Science Matters (30 page)

For much of the last two centuries, scientists studied planet Earth by looking at each of the great cycles—rocks, atmosphere, and oceans—in isolation. Today the focus is changing, and researchers are becoming more and more interested in seeing Earth as a single integrated system, with each cycle affecting and being affected by the others.

One of the most fascinating and critical global cycles involves the element carbon, the key element in all living things (see Chapter 15). Carbon plays important roles in all three of the great Earth cycles. It is an essential element of the rock cycle in sedimentary limestone, metamorphic marble, and a variety of igneous rocks. Carbon represents a significant component of the atmospheric cycle as the greenhouse gas carbon dioxide, which
has been implicated in global climate change (see Chapter 19). And the oceans are now recognized as a vital (though still not well understood) reservoir for carbon dioxide as well.

Given the importance of carbon to Earth’s climate and life, a major effort is under way to study the complex interchanges of carbon among rocks, atmosphere, and oceans. One key input is human activity: Burning fossil fuels such as coal and gasoline produces atmospheric carbon dioxide. How much carbon dioxide is being generated in this way, and can we find ways to reduce the amount? How rapidly do the oceans soak up carbon dioxide from the atmosphere, and is there a limit to how much carbon the oceans can hold? How do plants, which remove carbon dioxide from the atmosphere, affect the global balance?

Until recently scientists have focused almost exclusively on Earth’s surface in analyzing the global carbon cycle, but we now recognize possible links to the deep subsurface as well. Coal, oil, and other deep sources of fossil fuels have been known for thousands of years, and the assumption has been that these resources originated as plant material at Earth’s surface. New evidence suggests that at least some of this buried carbon originates from deep mantle sources and rises up along fracture zones. At the same time, carbon-rich rocks are taken from the surface down into the mantle in subduction zones. The picture is further complicated by discoveries of remarkable microbial life that ekes out a living in solid rock and processes carbon miles beneath Earth’s surface. Carbon cycle research will thus challenge chemists, biologists, and earth scientists for many decades to come.

I
MAGINE LYING OUT ON
a hill on a warm summer afternoon. All around you is physical evidence of planet Earth—rocks, clouds in the sky, perhaps a distant river or lake. But you are also surrounded by evidence of a different living Earth. The grass under your back, the insects you hear buzzing, the birds wheeling in the sky, and you yourself are all parts of a great web of living things that surround our planet. The web extends underneath the soil, to the depths of the ocean, to deserts and forests. It feeds you, supplies the air you breathe, and makes your life possible. And despite its diversity—despite the difference between a blade of grass and a giraffe—everything in this great web is related to everything else.

The most striking verification of this relationship is in your chemistry. Your body contains the same chemical compounds, derives its energy from the same chemical reactions, and utilizes the same chemical mechanisms as every other life-form. At the very core of your being, you are part of the living Earth.

You can think of life as arranged in a great ladder, starting
with the basic chemical compounds that make up living things, progressing upward to microscopic cells, then to collections of cells that make up organs, organ systems, and finally organisms themselves. The cells, midway up this ladder, are the nexus of life, a fact that can be summarized as:

Cells act as chemical factories, taking in materials from the environment, processing them, and producing “finished goods” to be used for the cell’s own maintenance and for that of the larger organism of which they may be part. In a complex cell, materials are taken in through specialized receptors (“loading docks”), processed by chemical reactions governed by a central information system (“the front office”), carried around to various locations (“assembly lines”) as the work progresses, and finally sent back via those same receptors into the larger organism. The cell is a highly organized, busy place, whose many different parts must work together to keep the whole functioning.

Each of the many different kinds of molecules that make up living things on our planet is built from an exact and orderly arrangement of atoms. Two important features characterize all of these molecules: (1) all are made from a few small modules, and (2) their properties depend mainly on their shapes.

No matter how big and complex an organic molecule gets (and some can contain millions of atoms), its basic structure is always
relatively simple, strung together from a few basic components. Every building, from a country cottage to the Empire State Building, is a different arrangement of common elements like bricks and windows. Similarly, you can think of every organic molecule, from simple sugars to complex proteins, as an assembly of simple building blocks. Four principal types of organic molecules, each built in a different way from different components, all share this basic property of modularity.

When molecules become large and complex, their three-dimensional shape becomes important in a way that doesn’t apply to relatively simple compounds like the minerals we described in Chapter 7. No matter how complex a molecule is, it must interact with other molecules by way of the same types of chemical bonds that hold smaller molecules together. Ultimately these bonds depend on the interactions between electrons of two neighboring atoms. Thus, in order to produce reactions between complex molecules, the appropriate atoms in each of the participants must be brought near each other so that their electrons can interact. Two complex molecules can interact only if their shapes exactly match, like two pieces of a jigsaw puzzle.

You can think of two large molecules that can interact with each other as long ropes haphazardly thrown into piles. Think of the atoms that want to form bonds as patches of Velcro, several on each rope. The ropes will not stick together if you press any two pieces at random; the probability of forming a bond by tossing one pile on top of the other is pretty small. A strong bond forms only if you arrange the ropes in such a way that the patches of Velcro can meet each other.

There are many ways that the piles of rope might not match. It might be, for example, that a patch on one rope is hidden inside a deep recess. In this case, only a rope with its Velcro at the end of a long loop could make proper contact. In the same way,
complex molecules can be made to bond only if they fit properly Therefore the interactions of these molecules depend on their shapes.

Enzymes are an extremely important class of large molecules whose sole task is to help other molecules interact with each other. In this linking process the enzymes themselves remain unchanged. (Molecules that facilitate such reactions between
inorganic
molecules are called catalysts.) In general, enzymes are remarkably specific—they link only two particular kinds of molecules and no others.

If you took the two piles of rope in our example and twisted them around so that all the Velcro pieces stuck together, you would be acting as an enzyme. You would grasp one rope, then the other, in such a way that the sticky patches faced each other. Once the ropes were stuck together, you would walk away unchanged, ready to work your magic on the next pile of rope.

Thus does an enzyme bring two specific molecules near each other, let their atoms form bonds, and then, its job done, go on its way unaffected, ready to begin the process all over again. Each kind of enzyme supervises one kind of reaction. For each of the thousands of chemical reactions that go on in each cell in your body every day, there has to be a separate molecule to act as an enzyme.

Large molecules must be constructed from atoms that are both plentiful and easy to hook together. Carbon, with four electrons in its outermost orbit, has both of these qualities. It also possesses
an even more important property, the ability to form strong covalent bonds with other carbon atoms. Thus, it is possible to put together long chains of carbon atoms with each atom in the chain having free electrons that can act as “hooks” to form covalent bonds with other atoms. This property of carbon explains why it is found in all molecules in living systems, and why we say that life on Earth is carbon based. We might, incidentally, also call it covalent based, since by far the greatest number of bonds between atoms in organic molecules are of this type.

In addition to carbon, organic molecules often contain five other types of atom—hydrogen, nitrogen, oxygen, phosphorus, and sulfur. (A simple mnemonic—CHNOPS—helps to keep these atoms in mind.) From these six elements we can construct all the basic modules needed to assemble the organic molecules themselves. Thus, on the scale of the atom, a basic simplicity underlies the diversity of life on our planet.

Four types of molecules are essential to the working of a cell. They are:

Nucleic acids
. These molecules (DNA and RNA) carry the blueprint that runs the cell’s chemical factories, and also are the vehicle for inheritance—the passing of genetic information from one generation to the next. Because of their unique role in biology, nucleic acids are discussed in the next chapter.

Proteins
. Proteins are the workhorses of the cell. In addition to their familiar role in the structure of living things (your hair and fingernails are made from protein, for example), proteins
serve as almost all of the enzymes that run chemical reactions in cells. Life would not be possible without these molecules.

Proteins are modular, built from hundreds or thousands of smaller molecules called amino acids. The basic structure of an amino acid consists of a group of hydrogen and nitrogen atoms on one side, a group of carbon, oxygen, and hydrogen on the other, and a “side group” labeled R in the diagram. There are hundreds of possible choices for this side group, each corresponding to a different amino acid.

Amino acids link together by having a hydrogen atom on one end of one molecule combine with the OH at the end of another molecule to form a water molecule (H
₂
O). Think of this bonding as two amino acids squeezing out a drop of water as they cement themselves together. Once two amino acids are linked in this way, a third can be added on, then a fourth, a fifth, and so on. Each different chain-like sequence of amino acids results in a different kind of protein molecule. Proteins can range in size from a few dozen amino acids (the building blocks of insulin are examples of this type of small protein) to giant chains containing hundreds of thousands of links.

Amino acids link together in long chains to form proteins. Twenty different amino acids, distinguished by different groups of atoms in the position R, are found in common proteins
.

Once an amino acid chain forms, it can take many shapes. The chains can coil up into a corkscrew (as they do in your hair), or they can wrap around each other to form a cable (as they do in the tendons that hold your muscles in place). Very long proteins may even have different structures along different parts of the chain. Once this so-called secondary structure has been established along a chain, large proteins can also fold up into complex, irregularly shaped globules. The nooks and crannies in the surfaces of these complex folded proteins make them ideal for use as enzymes in the cell. The smaller molecules that serve as the raw material for the cell’s chemical reactions fit into the surfaces of specific proteins.

One strange and as yet unexplained fact about the structure of proteins in living systems has important implications for evolution. Hundreds of amino acids are possible, but only twenty different kinds are actually found in the proteins of living things on Earth.

3.
Carbohydrates
. While proteins supervise the cell’s chemical factories, carbohydrates provide each factory’s fuel supply. The basic building blocks of carbohydrates are sugars—small ring-like molecules with perhaps two dozen atoms of carbon, oxygen, and hydrogen. Common sugars include glucose (an ingredient of many hospital IV solutions), fructose (found in many fruits), and sucrose (ordinary table sugar) made from a ring of glucose and a ring of fructose bound together.

Like the amino acids in proteins, sugars can “squeeze out
water” by combining an H from one ring and OH from another, thereby forming a bond that holds the rings together. And as was the case for proteins, these simple building blocks can be hooked together ad infinitum to form long chains. Strings of glucose molecules stacked head-to-tail in slightly different ways produce both starch and cellulose, two large molecules that are very important in the architecture of living systems. Starches store energy in cells, while cellulose is the principal fiber that stiffens the structure of plants.