Exam 1 by decree


									CHM381/Exam 2

                                          Exam 2
                                         CHM 381
                                 Fundamentals of Biochemistry


In keeping with Creighton University’s ideals and with the Academic Integrity Code adopted by
the College of Arts and Sciences, I pledge that this work is my own and that I have neither given
                      nor received inappropriate assistance in preparing it.

               Signature: ____________________________________________

                             No programmable calculators allowed
                                   Exam time: 50 minutes

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CHM381/Exam 2

1. (5 pts) The covalent catalytic mechanism of a particular enzyme depends on a single active
site cysteine whose pKa is 8. An amino acid mutation in a nearby residue (one that is part of this
enzyme’s catalytic triad) alters the microenvironment so that this pKa increases to 10. Would the
mutation cause the reaction rate to increase or decrease? Explain.

Active form of the enzyme contains the thiolate anion. The increased pK would increase
the nucleophilicity of the thiolate and thereby increase the rate of the reaction catalyzed by
the active form of the enzyme. However at physiological pH there would be less of the
active form of the enzyme and therefore the overall rate would be decreased.

2. (8 points) Match the compounds on the left with the important roles they play listed on the
right. (Answers are used only once.)

(a)   vitamin E                _h_ blood clotting
(b)   sphingolipids            _d_ rat poison, used as an anticoagulant
(c)   thromboxanes              _f_ stimulates smooth muscle contraction
(d)   warfarin                 _b_ important component of myelin membranes
(e)   vitamin D                _a_ prevention of oxidative damage
(f)   prostaglandins           _e_ formed in the skin from UV light
(g)   leukotrienes             _c_ synthesis inhibited by aspirin
(h)   vitamin K                _g_ synthesis inhibited by prednisone

3. (4 pts) Draw the structure of the fatty acid abbreviated 20:4 (5,8,11,14).

4. (6 pts) Why wouldn’t triacylglycerols make good membranes?
Triacylglycerols have three fatty acyl groups in ester linkage with glycerol; they are very
hydrophobic because the carboxyl groups, which are involved in the ester linkages, cannot
ionize. Phosphoglycerides have a polar region at their head group, where a phosphate in a
phosphodiester linkage bears a full negative charge. The head group itself (serine,
ethanolamine, choline, etc.) may also be charged and is in any case polar. Thus, the
phospholipid is amphipathic, having both polar and nonpolar regions, and it forms lipid
bilayers spontaneously in water.

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CHM381/Exam 2

5. (4 pts) A regulatory mechanism that is NOT readily reversible:
A) phosphorylation
B) allosteric control
C) proteolytic cleavage
D) all of the above
E) none of the above
Answer C

6. (4 pts) The main function of a coenzyme is to

A) extend the number of chemical reactions that can occur in the active site of enzymes.
B) stabilize the tertiary state.
C) increase the enzyme Km.
D) decrease the enzyme Vmax.
E) regulate enzymes through feedback inhibition.
Answer A

7. (4 pts) Indicate whether each of the following is true or false.

_____ Proteins and lipids account for almost all the mass of biological membranes.
_____ Proteins and lipids are the only components of biological membranes.
_____ The relative proportions of protein and lipid are the same in all biological membranes.
_____ Membranes with different functions have different proteins.
True, false, false, true

8. (7 pts) In the article “Cystic Fibrosis”, a description of the CFTR protein and how it is
mutated in cystic fibrosis patients is given. If the CFTR protein is not working correctly how
does this affect ion transport into and out of the cell?

Normally the CFTR protein helps pump Cl- out of the cell, but when it is defective Cl- stays
in the cell and more Na+ gets pumped into the cell. High [Cl-] in the cell leads to prolonged
life of bacteria outside the cell and frequent infections - damage to lungs. The mucus is
thicker outside the cell and more resistant to removal. Bacteria get trapped in the thick
mucus and fluorish here. Bacteria proliferate and attract immune cells which can damage
healthy tissue. These changes plug airway and lead to destruction.

9. (4 pts) The two active site histidines of ribonuclease A catalyze the hydrolysis of RNA
primarily by

A) acting as general acids and bases.
B) binding the substrate.
C) binding the intermediate.
D) orienting a molecule of water
E) binding the transition state of the rate limiting step.
Answer A
10. (4 pts) The hydropathy plot below provides which of the following information?

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CHM381/Exam 2

A) The protein being analyzed is a globular, peripheral membrane protein.
B) The protein being analyzed may be an integral membrane protein with seven
    membrane-spanning domains.
C) The membrane being analyzed has a high degree of fluidity.
D) The membrane being analyzed has a high proportion of long-chain fatty acids.
E) The protein being analyzed has extensive -barrel domains.
Answer B

11. (6 points) Describe two similarities and two differences between the -adrenergic receptor
(activated by epinephrine) and the insulin receptor (activated by insulin)

Similarities: Roles of phosphorylation and presence of amplification. Binding of signal starts
signal transduction process.

Differences: The adrenergic receptor indirectly activates a catalyst (adenylate cyclase), which
produces a second messenger (cAMP). The insulin receptor is itself a catalyst when occupied
with insulin; its tyrosine kinase activity phosphorylates and activates another protein kinase,
which initiates a cascade of phosphorylations of other proteins.

Insulin receptor is a standard hormone receptor. The adrenergic receptor is a serpentine receptor
that has an associated G protein.

12. (3 pts) On the molecule below circle and label those parts that make it amphipathic:
polar sugars and nonpolar fatty acid chains

13. (5 pts) Describe one way improper biosignaling can lead to cancer:

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CHM381/Exam 2

tumor suppressor genes

14. (6 pts) When a preparation of mitochondrial membranes was treated with high salt (0.5 M
NaCl), it was observed that 40% of the total protein in this preparation was solubilized. (a) What
kind of membrane proteins are in this soluble extract, and what forces normally hold them to the
membrane? (b) What kind of proteins constitute the insoluble 60%, and what forces hold these
proteins in the membrane?

(a) peripheral membrane proteins, which are associated with the membrane through ionic and
hydrogen bonds between their charged and polar side chains and the charged head groups of
phospholipids; (b) integral membrane proteins (which are held to the membrane by hydrophobic
interactions between their nonpolar side chains and the hydrophobic fatty acyl chains of
phospholipids), and those peripheral membrane proteins which are held to the membrane by a
covalent lipid anchor.

15. (5 pts) Why does the HIV virus only invade T cells?

HIV has two cell surface markers that is needs to recognize in order to infect a human cell.
These two markers (CD4 and CCR5) are found on the outer surface of T cells and
therefore T cells are targeted by HIV infections.

16. (4 pts) Refer to the graph below when answering this question. Line A represents the native
enzyme and line B the enzyme plus a fixed concentration of a modifier. The modifier

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CHM381/Exam 2

A) enhances the activity of the enzyme.
B) appears to increase the Km.
C) is a noncompetitive inhibitor.
D) is a competitive inhibitor.
E) is an allosteric inhibitor.
Answer D

17. (5 pts) You believe a substrate fits into a cleft like a key into a lock, but your roommate
does not. Who is right?

Answer: You are both partially correct. Like a lock and key, the substrate fits precisely
into the enzyme. However, the site is not a rigid cleft, but is flexible. Thus, it is possible
for the substrate to actually modify the shape of the site a bit, a hypothesis known as
induced fit. See textbook Figures 8.9 and 8.10 for further detail. Section: 8.3.2

18. (4 pts) When a bacterium such as E. coli is shifted from a warmer growth temperature to a
cooler growth temperature, it compensates by:

A)    increasing its metabolic rate to generate more heat.
B)    putting longer-chain fatty acids into its membranes.
C)    putting more unsaturated fatty acids into its membranes.
D)    shifting from aerobic to anaerobic metabolism.
E)    synthesizing thicker membranes to insulate the cell.
Answer C

19. (6 pts) You are studying the uptake of L-leucine by epithelial cells of the mouse intestine.
Measurements of the rate of uptake of L-leucine and several of its analogs, with and without Na+

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CHM381/Exam 2

in the assay buffer, yield the results given in the table. What can you conclude about the
properties and mechanisms of the leucine transporter?

                      Uptake in presence of Na+             Uptake in absence of Na+
Substrate                Vmax             Kt                 Vmax             Kt
L-leucine               420              0.24                 23              0.24
D-leucine               310               4.7                  5               4.7
L-valine                225              0.31                 19              0.31

The similar Kt values for L-leucine and L-valine indicate that the transporter binding site
can accommodate the side chains of both amino acids equally well; it is probably a
hydrophobic pocket of suitable size for either R group. The 20-fold higher Kt for D- than
for L-leucine indicates that the binding site recognizes differences of configuration about
the  carbon. Based on the lower Vmax in the absence of Na+ for all three substrates, we
know that Na+ entry is essential for amino acid uptake; the transporter acts by symport of
leucine (or valine ) and Na+.

20. (6 pts) Distinguish between simple diffusion (SD), facilitated diffusion (FD), and active
transport (AT) across a membrane for the following questions (circle your answer, more than one
may be true).

(a) Which processes are energy dependent?                       SD          FD               AT

(b) Which processes need some kind of carrier protein(s)?       SD          FD               AT

(c) Which processes can be saturated by substrate?              SD          FD               AT

(d) Which processes can establish a concentration gradient?     SD          FD               AT

Ans: (a) AT only; (b) FD and AT; (c) FD and AT; (d) AT only

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CHM381/Exam 2

EXTRA CREDIT (5 points)
What is the mechanism of action of the drug tamoxifen in the treatment of breast cancer?

Ans: Tamoxifen is an antagonist of estrogen, and competes with it for binding to the
estrogen receptor. Unlike the situation with estrogen, the tamoxifen-receptor complex,
though stable, cannot elicit significant changes in gene expression, thus slowing the growth
of hormone-dependent cancerous cells.

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