Chapter 7 Biosynthesis - PlanetaryBiology.com · The overall biosynthesis process has two main consequences that can lead life toward planet-changing stature: 1) By exchanging materials

94 Chapter 7

This DRAFT document is an excerpt from Principles of Planetary Biology, by Tom E. Morris.

Copyright© 1999 by Tom E. Morris. http://www.planetarybiology.com

Chapter 7

Biosynthesis7.1 Introduction

The collective activities of living things on a world caninfluence the planetary surface environment in manyways. For example, green forests can reduce theplanet’s albedo and help warm the atmosphere. On theother hand, the water vapor from forest trees helps tocool the forest by encouraging the formation of clouds.As the roots help make soil from solid rock, they speedup a process called rock weathering which helps coolthe planet by removing atmospheric carbon dioxide.But these changes in the environment are caused bylife acting on the mechanical level — pumping water,breaking rocks, absorbing light. Life also canprofoundly influence the planetary surfaceenvironment by acting on the chemical level.

Life possesses a diverse toolbox of chemical activity. Ifpresent in abundance, life’s chemistry can influencethe planetary surface environment in interesting ways.

Living things exploit the chemical properties of severalsubstances found in the Earth’s physical environment— the air, water and soil. Organisms use theseplanetary materials to build, maintain, operate andreproduce themselves. “Biosynthesis” is the term usedto describe the biochemical processes in which livingthings assemble many different kinds of newmolecules. As a consequence of this assembly process,life establishes its potential to chemically change theplanet.

The overall biosynthesis process has two mainconsequences that can lead life toward planet-changingstature:1) By exchanging materials with the Earth’s

environment, biosynthesis establishes life’spotential to change the chemical environment

2) By possessing the ability to assemble usefulmolecules, biosynthesis supports the dispersal oflife. Biosynthesis does this in two ways: a) byestablishing the basis for ecological processes likecompetition and predation — which in turn drivedispersal itself and the evolutionary phenomenonof natural selection; and b) by synthesizing specialmolecules that help living things to survive in theEarth’s many different environments.

Therefore, the purpose of this chapter is to describe theoverall process of biosynthesis on Earth. Its occurrencegives life the potential to chemically influence theplanetary surface environment.

7.2 Living things build themselves mostly from justa few elements

Living things are remarkable constructions of tinyparts called molecules (see panel 7.1). The molecules oflife are amazingly diverse in terms of their size, shape,makeup and what they do. For example, sugarmolecules (see panel 7.2) are small. Their main benefitis the ability to store energy. By contrast, enzymemolecules (a type of protein) are relatively large. Theyspeed up the chemistry of life. All living things areendlessly engaged in a process of self-construction(growth), self-maintenance and other energy-consuming operations like moving materials aroundinside (like pumping blood), or moving themselves toanother location. All of the activities of life that weobserve ultimately are dependent upon the presenceand action of the parts of life — the molecules. To theextent that a living thing runs out of a particular part,its health is diminished. This idea is veryunderstandable to anyone whose car has broken down.Cars, like living things, are collections of parts thatwork together as a whole system. The big difference isthat living things, unlike cars, build, fix and reproducethemselves. And in order to do that, living things needbuilding materials. They get those from the planet.

Living things build the molecules of life mainly out ofsmaller parts called atoms (panel 7.1). There are abouta hundred different kinds of atoms. Each variety ofatom is called an atomic element. Atoms are the mostbasic form of matter (if we ignore the subatomicparticles for the moment). Life mainly uses only aboutsix different kinds of atoms — six different elements.These main elements of life are shown in Table 7.1

Please note, living things require many other kinds ofelements in addition to the “main elements” shown inTable 7.1. Still, this chapter will focus on the six mainelements of life: carbon, hydrogen, oxygen, nitrogen,phosphorous, and sulfur. Not only are they the mostuseful to life, they also are the most significant in termsof life’s chemical influence on the planet. Their use on agrand scale by living things has resulted in importantconsequences to the planetary surface environment.

Author’s note (March 6, 2009): This DRAFT document was originally prepared in 1998 and has not been fullyupdated or finalized. It is presented here in rough draft form. Despite its unpolished condition, some might find itscontents useful.

Biosynthesis 95



Nitrogen gas

Oxygen gas

Carbon dioxide gas

Water

Water

WaterSulfate

Phosphate

Hydrosphere

Atmosphere

Lithosphere

Environmental Realms of Planet Earth

What is an atom?

To put it simply, an atom is the mostfundamental, independent unit of matter.They are extremely tiny. Atoms haverecognizable chemical properties and areidentif ied by them. For instance, thereare over 100 different kinds of atoms.Chemists call these the atomic elementsand they give each kind of atom a name.Life builds itself out of a handful ofelements, namely carbon, hydrogen,oxygen, nitrogen, phosphorous and sulfur.On Earth, atoms usually don’t existtotally free. They are usually attached toother atoms making crystals ormolecules.

What is a molecule?

A molecule is the smallest particle of asubstance that expresses the chemicalproperties of that substance. Generally,molecules are groups of atoms that areheld together with strong bonds. Forexample, a water molecule is made up oftwo hydrogen atoms attached to a singleoxygen atom. Water’s molecular formulais H

2O. The oxygen you breathe actually

is a molecule composed of two oxygenatoms stuck

What is a chemical reaction?

A chemical reaction involves two ormore chemical substances in which allparticipants are chemically changed insome way. For example, chemicalreactions can be represented in the formof a reaction equation. At right is areaction equation for photosynthesis.The chemical reaction starts with thereactants, shown on the lef t side of thereaction equation. The chemical reactionf inishes with the products, shown on theright side of the reaction equation.Notice that the products are differentsubstances from the reactants. Thatmeans that the reactants are no more,they have been transformed into theproducts. A chemical reaction is not amixing of chemicals, it is a rearranging ofthe parts of chemicals, turning them intosomething completely different.

Proton

Electron

Atomic Nucleus

Electron Shell

Atom of Hydrogen

Molecule of Methane (CH4)

Atom of Hydrogen

Atom of Hydrogen

Atom of Hydrogen

Atom of Hydrogen

Atom of Carbon

CO + H O + Sunlight Sugar + O (Reactants) (Products)

2 2 2

Panel 7.1. Realms of the Earth, and basic chemistry

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7.3 Life gathers materials from differentenvironmental realms of the planetary surfaceenvironment

Living things gather the elements they need byconsuming certain materials from the atmosphere,water, and soil in different forms (panels 7.1 & 7.2). Forexample, on Earth plants remove carbon dioxide (CO

2 )

from the atmosphere. They use the CO2 to build sugars

and other molecules. Plants also consume oxygen fromthe atmosphere, where it exists as molecular oxygen (O

2

). The O2 then combines with hydrogen inside the plant

to become water (H2O). Nitrogen is pulled out of the

atmosphere by bacteria that live in the soil or in thewaters of lakes and oceans. Sulfur and phosphorousmainly are taken out of the soil. Sulfur also spendssome time in the atmosphere after it is used up byliving things.

7.4 Biosynthesis involves the assembly of manykinds of useful molecules

Biosynthesis is a term that refers to the biologicalassembly of hundreds of thousands of different kindsof useful molecules.The molecules produced bybiosynthesis include: carbohydrates (including sugarsand starches); proteins (including enzymes); nucleicacids (including DNA); and lipids (including cellmembranes). Additional molecules synthesized by lifeinclude vitamins, hormones, alkaloids (like cocaine andcaffeine), various pigments (like melanin and carotene)and many kinds of poisons (like glycosides andaflotoxins). These special molecules have interestingadaptive value and will be discussed in chapter 13. Fornow, I wish to focus on the central “purpose” ofbiosynthesis, the making of carbohydrates, proteins,nucleic acids, and lipids.

Living things tend to conduct biosynthetic activitiesvery vigorously — as long as they can get the materialsand energy they need from their surroundings. Whichbrings us to the connection between life and the Earth.

Panel 7.2. Planetary Materials and Intermediate Poolmolecules

Table 4.1The Major Elements of Life and their Planetary Sources

Element Source in the Planetary EnvironmentCarbon (C) Carbon dioxide from the atmosphereHydrogen (H) Water from streams, river, lakes, oceans and

soil.In some cases from hydrogen sulf ide

Oxygen (O) Carbon dioxide from the atmosphereNitrogen (N) Nitrogen gas from the atmospherePhosphorous (P) Phosphate salts from the soil and dissolved

in surface waterSulfur (S) Sulfate minerals in soil, or as hydrogen

sulf ide gas in the soil

Oxygen

Oxygen

OxygenOxygen

Phosphorous

Phosphate(PO4 3- )

OxygenCarbon

Oxygen

Carbon dioxide gas(CO2 )

Hydrogen

Hydrogen

Oxygen

Water(H2O)

NitrogenNitrogen

Nitrogen gasor, molecular nitrogen

(N2 )

OxygenOxygen

Oxygen gasor, molecular oxygen

(O2 )

Sulfate(SO4 2- )

Oxygen

OxygenOxygen

Oxygen

Sulfur

Planetary Materials

HydrogenSulfur

Hydrogen

Hydrogen sulfide(H2S)

Hydrogen

Hydrogen

Nitrogen

HydrogenAmmonia

(NH3 )

Nitrogen

Oxygen

OxygenOxygen

Nitrate(NO3 - )

Sugar(C6H12O6 )

An exampleof a

carbon skeleton

Adenosine triphosphate(ATP)

Intermediate Pool Molecules

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It is appropriate now to make a statement that is veryobvious, but I want to make it anyway, for emphasis.Here it is. Living things do not inhabit the Earth astotally independent entities, free from Earthly needs.Instead, they exist in a state of constant need formaterials and energy. Why? Because biosyntheticprocesses endlessly consume building materials andenergy resources. Biosynthesis is responsible fordriving life’s demand for the Earth’s resources.Biosynthesis, in its vigorous efforts to make new livingmolecules, chemically interacts with the world. It islife’s point of contact with the Earth — the gatewaybetween the physical world and the living world, inwhich materials are passed back-and-forth.Biosynthesis is the link and the reason behind the link.Therefore, in order to understand the root cause forlife’s overall influence on the planet, we need to knowmore about how life does biosynthesis — its diverseoperations, its benefits to living things, and its potentialconsequences to the planet.

7.5 Our approach to biosynthesis is organizedaround a four-part model

Biosynthesis is an inherently complex set of processesthat involves thousands of different kinds ofbiochemical reactions. It includes dozens and dozens ofintermediate products and thousands of differentenzymes. It happens in different places in the cell, anddifferently in different kinds of organisms. Achieving acomprehensive understanding of biosynthesis wouldinvolve a lifetime of study in the fields of biochemistry,molecular biology, cell biology and microbiology. Ourobjective here is much more limited. The planetarybiologist is interested in biosynthesis, but only to theextent that it helps explain the planet. Therefore, manyof the details of biosynthesis do not concern us, and wewill ignore them. This is largely because ourperspective on biosynthesis is necessarily so muchdifferent from that of traditional biology. Our goals areto understand:1) the many ways biosynthesis interacts with the

global environment2) the basic kinds of molecules that biosynthesis

builds and how they are useful to living things —keeping in mind that their production, availabilityand acquisition are important drivers of ecologicalprocesses.

In order to condense this huge field of study into amore manageable and appropriate planetaryperspective, I invented a new model (figure 7.1). Thismodel organizes all of the processes of biosynthesis intofour main components:1) Planetary Materials2) Contact Biosynthesis3) Intermediate Pool4) Deep Biosynthesis

Although on its face this model is anything but simplelooking, it is based upon some very basic principlesthat should make understandable.

The Earth is made up of many materials, some ofwhich are important biologically. These include:nitrogen gas, oxygen gas, carbon dioxide gas, water,sulfur minerals and phosphate minerals (see panel7.2). Living things make use of these materials in orderto build, maintain, operate and reproduce themselves.Using energy from the sun and energy contained insome of the Earth’s own materials, living things take inthe planetary chemicals and assemble them into largemolecules. This overall assembly process is calledbiosynthesis and it happens in three main stages.According to this model, the first stage of biosynthesisis called “Contact Biosynthesis”.

Contact Biosynthesis includes all the major kinds ofbiosynthetic processes that directly exchange materialswith the environment. Included in this stage arefamiliar processes like photosynthesis and respiration,as well as nitrogen fixation and sulfur oxidation. Theproducts of Contact Biosynthesis include sugar, ATP(an energy-carrying molecule), carbon chains, ammoniaand hydrogen sulfide (see panel 7.2). These productsflow into the “Intermediate Pool”.

The Intermediate Pool is a hypothetical holding areawhich then feeds the products of Contact Biosynthesisback to some types of Contact Biosynthesis and to theultimate destination of biosynthesis — “DeepBiosynthesis”.

Deep Biosynthesis uses chemical energy andmaterials from the Intermediate Pool to assemble thelarge molecules of life — proteins, nucleic acids, lipids,carbohydrates and much more. Living things use thelarge molecules to build, maintain, operate andreproduce themselves.

A consequence of this process is that whilebiosynthesis is happening, living things are exertingtheir potential to change and redistribute planetarymaterials. In addition, pursuit of the means forbiosynthesis and the products themselves contribute todispersal of life by driving ecological processes that inturn drive evolutionary processes.

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Nitro

gen G

as (N

2)

Oxyg

en G

as (O

2)

Carb

on D

ioxide

Gas

(CO 2

)

Wate

r (H 2O

)

Sulfa

te Mi

nera

ls

Phos

phate

Mine

rals

Prote

ins

Nucle

ic Ac

ids

Lipids

Carb

ohyd

rates

Suga

r

ATP

Carb

on C

hains

Hydr

ogen

Sulf

ide (H

2S)

Ammo

nia (N

H 3 )

Nitra

te

Planetary Materials Contact Biosynthesis Intermediate Pool

Deep Biosynthesis

Direct uptake of phosphate

Oxygenic PhotosynthesisCarbon Fixation

Anoxygenic PhotosynthesisCarbon Fixation

NitrificationCarbon Fixation

Sulfur OxidationCarbon Fixation

Assimilative Nitrate ReductionAmmonia Production

Methanogenic Bacteria

Glycolysis

Denitrification(Anaerobic Respiration)

Fermentation

Sulfate-Reducing Bacteria

Aerobic Respiration

Methane

Sulfate

Energy Extraction

Nitrogen FixationAmmonia Production

Biosynthesis 99



7.6 Contact Biosynthesis directly exchangesmaterials with the planet

Contact Biosynthesis is unique when compared to theother stages of biosynthesis because it includesprocesses that directly exchange materials with theplanetary surface environment. Life makes contact withthe planet through the chemical processes of ContactBiosynthesis. It brings non-living materials into theliving world. It also converts living materials into non-living materials which are then returned to the planet.The main function of Contact Biosynthesis is to take inenergy and materials from the physical environmentand convert them into forms that can be used tosupport Deep Biosynthesis. The products of ContactBiosynthesis have two destinations. Some are releasedback to the planet, while others are fed into theIntermediate Pool.

In terms of life’s influence on the planet, ContactBiosynthesis is the most interesting to the planetarybiologist. These processes define the nature of life’splanet-changing capabilities. What follows are briefdiscussions of the most important forms of ContactBiosynthesis.

The different processes of Contact Biosynthesis fall intothree main categories: 1) Carbon fixation; 2) Energyextraction from sugar; and 3) Ammonia production.There are also other interesting processes that do notfit into these categories, such as calcium carbonateprecipitation (Panel 7.3), and dimethylsulfideproduction (Panel 7.4).

Figure 7.1 (Opposite page). Four-part modelfor studying biosynthesis from theperspective of planetary biology.

This diagram attempts to show a summaryof the major biosynthetic processesperfomed by living things on Earth. Thepurpose of the drawing is twofold: 1) todemonstrate the many ways living thingspass materials back-and-forth with theplanet; and 2) to show that the finaloutcome of this exchange process is thebiosynthesis and operation of the importantmolecules of life.

The drawing is organized around four mainconcepts: 1) Planetary Materials; 2) ContactBiosynthesis; 3) Intermediate Pool; and 4)Deep Biosynthesis. The biochemicaloperations in Contact Biosynthesis conferupon life the potential to change the planet,because of the many ways living thingsexchange of materials with the planet. Theproducts of Contact Biosynthesis are fed intoa hypothetical Intermediate Pool. This poolof resources partially feeds back to supplyseveral operations in Contact Biosynthesis.But ultimately, the Intermediate Pool feedsthe processes in Deep Biosynthesis.

Deep Biosynthesis is the “goal” of allbiosynthetic activities and includes the

assembly of such vital molecules as:proteins, nucleic acids, lipids andcarbohydrates. These molecules are whatliving things are made of. They help livingthings build, maintain, operate andreproduce themselves. But not all livingthings can perform Deep Biosynthesis fromthe materials in the Intermediate Pool. As aconsequence of their high value, livingthings vigorously pursue: 1) the means bywhich to conduct biosynthesis; or 2) the poolof Deep Biosynthetic products in other livingthings. The consequence of these pursuitssets the stage for interesting ecologicalprocesses.

7.7 Carbon Fixation attaches hydrogens to carbonto make carbon chain

Carbon fixation is the biosynthetic process thatattaches atoms of hydrogen to atoms of carbon, makingsmall carbon chains. Carbon chains are made up ofseveral carbon atoms surrounded by hydrogenattachments. Some carbon chains are later assembledinto sugar molecules. Otherwise, the carbon chains goon to make many different kinds of useful molecules.

Since living things build themselves out of carbon,hydrogen and oxygen, the process of carbon fixation isan essential first step. There are several ways to goabout fixing carbon into carbon chains. I will presentthe following ways below: 1) photosynthesis (oxygenicand anoxygenic); 2) sulfur oxidation; and 3)nitrification.

Regardless of the particular pathway toward carbonfixation, certain processes are common:1) Carbon fixation requires a source of energy and a

source of reducing power. The energy usuallycomes in the form of the energy-carrying molecule,ATP. Reducing power means the ability to attachhydrogen atoms to carbon atoms. The NADPHmolecule usually provides the reducing power forcarbon fixation.

2) Before proceeding with carbon fixation, ATP andNADPH must first be manufactured by theorganism. This is done in a variety of ways, as wewill see below.

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3) After the manufacture of ATP and NADPH, theactual process of carbon fixation follows, usuallycarried out by a recycling series of reactions knownas the Carbon Fixation Cycle (Figure 7.2 —otherwise known as the Calvin Cycle).

4) Upon completion of the Carbon Fixation Cycle,fixed chains of carbon may proceed to the finalsynthesis of sugar. But sometimes the CarbonFixation Cycle doesn’t complete itself. Instead,smaller chains of carbon may spin off in midstreamof the cycle. Those smaller chains don’t becomesugar molecules. Instead, they join theIntermediate Pool of carbon chains available forother forms of biosynthesis.

The synthesis of sugar has two important biologicalbenefits:1) The sugar molecule is a physical object of energy

storage. The chemical energy it contains can bemoved around and stored

2) Once fully formed, sugar also can serve as a sourceof carbon chains during its later disassembly in theprocesses of glycolysis, respiration, andfermentation (section 7.8). In any case, both theenergy and carbon chains that come from thesynthesis and disassembly of sugar are ultimatelyfed into Deep Biosynthesis.

7.7.1 Photosynthesis uses the sun’s energy to fixcarbon

Photosynthesis is one of the most important andpowerful processes of Contact Biosynthesis. Its sourceof energy for carbon fixation is the sun. Photosyntheticorganisms, make a large molecule that has the abilityto capture light energy. The molecule is called

chlorophyll, and it is what makes plants look green.Using chlorophyll, the process of photosynthesiscaptures light energy from the sun and uses it to makeATP and NADPH.

As we will see below (section 7.9.2), the process ofphotosynthesis also spins off the energetic molecule,NADPH, which is used by green plants to convertnitrate into the more useable ammonia (in assimilativenitrate reduction).

Photosynthesis contributes to big changes in the globalenvironment, mainly as a producer of oxygen gas.Virtually all of the oxygen gas in our atmosphere camefrom photosynthesis. Photosynthesis also has played aminor role as a remover of carbon dioxide gas from theatmosphere (calcium carbonate precipitation greatlyovershadows it).

Photosynthesis occurs in two main ways: 1) oxygenicphotosynthesis (which produces O2 gas); and 2)anoxygenic photosynthesis (which doesn’t produce O2gas).

7.7.2 Oxygenic Photosynthesis uses water as asource of hydrogens to fix carbon

Oxygenic photosynthesis is the most familiar andwidespread form of photosynthesis. On the continents,it occurs mostly in green plants (Figure 7.3). It is alsoprevalent in aquatic environments, like lakes, riversand oceans. There, oxygenic photosynthesis isperformed by algae, many protozoans, andcyanobacteria. Also, corals, lichens, giant clams and atleast one kind of tiny marine slug are photosyntheticbecause they are inhabited by symbiotic,photosynthetic microorganisms.

CarbonFixationCycle

ATPand

NADPH

Carbon dioxide

Carbon chains

Sugar

Input of:1) Energy2) Hydrogens

DeepBiosynthesis

Figure 7.2. Asimplified diagram of the process of carbon fixation.

Biosynthesis 101



Oxygenic photosynthesis is a complex process thatinvolves a cascade of biochemical reactions. In essence,however, it is fairly simple. The general reactionequation for oxygenic photosynthesis is shown below.

6CO2 + 6H2O+ Sunlight —> C6H12O6 (carbon chain)+6O2

[Carbon dioxide plus water plus sunlight react to makecarbon chains plus water plus oxygen gas.]

This reaction equation shows that the process ofphotosynthesis takes in carbon dioxide gas from theatmosphere, water from the soil (in the case of greenplants), and light energy from the sun. Photosynthesisthen uses these resources to make carbon chains. Thecarbon chains later can be used to make a variety ofmolecules including sugar. Note that water is used as asource of hydrogens. Oxygen gas is given off as a wasteproduct.

I want to draw yourattention for amoment to theissue of hydrogens.It turns out thatmuch of thediversity in ContactBiosynthesiscenters around theproblem of what todo with hydrogenatoms. In order tomake organicmolecules fromcarbon dioxide, youneed a source ofhydrogens. Andlater, in order tobreak down thosemolecules, youhave to get rid ofthose hydrogens. As we will see, the processes ofphotosynthesis, respiration and fermentation havedeveloped unique ways of dealing with hydrogens. Howthese processes manage hydrogen also has importantbiological, ecological and planetary consequences.

7.7.3 Anoxygenic Photosynthesis uses hydrogensulfide as a source of hydrogens to fixcarbon

Anoxygenic photosynthesis is probably the oldest formof photosynthesis, perhaps originating within ahundred million years or so after the appearance of life3.8 billion years ago. Its biochemistry is somewhatsimpler than oxygenic photosynthesis. Anoxygenicphotosynthesis occurs today in purple bacteria andgreen sulfur bacteria (Figure 7.4) that inhabit shallow,oxygen-free waters and muds in lakes, swamps, andoceans. Anoxygenic photosynthesis is different fromoxygenic photosynthesis in two main ways: 1) The

chemical compound, hydrogen sulfide (H2S) is usedinstead of water as a source of hydrogens; and 2)Mineral sulfur (S) is produced instead of oxygen gas.The general reaction equation for anoxygenicphotosynthesis is shown below.

6 CO2 + 12 H2S + Sunlight —> C6H12O6 (carbon chains)+ 6 H2O + 12 S

[Carbon dioxide plus hydrogen sulfide plus sunlightreact to make carbon chains plus water plus mineralsulfur.]

There are majorlimitations on thegeographicdistribution ofanoxygenicphotosynthesis. Inorder for it to occur,the environmentmust have acombination of threethings: 1) It must befree of oxygen gas;2) Hydrogen sulfidemust be available;and 3) Sunlightmust be available.An oxygen-less,hydrogen sulfide-rich environment (typical of deep lake waters or deep inmuddy environments) is difficult to find with goodexposure to sunlight.

7.7.4 Nitrification uses the chemical energy inammonia to fix carbon

Instead of light energy, the nitrifying bacteria usechemical ammonia (NH3 ) as an energy source for thesynthesis of ATP. Nitrifying bacteria are abundant insoils and shallow muds. Ammonia is present in theseenvironments due to the actions of the nitrogen-fixingbacteria (section 7.9.1). Ammonia possesses a smallamount of chemical energy which the nitrifyingbacteria can extract and use to make ATP. Once theATP is synthesized, it has two possible fates: 1) the ATPcan act as a general energy provider to the cell, helpingin biosynthesis or other operations; or 2) the ATP canbe used to synthesize NADPH.

In the case of nitrifying bacteria, much of the ATPproduced is used to energize the synthesis of NADPH.Then ATP and NADPH proceed to the Carbon FixationCycle and support the synthesis of carbon chains.

The composite reaction equation for nitrification andcarbon fixation is shown below.

6 CO2 + 6 NH3 + 6 O2 ——————> C6H12O6 + 6 HNO3

[carbon dioxide plus ammonia plus oxygen gas react tomake carbon chains plus hydrogen nitrite]

Figure 7.3. A tree as an example of agreen plant. Green plant engage inoxygenic photosynthesis.

Figure 7.4. Drawing of genericbacteria at about 5,000 times theiractual size. Bacteria are so small thatabout 1000 of them can fit on the dotof an "i".

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Nitrification is important ecologically since itreplenishes supplies of nitrate in the soil which thencan be used by the denitrifying bacteria (section 7.8.4).Nitrate also can be easily absorbed by plants which useit in their biosynthesis. However, the conversion ofammonia to nitrate by nitrifying bacteria presents aninconvenience to the process of biosynthesis. This isbecause nitrate must be reconverted back to ammoniabefore nitrogen can be used in biosynthesis. Thereconversion process is carried out by plants in aprocess called assimilation (section 7.9.2).

Globally, nitrification is another process that requiresmolecular oxygen. As a result, nitrification has thepotential to: 1) assist in the ultimate return of nitrogengas to the atmosphere (by supplying nitrate to thedenitrifying bacteria); and 2) reduce the quantity ofoxygen gas in the atmosphere.

7.7.5 Sulfur-Oxidation uses the chemical energyin hydrogen sulfide to fix carbon

Certain kinds of purple bacteria have the ability toextract the small amount of chemical energy stored insulfur minerals, including hydrogen sulfide (H2S) andmineral sulfur (S). Bacteria with these abilities arecalled the sulfur-oxidizing bacteria. Sulfur-oxidizingbacteria mainly inhabit oxygen-containing muds inaquatic environments like ponds, lakes and oceans.They sometimes live in acid pools. This is no smallwonder since one of the main products of sulfuroxidation is sulfuric acid.

They can tolerate high heat too. One species(Thermotrix) lives in sulfur hot springs at temperaturesup to 185° F (Figure7.5). Sulfur-oxidizing bacteriaform the ecologicalbase of deep seahydrothermal ventcommunities. Theseocean bottom hotsprings spew outsulfur and hydrogensulfide. Since theyoccur on oceanbottoms over 6000feet deep, there is nosunlight whatsoever.Photosynthesis isnot even remotelypossible. Instead,the sulfur-oxidizingbacteria perform thejob normally doneby photosynthesis.Overall, their energymanagementscheme is verysimilar to that of the

nitrifying bacteria just discussed. The sulfur-oxidizingbacteria use the chemical energy in sulfur minerals tomake ATP. The ATP then can either be used to supportother biosynthetic activities, or to make NADPH. Thenthe ATP and NADPH together feed the Carbon FixationCycle in which carbon dioxide is ultimately fixed tomake sugar.

The general reaction equation for sulfur-oxidation andcarbon fixation using hydrogen sulfide is shown below.

6 CO2 + 3 H2S + 6 H2O ——————> C6H12O6 + 3 H2SO4

[carbon dioxide plus hydrogen sulfide plus water reactto make carbon chains plus hydrogen sulfate,otherwise known as sulfuric acid]

NOTE: This reaction equation, like all shown in thischapter, is a summation and consolidation of a seriesof many reactions. Although not shown here, molecularoxygen (O2 ) is a necessary ingredient in the initialreactions leading to sulfur oxidation. Therefore, thisprocess does best in environments that have O2.

7.8 The energy stored in sugar is extracted in orderto make ATP

Once sugar molecules are made following carbonfixation, they have several possible fates:1) They can be fed directly into Deep Biosynthesis.

There, they can be chained together to makedurable energy storage molecules like starch orglycogen. Or they can be used to make ruggedstructural materials like cellulose

2) Sugar molecules can be utterly disassembled in theenergy-extraction processes of glycolysis,respiration, and fermentation. These processesremove the energy stored in sugar and use it tomake energy-carrying ATP molecules which areuniversally and instantly useful (Figure 7.6). ATPmolecules provide energy for the biosyntheticprocess and for the operation of the molecules thatresult from biosynthesis.

Sugar molecules also can be fed into Deep Biosynthesisby indirect means — but they are first broken apartinto carbon chains. For example, the processes ofglycolysis, respiration and fermentation spin off severaldifferent kinds of carbon chains that later are useful inthe synthesis of proteins, nucleic acids and lipids.

7.8.1 Glycolysis precedes respiration andfermentation

Glycolysis is the biochemical process that precedes thetwo main processes that will be discussed below. Theyare:1) respiration2) fermentation

Figure 7.5. Hydrogen sulfide andsteam are vented from hot sulfursprings in Yellowstone National Park.Sulfur-oxidizing bacteria use hydrogensulfide as a source of energy andhydrogens in the fixation of carbon.

Biosynthesis 103



Briefly, glycolysissplits sugarmolecules in two,making severalintermediatemolecules andending up at a finalmolecule calledpyruvate. Pyruvatecan be fed directlyinto fermentation.Or pyruvate can bechanged into acetylCoA and fed intorespiration. Some ofthe intermediate molecules generated during thecourse of glycolysis can be spun off to DeepBiosynthesis to be used in the formation of proteinsand nucleic acids.

7.8.2 Respiration is the most efficient producerof ATP

The discussion of respiration that follows is somewhatunconventional as biology books go. Typically,respiration is treated mainly, and often exclusively, asan energy management system and nothing more. Itsrole in biosynthesis frequently is overlooked. Perhapsdue to its total destruction of sugar molecules, manybiologists do not consider respiration to be amechanism of biosynthesis. However, because of itsrole in spinning off important carbon chains and insupplying ATP energy, respiration plays a vital part insupporting later biosynthesis — Deep Biosynthesis. Forthis reason, I believe it is appropriate to considerrespiration as a necessary part of the biosyntheticmachine.

Also, from a biochemical point of view, respiration isusually seen as only one part of a larger, multiple-partenergy extraction process consisting of: 1) the Krebscycle; and 2) the respiratory chain. Reasserting ourplanetary biological perspective, I think that dwellingon the intricate details of this system, as most biologybooks do, will not advance our efforts. So that we donot lose sight of the importance of respiration as itrelates to the global environment, I have chosen toignore the fascinating and abundant biochemical andthermodynamic details of the Krebs cycle andrespiratory chain. Instead, I have consolidated theminto a single process, which I will refer to simply asrespiration. Therefore, in the discussions of respirationthat follow, it is assumed that the components of theKrebs cycle, and respiratory chain are in place —although they will not be specifically referred to.

Respiration occurs in two main forms:1) Aerobic respiration (requiring O2 )

2) Anaerobic respiration (which happens in theabsence of O2 ). Anaerobic respiration is not to beconfused with fermentation, which will bediscussed later. In terms of total distribution,aerobic respiration is much more widespread thananaerobic respiration. Aerobic respiration happensin nearly every living thing you have ever seen. It isfound in many bacteria, protozoans, algae, fungi,plants and animals. On the other hand, anaerobicrespiration happens in organisms that are far lessfamiliar to you. It occurs in the methanogenicarchaeobacteria, denitrifying bacteria, sulfate-reducing bacteria, sulfur-reducing bacteria, andthe acetogenic bacteria.

Regardless of which specific type of respiration we aretalking about, all forms of respiration perform thefollowing important functions:1) Respiration totally disassembles sugar molecules

(or other small organic molecules) and releasescarbon dioxide

2) During sugar disassembly, respiration extracts theenergy from sugar and uses it to build ATPmolecules

3) In the end, respiration must somehow get rid ofwaste hydrogen atoms. Different solutions to thedilemma posed by the waste hydrogensdistinguishes aerobic respiration from anaerobicrespiration. If the hydrogens are not disposed of,then the whole process clogs up like a big trafficjam. A popular but less efficient side route aroundcongested respiration is the process offermentation, discussed later (section 7.8.5).

7.8.3 Aerobic respiration uses molecular oxygen(O2 ) to get rid of waste hydrogens

With aerobic respiration, molecular oxygen (O2 ) takesaway the waste hydrogens by reacting with them tomake water. The reaction equation for aerobicrespiration is shown below (Note: for brevity, ADP andPi are not shown):

C6H12O6 + 6 O2 —————> 6 CO2 + 6 H2O + ATP

[Sugar plus water plus molecular oxygen react to makecarbon dioxide plus water plus ATP]

In this reaction, sugar is utterly dismantled yieldingchemical energy along the way. The chemical energyliberated by respiration is captured in the form of theuniversally redeemable ATP molecule. ATP then is fedinto the Intermediate Pool.

7.8.4 Anaerobic respiration uses nitrate to get

Figure 7.6. A drawing of a molecule ofATP.

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rid of waste hydrogens (Denitrification)

Anaerobic respiration happens in oxygen-freeenvironments. When oxygen is not available, othersubstances are used to dispose of waste hydrogens.For example, denitrifying purple bacteria use thesubstance, nitrate, when molecular oxygen is notavailable. The general reaction equation for anaerobicrespiration using nitrate is shown below.

5 C6H12O6 + 24 HNO3 —> 30 CO2 + 42H2O + 12 N2 +ATP

[sugar plus hydrogen nitrate react to make carbondioxide plus water plus nitrogen gas plus ATP]

The denitrifying bacteria mostly are purple bacteria ofthe widely distributed genus Pseudomonas. Thesebacteria are interesting in that when molecular oxygenis available, they use aerobic respiration. But ifmolecular oxygen is not available, they shift over toanaerobic respiration using nitrate. They are alsointeresting to the planetary biologist since, in additionto carbon dioxide, they return nitrogen gas to theatmosphere. This may be a very important service tolife on the continents by replenishing the nitrogen gasremoved by nitrogen-fixing bacteria (section 7.9.1).

7.8.5 Fermentation is a popular but sluggishdetour when oxygen is not available

In environments where molecular oxygen is notavailable, the process of fermentation can take over.Fermentation occurs as a standby backup energyextraction process in all aerobic bacteria, protozoans,algae, fungi (including yeasts), plants, and animals.But it is the main mode of getting energy from sugar inmany anaerobic bacteria (except the methanogenicbacteria, sulfate-reducing bacteria and acetogenicbacteria — sections 7.8.6 and 7.8.7).

Basically, fermentation kicks in when there is abuildup of waste hydrogens at the end of therespiration process. Normally, molecular oxygen ornitrate are the removers of waste hydrogens. If they areabsent, such as in deep muds, soils, or stagnant water,then respiration stops because the hydrogens clog thesystem, causing a traffic jam. The carbon chainproducts of glycolysis (pyruvate) then are diverted ontoa side street called fermentation which continues theirdisassembly and ATP formation. The big difference isthat for each sugar molecule, fermentation producesabout 20 time less ATP than respiration. So,fermentation does not support vigorous activity.

For example, after you do sit-ups for awhile, you startgetting tired. That’sbecause yourmuscles aredemanding oxygenfaster than yourblood can supply it

(the oxygen youbreathe in is used tosupport respirationin your cells). Sincethey can’t supportrespiration anylonger (because oflack of oxygen), yourmuscle cells shiftover to fermentation.But since fermentation is much less efficient, yourability to continue sit-ups quickly falls off, and you arefinally too weak to continue.

Another big difference about fermentation compared torespiration is the large variety of waste productsfermentation makes. They include lactic acid, ethanol(the type of alcohol in beer and wine), and acetic acid(the acid that gives vinegar its sour “bite”).Fermentation in your tired muscles yields lactic acid.Although a buildup of lactic acid generally is not goodfor you (it can contribute to the making of soremuscles), lactic acid formation in bacteria is useful inthe making of yogurt and cheese (Figure 7.7). Ethanoland CO2 are produced by yeast and bacteria. This ishow champagne gets its sparkle, and its notoriousalcoholic ‘kick’. Bakers also benefit from thefermentation process as the production of CO2 byfermenting yeast cause the bread to rise from anotherwise solid blob of dough (Figure 7.8).

The waste products of fermentation occasionallyrepresent carbon chains which are useful in thebiosynthesis of larger molecules. More likely, however,fermentation wastes end up being released to theenvironment where they either cause a contaminationproblem (such as the death of yeast caused by theaccumulation of ethanol in a corked bottle of grapejuice/wine), or they are used by other microorganismsas a source of energy.

Some of the waste products of fermentation still containchemical energy. They are used by special groups ofbacteria including the methanogenic bacteria, and thesulfate-reducing bacteria who have no ability toperform glycolysis or fermentation themselves. Both ofthese types of bacteria live strictly in oxygen-freeenvironments. They are interesting ecologically becausethey cannot use sugar directly. Instead, methanogenicbacteria and sulfate-reducing bacteria live in closeassociation with other kinds of bacteria that producefermentation waste products.

7.8.6 Sulfate-reducing bacteria extract energy

Figure 7.7. Fermentation of milk,produces cheese.

Figure 7.8. Yeast, fermenting in breaddough, create tiny bubbles of carbondioxide, causing the dough to rise.

Biosynthesis 105



from fermentation waste products

Most sulfur in the Earth’s crust is found in the form ofsulfate minerals, mainly gypsum (Calcium sulfate) andsulfide minerals, like iron pyrite (FeS2 ). In the oceans,sulfur exists mainly in the form of dissolved sulfate.Certain bacteria, called sulfate-reducing bacteria, usesulfate to dispose of waste hydrogens.

The sulfate-reducing bacteria live only in environmentsthat have no molecular oxygen. They are widelydistributed in oxygen-free environments. For example,if you have ever dug up the black mud from a pond orstanding pool of water (Figure 7.9), you probablyremember smelling something like rotten eggs. Thatwas the hydrogen sulfide produced by the sulfate-reducing bacteria living in the mud. Sulfate-reducingbacteria use sulfate to get rid of waste hydrogens. Thegeneral reaction equation for anaerobic respirationusing sulfate is given below.

C2H4O2 + H2SO4 —————> 2 CO2 + 2 H2O + H2S + ATP

[acetic acid plus hydrogen sulfate react to make carbondioxide plus water plus hydrogen sulfide plus ATP]

Note that in this reaction equation I have shown aceticacid as the energy-carrying molecule. Acetic acid is oneof many different kinds of waste materials generatedfrom the process of fermentation.

Hydrogen sulfide can go straight into DeepBiosynthesis for the formation of amino acids andproteins. Sulfate-reducing bacteria are importantecologically because they return hydrogen sulfide to theenvironment, making it available again for anoxygenicphotosynthetic bacteria and sulfur-oxidizing bacteria.Regarding the global environment, sulfate-reducingbacteria are important because they return CO2 to theatmosphere.

7.8.7 Methanogenic bacteria extract energy fromfermentation waste products

Methanogenic bacteria live deep underground and inmuds along with sulfate-reducing bacteria. Theyflourish in the growing accumulations of municipalgarbage dumped in landfills. But they also areabundant in the guts of animals like cows, termites(Figure 7.10) and humans. These environments arethriving communities of different kinds of bacteria.Methanogenic bacteria take in waste hydrogens, wastecarbon dioxide, or waste acetic acid that are producedby fermentative bacteria. The methanogenic bacteriause these wastes as a source of energy, then produce anew waste of their own — methane gas. The generalreaction equation for methanogenesis is shown below.

C2H4O2 ——————> CH4 + CO2 + ATP

[acetic acid reacts to make methane plus carbondioxide plus ATP]

Another reaction equation for methanogenesis is givenbelow.

4H2 + CO2 ——————> CH4 + 2 H2O + ATP

[hydrogen gas plus carbon dioxide react to makemethane plus water plus ATP]

Methanogenic bacteria live in the rumen (sort of amultiple stomach) of cows and other grazing animals,like deer and Wildebeest. These animals burp out hugeamounts of methane produced by the methanogenic

Figure 7.9. A family of ducks swims along the banks of a marsh.The mud on the marsh bottom is black with stinky hydrogensulfide -- produced by sulfate-reducing bacteria.

Figure 7.10. A termite. Cellulolytic bacteria in the termite's gutbreaks down cellulose into simple sugar molecules. Some of thesugars are absorbed by the termite for its own use. Other sugarmolecules are fermented to acetic acid by anaerobic bacteria inthe termite's gut. Then methanogenic bacteria, also living in thetermite's gut, extract energy from acetic acid and release wastehydrogens as mehtane gas.

Termites may produce as much as half of the methane that getsinto the atmosphere.

106 Chapter 7



bacteria living inside. Termites harbor methanogenicbacteria in their intestines and are one of the largestsingle sources of methane emissions on the planet.Humans also serve as host to methanogenic bacteriawhich live in our intestines. Their busy work inside ofus is manifested occasionally in the most embarrassingway, as we release methane from the end of ourdigestive tract.

In terms of the global environment methane productionis very important since methane is a powerfulgreenhouse gas. Emissions of methane have been onthe rise because of increases in cattle populationsworldwide, and the increased cultivation of rice whoseflooded fields support mud-dwelling methanogenicbacteria.

7.8.8 In summation, energy extraction processesprovide energy and supplies to DeepBiosynthesis

This concludes the section on energy extraction fromsugar. Altogether, the biological aim of these processesis the production of the Intermediate Pool substance,ATP. ATP then is available as an energy source for DeepBiosynthesis. In the process of disassembling sugarmolecules, living things employ several interestingsolutions to deal with the problem of disposing of wastehydrogens. Aerobic respiration uses molecular oxygen.Anaerobic respiration uses nitrate. Fermentationreleases whole carbon chains with the hydrogens stillstuck to them. Sulfur-reducing bacteria intercept thefermentation wastes, then use sulfate to dispose ofwaste hydrogens. Methanogenic bacteria also consumefermentation wastes and dispose of waste hydrogens bymaking methane. Also, while sugar is beingdisassembled in this energy extraction process, some ofthe carbon chains spin off to become useful carbonchains.

In terms of the global environment, the energyextraction process in all forms represents one of life’smost diversified and vigorous planet-changing engines.It involves the mass movements of nitrogen gas, oxygengas, carbon dioxide gas, water, and sulfate.

7.9 Ammonia production makes nitrogen accessibleto Deep Biosynthesis

Nitrogen is a very important element that is used tomake proteins, nucleic acids, membranes and otheruseful molecules like ATP. On Earth, the greatest poolof nitrogen is in the atmosphere in the form of nitrogengas (N2 ). But just plain nitrogen gas cannot be used byliving things. Instead, it first must be converted toammonia (NH3 ). This is where the problem starts.

Unlike carbon, getting nitrogen into the living world isnot so easy. Nitrogen gas tends to be a very stablesubstance that rarely combines with other kinds ofatoms. So, breaking it up and attaching hydrogens to it

(making ammonia) is a difficult task that only certainkinds of bacteria are capable of. The process of makingammonia from nitrogen gas is called nitrogen fixation.Nitrogen is much more reactive while part of theammonia molecule. So, once the ammonia is produced,the nitrogen it carries can be easily incorporated intolarge molecules in Deep Biosynthesis. The mostaggressive ammonia consumers are the nitrifyingbacteria (section 7.7.4). They use ammonia as a sourceof hydrogens in the fixation of carbon. The nitrifyingbacteria produce nitrate as a waste product. Thatdoesn’t do other living things much good since thenitrate must again be changed to ammonia. Theprocess of changing nitrate to ammonia is calledassimilative nitrate reduction, and it is performed bygreen plants. Let’s discuss nitrogen fixation first.

7.9.1 Nitrogen fixation pulls nitrogen out of theair to make ammonia

Nitrogen fixation is an extremely important biologicalprocess. In this process, several different kinds ofbacteria remove nitrogen gas (N2 ) from the atmosphereand convert it to ammonia (NH3 ). Only certain kinds ofbacteria can perform nitrogen fixation, including somecyanobacteria, purple bacteria, the symbioticbacterium, Rhizobium, and the gram positivebacterium, Clostridium. Nitrogen is necessary in thebiosynthesis of ATP, NADPH, proteins, cell membranes(a type of lipid), nucleic acids and many other kinds ofmolecules. But biosynthesis cannot use nitrogen gasdirectly. So nitrogen fixation is important because itconverts nitrogen gas into a form that can be used bybiosynthesis — ammonia. The general reactionequation for nitrogen fixation is shown below:

C6H12O6 + 6 H2O + 4N2 ——————> 6 CO2 + 8 NH3

[sugar plus water plus nitrogen gas react to makecarbon dioxide plus ammonia]

Note that sugar is the ultimate source of hydrogens inthis reaction. And, this reaction actually consumesmore energy than it puts out.

In the sea, the mainnitrogen fixers arethe cyanobacteria.On land, nitrogen isfixed by bacteria inthe soil or mud. Thebacterium,Rhizobium, lives inspecial root nodulesof legume plants(like peas, beans,clover, alfalfa, andsoybeans). Insidethese nodules,Rhizobium fixesnitrogen toammonia which is

Figure 7.11. Living cells in tree leavesand other green parts of plants containchloroplasts. Photosynthesis happensinside the green chloroplasts. Oneproduct of photosynthesis is NADPH.Some of the NADPH is used to convertnitrate to ammonia.

Biosynthesis 107



absorbed directly by the plant roots. In addition to thesymbiotic Rhizobium, there are many free-livingbacteria that fix nitrogen gas. However, the ammoniaproduced by free-living soil bacteria is quicklyconsumed by another band of bacteria, the nitrifyingbacteria (section 7.7.4, above).

7.9.2 Assimilative nitrate reduction convertsnitrate to ammonia

The consumption of ammonia by nitrifying bacteriareduces the amount of ammonia in the soil. After usingammonia, the nitrifying bacteria release nitrate as awaste. As a result of this conversion process, theprimary source of nitrogen to most plants is nitrate.Nitrate is a kind of salt that can dissolve in water andbe taken in by the roots of plants. But once inside, thenitrate must be converted back to ammonia for use inbiosynthesis. The process that converts nitrate back toammonia for this purpose is called assimilative nitratereduction. This is an energy-consuming reaction.

Assimilative nitrate reduction happens inside thechloroplasts (tiny green objects inside leaf cells -Figure7.11) of green plants and uses light as its source ofenergy. It is a sort of side reaction that happensalongside photosynthesis. Remember that inphotosynthesis, NADPH is made with the help of lightenergy. The main function of NADPH is to transferhydrogen atoms to carbon atoms in the CarbonFixation Cycle. Assimilative nitrate reduction adds adifferent twist to this process. In assimilative nitratereduction, several NADPH molecules are diverted awayfrom the Carbon Fixation Cycle and their hydrogensare transferred to nitrogen instead of carbon. Theresult is the production of ammonia which then can beused in Deep Biosynthesis. The general reactionequation for assimilative nitrate reduction is shownbelow.

2 HNO3 + 2 H2O + Sunlight ——————> 2 NH3 + 4 O2

[Hydrogen nitrate plus water plus sunlight react tomake ammonia plus oxygen gas.]

This reaction equation should look very similar to thatof oxygenic photosynthesis. Water is consumed andused as a source of hydrogens and sunlight providesthe energy. Notice too that molecular oxygen isproduced. However, this does not really represent a netincrease in oxygen production. Remember that tworelated processes, nitrification/carbon fixation andaerobic respiration both consume molecular oxygen.So, if there is perfect coupling between these threereactions, all materials are completely recycled.

7.10 The reactions ofContactBiosynthesis arecoupled such thatthey recycle allmaterials

Looking at the manydifferent kinds ofprocesses in ContactBiosynthesis you shouldbegin to sense that,collectively, living thingsmake elegant use ofplanetary materials. As complicated as a single livingthings is, there are really only a few kinds of materialsthat it needs. And these same kinds of materials areused in very similar ways by all living things. Forexample, on Earth, carbon dioxide is the ultimatesource of carbon for the construction of biologicalmolecules. It is also the main carbon waste productfrom the dismantling of biological molecules duringenergy extraction. By the same token, water is theoverwhelming favorite source of hydrogens whenbuilding sugar, and it is returned to the physical worldwhen disassembling sugar for energy. So, carbondioxide and water are recycled by biological processes.

If we look at other processes, a very interesting patternbegins to emerge. We start to see opportunities forrecycling amongst all of the diverse biochemicaloperations we have dealt with so far. Table 7.2 (nextpage) organizes the various reaction equations into setsof coupled reactions in which all of the reactants andproducts are completely recycled. Notice that in eachset of coupled reactions is a source of energy, almostalways sunlight.

So, driven by the sun’s energy, the biochemicalprocesses of Contact Biosynthesis have the potential tochurn the planet. Left to their own devices, it seemsthat biosynthetic processes will continuously recycleplanetary materials as long as three conditions for idealrecycling (Figure 7.12) are met:

1) Reaction sets are perfectly coupled2) Coupled reactions are not somehow uncoupled or

otherwise interfered with3) There is a steady input of sunlight energy.

If all three conditions are satisfied, then life shouldhave little or no recognizable chemical impact on aplanet. It would just turn things round and round andthere would be no large net movement of materialsbetween the air, the water or the soil. But this is notwhat we see in the history of Earth.

Ideal Recycling inCoupled reactions

C6H12O6 CO2 H2O O2

CarbonFixation

Respiration

Figure 7.12. Ideal recycling incoupled reactions.

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Table 7.2Examples of Coupled Contact Biosynthetic Reactions

Carbon Fixation by Oxygenic Photosynthesis ................................................... 6 CO2 + 6 H2O + Sunlight è C6H12O6 + 6 O2

Aerobic Respiration ............................................................................................... C6H12O6 + 6 O2 è 6 CO2 + 6 H2O

Carbon Fixation by Nitrification ............................................................................ 6 CO2 + 6 NH3 + 6 O2 è C6H12O6 + 6 HNO3

Assimilative Nitrate Reduction ............................................................................. 2 HNO3 + 2 H2O + Sunlight è 2 NH3 + 4 O2

Aerobic Respiration ............................................................................................... C6H12O6 + 6 O2 è 6 CO2 + 6 H2O

Carbon Fixation by Oxygenic Photosynthesis ................................................... 6 CO2 + 6 H2O + Sunlight è C6H12O6 + 6 O2

Fermentation & Methane Production ................................................................... C6H12O6 è 3 CH4 + 3 CO2

Spontaneous Chemical Breakdown .................................................................... 3 CH4 + 6 O2 è 3 CO2 + 6 H2O

of Methane in Environment

Carbon Fixation by Anoxygenic Photosynthesis ................................................ 6 CO2 + 12 H2S + Sunlight è C6H12O6 + 12 S + 6 H2O

Fermentation and Mineral Sulfur Reduction ....................................................... C6H12O6 + 12 S + 6 H2O è 6 CO2 + 12 H2S

Carbon Fixation by Sulfur Oxidation .................................................................... 6 CO2 + 3 H2S + 6 H2O è C6H12O6 + 3 H2SO4

Fermentation and Sulfate Reduction ................................................................... C6H12O6 + 3 H2SO4 è 6 CO2 +3 H2S + 6 H2O

Carbon Fixation by Oxygenic Photosynthesis ................................................... 24 CO2 + 24 H2O + Sunlight è 4 C6H12O6 + 24 O2

Nitrogen Fixation .................................................................................................... 3 C6H12O6 + 18 H2O + 12 N2 è 18 CO2 + 24 NH3

Carbon Fixation by Nitrification ............................................................................ 24 CO2 + 24 NH3 + 24 O2 è 4 C6H12O6 + 24 HNO3

Denitrification (Nitrate Respiration) ...................................................................... 5 C6H12O6 + 24 HNO3 è 30 CO2 + 42 H2O + 12 N2

Biosynthesis 109



7.11 Geological burial of biosynthetic productsuncouples reaction sets

Instead of anunchanging planet,Earth’s chemicalenvironment hasevolved in manyways. For instance,the atmosphere hasexperienced bigincreases in oxygengas and bigdecreases in carbondioxide, and life hasbeen largelyresponsible. Buthow could this be ifthe coupledreactions soperfectly recyclematerials? In orderfor life to causesuch big changes,the ideal recyclingprocess must beinterrupted, thecoupled reactionsuncoupled. Suchdisruptions causenet movements ofmaterials out of onerealm and intoanother. The perfect circle is sometimes broken.

7.12 Oxygen builds up in the atmosphere because ofthe burial of fixed carbon

For example, in order for oxygen gas to build up in theatmosphere, there has to be less fixed carbon for it toreact with in the oceans and on the continents. This isaccomplished by geologic processes that bury theremains of living things (Figure 7.13). The burialprocess results in a one-way movement of carbondioxide and water into the Earth’s crust (in the form offixed carbon), and a one-way movement of oxygen gasinto the atmosphere. As a result, fixed carbonaccumulates deep in the Earth’s crust, and oxygen gasaccumulates in the atmosphere. It turns out that forthe processes we have discussed so far, the potentialfor life to chemically influence the planet ironically isdependent upon the planet interfering with thechemical cycles of life. It does this by disrupting theconnections between coupled reactions. But there areother forms of biosynthesis which exert their influencein slightly different ways — namely, the precipitation ofcalcium carbonate, and the production ofdimethylsulfide .

7.13 Calcium carbonate precipitation is a non-coupled biosynthetic process

The precipitation (solidification) of calcium carbonate isa form of non-coupled biosynthetic process. There isvirtually no recycling of solid calcium carbonate backto calcium and carbon dioxide. Therefore, the biologicalprecipitation of calcium carbonate is by far the greatestpermanent remover of atmospheric carbon dioxide ofall planetary processes. Please read about it in Panel7.3 (next page).

Geologic BurialUncouples Reactions

CarbonFixation

Burial of Fixed Carbon Molecules

Respiration

CO2 H2O O2

Figure 7.13. An example of howgeologic burial of fixed carbon canresult in net movements of materialsfrom one realm to another. In thiscase, fixed carbon accumulates in thethe Earth's crust (lithosphere), andoxygen gas accumulates in theatmosphere.

There has been recent interest in the biological productionof a substance called dimethylsulf ide (DMS). DMS is emit tedin large quantities over the oceans. Once in the atmosphere,DMS undergoes a series of reactions that convert it toairborne sulfate. The sulfate particles in the air then act asnuclei for the condensation of the tiny water droplets thatmake up clouds. So, the more DMS emit ted, the moreclouds. And clouds have the potential to warm the planet orcool it, depending upon how they form.

So, what is the biological reason for DMS production? Itturns out that DMS is made following the degradation ofdimethylsulfonium proprianate (DMSP). DMSP is made fromthe sulfur-containing amino acid methionine and it helpsmicroscopic marine algae regulate their internal waterbalance. When individual algae are consumed by marinebacteria (for example, after they die), the bacteria can useDMSP as an energy source. In this way, DMSP is degraded toDMS and released to the atmosphere. The general f low forthis process is shown below.

Methionine ——————> DMSP ———————> DMS

[Amino acid] [Helps in salt/water balance] [waste from DMSP breakdown]

Panel 7.4. Potential environmental consequences of DMSproduction

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CO2

The biosynthetic precipitation of calciumcarbonate is different from the processeswe have looked at so far because it isalmost entirely a non-coupled process.Calcium carbonate is a very hardsubstance. The sea shells you pick up atthe sea shore are constructed out of it.Calcium carbonate makes up coral reefsand the shells of hundreds of differentkinds of aquatic organisms, big and small.

In order for calcium carbonate to beused as a solid, it f irst must beprecipitated from its dissolved form.Chemical precipitation is a process thatmakes a solid out of a substance that isotherwise dissolved in water. Forexample, the soap scum that accumulateson the sides of your bathtub is a result ofthe precipitation process. Soap that isusually dissolved in water sticks to thebathtub walls as a solid.

In the waters of the oceans, lakes andrivers, calcium carbonate is dissolved.Calcium carbonate almost neverprecipitates on its own (except for thewhitings of the Bahamas). In nearly allcircumstances, living things areresponsible for the precipitation ofcalcium carbonate according to thefollowing process.

CaCO3 (Dissolved) ——> CaCO

3 (Solid)

[Dissolved calcium carbonate isprecipitated to solid calcium carbonate.]

Panel 7.3 Calcium carbonate precipitation is an example of a non-coupled biosynthetic process

The carbonate (CO3- - ) is formed

beforehand from carbon dioxide gas inthe atmosphere.

In terms of planetary biology, thesignif icance of the biosyntheticprecipitation of calcium carbonate is thatit is a non-coupled consumer ofatmospheric carbon dioxide. That meansit has great power to remove carbondioxide from the atmosphere and neverrecycle it. This is what has happened onEarth in great measure, starting about2.5 billion years ago. Solid calciumcarbonate has been very useful to livingthings because of its high strength anddurability. And because of its toughness,calcium carbonate tends to last a long,long time. In fact, calcium carbonateprecipitated by living things lastshundreds of millions of years. So, oncesolidif ied, calcium carbonate tends toaccumulate in the environment, settlingon ocean bottoms. Today, it forms thehuge volume of limestone deposits in theEarth’s crust. It is estimated that thereare about 4.4 x 1019 pounds of calciumcarbonate deposits in the crust (Holmanin Butcher et al.). That is 44 billion billionpounds, an amount equivalent to theentire surface of the Earth covered inCadillac cars 320 deep.

Since carbon dioxide is a greenhouse gas,its removal in such large amounts bycalcium carbonate precipitation probablyhad profound effects on the Earth’sglobal climate.

Unlike sugar, solid calcium carbonate isnot a consumable substance that can beused by Deep Biosynthesis or any otherbiochemical process. In other words,once calcium carbonate is formed, itstays calcium carbonate and is notbiologically recycled back into freecalcium and carbon dioxide. Thus is thenature and power of non-coupledbiosynthetic reactions to cause the one-way, net movement of materials fromone realm to another. In the case ofcalcium carbonate precipitation, carbondioxide leaves the realm of theatmosphere and is permanently stored inthe realm of the lithosphere (the Earth’scrust). (NOTE: After hundreds ofmillions of years, the carbon stored inlimestone can be slowly recycled backinto the atmosphere from volcanoesfollowing the tectonic processes ofsubduction.

Biosynthesis 111



7.14 The potential influence of dimethylsulfidedepends on sulfur cycling

The influence of dimethylsulfide (DMS) is greatest whilethe coupled reactions of the sulfur cycle remain intact.DMS is released as a waste product from themetabolism of sulfur compounds. Once in theatmosphere, DMS undergoes additional reactions thatmay increase the production of clouds over the openocean. Read about it in Panel 7.4.

7.15 In summary, uncoupled or non-coupled contactbiosynthetic processes have the greatestpotential to change the planet

Let us review for a moment here. We have seen that theprocesses of Contact Biosynthesis establish theirplanet-changing potential mostly when they areoccasionally uncoupled (as in burying fixed carbon) orwhen they occur in non-coupled form (as in theprecipitation of calcium carbonate). As a result, theseuncoupled or non-coupled biosynthetic reactions do

not recycle materials. Instead, they cause a one-waymovement of materials from one realm to another. As aconsequence, uncoupled or non-coupled biosyntheticreactions have the greatest potential to change thechemical environment of the planet by eventuallycausing gross re-distributions of planetary materials.We will see in chapter 15 that certain changes to thechemical environment are among the most importantways that life influences the planet.

Table 7.3 (next page) summarizes all of the reactionsdiscussed so far.

Keep in mind, living things do not engage in ContactBiosynthesis with the goal of changing the planet.Instead, Contact Biosynthesis is the first step thatsupports many further kinds of Deep Biosynthesis.Deep Biosynthesis, and not the planet, is the pointbehind Contact Biosynthesis.

7.16 The Intermediate Pool feeds Deep Biosynthesiswith energy and supplies

The Intermediate Pool is a theoretical holding area forthe products of Contact Biosynthesis. As we havealready seen, some of the Intermediate Pool materials(like sugar) feed back to support different ContactBiosynthetic processes. But ultimately, the materials ofthe Intermediate Pool are drawn upon by the needs ofDeep Biosynthesis.

Intermediate Pool

Deep Biosynthesis

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Sugar

Figure 7.14. Stages of Deep Biosynthesis.

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f auto

troph

icba

cteia

(Nitro

somo

nas) .

Ex

tracti

ng E

nerg

y fro

m Su

gar

Aero

bic R

espir

ation

C 6H 1

2O6 +

6 O 2

6

CO 2

+ 6

H 2O

Extra

ction

and u

se of

ener

gy st

ored

insu

gars,

star

ches

, fats.

O2 c

arrie

s off

waste

hydr

ogen

s as H

2O.

Aero

bic ba

cteria

; Mito

chon

dria

in alg

ae, fu

ngi, p

rotoz

oans

,pla

nts, a

nimals

Denit

rifica

tion (

Ana

erob

ic, N

itrate

Resp

iratio

n)5 C

6H12

O 6 +

24 H

NO3

30 C

O 2 +

42 H

2O +

12 N

2

Extra

ction

and u

se of

ener

gy st

ored

insu

gars,

star

ches

, fats.

Anae

robic

, den

itrifyi

ng ba

cteria

(Pse

udom

onas

)

Ferm

entat

ion &

Meth

ane P

rodu

ction

(Com

posit

e)C 6

H 12O

6

3 C

H 4 +

3 CO

2

Extra

ction

of en

ergy

stor

ed in

suga

rs,pr

oteins

, fatty

acids

in th

e abs

ence

ofO 2

.

Anae

robic

free

-living

bacte

ria;

yeas

ts; F

ungi;

symb

iotic

bacte

ria in

anim

al gu

ts

Ferm

entat

ion an

d Sulf

ate R

educ

tion (

Comp

osite

)C 6

H 12O

6 + 3

H 2SO

4

6 C

O 2 +

3 H2S

+ 6 H

2OEx

tracti

on of

ener

gy st

ored

in or

ganic

comp

ound

s rele

ased

by fe

rmen

ters.

Anae

robic

, pur

ple ba

cteria

and

arch

aeob

acter

ia.

Ferm

entat

ion an

d Mine

ral S

ulfur

Red

uctio

nC 6

H 12O

6 + 12

S +

6 H 2

O

6 C

O 2 +

12 H

2SEx

tracti

on of

ener

gy st

ored

in or

ganic

comp

ound

s rele

ased

by fe

rmen

ters.

Anae

robic

, pur

ple ba

cteria

and

arch

aeob

acter

ia.

Ammo

nia P

rodu

ction

Nitro

gen F

ixatio

nC 6

H 12O

6 + 6

H 2O

+ 4 N

2

6 C

O 2 +

8 NH

3

Prep

ares

nitro

gen f

or th

e mak

ing of

prote

ins, D

NA, c

ell m

embr

anes

. N2

carri

es of

f was

te H

as N

H 3.

Cyan

obac

teria,

and s

oilba

cteria

(Rhiz

obium

).

Assim

ilativ

e Nitra

te Re

ducti

on2 H

NO3 +

2 H 2

O +

Sunli

ght

2 N

H 3 +

4 O 2

Conv

erts

nitra

te to

ammo

nia fo

rma

king p

rotei

ns, D

NA, a

nd lip

idsOc

curs

in the

chlor

oplas

ts of

gree

n plan

ts.

Ca

lcium

Car

bona

te Pr

ecipi

tation

Biolo

gicall

y Enh

ance

d Roc

k Wea

therin

gCa

SiO 3

+ C

O 2

CaC

O 3 (d

issolv

ed in

wate

r)+ S

iO2

Spee

ded u

p bec

ause

land

plan

tsinc

reas

e amo

unt o

f CO 2

in th

e soil

.Re

spira

tion b

y roo

ts. D

ecay

ofpla

nt ma

terial

by so

il bac

teria.

Bi

ologic

al Pr

ecipi

tation

of C

alcium

Car

bona

teCa

CO3 (

disso

lved i

n wate

r)

CaC

O 3 (s

olid)

Calci

um ca

rbon

ate is

used

for s

hells

and o

ther s

tructu

ral s

uppo

rt.Aq

uatic

inve

rtebr

ates (

like

cora

ls an

d clam

s); al

gae

Dime

thyl

Sulfi

de P

rodu

ction

Synth

esis

of Me

thion

ine (a

sulfu

r-con

tainin

g ami

no ac

id)H 2

S +

Carb

on S

kelet

ons

Meth

ionine

Synth

esis

of im

porta

nt am

ino ac

idus

ed in

mak

ing pr

oteins

.Ba

cteria

and s

ome h

igher

plants

.

Deco

mpos

ition o

f Meth

ionine

to D

imeth

yl Su

lfide (

DMS)

Methi

onine

D

MSP

D

MSDM

SP fo

r salt

/wate

r bala

nce.

Used

byba

cteria

for e

nerg

y, wh

o rele

ase D

MS.

Plan

ts, M

arine

alga

e (co

cco-

lithop

hore

s, din

oflag

ellate

s)

Cons

eque

nces

to th

e Glob

al En

viron

ment

Redu

ces t

he gr

eenh

ouse

effec

t. The

buria

l of d

ead o

rgan

isms d

enies

O2 r

eacti

on op

portu

nities

, cre

ating

an O

2 sur

plus.

If not

replen

ished

, cou

ld re

sult i

n les

s atm

osph

eric O

2 , st

ress

ing lif

e dep

ende

nt up

on O

2-bas

ed bi

oche

mistr

y. Als

o, les

s O2,

less s

tratos

pheri

c ozo

ne.

Helps

tie up

hydro

gen a

toms i

n the

bodie

s of li

ving t

hings

. The

buria

l of d

ead o

rganis

ms al

so ca

n rem

ove h

ydro

gen f

rom at

mosp

heric

circu

lation

. May

help

plane

t con

serve

wate

r.Inc

rease

s the

gree

nhou

se ef

fect. T

he m

ore C

O2,

the w

armer

the p

lanet.

Biol

ogica

l pro

cess

es th

at cy

cle C

O2 in

& ou

t of th

e atm

osph

ere ha

ve th

e pote

ntial

to inf

luenc

e the

glob

al tem

perat

ure.

Increa

ses p

roduc

tion o

f stra

tosph

eric

ozon

e. Su

ppor

ts bio

logica

l proc

esse

s and

life f

orms

that

are d

epen

dent

upon

O2-b

ased

bioc

hemi

stry,

such

as m

any b

acter

ia, pr

otists

, fung

i, plan

ts an

d anim

als.

Relea

sing N

2 bac

k into

the a

tmos

pher

e allo

ws ni

troge

n to r

ecirc

ulate

over

the c

ontin

ents,

mak

ing la

rge, c

ontin

ental

ecos

ystem

s pos

sible.

Othe

rwise

, the p

lanet’

s nitro

gen w

ould

even

tually

all e

nd up

in th

e oce

ans.

Once

relea

sed i

nto th

e atm

osph

ere,

DMS

unde

rgoes

addit

ional

reac

tions

to m

ake a

sulfa

te pa

rticle.

Tiny

partic

les en

coura

ge cl

oud f

ormati

on. C

louds

(esp

. low

cloud

s) ca

n hav

e a co

oling

effec

t on t

he pl

anet.

Table

7.3.

Poten

tial E

nviro

nmen

tal C

onse

quen

ces o

f Con

tact B

iosyn

thesis

Biosynthesis 113



Deep Biosynthesis uses materials almost exclusivelyfrom the Intermediate Pool to assemble very largemolecules. The processes of Deep Biosynthesis are allbut entirely dependent upon the products of ContactBiosynthesis as a source of supplies and energy.

Deep Biosynthesis typically happens in two mainstages (Figure 7.14). Stage one uses Intermediate Poolenergy and supplies to make an assortment of buildingblock molecules. During stage two, these building blockmolecules are assembled into very big molecules,including proteins, nucleic acids, lipids, andpolysaccharides (chained carbohydrates). These bigmolecules then are capable of performing the importantbiological functions that help organisms complete theirlife cycles. Stage two represents the final assemblyprocess.

7.17 The products of biosynthesis are biologicallyuseful in a variety of ways

We have spent so much time on the processes ofbiosynthesis. Let’s now think about the products ofbiosynthesis. After all, what is the point? The endresult of the biosynthetic process is the production ofmolecules that are biologically useful. As I havementioned before, they help living things grow, operate,maintain and reproduce themselves. The molecularproducts of biosynthesis can be assembled ininteresting ways to make organs (such as a root systemor an eye), make useful structures (such as hardshells, or a seed casing), or provide useful services(such as storing energy, expediting chemical reactions,or fighting off infections). Some of these constructionsenable organisms to survive in harsh environments.For example, hot spring bacteria possess heat-tolerantenzymes, creosote bushes tolerate hot and dryconditions, and emperor penguins tolerate the extremecold of Antarctic winters.

These useful molecules are the products of evolution bynatural selection. We will consider them as molecularadaptations in chapter 13.

7.18 Biosynthesis has profound ecologicalconsequences

Let us review our interest in biosynthesis.Biosynthesis, in conjunction with geologic processes,establishes life’s potential to alter the planet’s chemicalenvironment. But the expression of this planet-alteringpotential will remain small if living things are confinedto only a few small geographic areas. Nonetheless, weknow that life has dispersed to essentially cover thesurface of the Earth, despite its extremely diverseenvironments. The process of evolution has spun newadaptive molecules and shaped them into new featuresthat have helped things live even in the harshest of

physical environments. The “wheel” of evolution isfanned by environmental stresses such as competition,predation, parasitism, and tolerance to the physicalenvironment.

Many environmental stresses are simply manifestationsof whole organisms seeking the means by which tosatisfy their own biosynthetic needs. In other words,biosynthesis is the reason for the pursuit of resources,and the pursuit of resources is the basis of manyenvironmental stresses.

Different kinds of organisms have different kinds ofbiosynthetic capabilities, so their resource needs aredifferent too. For example, carbon fixation can beperformed by green plants, cyanobacteria, and algae.But animals, fungi and many kinds of bacteria cannotfix carbon. Instead, they consume the bodies, wastes orremains of other organisms whose molecules arescavenged and incorporated into their own biosyntheticprocesses. Thus, living things compensate for their ownbiosynthetic shortcomings by exploiting thebiosynthetic capabilities of other organisms. In thisway, living things organize themselves into an ad hoceconomy of ecological processes — and the economy oflife can be stressful indeed. We will consider the natureof environmental stress in the next chapter.

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Chapter 7 Biosynthesis - PlanetaryBiology.com · The overall biosynthesis process has two main consequences that can lead life toward planet-changing stature: 1) By exchanging materials