CHAPTER 3

ENERGY, CATALYSIS, AND BIOSYNTHESIS

2009 Garland Science Puli!"in#
Ca$al%!i! and $"e &!e '( Ener#% % Cell!
3-1 Chemical reactions carried out by living systems depend on the ability of some organisms
to capture and use atoms from nonliving sources in the environment. The specific subset
of these reactions that breakdown nutrients in food can be described as _____________.
(a) metabolic
(b) catabolic
(c) anabolic
(d) biosynthetic
3-2 The second law of thermodynamics states that the disorder in any system is always
increasing. In simple terms, you can think about dropping aCl crystals into a glass of
water. The solvation and diffusion of ions is favored because there is an increase in
_____________.
(a) p!
(b) entropy
(c) ionic structure
(d) stored energy
3-3 The energy used by the cell to generate specific biological molecules and highly ordered
structures is stored in the form of _____________.
(a) "rownian motion
(b) heat
(c) light waves
(d) chemical bonds
3-4 #t first glance, it may seem that living systems are able to defy the second law of
thermodynamics. !owever, on closer e$amination it becomes clear that although cells
create organi%ation from raw materials in the environment, they also contribute to
disorder in the environment by releasing _____________.
(a) water
(b) radiation
(c) heat
(d) proteins
3-5 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 ne$t morning& 'hy or why not& !int( 'hat
happens to the atoms contained in the food as useful energy is derived from metaboli%ing
the food molecules&
3-6 'hich of the following statements are true or false& If a statement is false, e$plain why it
is false.
#. The second law of thermodynamics states that the total amount of energy in the
)niverse does not change.
". The ultimate source of energy for living systems is chlorophyll.
C. C*+ gas is fi$ed in a series of reactions that are light,dependent.
-. !+ is the most stable and abundant form of hydrogen in the environment.
3-7 Two college roommates do not agree on the best way to handle the clutter piled up in
your dorm room. .oommate / e$plains that chaos is inevitable, so why fight it&
.oommate + counters that maintaining an organi%ed environment makes life easier in
many ways, and that chaos is not inevitable. 'hat law of thermodynamics drives the
thinking of roommate /& 'hat thermodynamic argument can be used to support
roommate +&
3-8 #ssume that the average human adult re0uires +111 kilocalories per day to sustain all
normal processes and maintain a constant weight. If manufactured solar panels could
somehow provide power directly to the human body, what si%e solar panel would be
re0uired (in cm
+
)& #ssume there are /1 hours of sunlight per day, and that the usable
energy output for a typical solar panel is 231 k45ft
+
per hour.
Note: / kcal 6 7./27 k4
/ ft
+
6 8+8.19 cm
+
3-9 :ill in the blanks, selecting from the choices below.
;ight < _________ < _________ = _________ < heat < sugars
C*, C*+, *+, !+, !+*, +, *
3-10 -uring respiration, energy is retrieved from the high,energy bonds found in certain
organic molecules. 'hich of the following, in addition to energy, are the ultimate
products of respiration&
(a) C*+, !+*
(b) C!9, !+*
(c) C!+*!, *+
(d) C*+, *+
3-13 :or each of the pairs #>- in :igure ?9,/9, pick the more reduced member of the pair.
:igure ?9,/9
3-14 *$idation is the process by which o$ygen atoms are added to a target molecule.
@enerally, the atom that is o$idi%ed will e$perience which of the following with respect
to the electrons in its outer shell&
(a) a net gain
(b) a net loss
(c) no change
(d) an e0ual sharing
3-15 'hen elemental sodium is added to water, the sodium atoms ioni%e spontaneously.
)ncharged a becomes a
<
. This means that the a atoms have been _____________.
(a) protonated
(b) o$idi%ed
(c) hydrogenated
(d) reduced
3-16 #rrange the following molecules in order with respect to their relative levels of o$idation
(assign 3 to the most o$idi%ed and / to the most reduced).
_______ C!+* (formaldehyde)
_______ C!7 (methane)
_______ C!**! (formic acid)
_______ C!9*! (methanol)
_______ C*+ (carbon dio$ide)
3-17 *$idation and reduction states are relatively easy to determine for metal ions, because
there is a measurable net charge. In the case of carbon compounds, o$idation and
reduction depend on the nature of polar covalent bonds. 'hich of the following is the
best way to describe these types of bond&
(a) hydrogen bonds in a nonpolar solution
(b) covalent bonds in an a0ueous solution
(c) une0ual sharing of electrons across a covalent bond
(d) e0ual sharing of electrons across a covalent bond
3-18 Aeed oils are often dehydrogenated and added back into processed foods as partly
unsaturated fatty acids. In comparison with the original oil, the new fatty acids have
additional double carbon>carbon bonds, replacing what were once single bonds. This
process could also be described as _____________.
(a) isomeri%ation
(b) o$idation
(c) reduction
(d) protonation
3-20 Chemical reactions that lead to a release of free energy are referred to as Benergetically
favorable.C #nother common way in which these reactions are described is
_____________.
(a) uphill
(b) uncataly%ed
(c) spontaneous
(d) activated
3-21 DGE indicates the change in the standard free energy as a reactant is converted to product.
@iven what you know about these values, which reaction below is the most favorable&
(a) #-F < Fi = #TF DGE 6 <G.9 kcal5mole
(b) glucose /,phosphate = glucose H,phosphate DGE 6 >/.G kcal5mole
(c) glucose < fructose = sucrose DGE 6 <3.3 kcal5mole
(d) glucose = C*+ < !+* DGE 6 >H2H kcal5mole
3-22 Catalysts are molecules that lower the activation energy for a given reaction. Cells
produce their own catalysts called _____________.
(a) proteins
(b) en%ymes
(c) cofactors
(d) comple$es
3-23 :or each of the following sentences, fill in the blanks with the best word or phrase
selected from the list below. ot all words or phrases will be usedI each word or phrase
should be used only once.
"y definition, catalysis allows a reaction to occur more
__________________. Chemical reactions occur only when there is a loss
of __________________ energy. Jn%ymes act more
__________________ than other catalysts. # catalyst decreases the
__________________ energy of a reaction.
activation free slowly
chemical bond kinetic unfavorable
completely rapidly favorable
selectively
3-24 :igure ?9,+7 is an energy diagram for the reaction K=L. 'hich e0uation below
provides the correct calculation for the amount of free,energy change when K is
converted to L&
(a) a < b > c
(b) a > b
(c) a > c
(d) c > a
:igure ?9,+7
3-25 Jn%ymes facilitate reactions in living systems. :igure ?9,+3 presents an energy diagram
for the reaction K=L. The solid line in the energy diagram represents changes in energy
as the product is converted to reactant under standard conditions. The dashed line shows
changes observed when the same reaction takes place in the presence of a dedicated
en%yme. 'hich e0uation below indicates how the presence of an en%yme affects the
activation energy of the reaction (cataly%ed versus uncataly%ed)&
(a) d > c versus b > c
(b) d > a versus b > a
(c) a < d versus a < b
(d) d > c versus b > a
:igure ?9,+3
3-26 'hich of the following statements are true or false& If a statement is false, e$plain why it
is false.
#. Jn%ymes lower the free energy released by the reaction that they facilitate.
". Jn%ymes lower the activation energy for a specific reaction.
C. Jn%ymes increase the probability that any given reactant molecule will be
converted to product.
-. Jn%ymes increase the average energy of reactant molecules.
3-27 DG measures the change of free energy in a system as it converts reactant (L) into
product (K). 'hen MLN 6MKN, DG is e0ual to _____________.
(a) DGE < RT
(b) RT
(c) ln MKN5MLN
(d) DGE
3-28 :or the reaction L=K at standard conditions with MLN 6 / O and MKN 6 / O, DG is
initially a large negative number. #s the reaction proceeds, MLN decreases and MKN
increases until the system reaches an e0uilibrium. !ow do the values of DG and DGE
change as the reaction e0uilibrates&
(a) DG becomes less negative and DGE stays the same.
(b) DG becomes positive and DGE becomes positive.
(c) DG stays the same and DGE becomes less negative.
(d) DG reaches %ero and DGE becomes more negative.
3-29 The e0uilibrium constant (K) for the reaction L=K can be e$pressed with respect to the
concentrations of the reactant and product molecules. 'hich of the e$pressions below
shows the correct relationship between K, MLN, and MKN&
(a) K 6 MLN5MKN
(b) K 6 MLN P MKN
(c) K 6 MKN5MLN
(d) K 6 MKN > MLN
3-30 Isomeri%ation of glucose /,phosphate to glucose H,phosphate is energetically favorable.
#t 9GEC, DGE 6 >/.7+ log/1K. 'hat is the e0uilibrium constant for this reaction if DGE 6
>/.G7 kcal5mole at 9GEC&
(a) /H.82
(b) 1.18
(c) >1.18
(d) 1.98
3-31 *n the basis of the two reactions below, decide which of the following statements are true
and which are false. If a statement is false, e$plain why it is false.
/( #TF < L = L,F < #-F DG 6 >/11 kcal5mole
+( L,F < # = " DG 6 31 kcal5mole
#. .eaction / is favorable because of the large negative DG associated with the
hydrolysis of #TF.
". .eaction + is an e$ample of an unfavorable reaction.
C. .eactions / and + are coupled reactions, and when they take place together,
reaction + will proceed in the forward direction.
-. .eaction + can be used to drive reaction / in the reverse direction.
3-32 The potential energy stored in high,energy bonds is commonly harnessed when the bonds
are split by the addition of _______________ in a process called _____________.
(a) #TF, phosphorylation
(b) water, hydrolysis
(c) hydro$ide, hydration
(d) acetate, acetylation
3-33 'hen the polymer K,K,KQ is broken down into monomers, it is Bphosphoryly%edC
rather than hydroly%ed, in the following repeated reaction(
K,K,KQ < F = K,F < K,KQ (reaction /)
@iven the DGE values of the reactions listed in the following table, what is the e$pected
ratio of K,phosphate (K,F) to free phosphate (F) at e0uilibrium for reaction /&
(a) /(/1
H
(b) /(/1
7
(c) /(/
(d) /1
7
(/
(e) /1
H
(/
3-34 Consider the reaction K=L in a cell at 9GEC. #t e0uilibrium, the concentrations of K and
L are 31 RO and 3 RO, respectively. )sing the e0uations below and your new
knowledge, answer the following 0uestions.
DGE 6 >1.H/H ln Ke0
DG 6 DGE < 1.H/H ln MLN5MKN
.ecall that the natural log of a number z will have a negative value when z S /, positive
when z T /, and 1 when z 6 /.
#. 'hat is the value of Ke0 for this reaction&
". Is the standard free,energy change of this reaction positive or negative& Is the
reaction K=L an energetically favorable or unfavorable reaction under standard
conditions&
C. 'hat is the value of the standard free energy& .efer to Table 9,/ in the te$tbook
or use a calculator.
-. Imagine circumstances in which the concentration of K is /111 RO and that of L
is / RO. Is conversion of K to L favorable& 'ill it happen 0uickly&
J. Imagine starting conditions in which the reaction K=L is unfavorable, yet the
cell needs to produce more L. -escribe two ways in which this may be
accomplished.
3-35 If proteins # and " have complementary surfaces, they may interact to form the dimeric
comple$ #". 'hich of the following is the correct way to calculate the e0uilibrium
constant for the association between # and "&
(a) kon5koff 6 K
(b) K 6 M#NM"N5M#"N
(c) K 6 M#"N5M#NM"N
(d) (a) and (c)
3-36 Oatch the following general e0uations with the energy diagram that best describes the
free,energy transitions along the reaction pathway. Indicate your answer by filling in the
e0uation number in the bo$ under each respective curve. #fter you have identified a
match for each e0uation, indicate the positions of #, ", and C (if applicable) on the free,
energy curves. ot all of the energy diagrams will have a match.
3-37 The net distance a molecule travels as it diffuses through the cytosol is relatively short in
comparison with the total distance it travels. This is because movement governed by
diffusion alone is a ________________ process that is most effective for the dispersion
of small molecules over short distances.
(a) slow
(b) random
(c) regulated
(d) complicated
3-38 The small molecule cyclic #OF (c#OF) takes about 1.+ second to diffuse /1 Rm, on
average, in a cell. Auppose that c#OF is produced near the plasma membrane on one end
of the cellI how long will it take for this c#OF to diffuse through the cytosol and reach
the opposite end of a very large cell, on average& #ssume that the cell is +11 Rm in
diameter.
(a) 7 seconds
(b) /H seconds
(c) 21 seconds
(d) +11 seconds
3-39 The graph in :igure ?9,98 illustrates the relationship between reaction rates and
substrate concentration for an en%yme,cataly%ed reaction. 'hat does the Km value
indicate with respect to en%yme substrate interactions&
(a) the ma$imum rate of catalysis
(b) the number of en%yme active sites
(c) the en%yme>substrate binding affinity
(d) the e0uilibrium rate of catalysis
:igure ?9,98
3-40 The graph in :igure ?9,71 illustrates the change in the rate of an en%yme,cataly%ed
reaction as the concentration of substrate is increased. 'hich of the values listed below is
used to calculate the en%yme turnover number&
(a) UVma$
(b) Km
(c) Vma$
(d) Vma$ > Vm
:igure ?9,71
3-41 Frotein J can bind to two different proteins, A and I. The binding reactions are described
by the following e0uations and values(
J < A = JA Ke0 for JA 6 /1
J < I = JI Ke0 for JI 6 +
@iven the e0uilibrium constant values, which one of the following statements is true&
(a) J binds I more tightly than A.
(b) 'hen A is present in e$cess, no I molecules will bind to J.
(c) The binding energy of the JA interaction is greater than that of the JI interaction.
(d) Changing an amino acid on the binding surface of I from a basic amino acid to an
acidic one will probably make the free energy of association with J more
negative.
3-42 Indicate whether the following statements about en%ymes are true or false. If a statement
is false, e$plain why it is false.
#. Jn%ymes alter the e0uilibrium point of a reaction.
". Vma$ can be determined by measuring the amount of product accumulated late in
the reaction.
C. Competitive inhibitors bind irreversibly to the en%yme active site, lowering Vma$.
3-43 #. Lou are measuring the effect of temperature on the rate of an en%yme,cataly%ed
reaction. If you plot reaction rate against temperature, which of the graphs in
:igure ?9,79 would you e$pect your plot to resemble&
". J$plain why temperature has this effect.
:igure ?9,79
3-44 Consider a description of an en%ymatic reaction pathway that begins with the binding of
substrate A to en%yme J, and ends with the release of product F from the en%yme.
J < A = JA = JF = J < F
In many circumstances,
Km 6 MJN MAN 5 MJAN
#. 'hat proportion of en%yme molecules are bound to substrate when MAN 6 Km&
". .ecall that when MAN 6 Km, the reaction rate is UVma$. -oes your answer to part #
make sense in the light of this rate information&
3-45 :igure ?9,73 illustrates the amount of energy per molecule for a population in a
contained, controlled environment. Oost molecules will have the average energy of the
population, shown in region /. The number of molecules in the population with enough
energy to be converted to product is shown in region +. The number of molecules with
enough energy to react in the presence of en%yme is shown in region 9. )se this
information to e$plain how en%ymes cataly%e reactions.
:igure ?9,73
3-46 Chemical reactions are reversibleI they can proceed in both the forward and reverse
directions. If the DGE for the reaction L=K is energetically favorable, how can you
e$plain the fact that not all of the L molecules will be converted to K molecules&
3-47 Jn%ymes # and " cataly%e different reactions, but use the same reactant molecule as a
substrate. The graph in :igure ?9,7G presents the reaction rates observed when en%yme #
and en%yme " are mi$ed together in a single test tube containing molecule K. 'hat are
the Vma$ and the apparent Km values for each en%yme under these conditions& !ow might
these values change for en%yme " if it were analy%ed in the absence of en%yme #&
J$plain your answer.
:igure ?9,7G
Ac$i)a$ed Carrier *'lecule! and Bi'!%n$"e!i!
3-48 Consider an analogy between reaction coupling and money. In a simple economy, barter
provides a means of direct e$change of material goods. :or e$ample, the owner of a cow
may have e$cess milk and need eggs, whereas a chicken owner has e$cess eggs and
needs milk. Frovided that these two people are in close pro$imity and can communicate,
they may e$change or barter eggs for milk. "ut in a more comple$ economy, money
serves as a mediator for the e$changes of goods or services. :or instance, the cow owner
with e$cess milk may not need other goods until three months from now, or may want
goods from someone who does not need milk. In this case, the BenergyC from providing
milk to the economy can be temporarily BstoredC as money, which is a form of BenergyC
used for many transactions in the economy. )sing barter and money as analogies,
describe two mechanisms that can serve to drive an unfavorable chemical reaction in the
cell.
3-49 Lou are studying a biochemical pathway that re0uires #TF as an energy source. To your
dismay, the reactions soon stop, partly because the #TF is rapidly used up and partly
because an e$cess of #-F builds up and inhibits the en%ymes involved. Lou are about to
give up when the following table from a biochemistry te$tbook catches your eye.
'hich of the following reagents are most likely to revitali%e your reaction&
(a) a vast e$cess of #TF
(b) glucose H,phosphate and en%yme J
(c) creatine phosphate and en%yme #
(d) pyrophosphate
3-50 The anhydride formed between a carbo$ylic acid and a phosphate (:igure ?9,31#) is a
high,energy intermediate for some reactions in which #TF is the energy source. #rsenate
can also be incorporated into a similar high,energy intermediate in place of the phosphate
(:igure ?9,31"). :igure ?9,31C shows the reaction profiles for the hydrolysis of these
two high,energy intermediates. 'hat is the effect of substituting arsenate for phosphate
in this reaction&
:igure ?9,31
(a) It forms a high,energy intermediate of lower energy.
(b) It forms a high,energy intermediate of the same energy.
(c) It decreases the stability of the high,energy intermediate.
(d) It increases the stability of the high,energy intermediate.
3-51 The synthesis of glutamine from glutamic acid re0uires the production of an activated
intermediate followed by a condensation step that completes the process. "oth amino
acids are shown in :igure ?9,3/.
:igure ?9,3/
'hich molecule is added to glutamic acid in the activation step&
(a) phosphate
(b) !9
(c) #TF
(d) #-F
3-52 The synthesis of glutamine from glutamic acid re0uires the production of an activated
intermediate followed by a condensation step that completes the process. "oth amino
acids are shown in :igure ?9,3+.
:igure ?9,3+
In the condensation step, _______________ is displaced by ________________.
(a) *!, !9
(b) #-F, !+
(c) #TF, !9
(d) phosphate, !9
3-53 #-! and #-F! are activated carrier molecules that function in completely different
metabolic reactions. "oth carry two additional ________ and one additional
_____________. This combination can also be referred to as a hydride ion.
(a) protons, electron
(b) electrons, phosphate
(c) hydrogens, electron
(d) electrons, proton
3-54 The addition of a new deo$ynucleotide to a growing -# chain re0uires more energy
than can be obtained by the hydrolysis of #TF to #-F < Fi. 'hat alternative series of
reactions is used, and how does this help overcome the energy barrier for -# synthesis&