B. Alberts, A. Johnson, J. Lewis и др. - Molecular Biology of The Cell (6th edition) (1120996), страница 24
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They are able to produce tightbinding only when many of them are formed simultaneously. Although onlyelectrostatic attractions are illustrated here, in reality all four noncovalentforces often contribute to holding two macromolecules together (Movie 2.1).individual noncovalent attraction would be much too weak to be effective in theface of thermal motions, their energies can sum to create a strong force betweentwo separate molecules. Thus sets of noncovalent attractions often allow the complementary surfaces of two macromolecules to hold those two macromoleculestogether (Figure 2–3).Table 2–1 compares noncovalent bond strengths to that of a typical covalentbond, both in the presence and in the absence of water. Note that, by formingcompeting interactions with the involved molecules, water greatly reduces thestrength of both electrostatic attractions and hydrogen bonds.The structure of a typical hydrogen bond is illustrated in Figure 2–4.
This bondrepresents a special form of polar interaction in which an electropositive hydrogen atom is shared by two electronegative atoms. Its hydrogen can be viewed as aproton that has partially dissociated from a donor atom, allowing it to be sharedby a second acceptor atom. Unlike a typical electrostatic interaction, this bond ishighly directional—being strongest when a straight line can be drawn between allthree of the involved atoms.The fourth effect that often brings molecules together in water is not, strictlyspeaking, a bond at all.
However, a very important hydrophobic force is caused bya pushing of nonpolar surfaces out of the hydrogen-bonded water network, wherethey would otherwise physically interfere with the highly favorable interactionsbetween water molecules. Bringing any two nonpolar surfaces together reducestheir contact with water; in this sense, the force is nonspecific. Nevertheless, weshall see in Chapter 3 that hydrophobic forces are central to the proper folding ofprotein molecules.(A)donoratomSome Polar Molecules Form Acids and Bases in WaterOne 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 another atom dissolves in water.
The hydrogenatom in such a molecule has given up its electron almost entirely to the companionatom, and so exists as an almost naked positively charged hydrogen nucleus—inTABLE 2–1 Covalent and Noncovalent Chemical BondsStrength kJ/mole**Bond typeLength (nm)in vacuumin waterCovalent0.15377 (90)377 (90)ionic*0.25335 (80)12.6 (3)hydrogen0.3016.7 (4)4.2 (1)van der Waalsattraction (peratom)0.350.4 (0.1)0.4 (0.1)Noncovalent*An ionic bond is an electrostatic attraction between two fully charged atoms. **Values inparentheses are kcal/mole.
1 kJ = 0.239 kcal and 1 kcal = 4.18 kJ.hydrogen bond ~0.3 nm longacceptoratomMBoC6 m2.16/2.03NHOcovalent bond~0.1 nm long(B)OOON+NNdonoratomHHHHHHOONOONacceptoratomFigure 2–4 Hydrogen bonds. (A) Ball-andstick model of a typical hydrogen bond.The distance between the hydrogen andthe oxygen atom here is less than the sumof their van der Waals radii, indicating apartial sharing of electrons. (B) The mostcommon hydrogen bonds in cells.46Chapter 2: Cell Chemistry and BioenergeticsOCH3+COδ–OHHδ+acetic acidCH3OOwateracetateion(A)H(B)OHH OHH2OH2Oproton movesfrom onemolecule tothe other+CHHHO HH +++HO+HhydroniumionOH–H3OOHhydroniumionhydroxylionother words, a proton (H+).
When the polar molecule becomes surrounded bywater molecules, the proton will be attracted to the partial negative charge on theO atom of an adjacent water molecule. This proton can easily dissociate from itsoriginal partner and associate instead with the oxygen atom of the water molecule, generating a hydronium ion (H3O+) (Figure 2–5A). The reverse reaction alsotakes place very readily, so in the aqueous solution protons are constantly flittingto and fro between one molecule and another.Substances that release protons when they dissolve in water, thus formingH3O+, are termed acids.
The higher the concentration of H3O+, the more acidicthe solution. H3O+ is present even in pure water, at a concentration of 10–7 M, asa result of the movement of protons from one water molecule to another (Figure2–5B). By convention, the H3O+ concentration is usually referred to as the H+ concentration, even though most protons in an aqueous solution are present as H3O+.MBoC6 numbers,e2.14/2.05To avoid the use of unwieldythe concentration of H3O+ is expressedusing a logarithmic scale called the pH scale. Pure water has a pH of 7.0 and is saidto be neutral—that is, neither acidic (pH <7) nor basic (pH >7).Acids are characterized as being strong or weak, depending on how readilythey give up their protons to water.
Strong acids, such as hydrochloric acid (HCl),lose their protons quickly. Acetic acid, on the other hand, is a weak acid becauseit holds on to its proton more tightly when dissolved in water. Many of the acidsimportant in the cell—such as molecules containing a carboxyl (COOH) group—are weak acids (see Panel 2–2, pp. 92–93).Because the proton of a hydronium ion can be passed readily to many types ofmolecules in cells, altering their character, the concentration of H3O+ inside a cell(the acidity) must be closely regulated. Acids—especially weak acids—will give uptheir protons more readily if the concentration of H3O+ in solution is low and willtend to receive them back if the concentration in solution is high.The opposite of an acid is a base.
Any molecule capable of accepting a protonfrom a water molecule is called a base. Sodium hydroxide (NaOH) is basic (theterm alkaline is also used) because it dissociates readily in aqueous solution toform Na+ ions and OH– ions. Because of this property, NaOH is called a strongbase. More important in living cells, however, are the weak bases—those thathave a weak tendency to reversibly accept a proton from water.
Many biologicallyimportant molecules contain an amino (NH2) group. This group is a weak basethat can generate OH– by taking a proton from water: –NH2 + H2O → –NH3+ + OH–(see Panel 2–2, pp. 92–93).Because an OH– ion combines with a H3O+ ion to form two water molecules,an increase in the OH– concentration forces a decrease in the concentration ofH3O+, and vice versa. A pure solution of water contains an equal concentration(10–7 M) of both ions, rendering it neutral.
The interior of a cell is also kept closeto neutrality by the presence of buffers: weak acids and bases that can release ortake up protons near pH 7, keeping the environment of the cell relatively constantunder a variety of conditions.Figure 2–5 Protons readily move inaqueous solutions. (A) The reaction thattakes place when a molecule of aceticacid dissolves in water. At pH 7, nearly allof the acetic acid is present as acetateion. (B) Water molecules are continuouslyexchanging protons with each other toform hydronium and hydroxyl ions.
Theseions in turn rapidly recombine to form watermolecules.THE CHEMICAL COMPONENTS OF A CELLA Cell Is Formed from Carbon CompoundsHaving reviewed the ways atoms combine into molecules and how these molecules behave in an aqueous environment, we now examine the main classes ofsmall molecules found in cells. We shall see that a few categories of molecules,formed from a handful of different elements, give rise to all the extraordinary richness of form and behavior shown by living things.If we disregard water and inorganic ions such as potassium, nearly all themolecules in a cell are based on carbon. Carbon is outstanding among all theelements in its ability to form large molecules; silicon is a poor second. Becausecarbon is small and has four electrons and four vacancies in its outermost shell, acarbon atom can form four covalent bonds with other atoms.
Most important, onecarbon atom can join to other carbon atoms through highly stable covalent C–Cbonds to form chains and rings and hence generate large and complex moleculeswith no obvious upper limit to their size. The carbon compounds made by cellsare called organic molecules. In contrast, all other molecules, including water, aresaid to be inorganic.Certain combinations of atoms, such as the methyl (–CH3), hydroxyl (–OH),carboxyl (–COOH), carbonyl (–C=O), phosphate (–PO32–), sulfhydryl (–SH), andamino (–NH2) groups, occur repeatedly in the molecules made by cells.
Each suchchemical group has distinct chemical and physical properties that influence thebehavior of the molecule in which the group occurs. The most common chemicalgroups and some of their properties are summarized in Panel 2–1, pp. 90–91.Cells Contain Four Major Families of Small Organic MoleculesThe small organic molecules of the cell are carbon-based compounds that havemolecular weights in the range of 100–1000 and contain up to 30 or so carbonatoms. They are usually found free in solution and have many different fates. Someare used as monomer subunits to construct giant polymeric macromolecules—proteins, nucleic acids, and large polysaccharides. Others act as energy sourcesand are broken down and transformed into other small molecules in a maze ofintracellular metabolic pathways. Many small molecules have more than one rolein the cell—for example, acting both as a potential subunit for a macromoleculeand as an energy source.
Small organic molecules are much less abundant thanthe organic macromolecules, accounting for only about one-tenth of the totalmass of organic matter in a cell. As a rough guess, there may be a thousand different kinds of these small molecules in a typical cell.All organic molecules are synthesized from and are broken down into thesame set of simple compounds.
As a consequence, the compounds in a cell arechemically related and most can be classified into a few distinct families. Broadlyspeaking, cells contain four major families of small organic molecules: the sugars,the fatty acids, the nucleotides, and the amino acids (Figure 2–6).
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