B. Alberts, A. Johnson, J. Lewis и др. - Molecular Biology of The Cell (6th edition) (1120996), страница 56
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The enzyme first binds to the chain to form an enzyme–substrate complex (ES) and thencatalyzes the cleavage of a specific covalent bond in the backbone of the polysaccharide, forming an enzyme–product complex(EP) that rapidly dissociates. Release of the severed chain (the products P) leaves the enzyme free to act on another substratemolecule. (B) A space-filling model of the lysozyme molecule bound to a short length of polysaccharide chain before cleavage(Movie 3.8).
(B, courtesy of Richard J. Feldmann; PDB code: 3AB6.)Chapter 3: Proteins146SUBSTRATEPRODUCTSThis substrate is an oligosaccharide of six sugars,labeled A through F. Only sugars D and E are shown in detail.RAB CODRCH2OHEOOCH2OHESOHCRHCCHOODOC1 carbonOAsp52OOCHCH2OHOHOCH2EOOODCH HOO OCRRFEPOCH2OHEOORHOCAsp52atoms that speed up a reaction by using charged groups to alter the distribution ofelectrons in the substrates (Figure 3–52B). And as we have also seen, when a substrate binds to an enzyme, bonds in the substrate are often distorted, changing theMBoC6 m3.51/3.47substrate shape. These changes, along with mechanical forces, drive a substratetoward a particular transition state (Figure 3–52C). Finally, like lysozyme, manyenzymes participate intimately in the reaction by transiently forming a covalentbond between the substrate and a side chain of the enzyme. Subsequent steps inthe reaction restore the side chain to its original state, so that the enzyme remainsunchanged after the reaction (see also Figure 2–48).Tightly Bound Small Molecules Add Extra Functions to ProteinsAlthough we have emphasized the versatility of enzymes—and proteins in general—as chains of amino acids that perform remarkable functions, there are manyinstances in which the amino acids by themselves are not enough.
Just as humans(A) enzyme binds to twosubstrate molecules andorients them precisely toencourage a reaction tooccur between themORCThe Asp52 has formed a covalent bond betweenthe enzyme and the C1 carbon atom of sugar D.The Glu35 then polarizes a water molecule (red ),so that its oxygen can readily attack the C1carbon atom and displace Asp52.+EOHC–+OCH2OHOOIn the enzyme–substrate complex (ES), theenzyme forces sugar D into a strainedconformation. The Glu35 in the enzyme ispositioned to serve as an acid that attacks theadjacent sugar–sugar bond by donating a proton(H+) to sugar E; Asp52 is poised to attack theC1 carbon atom.OORROOOHOCH2EOOHGlu35CCH2OHOCOHDHCH2OHGlu35OHOCH2Oside chainon sugar ECCDAB CFORGlu35OThe final products are an oligosaccharide of four sugars(left) and a disaccharide (right), produced by hydrolysis.OCCAsp52The reaction of the water molecule (red )completes the hydrolysis and returns the enzymeto its initial state, forming the final enzyme–product complex (EP).Figure 3–51 Events at the active siteof lysozyme.
The top left and top rightdrawings show the free substrate and thefree products, respectively, whereas theother three drawings show the sequentialevents at the enzyme active site. Notethe change in the conformation of sugarD in the enzyme–substrate complex; thisshape change stabilizes the oxocarbeniumion-like transition states required forformation and hydrolysis of the covalentintermediate shown in the middle panel.It is also possible that a carbonium ionintermediate forms in step 2, but thecovalent intermediate shown in the middlepanel has been detected with a syntheticsubstrate (Movie 3.9). (See D.J.
Vocadlo etal., Nature 412:835–838, 2001.)–(B) binding of substrateto enzyme rearrangeselectrons in the substrate,creating partial negativeand positive chargesthat favor a reaction(C) enzyme strains thebound substratemolecule, forcing ittoward a transitionstate to favor a reactionFigure 3–52 Some general strategies ofenzyme catalysis.
(A) Holding substratestogether in a precise alignment. (B) Chargestabilization of reaction intermediates.(C) Applying forces that distort bonds in thesubstrate to increase the rate of a particularreaction.PROTEIN FUNCTION147TABLE 3–2 Many Vitamin Derivatives Are Critical Coenzymes for Human CellsVitaminCoenzymeEnzyme-catalyzed reactions requiring these coenzymesThiamine (vitamin B1)Thiamine pyrophosphateActivation and transfer of aldehydesRiboflavin (vitamin B2)FADHOxidation–reductionNiacinNADH, NADPHOxidation–reductionPantothenic acidCoenzyme AAcyl group activation and transferPyridoxinePyridoxal phosphateAmino acid activation; also glycogen phosphorylaseBiotinBiotinCO2 activation and transferLipoic acidLipoamideAcyl group activation; oxidation–reductionFolic acidTetrahydrofolateActivation and transfer of single carbon groupsVitamin B12Cobalamin coenzymesIsomerization and methyl group transfersemploy tools to enhance and extend the capabilities of their hands, enzymes andother proteins often use small nonprotein molecules to perform functions thatwould be difficult or impossible to do with amino acids alone.
Thus, enzymes frequently have a small molecule or metal atom tightly associated with their activesite that assists with their catalytic function. Carboxypeptidase, for example, anenzyme that cuts polypeptide chains, carries a tightly bound zinc ion in its activesite.
During the cleavage of a peptide bond by carboxypeptidase, the zinc ion formsa transient bond with one of the substrate atoms, thereby assisting the hydrolysisreaction. In other enzymes, a small organic molecule serves a similar purpose.Such organic molecules are often referred to as coenzymes. An example is biotin,which is found in enzymes that transfer a carboxylate group (–COO–) from onemolecule to another (see Figure 2–40). Biotin participates in these reactions byforming a transient covalent bond to the –COO– group to be transferred, beingbetter suited to this function than any of the amino acids used to make proteins.Because it cannot be synthesized by humans, and must therefore be supplied insmall quantities in our diet, biotin is a vitamin.
Many other coenzymes are eithervitamins or derivatives of vitamins (Table 3–2).Other proteins also frequently require specific small-molecule adjuncts tofunction properly. Thus, the signal receptor protein rhodopsin, which is made bythe photoreceptor cells in the retina, detects light by means of a small molecule,retinal, embedded in the protein (Figure 3–53A). Retinal, which is derived fromvitamin A, changes its shape when it absorbs a photon of light, and this changecauses the protein to trigger a cascade of enzymatic reactions that eventually leadto an electrical signal being carried to the brain.H3C CH3CH3H3CCOOHCOOHCH2CH2CH2CH2CH3+NNFeCH3H2CH3CCHO(A)HCN+CH3(B)NCH3HCCH2Figure 3–53 Retinal and heme.
(A) Thestructure of retinal, the light-sensitivemolecule attached to rhodopsin in the eye.The structure shown isomerizes when itabsorbs light. (B) The structure of a hemegroup. The carbon-containing heme ringis red and the iron atom at its center isorange. A heme group is tightly boundto each of the four polypeptide chains inhemoglobin, the oxygen-carrying proteinwhose structure is shown in Figure 3–19.148Chapter 3: ProteinsAnother example of a protein with a nonprotein portion is hemoglobin (seeFigure 3–19).
Each molecule of hemoglobin carries four heme groups, ring-shapedmolecules each with a single central iron atom (Figure 3–53B). Heme gives hemoglobin (and blood) its red color. By binding reversibly to oxygen gas through itsiron atom, heme enables hemoglobin to pick up oxygen in the lungs and releaseit in the tissues.Sometimes these small molecules are attached covalently and permanentlyto their protein, thereby becoming an integral part of the protein molecule itself.We shall see in Chapter 10 that proteins are often anchored to cell membranesthrough covalently attached lipid molecules.
And membrane proteins exposed onthe surface of the cell, as well as proteins secreted outside the cell, are often modified by the covalent addition of sugars and oligosaccharides.Multienzyme Complexes Help to Increase the Rate of CellMetabolismThe efficiency of enzymes in accelerating chemical reactions is crucial to themaintenance of life. Cells, in effect, must race against the unavoidable processesof decay, which—if left unattended—cause macromolecules to run downhilltoward greater and greater disorder.
If the rates of desirable reactions were notgreater than the rates of competing side reactions, a cell would soon die. We canget some idea of the rate at which cell metabolism proceeds by measuring therate of ATP utilization. A typical mammalian cell “turns over” (i.e., hydrolyzes andrestores by phosphorylation) its entire ATP pool once every 1 or 2 minutes. Foreach cell, this turnover represents the utilization of roughly 107 molecules of ATPper second (or, for the human body, about 1 gram of ATP every minute).The rates of reactions in cells are rapid because enzyme catalysis is so effective.Some enzymes have become so efficient that there is no possibility of further useful improvement.
The factor that limits the reaction rate is no longer the enzyme’sintrinsic speed of action; rather, it is the frequency with which the enzyme collideswith its substrate. Such a reaction is said to be diffusion-limited (see Panel 3–2,pp. 142–143).The amount of product produced by an enzyme will depend on the concentration of both the enzyme and its substrate. If a sequence of reactions is to occurextremely rapidly, each metabolic intermediate and enzyme involved must bepresent in high concentration.
However, given the enormous number of differentreactions performed by a cell, there are limits to the concentrations that can beachieved. In fact, most metabolites are present in micromolar (10–6 M) concentrations, and most enzyme concentrations are much lower. How is it possible, therefore, to maintain very fast metabolic rates?The answer lies in the spatial organization of cell components. The cell canincrease reaction rates without raising substrate concentrations by bringing thevarious enzymes involved in a reaction sequence together to form a large proteinassembly known as a multienzyme complex (Figure 3–54). Because this assemblyis organized in a way that allows the product of enzyme A to be passed directlyto enzyme B, and so on, diffusion rates need not be limiting, even when the concentrations of the substrates in the cell as a whole are very low.
It is perhaps notsurprising, therefore, that such enzyme complexes are very common, and theyare involved in nearly all aspects of metabolism—including the central geneticprocesses of DNA, RNA, and protein synthesis. In fact, few enzymes in eukaryoticcells diffuse freely in solution; instead, most seem to have evolved binding sitesthat concentrate them with other proteins of related function in particular regionsof the cell, thereby increasing the rate and efficiency of the reactions that theycatalyze (see p.
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