B. Alberts, A. Johnson, J. Lewis и др. - Molecular Biology of The Cell (6th edition) (1120996), страница 29
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A small organic molecule, for example, takesonly about one-fifth of a second on average to diffuse a distance of 10 μm. Diffusion is therefore an efficient way for small molecules to move the limited distances in the cell (a typical animal cell is 15 μm in diameter).Since enzymes move more slowly than substrates in cells, we can think of themas sitting still. The rate of encounter of each enzyme molecule with its substratewill depend on the concentration of the substrate molecule. For example, someabundant substrates are present at a concentration of 0.5 mM.
Since pure wateris 55.5 M, there is only about one such substrate molecule in the cell for every105 water molecules. Nevertheless, the active site on an enzyme molecule thatbinds this substrate will be bombarded by about 500,000 random collisions withthe substrate molecule per second. (For a substrate concentration tenfold lower,the number of collisions drops to 50,000 per second, and so on.) A random collision between the active site of an enzyme and the matching surface of its substrate molecule often leads immediately to the formation of an enzyme–substratecomplex. A reaction in which a covalent bond is broken or formed can now occurextremely rapidly.
When one appreciates how quickly molecules move and react,the observed rates of enzymatic catalysis do not seem so amazing.Two molecules that are held together by noncovalent bonds can also dissociate. The multiple weak noncovalent bonds that they form with each other willpersist until random thermal motion causes the two molecules to separate. Ingeneral, the stronger the binding of the enzyme and substrate, the slower theirrate of dissociation.
In contrast, whenever two colliding molecules have poorlymatching surfaces, they form few noncovalent bonds and the total energy of association will be negligible compared with that of thermal motion. In this case, thetwo molecules dissociate as rapidly as they come together, preventing incorrectand unwanted associations between mismatched molecules, such as between anenzyme and the wrong substrate.final distancetraveledFigure 2–26 A random walk.
Moleculesin solution move in a random fashion as aresult of the continual buffeting they receivein collisions with other molecules. Thismovement allows small moleculesMBoC6m2.48/2.26to diffuse rapidlyfromone part of thecell to another, as described in the text(Movie 2.3).The Free-Energy Change for a Reaction, ∆G, Determines WhetherIt Can Occur SpontaneouslyAlthough enzymes speed up reactions, they cannot by themselves force energetically unfavorable reactions to occur.
In terms of a water analogy, enzymesby themselves cannot make water run uphill. Cells, however, must do just that inorder to grow and divide: they must build highly ordered and energy-rich molecules from small and simple ones. We shall see that this is done through enzymesthat directly couple energetically favorable reactions, which release energy andproduce heat, to energetically unfavorable reactions, which produce biologicalorder.What do cell biologists mean by the term “energetically favorable,” and howcan this be quantified? According to the second law of thermodynamics the universe tends toward maximum disorder (largest entropy or greatest probability).Thus, a chemical reaction can proceed spontaneously only if it results in a netincrease in the disorder of the universe (see Figure 2–16). This disorder of the universe can be expressed most conveniently in terms of the free energy of a system, aconcept we touched on earlier.Free energy, G, is an expression of the energy available to do work—for example, the work of driving chemical reactions.
The value of G is of interest only whena system undergoes a change, denoted ∆G (delta G). The change in G is criticalbecause, as explained in Panel 2–7 (pp. 102–103), ∆G is a direct measure of theFigure 2–27 The structure of the cytoplasm. The drawing is approximatelyto scale and emphasizes the crowding in the cytoplasm. Only themacromolecules are shown: RNAs are shown in blue, ribosomes in green,and proteins in red. Enzymes and other macromolecules diffuse relativelyslowly in the cytoplasm, in part because they interact with many othermacromolecules; small molecules, by contrast, diffuse nearly as rapidly asthey do in water (Movie 2.4). (Adapted from D.S.
Goodsell, Trends Biochem.Sci. 16:203–206, 1991. With permission from Elsevier.)100 nmCATALYSIS AND THE USE OF ENERGY BY CELLSamount of disorder created in the universe when a reaction takes place. Energetically favorable reactions, by definition, are those that decrease free energy; inother words, they have a negative ∆G and disorder the universe (Figure 2–28).An example of an energetically favorable reaction on a macroscopic scale isthe “reaction” by which a compressed spring relaxes to an expanded state, releasing its stored elastic energy as heat to its surroundings; an example on a microscopic scale is salt dissolving in water.
Conversely, energetically unfavorable reactions with a positive ∆G—such as the joining of two amino acids to form a peptidebond—by themselves create order in the universe. Therefore, these reactions cantake place only if they are coupled to a second reaction with a negative ∆G so largethat the ∆G of the overall process is negative (Figure 2–29).The Concentration of Reactants Influences the Free-EnergyChange and a Reaction’s DirectionAs we have just described, a reaction Y ↔ X will go in the direction Y → X whenthe associated free-energy change, ∆G, is negative, just as a tensed spring left toitself will relax and lose its stored energy to its surroundings as heat.
For a chemical reaction, however, ∆G depends not only on the energy stored in each individual molecule, but also on the concentrations of the molecules in the reactionmixture. Remember that ∆G reflects the degree to which a reaction creates a moredisordered—in other words, a more probable—state of the universe. Recalling ourcoin analogy, it is very likely that a coin will flip from a head to a tail orientation ifa jiggling box contains 90 heads and 10 tails, but this is a less probable event if thebox has 10 heads and 90 tails.The same is true for a chemical reaction. For a reversible reaction Y ↔ X, alarge excess of Y over X will tend to drive the reaction in the direction Y → X.Therefore, as the ratio of Y to X increases, the ∆G becomes more negative for thetransition Y → X (and more positive for the transition X → Y).The amount of concentration difference that is needed to compensate for agiven decrease in chemical-bond energy (and accompanying heat release) is notintuitively obvious.
In the late nineteenth century, the relationship was determined through a thermodynamic analysis that makes it possible to separatethe concentration-dependent and the concentration-independent parts of thefree-energy change, as we describe next.61YENERGETICALLYFAVORABLEREACTIONXThe free energy of Yis greater than the freeenergy of X. ThereforeΔG < 0, and the disorderof the universe increasesduring the reactionY X.this reaction can occur spontaneouslyYENERGETICALLYUNFAVORABLEREACTIONXIf the reaction X Yoccurred, ΔG wouldbe > 0, and theuniverse wouldbecome moreordered.this reaction can occur only ifit is coupled to a second,energetically favorable reactionFigure 2–28 The distinction betweenenergetically favorable and energeticallyunfavorable reactions.MBoC6 m2.50/2.28CThe Standard Free-Energy Change, ∆G°, Makes It Possible toCompare the Energetics of Different ReactionsBecause ∆G depends on the concentrations of the molecules in the reaction mixture at any given time, it is not a particularly useful value for comparing the relative energies of different types of reactions.
To place reactions on a comparablebasis, we need to turn to the standard free-energy change of a reaction, ∆G°.The ∆G° is the change in free energy under a standard condition, defined as thatwhere the concentrations of all the reactants are set to the same fixed value of 1mole/liter. Defined in this way, ∆G° depends only on the intrinsic characters ofthe reacting molecules.For the simple reaction Y → X at 37°C, ∆G° is related to ∆G as follows:∆G = ∆G° + RT ln [X][Y]where ∆G is in kilojoules per mole, [Y] and [X] denote the concentrations of Y andX in moles/liter, ln is the natural logarithm, and RT is the product of the gas constant, R, and the absolute temperature, T. At 37°C, RT = 2.58 J mole–1.
(A mole is6 × 1023 molecules of a substance.)A large body of thermodynamic data has been collected that has made it possible to determine the standard free-energy change, ∆G°, for the important metabolic reactions of a cell. Given these ∆G° values, combined with additional information about metabolite concentrations and reaction pathways, it is possible toquantitatively predict the course of most biological reactions.YnegativeΔGpositiveΔGXDthe energetically unfavorablereaction X Y is driven by theenergetically favorablereaction C D, because the netfree-energy change for thepair of coupled reactions is lessthan zeroFigure 2–29 How reaction coupling isused to drive energetically unfavorablereactions.MBoC6 m2.51/2.2962Chapter 2: Cell Chemistry and BioenergeticsFigure 2–30 Chemical equilibrium.
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