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The highly stable benzene molecule, for example, consists of aring of six carbon atoms in which the bonding electrons are evenly distributed(although usually depicted as an alternating sequence of single and doublebonds, as shown in Panel 2-1).\ivhen the atoms joined by a single covalent bond belong to different elements, the two atoms usually attract the shared electrons to different degrees.compared with a c atom, for example, o and N atoms attract electrons relatively strongly, whereas an H atom attracts electrons more weakly.
By definition,a polar structure (in the electrical sense)is one with positive charge concentratedtoward one end (the positive pole) and negative charge concentrated toward theother (the negative pole). covalent bonds in which the electrons are sharedunequallyinthiswayarethereforeknown aspolarcoualentbonds(Figure2-10).For example, the covalent bond between oxygen and hydrogen, -O-H, orbetween nitrogen and hydrogen, -N-H, is polar, whereas that between carbonand hydrogen, -C-H, has the electrons attracted much more equally by bothatoms and is relatively nonpolar.Polar covalent bonds are extremely important in biology because they create permanent dipolesthat allow molecules to interact through electrical forces.Any large molecule with many polar groups will have a pattern of partial positiveand negative chargeson its surface.\Ay'hensuch a molecule encounters a secondmolecule with a complementary set of charges, the two molecules will beattracted to each other by electrostatic interactions that resemble (but areweaker than) the ionic bonds discussedoreviouslv.(A) ethane(B) etheneFigure2-9 Carbon-carbondouble bondsand singlebondscompared.(A)Theethanemolecule,with a singlecovalentbond betweenthe two carbonatoms,illustratesthe tetrahedralarrangementofsinglecovalentbondsformedby carbon.One of the CH3groupsjoined by thecovalentbond can rotaterelativeto theotheraroundthe bond axis.(B)Thedoublebond betweenthe two carbonatomsin a moleculeof ethene(ethylene)altersthe bond geometryof the carbonatomsand bringsall the atomsinto thesameplane(blue);thedoublebondpreventsthe rotationof one CH2grouprelativeto the other.THECHEMICALCOMPONENTSOFA CELL51An AtomOftenBehavesasif lt Hasa FixedRadius\.Vhena covalent bond forms between two atoms, the sharing of electrons bringsthe nuclei of these atoms unusually close together.
But most of the atoms thatare rapidly jostling each other in cells are located in separate molecules. \A/hathappens when two such atoms touch? RoshanKeab 02I-66950639For simplicity and clarity, atoms and molecules are usually representedschematically-either as a line drawing of the structural formula or as a balland-stick model. Space-fiIling models,however, give us a more accurate representation of molecular structure. In these models, a solid envelope representsthe radius of the electron cloud at which strong repulsive forces prevent a closerapproach of any second, non-bonded atom-the so-called uan derWaals radiusfor an atom.
This is possible because the amount of repulsion increases verysteeply as two such atoms approach each other closely.At slightly greater distances, any two atoms will experience a weak attractive force, knor,rryras a uan derWaalsattraction. As a result, there is a distance at which repulsive and attractiveforces precisely balance to produce an energy minimum in each atom's interaction with an atom of a second, non-bonded element (Figure Z-tl).Depending on the intended purpose, we shall represent small molecules asIine drawings, ball-and-stick models, or space-filling models. For comparison,the water molecule is represented in all three ways in Figure 2-l2.lMhenrepresenting very large molecules, such as proteins, we shall often need to furthersimplifu the model used (see,for example, Panel 3-2, pp. 132-133).6-lsFigure2-10 Polarand nonpolarcovalentbonds.Theelectrondistributionsin the oolarwatermolecule(H:O)and the nonpolaroxygenmolecule(Oz)are compared(6+,partialpositivecharge;6-, partialnegativecharge).Waterls the MostAbundantSubstancein CellsWater accounts for about 70% of a cell'sweight, and most intracellular reactionsoccur in an aqueous environment.
Life on Earth began in the ocean, and theconditions in that primeval environment put a permanent stamp on the chemistry of living things. Life therefore hinges on the properties of water.In each water molecule (HzO) the two H atoms are linked to the O atom bycovalent bonds (seeFigure 2-12). The two bonds are highly polar becausethe Ois strongly attractive for electrons, whereas the H is only weakly attractive.
Consequently,there is an unequal distribution of electrons in a water molecule, witha preponderance of positive charge on the two H atoms and of negative chargeon the O (see Figure 2-10). 'vVhen a positively charged region of one watermolecule (that is, one of its H atoms) approaches a negatively charged region(that is, the O) of a secondwater molecule, the electrical attraction between themcan result in a weak bond called a hydrogenbond (seeFigure 2-15). These bondsare much weaker than covalent bonds and are easily broken by the random thermal motions due to the heat energy of the molecules, so each bond lasts only ashort time. But the combined effect of many weak bonds can be profound.
Eachwater molecule can form hydrogen bonds through its two H atoms to two otherwater molecules, producing a network in which hydrogen bonds are being continually broken and formed (Panel 2-2, pp.f0B-109). It is only because of the. (+)IEUzU(-)v a n d e r W a a l sf o r c e e q u i l i b r i u ma t t h i s p o i n tFigure2-1 1 The balanceofvan derWaalsforces between two atoms.As the nucleiof two atomsapproacheachother,they initiallyshowa weakdue to theirbondinginteractionfluctuatingelectriccharges.However,thesameatomswill stronglyrepeleachotherif they are brought too closetogether.The balanceof thesevan derWaalsforcesoccursatattractiveand reoulsivethe indicatedenergyminimum.Thisminimumdeterminesthe contactdistancebetweenany two noncovalentlybondedatoms;this distanceis the sum oftheirvan der Waalsradii.By definition,zero energy(indicatedby the dotted redline)is the energywhen the two nucleiareat infiniteseparation.52Chapter2: CellChemistryand Biosynthesisvan derWaalsradiusofO=t+AoHH(A)(B)van derWaalsr a d i u so f Hi=1.24(c)";i.ill3l?ll,"l'hydrogen bonds that link water molecules together that water is a liquid atroom temperature, with a high boiling point and high surface tension-ratherthan a gas.Molecules, such as alcohols, that contain polar bonds and that can formhydrogen bonds with water dissolve readily in water.
Molecules carrying plus orminus charges (ions) likewise interact favorably with water. Such molecules aretermed hydrophilic, meaning that they are water-loving. A large proportion ofthe molecules in the aqueous environment of a cell necessarilyfall into this category including sugars, DNA, RNA, and most proteins. Hydrophobic (waterhating) molecules, by contrast, are uncharged and form few or no hydrogenbonds, and so do not dissolve in water. Hydrocarbons are an important example(see Panel 2-I, pp. 106-107). In these molecules the H atoms are covalentlylinked to C atoms by a largely nonpolar bond. Becausethe H atoms have almostno net positive charge, they cannot form effective hydrogen bonds to othermolecules.
This makes the hydrocarbon as a whole hydrophobic-a propertythat is exploited in cells,whose membranes are constructed from molecules thathave long hydrocarbon tails, as we shall see in Chapter I0.Some PolarMoleculesAre Acidsand BasesOne of the simplest kinds of chemical reaction, and one that has profound significance in cells,takes place when a molecule containing a highly polar covalentbond between a hydrogen and a second atom dissolvesin water. The hydrogenatom in such a molecule has largely given up its electron to the companion atomand so resembles an almost naked positively charged hydrogen nucleus-inother words, a proton (H+).\A/henwater molecules surround the polar molecule,the proton is attracted to the partial negative charge on the O atom of an adjacent water molecule and can dissociate from its original partner to associateinstead with the oxygen atoms of the water molecule to generate a hydroniumion (H3O+)(Figure 2-f 3A).
The reversereaction also takes place very readily, soone has to imagine an equilibrium state in which billions of protons are constantly flitting to and fro from one molecule in the solution to another.The same tlpe of reaction takes place in a solution of pure water itself. Asillustrated in Figure 2-13B, water molecules are constantly exchanging protonswith each other.
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