Undergraduate Biochemiostry Exam Syed A Jamal Fall 2016

1. November 20, 2016
Biochemistry
Exam 3
(1) Given the equation
E +S=ES=E +P
Label and number the 3 rate constants.
Write Km in terms of the 3 rate constants. Then, derive the units of Km.
(6 points)
(2) Given are two mechanisms for a well-known enzyme.
Name the enzyme. What are the mechanisms here? Explain the reasons behind your answer.
(6 points)

2. 3.
(a) Draw the mechanism of the reaction that leads to the formation of the second product in the
above reaction. (b) Does the overall reaction lead to the inversion or retention of configuration?
Why? Why not?
(6 points)

3. 4.

4. Label the types of inhibition shown above.
(3 points)
5) Beta-lactamase attacks the carbonyl carbon with its serine-OH group and an acyl linkage is
established. However, if you pay close attention to the structure of clavulanic acid in Fig 6.31, the
second nucleophilic attack converts the first beta-lactamase-clavulinic acid adduct into another adduct-
an enolate adduct- that can then form keto and enol tautomers. The beta-lactamase is inactivated.
Clavulinic acid has a beta-hydoxyethylidine moiety in the oxazolidine ring
a) Why is penicillin a good substrate for transpeptidase?
b) Why the attack of the beta lactamase not lead to thiazolidine ring opening.
c) Why clavulanic acid inactivates beta-lactamase but beta-lactamase inactivates penicillin?

5. (6 points)
Multiple choice:
6. Modulation of regulatory enzymes can occur
(a) by irreversible covalent modification
(b) by phosphorylation
(c) by proteolytic cleavage- zymogens in chymotrypsin and trypsin, and in blood coagulation.
(d) by inactivation
(e) a, b, and c
(2points)
7. Fill in the blanks: 10 points.
Diisopropylphosphofluoride inactivates acetylcholinesterase by binding irreversibly to ______ _______
of _______ ________ and causing irrevocable loss of catalytic activity
The parameters Kcat and Kcat/Km can be used to compare the activities of different enzymes.
Kcat is the turnover number of an enzyme or the number of substrate molecules converted into product
by an enzyme molecule per second when the enzyme is fully saturated with the substrate. Kcat is a
kinetic constant. It is a _____ order rate constant. The turnover number for biological enzymes with
physiological substrates ranges from 10 to 40,000,000 per second.
Another characterization of the kinetics of an enzyme is afforded by the parameter-kcat/Km, which is a
measure of the enzyme’s ____________ __________
Two closely related experimental variables that allow us to choose whether to determine rate of
catalysis by calculating Kcat, the turnover number or kcat/Km are ______ and _______.
8. Calculate the change in rate constant if the activation energy G for a reaction has been lowered from
8 kJ/mol to 4 kJ per mole.
h=6.212 *1012
s-1
; Boltzmann constant=1.38 *10-23
J/K; gas constant= 8.315 J/mol.K.
k 
kBT
h




exp
G
RT


 



6. (4 points)
9. Given that aA>>>>>P is a second order reaction, and knowing the units in the expression
Δ A/Δt, derive the units of k.
(4points)
10-12. In an enzyme catalyzed reaction, the following data set has been gathered.
[S] V0(no Inhibitor) V0 (inhibitor)
μM.s.-1
μM.s.-1
1 2.5 1.17
2 4.0 2.10
5 6.3 4.00
10 7.6 5.7
20 9.0 7.3
With the help of a generated graph, find Km, Vmax, and the type of inhibition.
(6 points)
13. Draw the cyclic (Haworth) and the Fischer projection formula(s) for glucose, C6H12O6. Label
the chiral centers in the Fischer formula.

7. (4 points)
(2 points)
14. Draw the structure of a disaccharide showing either the alpha, 1-4 or the beta, 1-4
glyosidic bond.
(4 points)
15. Refer to the passage below for the question(s) that follow.
Sialylation-sialic acid is a general term for N- or O-substituted derivatives of neuraminic
acid- a monosaccharide with a nine-carbon backbone. In humans, the highest
concentration of sialic acid is in the brain. Sialic acids occur at the end of sugar chains
connected to the surfaces of cells and soluble proteins. The function, stability, and
metabolism of glycoproteins depend on proper levels of sialylation.

8. Alterations in glycoprotein glycosylation, that include silaylation, have been observed in a class
of human diseases called congenital disorders of glycosylation (CDG) that are accompanied with
severe developmental disorders. Aberrations in glycosylation might also result from abnormal
activity of glycosidases.
Why would glycosylation disorders lead to developmental problems?
(4 points)
16. Lactose and sucrose, shown below, are both disaccharides. Which one is reducing and
which one is not? Why?
(3 points)

9. 17. Fill in the blanks: 10 points.
Glycophorins are _________ on __________ __________ ________.
Fibronectin is a cell-cell adhesion glycoprotein of the extracellular matrix that binds to ________
receptor. Fibronectin also binds _______ ________components such as collagen, fibrin, and heparin
sulfate proteoglycans like syndecans.

10. Glycosphingolipids are components of the _________ ________ where the hydrophilic head groups are
the oligosaccharides. As in glycoproteins, these sugars are recognition sites for lectins.
Glycosphingolipids have a role in ______________, ________-___________ and in signal transduction.
18. What are some of the properties of sugars that enable such a wide variety of
oligosaccharides that are also highly hydrated?
(2 points)
19. (a) Why does an egg left in a bowl on a countertop not serve as a conducive media for
bacteria to colonize?
(b)
Show above are crystal structures of lysozme and lactalbumin. Where is lactalbumin found?
What is its function?
(c) Breast milk contains as many as 600 different species of bacteria, including beneficial B.
adolescents, B. longum, B. bifidum, and B. dentium. It also contains a unique type of sugar, human
milk oligosaccharides(HMOs), not present in infant formula. Indigestible by the infant, HMOs make
up the intestinal flora. They also act as decoy receptors .and alter the response of immune cells,
which may benefit the infant.

11. In what ways would the above properties of human milk oligosaccharides benefit the infant?
(6 points)
20.
(a) Given that many receptors and hormone are glycoproteins with available sites for
glycosylation, how would high sugar levels affect the interactions between hormones
and receptors?
(b) The gp120 coat protein on the HIV virus mediates initial contact between the virus
and the CD4 receptor on white blood cells. The coat protein is heavily glycosylated
with 27 glycosylated residues. Can you suggest 2 advantages that glycosylation
would confer on the ability of the virus to infect the host?

12. (6 Points)
21. Refer to the diagram above.
Name a pathological process during which the activity at the cleavage site will be
excessively high.
Explain the process by which antithrombin binds Factor Xa to inhibit blood clotting.
(4 points).