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Chapter 8 Mechanisms and Inhibitors
Matching Questions
Use the following to answer questions 1–10.
Choose the correct answer from the list below. Not all of the answers will be used.
a) hydrolysis
b) affinity label
c) tyrosinase
d) chymotrypsin
e) pepsin
f) noncompetitive
g) uncompetitive
h) heterotropic
i) approximation and orientation
j) acid–base
h) competitive
4. ____________: The type of catalysis in which two substrates are brought into close proximity.
Ans: j
Section: 8.1
6. ____________: The inhibitor which binds only to the ES complex and lowers the Vmax and KM.
Ans: g
Section: 8.2
7. ____________: The enzyme inhibition that can be overcome by increasing the concentration of
substrate.
Ans: k
Section: 8.2
Chapter 8 Mechanisms and Inhibitors 2
10. ____________: An enzyme that is part of a pigment formation pathway and has a low optimum
temperature.
Ans: c
Section: 8.2
Fill-in-the-Blank Questions
11. An enzyme catalyst mechanism that uses a metal cation to stabilize a negative charge in the
active site is ________________.
Ans: metal ion catalysis Section: 8.1
12. A ________________ catalytic mechanism that forces two substrates into an appropriate three-
dimensional arrangement for the reaction to occur.
Ans: catalysis by approximation and orientation Section: 8.1
14. In conducting an experiment with a new drug, you find that regardless of the concentration of
substrate, the drug is able to inhibit the enzyme activity. You are likely to not have a(n)
________________ type of inhibitor.
Ans: competitive Section: 8.2
15. An uncompetitive inhibitor will have two ________________ lines on a double-reciprocal plot.
Ans: parallel Section: 8.2
17. The ________________ stabilizes the tetrahedral intermediate of the hydrolysis of a peptide
bond by chymotrypsin.
Ans: oxyanion hole Section: 8.3
18. A(n) ________________ inhibitor has a structure similar to the substrate and reversibly binds to
the active site of the enzyme.
Ans: competitive Section: 8.2
19. The straight-line kinetic plot of 1/V0 versus 1/S is called a ________________.
Ans: Lineweaver–Burk plot, or double-reciprocal plot Section: 8.2
Multiple-Choice Questions
21. What conclusion can be drawn concerning an inhibitor if the KM is the same in the presence and
absence of the inhibitor?
A) The inhibitor binds to the substrate.
B) The inhibitor has a structure that is not very similar to the substrate.
C) The inhibitor forms a reversible covalent bond with the enzyme.
D) The inhibitor binds to the same active site as the substrate.
E) The Vmax is larger in the presence of the inhibitor.
Ans: B Section: 8.2
23. In this type of inhibition, the inhibitor can only bind to the ES complex to form an ESI complex.
A) competitive
B) noncompetitive
C) irreversible
D) uncompetitive
E) None of the above.
Ans: D Section: 8.2
24. Which amino acids in chymotrypsin are found in the active site and are participants in substrate
cleavage?
A) his, ser, asp
B) his, ser
C) asp, lys
D) lys, arg
E) his, ser, arg
Ans: A Section 8.3
27. A protein that is optimally active at neutral pH is likely to have which in the active site?
A) the side chains of aspartate and glutamine
B) two histidine amino acid side chains
C) a glycine amino acid
D) one or more carboxyl groups
E) two amino groups
Ans: A Section: 8.2
28. The metal most commonly found at the active site of metalloproteases is:
A) zinc.
B) calcium.
C) selenium.
D) magnesium.
E) sodium.
Ans: A Section: 8.1
Short-Answer Questions
30. How are the types of inhibition kinetically distinguishable?
Ans: Competitive inhibition can be overcome by the presence of large amounts of substrate.
However, the apparent KM is increased. In noncompetitive inhibition, substrate can bind
to the enzyme-inhibitor complex; however, the Vmax is decreased. In mixed inhibition,
both values may be altered.
Section: 8.3
Chapter 8 Mechanisms and Inhibitors 5
31. Complete the structure of the catalytic triad of chymotrypsin by drawing the proper structure of
the missing residue side chain in the box provided. Show the proper hydrogen bonding involved
in this triad.
O H O
Asp C O CH2
Ser
CH2
Ans:
His
CH2
O N H O
H N
Asp C O CH2
Ser
CH2
Section: 8.3
32. What is the challenge for a protease to facilitate hydrolysis of a peptide bond?
Ans: The peptide bond contains a carbonyl that is not very reactive; therefore, the catalytic
mechanism must employ a feature that promotes nucleophilic attack of this carbonyl
group so the peptide bond can be cleaved.
Section: 8.3
33. How can covalent modification be used to determine the mechanism of action of an enzyme?
Ans: If a particular amino acid side chain is suspected of participating in a catalytic
mechanism, covalent modification of the residue may change it enough that the enzyme
activity is altered or inhibited. However, this method is usually confirmed by other
techniques, such as site-directed mutagenesis, to rule out other possible reasons for the
loss of activity, such as conformational change.
Section: 8.3
36. What caused a “burst” of activity followed by a steady-state reaction when chymotrypsin was
studied by stop-flow techniques?
Ans: Chymotrypsin cleaves peptide bonds in a two-step reaction, in which the first step,
formation of the acyl enzyme intermediate, is faster than the second step, hydrolysis.
Section: 8.3
Chapter 8 Mechanisms and Inhibitors 6
37. Designing drugs to inhibit enzymes is a large part of pharmaceutical research. What are some of
the enzymatic features that would be important?
Ans: The enzyme could be inhibited by the interaction of a potential drug at the active site or at
a site that alters conformation or regulation of the enzyme. The structure of natural
substrates and activators, and their binding sites, would be useful features to study for a
new drug design. The binding affinity and specificity would be important, and standard
enzyme assays would be used to determine the effect of the inhibitors on Kcat, KM, and
Vmax.
Section: 8.2
38. What factors should an enzymologist consider when designing an enzyme assay?
Ans: Factors an enzymologist should consider when designing an enzyme assay include the pH
for optimal substrate binding and enzymatic activity, the temperature for proper catalytic
function, and the additional regulatory compounds needed to measure the enzyme’s
activity.
Section: 8.2
39. There is a key difference between an enzyme that uses a covalent catalysis mechanism and one
that uses other catalytic strategies. What is this key difference?
Ans: For each of the other strategies of catalysis, a substrate and/or a cofactor are bound to the
site by noncovalent interactions with the amino acids of the enzyme. An enzyme that uses
a covalent catalyst strategy covalently binds the substrate to one or more of the amino
acids in the active site.
Section: 8.1
40. Which of the following curves (no inhibitor, inhibitor 1, or inhibitor 2) represents the rate of
reaction versus substrate concentration for a competitive and an uncompetitive inhibitor? Draw
the double-reciprocal plot for each case.
No I
I1
V0
I2
[S]
Ans: Inhibitor 1 is a competitive inhibitor; inhibitor 2 is an uncompetitive inhibitor .
Section: 8.2
42. Draw and describe the reaction pathway for a noncompetitive inhibitor.
Ans: The figure should resemble the reaction pathway shown in Figure 8.9. Here, the pathway
is demonstrating that the substrate can bind irreversibly to the enzyme alone or to the
enzyme already bound to the inhibitor. The ESI complex can continue in this pathway to
an ES + I state, but may not continue to an EI + P product.
Section: 8.2
44. Bacteria that become penicillin resistant express an enzyme called -lactamase. This enzyme
hydrolyses the lactam ring on penicillin. Suggest a reason why this protein allows cells to grow
in the presence of penicillin.
Ans: Penicillin is a suicide inhibitor of the transpeptidase enzyme that modifies the serine –OH
in the active site. -lactamase reduces the concentration of the inhibitor, allowing the cell
wall of the bacteria to properly form.
Section: 8.2
45. The initial reaction kinetics of some enzymes results in a quick burst of product in a short period
of time, followed by a slower but sustained increase in product formation over time. What does
this type of kinetic response tell an enzymologist about the mechanism of the catalysis?
Ans: These two-phase reactions (a rapid-burst phase and a steady-state phase) indicate that the
reaction takes place in two steps. The first step is very quick and will achieve equilibrium
rapidly; the second step of the reaction is slower.
Section: 8.3
47. How is the enzyme chymotrypsin bind and hydrolyze its substrate? How does this differ from
other proteases?
Ans: Chymotrypsin binds its substrate with a deep hydrophobic pocket, locking the substrate
into an appropriate conformation. If this binding site were altered or missing, the active
site would remain and the protein would bind many different substrates, as is the case for
some of the other proteases.
Section: 8.3
Chapter 8 Mechanisms and Inhibitors 8
49. You measure the initial velocity of an enzyme in the absence and presence of two inhibitors. In
each case, the inhibitor is at 10 µM. Shown in the table below is the primary data for all three
cases. Construct a Lineweaver–Burk plot for each case. Calculate the KM and Vmax for each case,
both graphically and mathematically. Determine the mechanism for each inhibitor and where
each will interact on the enzyme.
Initial Velocity (µmol/ml min)
Enzyme Enzyme Enzyme
[S] mM Alone + Inhibitor 1 + Inhibitor 2
0.33 1.65 1.05 0.79
0.50 2.13 1.43 1.02
1.00 2.99 2.22 1.43
2.00 3.72 3.08 1.79
5.00 4.00 3.80 2.00
Ans: Construct a double-reciprocal plot. From the intercept of the vertical axis, determine the
value for the intercept = 1/Vmax and the horizontal axis to determine the value for −1/KM.
Section: 8.2
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Volynia rose now against Volodislav. First Mystislav the Silent was
put forward, then Bailski, Leshko’s father-in-law, sent his brother,
Vsevolod, to attack the adventurer, and went himself later. Last of all
Daniel acted. After that, Leshko with Poles and men of Volynia
advanced against Volodislav. Volodislav left to his brothers the task
of defending the capital, and with hired forces hurried forth to meet
his opponents, but he was driven back and defeated. The victors
could not take Galitch, however. They fought at its walls till
exhausted, and then had to abandon the task. On the way home,
Leshko induced Bailski, now Prince of Volynia, to give two towns
near the capital to the orphans, who then moved thither from
Kamenyets, and, being near the capital, ceased not to sigh for it. “It
will come to us,” thought they. And it came earlier than they
expected.
Pakoslav now offered a second good counsel: “Let the prince, out of
love for the orphans, give them Vladimir of Volynia.” Immediately
Leshko sent this message to Bailski: “Give Vladimir to Vassilko and
Daniel. If thou wilt not consent, I will take it.” Bailski would not yield,
then Leshko constrained him, and installed Roman’s sons in
Vladimir.
Volodislav, now a prisoner, was put in fetters and died in
confinement. No prince would shelter his orphans, because their
father had aspired to sovereignty.
The King and Queen of Galitch, though mere children, were crowned
straightway. Andrei, seeing that the boyars were desirous of union
with Hungary, and remembering their statement that the people
would not oppose union, if their faith and its ceremonies were
respected, now wrote to the Pope on the subject: “Let it be known to
your Holiness that the princes of Galicia, and the people there under
us, wish as king our son, Koloman, and promise union with the Most
Holy Roman Church if they may keep their own ritual. Lest delay
harm a thing so useful to us and to you, give a written command, we
beg of you, to the Archbishop of Strigonia to anoint, at the earliest,
our son, the King of Galitch.”
Thus Galitch was lost for a time to Russian princes and the Orthodox
clergy. In Chernigoff and Kief, people were not thinking of Galitch;
they had their own troubles. Chermny and Rurik exchanged
principalities, Chermny went to Kief and Rurik to Chernigoff. Thus
the ancient home of Oleg and his descendants passed to a
descendant of Monomach, and Chermny, the senior of Oleg’s
descendants, not only took the old capital, but threatened to drive
from Kief regions all the descendants of Monomach. He declared
that through their fault a terrible crime had been committed. “Ye
caused the death of my cousins in Galitch, and put a great shame on
us. Ye have no part in Kief regions,” asserted he. Still after that
Chermny turned to Big Nest with [179]a prayer for peace and
friendship. He begged the metropolitan to bear this request to
Vladimir. Peace was granted, and that winter Big Nest strengthened
this peace by a marriage between his second son, Yuri, and the
daughter of Chermny.
Toward the end of his life, the Prince of Vladimir had many disputes
with Novgorod, which for years had been friendly. It was most
important for Novgorod to be at peace with Vladimir, to trade with its
broad regions, and receive grain, which in Novgorod was lacking at
all times. Nothing harmed Novgorod more than a quarrel with
Vladimir, whose prince could stop grain from reaching the city and
surrounding country, and arrest Novgorod merchants wherever he
found them in his own territory. But this was not sufficient to change
the quarrelsome disposition of Novgorod, where factions fought with
one another continually. When a posadnik displeased them, they
beat him, or hurled the man from the bridge to the river. Big Nest did
not interfere with their freedom. On the contrary he apparently
commended it. “Love him who seems good to you, but execute bad
men,” said he. And the Novgorod people carried out this instruction,
even against their own adherents, the Miroshiniches, with whom they
settled in real Novgorod fashion.
As this uprising was directed against all adherents of Big Nest, the
Novgorod people did not escape punishment. Again he arrested
Novgorod merchants and their goods throughout the lands of
Vladimir. Great inconvenience was felt by Novgorod people, and
Oleksa’s avengers spread complaints wherever they could against
Big Nest, who, being then at the height of his power and influence,
had no effective opponents. It seemed as though no man could
refuse him obedience.
Mystislav did at once all that was asked of him, and Big Nest fulfilled
his promise. Sviatoslav returned to his father, and Mystislav entered
Novgorod, rejoicing that he had passed through great peril without
bloodshed.
Big Nest was nearing the end of his earthly existence. He had
continued the task undertaken by his father and his brother to
[182]preserve and enlarge the principality of Vladimir. He had not
worked for all Russia, though he had tried to hold a share in the
Russia outside of Vladimir. During his rule, which was firm and at
times even terrible, he not only preserved unimpaired, but extended
and strengthened Vladimir. He established the beginning of a state in
the North and fixed its central region. Earlier than Big Nest, not only
in the time of his father, but also in that of Andrei, his brother, Rostoff
and Suzdal were remembered as belonging to Novgorod. Men did
not consider Vladimir or Moscow or any other place, as that Great
Russia which they were to obey, and to which they must gravitate.
Before Big Nest’s activity, Bailozersk and Galitch beyond the Volga,
and other places, if not claimed by Novgorod altogether, were
claimed at least partially. Now the Dvina country beyond the Volga
had become so connected with Vladimir that all was reconstituted.
That broad region looked on itself as Great Russia, and all men
began to regard it in that light. Lord Novgorod itself was forced to
count those lands as lost forever. Neither Rostoff nor Suzdal, from
the time of Big Nest, dared to think of their earlier primacy, the
memory of which became mingled with traditions of its ancient
connection with Novgorod. After Big Nest there could be no talk of
separation from Vladimir, for it became clear that not to Rostoff, or to
Suzdal did that Great Russia gravitate, but to Vladimir.
As his father had left Rostoff and Suzdal to his younger sons and
Vladimir to the eldest, so Big Nest, almost on the eve of his death,
gave Vladimir to his eldest son, Constantine, and left Rostoff to Yuri
his second son.
Constantine, who was in Rostoff at this time and enjoyed there great
friendship among boyars, was angry that his favorite city was given
not to him but to Yuri, and he would not abandon Rostoff for Vladimir
at the command of Big Nest. This was not his first disobedience. His
father had not forgotten the campaign of Ryazan, when Constantine
spoke against him in the presence of others. Big Nest repeated the
command. Constantine refused a second time, and sent a demand
that Rostoff should be given with Vladimir. The Grand Prince was
grieved and distressed at his son’s disobedience, and there was no
measure to his anger. As a result that took place which up to this
time had been unknown in Russia: Big Nest deprived his eldest son
of [183]seniority, and gave it to his second son, Yuri. From all the
districts and towns in Vladimir he summoned an assembly of priests,
merchants, nobles, and people, with Yoan, the bishop, at the head of
them, and in their presence gave the capital of Vladimir to Yuri,
imposing on him seniority. He commanded Yuri’s brothers to obey
him, and they kissed the cross to do so. Then the people kissed the
cross to the Grand Prince, that they would obey Yuri. From this came
endless contention in the family of Big Nest, who died shortly after.
He expired at the age of fifty-eight, Sunday, April 15, 1212, at the
hour when mass was ending in all the churches of Vladimir. They
buried him near his brother Andrei in the golden-domed cathedral,
the day following his death, as was the custom at that time.
Yuri freed the Ryazan and Murom princes imprisoned by his father.
Strengthened by them, he could war against his brother more
successfully. Constantine, leaving for a time his attempt on Vladimir,
continued hostile action in northern places. He seized Saligalsk, and
burned Kostroma. The whole principality was in conflict from Vologda
to Moscow. A second and a third year after the death of Big Nest this
struggle continued.
The Novgorod men were not pleased with themselves, and they
halted. “Lord brothers,” said Tverdislav, “what ye decide will be done
at all hazards. The question is ought we to abandon our prince at
this juncture. In their day our fathers and grandfathers marched to
suffer at Kief when their prince commanded. It is clear that we
should act in the old way.” Pleased with this speech, they turned,
and with hurried marches overtook Mystislav.
Daniel acted. He won back many towns, and warred against Leshko
successfully. Leshko doubted not that this winning was effected
through Mystislav’s counsel, and in view of this he changed [187]his
plans quickly. The Poles and Hungarians, from being enemies,
suddenly became friends. Leshko sent a message to Hungary that
he yielded Galitch gladly to Koloman, his son-in-law. With that Andrei
immediately allied himself with Leshko, and declared war against
Mystislav and Daniel. Leshko led in a strong army. A still greater
force came from Hungary. Mystislav wished to attack in the rear,
hence he moved toward Zbruch, and ordered his son-in-law to
defend Galitch. He summoned Bailski, also, and commanded both
allies to retire into Galitch and defend it. But Bailski left this difficult
task to Daniel, who had to bear the whole brunt of the attack of
Hungarian and Polish forces. He yielded no whit, however, and
defended the city successfully.
The allies now raised the siege and turned all their strength against
Mystislav, who was acting in their rear. Mystislav spared his scant
forces, and, while withdrawing, commanded Daniel to march out of
Galitch and join him. It was easy to give this command, but far from
easy to obey it. Mystislav himself, by deft action, slipped away
without loss, marching quickly to Kamenyets and thence to the Ros
River.
Daniel found himself now in a perilous position. The allies with united
strength, rushed at his army. It was difficult to withdraw from Galitch,
and extremely difficult to retreat along the whole course of the
Dniester, repelling the ceaseless attacks of keen enemies who
disputed each step that his men made. These enemies were much
encouraged by Mystislav’s withdrawal. Their forces were vastly
greater, and Daniel’s men lacked provisions. Night and day marches,
cold and hunger, fighting on horseback, riding without food and sleep
for nights and days in succession; all this the young warrior had to
live through in that murderous retreat down the Dniester. The glory of
this march was shared by his father’s chief boyars, who were with
him. Even they were astonished by the valor of their leader, still a
stripling. They saw with wonder how he fought entire days without
dismounting, how he rushed in pursuit of the enemy, who only saved
themselves through the swiftness of their horses.
Daniel, awaiting the time of fresh action, returned to his capital, but
Mystislav did not go directly to the Polovtsi. He appeared soon after
in Novgorod. During his absence many changes had taken place.
The prince sent from Vladimir by Yuri had been replaced by one sent
from Kief by Mystislav, son of the Smolensk prince, Roman. Neither
man pleased “Lord Novgorod.” The first, alarmed at disorders,
hastened home to his father; the second found still greater trouble.
Bloody battles took place on the streets, and again a posadnik was
murdered.
Novgorod turned to Yuri a second time. “If thy son will not stay with
us, send Yaroslav, thy brother,” said they. Yaroslav seemed indeed
just the prince needed in Novgorod, and the friends of Mystislav the
Gallant might think to find in him the prince for whom they had been
seeking a long time, for was he not intimate with Mystislav, being
married to his eldest daughter? Partisans also saw in him the best of
his family.
Yaroslav dismissed the priest without discussion. Not only did he not
free the prisoners, but those whom he held in Torjok he put in chains,
and sent to Pereyaslavl Beyond the Forest. Their property and
goods he distributed among his attendants. The moment that news
of this came to Novgorod, Mystislav commanded to sound the bell of
the assembly. The whole city came to him. “Let us go, brothers!” said
he. “Let us rescue our lands. Let us liberate our own people!”
The war from the very beginning assumed an unusual character. The
citizens of Novgorod had a single mind this time, and the prince was
at one with the people. To take vengeance for injustice was their
war-cry. Mystislav was not simply enraged against his son-in-law; he
hated in him that inborn pride of the Vladimir princes. Knowing well
that this unendurable haughtiness rested really on power, knowing
well that they had a great multitude of people behind them, and a
very large army, the strong warrior looked forward, not to a brilliant
victory in this unequal conflict, but rather to the crown of a martyr,
and prepared for the struggle with fear, but also with fortitude. He
summoned from Pskoff that brother of his whom Mystislav the Brave
on his death-bed had committed to Yuri Zaharitch, the boyar. This
brother, Vladimir, called to join him his cousin Vladimir, son of Rurik,
he who had taken the throne of Smolensk, when Mystislav, son of
Roman of Smolensk, went to rule Kief, the old capital.
Mystislav the Gallant worked untiringly. Novgorod assembled all
possible warriors, but in number they were insufficient. Mystislav
doubted not that Yaroslav and Yuri, Grand Prince of Vladimir, would
act as one man, but he counted on Constantine, who in his eyes
seemed another victim of Vladimir’s self-will and insolence. To
Constantine, and not to Yuri, belonged the throne of Vladimir, by
right of birth. To deprive a son of his God-given inheritance was a sin
in Mystislav’s eyes, and he thought that when he entered [191]the
Vladimir principality, proclaiming to Yaroslav and Yuri that he was
there to reinstate their eldest brother, Constantine would assist him.
To instate the senior son seemed to Mystislav just and proper.