

II: How do we get to RNA: 

5.- The problem of moving from an abiotic to a biotic environment 

6.- Where did the stuff of life come from 

7.- The Oparin-Haldane model 

8.- From simple inorganic to the building blocks of life 

9.- Early evidence of life 

III: When life went cellular: 

10.- Early evidence of cells 

11.- The phylogeny of all living things 

12.- The origin of organelles 

I: The RNA world: 

1.- Defining life 

1.1.- All living organisms possess both a genotype and a phenotype. In fact, when we 

consider what life really is, and how living systems can be distinguished from nonliving 

ones, the ability to store and transmit information (a genotype) and the 

ability to express that information (a phenotype) are perhaps the most important 

criteria that set life apart from nonlife. 

1.2.- Unfortunately, there is no neat list of characters that define life. Most biologists 

would include traits like growth and reproduction on such a list, but they cannot agree on 

what else should be used to exclude such life-like systems as a growing salt crystal or a 

computer virus. 

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1.3.- However, many now agree that the ability to evolve is a crucial component of any 

definition of life. Evolution - or change over time - requires both the ability to record 

and make alterations in heritable information, and some way of distinguishing valuable 

changes from detrimental ones. The former is carried out by the genotype, while the 

later is carried our by a phenotype. 

2.- Ribozymes as evidence for RNA as an early life form 

2.1.- In the early 1980s, two teams of scientists independently discovered small 

enzymes that could break and reform the chemical bonds that hold strings of 

nucleic acids intact. These enzymes are able to catalyze the breakage of a phosphodiester 

bond of other nucleotide molecules (most of the times mRNA). These enzymes are 

extremely important in the reactions of intron splicing, and splicing of precursors of 

tRNAs. 

2.2.- However these enzymes were made not of protein, but of nucleic acid - 

specifically RNA. Until 1982, all known enzymes were proteins. RNA was often 

considered to be DNA's poor cousin, relegated to the task of shuttling biological 

information from DNA, where the information is stored, to proteins, which 

carry out all the work of the cell. 

2.3.- The finding of RNA enzymes, or ribozymes has changed how biologists view 

the operations of the cell. Perhaps more importantly, the existence of ribozymes 

has forever changed how biologists view the origin of the first cells - how they 

believe life originated and evolved on the early Earth. 

2.4.- Understanding the origin of life presents an enormous challenge for scientists. 

By our best estimate, life arose on the Earth approximately 4 billion years ago. 

No physical record of biological events has survived for this long. Therefore 

the origins of life must be reconstructed using indirect evidence alone. 

2.5.- The solar system has an estimated age of 4.5 to 4.6 billions years. Therefore 

the newborn Earth remained inhospitable for at least a few hundred million years. 

At first, it was simply too hot for life. 

2.6.- In the course of all the studies about the origin of life, a quandary quickly 

became apparent. Which substance did life acquire first, proteins or DNA Proteins 

can do all sort of complicated biological tasks, but there is no evidence that proteins 

can propagate themselves; they cannot transmit the information needed to replicate. 

DNA, on the other hand, is perfectly suited to store and transmit information by 

complementary base pairing, but it was not known to be able to perform any 

biological work. This chicken-and-egg problem of which came first was essentially 

resolved with the discovery of catalytic RNA. Since RNA has a capacity for information 

storage and transmission and the ability to perform biological work, we now 

think that it preceded both proteins and DNA in the march toward the origin of life. 

2.7.- The hypothesis of an RNA world is based on the realization, since the discovery 



of ribozymes, that RNA can SIMULTANEOUSLY (!!!) possess both 

a genotype and a phenotype. The genotype is the primary sequence of nucleotides 

along the RNA. These ribozymes can fold back on themselves many times to form 

a three-dimensional structure that have an active site that enables the RNA molecule 

to catalyze a chemical reaction on a substrate, as do protein enzymes (!!). This 

reactivity gives RNA its phenotype. 

2.8.- Dozens of naturally occurring ribozymes have now been discovered, and the phenotypes 

of all of them involve the formation and breaking of phosphodiester bonds in RNA or DNA. 

The general chemistry of these reactions is precisely what is needed to replicate nucleic 

acids. This observation gives support to the idea of a primordial RNA world, where RNA 

would be responsible for replicating itself in order to persist. If a molecule of 

RNA could make a copy of itself while accommodating the possibility of mistakes, or 

mutations, then that molecule exhibit many of the characteristics of modern life and 

could therefore be considered alive. 

3.- The case for RNA as an early life form 

3.1.- The RNA World hypothesis posits that and RNA-based living system evolved into 

one more like the life we see today, with DNA storing the biological information and 

proteins manifesting this information. DNA is better suited as an information repository 

because it is chemically more stable than RNA. Especially when doubled stranded, DNA 

can better withstand high temperatures and spontaneous degradation by acids or bases. 

3.2.- What evidence do we have that RNA is ancient The existence of catalytic RNA 

is certainly critical, but there are other indicators as well. The most highly conserved and 

universal component of the information-processing machinery in cells, for example, is 

the apparatus for translation, the ribosome. This apparatus, while it incorporates proteins, 

is built on a frame made or RNA (rRNA), but they require RNA adaptors (tRNA) to carry 

out the task of protein synthesis. Furthermore, additional evidence indicates that it is the 

RNA portion of the ribosomes that actually carries out the catalytic steps in protein 

synthesis. 

3.3.- Another powerful argument for the antiquity of RNA is that the basic currency for 

biological energy, is ribonucleoside triphosphates such as ATP and GTP. These 

molecules are involved in almost every energy-transfer operation of all cells, 

and are even components of electron-transfer cofactors. 

4.- Self-replication 

4.1.- A puzzle piece that we lack for the RNA world is the demonstration that RNA 

can copy itself. The as-yet-undiscovered "RNA-dependent RNA autoreplicase" remains 

a Holy Grail for origins-of-life research. Whether the RNA World used only one type 

of self replicating RNA or a suite of interacting RNAs, and RNA with a replicase phenotype 

would be necessary. The acquisition of the ability to self-replicate by a collection of 



organic molecules, such as RNA, is arguably the point at which non-living matter 

came to life 

4.2.- The hypothesis that an RNA molecule could replicate itself, serving as a simple 

proto-organism, is testable. If the hypothesis is correct, then we should be able to 

make a self-replicating RNA molecule in the lab. This has not been achieved today, 

although a great of deal of research is currently being conducted in this field. 

II: How do we get to RNA: 

5.- The problem of moving from an abiotic to a biotic 

environment 

5.1.- The RNA world has many attractive features, and it solves the problem of having 

to propose the advent of proteins before DNA existed to encode them. But an RNA 

world come with troubles of its own. Some critics have claimed that it simply 

pushes the problem of the origin of self-replication one step back. The issue 

here is simple: How could any RNA sequences come into being from an abiotic 

environment. 

5.2.- The general consensus is that the RNA world was probably not the first 

self-replicating system. This is because the likelihood of making RNA abiotically 

is too minute (see below heading 8 of this lecture) . The first issue that we need to 

address is how information-containing biomolecules were made from simple 

inorganic compounds. Where did these molecules come from 

6.- Where did the stuff of life come from 

6.1.- On September 28, 1969 a meteor entered the Earth's atmosphere over the town of 

Murchison, Australia. Soon after, scientists collected some of the meteorites and carefully 

brought them back to the laboratory for chemical analysis. To their astonishment, the 

analyses showed that organic compounds were present in the interior of the rocks. 

In particular, the amino acids glycine, alanine, glutamic acid, valine, and proline were 

found in significant concentrations. These amino acids are among the ones used by 

modern organisms to make proteins. 

6.2.- The amino acids they found were racemic; that is, they included roughly equal 

proportion of the D- and L-stereoisomers. By contrast, biological amino acids 

are almost purely of the L-form, and thus terrestrial life could not be the source of 

the compounds the researchers found in the meteorites 

6.3.- Why were the Murchison meteorites significant The biomolecules of life, as well 

as their likely precursors, all require the elements carbon, hydrogen, oxygen, nitrogen, 

sulfur, and phosphorus in large amounts. If these building blocks could have 

been synthesized on the primitive Earth, then presumably they would have been 

available for condensation into larger biomolecules. But if they could not have been 



made on Earth, we would have to look to extraterrestrial sources, such as meteors, 

to account for their presence. 

6.4.- The problem with terrestrial sources is that, 4 billion years ago, the Earth's environment 

might not have been permissive for the synthesis of life's building blocks. A 

key feature of the environment is whether it was primarily oxidizing, with high 

abundance of molecular oxygen, and carbon dioxide or primarily reducing with high 

concentrations of hydrogen, methane, and ammonia. 

6.5.- Some feel that geochemical evidence points to an atmosphere that would not be 

favorable for the generation of biologically important molecules. Thus, many have 

explored an alternative hypothesis that certain critical biochemicals were made elsewhere 

in the solar system and delivered to the Earth in meteorites. In fact the young Earth 

experienced heavy bombardment by meteors and comets 

7.- The Oparin-Haldane model 

7.1.- Originally, there was great hope that the Earth itself could provide the "right" 

stuff for prebiotic synthesis. In 1953, Stanley Miller built an apparatus that boiled 

water and circulated the hot vapor through an atmosphere of methane, ammonia, 

and hydrogen, past an electric spark, and finally through a cooling jacket that condensed 

the vapor and directed it back into the boiling flask (Fig. 14.A). Miller identified the 

amino acids glycine, alpha-alanine, and beta-alanine in the final boiling flask. 

Similar experiments conducted by other scientists have documented the formation of 

a tremendous diversity of organic molecules. 

Figure 14.A.: Diagram of the apparatus Miller used to simulate 

the environmental conditions of a hypothetical reducing 

environment of early Earth 



7.2.- Miller used methane, ammonia, and hydrogen as in the 1950s it was thought that 

the atmosphere of the young Earth was highly reducing. However, many atmospheric 

chemists now believe that Earth's early atmosphere was not so reducing, being dominated 

by Carbon Dioxide rather than methane, and molecular nitrogen rather than ammonia. 

7.3.- Reaching a consensus on the prebiotic environment is important, because an 

atmosphere dominated by carbon dioxide and molecular nitrogen appears to be 

much less conducive to the formation of certain organic molecules. 

7.4.- The view that the Earth possessed all the necessary ingredients for the origin 

of life is perhaps the most thoroughly investigated hypothesis and holds great 

appeal for many scientists even today. This opinion dates back to the efforts of 

A. Oparin and J.B.S. Haldane, working in the first half of the 20th century. This 

scenario is often referred to as the Oparin-Haldane model 

8.- From simple inorganic to the building blocks of life 

8.1.- Previously, we saw the ease with which amino acids can be made from simple 

inorganic like methane, ammonia, and hydrogen. What about nucleotides. A 

second monumental achievement in origins-of-life research was the demonstration 

by Juan Oró (1961) that the nitrogenous base adenine (a purine) could be readily 

made from a thermodynamically favorable reaction involving only ammonia 



and hydrogen cyanide (HCN). 

8.2.- Other chemists have had similar results for other purine bases. Pyrimidines 

are slightly more difficult to construct abiotically, but chemists have had some 

successes. Finally, the ribose sugars that form nucleotides can, at least under 

the right environmental conditions, be derived from a cascade of condensation 

reactions that begin only from formaldehyde. 

8.3.- A major obstacle that has plagued biochemists for decades is the origin of 

chirality, or handedness. Living systems today use only one stereoisomer, or 

mirror-image form, of the amino acid in their proteins, and the same is 

true of nucleotides. In many of the chemical synthesis described by adherents 

to the Oparin-Haldane model, both mirror images of the building blocks are 

made in roughly equal quantities, and it is difficult to devise mechanisms that 

produce only one or the other. Exacerbating this problem is the fact that one 

mirror-image would inhibit the polymerization of the other during 

any type of polymer self-replication 

8.4.- Furthermore, as is the case with sugar formation, not only does the sugar 

that we see today in nucleic acids (ribose) constitute a very small percentage of 

all the sugar products of formaldehyde condensation, but there also exist multiple 

equally probable ways that the nitrogenous bases could be attached to the sugar. 

Each of these combinations produces a different nucleotide isomer than that 

used by contemporary RNA. To make matters worse, each building block 

(nucleotide) needs to be activated, or chemically charged before it can be incorporated 

into a polymer. Activation requires a pre-existing source of chemical energy. 

Without cell membranes to concentrate this energy (as ATP), it is challenging 

to understand how building blocks became activated in the RNA World. 

All these problems stress what we already mentioned in heading 5.2. of this 

lecture: "the likelihood of making RNA abiotically is too minute" 

8.5.- Many researchers now think that the RNA was likely to have been a 

later stage in an evolutionary lineage that derived from simpler genetic 

systems made of other kinds of polymers such as hybrids between peptides 

and nucleic acids, or composed of pyranose instead of ribose. 

9.- Earliest evidence of life 

9.1.- The oldest known sedimentary rocks to contain evidence suggesting that life 

was already established on Earth by 3.85 billion years ago. The rocks are from 

Akilia Island and Isua, both in Greenland and they contain apatite crystals. The high 

ratios of 12 C to 13 C found in these crystals indicate that the apatite has an biological 

origin. 

III: When life went cellular: 



10.- Early evidence of cells 

10.1.- Once self-replicating systems evolved on the Earth, at least one of them adapted 

to the use of DNA to store heritable information and to the use of proteins to express 

that information. This system eventually gave rise to all lineages of life on the planet 

today: We draw this conclusion because all life forms (except viruses) use DNA and 

proteins. In fact, all modern organisms use them in the same way; the same 

20 amino acids and the same basic structure of the genetic code have been found 

in all creatures studied to date. Thus, we apply the principle of parsimony to infer 

that all organisms share common ancestor 

10.2.- Because another shared feature of all extant life is the existence of cells, we 

also infer that the common ancestor was a cellular form. The advantages of 

cellular membranes, as well as internal organellar membranes would have been 

enormous. Cells allow for compartmentalization. This allowed life to accumulate 

its necessary constituents in much higher concentration than they are found free 

in solution. Cells allowed genotypes and phenotypes to be linked 

10.3.- The first place we might look in trying to identify the ancestral cells is the fossil 

record. The oldest fossils definitively established as those of living organisms are 

3.465 billion years old (Fig. 14.15). These fossils come from Western Australia. they 

show simple cells growing in short filaments 

Figure 14.15.: The oldest known fossils of living organisms. The 

fossils show filaments composed of individual cells lined up like 

beads of a string 



11.- The phylogeny of all living things 

11.1.- Another way to study the ancestral lineage is to reconstruct the phylogeny of all 

living things. A universal phylogeny should allow us to infer additional characteristics 

of the earliest life forms. 

11.2.- The challenge in using sequence data (nucleotide sequences from DNA) to estimate 

the evolutionary tree for all living things is to find a gene that shows recognizable sequence 

similarities even between species that are as distantly related as Escherichia coli and 

Homo sapiens. We need a gene that is present in all organisms, and that encodes a product 

whose function is essential and thus subject to strong stabilizing selection. Additionally the 

function of the gene must have remained the same in all organisms. One gene that meet all 

the criteria for use in reconstructing the universal phylogeny is the gene that codes for 

the small-subunit ribosomal RNA. Ribosomes are the machines responsible for translation. 

Translation is so vital, and organisms are under such strong natural selection to maintain 

it, that the ribosomal RNAs of humans and their intestinal bacteria show recognizable 

similarities in nucleotide sequence, even though humans and bacteria last shared a common 

ancestor billions of years ago. 

11.3.- An estimated of the universal phylogeny, based on sequences of the small-subunit 



rRNA, appears in Figure 14.16. 

Figure 14.16.: An estimate of the phylogeny of all living organisms. 

This tree is based on the analysis of nucleotide sequences of 

small-subunit rRNAs 

The whole-life rRNA phylogeny has prompted a dramatic revision of our traditional view 

of the organization of life, because it reveals that the five-kingdom system of 

classification [i.e., Plants, Animals, Fungi, Protists (this is the taxomic kingdom that 

comprises a variety of unicellular and some simple multinuclear and multicellular 

eukaryotic organisms, they include some algae, the protozoans, and multicellular 

or multinucleate autotrophs), and Monera (this is taxonomic kingdom that comprises 

the prokaryotes (bacteria and cyanobacteria))] bears only a limited resemblance to actual 

evolutionary relationships. 

11.4.- The prokaryotes, for example, which are all grouped in the kingdom Monera in 

the traditional classification, occupy two of the three main branches of the rRNA 

phylogeny. One of these two branches, the Bacteria, includes virtually all of the wellknown 

prokaryotes. The other prokaryote branch, the Archaea, is not well known. 

Many of the Archaea live in physiologically harsh environments like hot springs, and are 

difficult to grow in culture. They are also known as the Archebacteria 

11.5.- As the phylogeny in Figure 14.16 shows, the archebacteria are in fact more closely 

related to the eukaryotes than they are to the true bacteria. The most inclusive taxonomic 

units in the new classification are three domains corresponding to the three main branches 



on the tree of life: the Bacteria, the Archaea, and the Eucarya. It has been proposed 

that the these three branches are designated as kingdoms. 

11.6.- The universal rRNA phylogeny demonstrates, however, that the Animals, Plants, 

and Fungi, "the kingdoms" that have absorbed most of the attention of evolutionary 

biologists, are mere twigs on the tip of one branch of the tree of life. The multicellular, 

macroscopic organisms in these three "kingdoms" are newcomers on the evolutionary 

scene, with a relatively recent common ancestor 

12.- The origin of organelles 

12.1.- Evolution from the common ancestors to the extant Bacteria and Archaea 

appears to have been a process of gradual refinement. The Eucarya, on the other 

hand, are dramatically different. Among other things, eukaryotes have complex 

cells containing a variety of organelles, and dramatically more complicated genomes, 

in which the coding regions of genes are frequently interrupted by intervening 

sequences of noncoding DNA (introns). In addition many eukaryotes are 

multicellular, with differentiated cells and tissues. We will only consider one of these 

problems here, the evolutionary origin of organelles. 

12.2.- The organelles whose evolution is best understood are mitochondrial and 

chloroplasts. Most Eucarya have mitochondrial and many also have chloroplasts, 

but some early-branching eukaryotes (Giardia lamblia) have neither. Thus 

mitochondria and chloroplasts do not appear to be defining characteristics of the 

Eucarya; instead, they arose within the eukaryotic branch of the tree of life. 

12.3.- Superficially, mitochondria and chloroplasts resemble simple bacteria. With 

the discovery that mitochondria and chloroplasts have their own chromosomes, 

and that these chromosomes are small circular DNA molecules similar to 

those of bacteria, biologists began to take seriously an old idea that had been 

dismissed by all but a persistent few. This idea is that mitochondria and chloroplasts 

originated as bacteria that lived as internal symbionts of early eukaryotic cells. 

12.4.- The definitive test of this hypothesis was to sequence genes from mitochondrial 

and chloroplasts, such as the genes for the small-subunit ribosomal RNA, then determine 

their position on the universal phylogeny. If the organelles arose via symbiosis, then 

their rRNA genes should branch from within the Bacteria; if, instead, the organelles 

arose independently within the Eucarya, then their rRNA gene should branch from 

within the Eucarya. The results are in, and they prove that the endosymbiosis theory is 

correct (Fig. 14.24). Mitochondria are closely related to the protobacteria, 

previously called purple bacteria. Chloroplasts are cyanobacteria 

Figure 14.24.: An estimate of the universal phylogeny, showing 

the locations of the mitochondrial and chloroplasts. The 



mitochondria are represented by that of Zea mays.

Chapter 17. The origins of life and Precambrian evolution

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