Carbon anthe MolecDiversityKEY CONCEPTS

... Figure 4.1 What properties of carbon underlie its roleas the molecular basis of life'?

4.1 Organic chemistry is the study of carboncompounds

4.2 Carbon atoms can form diverse molecules bybonding to four other atoms

4.3 Asmall number of chemical groups are key tothe funclioning of biological molecules

is the studyof carbon compounds

Although water is the universal medium for life onEarth, living organisms. such as the plants and trilo-bite beetle in Figure 4.1, are made up of chemicals

that are based mostly on the element carbon. Carbon entersthe biosphere through the action of plants, which use solarenergy to transform atmospheric CO2 into the molecules oflife. These molecules are passed along to animals that feedon plants.Of all chemical elements, carbon is unparalleled in its ability

to form molecules that are large. complex, and diverse. and thismolecular diversity has made possible the diversity of organ-isms that have evolved on Earth. Proteins, DNA, carbohy-drates. and othermolecules that distinguish livingmatter frominanimate material are all composed ofcarbon atoms bondedto one another and to atoms ofother elements. Hydrogen (H),oxygen (0), nitrogen (I\T), sulfur (S), and phosphorus (P) areothercommon ingredientsofthese compounds, but it is theel-ement carbon (C) that accounts for the large of bio-logical molecules.Proteins and other very large molecules are the main focus

of Chapter 5. Here we investigate the properties of smallermolecules. We will use these molecules to illustrate conceptsofmolecular architecture that will help explain why carbon isso important to life. at the same time highlighting the themethat emergent properties arise from the organization ofmat-ter in living organisms.

58

For historical reasons, compounds containing carbon are saidto be organic, and the branch ofchemistry that specializes inthe study ofcarbon compounds is called organic chemistry.Organic compounds range from simple molecules. such asmethane (CKt), to colossal ones, such as proteins, with thou-sands of atoms. Most organic compounds contain hydrogenatoms in addition to carbon atoms.Theoverall percentages ofthe majorelements oflife-C, H,

0, N. S. and P-are quite uniform from one organism to an·other. Because ofcarbon's versatility. however, this limited as-sortment ofatomic building blocks, taken in roughly the sameproportions, can be used to build an inexhaustible variety oforganic molecules. Different species oforganisms, and differ-ent individuals within a species. are distinguished by varia-tions in their organic molecules.Since the dawn of human history, people have used other

organisms as sources of valued substances-from foods andmedicines to fabrics. The science oforganic chemistry origi-nated in attempts to purify and improve the yield of suchproducts. By the early IBOOs, chemists had learned to makemany simple compounds in the laboratory by combining ele·ments under the right conditions. Artificial synthesis of thecomplex molecules extracted from living matter seemed im-possible. however. At that time. the Swedish chemist JonsJakob Berzelius made the distinction between organic com-pounds. those thought to arise only in living organisms, andinorganic compounds, those found only in the nonliVingworld. Vitalism. the belief in a life force outside the jurisdic-tion of physical and chemical laws, provided the foundationfor the new discipline oforganic chemistry.

--Electrode

./........

.--.:'-., Coldwater

Cooled watercontainingorganicmolecules

t

In ui

OThecontained a mixture ofhydrogen gas (H2), methane 0 Sparks were(CH4), ammonia (NH3), and discharged to mimicwater vapor. olig,hc'c'O"O''i' _

---------- "Atmosphere"-------.. CH, /

( Water vapor .....

...,......Condenser

OThe watermixture in the

flask washeated; vaporentered the"atmosphere"flask.

\

•

Can organic molecules form under conditionsbelieved to simulate those on the early Earth?

" IHp I';0'"

,., /amPle for

/ analYSIS

4) As material cycled 'O"AC,CoC,CdC,",C"c,C,CooC,C,3d-through the apparatus, the atmosphere, rainingMiller periodically collected water and any dissolvedsamples for analysis. molecules down into the

sea flask.

In 1953. Stanley Miller set up a closed systemto simulate conditions thought to have existed on the early Earth,A flask of water simulated the primeval sea. The water washeated so that some vaporized and moved into asecond, higherflask containing the "atmosphere"-a mixture of gases. Sparkswere discharged in the synthetic atmosphere to mimic lightning.

EXPERIMENT

RESULTS Miller identified a variety of organic moleculesthat are common in organisms. These included simple com-pounds such as formaldehyde (CHlO) and hydrogen cyanide(HCN) and more complex molecules such as amino acids and longchains of carbon and hydrogen known as hydrocarbons.

Chemists began to chip away at the foundation of vitalismwhen they finally learned to synthesize organic compounds inlaboratories. In 1828, Friedrich Wohler, a German chemistwho had studied with Berzelius, attempted to make an "inor-

salt, ammonium cyanate, by mixing solutions of am-monium ions (NH4+) and cyanate ions (CNO-). Wohler wasastonished to find that instead he had made urea, an organiccompound present in the urine of animals. Wohler chal-lenged the vitallsts when he wrote, "I must tell you that 1canprepare urea without requiring a kidney or an animal, eitherman or dog:' However, one of the ingredients used in the syn-thesis, the cyanate, had been extracted from animal blood,and the vitalists were not swayed byWohler's discovery. A fewyears later, however, Hermann Kolbe, a student ofWohler's,made the organic compound acetic add from inorganic sub-stances that could be prepared directly from pure elements.Vitalism crumbled completely after several decades of lab-

oratory synthesis of some increasingly complex organic com-pounds. In 1953, Stanley Miller, a graduate student of HaroldUrey at the University of Chicago, helped bring this abiotic(nonliving) synthesis of organic compounds into the contextof evolution in a classic experiment described in Figure 4.2.Miller's experiment, testing whether complex organic mole-cules could arise spontaneously under conditions thought tohave existed on the early Earth, stimulated interest and furtherresearch on the origin oforganic compounds. Some scientistshave questioned whether the gases Miller used as starting ma-terials were really present in the primitive Earth's atmosphere.Recent work supports a slightly different recipe for earlyEarth's conditions; when used in the experiment, it led to thecompounds Miller found. Although the jury is still out, theseexperiments support the idea that abiotic synthesis of organiccompounds could have been an early stage in the origin ofHfe.The pioneers of organic chemistry helped shift the main-

stream of biological thought from vitalism to mechanism, theview that physical and chemical laws govern all natural phe-nomena, including the processes of life. Organic chemistry wasredefined as the study of carbon compounds, regardless of ori-gin. Organisms produce most ofthe naturally occurringorganiccompounds, and these molecules represent a diversity andrange of complexity unrivaled by inorganic compounds. How-ever, the rules of chemistry apply to all molecules. The founda-tion of organic chemistry is not some intangible life force, butthe unique chemical versatility of the element carbon.

CONCEPT CHECK

SOURCE

4.1I. What conclusion did Stanley Miller draw when hefound amino acids in the products of his experiment?

2. _','!:tnl. \'V'hen Miller tried the experiment inFigure 4.2 without the electrical discharge, no organiccompounds were found. What might explain this result?

For suggested answers. see Appendix A.

CONCLUSION OrganIC molecules, a first step in the origin oflife. may have been syntheSized abiotically on the early Earth (Wewill explore this hypothesis in more detail in Chapter 25.)

S. Milll'l", A produaion of amino ilCids undl'l" possiblepnmltive Earth conditIons. Science 11752&-529 (1953),

_'WU". If Miller had increased the concentration of NH] inhis experiment, how might the relative amounts of the productsHCN and CH20 have differed?

fOU Carbon and the Molecular Diversity of Life 59

can form diversemolecules by bonding to fourother atoms

The key to an atom's chemical characteristics is its electronconfiguration. This configuration determines the kinds andnumber of bonds an 3tom will form with other atoms.

The Formation of Bonds with CarbonCarbon has 6 electrons, with 2 in the first electron shell and 4in the second shell. Having 4 valence electrons in a shell thatholds 8, carbon would have to donate or accept 4 ele<trons tocomplete its valence shell and become an ion. Instead, a car-bon 3tom usually completes its valence shell by sharing its 4electrons with other atoms in covalent bonds so that 8 elec-trons are present. These bonds may include single and doublecovalent bonds. Each carbon atom thus acts as an intersectionpoint from which a molecule can branch offin as many as fourdirections. This letravalence is one facet ofcarbon's versatilitythat makes large, complex molecules possible.When a carbon atom forms four single covalent bonds,

the arrangement of its four hybrid orbitals causes the bondsto angle toward the corners of an imaginary tetrahedron(see Figure 2.l7b). The bond angles in methane (CH1) are109.5" (figure 4.3a), and they are roughly the same in anygroup ofatoms where carbon has four single bonds. For exam-ple, ethane is shaped like two overlapping tetrahedrons

(figure 4.3b). In molecules with more carbons, every group-ing of a carbon bonded to four other atoms has a tetrahedralshape. But when two carbon atoms are joined by a doublebond, all bonds around those carbons are in the same plane.For example, ethene isa flat molecule; its atoms all lie inthe same plane (figure 4.3c).We find it convenient to write allstructural formulas as though the molecules represented wereflat, but keep in mind that molecules are three-dimensionaland that the shape ofa molecule often determines its function.The electron configuration ofcarbon gives it covalent com-

patibility with many different elements. figure 4.4 shows thevalences of carbon and its most frequent partners-oxygen,hydrogen, and nitrogen. These are the four major atomic com-ponents oforganic molecules. These valences are the basis forthe rules ofcovalent bonding in organic chemistry-the build-ing code for the architecture oforganic molecules.Let's consider how the rules of covalent bonding apply to

carbon atoms with partners other than hydrogen. We'll look attwo examples, the simple molecules carbon dioxide and urea.In the carbon dioxide molecule (C02), a single carbon atom

is joined to two atoms of oxygen by double covalent bonds.The structural formula for CO2 is shown here:

o=c=oEach line in a structural formula represents a pair of sharedelectrons. The two double bonds formed by the carbon atomare the equivalent of four single covalent bonds. The arrange-ment completes the valence shells ofall atoms in the molecule.Because CO2 is a very simple molecule and lacks hydrogen, itis often considered inorganic, even though it contains carbon.

Name and Comment

(a) Methane. When acarbonatom has four single bonds toother atoms, the molecule istetrahedral,

(b) Ethane. A molecule may havemore than one tetrahedralgroup of single'bondedatoms. (Ethane consists oftwo such groups.)

(el Ethene (ethylene). Whentwo carbon atoms are Joinedby a double bond. all atomsattached to those carbonsare in the same plane; themolecule is flat.

MolecularFormula

CH,

StructuralFormula

HI

H-(-HIH

H HI I

H-(-(-HI IH H

Ball-and-StickModel

Space·FillingModel

.... Figure 4.3 The shapes of three simple organic molecules.

60 UNIT ONE TheChemistryofLife

Urea

oIIH C H'N/ 'N/

I IH H

Hydrogen Oxygen Nitrogen Carbon(valence" I) (valence" 2) (valence" 3) (valence" 4)

® - - -H· ·0: ·N· ·c·... Figure 4.4 Valences of the major elements of organicmolecules. Valence is the number of covalent bonds an atom canform. It is generally equal to the number of electrons required tocomplete the valence (outermost) shell (see Figure 2.9). All theelectrons are shown for each atom in the eledron distributiondia9rams (top). Only the electrons in the valence shell are presented inthe Lewis dot structures.',U.JIiMiI Refer to Figure 2.9 and draw the Lewis dot structures forsodium, phosphorus, sulfur, and chlorine.

\Vhether we call CO2 organic or inorganic, however, it isclearly important to the living world as the source of carbonfor all organic molecules in organisms.Urea, CO(NH2h. is the organic com-

pound found in urine that Wohler synthe-sized in the early 1800s. The structuralformula for urea is shown at the right.Again, each atom has the required num-ber of covalent bonds. In this case, onecarbon atom is involved in both single anddouble bonds.Urea and carbon dioxide are molecules with one carbon

atom. But as Figure 4.3 shows, a carbon atom can also useone or more valence electrons to form covalent bonds toother carbon atoms, linking the atoms into chains of seem-ingly infinite variety.

Molecular Diversity Arising from CarbonSkeleton VariationCarbon chains form the skeletons of most organic molecules(Figure 4.5). The skeletons vary in length and may be straight,branched, or arranged in closed rings. Some carbon skeletonshave double bonds, which vary in number and location. Suchvariation in carbon skeletons is one important source of themolecular complexity and diversity that characterize livingmatter. In addition, atoms ofother elements can be bonded tothe skeletons at available sites.

Hydrocarbons

All of the molecules that are shown in Figures 4.3 and 4.5 arehydrocarbons, organic molecules consisting of only carbonand hydrogen. Atoms of hydrogen are attached to the carbonskeleton wherever electrons are available for covalent bonding.Hydrocarbons are the major components of petroleum, whichis called a fossil fuel because it consists of the partially decom-posed remains oforganisms that lived millions ofyears ago.Although hydrocarbons are not prevalent in living organ-

isms, many of a cell's organic molecules have regions consist-ing of only carbon and hydrogen. For example, the moleculesknown as fats have long hydrocarbon tails attached to a non-hydrocarbon component (Figure 4.6, on next page). Neitherpetroleum nor fat dissolves in water; both are hydrophobiccompounds because the great majority of their bonds are rel-atively nonpolar carbon-to-hydrogen linkages. Another char-acteristic of hydrocarbons is that they can undergo reactionsthat release a relatively large amount of energy. The gasolinethat fuels a car consists of hydrocarbons, and the hydrocarbontails of fat molecules serve as stored fuel for animal bodies.

H H H H H H H H H HI

H c-( H H H H ( C ( ( H H C-C-C-C H, ,H H H H H H H HEthane Propane I-Butene 2-Butene

(a) length. Carbon vary in length.(c) Double bonds. The may have double bonds, which

can vary in location.

HCyclohexane Benzene

(d) Rings. Some carbon are arranged in rings. In theabbreviated structural formula for each compound (at the rightl.each corner represents a carbon and its attached hydrogens

H

H

HoH

H HH H H H H HI

H -C-(- H H HH H H H

Butane

(b) Branching. Skeletons may be unbranched or branched.

... Figure 4.5 Variations in carbon skeletons. Hydrocarbons. organic molecules consisting only of carbon andhydrogen. illustrate the diversity of the carbon skeletons of organic moleCllles.

fOU Carbon and the Molecular Diversity of Life 61

(a) Structural isomers differ in covalent partners, as shown inthis example of two isomers of (sH ll: pentane (left) and2-methyl butane (right),

Fat droplets (stained red)

H H H H HI I I I I

H-(-(-(-(-(-HI I I I IH H H H H

HI

H-(-HIH-(-H

H I HI IH-(-(-(-H

I I IH H H

(b) Geometric isomers differ in arrangement about a doublebond, In these diagrams. X represents an atom or group ofatoms attached to a double·bonded carbon,

t--<100l!m

(a) Mammalian adipose cells (b) A fat molecule

.... Figure 4.6 The role of hydrocarbons in fats. (a) Mammalianadipose cells stockpile fat molecules as a fuel reserve, Each adipose cell inthis micrograph is almost filled by a large fat droptet. which contains ahuge number of fat molecules, (h) Afat molecule consists of a small,noohydrocarbon component joined to three hydrocarbon tails. The tailscan be broken down to provide energy They also account for the hydro-phobic behavior of fats. (Black '" carbon: gray'" hydrogen; red '" oxygen.)

Isomers

x X, /C-c

/ "-H H

cis isomer: The two XS are onthe same side.

H X, /C-c

/ "-X H

trans isomer: The two XS are onopposite sides

... Figure 4.7 Three types of isomers. Compounds with thesame molecular formula but different structures, isomers are asourceof diversity in organic molecules,'·Jir.W"1 There are three structural isomers of CSHI2; draw theone not shown in (a).

(c) Enantiomers differ in spatial arrangement around anasymmetric carbon. resulting in molecules that are mirrorimages. like left and right hands. The two isomers aredesignated the Land 0 isomers from the Latin for leftand right (kvo and dextral, Enantiomers cannot besuperimposed on each other,

o isomerllsomer

change of rhodopsin, a chemical compound in the eye, fromthe cis isomer to the trans isomer (see Chapter SO).Enantiomcrs are isomers that are mirror images of each

other. In the ball·and-stick models shown in Figure 4.7(, themiddle carbon is called an asymmetric carbon because it is at-tached to four different atoms or groups of atoms. The fourgroups can be arranged in space around the asymmetric carbonin two different ways that are mirror images. Enantiomers are, inaway, left-handed and right-handedversions ofthe molecule. Justas your right hand won't fit into a left-handed glove, the workingmolecules inacell candistinguish the twoversions byshape. Usu-ally, one isomer is biologically active, and the other is inactive.Theconceptofenantiomers is important in the pharmaceutical

industrybecause the twoenantiomersofadrugmaynot beequally

Variation in the architecture oforganic molecules can be seenin isomers, compounds that have the same numbers ofatomsof the same elements but different structures and hence dif-ferent properties. Compare, for example, the two five-carboncompounds in Figure 4.7a. Both have the molecular formulaCsH l:b but they differ in the covalent arrangement oftheir car-bon skeletons. The skeleton is straight in one compound butbranched in the other. We will examine three types of isomers:structural isomers, geometric isomers, and enantiomers.Structural isomers differ in the covalent arrangements of

their atoms. The number ofpossible isomers increases tremen-dously as carbon skeletons increase in size. There are only 3forms of CSHI2 (2 are shown in Figure 4.7a), but there are 18variations ofCsH18 and 366,319 possible structural isomers ofCwl-42' Structural isomers may also differ in the location ofdouble bonds.Geometric isomers have the same covalent partnerships,

but they differ in their spatial arrangements. The differencesarise from the inflexibility ofdouble bonds. Single bonds allowthe atoms they join to rotate freely about the bond axis with-out changing the compound. In contrast, double bonds do notpermit such rotation, resulting in the possibility ofgeometricisomers. Ifa double bond joins two carbon atoms, and each Calso has two different atoms (or groups of atoms) attached toit, then two distinct geometric isomers are possible. Considera simple molecule with t\'>'O double-bonded carbons, each ofwhich has an H and an X attached to it (Figure 4.1b). Thearrangement with both Xs on the same side of the doublebond is called a cis isomer, and the arrangement with the Xson opposite sides is called a trans isomer. The subtle differ-ence in shape between geometric isomers can dramaticallyaffect the biological activities oforganic molecules. For exam-ple, the biochemistry of vision involves a light-induced

62 UNIT ONE TheChemistryofLife

For suggested answers, see Appendix A.

OHCH,Testosterone

o

Estradiol CH H,

HO

The Chemical Groups Most Importantin the Processes of life

.. Figure 4.9 Acomparison of chemical groups of female(estradiol) and male (testosterone) sex hormones. The twomolecules differ only in the chemical groups attached to a commoncarbon skeleton of four fused rings, shown here in abbreviated form.These subtle variations In molecular architecture (shaded in blue)influence the development of the anatomical and physiologICaldifferences between female and male vertebrates.

underlying framework for more complex organic molecules.A number ofchemical groups can replace one or more of thehydrogens bonded to the carbon skeleton of the hydrocarbon.(Some groups include atoms of the carbon skeleton, as we willsee.) These groups may participate in chemical reactions ormay contribute to function indirectly by their effects onmolecular shape. The number and arrangement of the groupshelp give each molecule its unique properties.

Consider the differences between testosterone and estradiol(a type of estrogen). These compounds are male and femalesex hormones, respectively, in humans and other vertebrates(Figure 4.9). Both are steroids, organic molecules with acom-mon carbon skeleton in the form of four fused rings. Thesesex hormones differ only in the chemical groups attached tothe rings. The different actions of these m'o molecules onmany targets throughout the body help produce the contrast-ing features ofmales and females. Thus, even our sexuality hasits biological basis in variations of molecular architecture.In the example of sex hormones, different chemical groups

contribute to function by affecting the molecule's shape. Inother cases, the chemical groups affect molecular function bybeing directly involved in chemical reactions; these importantchemical groups are known as functional groups. Each func-tional group participates in chemical reactions in a character-istic way, from one organic molecule to another.The seven chemical groups most important in biological

processes are the hydroxyl, carbonyl, carboxyl, amino,sulfhydryl, phosphate, and methyl groups. The first six groupscan act as functional groups; they are also hydrophilic and thusincrease the solubility of organic compounds in water. Themethyl group is not reactive, but instead often acts as a recog-nizable tag on biological molecules. Before reading further,study Figure 4.10 on the next two pages to familiarize yourselfwith these biologically important chemical groups.

5-Albuterol

R-Ibuprofen

IneffectiveEnantiomer

5-lbuprofen

4.2

R-Albuterol

EffectiveEnantiomer

Asthma

Condition

Pain;inflammation

CONCEPT CHECK

Albuterol

Ibuprofen

Drug

I. Draw a structural formula for C:2H.t.2. \\fhich molecules in Figure 4.5 are isomers? For eachpair, identify the type of isomer.

3. How are gasoline and fat chemically similar?4. -W:rUI• Can propane (C3Hs) form isomers?

effective (Figure 4.8). In some cases, one ofthe isomers mayevenproduce harmful effects. Thiswas the casewith thalidomide, adrugprescribed for thousands ofpregnantwomen in the late 1950sandearly 1960s. The drug ""'as a mixture of two enantiomers. Oneenantiomer reduced morning sickness, the desired effect, but theother causedseverebirthdefects. (Unfortunately, even ifthethalidomide enantiomer is used in purified form, some of it soonconverts to the enantiomer in the patient's body.) TIle differ-ingeffects ofenantiomers in the body demonstrate that organismsare sensitive to even the most subtle variations in molecular archi-tecture. Once again, we see that molecules have emergent proper-ties that depend on the specific arrangementoftheir atoms.

of chemicalgroups are key to the functioningof biological molecules

The distinctive properties ofan organic molecule depend notonly on the arrangement of its carbon skeleton but also on themolecular components attached to that skeleton. \X'e canthink ofhydrocarbons, the simplest organic molecules, as the

.. Figure 4.8 The pharmacological importance ofenantiomers. Ibuprofen and albuterol are examples of drugs whoseenantiomers have different effects (5 and Rare letters used in onesystem to distinguish two enantiomers.) Ibuprofen reducesinflammation and pain. It is commonly sold as a mixture of the twoenantiomers, The 5enantiomer is 100 times more effective than theother, Albuterol is used to relax bronchial muscles, improving airflow inasthma patients. Only R·albuterol is synthesized and sold as a drug; the5 form counteracts the active Rform,

fOU Carbon and the Molecular Diversity of Life 63

.. f9n4.10

Exploring Some Biologically Important Chemical Groups

Carbonyl

The carbonyl group (XO) consinsof a carbon atom joined to anoxygen atom by a double bond.

CHEMICALGROUP

STRUCTURE

Hydroxyl

._.I 0H

(may be wnnen HO-)

In a hydroxyl group (-oH), ahydrogen atom is bonded to anoxygen atom, which in turn isbonded to the carbon skeleton ofthe organic molecule. (Do notconfuse this functional group withthe hydroxide ion, OH .)

•-- l-(

\

Carboxyl

•--• ....1

When an oxygen atom is double-bonded to a carbon atom that isalso bonded to an -oH group,the entire assembly of atoms iscalled a carboxyl group (-COOH).

NAME OFCOMPOUNO

EXAMPLE

Alcohols (their specific namesusually end in-of)

H HI I

H-(-(-OHI IH H

Ethanol, the alcohol present inalcoholic beverages

Ketones if the carbonyl group iswithin a carbon skeleton

Aldehydes if the carbonyl groupis at the end of the carbonskeleton

H °I #H-C-CI C.......HH H....... \

H

Acetone, the simplest ketoneH H 0I I #H-C-C-CI I \H H H

Prooanal. an aldetwde

carboxylic acids, or organic acids

H °I #H-C-C

I 'oHHAcetic acid, which gives vinegar itssour taste

• Has acidic properties (is asource of hydrogen ions)because the covalent bondbetween oxygen and hydrogenis so polar; for example,

FUNCTIONALPROPERTIES

• Is polar as a result of theelectrons spending more timenear the electronegativeoxygen atom.

• Can form hydrogen bonds withwater molecules, helpingdissolve organic compoundssuch as sugars (see Figure 5.3).

• A ketone and an aldehyde maybe structural isomers withdifferent properties, as is thecase for acetone and propanal.

• These two groups are alsofound in sugars, giving rise totwo major groups of sugars:aldoses (containing analdehyde) and ketoses(containing a ketone).

HI l

H-C-CI 'oHH

AcetIC acid

H °I #I \H 0-

Acetate IOfl

64 UNIT ON! TheChemistryorUre

• Found in cells in the ionizedform with a charge of 1- andcalled a carboxylate ion (here,specifically, the acetate ion).

Amino Sulfhydryl Phosphate Methyl

HI

-N

'"I

-SH

(may bewritten HS -) •• ••.. -o-p-o-

I0-

HI-(-HIH

The amino group(-NH2) consists of anitrogen atom bondedto two hydrogen atomsand to the carbonskeleton,

Amines

o H HI I

(-(-N

He! \Glycine

Because it also has acarboxyl group, glycineis both an amine anda carboxylic acid;compounds with bothgroups are calledamino acids.

The sulfhydryl groupconsists of a sulfur atombonded to an atom ofhydrogen; resembles ahydroxyl group in shape.

Thiols

Cysteine is an importantsulfur-containing aminoacid.

In a phosphate group, aphosphorus atom is bonded tofour oxygen atoms; one oxygen isbonded to the carbon skeleton;two oxygens carry negativecharges. The phosphate group(-OPOl'-, abbreviated P) is anionized form of a phosphoric acidgroup (-OPOlH.; note the twohydrogens).

Organic phosphates

OHOHH 0I I I II

H-(-(-C-O-P-O-I I I IH H H 0-

Glycerol phosphate

In addition to taking part inmany important chemicalreactions in cells, glycerolphosphate provides thebackbone for phospholipids,the most prevalent molecules incell membranes.

Amethyl group consists of acarbon bonded to threehydrogen atoms. The methylgroup may be attached to acarbon or to a different atom.

Methylated compounds

NH,I

H........ -pC, /(H3

7 ic Co-p ........N/ 'HIH

5-Methyl cytidine

5-Methyl cytidine is acomponent of DNA that hasbeen modified by addition ofthe methyl group.

• Ionized, with acharge of 1+, undercellular conditions.

• Acts as a base; canpick up an W fromthe surroundingsolution (water, inliving organisms).

n Given the information in this figure and what you know about.. the electronegativity of oxygen, predict which of the following

molecules would be the stronger acid. Explain your answer.

;"-N

'"(nonionizedl

HI

-+N-HIH

(ionized)

• Two sulfhydryl groupscan react, forming acovalent bond. ThisHcross-linkingH helpsstabilize proteinstructure (seeFigure 5,21),

• Cross-linking ofcysteines in hairproteins maintains thecurliness or straightnessof hair. Straight hair canbe HpermanentlyH curledby shaping it aroundcurlers, then breakingand re-forming the cross-linking bonds.

• Contributes negative chargeto the molecule of which it isa part (2- when at the end ofa molecule, as above; 1-when located internally in achain of phosphates).

• Has the potential to reactwith water, releasing energy.

a, H H 0I I Ii

H-(-(-(I I 'OHH H

• Addition of a methylgroup to DNA, or tomolecules bound to DNA,affects expression of genes.

• Arrangement of methylgroups in male and femalesex hormones affects theirshape and function (seeFigure 4.9).

b. H 0 aI II I;

H-(-(-(I 'OHH

fOU Carbon and the Molecular Diversity of Life 65

1. What does the term amino acid signify about thestructure of such a molecule?

2. What chemical change occurs when ATr reacts withwater and releases energy?

3. MQ@\llfM Suppose you had an organic moleculesuch as glycine (see Figure 4.10, amino group exam-ple), and you chemically removed the-NH2 groupand replaced it with -COOH. Draw the structuralformula for this molecule and speculate about itschemical properties.For suggested answers. see Appendix A.

AlP: An Important Source of Energyfor Cellular ProcessesThe "Phosphaten column in Figure 4.10 shows a simple exam-ple of an organic phosphate molecule. A more complicatedorganic phosphate, adenosine triphosphate, or ATP, isworth mentioning because its function in the cell is so impor-tant. ATP consists ofan organic molecule called adenosine at-tached to a string of three phosphate groups:

o 0 0II II II

-O-P-O-P-O-P-O AdenosineI I I0- 0- 0-

CONCEPT CHECK 4.)

\'(fhere three phosphates are present in series, as in ATP, onephosphate may be split off as a result of a reaction with water.This inorganic phosphate ion, HOP03

2-, is often abbreviated®i in this book. Having lost one phosphate, ATP becomesadenosine diphosphate, or ADP. Although ATP is sometimessaid to "staTen energy, it is more accurate to think of it asing" the potential to react with water. This reaction releasesenergy that can be used by the cell. You will learn about this inmore detail in Chapter 8.

Reactswith H20

.. ill; + @-®-iAdenosinel + Energy

ATP Inorganic ADPphosphate

lhe Chemical Elements of life: AReviewLiving matter, as you have learned, consists mainly ofcarbon,oxygen, hydrogen, and nitrogen, with smaller amounts of sul-fur and phosphorus. These elements all form strong covalentbonds, an essential characteristic in the architecture of com-plex organic molecules. Of all these elements, carbon is thevirtuoso of the covalent bond. The versatility of carbon makespossible the great diversity of organic molecules, each withparticular properties that emerge from the unique arrange-ment of its carbon skeleton and the chemical groups ap-pended to that skeleton. At the foundation of all biologicaldiversity lies this variation at the molecular level.

C a terlJ .. •• •

-.m.It.• Go to the Study Area at www.masteringbio.comforBioFlix3-D Animations, MP3 Tutors, VideQs, Practice Tests, an eBook, and more.

SUMMARY OF KEY CONCEPTS

_i.lli'i'_ 4.1Organic chemistry is the study of carboncompounds (pp. 58-59)... OrganiC compounds were once thought to arise only withinliVing organisms, but this idea (Vitalism) was disproved whenchemists were able to synthesize organic compounds in thelaboratory.

-,.'I"i'- 4.2Carbon atoms can form diverse molecules by bondingto four other atoms (pp. 60-63)... The Formation of Bonds with Carbon Carbon. with a va-lence of 4. can bond to various other atoms, including 0, H,

66 UNIT ONE TheChemistryofLife

and N. Carbon can also bond to other carbon atoms, formingthe carbon skeletons oforganic compounds.

... Molecular Diversity Arising from Carbon SkeletonVariation The carbon skeletons oforganic molecules vary inlength and shape and have bonding sites for atoms ofotherelements. Hydrocarbons consist only of carbon and hydrogen.Isomers are compounds with the same molecular formula butdifferent structures and properties. Three types of isomers arestructural isomers, geometric isomers, and enantiomers.-t,j4o!,.•,\eIMtr DiversityofCarbon-Based MoleculesActi-.ity lromers

What Factors the Effectiveness of Drugs?

-, 'i"I'_4.3Asmall number of chemical groups are key to thefunctioning of biological molecules (pp. 63-66)... The Chemical Groups Most Important in lhe Processes oflife Chemical groups attached to the carbon skeletons ofor-ganic molecules participate in chemical reactions (functionalgroups) or contribute to function by affecting molecular shape.

6. \X'hich action could produce a carbonyl group?a. the replacement of the -OH ofa carboxyl group withhydrogen

b. the addition of a thiol to a hydroxylc. the addition of a hydroxyl to a phosphated. the replacement of the nitrogen of an amine with oxygene. the addition of a sulfhydryl to a carboxyl

+ ®-®--[AdenosineI +EnergyInorganic ADPphosphate

ATP

Reactswith H20

®-®-®-[Adenoslnel

... ATP: An Important Source of Energy for CellularProcesses

_M41f··Acti'ity Functional GroullS

... The Chemical Elements of life: AReview Living matteris made mostly of carbon, oxygen, hydrogen, and nitrogen,with some sulfur and phosphorus. Biological diversity has itsmolecular basis in carbon's ability to form a huge number ofmolecules with particular shapes and chemical properties.

7. \Vhich chemical group is most likely to be responsible for anorganic molecule behaving as a base?a. hydroxyl d. aminob. carbonyl e. phosphatec. carboxyl

For Self·Quiz answers, see Appendix A.

TESTING YOUR KNOWLEDGE-MH',. ViSit the Study Area at www.masteringbio.(om lor aPractice Test

SELF·QUIZ EVOLUTION CONNECTION

3. Choose the term that correctly describes the relationshipbetween these two sugar molecules:

8. ••I;t-W"I Some scientists believe that life elsewhere in theuniverse might be based on the element silicon, rather thanon carbon, as on Earth. Look at the electron distribution dia-gram for silicon in Figure 2.9 and draw the Lewis dot struc-ture for silicon. What properties does silicon share withcarbon that would make silicon-based life more likely than,say, neon-based life or aluminum-based life?

SCIENTIFIC INQUIRY

9. In 1918, an epidemic of sleeping sickness caused an unusualrigid paralysis in some survivors, similar to symptoms of ad-vanced Parkinson's disease. Years later, L-dopa (below, left), achemical used to treat Parkinson's disease, was given to someof these patients, as dramatized in the movie Awakenings.L-dopa was remarkably effective at eliminating the paralysis, atleast temporarily. However, itsenantiomer, o-dopa (right),was subsequently shown tohave no effect at all, as is thecase for Parkinson's disease. L-dopa o-dopaSuggest a hypothesis to explainwhy, for both diseases, one enantiomer is effective and theother is not.

H, -v0CI

H-C-OHI

H-C-OHIH

c. enantiomersd. isotopes

HI

H-C-OHIC=OI

H-C-OHIH

a. structural isomersb. geometric isomers

I. Organic chemistry is currently defined asa. the study of compounds made only by living cells.b. the study of carbon compounds.c. the study of vital forces.d. the study of natural (as opposed to synthetic) compounds.e. the study of hydrocarbons.

2. \Vhich ofthe following hydrocarbons has a double bond in itscarbon skeleton?a. C3Hgb. C2H6C. CH4

4. Identify the asymmetric carbon in this molecule:

5. Which functional group is not present in this molecule?

o OHH H H'C-C-C-C-C-H

HI U U

HO, -v0C HI I

H-C-C-OHI IN H

H/ 'H

SCIENCE, TECHNOLOGY, AND SOCIETY

10. Thalidomide achieved notoriety 50 years ago because of awave of birth defects among children born to women whotook thalidomide during pregnancy as a treatment formorning sickness. However, in 1998 the U.S. Food and DrugAdministration (FDA) approved this drug for the treatmentof certain conditions associated with Hansen's disease (lep-rosy). In clinical trials. thalidomide also shows promise foruse in treating patients suffering from AIDS. tuberculosis,and some types of cancer. Do you think approval of thisdrug is appropriate? If so. under what conditions? \Vhat cri-teria do you think the FDA should use in weighing a drug'sbenefits against its dangers?c. hydroxyl d. aminob. sulfhydryla. carboxyl

fOU Carbon and the Molecular Diversity of Life 67