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THE HISTORICAL PLANET



been metamorphosed (subjected to episodes of modest pressure

and high temperature) in a way that suggests processing in and

beneath a primitive basaltic crust. Also present in these rocks

are rounded pebbles that appear to be sedimentary, that is, laid

down in an environment containing liquid water. Belts of these

rocks appear to be the remnants of the earliest continents. They

indicate that continental-type crust, floating buoyantly atop a

denser mantle, began to appear about 500 million years after the

formation of Earth; whether continents could have formed much



earlier is unknown. The chemistry of oceanic and continental

rock formation is explored in more detail in Chapter 16.

This Hadean Earth, while vastly different from the present

planet, set the stage for what was to follow. By 3.8 to 4.0 billion

years ago, the growth of continents, the stabilization of liquid

water, and the decreasing impact rate made for an increasingly

predictable and benign environment. Increasing environmental

stability characterized the transition from the Hadean era to the

Archean eon of Earth.



Summary

The Hadean era of the Earth spans the time from formation

to the presence of the first whole rocks in the geologic record.

This is therefore the era in which information on the state of the

Earth must be derived from meteorites, from the Moon, and

from modeling of planetary processes. The planets of the solar

system can be divided according to their density into the solid

terrestrial planets, made mostly of rock and metal, and the giant

planets, made mostly of hydrogen and helium. Uranus and

Neptune are distinguished from Jupiter and Saturn by having

far less hydrogen and helium, and proportionately more water.

A third class of bodies is made of various proportions of water

ice and rock (plus metal); these are the icy moons of the outer

solar system, and dwarf planets like Pluto and other Kuiper Belt

objects. The Earth’s internal structure, revealed through careful measurement of seismic waves propagated by earthquakes,

includes a chemically distinct core that is divided into an outer

liquid and an inner solid core. The core is mostly iron and other

metals with an admixture of oxygen or sulfur. Above the core

is the mantle, which itself may be layered chemically, but is

made largely of silicates. It is solid, but flows slowly in the same

manner as glass does in very old windows. At the core–mantle



boundary a complex mixing of the molten iron and solid silicates may be taking place. Above the mantle is the solid crust

of the Earth, another chemically distinct layer rich in silicon and

aluminum compared to the mantle. The growth of the planets

and their moons by addition of material resulted in the release

of heat, leading to substantial melting of their interiors. In the

case of the Earth, collisions with lunar- and Mars-sized bodies

occurred multiple times during its growth, the last of which was

a glancing blow that enabled material to remain in orbit, forming the Moon. Meanwhile in the outer solar system, the giant

planets may have been spaced more closely together than they

are now, orbiting between 5.5 and 17 AU. However, interactions with the remnant disk of debris, and between the giant

planets themselves, could have led to a dramatic reshuffling

of orbits that is seen in the lunar cratering record as the “Late

Heavy Bombardment”. The cooling of the Earth after its formation continues to the present, with heat transported from the

interior not only from the energy of formation but also from

the decay of radioactive elements that progressively became

concentrated in the crust.



Questions

1. Some meteorite properties suggest that rocky bodies were



3. What might have been different about Earth’s Hadean and



strongly heated by 26 Al, a very short-lived radioisotope of

aluminum. How might the asteroids help determine whether

this heating actually occurred? What would you look for?

2. Calculate the temperature rise associated with the formation

of the Earth’s iron core, assuming that the iron started out

fully mixed with the silicates throughout the Earth (this is an

oversimplification of what happened, but one still derives a

useful number).



Archean history had the Moon not been present?

4. Go online to the exoplanet encyclopedia (http://exoplanet.

eu/) and examine the orbits of planets in multiple planet systems. Do the configurations you find there seem to argue

for or against, or are neutral with respect to, the Nice

model?



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129



General reading

Broecker, W. S. 1985. How to Build a Habitable Planet. Eldigio

Press, Palisades, NY.

Cloud, P. 1988. Oasis in Space: Earth History from the Beginning.

W. W. Norton, New York.

Press, F. and Siever, R. 2001. Understanding Earth. W. H. Freeman,

New York.



References

All´ gre, C., Poirer, J.-P., Humler, E., and Hofmann, A. W. 1995.

e

The chemical composition of the Earth. Earth and Planetary

Science Letters 134, 515–26.

Gomes, R., Levison, H. F., Tsiganis, K., and Morbidelli A. 2005.

Origin of the cataclysmic Late Heavy Bombardment period of

the terrestrial planets. Nature 435, 466–8.

Jeanloz, R. and Lay, T. 1993. The core-mantle boundary. Scientific

American 268(5), 48–55.

Mason, S. F. 1991. Chemical Evolution. Clarendon Press, Oxford.

Melosh, H. J., Vickery, A. M., and Tonks, W. B. 1993. Impacts and

the early environment and evolution of the terrestrial planets.

In Protostars and Planets III (E. H. Levy and J. I. Lunine, eds).

University of Arizona Press, Tucson, pp. 1339–70.

Owen, T. and Bar-Nun, A. 1995. Comet, impacts and atmospheres.

Icarus 116, 215–16.

Press, F. and Siever, R. 1978. Earth. W. H. Freeman and Company,

San Francisco.



Spudis, P. D. 1992. Moon, geology. In The Astronomy and Astrophysics Encyclopedia (S. P. Maran, ed.). Van Nostrand Reinhold, New York, pp. 452–5.

Squyres, S., Reynolds, R. T., Cassen, P. M., and Peale, S. J. 1983.

Liquid water and active resurfacing on Europa. Nature 301,

225–6.

Tackley, P. J. 1995. Mantle dynamics: influence of the transition

zone. Reviews of Geophysics 33 (Suppl.), 275–82.

Tackley, P. J., Stevenson, D. J., Glatzmaier, G. A., and Schubert, G.

1994. Effects of mantle phase transitions in a 3-D spherical

model of convection in the Earth’s mantle. Journal of Geophysical Research 99, 15,877–901.

Taylor, S. R. and McLennan, S. M. 1995. The geochemical evolution

of the continental crust. Reviews of Geophysics 33, 241–65.

Weissman, P. 1992. Comets, Oort cloud. In The Astronomy and

Astrophysics Encyclopedia (S. P. Maran, ed.). Van Nostrand

Reinhold, New York, pp. 120–3.



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12

The Archean eon and the origin of life

I Properties of and sites for life

Introduction

The close of the Hadean and opening of the so-called Archean

eon is defined and characterized by the oldest whole rock samples found on Earth, 4.0 billion years old. At the opening of the

Archean, Earth had an atmosphere rich in carbon dioxide, with

perhaps some nitrogen and methane but little molecular oxygen, and liquid water was stable on its surface. Mantle convection had begun producing oceanic basalts and continental-type

granitic rocks. The rate of impacts of asteroidal and cometary

fragments had decreased significantly. The Moon, formed from

Earth at the end of accretion some half billion years before,

could be seen in the terrestrial sky.

By 3.5 billion years ago, rocks were present that record definitive evidence for life; more controversial evidence exists back

to almost 3.9 billion years. Large sedimentary or layered formations in ancient limestones contain concentric spherical shapes,

stacked hemispheres and flat sheets of calcium carbonates (calcite), and trapped silts. These stromatolites are best understood

as the work of bacteria from 3.5 billion years ago, precipitating calcium carbonate in layers as one of the byproducts of



primitive photosynthesis. (Present-day active stromatoliteforming colonies can be found in Shark Bay, Australia.) If

the interpretation is correct, life on Earth was present then

and somewhat earlier as well, because such bacteria constitute

already reasonably well-developed organisms.

It therefore appears that, as Earth settled down from the

chaos of accretion, core formation, and impacts, life was able

to exist on its surface (Figure 12.1). The same might be true for

Mars, but the evidence discussed later in the chapter is vague

and controversial. How did life arise on the Earth? Could it have

arisen on the neighboring planets as well? Is there life in other

planetary systems? Why was Earth able to sustain life over billions of years of change, and the other terrestrial planets not?

How did life alter the Earth environment?

These are questions whose explorations constitute the

remainder of the book, including Part IV, where human kind’s

role is examined. In the present chapter, we outline the

definition of life and the essential structures that make it

possible.



12.1 Definition of life and essential workings

12.1.1 What is life?

No completely satisfactory definition of life – or of “living

things” – has yet been devised. Most simple definitions of

life – something that grows spontaneously, or something that

replicates itself – fail because they either include demonstrably

nonliving things or exclude certain particular living organisms.

Crystals such as snow or pyrite grow but are not biological in

nature; offspring of separate but related species such as mules

(offspring of a donkey and a horse) are almost invariably unable

to reproduce, yet clearly are living.

Some biologists lean toward a definition that incorporates

the concept of Darwinian evolution, defined broadly to mean



reproduction, variation of characteristics from one generation

to another, and natural selection whereby some individuals with

specific traits gain an advantage over others and hence are more

successful in producing offspring. In this context, one working definition of life might be “a self-sustained chemical system

capable of undergoing Darwinian evolution,” as devised by University of California biologist Gerald Joyce and colleagues.

There are two major drawbacks to this definition. First, it

has become clear that, although species do evolve, the classical

Darwinian concept of natural selection is only one factor that

comes into play in such evolution. Second, the definition may



131



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.9

.7



megascopic eukaryotes

develop and diversify



.9



1.4



1.6



.6

.5



mass

extinction



early vascular plants



.4



mass

extinction



.2



gymnosperms



.2



mass

extinction

(asteroid impact)



0



100



200



300



0



700



800



900



angios



100



200



300



perms



sent

r e pre

ars befo

illions of ye

geologic time, b

.3 pteridophytes



mass

extinction



aerobic

prokaryotes

diversify



mass

extinction



youngest detrital uraninites



major banded iron formations



nonvascular land plants and others

(this black section)



1.8



3.0



400



500



0



700



0



100



200



300



400



500



600



land

plant

species

(incomplete)



(known)

marine

vertebrate

and

invertebrate

families



land vertebrate

families



land arthropod

and other families



Figure 12.1 Schematic history of life on Earth, showing where key milestones in the history of life likely occurred relative to geologic events on Earth. Beginning at the Vendian–Cambrian

diversification of life (Chapter 18), the rise and fall with time of the number of families of land and marine creatures is depicted.



oldest body fossils

of invertebrates



oldest traces of invertebrates;

oldest large algae



1.0



1.2



eukaryotes develop

(or earlier)



eukaryotes diversify;

sexual reproduction

develops



2.2



2.0



2.8



photosynthetic bacteria



first

anaerobic

bacteria



oldest fossil-like objects



Present time



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O2-rich atmosphere;

aerobic respiration develops;

some anaerobes become extinct



aerobic

photosynthesis

develops



2.4



2.6



3.5



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ARCHEAN EON: PROPERTIES OF AND SITES FOR LIFE



be unnecessarily narrow in that “life” on other planets might

not undergo Darwinian evolution, but might still involve biochemical reactions resembling those on Earth; non-Darwinian

evolution might have occurred in the very earliest, primitive

organisms on our planet as well. The definition also excludes

“artificial life,” experiments in computer information replication described in Chapter 13, but could easily allow inclusion of

such experiments by replacing the phrase “chemical system” by

“material system,” as has been suggested by NASA Ames planetary scientist Chris McKay. Finally, a more general definition of

life – perhaps too general in that it might apply to some nonliving

systems – is “a system that possesses the ability (homeostasis)

of maintaining form and function through feedback processes

in the face of changing environments.”

What is required to maintain terrestrial life? Many different

things are required for different forms of life, but the essentials are organic (carbon-based) molecules for structure and processes, liquid water as an energy and information transporting

medium, and a source of usable energy (most often from the

Sun, but Earth’s heat can be a source as well).



133



oxygen

carbon

nitrogen



hydrogen



(a)



H

O

R



C



C



12.1.2 Basic structure of life

All known life-forms live on Earth and are based on the same

small set of molecular units and chemical reactions. Four types

of essential molecules are organic (contain carbon and hydrogen) and account for most biological processes and structures:

proteins, nucleic acids, carbohydrates, and lipids. Carbohydrates are molecules in which the hydrogen and oxygen atoms

form a whole number (that is, 1, 2, 3 . . . ) of water molecules.

Some classes of carbohydrates (sugars) are produced by plants

using sunlight as an energy source, and water and carbon dioxide as the raw materials. This process, photosynthesis, led to

fundamental changes in Earth’s atmospheric composition early

in its history, as we see in Chapter 17.

The molecules that provide the primary structural material

for life, as well as contribute crucially to its functioning, are

called proteins (from the Greek word proteios, or primary, hence

“primary substance”). Proteins are long chains (or polymers) of

relatively small molecular units (monomers), called amino acids.

An example structure of an amino acid is shown in Figure 12.2.

The “R” group distinguishes the particular amino acid – it could

be hydrogen or methyl (CH3 ) or more complicated combinations

of hydrogen, carbon, and oxygen. Of the vast variety of possible

amino acids, only about 20 are found to be the building blocks

of the major proteins of life.

Long-chain proteins fold into tight bundles, which give rise to

the physical and chemical behaviors associated with particular

proteins. A typical protein chain may contain from about 50 to

1,000 amino acid molecules strung together. The total number

of possible proteins is vastly more than the relatively few (of

order 100,000) that actually occur in terrestrial life. Of those

that do occur in cells, some play a role in defining the cellular

structure, some act to transport or store molecular compounds,

and others act as catalysts to control the rates of biochemical

reactions; the latter are called enzymes.

Proteins cannot make copies of themselves; in the absence

of some directive agent or template, the faithful production of



OH



N

(b)



H



H



Figure 12.2 (a) Atomic structure of the amino acid alanine, used in

proteins. (b) Schematic structure of many amino acids, including most

biological ones, where “R” represents a functional group of atoms that

defines the particular amino acid.



proteins from the simpler amino acids would not occur in cells.

Nucleic acids are molecules that form the building blocks of the

templates, which we consider next.



12.1.3 Information exchange and replication

The information-carrying and replicating (or genetic) components of terrestrial life are types of nucleic acids called DNA

(deoxyribonucleic acid) and RNA (ribonucleic acid). DNA

molecules are long double chains normally twisted into a helical

structure. The side rails of the double chains consist of a string

of alternating sugar and phosphate molecules. Sugar is a simple

carbohydrate. Many common sugars, such as glucose, have the

chemical formula C6 H12 O6 ; others have slightly different ratios

of carbon to hydrogen and oxygen. Phosphate molecules, or

phosphate groups, form high-energy bonds in living systems; a

phosphate group involves phosphorus and, for example, would

have the formula PO3 H2 .

The cross-ties of the DNA chain consist of pairs of four different types of bases: adenine (A), thymine (T), guanine (G), and

cytosine (C). These bases consist of carbon, nitrogen, oxygen,

and hydrogen in complicated ring structures (Figure 12.3). The

combination of a base with the sugar and phosphate backbone

is called a nucleotide.

The pairing of the nucleotide bases is restricted: A with T,

and G with C. Thus, the two sides of the chain (conjugates) are



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Pyrimidines:

O



H



N



H N

O



N



Nucleotides:

O



NH2



O



H

uracil



O



N



CH3



N3



H

cytosine



beta-glycoside link

to purine or pyrimidine



O

−O



P



O



O



−O



N

H

thymine



HO OH

Beta-D-ribonucleotide



Purines:

O

N



N

N

adenine



beta-glycoside link

to purine or pyrimidine



O



NH2



N



N



H N

H2N



H



(a)



N



−O



P



O



O



−O



N



HO H

Beta-D-deoxyribonucleotide



H

guanine

(b)



Figure 12.3 (a) The five types of nucleic acid bases in DNA and RNA, showing the characteristic ring structure. (b) Two types of nucleotides are

produced from the bases: (top) a ribonucleotide that is the foundation for RNA and (bottom) a deoxyribonucleotide that is the foundation for DNA.

Empty vertices correspond to carbon paired with zero or one hydrogen atoms; double lines indicate two shared pairs of electrons. Redrawn from

Mason (1991).



redundant to each other because, from the letter on one side, you

know what the letter on the other side must be. In replication,

the net result is that the two sides of the chain are split, with

each side reconstituting (through the mediation of enzymes) its

conjugate, resulting in two copies of the original DNA.



12.1.4 Formation of proteins

Protein synthesis is governed by DNA, through the intermediation of RNA. The synthesis begins when DNA, instead of

replicating to make new DNA, transcribes RNA. RNA differs

from DNA in two aspects: the sugar is of a different form, and the

nucleic acid base uracil (U) is present in place of thymine (T).

These are relatively minor structural changes in the molecule

(Figure 12.3), a fact that we return to in Chapter 13 as we consider the origin of the genetic code.

Thus, a chain of RNA contains a long sequence of molecular

monomers chosen from among the four nucleic acid bases A, U,

G, C. This chain of monomers can be “read” as a sequence of

three-letter “words” constructed from a four-letter “alphabet.”

Each three-letter word is called a codon. Some examples of

words are GUA, AAG, UGA. The number of possible words is

4 × 4 × 4 = 64.

Each codon codes for a specific amino acid; thus, the sequence

of codons in an RNA molecule (which, remember, is ultimately

derived from the sequence in the original DNA) specifies a

sequence of amino acids. This amino acid sequence constitutes the synthesized protein. A particular amino acid generally

is coded for by more than one codon, because 64 codons are

available for the 20 amino acids commonly used in terrestrial

biology.

The actual protein synthesis is a bit more complicated, with

messenger RNA carrying the protein-structure information from



the DNA, transfer RNA attaching to specific amino acids and

aligning them based on the messenger RNA sequence, and

ribosomal RNA (located in a cellular structure called the ribosome) receiving the ordered amino acid sequence (ferried by

the transfer RNA) and acting as a catalyst for final assembly

of the amino acid chains. Other RNA molecules assist in DNA

replication and in the construction of the messenger RNA. This

diverse range of roles for a single kind of molecule makes tempting the proposal that, at some time in the distant past, RNA was

central to the genesis of life as we know it. By contrast, DNA,

which is not terribly dissimilar to RNA, has a very specialized

function as a record of the genetic information of the individual

organism and (in separate DNA strands) of certain structures in

the cell. This essential but much more limited role compared

to that of RNA suggests that DNA is a subsequent, derived

molecule.

A length of DNA that carries the genetic information that

is ultimately expressed as a single protein is called a gene.

The genetic code is the complete sequence of nucleotides in

DNA, which determines the form and function of an organism’s

proteins. All living organisms on Earth that have been examined

use DNA and RNA to record and express the proteins of which

they are made.



12.1.5 Mutation and genetic variation

The replication process sketched above operates with high

fidelity. Errors are rare but occur. These errors are called mutations. Such errors, changes in the structure of the DNA, may

have a variety of causes such as chemical impurities in the environment or radiation (ultraviolet photons or particle radiation).

Other errors or changes may be a result of accidental mixing or

crossover of DNA chains in normal cells. Mutations give rise to



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(a)



Eukaryotic cell



135



microtubules

lysosome

peroxisome

Golgi apparatus

mitochondria

DNA



endoplasmic reticulum

nuclear envelope



10



–3



0m



icr



on



s



chloroplast



cell membrane



ribosome

cytoplasm



cell wall

DNA



1 micron

(b)



Prokaryotic cell



flagella



Figure 12.4 (a) Generalized eukaryotic cell, with structures and organelles shown. (b) Prokaryotic cell (a bacterium).



changes in organisms. This genetic variation is usually harmful

but sometimes not.

Such variation forms the biochemical basis for the evolution of one species from another, via natural selection within

a given environment or through environmental changes in

the ecosystem itself. The large-scale pressures for the evolution of species are discussed in Chapter 18, but, without the

imperfection and vulnerability in the genetic code that allows

changes (both good and bad), such evolution would not be

possible, or too slow to be relevant to the history of life on

Earth.

Since it is now possible to analyze the genome of an organism

and determine the sequence of base pairs, the concept of a molecular clock based on the mutation rate has assumed great importance in estimating when different organisms diverged from one

another. The rate of mutation varies from species to species,

and even between different components of DNA within a given

species – for example the mutation rate of DNA contained in the

mitochondria of eukaryotes (see next section) is generally higher

than that of the DNA in the nucleus. This molecular clock may

have errors of factors of ten or more. In some cases, the mutation rate can be cross-checked with other evidence. For example,

the differences in DNA among different peoples can be crosschecked with the migration patterns established by archeology

to determine a mutation rate. And in closely related species, such

as humans and chimpanzees, it is reasonable to assume mutation

rates that are similar, allowing a molecular determination of how

long ago the two lineages diverged from a common lineage; to

some extent this can be cross-checked by dating fossil remains

(Chapter 20).



12.2 The basic unit of living organisms:

the cell

With the exception of viruses and virons, which are essentially

strands of DNA or RNA sheathed in proteins and which cannot

survive independently of other organisms, all Earth life is organized into cells. These structures provide a boundary or membrane for separating the outside environment from the internal

one where biochemical reactions occur, and house the DNA and

RNA genetic machinery for replicating the particular organism.

Two basic types of cells exist today on Earth (Figure 12.4).

Prokaryotic (from the Greek “pro” for before and “karyon”

for nut, hence seed or nucleus) cells include the common bacterium. The interiors of the prokaryotic cells are dominated by

cytoplasm (a salt-water medium containing proteins) in which

are contained a loop of DNA and ribosomes – structures hosting

the RNA for protein production. The cell walls are composed of

sugars and peptides, chains of amino acids that are shorter than

the full-fledged proteins. These simple cells are as small as 10−6

meters, are able to store energy by either aerobic or anaerobic

processes, and divide by a simple splitting process. Most can

move by means of attached protein strands called flagellum.

Eukaryotes (from the Greek “eu” for good, hence true, and

“karyon” for nucleus) are much bigger, more complex cells.

The DNA is housed in a nucleus, and other structures called

organelles also occupy the cytoplasmic space. These include

plastids (the commonly known green ones being chloroplasts)

in plants, which are the sites of photosynthesis (see section

12.4), and mitochondria, within which respiratory processes

take place. Most eukaryotes are obliged to utilize oxygen in



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their sustaining processes; there are a lesser number of anaerobic

eukaryotes. Furthermore, the cells are 10 to 100 times larger in

diameter than prokaryotic cells, and reproduce by somewhat

more complex processes, which ensure the presence of nucleus

and organelles in each new cell.

Clues to the origin of eukaryotic cells lie in the ability of most

to take advantage of oxygen and the resemblance of organelles

in size and structure to bacteria. They seem to be later arrivals in

the history of life, though how late is controversial, with some

well preserved organic molecules typical of photosynthesizing

eukaryotes dating back to 2.7 billion years.



12.3 Energetic processes that sustain life

Chapter 13 considers life as a phenomenon of nonequilibrium

thermodynamics, driven and sustained by substantial flows of

energy. Life on Earth primarily utilizes the Sun for energy,

with heat from Earth’s interior as a secondary source. To

appreciate the coupling of life to such energy sources, we

must understand how they are utilized by living organisms on

Earth.



12.3.1 Common metabolic mechanisms

Energy for living processes requires a usable raw material and

suitable chemical reactions to store energy in chemical bonds,

which then can be utilized by the organism. Fermentation and

respiration are the most common metabolic processes used by

organisms today (Figure 12.5). In each case, energy is stored

by the organism in bonds involving the element phosphorus.

Molecules such as adenosine triphosphate serve as the storage

medium through their phosphate bonds; a single phosphate bond

stores 7.3 kilocalories of energy, a large amount. (Biochemists

use the unit calorie, but so do nutritional scientists: confusingly,

the nutritional “calorie” listed on a cereal box is 1,000 times that

of the physicists’ calorie, or 1 kilocalorie. Only the physicists’

calorie is used in this book.)

In fermentation, which is practiced by bacteria, the sugar, glucose, is split into two molecules of pyruvate. Two phosphatebonds worth of energy are used to break the bond, but the resulting reaction produces a total of four phosphate-bonds worth of

energy. The pyruvate then is converted into ethanol and carbon

dioxide, or into lactic acid (depending on the type of bacteria)

as waste products. Net energy gain is two phosphate-bonds or

14.6 kilocalories of energy per glucose molecule.

Respiration takes advantage of the presence of free oxygen

(O2 ) in Earth’s atmosphere to extract much more energy from the

glucose molecule than fermentation can. Pyruvate again is produced as in fermentation, but instead of immediate conversion

of pyruvate into waste products, a complex series of chemical

reactions with six oxygen molecules leads to the production

of carbon dioxide, water, and 34 additional phosphate-bonds

worth of energy. The net result is 36 phosphate-bonds, or 263

kilocalories, worth of energy. A number of biological catalysts,

that is, enzymes, are required to mediate and control the citric acid cycle that produces the additional 32 phosphate bonds.

Although some bacteria do undertake respiration, eukaryotes

take the greatest advantage of this process. As we discuss in



Chapter 18, the onset of oxygen in Earth’s atmosphere was

likely the enabling factor for the dominance of multicellular

eukaryotic life, with its specialization of cells and high degree of

mobility. Confined to only one-eighteenth the amount of energy

per glucose molecule, as is the case in fermentation, living

processes would be much too sluggish to sustain macroscopic

animals.



12.3.2 Photosynthesis

The source of glucose and other sugars used in metabolic processes must lie in an energy-collecting process. Without some

means to create such sugar, limitations of food supply for

metabolic processes would be far more severe than they actually

are. Photosynthesis is the production of sugars from water and

carbon dioxide, using sunlight as the energy source. Chemically

the reaction (in plants) is 6 CO2 + 6 H2 O → C6 H12 O6 + 6 O2 ,

where the sugar (glucose) appears as the first compound on the

right side of the equation. Energetically, sunlight charges a natural battery in the plant: a molecule called chlorophyll is able to

donate an electron upon absorption of photons. The source of

the electron in plants and most photosynthesizing bacteria is a

water molecule. The electrons so liberated then are used to drive

the formation of high-energy phosphate bonds, which, in turn,

the plant uses to produce sugars.

There are several varieties of chlorophyll and chlorophylltype molecules utilized by different photosynthesizing organisms. Modern plants employ water as the electron source, and

produce molecular oxygen as a waste product. Some bacteria

use a less efficient cycle in which the chlorophyll-type molecule

is the electron source itself, and the electron then is returned to

the donor molecule. This more primitive cyclic photosynthesis

does not produce molecular oxygen, and captures less energy

from a given amount of sunlight than does plant photosynthesis. One type of cyclic photosynthesis, as an example, begins

with hydrogen sulfide and ends with sulfur: 2 H2 S + CO2 →

CH2 O + H2 O + 2 S.

Some bacteria that conduct cyclic photosynthesis are in fact

intolerant of oxygen. Others switch between oxygen-free photosynthesis and respiration. As discussed in Chapter 19, the rather

late occurrence of large amounts of molecular oxygen in Earth’s

atmosphere suggests that the less efficient cyclic photosynthesis dominated early on, and that the oxygen-producing form of

photosynthesis was a later innovation.



12.4 Other means of utilizing energy

Respiration and photosynthesis are currently the predominant

means of producing storable energy from sunlight and then

utilizing that energy for biological processes. However, other

mechanisms are employed by organisms that are not in environments where they can photosynthesize or gain access to photosynthesized sugars. Chemisynthesis is employed by organisms

that live in the environment around deep-sea volcanic vents,

where hot, hydrogen sulfide-rich waters pour out of newly

formed ocean crust (Figure 12.6). Such waters, compared to

the colder, sulfide-poor adjacent regions, have an abundant supply of free energy. This term refers to a source of energy that



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ARCHEAN EON: PROPERTIES OF AND SITES FOR LIFE



Anaerobic

fermentation



(a)



glucose

O

H HO H



H

OH C



C



C



H



H



OH H



P



C C



Bacterial

fermentation



(b)



H

C OH



OH H



OH C



C



C



H



H



OH H



P

P



C C



Respiration



(c)



glucose

O

H HO H



glucose

O

H HO H



H

C OH



OH C



C



C



H



H



OH H



OH H



137



P



P



C C



C OH



OH H



gluconeogenesis



P

pyruvate



glycolysis



glycolysis



glycolysis

pyruvate



P



P



P



P P



P



P P



P P

P



P



pyruvate



pyruvate



pyruvate



pyruvate



lactic

acid



pyruvate

pyruvate



lactic

acid



P

P P

P PP

ethanol



+

ethanol



P



CO2

CO2



P



2 phosphate bonds

(molecules of ATP)



lactic

acid



citric

acid cycle



PP

P

PP

P

P

PP

P

P

P

P P P P P

P P

P P

P

P P PP P

P

P P

P

P P

P



lactic

acid



P



P



2 phosphate bonds

(molecules of ATP)



CO2

CO2



CO2 CO2

CO2 CO2



+

H2 O

H2O



H2O H2O

H2O H2O



P P P P P P

P P P P P P

P P P P P P

P P P P P P

P P P P P P

P P P P P P



36 phosphate bonds

(molecules of ATP)

Figure 12.5 Comparison of the common metabolic processes of fermentation and respiration. Various molecules involved in the process are

indicated by circular boxes, but only glucose’s structure is shown. Square boxes refer to processes; for example gluconeogenesis is the production

of glucose. Phosphate bonds are symbolized by a P. Note that fermentation sequesters for the organism, in the end, two phosphate-bonds worth of

energy; respiration sequesters 36 such bonds. Modified from Gould and Gould (1989).



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THE HISTORICAL PLANET



(a) Photosynthesis

energized

electron

e



charged

membrane

enzyme



enzyme



ATP



ADP



P



ADP



P



photon

e

unenergized

electron in

chlorophyll



(b) Chemisynthesis

charged

membrane



energized

electron

e

H2S



enzyme



enzyme



ATP



e

free

chemical

energy

Figure 12.6 Comparison of photosynthesis and chemisynthesis: both allow organisms to sequester useful energy for cellular functions in the

form of the phosphate bonds of the molecule adenosine triphosphate (ATP). However, photosynthesis derives energy from sunlight whereas

chemisynthesis garners energy from reduced molecules (such as H2 S) not in chemical equilibrium with their surroundings. ATP is symbolized as

the energized weightlifter; the preceding molecular form that does not have the energetic phosphate bond is adenosine diphosphate (ADP).

Redrawn and modified from Gould and Gould (1989).



can be utilized readily to do some form of work, such as sustain

biological processes, or can be stored in high-energy phosphate

bonds.

One readily available means to extract energy from the vents is

to combine hydrogen sulfide with oxygen to form sulfur dioxide

with production of energy. Such a process is possible in an

ocean that has free oxygen available, but would not work on the

primitive, pre-oxygen-rich Earth. Other biochemical cycles that

use sulfur but not oxygen are conducted by some prokaryotic

organisms, but these capture much less energy than the oxygendriven cycles. As with fermentation, chemisynthesis without

free oxygen was the hallmark of a rather sluggish primitive

biota.



12.5 Elemental necessities of life: a brief

examination

12.5.1 Why carbon?

Why is the element carbon the basis for biochemistry? Of all

elements, carbon possesses the greatest tendency to form covalent bonds and, in particular, has a remarkable tendency to bond

with itself. These characteristics reside to some extent with all

elements near the center of the periodic table (Figure 2.6), for

which there is not a strong tendency to favor donation over

acquistion of electrons. However, carbon is most distinguished

in this regard as a small element (few electron shells) and being



positioned in the central column IVA of the table. It readily

forms a variety of long-chain, sheet, and ring structures, many

of which play important roles in the basic biological molecules,

as seen in Figures 12.2 and 12.3. In addition, carbon is the fourth

most abundant element in the cosmos (after hydrogen, helium,

and oxygen), being made readily from helium fusion in stars.

The element silicon has chemical-bonding properties very

similar to those of carbon, being one row below the latter in

the periodic table. Silicon also forms chain, sheet, and ring

structures with nearly (but not quite) the same ease and variety as does carbon. It is not nearly as abundant as carbon in

the cosmos because it is the product of a later stage of fusion

reactions achieved only in massive stars, but, after oxygen, it is

the primary constituent of the crust of Earth. The similarities in

silicon’s properties to those of carbon and its high abundance in

geologic materials are responsible for the lithification of biological remains in the form of fossils, as discussed in Chapter 8. It

is natural to ask whether silicon might be the elemental basis for

biology on another planet in another planetary system, perhaps

one on which conditions are not quite suitable for carbon-based

life because of higher temperatures, or where carbon-bearing

molecules were not supplied to the planet’s surface, for whatever reason.

The biologist A. Cairns-Smith has proposed that, on the early

Earth, layers of crystalline silicates might have served as the

basis for a very primitive kind of life, which served in turn as

a sort of template for, and gradually evolved into, carbon-based

life. Certainly, some clay minerals have a surface upon which

organic molecules can adhere, in favorable positions, which



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