Theoretical Exam 1 Answer keys

Question Answer Question Answer Question Answer Question Answer Question Answer
1 F 42 T 83 F 124 T 165 F
2 T 43 F 84 F 125 F 166 F
3 T 44 F 85 T 126 T 167 F
4 F 45 T 86 T 127 T 168 T
5 T 46 T 87 F 128 F 169 F
6 T 47 F 88 F 129 F 170 F
7 F 48 T 89 T 130 F 171 T
8 T 49 F 90 F 131 T 172 T
9 T 50 F 91 T 132 T 173 F
10 F 51 T 92 T 133 T 174 T
11 T 52 T 93 F 134 F 175 T
12 T 53 T 94 F 135 T 176 T
13 T 54 T 95 F 136 T 177 F
14 T 55 T 96 T 137 F 178 T
15 F 56 T 97 T 138 T 179 T
16 T 57 T 98 F 139 F 180 F
17 T 58 F 99 F 140 T 181 T
18 F 59 F 100 F 141 F 182 F
19 T 60 F 101 F 142 T 183 F
20 F 61 T 102 F 143 F 184 F
21 F 62 T 103 T 144 F 185 F
22 T 63 F 104 F 145 T 186 T
23 F 64 F 105 T 146 F 187 F
24 F 65 F 106 F 147 T 188 T
25 T 66 T 107 T 148 T 189 F
26 F 67 F 108 F 149 F 190 F
27 F 68 F 109 F 150 F 191 F
28 F 69 T 110 T 151 T 192 T
29 T 70 T 111 F 152 F 193 T
30 F 71 T 112 T 153 T 194 F
31 F 72 F 113 F 154 F 195 F
32 T 73 F 114 F 155 T 196 F
33 F 74 T 115 T 156 F 197 T
34 T 75 T 116 T 157 F 198 F
35 T 76 F 117 T 158 T 199 T
36 T 77 F 118 T 159 F 200 F
37 T 78 T 119 F 160 T 201 F
38 F 79 T 120 F 161 F 202 T
39 F 80 T 121 F 162 F
40 F 81 T 122 T 163 F
41 T 82 T 123 F 164 T
Each correct answer scores 1 marks, each incorrect or missing
answer score 0 marks.

Biochemistry
Q1(citrate and aconitase)

No. 1 2 3 4
Answer False True True False

Answers: A, F; B, T; C, T; D, F
Citrate is not chiral but stereochemically recognized by aconitase. The two -CH2COO–
groups of enzyme-bound citrate can be distinguished by aconitase, because the substrate-
binding site of the enzyme is not symmetric. This was a critical issue when the citric acid
cycle was proposed but later questioned by Krebs himself, and “TCA (tricarboxylic acid)
cycle” was proposed instead of the “citric acid cycle”. Now we know the first product,
citric acid, can be stereochemically recognized by aconitase.

Q2 (respiratory control)

No. 5 6 7 8
Answer True True False True

Answer: A, T; B, T; C, F; D, T
From the graphs, intact mitochondria respire.
The major role of the mitochondria is to produce ATP. The enhanced respiration by
addition of ADP can be regarded as coupling of ATP synthesis and respiration in intact
mitochondria. DNP, however, stimulated respiration in the absence of ATP synthesis,
because ADP was fully consumed before the addition of DNP. On the other hand, DCCD
stopped the respiration before ADP was fully consumed in the figure on the right. These
interpretations can be inferred only from the graphs and do not require the knowledge of
DNP and DCCD.
As a side note, typical cellular membranes are impermeable to ions like ATP, but
mitochondrial membranes possess ATP/ADP translocators. DNP, the uncoupler, acts as a
transporter of H+ ion across the mitochondrial membrane, because both DNP and DNP/H+
are lipophilic. DCCD binds covalently to the H+ channel of the ATP synthase and blocks
the ATP synthesis.

Q3 (RubisCO and PEPC)

No. 9 10 11 12
Answer True False True True

Answers: A, T; B, F; C, T; D, T
Reaction 1 is catalyzed by phosphoenolpyruvate carboxylase (PEPC), which shows
specificity to HCO3– ion. Reaction 2 is catalyzed by ribulose 1,5-bisphosphate
carboxylase/oxygenase (RubisCO), which shows specificity to CO2.

Cell Biology
Q4 (sedimentation coefficient)

No. 13 14 15 16
Answer True True False True

The questions are related to the sedimentation coefficient of specimens. The S-value,
which indicates the rate of specimen sedimentation during centrifugation, is a parameter
that appears in every textbook of biochemistry, but is simply described to be
corresponding to specimen size or density. This question is intended to allow the students
to gain more detailed insight into how the S-value is a number that changes under other
experimental conditions, such as temperature, viscosity, and specimen shape.

Answers
A. True: From equation (2), it is clear that the S-value is proportional to the density
difference between the specimen and the solvent, 𝜌 − 𝜌! . Thus, we can estimate
the density difference of organelles from the S-values if we can fix other
parameters, such as Vm (molar volume) and r (estimated radius).
B. True: From equation (2), it is clear that the S-value is proportional to Vm/r. This
parameter changes depending on the size of the specimen (more precisely,
 proportional to the surface area), thus we can distinguish the size difference of
specimens from the S-values if we can fix the density of specimens, 𝜌, to be 1.3–
1.4.
C. False: From equation (2), it is clear that the S-value is proportional to Vm/r, but not
to the specimen volume, Vm. Thus, the S-value is not twice as large when the
molecular weight is doubled. It is estimated to be of a value of approximately 1.4-
fold higher, or the square root of 2, if the globular shape of ribosomes does not
change much after forming a compound.
D. True: From equation (2), it is clear that the S-value is inversely proportional to η,
the viscosity coefficient of the solvent. Thus, the S-value should decrease when η
increases at low temperatures.

Questions were prepared with reference to the following document that explains how the
sedimentation coefficient relates to the shapes of biomolecules.

References
H. P. Erickson. Shape of protein molecules at the nanometer level determined by sedimentation, gel filtration,

and electron microscopy. Size and Biol. Proc. Online, 11(1):32-51 (2009).

Q5 (Squid axon & Na-pump)

No. 17 18 19 20
Answer True False True False

A mechanism for maintaining the sodium/potassium ion gradient between the inside
and outside of nerve cells is crucial for maintaining the activity of excitation. This
question yields a result from classical experiments that determined the efflux rate of
sodium ions (Na+) by the Na+ pump using the 24Na+ radiation isotope. We can establish
whether students understand the basic properties of the Na+ pump that is supported by
ATP derived from mitochondria.

A. True: The experiment clearly shows that the activity of Na+ efflux was inhibited by
 DNP, an uncoupler of ATP generation in mitochondria. Thus, the experimental
conditions should have been designed to maintain the continuous respiration activity
of mitochondria by supplying enough oxygen to the specimen, a squid giant axon.
B. False: The observed time course of DNP inhibition indicates that the efflux activity
of Na+ is decreased to approximately 1/40 (inhibited by 98%) of the original
activity. Thus, the remaining portion of this Na+ efflux can partially correspond to
the leaking flux of Na+ (plus efflux depending on the glycolytic ATP production),
but it is quite small compared with the pumping activity supported by ATP from
mitochondria (without DNP).
C. True: The delayed decrease of Na+ efflux after the application of DNP implies that
this chemical does not directly inhibit the activity of the Na+ pump. Thus, the
delayed decrease is reasonable as we can expect that the Na+ pump activity depends
on intracellular ATP remaining inside the nerve axon even if cell respiration is
blocked completely.
D. False: From the experimental results, we can calculate the rate of Na+ efflux to be
decreased approximately from 50 to 40 (decrease by 20%) in 50 min. This may be
corresponding to the decrease or dilution of 24Na+ inside the axon. This experiment
does not show any evidence of increasing intracellular Na+.

References
K. Schmidt-Nielsen, Animal physiology. 5th ed. Cambridge Univ. Press (1997).

A.L. Hodgkin & R.D. Keynes, Active transport of cations in giant axons from Sepia and Loligo. J.
Physiol., 128:28-60 (1955).

Q6

No. 21 22 23 24
Answer False True False False

A. False. Under this condition, the Nernst equilibrium potential of K+ is −120 mV.
Since the membrane potential is −150 mV, the cation K+ is passively transported
into the cell.
B. True. Under this condition, the Nernst equilibrium potential of K+ is −240 mV.
 Since the membrane potential is −150 mV, the cation K+ must be actively
transported into the cell.
C. False. Under this condition, the Nernst equilibrium potential of Cl− is +60 mV.
Since the membrane potential is −150 mV, the anion Cl− must be actively
transported into the cell.
D. False. Under this condition, the Nernst equilibrium potential of Cl− is 0 mV. Since
the membrane potential is −150 mV, the anion Cl− must be actively transported into
the cell.

Q7

No. 25 26 27 28
Answer True False False False

A. True. In wild plants, the outer lamina is bitten by insect larvae less often. On the
other hand, in mutant plants that cannot synthesize glucosinolate, both laminae were
equally bitten. Therefore, the outer lamina is supposed to accumulate more
glucosinolate than the inner lamina.
B. False. This mutant cannot synthesize glucosinolate.
C. False. We cannot judge whether Arabidopsis accumulates only glucosinolate as a
repellent to this larva, because certain repellents may distribute equally.
D. False. In wild plants, inner lamina is damaged more by this larva. The outer lamina
is supposed to be more important for this plant.

Q8

No. 29 30 31 32
Answer True False False True

A. True. The CO2 released from malic acid can be used for photosynthesis during
daytime. Therefore, more and more malic acid should be stored during night. It is
likely that malic acid concentration is the highest just before sunrise.
B. False. Since this is a freshwater environment, there is no reason to believe that water
 is scarce.
C. False. This plant is not a C4 plant. Therefore, it does not have bundle sheath cells
with well-developed chloroplasts.
D. True. In shallow waters receiving a high amount of sunshine, CO2 concentrations
decrease due to the activities of other photosynthetic organisms. In other words, CO2
tends to be scarce during the daytime. Therefore, the strategy of concentrating CO2
as malate during the night would be advantageous.

Genetics
Q9

No. 33 34 35
Answer False True True

Experiment (1) shows that only the first AUG codon of mRNA may be translated in yeast.
From Experiment (2), it is presumed that some condition exists in the AUG codon that
functions as the translation initiation in E. coli.
In eukaryotes, ribosome binds to the 5' terminal of mRNA, scans the nucleotide sequence,
and starts translation from the first AUG codon.
In prokaryotes, translation begins at the AUG codon located approximately 10 bases
downstream of the SD sequence which is complementary to the 3' terminal sequence of
16S ribosomal RNA (-CCUCCUA) in the mRNA sequence.

A. False. In E. coli, the second and subsequent AUG codons in mRNA can also serve
as translation initiation codons.
B. True. In yeast mRNA, the first AUG codon is the translation initiation codon.
C. True. In E. coli mRNA, translation begins at the AUG codon linked to the SD
sequence.

Q10

No. 36 37 38 39
 Answer True True False False

The NH2 group in the Cytosine base often reacts with H2O molecule even under natural
conditions to be converted into a carbonyl group, and then Cytosine base is converted
into an Uracil base. Therefore, all organisms have repair mechanisms that detect Uracil
bases in the DNA strands and replaces them with Cytosine bases.

A. True. Since RNA is not transmitted to the next generation, it does not need to be
repaired even if there is a chemical change in the base.
B. True. If Uracil base is used in the DNA strand, chemical conversions of Cytosine-to-
Uracil base cannot be detected.
C. False. It is the C-G base pairs that are more likely to have mutations in mutant cells
with defective Cytosine base repair mechanism.
D. False. Uracil base has no NH2 group, so chemical changes do not occur easily.

Q11

No. 40 41 42 43
Answer False True True False

A. False. Alfa is not a dominant allele because A10, which exhibits the trait, is a progeny
of A3 and A4, none of which show the trait.
B. True. Charlie cannot deny the possibility of a dominant allele because all the children
with the trait have parents with the trait.
C. True. In family B, both B1 and B3 are presumed to be carriers.
D. False. In family C, both C1 and C8 are presumed to be carriers.

Q12

No. 44 45 46 47
Answer False True True False
A. False. Uracil is an inducer for RutR repressor, and RutR becomes inactive in the
presence of uracil. Since the repression by the RutR repressor is derepressed by
increasing the concentration of uracil, the expression level of the rut operon increases.
B. True. When the affinity between the RutR repressor and uracil decreases, the
sensitivity of the RutR to uracil also decreases. Therefore, the RutR repressor is less
likely to be in inactive form. As a result, the repression of the rut operon is enhanced,
and the expression level of the rut operon is reduced.
C. True. When the DNA binding affinity of the RutR repressor decreases, repression by
the RutR repressor is reduced. As a result, the expression level of the rut operon
increases.
D. False. When a change occurs in the RutR repressor binding sequence of the Prut
promoter, the affinity to the RutR repressor may decrease or increase. Therefore, it
cannot be concluded that the expression level always increases.

Q13

No. 48 49 50 51
Answer True False False True

A. True. Under conditions where glucose is available, lactose metabolism is suppressed.

B. False. The first step in glycogen metabolism is the addition of a phosphate group to
glycogen to produce glycogen-1-phosphate. Therefore, glycogen metabolism is
suppressed under the phosphate depletion condition.
C. False. The metabolism of fatty acids is an oxidative reaction. Therefore, transcription
factors that activate the expression of fatty acid metabolism genes are generally
activated in the presence of oxygen.
D. True. Since biofilm formation is promoted by cell adhesion, motility is suppressed.

Q14

No. 52 53 54 55
Answer True True True True
A. True. In situ hybridization is used to examine mRNA expression and localization in
tissues.
B. True. Quantitative RT-PCR can quantitatively analyze the expression levels of
specific genes.
C. True. Bacillus subtilis cultured in media with different concentrations of nitrogen
sources can be screened for genes with altered expression level using the DNA
microarray, which can comprehensively measure the expression levels of the entire
genome.
D. True. Metagenome analysis is a technology for sequencing genomic DNA extracted
from microbial groups in compost for comprehensive analysis of the microbial
species.

Q15

No. 56 57 58 59
Answer True True False False

A. True. Germination of mutant seeds is delayed because gibberellin, a hormone that

promotes germination, is not produced.
B. True. In the ent-kaurene synthase knockout mutant, ent-kaurene is not produced, but
the downstream biosynthetic genes function normally. Thus, the treated ent-kaurene
is converted into gibberellin, and it promotes germination.
C. False. GA20 oxidase is an enzyme acting downstream of ent-kaurene. Therefore the
treated ent-kaurene is not converted into gibberellin, and thus germination is not
promoted.
D. False. Since the strain of overexpressing the CYP707A enzyme gene showed to
promote germination more than the wild type seed, it is considered that 8'-
hydroxyabscisic acid has a weaker germination suppressing effect than ABA.

Q16

No. 60 61 62 63
 Answer False True True False

A. False. Translation is initiated at the start codon ATG. Protein X mRNA is not
translated correctly because of a frameshift.
B. True. Designed correctly.
C. True. Designed correctly.
D. False. The reverse primer, which must be designed starting from the 3'-end in the 3'-
to-5' direction to match the complementary strand, is designed in the opposite
direction and therefore does not match the template.

Q17

No. 64 65 66 67
Answer False False True False

A. False. Since the insertion of a single base causes a frameshift, it is considered that
the function of the protein encoded by this gene is lost.
B. False. Since the deletion of one base causes a frameshift, it is considered that the
function of the protein encoded by this gene is lost.
C. True. One amino acid is missing due to the deletion of 3 bases. If this amino acid is
not critical for protein function, the function of the encoded protein may be conserved.
D. False. One codon is added by inserting three bases. Although no frameshift has
occurred, it is considered that the function of the encoded protein is lost due to the
appearance of the stop codon TAA.

Q18

No. 68 69 70 71
Answer False True True True

A. False. The transcription/translation control system by attenuation is based on the

premise that the rate of ribosome progression is equal to or higher than the rate of
 RNA polymerase progression. It has been found that prokaryotic transcription rate is
50–100 bases/second and translation rate is 20 amino acids/second.
B. True. When the operator sequence is mutated, the repressor cannot bind to it, so trp
mRNA is always transcribed. But most transcription events terminate halfway
because the translation of the leader peptide is not stagnant.
C. True. Even if Trp is depleted in the intestinal bacterium, the translation of the leader
peptide ends, so that Region 3 and Region 4 form a pair and transcription of the trp
operon is stopped.
D. True. Since the ribosome is likely to be stagnant in the leader peptide, it is considered
that the trp operon mRNA is easily transcribed and translated even in the presence of
low concentration of Trp, and the intracellular Trp concentration of E. coli is
increased.

Animal biology
Q19 (Glucagon receptor)

No. 72 73 74 75
Answer False False True True

The magnitude of hormonal effects in animals depends on hormone concentration. At

the same time, it also depends on the amount of receptors in recipient tissues or cells. We
provided the students with experimental data measuring the amount of mRNA considered
to be corresponding to the expression level of receptors (glucagon receptor, GLR) and
asked them to discuss the given results in the context of textbook knowledge.

A. False: The liver responds to glucagon and functions as a glucose source. It uptakes
and stores glucose in response to another hormone, insulin.
B. False: It may be true that brain tissue has little GLR mRNA according to the
experimental data (Hansen, 1995), but this does not mean that the brain never needs
glucose. I also expect that the examinees know that glucose is the major source of
energy for brain tissues.
C. True: Hansen’s data indicate muscle has little GLR. This is consistent with the
properties of muscles such that they just consume ATP (working as ATP sinks) but
 need not operate as ATP sources for other tissues/cells.
D. True: Hansen’s data may be consistent with textbook knowledge indicating that
adipose tissue is working as a glucose source in starvation.

Reference
L.H. Hansen et al., Glucagon receptor mRNA distribution in rat tissues. Peptides, 16(6):1163-
1166 (1995).
M.A. Abraham & T.K.T. Lam, Glucagon action in the brain. Diabetlogia, 59:1367-1371 (2016).

Q20 (Athlete metabolism)

No. 76 77 78 79
Answer False False True True

Without any knowledge of exercise physiology, the given table would help the
examinees understand that there are multiple energy sources besides stored ATP in our
skeletal muscles. Crucial points I wish the students to understand are the differences in
the amount and rate of power output depending on the involved metabolic pathways. The
questions were prepared to ask examinees about the rationale underlying how the energy
source is used during exercise.

A. False: For 100-meter sprinters, their muscles require energy sources with a high
output rate to maintain running speed, which is sometimes faster than 10 m/s. From
the data shown in the table, ATP and CP should be the main energy sources needed
for such a high rate of power output. CP would be providing additional ATP
molecules as the stored 8 mM ATP inside muscle cells that should be consumed
within a few seconds during sprinting. Both are supported by anaerobic process
metabolism (without respiration).
B. False: In any kind of sport, the substrate for myosin motors during muscle
contractions is ATP alone. I intended for the students to infer that some amount of
ATP concentration must never be depleted even if the stored ATP and CP are
numerically depleted to be zero. It is quite reasonable to expect that ATP converted
from stored fat or glycogen are the main energy sources for long-distance runners.
C. True: For 1,500 m athletes who need to run longer than 1 min, it is clear that stored
ATP and CP are not sufficient. I intended for the examinees to infer that ATP supply
from both anaerobic (glycolysis) and aerobic (cell respiration) metabolism are
crucial, i.e., an intermediate state of energy consumption between sprinters and
marathon runners.
D. True: As explained above, ATP enables aerobic metabolism crucial for long-
distance runners, thus both stored glycogen and fat should be used during a
marathon.

Reference
K. Schmidt-Nielsen, Animal physiology. 5th ed. Cambridge Univ. Press (1997).

Q21 (Huntington Disease)

No. 80 81 82 83
Answer True True True False

Huntington's disease is a neurological disease that has been known for a long time, but
the molecular mechanism of its manifestation was clarified only recently. This question
was prepared based on a review of the causative gene mutations (glutamate repeat) in
Huntington's disease as well as the results from cell biological research (defects in axonal
glycolysis). Contrary to common sense held by examinees, the latter document (Zala et
al., 2013) provides clear experimental evidence that axonal transport is mainly dependent
on glycolytic ATP. This is a question to assess the examinee's adaptive thinking when
exposed to new information that may be contradictory to their textbook knowledge.

A. True: The base sequence, CAG (glutamate), is found at the transcriptional initiation
site of the HTT gene as described in the text. Thus, the N-terminal in translated HTT
proteins has some sets of repeated glutamate amino acids.
B. True: As described in the text, Zala et al. observed that HTT, motor proteins (FAT
transporter), and GAPDH (glycolysis enzyme) were all located within synaptic
vesicles. In addition, the FAT of synaptic vesicles cannot be observed in HTT-
depleted axons (by RNAi). This evidence implies that HTT helps to maintain the
 functioning of both FAT motors and GAPDH in synaptic vesicles. Anchoring by
HTT is one of the most possible assumptions.
C. True: As described in the text, RNAi of HTT as well as iodoacetate stopped the FAT
of synaptic vesicles, but it had no effects on mitochondrial FAT. Thus, ATP produced
by mitochondria cannot be utilized by synaptic vesicles, even if there is an adequate
amount of ATP in axons, contrary to our textbook knowledge.
D. False: As described in the table, iodoacetate cannot stop mitochondrial FAT. Thus,
ATP produced by glycolysis is not critical.

References
D. Zala et al., Vesicular glycolysis provides on-board energy for fast axonal transport. Cell, 152:
479–491 (2013).

J.A. White II et al., Huntingtin differentially regulates the axonal transport of a sub-set of Rab-
containing vesicles in vivo. Human Mol. Genetics, 24(25):7182-7195 (2015)
F. Saudou & S.Humbert, The biology of huntingtin. Neuron, 89: 910-926 (2016).

F. Saudou & S. Humbert, The biology of Huntingtin. Neuron, 89:910-926 (2016).

Q22

No. 84 85 86 87
Answer False True True False

A. False. Beaver excretes urine with low concentration. It is expected that the JM/C
ratio will be small, thus the answer is False.
B. True. Kangaroo rat urine concentration is 5500. At the >4000 plots, they are all over
1.5, so this statement is True.
C. True. Medullary salt reabsorption and increased medullary salt concentration
promote passive water transport by aquaporins, resulting in decreased urinary water
content. Therefore, this statement is True.
D. False. It is obvious that the JM/C ratio of animals living in arid climate is higher than
that of animals living in freshwater. Therefore, this statement is False.
Q23

No. 88 89 90 91
Answer False True False True

A. False. In Fig. 1, the recording neuron is depolarized from around -50 mV in response
to the application of GABA. In Figs. 2 and 3, GABA induced inward current when
the membrane potential is -50 mV, and the current direction reversed when the
membrane potential is -10 mV. That means the cell is more hyperpolarized. Therefore,
this statement is False.
B. True. From Table 1, the equilibrium potential of chloride ions is -28 mV, which is
higher than the resting membrane potential of recording neurons (approximately -50
mV). Therefore, this statement is True.
C. False. GABA treatment induces depolarization of the recording neurons and does not
induce action potentials because of the blockade of Na+ channels by tetrodotoxin. In
this situation, the membrane potential of the recording neurons will approach the
equilibrium potential of Cl- (-29 mV) and will not depolarize beyond the equilibrium
potential of Cl-. Therefore, this statement is False.
D. True. In the “other” neuron described in this statement, the membrane potential is
hyperpolarized by GABA treatment. In such a situation, Cl- are expected to move
inward (this is a “well-known” GABA reaction). Since Cl channels open and Cl ions
flow inside, it is suggested that the intracellular Cl- concentration is lower than that
of the neurons investigated this time. Therefore, this statement is True.

Q24

No. 92 93 94 95
Answer True False False False

A. True. The nuclear/cytoplasmic ratio increases in both polyspermy and enlargement

of the nuclear envelope. At both experiments, the MBT takes place earlier. Thus, this
statement is True.
B. False. The cell cycle includes interphase after MBT. Thus, it is considered that the
earlier the MBT takes place, the longer is the time required for division until the 12th
round. Accordingly, this statement is False.
C. False. The change in the timing of MBT in the experiments of polyspermy and
manipulation of nuclear size indicate that the timing of MBT is not determined by
the number of cell divisions. Thus, this statement is False.
D. False. MBT occurs earlier as the nuclear size increases. It is possible that the
concentration of histones in the nucleus is affected. Because the text states that the
amount of histones does not change during the manipulation performed in this
experiment, we can assume that MBT occurs when the concentration of histones gets
small. The sentence states the opposite: the concentration of histone becomes BIG.
Thus, this statement is False.

Q25

No. 96 97 98 99
Answer True True False False

A. True. It is described that the head is disrupted due to the inhibition of organizer
formation. GSK3β inhibits the formation of the organizer because the head defect
occurs when GSK3β is injected dorsally. Accordingly, this statement is True.
B. True. Injection with β-catenin on the ventral side induces a secondary axis, and co-
injection with GSK3β has no effect. So, this statement (GSK3β inhibits β-catenin) is
True. The possibility that β-catenin inhibits GSK is also eliminated because DN-
GSK3β/dorsal injection has no effect.
C. False. If β-catenin is absent on the ventral side, the secondary axis cannot be formed
even if the GSK3β is suppressed. Thus, the statement is False.
D. False. It is expected that suppression of β-catenin causes head defects even if GSK3β
is not activated. Accordingly, this statement is False.
Q26

No. 100 101 102 103

Answer False False False True

A. False. Body temperatures of some ectotherms is higher than those of endotherms.

B. False. When the temperature of hypothalamus elevates, it signals to decrease the
body temperature of the whole body.
C. False. When incubating, the python requires more energy to warm the egg.
D. True. Exotherms consume less energy because they rely on extracorporeal
temperature.

Q27

No. 104 105 106 107 108

Answer False True False True False

A. False. From this experiment, it is not clear that introduction of only 3 genes are
enough to induce colonies.
B. True. This experiment shows requirement of each gene for colony induction.
C. False. The long bar in 9 indicates that 9 is unnecessary.
D. True. To find the smallest set of genes, we need to add another gene to 14/15/20 to
test whether the colonies are actually induced.
E. False. This experiment shows that the addition of the gene set into fibroblasts induces
colonies, but does not show whether 14, 15, or 20 is expressed.

Q28

No. 109 110 111 112

Answer False True False True

A. False. DNA fragments do not reflect the size of the light chain gene. Also, even if
they did, they would be long.
B. True. The difference in migration distance depends on the length of hybridized DNA.
C. False. The entire DNA fragment that hybridizes with 3'-terminal of mRNA differs
between myeloma cells and embryo center cells. But, when considered alone, the
hybridized region is the same in myeloma cells and germinal center cells.
D. True. Two peaks were observed in the hybrid of full-length mRNA and DNA from
embryo center cells. This indicates that there are two DNA fragments that can
hybridize with the mRNA sequence.

Plant biology
Q29

No. 113 114 115 116

Answer False False True True

A. False. The absolute humidity of the air is directly reflected in Δw. Therefore, if the
absolute humidity determines relative stomatal aperture, it should be the same in
the Air and Helox conditions, which are same in Δw, and it should be different in
the Air and Helox1/2.33 conditions, which are different in Δw. However, this is not
the case.
B. False. While dwater is 2.33 times larger in Helox than in Air, Figure 1 shows that
relative stomatal aperture is about 2.33 times smaller in Helox than in Air. The
Helox and Air conditions are same in Δw and thus have the same humidity. Taken
together, transpiration rate, which is proportional to dwater, Δw, and relative stomatal
aperture, is calculated to be the same in Helox and normal air at the same humidity.
C. True. Relative stomatal aperture decreases as the humidity decreases, CO2 uptake
decreases as relative stomatal aperture decreases, and the concentration of CO2 in
the leaf decreases as CO2 uptake decreases. Because the rate of photosynthesis is
dependent on the concentration of CO2 in the leaf, the low humidity condition
causes a reduction in the rate of photosynthesis.
D. True. Figure 1 shows that, even under the conditions with different humidity and
Δw, changes of relative stomatal aperture offset such differences to keep the
transpiration rate constant. In other words, at a low humidity, Δw increases but the
 transpiration rate remains constant as the relative stomatal aperture decreases.

Reference
K. A. Mott, D. F. Parkhurst (1991) Stomatal responses to humidity in air and helox. Plant, Cell
and Environment 14, 509–515.

Q30

No. 117 118 119 120

Answer True True False False

A. True. Protease inhibitor gene expression is not induced in the wild-type scion
grafted to the spr1 stock, which cannot perceive systemin in the proximity of the
wound site.
B. True. Protease inhibitor gene expression is not induced in the wild-type scion
grafted to the spr2 stock, which cannot synthesize jasmonates in the proximity of
the wound site, while it is normally induced in the spr2 scion grafted to the wild-
type stock.
C. False. Protease inhibitor gene expression is induced in the wild-type scion grafted
to the jai1 stock, which cannot perceive jasmonates in the proximity of the wound
site.
D. False. Protease inhibitor gene expression is induced in the spr1 scion grafted to the
wild-type stock, while it is not induced in the wild-type scion grafted to the spr1
stock, suggesting that protease inhibitor gene expression is induced only when
systemin is perceived in the proximity of the wound site. Therefore, systemin is not
likely to be the mobile signaling molecule responsible for long-distance wound
signaling.

References
G. I. Lee, G. A. Howe (2003) The tomato mutant spr1 is defective in systemin perception and

the production of a systemic wound signal for defense gene expression. The Plant Journal 33,
567–576.
L. Li, C. Li, G. I. Lee, G. A. Howe (2002) Distinct roles for jasmonate synthesis and action in the
 systemic wound response of tomato. Proceedings of the National Academy of Sciences of the
United States of America 99, 6416–6421.
J.-Q. Sun, H.-L. Jiang, C.-Y. Li (2011) Systemin/jasmonate-mediated systemic defense signaling
in tomato. Molecular Plant 4, 607–615.

Q31

No. 121 122 123 124

Answer False True False True

A. False. The results of grafting between max2 and WT showed that MAX2 function
in the shoot is required for the control of branching. This indicates that SL is
perceived in the shoot to control branching.
B. True. The results of grafting between max1 and WT showed that branching is
normally controlled by SL if either one of the root or shoot has functional MAX1.
This indicates that CL is synthesized both in the root and shoot in WT plants. Note
that a normal branching phenotype obtained in grafting of the max1 shoot scion to
the WT rootstock indicates that SL synthesized in the root is transported to the shoot.
C. False. Grafting of the max4 shoot scion to the max1 rootstock resulted in a normal
branching phenotype, which indicates that CL synthesized in the root is transported
to the shoot and converted to SL. However, grafting of the max1 shoot scion to the
max4 rootstock resulted in a hyper-branching phenotype, which indicates that CL
synthesized in the shoot is not transported to the root. (If CL synthesized in the shoot
was transported to the root in this plant, CL would be converted to SL in the root
and then transported back to the shoot to control branching. This does not agree
with the phenotype.)
D. True. As MAX2 functions in the shoot, this grafting creates practically the same
situation as grafting of the max4 shoot scion to the WT rootstock. In this grafted
plant, it is expected that SL synthesized in the root is transported to the shoot and
controls branching and also that CL synthesized in the root is transported to the
shoot and converted to SL in the shoot and controls branching.

Reference
 J. Booker, T. Sieberer, W. Wright, L. Williamson, B. Willett, P. Stirnberg, C. Turnbull, M.
Srinivasan, P. Goddard, O. Leyser (2006) MAX1 encodes a cytochrome P450 family member
that acts downstream of MAX3/4 to produce a carotenoid-derived branch-inhibiting hormone.
Developmental Cell 8, 443–449.

Q32

No. 125 126 127 128

Answer False True True False

A. False. Obvious from comparison of Figure 1(a)·(b) with Figure 1(c).

B. True. Obvious from Figure 1(a) and (b).
C. True. Zn content in the root was decreased by addition of excess Fe2+, while Zn
content in the shoot was not changed by excess Fe2+.
D. False. Addition of excess Fe2+ did not change Zn content of dry weight basis in the
shoot but increased dry weight of the shoot, and therefore increased total Zn amount
in the shoot.

Reference
V. Shanmugam, J.-C. Lo, C.-L. Wu, S.-L. Wang, C.-C. Lai, E. L. Connolly, J.-L. Huang, K.-C.
Yeh (2011) Differential expression and regulation of iron-regulated metal transporters in

Arabidopsis helleri and Arabidopsis thaliana – the role in zinc tolerance. New Phytologist 190,
125–137.

Q33

No. 129 130 131 132

Answer False False True True

A. False. In the inflorescence of sunflower, as is typical for the Compositae

inflorescence, florets in the outer region are formed earlier than florets in the inner
region. The sunflower florets in the outer region are ligulate and thus bilateral,
suggesting that these florets have high expression of gene G’.
B. False. In variant x, the inner florets, which are normally tubular (radially symmetric),
are changed to be ligulate (bilateral). This suggests that expression of gene G’ is
increased in variant x.
C. True. In variant y, all florets are tubular (radially symmetric). The disappearance of
bilaterality from florets indicates that this variant is a loss-of-function mutant of gene
G’.
D. True. There is an insertion shared by variants x and y, while there is no common
insertion between variants y and z.

Reference
M. A. Chapman, S. Tang, D. Draeger, S. Nambeesan, H. Shaffer, J. G. Barb, S. J. Knapp, J. M.
Burke (2012) Genetic analysis of floral symmetry in Van Gogh's sunflowers reveals

independent recruitment of CYCLOIDEA genes in the Asteraceae. PLoS Genetics 8,

e1002628.

Q34

No. 133 134 135 136

Answer True False True True

The increase of combined dry biomass in the connected ramets compared to the severed
ramets showed that the connection released the restriction of photosynthesis by light or
nitrogen availability, indicating exchange of nitrogen and photosynthetic assimilates
between connected ramets.
A. True. In a severed ramet under the high PFD and low nitrogen condition, the
absorption of nitrogen in the root limits photosynthesis, and as an adaptive response,
the ramet increases the absorption of nitrogen by decreasing the shoot/root ratio
with the sacrifice of light absorption in the shoot. However, in a connected ramet
under high PFD and low nitrogen condition, nitrogen is not a limiting factor of
photosynthesis because of the nitrogen supply from its partner, and such adaptive
response does not occur.
B. False. In a severed ramet under the low PFD and high N condition, availability of
light, instead of nitrogen, limits photosynthesis.
C. True. Under uniform conditions, exchange of nitrogen and photosynthetic
assimilates between ramets does not complement resource deficiencies in each
ramet.
D. True. As discussed above, nitrogen and photosynthetic assimilates are exchanged
between connected ramets, which is mediated by translocation via stolons.

Reference
D. Friedman, P. Alpert (1991) Reciprocal transport between ramets increases growth of Fragaria
chiloensis when light and nitrogen occur in separate patches but only if patches are rich.

Oecologia 86, 76–80.

Q35

No. 137 138 139 140

Answer False True False True

A. False. Mutant x responded to sorbitol in a manner similar to the wild type, indicating
that x is normal in sensing and responding to osmotic stress.
B. True. While osmotic stress response of mutant x is normal, its response to NaCl was
very small, indicating that x is defective in sensing ionic stress. The response of
mutant y to NaCl was smaller than the wild type but much larger than mutant x
defective in sensing ionic stress. This indicates that mutant y can sense and respond
to ionic stress. The reduction in response of mutant y to NaCl is attributable to the
defect of osmotic stress sensing, in consideration of the limited response of y to
sorbitol.
C. False. While both osmotic stress response and ionic stress response are compromised
in the x y double mutant, mutant x is defective only in ionic stress response. Because
NaCl elicits both osmotic and ionic stresses, the phenotype of the x y double mutant
will be more severe than that of the x single mutant.
D. True. Because sorbitol elicits only osmotic stress, the phenotype of the x y double
mutant will be equivalent to that of the y single mutant, whose response to the
osmotic stress is compromised.
Reference
Z. Jiang , X. Zhou, M. Tao, F. Yuan, L. Liu, F. Wu, X. Wu, Y. Xiang, Y. Niu, F. Liu, C. Li, R. Ye,
B. Byeon, Y. Xue, H. Zhao, H.-N. Wang, B. M. Crawford, D. M. Johnson, C. Hu, C. Pei, W.
Zhou, G. B. Swift, H. Zhang, T. Vo-Dinh, Z. Hu, J. N. Siedow, Z.-M. Pei (2019) Plant cell-
surface GIPC sphingolipids sense salt to trigger Ca2+ influx. Nature 572, 341–346.

Evolution
Q36

No. 141 142 143 144

Answer False True False False

A. False. The frequency of CBCB is about 49%. p2: 2pq: q2, q2 = 0.09, q = 0.3, p = 0.7,
p2 = 0.49
B. True.
C. False. Random genetic drift is a more plausible explanation.
D. False. A small population is more sensitive to random genetic drift than a large
population. Therefore, fixation probability of slightly deleterious mutations is higher
in a small population than in a large population.

Q37

No. 145 146 147 148

Answer True False True True

This figure was modified from Zhang et al. 1998 PNAS

A. True. Tamarin has only the EDN gene. In addition, Tamarin EDN has a sister-
relationship with both of ECP and EDN genes of all Old World monkeys. That
suggests that there is only EDN in the common ancestor of primates.
B. False. ECP genes of human, chimpanzee, gorilla, orangutan, and macaque were
derived from only one gene duplication from EDN in the common ancestor of them
and split into each species according to the speciation.
C. True. X to human ECP gene: 3+2+0+0+0=5, X to human EDN gene: 3+5+3+0+2=13.
 Number of synonymous substitutions on the branches from X to human ECP is
smaller than EDN.
D. True. So many non-synonymous substitutions occurred on the branch of the common
ancestor of ECP (33) although the number of synonymous substitutions seems to be
comparable to the other branches, implying the operation of positive selection.

Q38

No. 149 150 151 152 153 154

Answer False False True False True False

A. False. Zebrafish SWS is equally closely related to RH and zebrafish MWS1 to 4. So,
Zebrafish SWS is not “most closely related” to RH.
B. False. Common ancestor possesses five opsin gene.
C. True.
D. False. Zebrafish has acquired four opsin genes.
E. True.
F. False. The ancestor had a gene encoding SWS. The gene was lost in the human
lineage, but human acquired a new SWS gene via amino acid changes from a UVS
gene.

Q39

No. 155 156 157 158

Answer True False False True

This figure was modified from Hoekstra et al. (2006)

A. True. MC1R largely contributes to the body color. However, C allele is not fixed in
white color population, suggesting that other genes also contribute to the body color.
Indeed, such genes were discovered in a latter paper.
B. False. Opposite
C. False. The mutations in C allele occurred only one time. The existence of the C
 alleles in each localities ①-③ was explained by the changes of frequency.
D. True.

Q40

No. 159 160 161 162

Answer False True False False

This question is in reference to Seehausen et al. (2008) Nature.

A. False. Female cichlids choose male cichlids.
B. True.
C. False. It is explained by sexual selection through female mate choice on male body
coloration.
D. False. The opsin gene is not differentiated between males and females of the same
species because the opsin adapted to light conditions in the habitat of each species.

Q41

No. 163 164 165 166

Answer False True False False

A. False. More slowly evolving gene should be used to infer the older divergence.
Substitution will be saturated in the case of rapidly evolving genes.
B. True.
C. False. We should select organisms that are as closely related as possible.
D. False. Biological species concept does not require the monophyly of the species.

Q42

No. 167 168 169 170

Answer False True False False

A. False. We cannot judge terrestrial or amphibious in the common ancestor of whales

 and hippos.
B. True.
C. False. Remingtonocetus and Miacetus ate seawater fish, implying the invasion of the
oceanic environment whereas their lifestyles were amphibious. This suggests that the
acquisition of fully aquatic lifestyle may occur after the invasion of the oceanic
environment.
D. False. Loss of enamelin gene should be after the divergence of toothed whales and
baleen whales.Q43

No. 171 172 173 174

Answer True True False True

T This figure is modified from Barton et al. (2007) “Evolution”

A. True.
B. True.
C. False. Loss of Ubx in T3 alters the identity of the segment. The loss of Ubx in T3
does not have an effect on the other hox genes.
D. True.

Q44

No. 175 176 177 178

Answer True True False True

This figure was modified from Gilbert (2015) “Developmental Biology”

A. True. Because the freshwater sticklebacks are observed in remote rivers all over the
world, they are likely to be independently evolved from oceanic populations in each
environment.
B. True. The paper was published to propose this hypothesis.
C. False. Because KO of Pitx1 results in the loss all organs (ventral spine, thymus and
sensory canal), the phenotype will not be the same as in the freshwater population
(Indeed, they are lethal).
D. True.
Ecology
Q45

No. 179 180 181 182

Answer True False True False

1. True. Asexually reproductive species do not need mating partners, but sexually
reproductive species need to find a mating partner. Therefore, at low densities, the
rate of increase in sexually reproduced species may decrease, but not in asexual
reproduction.
2. False. A and D are stable equilibrium points, but B is an unstable equilibrium point
that disrupts the directions of population changes. Thus, population density is not kept
constant at around B in a density dependent manner.
3. True. Since there is a positive association between density and growth rate below C,
aggregation is beneficial.
4. False. Extinction vortex is caused by accelerated reductions of population size with
decreasing density. This is more likely to occur in type 2 than in type 1, because
population growth rate is negative under low densities in type 2.

Q46

No. 183 184 185 186

Answer False False False True

A. False. Large territory size does not lead to enhanced food consumption rate and food
depletion. Rather, limits on foraging time and food requirement lead to the saturation
pattern.
B. False. Optimal territory size is the point at which (benefit - cost) or (benefit/cost) is
maximized.
C. False. When resources become scarcer, the slope of the benefit curve becomes less
steeper and the intersection of the curve and the cost line should move to the left.
Since territory size is determined in a way that maximizes the net benefit gain of
individual animals, optimal territory size will become smaller (see below figure).
 Notice that this does not mean home range becomes smaller, instead probably
becoming larger; this is out of the scope of this question.

D. True. The cost line becomes steeper with increasing intensity of competition. Above
a certain threshold, the cost is always larger than benefit, which makes territory
establishment nonsense. Notice that this does not mean home range becomes smaller.

Q47

No. 187 188 189 190

Answer False True False False

A. False. Comparison of the number of seeds between (1) and (2) reveals the nighttime
contributions.
B. True. The treatment 4 indicates evidence for selfing.
C. False. The treatment 3 shows a large variability in nighttime pollinations.
D. False. Comparison of the number of seeds between (5) and (1) indicates pollinator
limitation to some degree under natural conditions.

Q48

No. 191 192 193 194

Answer False True True False

A. False. The presence of heterozygotes indicates the presence of the resistance allele.
B. True. The increase of the resistance allele frequency indicates natural selection.
C. True. The decrease of allele r after cessation of insecticide application indicates its
lower fitness in ordinal conditions.
D. False. The allele frequency of r was 21% in 1990, while it was 94% in 1995.

Q49

No. 195 196 197 198

Answer False False True False

A. False. The number of species in 50 years was lower than that in the first 2 years.
B. False. The decrease in dominance of species A does not indicate competitive
exclusion by itself.
C. True. The abundances of the top 3 species exceed 85% of the total.
D. False. The gradual decrease in the slope of the rank-abundance curve indicates the
increase in evenness with time.

Q50

No. 199 200 201 202

Answer True False False True

A. True. Niche differentiation indicates more efficient use of available nutrients, which
results in higher productivity.
B. False. The highest biomass was found at the plot with 9 species.
C. False. Additional 6 species will achieve 0.1 kg increase in a plot on average.
D. True. Sampling effect denotes the higher chance of inclusion of more productive
species in species-rich plots, which is an inevitable consequence.