BCH 3023 Final Part 1

Due in class on Monday, December 10.

For questions 1-4, consider the structure of the coenzyme NADP

O
B
O NH 2

O P O N

A H
O
H
O
H H
OH OH NH2
O P O
N
C
N
O
N
N

H
O
H
D
H H
OH O
E
O P O

1. Which arrow points at a phosphate ester bond?

A) A
B) B
C) C
D) D
E) E

2. Which arrow points at an amide bond?

A) A
B) B
C) C
D) D
E) E

3. Which arrow points at an anhydride bond?

A) A
B) B
C) C
D) D
E) E

1
4. Which arrow points at a glycosidic bond?
A) A
B) B
C) C
D) D
E) E

5. Enzymes accelerate biochemical reactions by

A) d G for the reactions.
G for the reactions.
C) establishing a ‘closed system’ for each reaction.
G.
E) providing a more favorable pathway for the reactions.

6. The strongest noncovalent interactions are

A) ionic interactions.
B) hydrogen bonds.
C) dipole-dipole interactions.
D) London dispersion forces.
E) van der Waals forces.

7. Hydrogen bonds within liquid water

A) are attractions between protons and oxygen nuclei.
B) are attractions between two hydrogen atoms.
C) are attractions between protons and hydroxide ions.
D) are ion-induced dipole attractions.
E) are dipole-dipole attractions.

8. Urea is a water-soluble product of nitrogen metabolism. How many hydrogen bonds can one
urea molecule donate to surrounding water molecules?

A) 2
B) 3
C) 4
D) 5
E) 6

2
9. In a hydrogen bond between a water molecule and another biomolecule
A) a hydrogen ion on the water molecule forms an ionic bond with a hydride ion on the other
molecule.
B) the partial charge on a hydrogen of the water molecule interacts with the partial charge on a
hydrogen of the other molecule.
C) the hydrogen bond will typically form between a hydrogen atom of the water molecule and
either a nitrogen, sulfur, or oxygen atom of the other molecule.
D) a hydrogen on the water molecule forms a covalent bond with a hydrogen atom on the other
molecule.
E) the hydrogen atom is located between an oxygen atom of the water and a carbon atom of the
other molecule.

10. The boiling point of water is 264°C higher than the boiling point of methane because
A) the molecular mass of methane is much lower than that of water.
B) methane molecules tend to avoid contact with each other.
C) water molecules are connected to each other by H-bonds.
D) methane molecules do not undergo London dispersion forces.
E) all of the above

11. Molecules such as methanol and ethanol are very soluble in water because
A) they tend to avoid contact with each other.
B) they contain C─H groups that donate H-bonds to water.
C) they contain C─H groups that accept H-bonds from water
D) they contain O─H groups that can form multiple H-bonds with water.
E) they do not form intermolecular H-bonds

12. Fatty acids such as palmitate and oleate are usually characterized as
A) hydrophobic.
B) hydrophilic.
C) polar.
D) water soluble.
E) amphiphilic.

13. Globules of up to several thousand amphiphilic molecules arranged with the hydrophilic
groups on the surface and the hydrophobic groups buried in the center that form in water are
called
A) micelles.
B) liposomes.
C) vacuoles.
D) bilayer membranes.
E) none of the above

3
14. Weak acids
A) are only partially ionized in an aqueous solution.
B) give solutions with a high pH.
C) do not provide hydronium ions.
D) are almost insoluble in water.
E) are of no value in a buffering system.

15. A solution is made by mixing 0.05 mL of 1.0 M HCl with 999.95 mL of pure water.
Calculate the pH of the resulting solution (assume the total volume is 1.0 L).
A) 2.7
B) 4.3
C) 9.7
D) 7.0
E) 5.0

16. The pH of coffee is 5.6. The pH of grapefruit juice is 2.6. This means that the proton
concentration in coffee is
A) a thousand times higher than in grapefruit juice.
B) a thousand times lower than in grapefruit juice.
C) 3000 times lower than in grapefruit juice.
D) 3 times the proton concentration of grapefruit juice.
E) 3000 times higher than in grapefruit juice.

17. You mix 999 mL pure water and 1 mL of 2.0 M NaOH. Calculate the pH of the resulting
solution. (assume the total volume is 1.0 L).
A) 0.3
B) 0.7
C) 2.7
D) 11.3
E) 13.7

18. Phosphoric acid is a polyprotic acid, with pK values of 2.14, 6.86, and 12.38. Which ionic
form predominates at pH 9.3?
A) H3PO4
B) H2PO41−
C) HPO42−
D) PO43−
E) none of the above

19. To make an acetate buffer at pH 4.76 starting with 500 mL of 0.1 M sodium acetate (pK
acetic acid = 4.76), you could add
A) 0.1 mol of NaOH.
B) 0.2 mol of HCl.
C) 0.025 mol of HCl.
D) 0.1 mol of HCl.
E) You can't make a buffer by adding HCl or NaOH.

4
20. A graduate student at UCF wants to measure the activity of a particular enzyme at pH 4.0.
To buffer her reaction, she will use a buffer system based on one of the acids listed below, which
acid is most appropriate for the experiment?
A) Formic acid (Ka 1.78 × 10−4)
B) MES (Ka 8.13 × 10−7)
C) PIPES (Ka 1.74 × 10−7)
D) Tris (Ka 8.32 × 10−9)
E) Piperidine (Ka 7.58 × 10−12)

Matching 21-30. Answers may be used more than once, or there may be more than once
answer accepted for these questions.

A) glutamate
B) uncharged
C) deprotonated
D) three
E) amino group
F) two
G) C-terminus
H) lysine
I) racemic mixture
J) cysteine
K) zero
L) protonated
M) isoleucine
N) tryptophan
O) phenylalanine
P) N-terminus

21. The net charge of the zwitterion form of Gly is ______.

22. When a peptide bond is formed, an ______ reacts with a carboxylate group.
23. At a pH above its pKa, the phenol group of tyrosine is ______.
24. In the tripeptide Lys─Pro─Ile, there are ______ charged groups at pH 7.

25. At a pH below its pKa, the -amino group of lysine is ______.

26. At a pH below its pKa, the -carboxylate group of Asp is ______.

27. In the peptide Trp─Ser─Val, valine is at the ______.
28. In the tripeptide Trp─Val─Phe, the N-terminal residue is ______.
29. In the tripeptide Lys─Pro─Ile, the C-terminal residue is _________.
30. Biological systems usually produce a single enantiomer, whereas chemical synthesis
produces a ______.

5
31. Which of the following amino acids would be last to elute at pH 8.0 from an anion-exchange
column?
A) lysine
B) alanine
C) glutamic acid
D) asparagine
E) glycine

32. Which of the following links two b sheets?

A) A, C, D
B) B and C
C) A only
D) A, B, and D
E) C only

33. When solving a protein structure using X-ray crystallography, the crystallographer generates
a 3-D grid called an electron density map based on the observed diffraction pattern. The higher
the resolution, the more detailed the electron density map and therefore the easier it is to identify
what atoms (and therefore what amino acids) are in a given position. Based on the three choices
below, in which of the following groups could the two of amino acids be the easiest to
differentiate regardless of resolution?

I. Leucine vs. Isoleucine

II. Phenylalanine vs. Alanine
III. Glutamate vs. Glutamic acid

A) Those in both groups I and II could be differentiated

B) Those in both groups I and III could be differentiated
C) Only those in group II could be differentiated
D) Only those in group III could be differentiated
E) Only those in groupI could be differentiated

6
This figure is used in questions 34-36.

34. The structure shown in the figure above represents a

A) glucopyranose.
B) ribofuranose.
C) myo-inositol.
D) fructofuranose.
E) glucofuranose.

35. Which of the carbon atoms shown in the figure above represent the anomeric carbon?
A) A
B) B
C) C
D) D
E) E

36. The configuration around which carbon atom shown in the figure above determines whether
this is a D or an L sugar?
A) A
B) B
C) C
D) D
E) E

7
37. The structure below shows a Fischer projection of D-idose.

Which of the structures below represents -D-idopyranose

38. Which of the following is an example of a heteropolysaccharide?

A) cellulose
B) chitin
C) starch
D) glycogen
E) hyaluronic acid

8
39. The drawing below shows the structure of the disaccharide sucrose.

a. What are the names of the two monosaccharides that form sucrose?
b. Draw squares around the carbons that determine the designation D or L for each of the
monosaccharides.
c. Draw circles around the anomeric carbon atoms on the drawing.
d. Indicate on the drawing for each of the anomeric carbon atoms whether they are in the  or
the  configuration.
e. Is sucrose a reducing sugar? Explain your answer in one sentence. (all must be correct for
credit!)

40. Rank the melting points of the following fatty acids from highest to lowest:
(1) cis-oleic(18:1)
(2) trans-oleic (18:1)
(3) linoleic (18:2)
(4) steraic (18:0)
(5) palmitic (16:0)

A) 1 > 2 > 3 > 5 > 4

B) 4 > 5 > 2 > 1 > 3
C) 4 > 5 > 3 > 2 > 1
D) 5 > 4 > 2 > 1 > 3
E) none of the above

41. Sphingolipids

I. contain a glycerol core with a phosphocholine headgroup.

II. contain a modified sphingosine.
III. often function as receptor components of membranes.
IV. function as a precursor to sterols.

A) I, II, IV
B) II, IV
C) I, II, III
D) II, III
E) II, III, IV

9
42. Which of the following structures correctly represents a glycerophospholipid?

A) Structure A
B) Structure B
C) Structure C
D) Structure D
E) None of the above

10
43. Consider the following portion of the glycolytic sequence catalyzed by the enzymes
above the arrows. Which products(s) will produce ATP?
O
-
C H CO2
E1 E2 E3 E4 -2 E5 E6
HC OH I. II. III. C OPO3 IV. V.
CH2OPO3-2 CH2

A) I, IV
B) II, IV
C) II only
D) III, IV
E) IV only

44. Which of the following compounds contains a “high-energy” bond and is used to produce
ATP by substrate-level phosphorylation in glycolysis?
O
C H
C OH
CH2OPO 3-2
a.
O
-
C O
C OPO 3-2
CH2OPO 3-2
b.
-
CO2
-2
C OPO3
CH2
c.
O
CH3CCO2-
d.
O
CH3C OPO3-2
e.

11
45. Methanol is highly toxic, not because of its own activity, but because it is converted
metabolically into formaldehyde, which is the actual poison. What enzyme catalyzes this
conversion?

A) methanol caboxylase
B) methanol transferase
C) alcohol transmutase
D) alcohol carboxylase
E) alcohol dehydrogenase

46. Condensation of ____ with oxaloacetate yield citrate.

a. acetyl-CoA
b. α-ketoglutarate
c. isocitrate
d. citrophosphate
e. oxalosuccinate

47. During the oxidation of isocitrate, _____ is decarboxylated to form -ketoglutarate.

a. hydroxyethyl-TPP
b. carboxybiotin
c. oxalosuccinate
d. succinyl-phosphate
e. none of the above

12
48. If acetyl-CoA labeled with 14C, as shown in the figure to the right,
O
were used as the substrate for the citric acid cycle, which of the
CoAS C *CH3
following intermediates would be produced during the first round
of the cycle?
OH H
O2*C C C CH2 CO2
H CO2
a.
OH H
O2C C C *CH2 CO2
H CO2
b.
OH H
O2C C C CH2 *CO2
H CO2
c.
OH H
O2C *C C CH2 CO2
H CO2
d.
OH H
O2C C *C CH2 CO2
H CO2
e.

49. Which of the following enzymes catalyzes a reaction with the

pictured compound as an intermediate? COO-

a. a-ketoglutarate dehydrogenase CH2

b. succinyl-CoA synthetase
c. succinate dehydrogenase CH2
d. fumarase
C
e. malate dehydrogenase 2-O P
3 O O

13
50. Considering the reactions within the citric acid cycle, which of the
following molecules will be produced from the intermediate pictured on O O-
C
the right?
CH 2
a. citrate C COO -
b. isocitriate -
c. succinate HC COO
d. succinyl-CoA
e. α-ketoglutarate

14