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CHAPTER 3ENERGY, CATALYSIS, AND BIOSYNTHESIS

2004 Garland Science Pu li!"in#

Ca$al%!i! and $"e &!e '( Ener#% % Cell!

3-1 If you weigh yourself on a scale one morning then eat four pounds of food during the day,will you weigh four pounds more the next morning? Why or why not? Hint: Whathappens to the atoms contained in the food and the energy stored in the chemical bondsof food molecules?

3-2 Living organisms require a continual supply of energy to exist because theya! defy the laws of thermodynamics"b! convert it into heat energy, which powers biosynthetic reactions"c! create order out of disorder inside their cells"d! cause the entropy in the universe to decrease"e! are closed systems isolated from the rest of the universe"

3-3 Life is thermodynamically possible because living thingsa! release heat to the environment"b! increase the degree of order in the universe"c! reproduce themselves"d! carry out energetically favorable reactions only"e! can carry out a chain of reactions that is energetically unfavorable"

3-4 #he energy required by a human cell to grow and reproduce is provided bya! the generation of order inside it"b! its anabolic metabolism"c! its catabolic metabolism"d! generation of heat"e! its biosynthetic reactions"

3-5 Which of the following statements about photosynthesis are #$%&?a! 'hotosynthesis is irrelevant to the existence of animals"b! 'hotosynthesis converts light energy into heat energy and chemical bond energy"c! 'hotosynthesis consumes activated carrier molecules"

d! 'hotosynthesis is the opposite of carbon fixation in the &arth(s carbon cycle"e! 'hotosynthesis increases global warming"

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3-6 )" *omplete the equation for respiration:

+ugars --------- --------- H . / heat energy --------- energy

0" What does this process have in common with a fire that burns the polysaccharides

in wood? How does it differ?

3-7 1or each of the pairs )23 in 1igure 4567, pic8 the more reduced member of the pair"

1igure 4567

3-8 )re the following statements #$%& or 1)L+&? &xplain")" If oxidation occurs in a reaction, it must be accompanied by a reduction"0" #he hydrogenation of an unsaturated fatty acid to a saturated fatty acid, as in the

conversion of vegetable oil to margarine, is an example of an oxidation reaction"*" #he oxidation state of an atom influences its diameter"

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3-9 1or each of the following sentences, fill in the blan8s with the best word or phraseselected from the list below" 9ot all words or phrases will be used each word or phraseshould be used only once"

0y definition, catalysis allows a reaction to occur more

------------------" *hemical reactions occur only when there is aloss of ------------------ energy" &n;ymes act more ------------------ than other catalysts" ) catalyst reduces the ------------------ energy of a reaction"

activation free slowlychemical bond 8inetic unfavorablecompletely rapidlyfavorable selectively

3-10 Which of the following reactions are energetically favorable?

a! base sugar phosphate nucleotideb! amino acid amino acid peptidec! */ . H . / sugar d! sucrose */ . H . /e! 9 . H . ammonia

3-11 Which of the following statements about en;ymes is correct?a! *atalysis of an energetically unfavorable reaction by an en;yme will enable that

reaction to occur"b! )n en;yme can direct a molecule along a particular reaction pathway"

c! )n en;yme can cataly;e many chemically different reactions"d! )n en;yme can bind to many structurally unrelated substrates"e! &n;ymes are permanently altered after cataly;ing a reaction"

3-12 Which of the following *)99/# be a reason that cells use en;ymes rather than heat toincrease the rate of biochemical reactions?

a! #he temperature increase required to speed up a reaction by an appreciable extentis often huge"

b! $eactions cannot be coupled without en;ymes"c! )n en;yme cataly;es

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3-13 #he graph 456=5 is an energy diagram for an energetically favorable reaction of substrate+ converted to product '" Indicate the following on the graph")" #he activation energy for the reaction0" #he free energy change for the reaction*" 3raw a new curve on the graph to indicate how an en;yme that converts + to '

will change the energetics of the reaction"

1igure 456=5

3-14 &nergetically favorable reactions are those thata! decrease the entropy of a system"b! increase the free energy of a system"

c! have a positive G"d! decrease the free energy of a system"e! create order in a system"

3-15 )" Which one or more of the following reactions will 9/# occur spontaneouslyunder the standard conditions that specify G?

a! )3' ' i )#' G > 7"5 8cal moleb! glucose6=6phosphate glucose6@6phosphate G > 2="7 8cal molec! glucose fructose sucrose G > A"A 8cal moled! glucose */ . H . / G > 2@B@ 8cal mole

0" Which of the reactions in ) could be coupled to any of the energeticallyunfavorable reactions to enable them to occur?

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3" 9o change in G and no change in activation energy"

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3-17 )ny reaction ) 0 is at equilibrium whena! G > C"b! G > C"c! D)E > D0E"d! G > G "e! both forward and bac8ward rates reach ;ero"

3-18 *onsider the reaction F G in a cell at 57 *" )t equilibrium, the concentrations of Fand G are AC and A , respectively" %sing the equations below and your new8nowledge, answer the following questions"

G > 2C"@=@ ln K eqG > G C"@=@ ln DGE DFE

$ecall that the natural log of a number z will have a negative value when z J =, positive

when z K =, and C when z > =")" What is the value of K eq for this reaction?0" Is the standard free energy change of this reaction positive or negative? Is the

reaction F G an energetically favorable or unfavorable reaction under standardconditions?

*" What is the value of the standard free energy? $efer to #able 56= in the textboo8or use a calculator"

3" Imagine circumstances in which the concentration of F is =CCC and G is= " Is conversion of F to G favorable? Will it happen quic8ly?

&" Imagine starting conditions in which the reaction F G is unfavorable, yet thecell needs to produce more G" 3escribe two ways that this may be accomplished"

3-19 #he equilibrium constant for the binding of a protein to its ligand can depend on all of thefollowing &F*&'# the

a! number of noncovalent bonds formed between the protein and the ligand"b! concentration of the ligand"c! exact fit of the binding site to the ligand"d! temperature"e! pH"

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3-20 'rotein & can bind to two different proteins, + and I" #he binding reactions are described by the following equations and values:

& + &+ K eq for &+ > =C& I &I K eq for &I > .

0ased on the equilibrium constant values, which one of the following statements is#$%&?

a! & binds I more tightly than +"b! When + is present in excess, no I molecules will bind to &"c! #he binding energy of the &+ interaction is greater than that of the &I interaction"d! *hanging an amino acid on the binding surface of I from a basic amino acid to an

acidic one will li8ely ma8e the free energy of association with & more negative"e! 0inding of + to & will decrease the entropy of these two proteins, and thus it is an

unfavorable reaction"

3-21 When the polymer F6F6F""" is bro8en down into monomers, it is phosphoryly;edMrather than hydroly;ed, in the repeated reaction:

F6F6F""" ' F6' F6F""" reaction =!

Niven the G values of the reactions shown in #able 456.=, what is the expected ratioof F6phosphate F6'! to free phosphate '! at equilibrium for reaction =?

a! =:=C@

b! =:=COc! =:=d! =CO:=e! =C@:=

#able 456.=F6F6F""" H . / F F6F""" G > 2O"A 8cal moleF )#' F6' )3' G > 2."B 8cal mole)#' H . / )3' ' G > 27"5 8cal mole

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3-22 #he following reactions ta8e place in a cell located next to a blood vessel"

F G G > 2=C 8cal moleG / . P */ . G > C"A 8cal mole

9ormally, the blood vessel brings in oxygen and ta8es away carbon dioxide, but years ofoverindulgence have ta8en their toll, and it has become completely clogged withcholesterol, cutting off the blood supply" Which of the following molecules would beexpected to accumulate in large amounts?

a! Fb! Gc! Pd! G and Pe! F and P

3-23 1igure 456.5 shows graphs of energy diagrams for the unfavorable reaction F G, thefavorable reaction G P, and the composite reaction F P"

)" 3raw lines near the composite reaction curve to indicate the free energy changefor each of the three reactions: G FG!, G GP!, and G FP!"

0" Is the composite reaction favorable or unfavorable?

1igure 456.5

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3-24 )" Gou are measuring the effect of temperature on the rate of an en;yme6cataly;edreaction" If you plot reaction rate against temperature, which of the graphs in1igure 456.O would you expect your plot to resemble?

0" &xplain why temperature has this effect"

1igure 456.O

3-25 )re the following statements about diffusion #$%& or 1)L+&?)" #he diffusion rate for small molecules is much slower in the dense gel of thecytoplasm than in pure water"

0" #he diffusion rate is faster for large macromolecules than for small molecules"*" #he rate of diffusion determines the association rate of all binding reactions"3" #he number of reactions per second that an en;yme cataly;es is independent of

diffusion"&" 3iffusion causes a molecule to move along a fairly straight path"

3-26 Which of the following features generally tend to increase the number of catalytic eventsan en;yme accomplishes per second?

a! Increased substrate concentrationb! ore positive free energy of binding between en;yme and substratec! 3ecreased strength of binding between en;yme and productd! Increased diffusion rate of substratee! Increased salt concentration

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How We Know: Using Kinetics to Model and Manipulate MetabolicPathways

3-27 #he product G of an en;ymatic reaction absorbs light at the wavelength .@C nm and the product P of another reaction absorbs at 5OC nm, unli8e the common substrate of the

reactions" ) spectrophotometer was used to measure the initial rate of production of Gand P by the reactions shown in 1igure 456.7)"

#he initial rates were measured for several independent reactions, all containing equalamounts of en;yme ) or en;yme 0 and differing amounts of substrate F" ) graph wasmade of the initial reaction rate v! plotted against the concentration of F DFE! 1igure456.7!" Niven the data shown, are the following statements #$%& or 1)L+&?

1igure 456.7

)" V max )! J V max 0!"

0" )t DFE > =C , the amounts of en;ymes ) and 0 limit the rate of reaction"*" K )! K K 0!" Hint: D+E > K when v > V max ."!3" #he turnover number of en;yme ) is greater than the turnover number of en;yme

0" Hint: #urnover number > V max Den;ymeE"!&" If DFE > = and both en;ymes are present, most of the substrate will be

converted to G rather than P"

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3-28 *onsider a description of an en;ymatic reaction pathway that begins with the binding ofsubstrate + to en;yme & and ends with the release of product ' from the en;yme"

& + &+ &' & '

%nder many circumstances,

K > D&E D+E D&+E

)" What proportion of en;yme molecules are bound to substrate when D+E > K ?0" $ecall that when D+E > K , the reaction rate is V max ." 3oes your answer to 'art

) ma8e sense in light of this rate information?

Activated Carrier Molecules and Biosynthesis

3-29 Which of the following is 9/# a crucial benefit of using en;ymes to cataly;e biologicalreactions?

a! &n;ymes are highly selective in which reactions they cataly;e"b! &n;ymes can drive an unfavorable reaction by coupling it to a favorable reaction,

either directly or via activated carrier molecules"c! &n;ymes ma8e reactions occur faster than without catalysis"d! &n;ymes change the equilibrium of a reaction to ma8e it more favorable"e! #he activity of en;ymes can be modulated by inhibitors and other small molecules

to respond to the needs of the cell at each moment"

3-30 *onsider an analogy between reaction coupling and money" In a simple economy, barter provides a means of direct exchange of material goods" 1or example, the owner of a cowmay have excess mil8 and need eggs, whereas a chic8en owner has excess eggs andneeds mil8" 'rovided these two people are in close proximity and can communicate, theymay exchange or barter eggs for mil8" 0ut in a more complex economy, money serves asa mediator for the exchanges of goods or services" 1or instance, the cow owner withexcess mil8 may not need other goods until three months from now or may want goodsfrom someone who does not need mil8" In this case, the energyM from providing mil8 tothe economy can be temporarily storedM as money, which is a form of energyM used formany transactions in the economy" %sing barter and money as analogies, describe twomechanisms that can serve to drive an unfavorable chemical reaction in the cell"

3-31 ) common means of providing energy to an energetically unfavorable reaction in a cell is by

a! generation of a higher temperature by the cell"b! transfer of a phosphate group from the substrate to )3'"c! en;yme catalysis of the reaction"d! coupling of )#' hydrolysis to the reaction"e! coupling of the synthesis of )#' to the reaction"

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3-33 Gou are studying a biochemical pathway that requires )#' as an energy source" #o yourdismay, the reactions soon stop, partly because the )#' is rapidly used up and partly

because an excess of )3' builds up and inhibits the en;ymes involved" Gou are about togive up when the following table from a biochemistry textboo8 catches your eye"

Hydrolysis reaction G

creatine )#'

en;yme ) creatine phosphate )3' 5 8cal mole

)#' H . /en;yme 0

)3' phosphate 27"5 8cal mole

pyrophosphate H . /en;yme 3

. phosphate 27 8cal mole

glucose @6phosphate H . /en;yme &

glucose phosphate 25"5 8cal mole

Which of the following reagents are most li8ely to revitali;e your reaction?a! ) vast excess of )#'b! Nlucose @6phosphate and en;yme &c! *reatine phosphate and en;yme )d! 'yrophosphatee! 'yrophosphate and en;yme 3

3-34 Which of the following statements is #$%&?a! #he oxidation of food molecules generates 9)3 "b! 9)3H and 9)3'H are found in mutually exclusive parts of the cell"c! #he ratio of 9)3'H:9)3' is higher than the ratio of 9)3H:9)3 because

each molecule of 9)3'H is a stronger reducing agent than a molecule of 9)3H"d! any en;ymes can use 9)3'H and 9)3H interchangeably"e! /ne molecule of 9)3'H can cause the transfer of two hydrogen atoms"

3-35 atch the activated carrier molecules in List = with the groups they transfer, selectedfrom List ." Write the appropriate number beside each item in List ="

List 1 List 2)" )#' =" 2*// 2

0" )cetyl *o) ." e 2 and H*" 9)3'H 5" Nlucose3" *arboxylated biotin O" 2'/ O52

&" S 6adenosylmethionine A" 2*H 5@" 9ucleotide7" 2*/*H 5B" )mino acid

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3-36 Which of the following processes must be coupled to an energetically favorable reactionin order to occur?

a! *onversion of protein into amino acidsb! 'olymeri;ation of amino acids into polypeptidesc! *onversion of glucose to carbon dioxide and water

d! 1ormation of a bilayer from phospholipids in water e! #he hydrolysis of )#'

3-37 #he en;ymes that cataly;e the synthesis of macromolecules do not also cataly;e their brea8down by hydrolysis because

a! en;ymes can cataly;e reactions in only one direction"b! hydrolysis is not an energetically favorable reaction"c! the hydrolytic reaction is not the reverse of the reaction pathway that is used for

biosynthesis"d! en;ymes are destroyed immediately after synthesis is completed"e! biosynthesis proceeds more rapidly than hydrolysis"

3-38 #he energy required for the addition of a * nucleotide subunit * '! to a growing polynucleotide chain is originally derived from the hydrolysis of )#'" &xplain how this isachieved"

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An!/er!

3-1 9o, you will not weigh four pounds more the next morning because only a small portionof the mass of the food will form components of the body" uch of the mass of food isreleased as */ . that is breathed out into the atmosphere or is released into the

environment as waste products" ost of the energy contained in the chemical bonds ofthe food molecules is converted to energy to maintain order among molecules in the

body, energy to move and thin8, and energy for anabolic or biosynthetic reactions torearrange the atoms from food into useful chemical structures biological small moleculesand macromolecules!" )s part of the process, a great deal of the bond energy is alsoconverted to heat"

3-2 *hoice c! is the answer" *hoice a! is incorrect as no system, living or otherwise, candefy the laws of thermodynamics" *hoice b! is incorrect as living organisms do not useheat to power biochemical reactions" Heat is produced in the course of biochemicalreactions" *hoice d! is incorrect: although living organisms are causing a local decreasein entropy, they cannot cause a decrease in the entropy of the universe as a whole as thatwould be a thermodynamic impossibility" *hoice e! is incorrect as living organisms arenot closed systems"

3-3 a! 0y releasing heat to their environment, living things increase the entropy of theenvironment, thus compensating for the decrease in entropy inside cells" Livingthings, therefore, satisfy the second law of thermodynamics" #hey use special

pathways for all their reactions that allow them to be energetically favorable"

3-4 *hoice c! is the answer" *atabolic reactions are the reactions in which a cell brea8sdown food molecules, releasing the energy held within their chemical bonds" *hoices

a!, b!, and e! are energy6requiring processes"

3-5 *hoice b! is true" 'hotosynthesis harvests light energy from the sun and converts it intochemical bond energy" *hoice a! is false because food molecules and oxygen produced

by photosynthesis are the sole source of the energy that powers nearly all living non6 photosynthetic organisms" 'hotosynthesis activates carrier molecules as intermediates inthe fixationM of inorganic carbon dioxide into organic sugar molecules so choices c!and d! are false!" 0y consuming carbon dioxide and producing oxygen photosynthesislessens global warming cause by the greenhouse effect choice e! is false!"

3-6 )" +ugars / . */ . H . / heat energy chemical bond energy0" 0oth respiration and burning are reactions that use oxygen gas to oxidi;e complex

organic carbon molecules into */ . H . /" 0urning is an uncontrolled oxidationin which the energy is all dissipated as heat respiration is a multi6step, controlledoxidation that harnesses the energy in high6energy chemical bonds that are usefulfor anabolic reactions of cells"

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3-7 )Qii 0Qii *Qi 3Qii" ore reducedM means having more electrons gain ofelectrons can result in an increased negative charge or a decreased positive charge andcan be due to an increase in the number of hydrogen atoms in a molecule"

3-8 )" #rue" ) redox reaction involves the complete or partial transfer of electrons from

one molecule or atom to another" #he donor is oxidi;ed and the recipient isreduced in the reaction"0" 1alse" Hydrogenation is a special 8ind of reduction reaction, involving receipt of

an electron from a donor molecule and acquisition of a proton, usually fromwater" Hydrogenation increases the number of *6H bonds in a molecule"

*" #rue" #he diameter of an atom is influenced by the amount of negative charge, orelectron density, surrounding it" #he more reduced an atom becomes, the largerwill be its electron cloud"

3-9 0y definition, catalysis allows a reaction to occur more rapidly " *hemical reactionsoccur only when there is a loss of free energy" &n;ymes act more selectively than other

catalysts" ) catalyst reduces the activation energy of a reaction"

3-10 d!

3-11 b!

3-12 d! &n;ymes change only the activation energy of a reaction, not the free energydifference between reactants and products and thus cannot change the equilibriumconcentrations of reactants and products"

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3-13 +ee 1igure )56=5"

1igure )56=5

)" )ctivation energy is a minus b!"0" *hange in free energy for the reaction is b minus c!"*" )n en;yme will ma8e the value of a! smaller and leave the values for b! and c!

unchanged"

3-14 d!

3-15 )" a! and c!" /nly reactions with a negative G can occur spontaneously"0" *oupling of reaction d! to either of the reactions a! or c! would provide anoverall negative G for the coupled reactions, thus enabling them to occur"

3-16 )Q. 0Q5 *Q= 3QO" Nraph O is the same as the graph for the original reaction interms of the relative energetic differences between substrates, transition states, and

products the reaction diagram curve is simply positioned higher on the y6axis"

3-17 *hoice a! is correct" #he value of G for the reaction ) 0 is ;ero when there is no net tendency for either ) 0 or 0 ), which is the definition of equilibrium" G is aconstant and is thus always the same regardless of whether the reaction has reachedequilibrium or not" #hus choices b! and d! are incorrect" *hoice c! is an incorrectanswer although a particular reaction might be at equilibrium when the concentration ofsubstrate equals that of product, this is not true for most reactions" *hoice e! is not adefinition of equilibrium, but of a reaction that is not occurring at all"

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3-21 c! $eaction = can be written as the sum of the three reactions given, since the )#'used in +tep . is restored in +tep 5"

F6F6F""" H . / F F6F""" G > 2O"A 8cal moleF )#' F6' )3' G > 2."B 8cal mole

)3' ' )#' H . / G > 7"5 8cal mole

+ince G values are additive, G total > C, and if G > C, K eq > =, meaning thatDproductsE DreactantsE > =, and the ratio of F6' to ' is =:="

3-22 b! #he constant removal of */ . and replenishment of / . by the blood normallydrives the reaction G P" #herefore, when */ . is allowed to accumulate and / .drops, G will accumulate" 0ecause the G of the first reaction is very negative,G can accumulate to a very high level without causing significant amounts of F to

build up"

3-23 )" +ee 1igure )56.5 for correct labeling of figure"

1igure )56.5

0" 1avorable

3-24 )" Nraph =0" 0y increasing thermal motion, increasing the temperature increases the rate of

diffusion of components and the number of collisions of sufficient energy toovercome the activation energy" )n increase in temperature will thus increase thereaction rate initially" However, en;ymes are proteins and are held together by

noncovalent interactions, so at very high temperatures, the en;yme will begin todenature and the reaction rate will fall"

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3-32 *hoice c! is correct" #he activation energy of the arsenate compound is extremely low,as can be seen from the reaction profile, meaning that its high6energy intermediate is veryunstable and will be spontaneously hydroly;ed more rapidly than the phosphatecompound" In fact, this hydrolysis occurs rapidly without en;yme catalysis, even incellular conditions" #hus choices d! and e! are false" *hoices a! and b! are false as

more energy is released by the hydrolysis of the arsenoanhydride bond as inferred by thegreater difference in energy level between reactants and products in 1igure 4565.! so, bydefinition, the arsenoanhydride bond is said to have more energy than the

phosphoanhydride bond"

3-33 c! )n excess of )#' will initially restore the reactions, but as )#' is hydroly;ed,)3' will build up and inhibit the en;ymes again" 'yrophosphate does not loo8li8e )#' and is therefore unli8ely to be used by the en;ymes as an alternativeenergy source" 'yrophosphate en;yme 3 will

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3-37 c! Hydrolysis is not the reverse of the reactions cataly;ed by biosynthetic en;ymes"1or instance, the reactions involved in $9) biosynthesis are:

polynucleotide n! 9#' polynucleotide n =! '' i'' i H . / . ' i"

#he reverse reactions are:. ' i '' i H . /'' i polynucleotide n =! polynucleotide n! 9#',

9ot: polynucleotide n =! H . / polynucleotide n! 9 ' nucleoside

monophosphate!,

which is the reaction by which $9) is hydroly;ed" a! and b! are untrue:

en;ymes cataly;e both forward and reverse reactions, and hydrolysis is anenergetically favorable reaction" d! is untrue, since en;ymes are unchanged by

participating in catalysis" Whether e! is true or not for any particular reaction isirrelevant"

3-38 In order to add the * nucleotide to the polynucleotide chain, it must be in the form of a*#' cytidine triphosphate!" *onversion of * ' to *#' occurs by the sequential transfer of two terminal phosphate groups from two molecules of )#'" #hus, hydroylysis of )#'is coupled to phosphorylation of * ' and then to phosphorylation of *3'" +ubsequently,the reaction that adds * ' to the polynucleotide chain releases pyrophosphate '' i!,which is hydroly;ed to inorganic phosphate this favorable reaction provides the energetic

drive for the overall condensation or polymeri;ation! reaction"

+*