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Biological Molecules
Test 1
Time: 23 Minutes*
Number of Questions: 18
* The timing restrictions for the science topical tests are optional. If
you are using this test for the sole purpose of content
reinforcement, you may want to disregard the time limit.
MCAT
2
He
4.0
3
Li
6.9
4
Be
9.0
5
B
10.8
6
C
12.0
7
N
14.0
8
O
16.0
9
F
19.0
10
Ne
20.2
11
Na
23.0
12
Mg
24.3
13
Al
27.0
14
Si
28.1
15
P
31.0
16
S
32.1
17
Cl
35.5
18
Ar
39.9
19
K
39.1
20
Ca
40.1
21
Sc
45.0
22
Ti
47.9
23
V
50.9
24
Cr
52.0
25
Mn
54.9
26
Fe
55.8
27
Co
58.9
28
Ni
58.7
29
Cu
63.5
30
Zn
65.4
31
Ga
69.7
32
Ge
72.6
33
As
74.9
34
Se
79.0
35
Br
79.9
36
Kr
83.8
37
Rb
85.5
38
Sr
87.6
39
Y
88.9
40
Zr
91.2
41
Nb
92.9
42
Mo
95.9
43
Tc
(98)
44
Ru
101.1
45
Rh
102.9
46
Pd
106.4
47
Ag
107.9
48
Cd
112.4
49
In
114.8
50
Sn
118.7
51
Sb
121.8
52
Te
127.6
53
I
126.9
54
Xe
131.3
55
Cs
132.9
56
Ba
137.3
57
La *
138.9
72
Hf
178.5
73
Ta
180.9
74
W
183.9
75
Re
186.2
76
Os
190.2
77
Ir
192.2
78
Pt
195.1
79
Au
197.0
80
Hg
200.6
81
Tl
204.4
82
Pb
207.2
83
Bi
209.0
84
Po
(209)
85
At
(210)
86
Rn
(222)
87
Fr
(223)
88
Ra
226.0
89
Ac
227.0
104
Unq
(261)
105
Unp
(262)
106
Unh
(263)
107
Uns
(262)
108
Uno
(265)
109
Une
(267)
58
Ce
140.1
59
Pr
140.9
60
Nd
144.2
61
Pm
(145)
62
Sm
150.4
63
Eu
152.0
64
Gd
157.3
65
Tb
158.9
66
Dy
162.5
67
Ho
164.9
68
Er
167.3
69
Tm
168.9
70
Yb
173.0
71
Lu
175.0
90
Th
232.0
91
Pa
(231)
92
U
238.0
93
Np
(237)
94
Pu
(244)
95
Am
(243)
96
Cm
(247)
97
Bk
(247)
98
Cf
(251)
99
Es
(252)
100
Fm
(257)
101
Md
(258)
102
No
(259)
103
Lr
(260)
as developed by
HO
H CH2 OH
O
H+
HO
OH
O
CH 2OH
HO
Sucrose
CH2 OH
O
CH2 OH O
HO
HO
OH +
HO
OH
CH 2OH
OH
HO
D Glucose
Table 1
Specific rotation []D
DFructose (I)
Figure 1
Under acidic conditions, D-glucose undergoes
mutarotation giving an equilibrium mixture of - and anomers, whereas D-fructose exists as four different
isomers (isomer IV being the predominant form):
OH
HOCH2
O
O
OH
CH 2OH
HO
OH
CH 2OH
OH
Solution before
hydrolysis
Solution after
hydrolysis
+66/5
Negative
19.9
Positive
OH
HO
II
OH
OH
I
IV
I
CH 2OH
HOCH2
O
OH
CH2OH O
OH
HO
HO
CH2OH
HO
Benedicts
Test
HO
H CH OH
2
O
HO
OH
O
CH2 OH
OH
HO
V
III
IV
III
II
Figure 2
A student carried out the hydrolysis of sucrose using
the following procedure:
A.
B.
C.
D.
I
II
III
IV
KAPLAN
MCAT
2 . Sucrose does NOT produce a positive test when
treated with Benedicts solution because:
A . the carbonyl functionalities of both subunits are
involved in the formation of a glycosidic linkage.
B . it undergoes mutarotation.
C . the molecule is not oriented correctly for a
reaction to occur.
D . disaccharides do not possess free hemiacetal or
hemiketal groups.
-D-Glucopyranosyl -D-fructofuranoside
-D-Glucofuranosyl -D-fructopyranoside
-D-Fructofuranosyl -D-glucopyranoside
-D-Fructofuranosyl -D- glucopyranoside
I only
I and III only
II and III only
II and IV only
and the
rotation
rotation
and the
as developed by
HNCHCO
F + H2NCHCO
R
etc
Isoelectric point
(pI)
2.92
9.62
9.74
9.74
9.74
Molecular
COOH
pK a
NH3+
group
weight
Glycine (Gly)
2.34
9.63
75
Valine (Val)
2.32
9.62
117
CH(CH3)2
HCO 3
Glutamic
2.19
9.67
4.25
147
(CH2)2COOH
(HF)
acid (Glu)
2.10
9.8
3.9
133
CH2COOH
Lysine (Lys)
2.18
8.95
10.53
146
(CH2)4NH2
Isoleucine (Ile)
2.36
9.68
131
CH(CH3)C2H 5
Phenylalanine
1.83
9.13
165
CH 2 Ph
2.28
9.21
149
(CH2)2SCH 3
Cysteine (Cys)
1.96
10.8
8.3
121
CH 2SH
Serine (Ser)
2.21
9.15
105
CH2OH
R'
Name
Aspartic
NO2
pK a
R group
acid (Asp)
2,4-Dintrofluorobenzene
O 2N
Table 1
Molecular weight
(Daltons)
418
336
203
146
650
Fragment
number
1
2
3
4
5
Polypeptide
NHCHCO
NHCHCO
R'
etc
H 3O +
(Phe)
Methionine
(Met)
NO2
Labeled polypeptide
+
NHCHCOOH + H 3NCHCO2
O 2N
R'
NO2
Labeled amino acid
Reaction 1
KAPLAN
MCAT
7 . If the fragments shown in Table 1 are subjected to
electrophoresis at a pH of 4, in which direction will
fragment 5 move?
A.
B.
C.
D.
Lys-Gly
Gly-Asp-Val-Glu
Gly-Asp-Val
Lys-Cys-Ser
A.
B.
C.
D.
Aspartic acid
Lysine
Phenylalanine
Glycine
9.80
6.80
5.95
3.00
as developed by
A.
B.
C.
D.
C.
hydrogen bonding.
hydrophobic interactions.
electrostatic interactions.
peptide bonds.
A.
CH2
and
CH2OH
(CH 2) 2 COOH
and
CH2
B.
C=O
14
B.
19
19
D. 1
C.
CH3
CH
10
NH
14
D.
O=C
CH3
CH3
and
CH
CH2CH3
CH3
and
CH2COOH
CH3
CH
19
19
primary structure.
secondary structure.
tertiary structure.
quaternary structure.
C.
O
C
NH O
B.
D.
KAPLAN
END OF TEST
MCAT
ANSWER KEY:
1.
C
2.
A
3.
A
4.
B
5.
D
6.
7.
8.
9.
10.
B
A
C
D
B
11.
12.
13.
14.
15.
C
A
B
D
B
16.
17.
18.
D
D
C
as developed by
KAPLAN
MCAT
is oriented upwards or equatorially, making it a beta-anomer, so the alpha anomers are II and IV making choice B the correct
response.
5.
The correct answer here is choice D. As I mentioned at the end of the explanation to question 2, maltose is
a disaccharide, but it differs from sucrose in that it is a reducing sugar. Maltose is made up of two glucose sub-units, but
only one of the units is a glucoside. The other sub-unit is present in the hemiacetal form, hence it can mutarotate.
Mutarotation is characterized by an equilibrium between alpha and beta anomers; the conversion between these two proceeds
through an open chain form which possesses a free carbonyl group that can reduce Benedict's reagent--giving the characteristic
brick-red precipitate. Therefore, choice D is the correct answer as maltose contains one free hemiacetal group.
Choice A is incorrect since Benedict's test has nothing to do with the glycosidic bond, so you should be able to
eliminate this answer choice right away. Choice B is also incorrect because as I said before, sucrose is not a reducing sugar,
due to the lack of hemiacetal and hemiketal groups. Choice C is also wrong. Although it is stating the opposite to choice
A, it is still an incorrect statement because it is not relevant to the question anyway. Again, choice D is the correct answer.
6.
For question 6, the correct answer is choice B. A common way to name cyclic monosaccharides is
according to the ring size, and if you recall heterocyclic chemistry, you will know that pyran corresponds to a 6-membered
ring, while furan corresponds to a 5-membered ring. It's logical then that a five-membered fructose ring would be a
fructofuranose, while a 6-membered glucose ring would be a glucopyranose, but as I said before, the sub-units in sucrose are
glycosides, so the acetal forms of glucose and fructose would be glucopyranoside and fructofuranoside. Straight away then,
you can eliminate choice II, since this states that glucose will be a furanoside, not a pyranoside and that fructose will be a
pyranoside, not a furanoside--so choices C and D are wrong.
You should also be aware that the prefix for a glycoside is -osyl, so that fructofuranoside is fructofuranosyl and so
on. Sucrose can therefore be named as a fructofuranosyl-glucopyranoside or a glucopyranosyl-fructofuranoside; statements I,
III and IV are possible answer choices. The last thing to look at is the alpha and beta designations. The glucoside has an
alpha linkage, while the fructoside has a beta linkage. If you can't remember this, rewind the tape to the explanations to
questions 1 or 4 where I discuss these anomers in more detail. You should be able to see that choice IV is wrong, as this
describes the fructofuranoside as alpha, while the glucopyranoside is beta. This confirms answer choice D as being wrong,
but you could have discarded this on the strength of what we discussed earlier.
As sucrose can be named as a fructofuranoside or a glucopyranoside, statements I and III are equally viable. The ring
size and the anomeric designations are correct, and so choice A can be eliminated, leaving B as the correct answer.
Passage II (Questions 713)
7.
The correct answer here is choice A. From Table 1, you can see that the isoelectric point of fragment 5 is
9.74. The isoelectric point is defined as the point where the negative and positive charges in the amino acid cancel out, so the
molecule has a zero net charge and will not move when placed in an electric field. At a pH below 9.74, the molecule will be
protonated and hence positively charged, whereas at a pH higher than 9.74, the molecule will be deprotonated and so
negatively charged. Since fragment 5 is in a buffer at pH 4 (which is below its isoelectric point of 9.74) it will be positively
charged and so will migrate to the negatively charged electrode; namely the cathode. This makes choice A the correct
response.
Choice B is incorrect since the buffer would have to be at a pH above 9.74 in order for fragment 5 to migrate toward
the anode. Choice C is incorrect because as I said, an amino acid that will not move when placed in an electric field is one
which is at its isoelectric point. The only point which fragment 5 would be at its isoelectric point would be if the pH of the
buffer was 9.74. Obviously from the question stem it isn't, so choice C can also be discarded. Finally, choice D is wrong
since you can tell just from the fragment's isoelectric point and the pH of the environment which way the molecule will
move. Again, choice A is the correct response.
8.
The correct answer to question 8 is choice C. In order to answer this question, you need to look to the
discussion of the proteolytic enzyme just before Table 1 in the passage. Here it states that the enzyme is specific for the Nterminal end of an amino acid (conventionally written on the left) which itself possesses an amino or basic side chain. Out of
all of the amino acids listed, the only one that possesses an amino side chain is lysine. Therefore, we would expect the
proteolytic enzyme to cleave the polypeptide at the N-terminal residue of lysine; on the left hand side.
Looking at the answer choices, you can see that choice A is incorrect, since the polypeptide in Figure 1 could be
cleaved between the glutamic acid and the lysine residue and the glycine and lysine residue to form the fragment shown.
The fragment in choice B also forms due to cleavage of the glutamic acid-lysine linkage alone (but obviously it's an
end fragment since it constitutes the first four amino acids in the polypeptide, so no other linkages have to be cleaved). As in
choice B, the sequence in choice D is the end fragment of the polypeptide; more specifically the last three amino acids on the
right hand side of the molecule. This can also be formed by cleavage of the methionine-lysine linkage, so D is also out.
This leaves choice C as the correct response. In order to form this fragment, the enzyme would have to cleave the polypeptide
at the N-terminal end of glutamic acid. This amino acid possesses a carboxyl or acidic side chain but you are told that the
10
as developed by
KAPLAN
11
MCAT
Finally, choice D is incorrect since the R group for serine doesn't even possess a pKa, so you cannot tell whether it will even
dissociate at pH 6 to 7. Again, choice A is the correct response.
13.
The correct answer to question 13 is choice B. As I discussed in question 12, lysine has a basic side
chain which has a pretty high pKa value. In other words, the protonated form of this side chain is a weak acid. This makes
the free NH2 a strong base and choice B the correct response.
Basic R groups are recognized by the presence of the amino group in the R group structure. Of all of the amino
acids in the passage, only lysine possesses this basic side chain. Glycine has a side chain consisting of hydrogen which is
definitely not as basic, so choice D is wrong. Phenylalanine possesses a side chain which isn't even polar, so C is also
wrong. Finally, choice A is wrong as aspartic acid contains an acidic side chain; obviously a much weaker base than the
amino side chain in lysine. Again, choice B is the correct response.
Discrete Questions
14.
The correct answer here is choice D. This bond is characteristic of a disulfide linkage which contributes to
the primary structure of a protein. Disulfide linkages often arise due to the covalent interaction between two cysteine
residues; this is the case here, where the cysteine residues numbered 10 and 16 cross link.
Ester linkages such as that shown in choice A do not arise between polypeptide chains, so this can be discarded. In
addition, peptide linkages like that shown in choice B also do not arises between chains. These linkages arise within peptide
chains to link amino acids; but not between peptide chains to link amino acids. Therefore, choice B is incorrect as well.
Finally, choice C is wrong as a 'dinitride' linkage does not occur at any level of protein structure. Again, choice D is the
correct response.
15.
The correct answer to question 15 is choice B. A polypeptide chain can undergo short range bending and
folding to form sheets or helices. These structures arise as the peptide bonds can assume partial double bond character and so
adopt different conformations. The arrangement of groups around the relatively rigid amide bond can cause R groups to
alternate from side to side and hence interact with each other. In addition, the carbonyl oxygen in one region of the
polypeptide chain could become hydrogen bonded to the amide hydrogen in another region of the polypeptide chain. This
interaction often results in the formation of a beta-pleated sheet or an alpha helix.
Localized bending and folding of a polypeptide does not constitute a proteins primary structure. The primary
structure of a protein is the amino acid sequence; individual amino acids are linked to each other usually through peptide
linkages. Therefore, choice A is incorrect. Choice C is incorrect since the tertiary structure of a protein is the 3D shape that
arises by further folding of the polypeptide chain. Usually these non random folds are superimposed on an alpha helix and
serve to give the protein a particular function. Finally, choice D is wrong since quaternary structure is the spatial
arrangement between two or more associated proteins. Again, choice B is the correct response.
16.
For question 16, the correct answer is choice D. The CO-NH linkage that arises between individual
amino acids are known as amide linkages or more commonly, peptide linkages. This linkage forms when the carboxyl group
of one amino acid reacts with the amino group of another. This process is characteristic of a condensation reaction and so
results in the loss of water as well as peptide bond formation. These bonds can link an amino acid sequence to form a
dipeptide, tripeptide or a polypeptide.
Choice A is incorrect because this is an ester bond. Choice C is also wrong because this is an ether bond. Finally,
choice B is incorrect because this bond is a hydrogen bond. While this bond may be important in determining the secondary
and tertiary structures of proteins, it does not hold amino acids together in the chain. Again the correct answer is choice D.
17.
The correct answer to question 17 is choice D. As I discussed earlier, peptide bonds link the primary
sequence of amino acids in a protein. These bonds form between individual amino acids that can then go on to form a peptide
chain. Peptide bonds are never observed when a polypeptide bends or folds to form a secondary structure. In addition, when
the polypeptide folds into a three dimensional shape (which is the tertiary structure of a protein) peptide bonds do not form.
Choice A is incorrect because hydrogen bonds are involved in both the secondary and tertiary structure of a protein.
In the secondary structure, the polypeptide chain can fold so as to allow the carbonyl oxygen and the amine hydrogen to lie in
close proximity to each other. As a result, hydrogen bonding can occur to form sheets, helices or turns. Likewise, hydrogen
bonding may serve to stabilize the tertiary structure of a protein. Hydrophobic interactions can also play an important role in
the tertiary structure of a protein. For example, in an aqueous environment, the hydrophobic side chains of the amino acids
may interact so as to arrange themselves towards the inside of the protein. Therefore, choice B is also incorrect. Finally,
choice C is wrong since interactions between charged groups (often called electrostatic interactions) can arise, especially in the
tertiary structure of a protein. Again the correct answer is choice D.
18.
The correct answer here is choice C. The association rule in proteins is similar to the solubility rule you
learned in general chemistry. Groups of similar polarity will tend to group together and influence the secondary and tertiary
structure of a protein. Choice C is correct since both groups are hydrocarbons and non polar in nature. If these were side
12
as developed by
KAPLAN
13