B. Alberts, A. Johnson, J. Lewis и др. - Molecular Biology of The Cell (6th edition) (1120996), страница 40
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Mono-,di-, and triphosphates are common.A nucleotide consists of a nitrogen-containingbase, a five-carbon sugar, and one or morephosphate groups.OO–O–O–OPOOPO–O–OOPOO–POCH2–OPOCH2HO–POCH2as inATPO–The phosphate makes a nucleotidenegatively charged.Nucleotidesare thesubunits ofthe nucleic acids.HHOCH2C 5’a five-carbon sugar4’3’HH2’1’HOHtwo kinds are usedHOCH2Each numbered carbon on the sugar of a nucleotide isfollowed by a prime mark; therefore, one speaks of the“5-prime carbon,” etc.Hβ-D-riboseused in ribonucleic acidOHOHOβ-D-2-deoxyriboseused in deoxyribonucleic acidHHHOHHOHOHO2C1The base is linked tothe same carbon (C1)used in sugar–sugarbonds.OHSUGARSUGARSPENTOSE3HHOHSUGAR4OOOOONO–N5Oas inADPNH2BASENPHOSPHATECNN-glycosidicbondNH2as inAMPCH2GCNHNHBASIC SUGARLINKAGEBASEOPCHCPHOSPHATES–OCNguanineCCHNO68NACNHCCCHCOOOCNadenineNHH101NOMENCLATUREA nucleoside or nucleotide is named according to its nitrogenous base.baseSingle-letter abbreviations are used variously asshorthand for (1) the base alone, (2) theNUCLEOSIDEABBR.nucleoside, or (3) the whole nucleotide—sugarthe context will usually make clear which ofadenosineAthe three entities is meant.
When the contextBASE + SUGAR = NUCLEOSIDEis not sufficient, we will add the terms “base”,guanosineG“nucleoside”, “nucleotide”, or—as in theexamples below—use the full 3-letter nucleotidebasecytidineCcode.PBASEadenineguaninecytosineuraciluridineUthyminethymidineTNUCLEIC ACIDSAMPdAMPUDPATPNUCLEOTIDES HAVE MANY OTHER FUNCTIONSNucleotides are joined together by aphosphodiester linkage between 5’ and3’ carbon atoms to form nucleic acids.The linear sequence of nucleotides in anucleic acid chain is commonlyabbreviated by a one-letter code, such asA—G—C—T—T—A—C—A, with the 5’end of the chain at the left.O–OPOThey carry chemical energy in their easily hydrolyzed phosphoanhydride bonds.CH2NH2phosphoanhydride bondsNO–OOPOPO–ONOOO–PONCH2O–OHexample: ATP (or ATP )NOOHsugar+OP1baseO––O= adenosine monophosphatesugar= deoxyadenosine monophosphate= uridine diphosphateBASE + SUGAR + PHOSPHATE = NUCLEOTIDE= adenosine triphosphateOOH2baseCH2O–HSHHCCHOHHNHOHHCCCHHNHOH CH3 HCCCCOOOPOO–HO CH3 HNPOCH2O–example: coenzyme A (CoA)–OO5’ end of chainPO5’CH2O–phosphodiester–OlinkageO3sugarThey are used as specific signaling molecules in the cell.NH23’ O5’ CH2PO–example: cyclic AMP (cAMP)NNOOexample: DNAObaseOPNNOsugarH2ONH2They combine with other groups to form coenzymes.baseCH2ONOOsugarO3’ OH3’ end of chainPO–OOHNNOOH–O102PANEL 2–7: Free Energy and Biological ReactionsTHE IMPORTANCE OF FREE ENERGY FOR CELLSLife is possible because of the complex network of interactingchemical reactions occurring in every cell.
In viewing themetabolic pathways that comprise this network, one mightsuspect that the cell has had the ability to evolve an enzyme tocarry out any reaction that it needs. But this is not so. Althoughenzymes are powerful catalysts, they can speed up only thosereactions that are thermodynamically possible; other reactionsproceed in cells only because they are coupled to very favorablereactions that drive them.
The question of whether a reactioncan occur spontaneously, or instead needs to be coupled toanother reaction, is central to cell biology. The answer isobtained by reference to a quantity called the free energy: thetotal change in free energy during a set of reactions determineswhether or not the entire reaction sequence can occur. In thispanel, we shall explain some of the fundamental ideas—derivedfrom a special branch of chemistry and physics called thermodynamics—that are required for understanding what freeenergy is and why it is so important to cells.ENERGY RELEASED BY CHANGES IN CHEMICAL BONDING IS CONVERTED INTO HEATBOXCELLSEAUNIVERSEAn enclosed system is defined as a collection of molecules thatdoes not exchange matter with the rest of the universe (forexample, the “cell in a box” shown above).
Any such system willcontain molecules with a total energy E. This energy will bedistributed in a variety of ways: some as the translational energyof the molecules, some as their vibrational and rotational energies,but most as the bonding energies between the individual atomsthat make up the molecules. Suppose that a reaction occurs inthe system. The first law of thermodynamics places a constrainton what types of reactions are possible: it states that “in anyprocess, the total energy of the universe remains constant.”For example, suppose that reaction A B occurs somewhere inthe box and releases a great deal of chemical-bond energy.
Thisenergy will initially increase the intensity of molecular motions(translational, vibrational, and rotational) in the system, whichis equivalent to raising its temperature. However, these increasedmotions will soon be transferred out of the system by a seriesof molecular collisions that heat up first the walls of the boxand then the outside world (represented by the sea inour example). In the end, the system returns to its initialtemperature, by which time all the chemical-bond energyreleased in the box has been converted into heat energy andtransferred out of the box to the surroundings.
According tothe first law, the change in the energy in the box (ΔEbox, whichwe shall denote as ΔE) must be equal and opposite to theamount of heat energy transferred, which we shall designateas h: that is, ΔE = _h. Thus, the energy in the box (E) decreaseswhen heat leaves the system.E also can change during a reaction as a result of work beingdone on the outside world. For example, suppose that there isa small increase in the volume (ΔV) of the box during a reaction.Since the walls of the box must push against the constantpressure (P) in the surroundings in order to expand, this doeswork on the outside world and requires energy. The energyused is P(ΔV), which according to the first law must decreasethe energy in the box (E) by the same amount.
In most reactions,chemical-bond energy is converted into both work and heat.Enthalpy (H) is a composite function that includes both of these(H = E + PV). To be rigorous, it is the change in enthalpy(ΔH) in an enclosed system, and not the change in energy, thatis equal to the heat transferred to the outside world during areaction. Reactions in which H decreases release heat to thesurroundings and are said to be “exothermic,” while reactionsin which H increases absorb heat from the surroundings andare said to be “endothermic.” Thus, _h = ΔH. However, thevolume change is negligible in most biological reactions, so toa good approximation_h = ΔH ~= ΔETHE SECOND LAW OF THERMODYNAMICSConsider a container in which 1000 coins are all lying heads up.If the container is shaken vigorously, subjecting the coins tothe types of random motions that all molecules experience dueto their frequent collisions with other molecules, one will endup with about half the coins oriented heads down.
Thereason for this reorientation is that there is only a single way inwhich the original orderly state of the coins can be reinstated(every coin must lie heads up), whereas there are many differentways (about 10298) to achieve a disorderly state in which there isan equal mixture of heads and tails; in fact, there are more waysto achieve a 50-50 state than to achieve any other state. Eachstate has a probability of occurrence that is proportional to thenumber of ways it can be realized. The second law of thermodynamics states that “systems will change spontaneously fromstates of lower probability to states of higher probability.”Since states of lower probability are more “ordered” thanstates of high probability, the second law can be restated:“the universe constantly changes so as to become moredisordered.”103THE ENTROPY, SThe second law (but not the first law) allows one to predict thedirection of a particular reaction.
But to make it useful for thispurpose, one needs a convenient measure of the probability or,equivalently, the degree of disorder of a state. The entropy (S)is such a measure. It is a logarithmic function of the probabilitysuch that the change in entropy (ΔS) that occurs when thereaction A B converts one mole of A into one mole of B isΔS = R In p B /pAwhere pA and pB are the probabilities of the two states A and B,_R is the gas constant (8.31 J K–1 mole 1), and ΔS is measuredin entropy units (eu).
In our initial example of 1000 coins, therelative probability of all heads (state A) versus half heads andhalf tails (state B) is equal to the ratio of the number of differentways that the two results can be obtained. One can calculatethat pA = 1 and pB = 1000!(500! x 500!) = 10299. Therefore,the entropy change for the reorientation of the coins when theircontainer is vigorously shaken and an equal mixture of headsand tails is obtained is R In (10298), or about 1370 eu per mole ofsuch containers (6 x 1023 containers).
We see that, because ΔSdefined above is positive for the transition from state A tostate B (pB /pA > 1), reactions with a large increase in S (that is,for which ΔS > 0) are favored and will occur spontaneously.As discussed in Chapter 2, heat energy causes the randomcommotion of molecules. Because the transfer of heat from anenclosed system to its surroundings increases the number ofdifferent arrangements that the molecules in the outside worldcan have, it increases their entropy. It can be shown that therelease of a fixed quantity of heat energy has a greater disordering effect at low temperature than at high temperature, andthat the value of ΔS for the surroundings, as defined above(ΔSsea), is precisely equal to h, the amount of heat transferred tothe surroundings from the system, divided by the absolutetemperature (T ):ΔSsea = h / TTHE GIBBS FREE ENERGY, GWhen dealing with an enclosed biological system, one wouldlike to have a simple way of predicting whether a given reactionwill or will not occur spontaneously in the system.
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