Chapter1 The Chemistry of Life.pdf

C H A P T E R S

1 The Chemistry of Life

2 Energy, Life, and the Biosphere

3 Exchanging Materials with the Environment

4 Autotrophy: Collecting Energy from theNonliving Environment

5 Cell Respiration: Releasing Chemical Energy

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Nonliving things are passive; they cannot control how the environment affects them. Living things, in contrast, select whatthey absorb and what they retain or release. How do they do this? This

is an important question that biologists, scientists who study living things, tryto answer. In this unit, you will learn some important ideas that scientists useto understand life. In particular, you will learn about the molecular approach tobiology. This approach seeks to answer these questions by using the laws ofchemistry and physics that describe all things, not just living ones.

This unit is your introduction to the molecular approach. Here you will learn about the substances that make up living things and how energydrives their activities. You will find out how living things selectively take in some substances from their environment, while rejecting or releasingothers. Finally, this unit will explain how living things collect energy fromthe environment and use it to survive.

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U N I T

1

How do these tiny living things benefit from

living inside their glass shells?

Can scientists explain the structure of glass

made by living things in the same way that

they explain the structure of glass made in a

factory from sand?

Energy, Matter, and Organization

Energy, Matter, and Organization

� About the photo This photo showsdiatoms viewedthrough a lightmicroscope (�400).

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C O N T E N T S

GENERAL CHEMISTRY

1.1 Atoms, Molecules, and Compounds1.2 The Structure of Atoms

REACTIONS IN LIVING CELLS

1.3 Chemical Reactions1.4 Chemical Bonds1.5 Ions and Living Cells

BIOCHEMISTRY

1.6 Organic Compounds and Life1.7 Carbohydrates1.8 Lipids1.9 Proteins1.10 Nucleic Acids

GENETIC CODING IN CELLS

1.11 The Double Helix1.12 The Functions of DNA

L E A R N I N G O U T C O M E S

By the end of this chapter you will be able to:

A Explain the relationships among atoms, molecules, elements, and compounds.

B Describe the types of chemical bonds.

C Explain the pH scale and its use.

D Relate the characteristics and functions of the four classes of macromolecules.

E Recognize the importance of nucleic acids in inheritance.

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The Chemistry of Life

23

From the time of ancient Greece until the eighteenth century, mosteducated people believed that all things were made of earth, fire,air, and water. A brilliant scientist named Lavoisier challenged that

thinking with his discovery that fire is not a substance but rather a process(combustion) that can convert matter from one form to another. Lavoisierused physical laws and measurement to understand how chemicals react. In doing so, he founded modern chemistry.

Over time, biologists began to recognize that all organisms (livingthings) are composed of chemicals and that an understanding of liferequires an understanding of chemistry. Biochemistry—the chemistry of living organisms—plays a central role in our understanding of today’sbiological questions. Information about causes and treatments of cancer,AIDS, and mental illness is being found in the biochemistry of human cells. Evolutionary relationships are being more clearly defined throughcomparisons of chemicals in different organisms.

This chapter presents some principles of general chemistry and of biochemistry that are important for an understanding of how living cells function.

The Chemistry of LifeWhat roles do chemicals play in life?

What evidence do you see of chemicals in this

hot spring?

C H A P T E R

1

� About the photo The photo to the leftshows the ChampagnePool, a mineral rich hotspring at WaiotapuThermal Park in NewZealand.

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FIGURE 1.1 Elements that make up water. Hydrogen, a flammable gas, was used in dirigible balloonsuntil the German airship Hindenburg (a) exploded at Lakehurst, New Jersey, in 1937. Oxygenis a gas needed by most life forms. People with breathing problems are often givenconcentrated oxygen to breathe (b). Both elements behave very differently from water.

24 UNIT 1 Energy, Matter, and Organization

General Chemistry1.1 Atoms, Molecules, and Compounds

Water is abundant on Earth today, and it exists in three physical states—as a gas, as a liquid, and as a solid. The physical state of water dependson temperature. If the temperature is high enough, water is a gas. If thetemperature is low enough, water freezes and forms ice. Although the formsof water may vary, its chemical composition remains the same. Water has someunusual physical and chemical properties that have had a powerful effect onthe evolution of life. This may seem surprising, but living things are mostlywater. Thus a close look at the chemistry of water can provide informationabout the chemical nature of matter and about the function of organisms.

Suppose you found a way to subdivide a drop of water into smaller andsmaller droplets until you could not see them even under a microscope. Nomatter how small the water droplet, it would still be made of identical unitscalled molecules. Molecules of water are the smallest units into which watercan be subdivided and still have the essential chemical properties of water.

When an electric current flows through water under proper conditions, a remarkable change occurs: water becomes two gases. One is the lightest gas,hydrogen, which burns with a very hot flame in air. The other gas is oxygen.Thus under certain conditions, water molecules can break down into twodifferent substances (which are also molecules), hydrogen and oxygen. Neithersubstance has the appearance or any other property of water (Figure 1.1).

Hydrogen and oxygen are elements—substances that cannot be brokendown chemically into simpler substances. In 1805, the British teacher andchemist John Dalton finished a long series of experiments and measurements

(bl)Hulton-Deutsch Collection/CORBIS, (br)Larry Mulvehill/Photo Researchers

a b

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a- = not (Greek)tomo- = cut or divide (Greek)

An atom is a particle that cannot bedivided into smaller particles of thesame substance.

E T Y M O L O G Y

CHAPTER 1 The Chemistry of Life 25

that indicated every element is made of minute particles. Dalton believedthese particles could not be broken into smaller particles, so he named thematoms. Atoms are the smallest unit of an element that still has the chemicalproperties of that element. Dalton stated several principles to describe anatom’s chemical behavior. Those principles form the basis of the mostimportant of all chemical theories, the atomic theory. New data havechanged the atomic theory since Dalton’s time, but this theory is still basicto an understanding of chemistry and biology.

Molecules are made of atoms (the smallest units of elements) that havecombined chemically. Molecules may be made from more than one type ofatom (in which case the molecule is called a compound, such as water), or from atoms of the same type. For example, hydrogen gas consists ofhydrogen molecules, each of which consists of two hydrogen atoms linkedtogether (see Figure 1.2). Similarly, an oxygen molecule consists of twooxygen atoms. (Oxygen also forms molecules of ozone, which contain threeatoms of oxygen.) Elements can combine chemically in many ways to form the millions of compounds that give Earth its variety of materials.

Chemists have given each element a symbol of letters from the element’sname. H stands for hydrogen, O for oxygen, C for carbon, and N for nitrogen.Iron, however, has two letters. Its symbol is Fe, derived from the wordferrum, reflecting that some symbols come from an element’s Latin or Greek name. (See Appendix 1A, “The Periodic Table of the Elements.”)

Despite all the variety of materials, organisms are made of a limitednumber of compounds, of which water is the most abundant. About 97% of the compounds present in organisms contain only six elements—carbon(C), hydrogen (H), oxygen (O), nitrogen (N), phosphorus (P), and sulfur (S).The remaining 3% contain small amounts of other elements. The basic sixelements are essential to every organism. Some 20 others are essential, too, but only in smaller amounts (Figure 1.3).

The number of atoms of each element in a molecule is shown by thenumber, called a subscript, following the symbol for the element (thenumber 1 is always understood and not written). For example, the formulafor carbon dioxide, CO2, means that a molecule of this gas contains onecarbon atom and two oxygen atoms. A molecule of ammonia, written asNH3, contains one nitrogen atom and three hydrogen atoms. The formulatells what elements are in each molecule and how many atoms of eachelement the molecule contains.

watermolecule

oxygenatom

oxygenatom

oxygenatom

2 hydrogenatoms

hydrogenatom

hydrogenatom

hydrogenmolecule

oxygenmolecule

FIGURE 1.2 Structures of some simplemolecules. Molecules of water,hydrogen, and oxygen are madefrom combinations of atoms, asshown in these models.

FIGURE 1.3 Elements present in the humanbody. The large proportions ofhydrogen and oxygen reflect thefact that living organisms consistmostly of water. The dry matter inorganisms consists mostly ofvarious compounds of carbon with other elements, especially,hydrogen, oxygen, and nitrogen.

hydrogen10%

oxygen64%

nitrogen 3%phosphorus 1%sulfur 0.75%trace elements 3.25%

carbon18%

C O N N E C T I O N SC O N N E C T I O N SThe presence of the same sixelements in all living organismsis an example of patterns innature.

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sub- = below or under (Latin)

Atoms are made up of subatomicparticles; these particles are smallerthan, or “below” the level of atoms.

E T Y M O L O G Y


1.2 The Structure of AtomsAlthough Dalton didn’t know it, atoms themselves are built of many

smaller subatomic particles. The subatomic particles of atoms that arebasic to an understanding of biology are electrons, protons, and neutrons.The electron carries a negative electric charge. A proton has a positivecharge, and a neutron has no charge (it is neutral).

Protons and neutrons remain in the center, or nucleus, of the atom. Theelectrons, however, seem to be everywhere at once except in the nucleus.The rapidly moving electrons form a negatively charged “cloud” around thenucleus. Electrons tend to stay in this cloud because their negative chargesare attracted to the positive charges of the protons in the nucleus. Electronsare distributed throughout the cloud based on differing levels of energy (orattraction) called electron shells. Electrons in shells near the nucleus areheld more tightly than those in shells farther from the nucleus.

The simplest of all atoms is hydrogen. A hydrogen nucleus has a singleproton, no neutron, and a single electron that orbits in the energy shellclosest to the nucleus (Figure 1.4a). Because two electrons can fit in thatshell, hydrogen has room for another electron. That vacancy makeshydrogen very reactive.

Atoms of other elements are more complex than the hydrogen atom. For example, an atom of carbon (Figure 1.4b) has six protons and sixneutrons in its nucleus and six electrons orbiting the nucleus (two in the innermost shell, four in an outer shell). The number of neutrons mayvary, but carbon atoms always contain six protons. Similarly, nitrogen has seven protons and seven electrons, and oxygen has eight protons and eight electrons (Figure 1.4c, d). In both nitrogen and oxygen, there are twoelectrons in the innermost shell. Nitrogen has five electrons in its outer

Molecular ModelsWhat is a model of a molecule? In a sense, a

molecular model has some things in common withmodels of planes, ships, and automobiles that you can purchase in a hobby shop. A model of a ship, forexample, is an approximation of the real object, exceptthat the model is much smaller and probably does notfunction the way the ship does. The model makes iteasier to understand how a ship is built and how itoperates, but it is not the real thing.

In a similar way, a molecular model gives an idea of a molecular structure. Unlike the ship, however, wedo not know what the molecule actually looks like. It is impossible to observe the structure of a moleculedirectly because a molecule is too small for the eye to

see, even with a microscope. Molecular models areconstructed from inferences—conclusions that followlogically from laboratory data such as X-ray diffraction.As more is learned about a molecule, the model ischanged and improved to be consistent with the newinformation. In this way, a model can serve as a learningtool and be used in developing new hypotheses. Thesymbol H2O represents a molecule of water. H and O are printed symbols used to represent the elementshydrogen and oxygen in water, and H2O is a printedmodel of a molecule of water. As you will see, the 2indicates that there are two atoms of hydrogen in onewater molecule. (In one drop of water there are about abillion trillion molecules of H2O.)

The figures and symbols used in this chapter aremodels that can help you visualize and understand thestructure and the function of elements and molecules.

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shell, and oxygen has six in its outer shell. That second shell can hold eightelectrons, as can the third shell. Atoms with filled electron shells, such ashelium and neon, are more stable than atoms with unfilled shells, such asnitrogen and oxygen.

Every atom has an equal number of protons and electrons. Thus, thecharges are balanced, and the atom itself has no overall electric charge.However, the atoms of most elements can undergo chemical change bygaining, losing, or sharing one or more electrons with other atoms. Atomswith unfilled shells have a strong tendency to lose or gain electrons tocomplete their outer shells. As you will see in the next section, this is thebasis of chemical reactions.

Atoms of different elements differ in their number of protons, neutrons,and electrons. Atoms of the same element always have the same number ofprotons and electrons, but they may differ in their number of neutrons.Atoms of the same element that differ in their number of neutrons are calledisotopes. For example, 99% of oxygen atoms are like the one in Figure 1.4d.This atom is called the oxygen-16 isotope, named for the sum of its 8 protonsand 8 neutrons. Oxygen-17 and oxygen-18 also exist, with 9 and 10 neutrons,respectively. Some isotopes have unstable atomic nuclei that break down,releasing radiation energy. These isotopes are called radioisotopes. They areuseful in biological research because they can help to determine some of thechemical reactions organisms carry out. (See Appendix 1B, “Radioisotopesand Research in Biology.”)

FIGURE 1.4Some simplified models of atoms. Simplified models of hydrogen (a), carbon (b), nitrogen(c), and oxygen (d), are shown here. The models show electrons as a cloud of negative chargearound the nucleus. The number of electrons in the outer level determines the chemicalactivity. Protons are shown in blue, and neutrons are shown in brown.

a hydrogen atom(1 proton, 1 electron)

b carbon atom(6 protons, 6 neutrons, 6 electrons)

c nitrogen atom(7 protons, 7 neutrons, 7 electrons)

d oxygen atom(8 protons, 8 neutrons, 8 electrons)

Check and Challenge1. What is the relationship between atoms and elements?

2. What are the particles of an atom and how do they interact?

3. What six elements are most important in organisms?

iso = equal (Greek)topos = place (Greek)

Isotopes of a chemical elementoccupy the same position in theperiodic table of the elements.

E T Y M O L O G Y

BiologyBiology

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Reactions in Living Cells1.3 Chemical Reactions

Chemical bonds are the attraction, sharing, or transfer of outer shellelectrons from one atom to another. Those bonds between atoms can bebroken, the atoms rearranged, and new bonds formed. A chemical reaction

involves the making and breaking of chemical bonds. During a chemicalreaction, substances interact and form new bonds and new substances.

Only electrons in the outer shells of the atoms pictured in Figure 1.4 are involved when the atoms react during a chemical change. For atoms with electrons in more than one energy shell, only the outermost electronsnormally interact during chemical changes. The outer electrons are a reliableindicator of the reactivity of an atom, but the structure of the entire atomalso influences chemical reactions.

Chemical reactions occur in the cells of all living organisms. Cells are thebasic units of life, much as atoms are the basic units of matter (Figure 1.5).Chemical reactions are important to a cell for two reasons. First, they arethe only way to form new molecules that the cell requires for such things asgrowth and maintenance. Second, the making and breaking of bonds involveschanges in energy. As a result of chemical reactions in a cell, energy may bestored, used to do work, or released.

Chemical reactions can be represented as short statements calledchemical equations. For example, the breakdown of water can berepresented by the following equation:

Why is it necessary to use two molecules of water in the equation?Remember that hydrogen and oxygen molecules each consist of two atoms.A single molecule of water does not yield enough oxygen atoms to make anoxygen molecule, but two molecules of water do. The equation is written to

FIGURE 1.5 A generalized animal cell. Amembrane encloses all cells. Inanimals, the genetic material isenclosed in a structure called thenucleus.

cell membrane

cell interior

nucleus

electric2 H2O 2 H2 + O2energy

2 molecules 2 molecules 1 moleculeof water of hydrogen of oxygen

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balance the number of atoms on both sides of the arrow. Balancing chemicalequations illustrates one of the most basic laws of chemistry: the law of

conservation of matter, which states that matter is neither created nordestroyed in chemical reactions.

The direction of the arrow in a chemical reaction points from reactantsto products. Notice that the number of molecules is shown by a numeralpreceding the formula for the molecule. Figure 1.6 shows models thatrepresent chemical reactions.

When molecules collide, they may or may not react, depending on theenergy and orientation of the molecules. Activation energy is the energyneeded to get a chemical reaction started. Sometimes an outside source ofextra energy is necessary to initiate a reaction. For example, hydrogen (H2)and oxygen (O2) gases can be mixed without reacting until a lighted match, a spark, or ultraviolet light adds energy. This relatively small amount ofenergy causes some hydrogen molecules and oxygen molecules to react toform water. The reaction releases energy that heats the remaining moleculesof hydrogen and oxygen, causing them to react to form more water. Thereaction is often explosive. The product, water, has less energy than thehydrogen and oxygen gases had separately in the mixture. The difference in energy is accounted for mainly in the form of light and heat produced by the reaction.

1.4 Chemical BondsWhen atoms interact, they can form several types of chemical bonds.

One type forms when electrons move from one atom to another atom. Thistype of chemical bond occurs in many substances, including table salt, alsoknown as sodium chloride (NaCl). As the latter name suggests, table salt ismade of two elements, sodium (Na) and chlorine (Cl). When atoms of thesetwo elements react, an electron passes from a sodium atom to a chlorineatom (Figure 1.7). The resulting sodium atom is positively charged, for it has one less electron than protons. It becomes a sodium ion, written as Na+.

FIGURE 1.6 Models of chemical reactions. In the decomposition of water, twice as many hydrogenmolecules as oxygen molecules are produced.

one atom ofhydrogen

one atom ofoxygen

one atom ofhydrogen

one atom ofoxygen

one molecule ofhydrogen (H2)

two moleculesof hydrogen (H2)

electricspark

two moleculesof water (H2O)

one molecule ofoxygen (O2)

one molecule ofoxygen (O2)

+

+

+

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An ion is an atom or a molecule that has acquired a positive or negativecharge as a result of gaining or losing electrons. The chlorine atom isnegatively charged, for it has one more electron than protons. It becomes achloride ion, written as Cl�. Note the change in name from chlorine tochloride. An ionic bond is the attraction between oppositely charged ions,such as the sodium chloride bond (Figure 1.7).

In a second type of chemical bond, called a covalent bond, two atomsshare one or more pairs of electrons (Figure 1.8). Two atoms of hydrogenjoin to form a molecule of hydrogen gas (H2) by sharing a pair of electrons.This sharing gives each hydrogen atom a filled electron shell. In a moleculeof water, each of the two hydrogen atoms shares a pair of electrons with thesame oxygen atom. This gives each hydrogen atom two electrons and fillsthe outer shell of oxygen with eight electrons.

The chemical behavior of water indicates that the atoms do not share the electrons equally. The larger oxygen atom attracts the electrons morestrongly than the smaller hydrogen atoms do. If the electrons of a bond arenot shared equally, the bond is called a polar covalent bond. In contrast, theelectrons in a molecule of hydrogen gas are shared equally, and the resultingcovalent bond is said to be nonpolar.

The unequal sharing of electrons in a water molecule gives the oxygenatom a slight negative charge and each hydrogen atom a slight positivecharge (Figure 1.9). Such a molecule is known as a polar molecule. Thepolar nature of water is biologically significant. Most cells and tissues

FIGURE 1.8An example of covalent bonding.Covalent bonds form when twoatoms share a pair of electrons.Only electrons in the outer energylevels are shown here.

H2

H2O

H

O

H

HH

FIGURE 1.7 An example of ionic bonding. (a) Sodium and (b) chlorine can react to form (c) the saltsodium chloride (NaCl). By losing one electron, sodium achieves two filled shells (2 + 8) andbecomes a stable positive ion. By gaining one electron, chlorine achieves three filled shells (2 + 8 + 8) and becomes a stable negative ion, chloride.

sodium ion (Na+)

chloride ion (Cl-)

sodium atom c

sodium + chlorine sodium chloride

chlorine atom

11 electrons

17 electrons

10 electrons

18 electrons

1 electron

(+)

(–)

a

b

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contain large amounts of water—up to 95% in some, with an average of70–80% water throughout all organisms. Molecules must dissolve in water in order to move easily in and between living cells. Polar molecules, such as sugar, and ions, such as Na+, dissolve in water because of the electricattraction between them and the water molecules. Nonpolar molecules, such as fats and oils, do not dissolve in water.

Polar molecules may form still another type of chemical bond. A weakattraction can occur between a slightly positive hydrogen atom in a moleculeand a nearby slightly negative atom of another molecule (or of the samemolecule if it is large enough). This type of attraction is called a hydrogen

bond (Figure 1.10). In compounds found in organisms, hydrogen bondsusually involve hydrogen atoms that are bonded to oxygen or nitrogen.Hydrogen bonds provide an attractive force between water molecules,which explains why water is a liquid at room temperature and not a gas. A large number of hydrogen bonds can be quite strong, but single hydrogenbonds are much weaker than covalent bonds.

1.5 Ions and Living CellsWhen table salt dissolves in water, the ionic bonds are broken. Na+

and Cl� ions separate, or dissociate, but remain as ions in solution. Thepositive sodium ion is attracted to the slightly negative end of water, and the negative chloride ion is attracted to the slightly positive end. Sodiumions are important in regulating water balance in organisms. Other ions,

Structural FormulasStructural formulas are models that show both the

number and arrangement of atoms in molecules. Inwriting structural formulas of compounds, a covalentbond is indicated by a line. For example, the structuralformula for hydrogen gas is written H—H. Sometimestwo atoms share two pairs of electrons between them,forming a double bond that is shown by a double line(=), as in O=C=O, carbon dioxide. When three pairs ofelectrons are shared by two atoms, they form a triplebond that is represented by three lines ( ). Forexample, the nitrogen gas (N2) that makes up most ofthe atmosphere consists of pairs of nitrogen atomsjoined by a triple bond. Figure 1.11 shows severalmethods of representing molecules. Note that themolecular formula tells you only the number of atomsof each type present in the molecule, whereas thestructural formula indicates how the atoms are bonded.The space-filling and ball-and-stick models providepictures of the spatial arrangements of the atoms.

FIGURE 1.11Several ways of representing the structures of molecules.A variety of symbols and models are used to representchemical formulas.

FIGURE 1.9 The polar nature of water. An oxygenatom attracts electrons more stronglythan hydrogen, giving the oxygen aslight negative charge and eachhydrogen a slight positive charge. Thenet charge of the molecule is zero.

name/molecularformula

structuralformula space-

filling

models

ball-and-stick

hydrogen/H2 H H

water/H2O H O H

H N Hammonia/NH3

methane/CH4

H

H C H

H

H

FIGURE 1.10Hydrogen bonding. A hydrogenbond is a weak attraction between aslightly positive hydrogen atom inone polar molecule and a slightlynegative atom in another. This watermolecule is forming hydrogen bondswith four other water molecules.

+

+

++

+

+

+

+

+

+hydrogenbondH

HH

+ +

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including potassium ions (K+) and calcium ions (Ca+2), are involved in many reactions inside cells.

When a nonionic compound, such as water, is converted to ions, theprocess is called ionization. The ionization of water is a vital reaction inliving cells. When a water molecule separates, one of its H—O bondsbreaks. The result is a positively charged hydrogen ion (H+) and anegatively charged hydroxide ion (OH�). The hydrogen ion—a proton—quickly combines with a water molecule to form a hydronium ion (H3O+). Itstill is convenient, however, to refer to the number of hydrogen ions (H+) ina solution, even though that really means the concentration of hydroniumions (H3O+).

Only about one in every 500 million water molecules ionizes in livingcells, yet all life processes depend on this tiny amount of ionization. Indeed, living cells must maintain their internal levels of H+ and OH�

ions within narrow limits, because even small changes greatly influenceimportant reactions.

The level of H+ and OH� ions in solution is described by a range ofnumbers known as the pH scale (Figure 1.12). The scale runs from 0 to 14. A solution (a mixture in water) that has the same number of H+ and OH� ions is neutral and has a pH of 7. Pure water has a pH of 7. A solution having more H+ than OH� is acidic and has a pH less than 7 (low pH). Asolution that has more OH� than H+ ions is basic (or alkaline) and has a pH greater than 7 (high pH). Thus a solution with a pH of 2 is highly acidic, and a solution with a pH of 10 is highly basic.

The pH scale is a logarithmic scale. This means that a change of one pH unit is equal to a tenfold change in the level of H+ ions. For example, asolution with a pH of 3 is 10 times more acidic than a solution with a pH of 4. Figure 1.13 shows the pH of several common substances.

pH is important in biology because the pH of a cell’s interior helpsregulate the cell’s chemical reactions. As discussed earlier, all cells rely onchemical reactions for growth and survival. Thus, it is not surprising thatorganisms have ways to control pH and to respond to changes in the pH of their environment (Figure 1.14). For example, certain fungi and bacteriacan grow in acidic solutions but not in basic ones. Some marine organismshave become so adapted to the slightly basic pH (7.8–8.6) of seawater thatthey cannot live in less basic solutions. The pH of normal urine is about 6,but human blood must remain near pH 7.4. Death nearly always results if the blood pH falls to and stays at 6.8 or rises to and stays at 8.0. Failedkidney function is most often the reason a person cannot maintain normalblood pH.

FIGURE 1.13 The pH of some commonsubstances. Note that mostbiological substances are slightlyacidic (pH 6–7). The greater acidityof soft drinks (pH 3) is partlyresponsible for contributing to tooth decay.

sodium hydroxide

oven cleaner

hair remover

household ammonia

milk of magnesia

bleach, phosphatedetergentsseawatereggsbloodmilkurine

normal rainwater

black coffee

tomatoes, grapes

vinegar, soft drinks

gastric juice

hydrochloric acid

14

13

12

11

10

9

8

7

6

5

4

3

2

1

0

incr

easi

ngly

bas

icin

crea

sing

ly a

cidi

c

neutral

milk of magnesia

pH

0 1 2 3 4 5 6 7 8 9 10 11 12 13 14

more acidic neutral more basic

FIGURE 1.12 The pH scale. This scale is used to denote the acidity and alkalinity of solutions.

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Check and Challenge1. How are chemical reactions important in cells?

2. Distinguish among the various types of chemical bonds.

3. Describe the law of conservation of matter.

4. Why is pH important to living organisms?

5. How does the polarity of water assist the movement of molecules?

FIGURE 1.14Adaptations of organisms to differences in soil pH. (a), Conifers (needle-leaf trees) suchas these Douglas firs thrive in the acidic soil of Olympic National Forest in Washington state.(b), Deciduous hardwood trees such as oaks, maples, and beeches compete moresuccessfully in the less acidic soil of this forest.

a b

Biochemistry1.6 Organic Compounds and Life

Many chemical compounds besides water are needed for life to exist.The most important are organic compounds, in which carbon atoms arecombined with hydrogen and usually oxygen. Organic compounds frequentlyalso contain nitrogen, sulfur, or phosphorus. A few carbon compounds are not included with organic compounds: carbon dioxide (CO2), carbonmonoxide (CO), and carbonic acid (H2CO3).

The word organic was coined long ago when it was thought thesecompounds could be formed only by living cells. Since then, millions of different organic compounds have been synthesized in the laboratory. There is no longer any reason to call these compounds organic, but the name is so well established that it is still widely used to describe nearly all carbon compounds, essential for life or not.

Try Investigation 1A Organismsand pH.

Try Investigation 1B Compoundsof Living Things.

BiologyBiology

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Carbon atoms can combine in long chains that form the backbone oflarge complex molecules, or macromolecules. The backbone of carbonatoms is called the carbon skeleton (Figure 1.15). Other atoms andmolecules can attach to the carbon skeleton, giving each macromoleculea particular structure and, therefore, a particular function. The followingsections of the chapter discuss the characteristics of the four mostimportant classes of molecules in living cells—carbohydrates, lipids,proteins, and nucleic acids. Figure 1.16 shows the relationship between the cell’s building-block molecules and their macromolecular forms.

1.7 CarbohydratesAll known types of living cells contain carbohydrates. In addition to

carbon atoms, carbohydrates contain hydrogen and oxygen atoms in thesame two-to-one ratio as water. The simplest carbohydrates are single sugarscalled monosaccharides, which may contain three to seven carbon atomsin their carbon skeletons. Figure 1.17a shows the structural formulas of twoforms of the common monosaccharide glucose. Most organisms use glucose(which is also referred to as blood sugar) as a source of energy. The energyin glucose, and in all molecules, is contained in the atoms and bonds of themolecule itself.

Biologically important sugars often have a phosphate group attached tothe carbon skeleton and are called sugar-phosphates. The phosphate

FIGURE 1.15Structural formulas of some carbon compounds. Carbon atoms (black) make up a carbonskeleton and link with other atoms, such as hydrogen (white). In each formula, a short lineindicates a covalent bond: (a), a molecule of methane; (b), part of the carbon skeleton of a largermolecule; (c), a view of (b) that indicates the three-dimensional structure of the molecule. Otheratoms, such as oxygen (usually shown in red) or nitrogen (usually shown in blue), can beattached to the carbon skeleton instead of hydrogen.

carbo- = carbon (French, Latin)hydro- = water (Greek)mono- = single (Latin)di- = two (Greek)poly- = many (Greek)saccharo- = sweet or sugar (Latin,Greek)

Carbohydrates are compounds ofcarbon, hydrogen, and oxygen in thesame 2:1 proportion in which theyoccur in water (CH2O). Amonosaccharide is a single sugarmolecule. A disaccharide consistsof two joined sugar molecules, and apolysaccharide is composed ofmany sugar subunits.

E T Y M O L O G Y

H

H H H H H H H H

HH

HH

HH

HHH

H

C

C

C

C

C

C

C

C

C

C

c

a

HH

CCCCCCH

H HH H

HHHH

HCH

H

H

H H

HH

CCC

H H

H

H

b

SWP2618_CH01_020-049 10/4/04 10:58 AM Page 34


group, which is composed of an atom of phosphorus and four atoms ofoxygen (see Figure 1.17b).

Two simple sugar molecules, or monosaccharides, (Figure 1.18a) maybond to form a double sugar, or disaccharide, represented in Figure 1.18b.The most familiar of all disaccharides is sucrose, commonly called table sugar.Sucrose contains glucose and another monosaccharide, fructose. Lactose, ormilk sugar, is a disaccharide formed of glucose and the monosaccharidegalactose. Maltose, or malt sugar, is a common disaccharide made of twoglucose molecules.

Several glucose molecules may bond to form complex carbohydratescalled polysaccharides (Figure 1.18c). Starch and cellulose are the complexcarbohydrates commonly formed by plants. Starch is an energy-storage andcarbon-reserve compound in many plants and is an important food sourcefor humans. Cellulose is a structural molecule found in the rigid wallssurrounding plant cells, and it is an important part of wood and cottonfibers. The human liver and muscles store carbohydrates in the form ofglycogen, also called animal starch. Molecules of starch, cellulose, andglycogen consist of thousands of glucose units and have no fixed size.

FIGURE 1.16The building blocks of the cell.Most macromolecules arepolymers—long chains of similarsubunits (monomers). For example,proteins are polymers made frommany amino-acid monomers.Sugars and polysaccharides arecarbohydrates.

sugars

amino acids

nucleotides

polysaccharides

fats and lipids

proteins

nucleic acids

importantmacromolecules

building blocksof the cell

fatty acids

FIGURE 1.17 The structures of a sugar and a sugar-phosphate. (a), In solution, glucose, a 6-carbonsugar, can exist in two forms: a straight chain and a ring form. The ring form, in which fivecarbon atoms and an oxygen atom form a closed ring, is by far the most abundant. Althoughnot shown, carbon atoms exist at the points of the hexagon. Also, actual glucose molecules are not solid, as depicted; their centers are mostly open space. (b), The two forms of glucose-6-phosphate are shown. Cells often add a phosphate group to glucose after glucose enters the cell.

O

a glucose

straight chain form

H

C

H C OH

C

OHH

HO C H

C

H C

O

OHH

H OH

b glucose-6-phosphate

ring form

H

HOH

OH

OH

H

OH

H

H

CH2-O-PO3–2

ring form

H

HO

O

H

OH

OH

H

OH

H

H

CH2-OH

straight chain form

C

HO C H

C

OHH

H C OH

CO

H OH

H

CH2-O-PO3–2

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1.8 LipidsLipids, or fats and oils, are macromolecules that have two primary

functions: long-term storage of energy and carbon and building of structuralparts of cell membranes. Lipids generally do not dissolve in water, becausethey are nonpolar. Like carbohydrates, lipids contain carbon, hydrogen, andoxygen, but not in a fixed ratio. Building blocks of lipids, called fatty acidsand glycerol, make up the simple fats most common in our diets and bodies.Three fatty-acid molecules and one glycerol molecule join to form a simplefat, or triglyceride, as shown in Figure 1.19.

The biologically important properties of simple fats depend on their fattyacids. For example, the fats in meat are different from the oils in vegetablesbecause the fatty acids are different. The properties of fatty acids, in turn,depend on the length of the carbon chains and the type of bonds betweenthe carbons. Common fatty acids have a total of 16 or 18 carbon atoms. Fattyacids in which single bonds join the carbon atoms are saturated fatty acids(one way to remember this: the carbon atoms are saturated with hydrogens).Unsaturated fatty acids are fatty acids in which double bonds join some ofthe carbon atoms. Figure 1.19 shows both types of fatty acids.

Unsaturated fats (fats containing unsaturated fatty acids) tend to be oilyliquids at room temperature. Olive oil, corn oil, and sunflower oil consist

FIGURE 1.18 Formation of complex carbohydrates. Monosaccharides (a), can combine to formdisaccharides (b). Starch and cellulose (c), are polysaccharides formed by linking togethermany monosaccharide subunits. Glycogen has a structure very similar to starch. Note theglucose subunits are linked differently in cellulose and starch. Human digestive enzymescannot break down the linkages in cellulose; hence we cannot digest it.

OOO

glucose fructose

H

H

OH

H OH

OH

HH

HO

water

disaccharide(double sugar)

CH2OH

HO

CH2OH

OH

H HO

CH2OH

H

H

b

polysaccharides

cellulose

O

O

O O

HOH++

sucrose

CH2OH

H

OH

H

HO

H

H

OH

H

O

CH2OH

H

OH

HO

H

H

CH2OH

monosaccharides(single sugars)

a

starch or glycogen

O O O

CH2

O

O O OO

c

O

O O OO

OO O

OO

O

O

O

O

O

SWP2618_CH01_020-049 10/4/04 10:59 AM Page 36


mostly of unsaturated fats. Saturated fats tend to be solids at roomtemperature. Butter and lard consist mostly of saturated fats. Fats are amore efficient form of energy storage than are carbohydrates because fatscontain a larger number of hydrogen atoms and less oxygen. You will learnlater how the amount of hydrogen and oxygen in fats and carbohydratesrelates to energy, as well as the important roles that saturated andunsaturated fats play in the diet.

Two other types of lipids important in cells are phospholipids andcholesterol. Phospholipids form when a molecule of glycerol combines withtwo fatty acids and a phosphate group (Figure 1.20a and b). The polarphosphate group allows one end of the lipid molecule to associate withwater. Together with proteins, phospholipids form cellular membranes(Figure 1.20c). Membranes are critical to cell survival because they separatea cell’s internal chemical reactions from the outside environment. They alsohelp control which chemicals enter and leave the cell. Cholesterol (Figure1.20d) is part of the membrane structure of animal cells and is important innutrition. Cells in the human body manufacture many essential substances,such as sex hormones, from cholesterol.

1.9 ProteinsEvery living cell contains from several hundred to several thousand

different macromolecules known as proteins. Proteins are structuralcomponents of cells as well as messengers and receivers of messages (alsocalled receptors) between cells. They play an important role in defense

FIGURE 1.19Formation of a fat molecule. To form a fat, one molecule of glycerol combines with threemolecules of fatty acids. The fatty acids in one fat may be alike or different. Examine thediagram. What is a by-product of this reaction?

H

HCOH

C

HCOH

H

OH H ++

glycerol triglyceride water

3HOH

H HH

H C C C CC O C H

H O

HHH O

HCOCC C

H

CCCCH

H HH H H

HHHH

H HH

H C C C CC C O C H

H

H H O

HH

HH H H H

C

fatty acids

(unsaturated fatty acid)

H H H HH

H C C C CC

H H H

CO

OH

H H H HH

C C C CC

H H H

CO

OH

H H HH

H C C CC

H H

CO

OH

H H

HH

(saturated fatty acids)

H

H

H

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against disease. Skin, hair, muscles, and parts of the skeleton are made ofproteins. Their most essential role, however, is as enzymes, specializedmolecules that assist the many reactions occurring in cells.

Cells make proteins by linking building blocks called amino acids.Amino acids are small molecules that contain carbon, hydrogen, oxygen,and nitrogen atoms; two also contain sulfur atoms. Figure 1.21 shows thegeneral structural formula for an amino acid. Amino acids have a centralcarbon atom to which is attached a hydrogen atom, an amino group (—NH2),an acid group (—COOH), and a variable group, symbolized by R, which maybe one of 20 different atoms or groups of atoms. Observe in Figure 1.22a thatin the amino acid glycine, R is an H atom, and in alanine, R is a —CH3 group.Some R groups are polar, such as the amino group in lysine; others arenonpolar, such as the carbon chain in leucine. The polarity of amino acidsaffects their ability to dissolve in water.

Any two amino-acid molecules may combine when a chemical bondforms between the acid group of one molecule and the amino group of the

variablegroup

R

C C

HOH

Oacid groupamino group

NH

H

FIGURE 1.21The structure of an amino acid.Amino acids (except for proline)have a central carbon atom bondedto a hydrogen atom, an aminogroup, an acid group, and an R-group. The R-group is any of20 arrangements of C, H, O, N,and S atoms, depending on, andgiving unique structure to, eachamino acid.

FIGURE 1.20Structures of two types of complex lipids. Glycerol joins with two fatty acids and a polarphosphate group to form a phospholipid (a) and (b). When phospholipids form membranes (c), thepolar head associates with water on the membrane surface, and the nonpolar tail faces the interiorof the membrane, away from water. Membranes prevent the cell contents from mixing with theexternal environment. Cholesterol (d), has a fused four-ring structure with additional side groups.Cholesterol is important in membrane structure, and the sex hormones are derived from it.

water

membrane

water

glycerol

phosphate

(b) phospholipid molecule (c) phospholipid membrane

polarhead

nonpolartails(fatty acids)

CH2 — N(CH3)3

——

CH2

C

—

CH2 — CH— CH2

O — P — O —

O

——

O

—

—O

O—

—

CH2

—

CH2

—

CH2

—

CH2

—

CH2

—

CH2

—

CH2

—

CH2

—

CH2

—

CH2

—

CH2

CH2

—

CH2

—

CH2

—

CH2

—

CH2

—

CH2

—

CH

—

CH

——

CH2

CH2

—

CH2

—

CH2

—

CH2

—

CH2

—

CH2

—

CH3

—

—

O

——

—— C O

—

——

—

CH2

—

CH2

—

CH2

—

CH2

—

CH2

—

CH2

—

CH3

hydr

ophi

lic h

ead

hydr

ophi

lic ta

il

(a) phospholipid structural formula

choline

fatty acids

glycerol

phosphate

CH3

HHH

CCCCCCH

H HH H

HHHHC

C H

CH3

HO

HH

HH

(d) cholesterol

SWP2618_CH01_020-049 10/4/04 10:59 AM Page 38


other (Figure 1.22a). Covalent bonds of this sort, formed between aminoacids, are called peptide bonds. Additional peptide bonds may form,resulting in a long chain of amino acids, or polypeptide (Figure 1.22b).Longer polypeptide chains form proteins; protein molecules range fromabout 50 to 3,000 amino-acid units. The type, number, and sequence of itsamino acids distinguishes a protein from all others.

The sequence of amino acids in a polypeptide chain forms the primary

structure (Figure 1.23a) of a protein. In most proteins, the chain folds ortwists to form local structures known as secondary structures (Figure1.23b). The most common secondary structures, alpha helices and betasheets, are stabilized by hydrogen bonds. More complex folding creates atertiary structure (Figure 1.23c), which usually is globular, or spherical.One of the major forces controlling how a protein folds is hydrophobicity,

or the tendency for nonpolar amino acids to avoid water. As a result,nonpolar amino acids tend to be buried inside folded proteins, where theyare shielded from contact with water. Some proteins have nonpolar aminoacids on the outside, where they can interact with lipid membranes.

The sequence of amino acids in a protein (primary structure) determinesits three-dimensional shape (secondary and tertiary structure). The tertiarystructure, in turn, determines a protein’s function. Each individual proteinhas a unique shape and, therefore, a specific function. A few proteins

FIGURE 1.22Formation of a polypeptide. A peptide bond forms when the acid group (—COOH) of oneamino acid joins to the amino group (—NH2) of another amino acid (a). The acid group losesan atom of hydrogen and an atom of oxygen. The amino group loses an atom of hydrogen.These atoms combine to form a water molecule. More peptide bonds can form in the sameway, joining a chain of amino acids to form a polypeptide (b).

glycine(amino acid)

alanine(amino acid)

acidgroup

aminogroup

variablegroup

glycylalanine(dipeptide)

peptide bond

polypeptide chain

a

bH

C

C

H

H

C

C

H

H

C

C

H

HH

C

CH3H

CO

OH= C

O

OH=C

HH

C

CO

OH=

C

HH3C

HOHH

N

HH

N

H H

N

H

H

CO

N

=

++

hydro- = water (Greek)-phobic = fear or dislike (Greek)tert- = third (Latin)quaterni- = four (Latin)

Hydrophobic molecules or parts ofmolecules do not mix easily withwater. Tertiary structure is the thirdlevel of protein structure;quaternary structure is the fourth level.

E T Y M O L O G Y

C O N N E C T I O N SC O N N E C T I O N SThe structure-function conceptis critical in understanding therelationship between chemistryand biology. Biological functiondepends on chemical structure.Biological molecules do whatthey do because of their uniquechemical structures.

SWP2618_CH01_020-049 10/4/04 11:00 AM Page 39


become active only when two or more tertiary forms combine to form acomplex quaternary structure (Figure 1.23d). Specific geometric andchemical interactions determine which surfaces of the proteins combine to create the quaternary structure.

1.10 Nucleic AcidsNucleic acids are macromolecules that dictate the amino-acid sequence

of proteins, which in turn control the basic life processes. Nucleic acids alsoare the source of genetic information in chromosomes, which are passedfrom parent to offspring during reproduction. Nucleic acids are thus thechemical link between generations, dating back to the beginning of life onEarth. How can one type of molecule play such a dominant role in all livingthings? The answer lies in the structure of the molecules.

Nucleic acids are made of relatively simple units called nucleotides

connected to form long chains. Each nucleotide consists of three parts. One part is a 5-carbon sugar (a pentose), which may be either ribose or deoxyribose. Compare the structural formulas in Figure 1.24. Whatdifferences can you see? Attached to the sugar is a nitrogen-containing base,

OH

deoxyribose

H

C

H

OHH

H

HO

H

H

H

OHO

H

OH

H

H

ribose

H

OH

R D

C

H

OHHO

FIGURE 1.24Two sugars found in nucleotides.Ribose and deoxyribose form ringstructures with four of their carbonatoms joined by an oxygen atom.The blue boxes highlight thedifference between the two sugars. Ribose has a hydroxylgroup (—OH), whereas deoxyribosehas only a hydrogen atom at thesame carbon. Compared to ribose,deoxyribose is missing one oxygenatom; deoxy in the name means“minus oxygen.”

FIGURE 1.23Stages in the development of afunctional protein. Only thebackbone atoms of the secondarystructures are shown, not the entireamino acid.

alpha helix

a primary structure

b secondary structure

c tertiary structure

d quaternary structure

amino acid sequence

beta sheet

alpha helix

bending betweenadjacent amino acids

active form of protein

several polypeptidescombine to formquaternary structure

SWP2618_CH01_020-049 10/4/04 11:00 AM Page 40


which is a single or double ringlike structure of carbon, hydrogen, andnitrogen (Figure 1.25). The third part of a nucleotide is a phosphate groupP (see Figure 1.26).

Nucleic acids that contain ribose in their nucleotides are calledribonucleic acids, or RNA. Nucleotides containing deoxyribose formdeoxyribonucleic acids, or DNA. In DNA, each of the four differentnucleotides contains a deoxyribose, a phosphate group, and one of the four bases—adenine, thymine, guanine, or cytosine. The possible DNA nucleotides that can form from these bases are illustrated in Figure 1.26. Figure 1.27 shows a chain of nucleotides connected to form a nucleic-acid molecule.

FIGURE 1.26The components of DNA. Each nucleotide contains one of the bases, one sugar, and onephosphate group. The sugar is deoxyribose, making these the four nucleotides of DNA.

G

O

CC

C

N

CN

HN

C

N

H

HNH2

H

O

CC

C

N

CN

HO

H

H

H

H

guanine

thymine

TC

cytosine H

NH2

CC

C

N

CN

HO

H

C

adenine

A

NH2

CC

C

N

CN

H

N

C

N

H

H

FIGURE 1.25Four nitrogen bases that occur in nucleotides. In this book, symbols are used to representthe nucleotides adenine, guanine, cytosine, and thymine. Note that cytosine and thymine havea single-ring structure; adenine and guanine have a double ring.

thymine nucleotide

T

adenine nucleotide

A

cytosine nucleotideguanine nucleotide

C

phosphatedeoxyribose

P

PP

P

PD

CG

C

C

G

T

A

T

P

P

P

P

P

P

FIGURE 1.27A short section of a model ofnucleic acid. The bases adenine,guanine, thymine, and cytosine are attached to a backbone ofalternating deoxyribose sugar and phosphate groups.

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42 UNIT 1 Energy, Matter, and Organization BSCSblue.com/check_challenge

P

P

uracilU

phosphate

R ribose

H

O

CC

C

N

CN

HO

H

H

uracil

uracil nucleotide

RU

FIGURE 1.28Another difference between DNA and RNA. In addition to containing ribose in place ofdeoxyribose, RNA contains uracil nucleotides in place of the thymine nucleotides found in DNA.

Check and Challenge1. Describe how building-block molecules combine to form each of the

four types of biological macromolecules.

2. What is the relationship between the primary and tertiary structureof a protein?

3. Describe the three-part structure of a nucleotide.

4. How do the chemical structures of ribose and deoxyribose differ?

RNA is a nucleic acid much like DNA, except that it contains the sugar ribose instead of deoxyribose. Also, in RNA the nitrogen base uracil, shown in Figure 1.28, replaces the base thymine. The other threebases, adenine, guanine, and cytosine, are the same in RNA and DNA.

Structurally, there is another difference between DNA and RNA. DNAalways occurs in cells as a double-stranded helix (Section 1.11); RNA issingle stranded, although it can fold into complex shapes. There are threetypes of RNA in cells, each of which performs a different role in thesynthesis of proteins.

The number and arrangement of the nucleotides vary in RNA as they doin DNA. The different arrangements of nucleotides in a nucleic acid providethe key to how these molecules contribute to the diversity of organismsliving on Earth.

BiologyBiology

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(bl)A. Barrington Brown/Science Source/Photo Researchers, (bc) Photo Researchers, (br)AP/Wide World Photos


Genetic Coding in Cells1.11 The Double Helix

In a short scientific paper published in 1953, James Watson and Francis Crick (Figure 1.29a and b) proposed a model for the structure of the DNA molecule that is still accepted today (although with somemodification). They founded their model on the principle of specific pairing of the nucleotides, shown in Figure 1.30. Hydrogen bonds form only between the nucleotide bases of adenine (A) and thymine (T) orcytosine (C) and guanine (G). In other words, there is a specific interactionbetween the surfaces of the nucleotide molecules. Experiments done byRosalind Franklin (Figure 1.29c) in the laboratory of Maurice Wilkins(Figure 1.29d) suggested to Watson and Crick that DNA molecules have adouble-helix structure.

The DNA double helix is composed of two long chains of nucleotides.The nucleotides of each chain are connected between their deoxyribosesugars by phosphate groups. (This forms a so-called sugar-phosphatebackbone.) The two chains run next to each other, but, chemically speaking,the sugar-phosphate backbones run in opposite directions. The two chainsare connected by hydrogen bonding between nitrogen bases to form a longdouble-stranded molecule. Because of the specific pairing between bases,

You can model a single helix bywrapping a pipe cleaner around a pencil.

CHEMISTRY TIPCHEMISTRY TIP

FIGURE 1.29The discoverers of the DNA structure. In 1953, James Watson (a), and Francis Crick (b),proposed a model for the DNA molecule based partly on the X-ray diffraction studies of RosalindFranklin (c), and Maurice Wilkins (d). Watson, Crick, and Wilkins shared the Nobel Prize in 1962.Franklin died in 1958 and was therefore not eligible for the Nobel Prize.

a, b c d

SWP2618_CH01_020-049 10/4/04 11:01 AM Page 43


each strand is the complement of the other. For example, a guanine on onestrand indicates the presence of cytosine on the other strand, and vice versa.(As you will see later, complementarity is the basis for copying DNA.) Thetwo strands intertwine, forming a double helix that winds around a centralaxis like a spiral staircase (Figure 1.31). As mentioned earlier, RNA also canfold into complex shapes, although those shapes result from interactionswithin a single-stranded molecule (or with proteins). Nonetheless, the foldsin RNA are held together by the same type of base pairing as in DNA (Figure 1.32).

1.12 The Functions of DNADNA forms the genes, units of genetic information, that pass from

parent to offspring. The structure of DNA explains how DNA functions as the molecule of genetic information. In brief, DNA stores information

nitrogen

carbon

hydrogen

oxygen

phosphorus

hydrogen bonds

other bonds

cytosine guanine thymine adenine

FIGURE 1.30A diagram showing the pairing of two nitrogen bases. Hydrogen bonds connect cytosine toguanine and thymine to adenine.

thymine nucleotide

T

adenine nucleotide

A

cytosine nucleotideguanine nucleotide

C

phosphatedeoxyribose

P

PP

P

PD

CG

C O N N E C T I O N SC O N N E C T I O N SThe observation that DNA is thegenetic material in all organismsis evidence of a commonevolutionary origin for life.

SWP2618_CH01_020-049 10/4/04 11:02 AM Page 44


FIGURE 1.32A model of a folded RNAmolecule, showing single- anddouble-stranded regions. Most ofthe molecule is single stranded, butthe shaded region shows hydrogenbonding between base pairs, whichforms a double-stranded region.Note the four bases in RNA.

FIGURE 1.31 The structure of DNA. Thebackbone of each chain (shown asribbons) is composed of alternatingsugar and phosphate molecules thatconnect the nucleotides. The twochains are held together by specificpatterns of hydrogen bondingbetween pairs of bases—A to T and G to C—and the chains coilaround a central axis to form adouble helix. The diameter of thedouble helix is equal along its lengthbecause a double-ring A or G base(called purines) always pairs with asingle-ring T or C base (calledpyrimidines). There are tennucleotides per turn of the helix,and only a small portion of a modelof a DNA molecule is shown.

G

G

G

G

GC

CC

C

C

C

C

C

C

C

A

A

A

A

A

A

A

AA

A

A

A

A

A

T

T

T

T

T

T

T

T

T

TT

T

T

T

T

GG

G

GG

sugar-phosphatebackbone

base

hydrogenbonds

G

G

G

G

G

GG

G

G

G

CC

C

C

C

C

C

C

A

A

A

A

A

A

A

A

A

U

U

U

U

U

U

U

U

sugar-phosphatebackbone

bases

in a code consisting of units that are three nucleotides long; these shortsequences are called triplet codons. Certain codons are translated by the cell to mean certain amino acids. For example, the codon GGA meansglycine when translated by the cell. Thus the sequence of nucleotides inDNA can indicate a sequence of amino acids in protein. As you have seen,the sequence of amino acids in a protein determines its shape, which then

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46 UNIT 1 Matter, Energy, and Organization

The Scanning TunnelingMicroscope

Electron microscopes are powerful tools forexploring the structure of microscopic objects suchas cells. Unlike light microscopes, which use lightand glass lenses to make details visible, electronmicroscopes use electron beams and magneticcoils. Electron microscopes permit much greatermagnification of cellular structures than do lightmicroscopes. The scanning tunneling microscopeuses electrons already in the sample, rather thanan external electron beam. This allows scientiststo see surface structures clearly. A characteristicof all materials is that some electrons form anelectron cloud around the material. The scanningtunneling microscope probes this electron cloudto reveal structure.

To scan the surface of a sample, the tip of themicroscope (a needle) is pushed toward the sampleuntil the electron clouds of the tip and the sampletouch. Then an electric voltage is applied betweenthe tip and the sample, causing electrons to flowthrough a narrow channel in the electron clouds.This electron flow is called the tunneling current.The tunneling current is extremely sensitive tothe distance between the microscope tip andthe surface of the sample and allows precisemeasurements of the vertical surface features ofthe sample. A feedback mechanism maintains thetip at a constant height as it sweeps across thesample surface, following the contours of thesurface atoms. The motion of the tip is read andprocessed by a computer and displayed on ascreen. A three-dimensional image of the surfaceis obtained by sweeping the tip in parallel lines (seeFigure 1.33). To achieve high-resolution images ofsurface structures, the microscope must be shieldedfrom even the smallest of vibrations, such as afootstep or sound.

Investigators probing the structure of DNA havegenerated images depicting the helical twists andturns of a strand of DNA (Figure 1.34). Becausescanning tunneling microscopes can operate equallywell with samples in air or liquid, the DNA can beobserved under normal atmospheric conditions. (Inan electron microscope, samples must be observed in a vacuum.)

FIGURE 1.33Mechanism of the scanning tunneling microscope. Theshape of the electron cloud above a surface reveals themolecular structure of the surface.

scanningneedle

scanningneedle tip computer screen

sam

ple

electron cloud

surface of sample

FIGURE 1.34A DNA molecule seen with the scanning tunnelingmicroscope, (�2,000,000). The microscope reveals the shapeof the DNA molecule.


T E C H N O L O G Y

(b)Driscoll, Youngquist & Baldeschwieler, Caltech/SPL/Photo Researchers

SWP2618_CH01_020-049 10/4/04 11:03 AM Page 46


Check and Challenge1. What determines which nitrogen bases form pairs in DNA?

2. If one DNA strand has the sequence AGTTC, what is the sequence ofthe opposite, or complementary, strand?

3. List four life processes in which DNA plays an important role.

copiesof genes

are composed of

stores

is translatedthrough

is copiedthrough

produce produces

functionin arise through arise through

genes

DNA

geneticinformation

RNA synthesisand

protein synthesisDNA synthesis

growth cells mutations

basic unitof life

newgenes

are

affect

metabolism

affect

recombination

developmentstructure

and function

may produce

evolution reproduction

can affect can affect

affecthave

coordinated

proteins

FIGURE 1.35Functions of DNA. This concept map summarizes the major cellular processes that involveDNA. Note that both the information stored in the structure of DNA and the copying of thatinformation during DNA synthesis have important effects on the life of a cell.

determines function. Proteins perform most of the chemical reactions thatkeep cells alive. The structure of DNA also accounts for its ability to becopied and passed through inheritance from one generation to the next. You will learn more about these processes in later chapters, but for now they are summarized in the concept map in Figure 1.35.

BiologyBiology

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48 UNIT 1 Energy, Matter, and Organization48 UNIT 1 Energy, Matter, and Organization BSCSblue.com/vocabulary_puzzlemaker

Summary

Chemical reactions occur continuously in cells,the basic units of life. Cells carry out their biologicalfunctions through chemical reactions. Elements arematerials that cannot break down into substanceswith new or different properties. They are the basicchemical form of matter. Atoms contain acharacteristic number of positively charged protons,negatively charged electrons, and neutral neutrons.All elements are composed of atoms. Ions are atomsor molecules that have gained or lost electrons; ionshave a positive or negative charge. Chemical bondshold atoms together to form molecules. When thosebonds involve the sharing of electrons, the bonds arecalled covalent bonds. When those bonds involve theattraction of two oppositely charged ions, the bondsare called ionic bonds. Weak bonds involving apartially positive hydrogen atom are called hydrogenbonds.

In chemical reactions, molecules interact andform different substances. Those interactions areaccompanied by energy changes that drive thereactions living cells use for growth, reproduction,and all other functions. The membranes thatsurround cells enclose the chemical reactions of thecells and isolate them from the outsideenvironment.

Organisms contain four major types ofmacromolecules. Carbohydrates store and transferenergy in cells and contribute to cell structure.Lipids store energy and form a major part ofmembranes. Proteins are structural components ofcells, enzymes, and messengers and receivers ofmessages. The nucleic acids DNA and RNA store,transfer, and direct the expression of geneticinformation. Chemical compounds have biologicalactivity because of their specific chemical structures.Chemical structure dictates biological function.

Key Concepts

Below is the beginning of a concept map. Use theconcepts that follow to build a more complete map.Add as many other concepts from the chapter as youcan. Include appropriate linking words.

• atoms • lipids• carbohydrates • macromolecules• chemical bonds • molecules• chemical reactions • nucleic acids• elements • proteins

Reviewing Ideas

1. What type of information does the periodic tableof elements provide?

2. State in your own words the relationship amongatoms, protons, neutrons, and electrons.

3. What are isotopes and why are they biologicallyimportant?

4. How does an ion differ from the atom fromwhich it was formed?

5. Compare ionic, nonpolar covalent, and polarcovalent bonds.

6. What is the importance of water in cells?7. What is meant by pH, and how does pH affect

cells and cellular processes?

are made of

may be may be

organisms

chemicals

inorganic organic

HIGHLIGHTSC h a p t e r

HIGHLIGHTS

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8. Describe the structure of an amino acid. Whattype of bond forms the link between aminoacids?

9. What are the building blocks of nucleic acids?Why are nucleic acids important in biology?

10. Why are lipids important to cell structure andfunction?

Using Concepts

1. Using simple molecular models, draw theelectric attractions that allow sodium andchloride ions to dissolve in water. (Hint:Represent water as in Figure 1.9.)

2. Distinguish between amino acids and peptidesand between simple peptides and polypeptides.

3. You are an analytical chemist working in anutritional analysis laboratory. Someone bringsyou a tropical food made of only one type ofmacromolecule. How would you determinewhether it is carbohydrate, fat, protein, ornucleic acid? (Reference: Investigation 1B)

4. You are given two samples of carbohydrates.One contains 6 carbon atoms per molecule(molecular formula C6H12O6), and the othercontains 12 carbon atoms (C12H22O11). Whichone is glucose and which one is sucrose?Explain your answer.

5. Animals usually store energy reserves as lipids;plants store them as polysaccharides. What isthe advantage to animals of using lipids asstorage molecules?

6. Margarine is produced by hydrogenating liquidvegetable oils so that they become solids likebutter. What chemical change has taken place inthe fatty acids?

Synthesis

Fat is more abundant in some cells of your bodythan in other cells. Explain how natural selectioncould account for that variation.

Extension

DNA is the source of genetic information for allliving organisms, but the sequence of DNAnucleotides in organisms differs. In fact, thesequences of DNA can be characteristic for differentspecies. If you were to compare the sequence ofDNA nucleotides of similar and dissimilar organisms,what patterns would you observe? How is thisevidence of evolutionary relatedness?

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Web Resources

Visit BSCSblue.com to access• Resources to help you understand important

chemical concepts and the chemical basis of life• Explanations and self-tests on biochemistry

and an explanation of the chemical basis ofyour sense of taste and smell

• Web links related to this chapter

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Chapter1 The Chemistry of Life.pdf

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