H. Lodish - Molecular Cell Biology (5ed, Freeman, 2003) (796244), страница 14
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Inaddition to the covalent bonds that hold the atoms of an amino acidtogether and link amino acids together, noncovlent interactions helpdefine the structure of each individual protein and serve to help holdthe complementary structures together. (b) Small molecules serveas building blocks for larger structures. For example, to generatethe information-carrying macromolecule DNA, the four smallnucleotide building blocks deoxyadenylate (A), deoxythymidylate (T),deoxyguanylate (G), and deoxycytidylate (C) are covalently linkedtogether into long strings (polymers), which then dimerize into thedouble helix.
(c) Chemical reactions are reversible, and the distributionof the chemicals between starting compounds (left) and the productsprinciples of biochemical energetics, including the centralrole of ATP (adenosine triphosphate) in capturing and transferring energy in cellular metabolism.2.1 Atomic Bonds and MolecularInteractionsStrong and weak attractive forces between atoms are the gluethat holds them together in individual molecules and permitsinteractions between different biological molecules. Strongforces form a covalent bond when two atoms share one pairof electrons (“single” bond) or multiple pairs of electrons(“double” bond, “triple” bond, etc.). The weak attractiveforces of noncovalent interactions are equally important inAdenosinetriphosphate(ATP)of the reactions (right ) depends on the rate constants of theforward (kf, upper arrow) and reverse (kr, lower arrow) reactions.In the reaction shown, the forward reaction rate constant isfaster than the reverse reaction, indicated by the thickness of thearrows.
The ratio of these Keq, provides an informative measureof the relative amounts of products and reactants that will bepresent at equilibrium. (d) In many cases, the source of energyfor chemical reactions in cells is the hydrolysis of the moleculeATP. This energy is released when a high-energy phosphoanhydridebond linking the α and β or the β and γ phosphates in the ATPmolecule (yellow) is broken by the addition of a water molecule.Proteins can efficiently transfer the energy of ATP hydrolysis toother chemicals, thus fueling other chemical reactions, or toother biomolecules for physical work.determining the properties and functions of biomoleculessuch as proteins, nucleic acids, carbohydrates, and lipids.There are four major types of noncovalent interactions: ionicinteractions, hydrogen bonds, van der Waals interactions,and the hydrophobic effect.Each Atom Has a Defined Numberand Geometry of Covalent BondsHydrogen, oxygen, carbon, nitrogen, phosphorus, and sulfurare the most abundant elements found in biological molecules.
These atoms, which rarely exist as isolated entities,readily form covalent bonds with other atoms, using electrons that reside in the outermost electron orbitals surrounding their nuclei. As a rule, each type of atom forms a2.1 • Atomic Bonds and Molecular Interactionscharacteristic number of covalent bonds with other atoms,with a well-defined geometry determined by the atom’s sizeand by both the distribution of electrons around the nucleusand the number of electrons that it can share.
In some cases(e.g., carbon), the number of stable covalent bonds formed isfixed; in other cases (e.g., sulfur), different numbers of stable covalent bonds are possible.All the biological building blocks are organized aroundthe carbon atom, which normally forms four covalent bondswith two to four other atoms. As illustrated by the methane(CH4) molecule, when carbon is bonded to four other atoms,the angle between any two bonds is 109.5º and the positionsof bonded atoms define the four points of a tetrahedron(Figure 2-2a). This geometry helps define the structures ofmany biomolecules.
A carbon (or any other) atom bonded tofour dissimilar atoms or groups in a nonplanar configurationis said to be asymmetric. The tetrahedral orientation of bondsformed by an asymmetric carbon atom can be arranged inthree-dimensional space in two different ways, producingmolecules that are mirror images of each other, a propertycalled chirality. Such molecules are called optical isomers, or(a) MethaneHH109.5°HCHCHHHH(b) FormaldehydeOHCOHHC~120°HChemicalstructureBall-and-stickmodelSpace-fillingmodel▲ FIGURE 2-2 Geometry of bonds when carbon is covalentlylinked to four or three other atoms.
(a) If a carbon atom formsfour single bonds, as in methane (CH4), the bonded atoms (all Hin this case) are oriented in space in the form of a tetrahedron.The letter representation on the left clearly indicates the atomiccomposition of the molecule and the bonding pattern. The ball-andstick model in the center illustrates the geometric arrangement ofthe atoms and bonds, but the diameters of the balls representingthe atoms and their nonbonding electrons are unrealistically smallcompared with the bond lengths. The sizes of the electron cloudsin the space-filling model on the right more accurately representthe structure in three dimensions. (b) A carbon atom also can bebonded to three, rather than four, other atoms, as in formaldehyde(CH2O). In this case, the carbon bonding electrons participate intwo single bonds and one double bond, which all lie in the sameplane.
Unlike atoms connected by a single bond, which usually canrotate freely about the bond axis, those connected by a doublebond cannot.TABLE 2-1Atomand OuterElectrons31Bonding Properties of Atoms MostAbundant in BiomoleculesUsual Numberof Covalent BondsBond GeometryHH1O2OS2, 4, or 6SN3 or 4NP5PC4Cstereoisomers. Many molecules in cells contain at least oneasymmetric carbon atom, often called a chiral carbon atom.The different stereoisomers of a molecule usually have completely different biological activities because the arrangementof atoms within their structures differs, yielding their uniqueabilities to interact and chemically react with other molecules.Carbon can also bond to three other atoms in which allatoms are in a common plane.
In this case, the carbon atomforms two typical single bonds with two atoms and a double bond (two shared electron pairs) with the third atom(Figure 2-2b). In the absence of other constraints, atomsjoined by a single bond generally can rotate freely about thebond axis, while those connected by a double bond cannot.The rigid planarity imposed by double bonds has enormoussignificance for the shapes and flexibility of large biologicalmolecules such as proteins and nucleic acids.The number of covalent bonds formed by other commonatoms is shown in Table 2-1.
A hydrogen atom forms onlyone bond. An atom of oxygen usually forms only two covalent bonds, but has two additional pairs of electrons that canparticipate in noncovalent interactions. Sulfur forms two covalent bonds in hydrogen sulfide (H2S), but also can accommodate six covalent bonds, as in sulfuric acid (H2SO4) andits sulfate derivatives. Nitrogen and phosphorus each havefive electrons to share. In ammonia (NH3), the nitrogen atomforms three covalent bonds; the pair of electrons around theatom not involved in a covalent bond can take part in noncovalent interactions. In the ammonium ion (NH4), nitrogen forms four covalent bonds, which have a tetrahedralgeometry.
Phosphorus commonly forms five covalent bonds,as in phosphoric acid (H3PO4) and its phosphate derivatives,which form the backbone of nucleic acids. Phosphate groupsattached to proteins play a key role in regulating the activity of many proteins (Chapter 3), and the central moleculein cellular energetics, ATP, contains three phosphate groups(see Section 2.4).32CHAPTER 2 • Chemical FoundationsElectrons Are Shared Unequallyin Polar Covalent Bondsδ−In many molecules, the bonded atoms exert different attractions for the electrons of the covalent bond, resulting in unequal sharing of the electrons. The extent of an atom’s abilityto attract an electron is called its electronegativity. A bondbetween atoms with identical or similar electronegativitiesis said to be nonpolar. In a nonpolar bond, the bonding electrons are essentially shared equally between the two atoms,as is the case for most COC and COH bonds.
However, iftwo atoms differ in their electronegativities, the bond between them is said to be polar.One end of a polar bond has a partial negative charge(), and the other end has a partial positive charge (). Inan OOH bond, for example, the greater electronegativity ofthe oxygen atom relative to hydrogen results in the electronsspending more time around the oxygen atom than the hydrogen.
Thus the OOH bond possesses an electric dipole, a positive charge separated from an equal but opposite negativecharge. We can think of the oxygen atom of the OOH bondas having, on average, a charge of 25 percent of an electron,with the H atom having an equivalent positive charge. Because of its two OOH bonds, water molecules (H2O) aredipoles that form electrostatic, noncovalent interactions withone another and with other molecules (Figure 2-3).
Theseinteractions play a critical role in almost every biochemicalinteraction and are thus fundamental to cell biology.The polarity of the OUP double bond in H3PO4 resultsin a “resonance hybrid,” a structure between the two formsshown below in which nonbonding electrons are shown aspairs of dots:HOHHOOPOOHHOPOO−δ−Dipolemomentδ+H104.5°Hδ++▲ FIGURE 2-3 The dipole nature of a water molecule. Thesymbol represents a partial charge (a weaker charge than theone on an electron or a proton). Because of the difference inthe electronegativities of H and O, each of the polar HOO bondsin water has a dipole moment.
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