Name:
BIOCHEMISTRY (CHEM 360)
EXAM 2
October 25, 2013
There are six pages, ELEVEN questions, and a total of 116 points in this exam.
Please read each question carefully and possibly more than once. Good luck…
(9)
1.
The active site of chymotrypsin is illustrated below. Show the acyl enzyme formed after the
hydrolysis of the heptapeptide below (but before the hydrolysis of the acyl enzyme). You can use
the template for the active site, but you need to show the full structure of the acyl group.
1.1.
Circle the portion of the heptapeptide which fits into the specificity pocket.
(6)
2.
Explain the physiological basis for the intravenous administration of bicarbonate to shock victims (when
there is a critical deprivation of oxygen to the tissues)
Bicarbonate administered provides a source of carbon dioxide, which forms carbonic acid and decreases
the pH of blood (makes it more acidic); thus allowing more extensive interactions with 2,3-BPG. This
decreases the affinity of hemoglobin for oxygen and facilitates the release of oxygen to the tissues.
(12)
3.
Provide structures for the missing species in the reaction below. Make sure not to skip any steps, and only
give the intermediate for the specific step (where appropriate).
3.1.
Give the final product following the cleavage of TPP.
(14)
4.
In the equations below reactions of certain well known metabolites in the presence of “generic enzymes”
are shown. Any coenzymes needed or any other substrates are not shown.
(i) Predict the final product for each reaction
(ii) Indicate (classify) the type of reaction observed
4.1.
4.2.
Submitted by Chelcey
4.3.
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5.
Circle the best correct answer for the multiple choice questions given below:
5.1.
Lysozyme catalyzes the cleavage of bacterial cell wall polysaccharides. A cleavage point
representation is shown below:
Which of the following is not considered as one of the catalytic effects of lysozyme?
(1) Hydrophobic effect
(2) Transition-state stabilization
(3) Acid-base catalysis
(4) Raising the ground-state energy level
5.2.
Which of the following is not characteristic of chaotropic agents
(1) they disrupt hydrophobic interactions
(2) they disrupt hydrogen-bonding
(3) they inhibit enzymes irreversibly
(4) they denature proteins
5.3.
Which of the partial amino acid residues in the -unit of hemoglobin shown below binds
most tightly to 2,3-bisphosphoglycerate (2,3-BPG) at metabolic pH?
The pKa values of the amino acid side chains shown are given below.
O2C
H3N
pKa 3.9
pKa N/A
(1)
(2)
pKa 10.5
(3)
OH
pKa N/A
(4)
5.4.
Which of the following statements is correct for an enzyme catalyzed reaction?
(1) A tightly bound enzyme-substrate complex increases the rate of a reaction.
(2) A loosely bound enzyme-substrate complex increases the rate of a reaction.
(3) The enzyme-substrate complex is the transitions state of the reaction.
(4) The enzyme substrate complex does not alter the rate of a reaction, since it is not the
transition state.
5.5.
Circle the most acidic hydrogen out of those indicated on the coenzyme structure below.
Page 3
(8)
6.
Collagen is a fibrous protein, which is particularly strong due to covalent cross-linking, as shown
below, within a triple helix structure. Complete the following reaction to illustrate how the
cross-linking has occurred. Identify (name) one of the amino acid residues.
lysine
(6)
7.
The nerve agent sarin has been in the news (again) recently. A great majority of the world is becoming
increasingly aware of the atrocities committed using chemical weapons and welcoming international
efforts to ban their use. Measures for the destruction of chemical weapons stockpiled are under way.
As a minor contribution to these efforts suggest a simple method to make sarin ineffective as a nerve
agent. Give brief experimental details.
OH
bubble sarin gas through a
concentrated NaOH solution
O
P
O
(6)
8.
The functional site of hemoglobin is illustrated below. Insert key structural components of missing
histidine residues and draw/show clearly how they interact with any of the structural units in the
illustration. You need to be specific about each interaction (identifying lone pairs, hydrogens, and/or
any other relevant features)
N
N
H
N
N
H
Page 4
OH
F
O
P
O
(18)
9.
One of the most significant steps in the cross-linking process of peptidoglycans in bacterial cell
walls (of S. aureus) is the formation of an amide bond between the carboxyl group of D-alanine
residue and a pentaglycine bridge.
9.1.
Ironically, the amide bond formation is catalyzed by a “carboxypeptidase” enzyme,
which is known to catalyze the hydrolysis of amide bonds, not the formation of amide
bonds. Outline the process of the amide bond formation. Speculate on the structural
features of the “carboxypeptidase” active site.
Note that the tetrapeptide, ala.glu.lys.ala, may be incomplete for the purposes of the
amide-linkage process.
D-ala
O
N H
O
H N
Enz
N H
HO
O
serine protease
O2C
9.2.
O
O
Enz
There is an additional D-ala in the
polypeptide chain connected to
the muramic acid which gets
cleaved by the carboxypeptidase.
The resulting acyl enzyme is a
“C-activated” D-ala, which can
form the amide linkage with gly.
It is likely that the
carboxypeptidase is a serine
protease.
The “carboxypeptidase” enzyme mentioned above can be inhibited by penicillin
derivatives, an example of which is given below. Describe two structural features of
penicillin, to which the inhibitory activity can be attributed.
(1) the structure resembles D-ala.D-ala moiety
(2) nucleophilic attack by the carboxypeptidase
is more likely to occur to the -lactam ring than
the ala.ala amide link (in view of the relief from
angle strain for the former)
(
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
Circle the correct statement (only one) with reference to penicillin resistant bacteria
 Penicillin resistant bacteria no longer utilize the “carboxypeptidase” enzyme for the
formation of an amide bond between the carboxyl group of D-alanine residue and a
pentaglycine bridge.
 Penicillin resistant bacteria have evolved to utilize a -lactamase enzyme for the
formation of an amide bond between the carboxyl group of D-alanine residue and a
pentaglycine bridge.
 Both (1) and (2)
 Penicillin resistant bacteria have developed a -lactamase enzyme for a
nucleophilic attack directed to the -lactam ring of penicillin derivatives 
(11)
In the Lineweaver-Burke graph below both the “control” activity (enzyme without the
inhibitor) and the activity upon addition of inhibitor are shown. Write a generic “steady state”
equation which illustrates how the type of inhibitor added influences the activity (as seen in the
plot).
10.
10.1.
E
+
S
On the basis of the change in a parameter in the plot discuss whether you can estimate if
the enzyme-substrate complex is more tightly or more loosely bound after the inhibitor is
added. Identify the parameter which is used as a criterion and indicate its position on the
graph.
ES
E
+
P
I
ESI
The plot shows a increase in
the absolute value of 1/Km,
(thus an increase in the value
of Km), with addition of the
inhibitor, which suggests a
more tightly bound ES
complex (also suggested by
the steady-state equilibria)
1/Km
(11)
11.
The reaction shown below is a key step in histamine production. Write structures for the missing
substrate and the products.
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