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Name: ___________________________Lab Section __________________ 3/28/11

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BIO 10100 Exam 2 Version 3
Prior to completing this exam, please read the following statement and sign below to indicate
that you have read and understood the statement. No exam will be graded unless the pledge is
signed.
I pledge that I have neither given nor received unauthorized assistance on this exam. I
understand that if I am charged with cheating, my name will be submitted to the Dean for
disciplinary action.

__________________________________________________ _____________________
Name Date

Please make sure you have all 12 pages of the exam. Write your name and lab section on all
sheets. Please read each question carefully. If you do not understand the meaning or intention
of a question, please ask. Please pace yourself and use your time efficiently.
Please put away your cell phones, blackberries, iPods, laptop computers, etc. Write your
answers using a pen. Answers written in pencil will not be accepted.
Each T/F or multiple-choice question is worth 2 points. Note that a correct statement is not
necessarily the best answer to a multiple-choice question. For each multiple-choice question,
circle the best answer. You will receive ZERO credit for any question for which we cannot tell
what your final answer is. If you cross out an answer, please make it clear as to which answer is
your final answer.
Please pace yourself and use your time efficiently; allow time for the essay type questions. If a
question states answer a or b, not both: if you answer both, then we will read only the answer
to a, regardless of how much better your answer to b might be.
1. Below is an excerpt from a set of research experiments.
Experiment 1: Mitochondria are isolated from cells and placed in a medium at pH 9. This
results in a low H
+
concentration on both sides of the inner mitochondrial membrane. Half of
the mitochondria are removed quickly to a neutral medium (pH 7) as shown in the figure.
ATP is synthesized in these mitochondria. The other half of the mitochondria are kept in a
test tube at pH 9 (not shown in the figure). No ATP is synthesized in these mitochondria.

Experiment 2: A set of artificial vesicles is made and a bacterial proton pump is inserted in
the membrane of the artificial vesicles. The bacterial pump actively transports protons (H
+
)
into the vesicles. This establishes a large proton gradient across the vesicle membrane (more
protons on the inside, fewer protons on the outside). ADP and Pi are provided on the outside
of the vesicle. No ATP is synthesized. The vesicles are divided into two test tubes. ATP
synthase from the mitochondria of a mammal is isolated and then inserted into the membrane
of half of the artificial vesicles in the orientation shown in the figure on the right. These
vesicles are placed in test tube 1. The vesicles that do not have the ATP synthase inserted in
their membrane are in test tube 2 (not shown). There is ATP synthesis in test tube 1. There
is no ATP synthesis in test tube 2.
Name: ___________________________Lab Section __________________ 3/28/11
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Experiment 1 Experiment 2
a. Identify the alternative and null hypotheses being tested and the experimental predictions.

(4 points) Alternative:
Exp 1: A proton gradient is required (or is enough in the absence of electron transport)
for ATP synthesis.

Exp 2: The protein ATP synthase is required (or proton gradient is not enough) for ATP
synthesis.

(4 points) Null:
Exp 1: The presence of a proton gradient is not required (or is not enough in the absence
of electron transport) for ATP synthesis.

Exp 2: The protein ATP synthase is not required (or proton gradient is enough) for ATP
synthesis.

(4 points) Experimental prediction:
Exp 1: If isolated mitochondria are incubated in pH 9 solution to equilibrate to pH 9 and
then moved to pH 7 to create a proton gradient across the cristae with more protons on
The Immoital Bevil

1. What is BFTB. Bow uoes it spieau.
devil facial tumor disease, its spread by contact

2. What is meant by the following. "All canceis aie piouucts of natuial selection
playeu out on the level of cells iathei than species."

Its ability to iepiouuce anu uiviue
Biviue iapiuly anu kill anu in conflict with the inteiest of the host oiganism.

S. Why is the suivival of the Tasmanian Bevil so impoitant to the ecology of the
islanu.

Tamsanians aie the top pieuatois, especially of non-native cats anu foxes, if they uie
these woulu take oveis

4. What uiu the stuuy of the chiomosomes of the cancei cells tell the ieseaicheis
about the souice of the cancei in the uevils. What is the "immoital uevil".

all the cancei cells aie iuentical in eveiy oiganism, came fiom xx chiomosome.
Came fiom one oiiginal female Tasmanian, that is living thiu otheis.


S. What weie the alteinative hypotheses foi why the immune system of the uevils
wasn't able to uetect the cancei invasion. Which one is suppoiteu.

veiy inbieu that theii cells look iuentical to theii immune systems iuleu out by skin
tiansplants uiun't take.
Tumoi was obscuiing its foieign iuentity caiu. tuineu out that they hau no iuentity
caiu at all.

6. What is the iole of the NBC genes in BFTB. Bow uiu use of inteifeion-gamma
help Siuule.
Role is to piouuce the iuentity caiu
The inteifeion is a chemical messengei that inuuces anu immune iesponse anu it
activateu the mhc genes anu the tumoi cell's iuentity caiu showeu up.


7. What is the pioposal foi making a vaccine foi BFTB. Woulu it woik foi the wilu
population.
uiow cultuie give the inteifeion, tuin on gene, tiansfei to healthy uevils, let it fight
it off, anu then they will have
0, because it woulu have to be uone inuefinitely

8. What is CTvT. What uoes it tell us about the evolution of the paiasitic
ielationship it has with its host. Woulu this be a iealistic expectation foi futuie
evolution of BFTB.

11k ya Infectious cancei Bog veneieal uisease

When it affects a uog, it uoesn't show its caiu, but latei on it shows, it's consiueiate
of its host.

Name: ___________________________Lab Section __________________ 3/28/11
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the outside, then in the absence of electron transport ATP will be synthesized by the
mitochondria.

Exp 2: If a proton gradient is created in an artificial vesicle with the use of a bacterial
proton pump, and an ATP synthase from mitochondria is inserted into the vesicle in the
correct orientation, then ATP will be synthesized in the presence of the substrates ADP
and Pi.

b. (4 points) What, if anything, is the control treatment in each experiment?
Exp 1: Keeping the mitochondria in a test tube at pH 9 for the entirety of the experiment.

Exp 2: Not adding the ATP synthase to the vesicles in test tube 2.

Theodor W. Engelmann illuminated a filament of algae with light that passed through a prism,
thus exposing different segments of algae to different wavelengths of light. He added aerobic
bacteria and then noted in which areas the bacteria congregated. A diagram showing the outcome
of the experiment is shown below.


Aerobic Bacteria



Filament of Alga

Blue Green Yellow Red
2. An outcome of this experiment was to help determine
a. the relationship between the concentration of carbon dioxide and the rate of photosynthesis.
b. the relationship between the concentration of oxygen and the rate of photosynthesis.
c. the relationship between wavelengths of light and the oxygen released during photosynthesis.
d. the relationship between wavelengths of light and the rate of aerobic respiration.
e. the relationship between the concentration of oxygen and the rate of aerobic respiration.

3. 4 points: Refer to the diagram below. You are testing the ability of two different strains of
yeast to grow in an anaerobic environment. You provide the yeast with glucose as a source
of energy. The first batch of yeast lives on. The second batch of yeast dies quickly. You
test the contents of the test tubes and find that there is ethanol produced in the first batch, but
there is no ethanol produced in the second batch. In the second batch, there is plenty of
glucose left and some acetaldehyde has been produced. Therefore, both strains have the
enzyme to break down glucose to make ATP from it. Explain why the second batch of yeast
did not survive.
The second batch was not able to turn the acetaldehyde into ethanol and recycle the needed
NAD
+
for glycolysis to continue, probably because of a mutation in the enzyme needed for
that reaction. Therefore, as the supply of NAD
+
in the cell runs out in the absence of aerobic
respiration (anaerobic environment) and in the absence of alcohol fermentation (cant turn
Name: ___________________________Lab Section __________________ 3/28/11
%
acetaldehyde into ethanol), glycolysis comes to a halt, and the cells are not getting the ATP
they need to survive, unlike the cells in batch 1.



4. Review the figure below.

a. 2 points. Describe one reason why the global CO
2
concentration is increasing steadily.
Here are several reasons: The concentration of CO
2
in the atmosphere has been increasing
steadily due to human activity. As human population has grown and our reliance on fossil
fuels has grown, more and more fossil fuels are being burned releasing CO
2
in ever
increasing amounts into the atmosphere. In addition, a growing human population has also
meant more deforestation to create space for housing and other buildings/roads, etc., as well
as more deforestation to replace the forests with agricultural fields that are less productive
than forests, that is they have lower rates of photosynthesis and thus take less CO
2
out of the
atmosphere than forests would.
Name: ___________________________Lab Section __________________ 3/28/11
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Image Source: http://www.esrl.noaa.gov/gmd/obop/mlo/programs/coop/scripps/img/img_scripps_co2_record.gif
b. 4 points. Briefly describe why what happens in the Northern Hemisphere dominates in terms
of the seasonal maxima and minima for the concentration of CO
2
measured.
The reason is that there are more land masses in the Northern Hemisphere and thus
both more people and more forests. Therefore, the Northern Hemisphere dominates
the global CO
2
cycle. During the winter more fossil fuels are being burnt for heating
and rates of photosynthesis are lower due to dormancy or death of plants. Since
there are more people and more forests in the Northern Hemisphere, the winter of
the Northern Hemisphere dominates over the summer of the Southern Hemisphere
and so the maximum CO
2
concentrations are reached then. For the same reason, the
summer of the Northern Hemisphere dominates over the winter of the Southern
Hemisphere and the minimum CO
2
concentrations are reached during the summer
of the Northern Hemisphere when there is less fossil fuel burning and higher rates
of photosynthesis.
c. 2 points. Briefly describe why the seasonal effects can be observed even in Hawaii!
The reason is the global air circulation patterns that distribute the gases throughout the globe
so that even in Mauna Loa the effects of the rest of the globe can be measured.

The following 2 questions are based on the reaction A + B ! C + D shown above.
5. Which of the following represents the !G of the reaction?
a. a
b. b
c. c
d. d
e. e
6. Which of the following represents the activation energy required for a noncatalyzed reaction?
a. a
b. b
c. c
d. d
e. e
7. When you have a severe fever, what may be a grave consequence if this is not controlled?
Name: ___________________________Lab Section __________________ 3/28/11
'
a. removal of the amino acids in active sites
b. binding of enzymes to inappropriate substrates
c. removal of amine groups from your proteins
d. destruction of your enzymes' primary structure
e. change in the folding of enzymes
8. 12 points. Answer either a or b, not both:
a. Pepsin and trypsin are both enzymes that help break down proteins in your digestive
tract. Pepsin has a pH optimum of 2, and a pH range of approximately 0-3.5. Trypsin
has a pH optimum of 8, and a pH range of approximately 5.5 to 10. On the blank graph
provided below, graph the pH range / optima curves for these two enzymes. Make sure
to label the axes. Identify the dependent and independent variables on your graph.


Pepsin Trypsin

Activity (rate of reaction)
of Enzyme (dependent)






"

0 2 4 6 8 10
pH (independent)

b. HIV (the human immunodeficiency virus) has a protease (an enzyme that breaks
down proteins) that is essential for its function. Ritonavir is a drug being used to treat
HIV infected patients. It resembles the protein that is the normal substrate of the
protease mentioned above and can substitute for the protein in the active site. On the
blank graph provided below, graph the effects of substrate protein concentration on
the rate of the reaction catalyzed by the HIV protease in the presence of a constant
dose (constant amount) of the drug Ritonavir. Make sure to label the axes. Identify
the dependent and independent variables on your graph.

Name: ___________________________Lab Section __________________ 3/28/11
(






Rate of reaction of
Protease (dependent)






"

0 #
Substrate protein concentration (independent)

9. 6 points. Fill in the blanks. Ethylene is a plant hormone involved in fruit ripening in fruits
such as tomatoes, bananas, and apples. Ethylene is a gas and diffuses from its point of
synthesis through air. Synthesis of ethylene involves a multi-step pathway of several
enzyme-catalyzed reactions, and requires oxygen and is inhibited by CO
2
. Apples can be
picked in the fall and stored for several months without spoilage if the storage area has high
concentrations of CO
2
and low concentrations of O
2
and the temperature is kept low.

10. A receptor protein in a membrane that recognizes a chemical signal is most similar to which
of the following?
a. RNA specifying the amino acids in a polypeptide.
b. a particular metabolic pathway operating within a specific organelle.
c. the active site of an enzyme that binds to a specific substrate.
d. an enzyme with an optimum pH and temperature for activity.
11. In general, a signal transmitted via phosphorylation of a series of proteins
a. requires binding of a hormone to a cytosol receptor.
b. occurs in cells that do not have active phosphatases.
c. brings a conformational change to each protein.
d. allows target cells to change their shape and activity.
12. Binding of a signaling molecule to which type of receptor leads directly to a change in
distribution of ions on opposite sides of the membrane?
a. ligand-gated ion channel
b. receptor tyrosine kinase
c. G protein-coupled receptor
d. receptor tyrosine kinase dimer
e. intracellular receptor
13. An inhibitor of adenylyl cyclase activity would have which of the following effects?
a. increase the amount of cAMP in the cytoplasm in response to a signal
Name: ___________________________Lab Section __________________ 3/28/11
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b. block the activation of protein kinase A despite having a signal
c. block the activation of G proteins in response to a signal
d. prolong the effect of a signal by maintaining elevated cAMP levels
14. An inhibitor of which of the following could be used to block the release of calcium from the
endoplasmic reticulum?
a. tyrosine kinases
b. phospholipase C
c. serine/threonine kinases
d. phosphodiesterase
e. adenylyl cyclase




Name: ___________________________Lab Section __________________ 3/28/11
*

15. The primary role of oxygen in cellular respiration is
a. To form water in the mitochondrial matrix
b. To oxidize glucose into pyruvate
c. To link glycolysis and ATP synthesis
d. To act as the final electron acceptor

16. If an uncoupler is added to the mitochondrial membrane, that would lead to
a. Accumulation of protons in the matrix so ATP synthesis would stop
b. Accumulation of protons in the matrix so ATP synthesis would speed up
c. Dissipation of the proton gradient so electron transport would stop
d. Accumulation of protons in the matrix so electron transport would speed up
e. Dissipation of the proton gradient so ATP synthesis would stop
17. 6 points. Ca
2+
is a secondary messenger in some signal transduction pathways. Ca
2+
pumps
actively transport Ca
2+
from the cytosol to either the extracellular fluid or the cellular
organelles. Explain why it is important for the Ca
2+
pumps to reduce the concentration of
Ca
2+
in the cytosol.

For Ca
2+
to act as a secondary messenger the cytosolic concentration must be kept low so that the
release of calcium in response to a signal is recognized as a secondary messenger. If the
concentration of calcium is high to begin with, addition of a few more ions from the internal
reserves in response to a signal does not lead to a big change in concentration and would not be a
noticeable change in the cell (for example 5% concentration change). But if the internal
concentration is low, addition of a few ions would be a big change in relative concentration (for
example 50%) and that would be a noticeable change in the cell, and could be a useful way to
transmit a signal to cause a cellular response. Also, since it is a secondary messenger, it has to
be removed from the cytosol for the response to end otherwise the pathways turned on by the
Ca
2+
would remain activated all the time.
Name: ___________________________Lab Section __________________ 3/28/11
"+

An inhibitor blocks the citric acid cycle at step 7 below (conversion of fumarate to malate).
18. True/False: With the inhibitor present the citric acid cycle produces fewer NADH molecules,
but the same number of ATP and FADH
2
as when the inhibitor is absent.

The figure on the right below illustrates some of the steps (reactions) of glycolysis in their proper
sequence. Each step is lettered.
19. Which step involves an endergonic reaction?
a. A
b. B
c. C
d. D
e. E
20. The ATP made during glycolysis is generated by what process?
a. Substrate-level phosohorylation
b. Oxidative phosphorylation
c. Photophosphorylation
d. Redox-level phosphorylation
Name: ___________________________Lab Section __________________ 3/28/11
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Citric Acid Cycle Glycolysis



21. (20 points) Please write a short essay in response to only one (either a or b, but not both)
of the following questions. You are expected to write a logically constructed answer;
organization does count. You may want to outline your answer first.
a. Consider the single cell amoebas, facultative multicellularity, the sexual cycle, and the
asexual cycle in the life of Dictyostelium. What might be the evolutionary impetus (original
driving force) for the complex life cycle of Dictyostelium? What evolutionary sequence do
we think might explain the evolution of the complex life cycle of Dictyostelium? Explain the
sequence and how each step relates to the original driving force.
2 points: Evading the predatory nematodes might have been the evolutionary impetus for the
evolution of the complex life cycle of Dictyostelium.

4 points: We expect the sequence to go from a) forming a small cyst to b) forming a large
and protected cell through sexual reproduction to c) forming the complicated structure in
Name: ___________________________Lab Section __________________ 3/28/11
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asexual reproduction that includes a facultatively multicellular stage. The reason is that this
sequence goes from the simplest structure to the most complex structures and evolutionarily
it makes sense for the most complex steps to have evolved later. Alternative 2 points:
Facultative multicellurity involves several individual organisms coming together to act as a
single multicellular organism.

4 points: Individual Dictyostelium amoeba can turn into isolated cysts covering themselves in
a tough cellulose coating which allows them a chance to pass through a nematodes gut
without being digested. This is the simplest method.

2 points: However, a better way would be to avoid getting eaten altogether: a larger organism
that is too large for the nematodes to swallow would be the answer.

4 points: In sexual reproduction of Dictyostelium, two amoebas will fuse. They begin
sending out cAMP to their neighbors who then crawl toward the signal. The mating pair then
swallow the incoming amoebas and digest them. The cell grows very large and coats itself
with cellulose and turns dormant, waiting for the right conditions to germinate. This large
cell is too large for the nematodes to eat (dont expect all of the details; as long as the gist of
the idea is explained). Alternative 2 points: This stage uses the protective layer (cyst-like)
also. By this stage large size, cAMP as a communication signal, and sacrificing some cells
for the benefit of others have evolved

4 points: The asexual life cycle is even more complex, but uses the same signal, cAMP. In
asexual reproduction amoebas come together through the use of the cAMP signal to form a
facultatively multicellular organism that crawls to the surface of the soil where the organism
forms a complicated structure with a stalk and a globe where asexual spores are produced
and are protected by a protective cellulose covering. The facultatively multicellular
organism is also too large for the nematodes to eat. It is much more complicated than the
other stages described above and so expected to have evolved later (dont expect all of the
details; as long as the gist of the idea is explained). Alternative point: for example it can
sense light and heat and direct its movement. Alternative 2 points: The asexual life cycle
builds on the cAMP signal, the protective cyst-like layer, sacrifice of some cells, and large
size.

b. Review the pictures of the horizontal and vertical leaves shown below. Explain the
differences in the anatomy of these leaves with regards to the role of the different cell types:
mesophyll cells and guard cells (with their stomata). Explain how these differences relate to
the physiology of the leaf: light absorption and gas exchange for photosynthesis as well as
transpiration (evaporation of water). Explain how the location of the stomata would help
each leaf type with both conservation of water and maximal use of CO
2
within the leaf.
Explain how the differential opening of stomata (some may be open while others may be
closed at a given time) would especially help vertically oriented leaves with both
conservation of water and maximal use of CO
2
within the leaf.

4 points: Horizontally oriented leaves receive most of their light from above, with the light
coming down on the top surface of the leaves. Vertically oriented leaves receive light from
Name: ___________________________Lab Section __________________ 3/28/11
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all directions. For a vertically oriented leaf, during some part of the day one side of the leaf
receives more direct light, while during other parts of the day the other side of the leaf
receives more direct light.

4 points: This translates into the differences in the anatomy observed. Horizontal leaves have
palisade mesophyll cells on the upper surface and spongy mesophyll cells towards the lower
surface. (Alternative 2 points: Palisade mesophyll cells are tightly packed and vertically
stacked and are packed with chloroplasts). Thus maximal absorption of high intensity light
coming from above happens as the light passes through the palisade mesophyll. The spongy
mesophyll cells are loosely packed with lots of air spaces and fewer chloroplasts. Therefore
as the lower intensity light filters down through the palisade to the spongy mesophyll, the
few chloroplasts there absorb the light.

4 points: This also means that the demand for CO
2
is highest in the upper level of palisade
and lowest in the lower level of spongy mesophyll cells due to the relative rates of
photosynthesis (high to low from top to bottom). And the top surface of the leaf is the
warmer due to the high intensity light being absorbed while the bottom surface is cooler due
to the relative shade. So, stomata are located on the bottom surface so that less water is lost
from the cooler lower surface when stomata open to allow CO
2
to go in for photosynthesis.
And, since the highest demand and lowest internal CO
2
concentration is at the top surface of
the leaf, the gradient favors the diffusion of the gas from the lower to the upper surface of the
leaf and all mesophyll cells get some CO
2
along the way. Alternative 2 points: If the stomata
were on the upper surface, not only would the leaf lose too much water from the warmer
surface, the CO
2
coming in from the top would be used by the palisade cells and probably
wouldnt diffuse down to the spongy mesophyll with their lower demand

4 points: In vertically oriented leaves, since both sides of the leaf receive direct light at some
point, mesophyll cells are uniform throughout the leaf since at some point during the day
they will receive the highest intensity light regardless of which side of the leaf they are
located. And since both sides of the leaf will be the warmer side at some point during the
day, location of stomata on one side only will not be beneficial in terms of water loss. In
fact, during the time of the day when that side is receiving direct light, it would be
detrimental to open stomata on that side.

4 points: So, having stomata on both sides, and then regulating which ones open (open when
they are shaded and cooler, and close when they are in direct light and thus warmer) will help
with minimizing water loss. And, this differential opening and closing also helps with the
CO
2
gradient as described above to allow all mesophyll cells to get some CO
2
as the gas
diffuses from the open stomata throughout the leaf to the opposite surface that is receiving
the highest light levels and has the highest demand for CO
2
.
Name: ___________________________Lab Section __________________ 3/28/11
"%


Stomata Mesophyll


Name: ___________________________Lab Section __________________ 7/6/11
"
BIO 10100 Exam 2 Version 1
Prior to completing this exam, please read the following statement and sign below to indicate
that you have read and understood the statement. No exam will be graded unless the pledge is
signed.
I pledge that I have neither given nor received unauthorized assistance on this exam. I
understand that if I am charged with cheating, my name will be submitted to the Dean for
disciplinary action.

__________________________________________________ _____________________
Name Date

Please make sure you have all 14 pages of the exam. Bonus 2points: write your name and lab
section on all sheets. Please read each question carefully. If you do not understand the meaning
or intention of a question, please ask. Please pace yourself and use your time efficiently.
Please put away your cell phones, blackberries, iPods, laptop computers, etc. Write your
answers using a pen. Answers written in pencil will not be accepted.
Each multiple-choice question is worth 2 points. Note that a correct statement is not necessarily
the best answer to a multiple-choice question. For each multiple-choice question, circle the best
answer. You will receive ZERO credit for any question for which we cannot tell what your final
answer is. If you cross out an answer, please make it clear as to what is your final answer.
Please pace yourself and use your time efficiently; allow time for the essay type questions. If a
question states answer a or b, not both: if you answer both, then we will read only the answer
to a, regardless of how much better your answer to b might be.
1. 5 points. How is multicellularity in Dictyostelium similar to or different from that in animals?
In animals, all cells in the individual are derived from the same parent zygote cell. In a
facultatively multicellular Dictyostelium, different individual cells have come together to act
as a multicellular organisma, but they are not all derived from the same parent amoeba. They
are similar in that they show division of labor and specialization of the cells.

2. 2 points. In one sentence state what the evolutionary impetus for the complex life cycle of
Dictyostelium might be.
Evading the predatory nematodes might have been the evolutionary impetus for the evolution
of the complex life cycle of Dictyostelium.

3. 4 points. What evolutionary sequence do we think might explain the evolution of the life
cycle of Dictyostelium? List the currently accepted sequence.
We expect the sequence to go from a) single cell amoeba, to b) forming a small cyst to c)
forming a large and protected cell through sexual reproduction to d) forming the complicated
structure in asexual reproduction that includes a facultatively multicellular stage.

4. 10 points. Using a series of arrows, draw the branched metabolic reaction pathway described
Name: ___________________________Lab Section __________________ 7/6/11
#
by the following statements, then answer the question at the end.
! L can form either M or N.
! M can form O.
! O can form either P or R.
! P can form Q.
! R can form S.
! N can form T.
! O inhibits the reaction of L to form M.
! O promotes the reaction of L to form N.
! Q inhibits the reaction of O to form P.
! S inhibits the reaction of O to form R.



+

Which reaction would prevail if both Q and S were present in the cell in high concentrations?

Conversion of L to N and N to T.


The following question is based on the reaction A + B ! C + D shown below.
Figure 1

5. 5 points. Fill in the blanks: The reaction above is __________ (select one: endergonic /
exergonic) because the !G of the reaction, depicted as ___ (select one: a, b, c, d, or e) is
_________ (select one: positive / negative). An enzyme makes the reaction go faster because
it reduces the activation energy from __ (select one: a, b, c, d, or e) to __ (select one: a, b, c,
d, or e).

6. Which of the following types of reactions would decrease the entropy within a cell?
a) dehydration
b) hydrolysis
$
Name: ___________________________Lab Section __________________ 7/6/11
%
c) respiration
d) digestion
e) catabolism

The next 3 questions refer to the curves shown below in Figure 2.
Figure 2.

7. Which curve represents the behavior of an enzyme taken from a bacterium that lives in hot
springs at temperatures of 70C or higher?
a) curve 1
b) curve 2
c) curve 3
d) curve 4
e) curve 5

8. Which curve was most likely generated from analysis of an enzyme from a lake with mildly
alkaline water?
a) curve 1
b) curve 2
c) curve 3
d) curve 4
e) curve 5

9. 2 points. Explain your answer to the last question.
An enzyme from an alkaline lake might be expected to work optimally at a pH slightly above
neutral. Curve 5 shows the pH range and optimum for an enzyme that would fit this
requirement.

10. Ethanol is metabolized in the body by oxidation to acetaldehyde, which is in turn further
oxidized to acetic acid by aldehyde oxidase enzymes. Methanol poisoning occurs because
Name: ___________________________Lab Section __________________ 7/6/11
&
methanol is oxidized to formaldehyde and formic acid which attack the optic nerve causing
blindness. Ethanol is given as an antidote for methanol poisoning because ethanol is
oxidized in preference to methanol by the same enzymes and consequently the toxic by-
products of methanol oxidation do not have a chance to accumulate.
a) 4 points. What kind of inhibition (competitive or non-competitive) is occurring when
ethanol is used as an antidote to fight methanol poisoning? How do you know?
Competitive. Both substances (methanol and ethanol) are substrates for the same enzyme
(they bind to the active site of the enzyme and their oxidation reactions are catalyzed by
the enzyme).

b) 8 points. On the blank graph provided below, graph the effects of methanol concentration
on the rate of oxidation of methanol in both the presence and the absence of a constant
dose of ethanol as an antidote. Make sure to label the axes. Identify the dependent and
independent variables on your graph. Make sure the curves for the presence and absence
of ethanol are distinguishable.


Rate of
oxidation
of methanol
(dependent)




Methanol concentration (independent)

Without ethanol With ethanol

11. During glycolysis, when glucose is catabolized to pyruvate, most of the energy of glucose is
a) transferred to ADP, forming ATP.
b) transferred directly to ATP.
c) stored in the NADH produced.
d) retained in the pyruvate.

12. The ATP made during glycolysis is generated by what process?
a) Oxidative phosphorylation
b) Photophosphorylation
c) Substrate-level phosohorylation
d) Redox-level phosphorylation

13. Cyanides attach to the iron within cytochrome c oxidase and inhibit its activity. This could
act as a metabolic poison because
a) It stops formation of cytochrome c in the mitochondria
b) It reduces cytochrome c instead of oxidizing it
c) It disrupts electron flow and the formation of a H
+
gradient
Name: ___________________________Lab Section __________________ 7/6/11
'
d) It stops the formation of ATP in the process of glycolysis

14. Which of the following processes in eukaryotic cells will proceed normally whether oxygen
(O
2
) is present or absent?
a) glycolysis
b) electron transport
c) the citric acid cycle
d) oxidative phosphorylation
e) chemiosmosis

15. Starting with one molecule of isocitrate and ending with fumarate, what is the maximum
number of ATP molecules that could be made through substrate-level phosphorylation?
a) 1
b) 2
c) 11
d) 12

16. 2 points. On the figure below (on the left), circle the step where substrate-level
phosphorylation happens. See red circle.

The figure below (on the right) illustrates some of the steps (reactions) of glycolysis in their
proper sequence. Each step is lettered. Use these letters to answer the next two questions.
17. 2 points. Which step shows a split of one molecule into two smaller molecules? B
18. 2 points. Which step is the energy investment phase? A
19. A young animal has never had much energy. He is brought to a veterinarian for help and is
sent to the animal hospital for some tests. There they discover his mitochondria can use only
fatty acids and amino acids for respiration, and his cells produce more lactate than normal.
Of the following, which is the best explanation of his condition?
Name: ___________________________Lab Section __________________ 7/6/11
(
a) His mitochondria lack the transport protein for pyruvate.
b) His cells cannot move NADH into the mitochondria.
c) His cells contain something that inhibits oxygen use in his mitochondria.
d) His cells lack the enzyme in glycolysis that forms pyruvate.
e) His mitochondria have a defective electron transport chain.

Citric Acid Cycle Glycolysis

20. One function of both alcohol fermentation and lactic acid fermentation is to
a) reduce NAD
+
to NADH.
b) reduce FAD
+
to FADH
2
.
c) oxidize NADH to NAD
+
.
d) reduce FADH
2
to FAD
+
.
e) none of the above
21. In the thylakoid membranes, what is the main role of the antenna pigment molecules?
a) synthesize ATP from ADP and Pi
b) split water and release oxygen to the reaction-center chlorophyll
c) harvest photons and transfer light energy to the reaction-center chlorophyll
d) transfer electrons to ferredoxin and then NADPH
Name: ___________________________Lab Section __________________ 7/6/11
)
e) concentrate photons within the stroma
22. Answer either a or b, not both:
a) Below is an excerpt from a set of research experiments.
Experiment 1: Mitochondria are isolated from cells and placed in a medium at pH 9. This
results in a low H
+
concentration on both sides of the inner mitochondrial membrane. Half of
the mitochondria are removed quickly to a neutral medium (pH 7) as shown in the figure.
ATP is synthesized in these mitochondria. The other half of the mitochondria are kept in a
test tube at pH 9 (not shown in the figure). No ATP is synthesized in these mitochondria.

Experiment 2: A set of artificial vesicles is made and a bacterial proton pump is inserted in
the membrane of the artificial vesicles. The bacterial pump actively transports protons (H
+
)
into the vesicles. This establishes a large proton gradient across the vesicle membrane (more
protons on the inside, fewer protons on the outside). ADP and Pi are provided on the outside
of the vesicle. No ATP is synthesized. The vesicles are divided into two test tubes. ATP
synthase from the mitochondria of a mammal is isolated and then inserted into the membrane
of half of the artificial vesicles in the orientation shown in the figure on the right. These
vesicles are placed in test tube 1. The vesicles that do not have the ATP synthase inserted in
their membrane are in test tube 2 (not shown). There is ATP synthesis in test tube 1. There
is no ATP synthesis in test tube 2.


Experiment 1 Experiment 2
Name: ___________________________Lab Section __________________ 7/6/11
*
Identify the alternative and null hypotheses being tested and the experimental predictions
below.
4 points. Alternative:
Experiment 1
A proton gradient is required (or is enough in the absence of electron transport) for ATP
synthesis.
Experiment 2
The protein ATP synthase is required (or proton gradient is not enough) for ATP
synthesis.

4 points. Null:
Experiment 1
The presence of a proton gradient is not required (or is not enough in the absence of
electron transport) for ATP synthesis.
Experiment 2
The protein ATP synthase is not required (or proton gradient is enough) for ATP
synthesis.

4 points. Experimental prediction:
Experiment 1
If isolated mitochondria are incubated in pH 9 solution to equilibrate to pH 9 and then
moved to pH 7 to create a proton gradient across the cristae with more protons on the
outside, then in the absence of electron transport ATP will be synthesized by the
mitochondria.

Experiment 2
If a proton gradient is created in an artificial vesicle with the use of a bacterial proton
pump, and an ATP synthase from mitochondria is inserted into the vesicle in the correct
orientation, then ATP will be synthesized in the presence of the substrates ADP and Pi.

4 points. What, if anything, is the control treatment in each experiment?
Experiment 1
Keeping the mitochondria in a test tube at pH 9 for the entirety of the experiment.

Experiment 2
Not adding the ATP synthase to the vesicles in test tube 2.
b) Chloroplast thylakoids are isolated from plant cells and placed in a medium at pH 4 and
allowed to equilibrate. This results in a high H
+
concentration on both sides of the
thylakoid membrane. The thylakoids are removed to a slightly alkaline medium (pH 8).
These test tubes are placed in the dark. ATP is synthesized in the test tube in the dark
given that ADP and Pi are provided.

Identify the alternative and null hypotheses being tested and the experimental prediction
below.
2 points. Alternative:
Name: ___________________________Lab Section __________________ 7/6/11
+
In the thylakoids a proton gradient is enough to power ATP synthesis in the absence of
electron transport.

2 points. Null:
In the thylakoids a proton gradient is not enough to power ATP synthesis in the absence
of electron transport.

2 points. Experimental prediction:
If we isolate thylakoid membranes and create a proton gradient across the membranes by
first incubating them in pH4 to lower the pH in the lumen and then moving them to pH 8,
in the absence of electron transport in the dark the thylakoids will produce ATP if
provided with ADP and Pi.

2 points. What, if anything, should be the control treatment for this experiment?
Keep some of the thylakoids in identical conditions as above with the exception of the pH
gradient: keep them in pH 4 the whole time (or in pH 8 the whole time).

8 points. In the blank graph provided below, draw a column graph to show the results of
the experiment for both the experimental and the control treatments for the experiment
described above. Make sure to label the axes properly. Suppose an uncoupler were to be
added to the thylakoids in both the experimental and the control treatments. Add the
expected results from these treatments to your graph. Make sure to distinguish the
various treatments on your graph.






Amount of
ATP produced



+ pH gradient - pH gradient
Treatment
With uncoupler
Without uncoupler
23. 6 points. In the figure below identify and mark the 3 steps of the Calvin cycle:
carboxylation, reduction, and regeneration.


Name: ___________________________Lab Section __________________ 7/6/11
",




Theodor W. Engelmann illuminated a filament of algae with light that passed through a prism,
thus exposing different segments of algae to different wavelengths of light. He added aerobic
bacteria and then noted in which areas the bacteria congregated. A diagram showing the outcome
of the experiment is shown below.


Aerobic Bacteria



Filament of Alga

Blue Green Yellow Red
24. If you ran the same experiment without passing light through a prism, what would you
predict?
a) There would be no difference in results.
b) The bacteria would be relatively evenly distributed along the algal filaments.
c) The number of bacteria present would decrease due to an increase in the carbon dioxide
concentration.
d) The number of bacteria present would increase due to an increase in the carbon dioxide
Name: ___________________________Lab Section __________________ 7/6/11
""
concentration.
e) The number of bacteria would decrease due to a decrease in the temperature of the water.

25. 6 points. Review the figure below. Briefly describe the reason that what happens in the
Northern Hemisphere dominates in terms of the seasonal maxima and minima for the
concentration of CO
2
measured.

Image Source:
http://www.esrl.noaa.gov/gmd/obop/mlo/programs/coop/scripps/img/img_scripps_co2_record.gif
The reason is that there are more land masses in the Northern Hemisphere and
thus both more people and more forests. Therefore, the Northern Hemisphere
dominates the global CO
2
cycle. During the winter more fossil fuels are being
burnt for heating and rates of photosynthesis are lower due to dormancy or death
of plants. Since there are more people and more forests in the Northern
Hemisphere, the winter of the Northern Hemisphere dominates over the summer
of the Southern Hemisphere and so the maximum CO
2
concentrations are reached
then. For the same reason, the summer of the Northern Hemisphere dominates
over the winter of the Southern Hemisphere and the minimum CO
2
concentrations
are reached during the summer of the Northern Hemisphere when there is less
fossil fuel burning and higher rates of photosynthesis.

26. Review the figure below. Which of the following are directly associated with photosystem I?
a) harvesting of light energy by ATP
b) receiving electrons from plastocyanin (PC)
c) extraction of hydrogen electrons from the splitting of water
d) passing electrons to plastoquinone (PQ)
e) oxidation of NADPH

Name: ___________________________Lab Section __________________ 7/6/11
"#





Rubisco
Name: ___________________________Lab Section __________________ 7/6/11
"%

27. 20 points. Please write a short essay in response to only one (either a or b, but not both) of the
following questions. You are expected to write a logically constructed answer; organization does
count. You may want to outline your answer first.
a) Why is oxygen a problem in photosynthesis? Why is it more of a problem with warmer
temperatures? What process has evolved in typical, C3 plants to deal with the problem with
oxygen? What are the costs and benefits of this process? As concentration of CO
2
rises globally,
how might that alone affect the problem with oxygen? Explain.
Background: The first reaction in the Calvin cycle involves the enzyme Rubisco that takes a molecule
of CO
2
and attaches it to the 5-carbon sugar RuBP forming a 6-carbon compound that then splits to
make two 3-carbon compounds (PGA). This is the carboxylation step that adds a C to the body of the
plant.

5 points. If oxygen is present, it can also react with the 5 C sugar RuBP through the activity of the
enzyme Rubisco. However, when oxygen reacts with RuBP, no C is added to the body of the plant.
Instead, the 5-carbon compound is split to make a 3-carbon compound (PGA) that can be used by the
plant, and a 2-carbon compound (phosphoglycolate) that is not useful to the plant. Figure included
above. Hence the plant is not gaining any carbon from this reaction, and could potentially lose 2
carbons it already had. That is a problem.

5 points. This problem becomes more serious as temperatures rise. Higher temperatures mean lower
solubility for gases in an aqueous solution such as the stroma of the chloroplast. As temperatures
rise, the solubility of CO
2
decreases faster than that of O
2
and thus the potential for O
2
to react
through Rubisco with RuBP increases. Thus the carboxylation to oxygenation ratio goes down and
the plant could potentially lose a lot more carbon to the reaction with O
2
.

5 points. Plants have evolved a mechanism to salvage the carbons in the potentially useless 2-carbon
compound that is produced through the oxygenation reaction. This process involves the chloroplasts,
mitochondria, and peroxisomes (Figure included above). Through this process, the plant can
salvage three quarters of the carbons that would have otherwise been useless to it. That means, for
every 2 molecules of phosphoglycolate (total of 4 carbons) that go through this process, 3 carbons are
salvaged as one molecule of useful PGA, and only 1 carbon is lost as CO
2
. Costs and benefits: This
process does cost ATP, however. So, the plant salvages ! of the C it would have lost otherwise, but
loses one C it already had without gaining any new C, and loses some ATP in the process as well.

5 points. As concentrations of CO
2
rise globally, that could help the plants with the problem with the
oxygenation reaction. More CO
2
in the atmosphere means more CO
2
in the solution in the stroma and
so a lower chance that Rubisco will react with oxygen; that means a higher carboxylation to
oxygenation ratio, which is good for the plants.

The following is additional but not required, 3 alternative points: However, the increase in CO
2

concentrations in the atmosphere have other consequences as well, such as a potential increase in air
temperature and prolonged droughts and closure of stomata, etc., so the benefits are not straight
forward.







Name: ___________________________Lab Section __________________ 7/6/11
"&
b) Consider horizontally and vertically oriented leaves. Explain the differences in the anatomy of
these leaves with regards to the role of the different cell types: different mesophyll cells and
guard cells (with their stomata). Explain how these differences relate to the physiology of the
leaf: light absorption and gas exchange for photosynthesis as well as transpiration (evaporation of
water). Explain how the location of the stomata would help each leaf type with both conservation
of water and maximal use of CO
2
within the leaf. Explain how the differential opening of
stomata (some may be open while others may be closed at a given time) would especially help
vertically oriented leaves with both conservation of water and maximal use of CO
2
within the
leaf.

4 points: Horizontally oriented leaves receive most of their light from above, with the light coming
down on the top surface of the leaves. Vertically oriented leaves receive light from all directions.
For a vertically oriented leaf, during some part of the day one side of the leaf receives more direct
light, while during other parts of the day the other side of the leaf receives more direct light.

4 points: This translates into the differences in the anatomy observed. Horizontal leaves have
palisade mesophyll cells on the upper surface and spongy mesophyll cells towards the lower surface.
(Alternative 2 points: Palisade mesophyll cells are tightly packed and vertically stacked and are
packed with chloroplasts). Thus maximal absorption of high intensity light coming from above
happens as the light passes through the palisade mesophyll. The spongy mesophyll cells are loosely
packed with lots of air spaces and fewer chloroplasts. Therefore as the lower intensity light filters
down through the palisade to the spongy mesophyll, the few chloroplasts there absorb the light.

4 points: This also means that the demand for CO
2
is highest in the upper level of palisade and lowest
in the lower level of spongy mesophyll cells due to the relative rates of photosynthesis (high to low
from top to bottom). And the top surface of the leaf is the warmer due to the high intensity light
being absorbed while the bottom surface is cooler due to the relative shade. So, stomata are located
on the bottom surface so that less water is lost from the cooler lower surface when stomata open to
allow CO
2
to go in for photosynthesis. And, since the highest demand and lowest internal CO
2

concentration is at the top surface of the leaf, the gradient favors the diffusion of the gas from the
lower to the upper surface of the leaf and all mesophyll cells get some CO
2
along the way.
Alternative 2 points: If the stomata were on the upper surface, not only would the leaf lose too much
water from the warmer surface, the CO
2
coming in from the top would be used by the palisade cells
and probably wouldnt diffuse down to the spongy mesophyll with their lower demand

4 points: In vertically oriented leaves, since both sides of the leaf receive direct light at some point,
mesophyll cells are uniform throughout the leaf since at some point during the day they will receive
the highest intensity light regardless of which side of the leaf they are located. And since both sides
of the leaf will be the warmer side at some point during the day, location of stomata on one side only
will not be beneficial in terms of water loss. In fact, during the time of the day when that side is
receiving direct light, it would be detrimental to open stomata on that side.

4 points: So, having stomata on both sides, and then regulating which ones open (open when they are
shaded and cooler, and close when they are in direct light and thus warmer) will help with minimizing
water loss. And, this differential opening and closing also helps with the CO
2
gradient as described
above to allow all mesophyll cells to get some CO
2
as the gas diffuses from the open stomata
throughout the leaf to the opposite surface that is receiving the highest light levels and has the highest
demand for CO
2
.

The Nicotine Fix

1. According to the 2012 study, how useful is nicotine replacement therapy for those wishing to
quit smoking? What are the independent and dependent variables in this study?
2. What did the study by Kahn in 1966 suggest? Were his results correlation or causation?
3. What was Chesselets discovery in 1979?
4. What is L-dopa and what does it do? Why was it included in the study by Quik? What did
her study show about nicotine? What would you expect the experimental design be for her
study?
5. What is the experimental design for Boyds study on the effect of nicotine on impulsivity?
6. How were the neuroprotective effects of nicotine studied in Alzheimers patients? How
about enhancing attention in ADHD patients?
7. How would you design a study to determine whether nicotine improves the ability of people
with schizophrenia to focus their attention better than haloperidol?
8. How did the rat studies show that other chemicals found in tobacco are likely to be involved
in the addiction behavior that people normally associate with nicotine? What would be the
study design?
1.
Not useful, those that used it had the same results
ind var- nicotine replacement therapy
dep var- relapse rate
standardized- recently quit smoking, length of study, adults.
2. cancer and emphysema were more common in non-smoker, more parkinsons in smokers
correlation- because you are not manipulating conditions, variable.
cigarette smokers were 11 times as likely to have died of lung cancer as nonsmokers, and 12 times as likely to have died of
emphysema. Death due to Parkinsons disease occurred at least three times as often in nonsmokers as in smokers.
Experimental design nicotine or anatabine
???????
3. ????? What was Chesselets discovery in 1979?
increase dopamine
4. ????
in rats w/ parkinsons
inde var- nicotine
dep var- rate of tremor per minute
standad- sample size, nicotine
5. parkinson-low risk, because of decreasing dopamine
give l-dopa- higher risk because of increasing dopamine
if you give nicotine, it brings them into a middle ground because nicotine regulates l-dopa
6. subjects are humans with alzheiers but mild memory/cognitive issues.
blind randomized clinical trial, half placebo, half medication.
ind v- 15mg
dep v- attention, memory, and psychomotor speed
adhd-
ind v- nicotine patch
stand-nonsmoking, time,
dep v- impulse inhibiton, reward daleying, remembereing image
7. ind v- nicotine
dep v- attention during task
control baseline on all patients, then half haloperidol, the other nicotine.
8. ?????
Name: ___________________________Lab Section __________________ 3/17/14
1
1oLal olnLs: _____
BIO 10100 Exam 2 Version 1
Prior to completing this exam, please read the following statement and sign below to indicate
that you have read and understood the statement. No exam will be graded unless the pledge is
signed.
I pledge that I have neither given nor received unauthorized assistance on this exam. I
understand that if I am charged with cheating, my name will be submitted to the Dean for
disciplinary action.

__________________________________________________ _____________________
Name Date

Please make sure you answer all 21 questions on the exam. Please read each question carefully.
If you do not understand the meaning or intention of a question, please ask. Please put away
your cell phones, blackberries, iPods, laptop computers, etc., otherwise you will receive a grade
of 0. Please separate the last sheet from the rest of the exam. Write the answer to only the last
question on the last sheet. The last sheet is graded separately from the rest of the exam.
Note that a correct statement is not necessarily the best answer to a multiple-choice question.
Each multiple-choice question is worth 2 points. If a question states Select all that apply then
select all of the correct choices. For each multiple-choice question write the letter for the best
answer in the space provided. Note: circling your answer, a , or an x wont count. You will
receive ZERO credit for any question for which we cannot tell what your final answer is. If you
cross out an answer, please be clear as to what your final answer is. Please pace yourself and use
your time efficiently; allow time for the essay type questions. If a question states Answer
either a or b, not both: if you answer both, then we will read only the answer to a, regardless
of how much better your answer to b might be. Write your answers using a pen. Answers
written using pencils will not be graded.

2 Bonus Points: Write your name and lab section on all sheets.

1. A fungal cell has a potential of -180 mV (negative inside). There is more Ca
2+
outside the
cell than inside the cell. What can we conclude about the movement of Ca
2+
in this case?
a. Ca
2+
will enter the cell through open channels via passive transport.
b. Ca
2+
will exit the cell through open channels via passive transport.
c. Ca
2+
will enter the cell only through active transport.
d. Ca
2+
will exit the cell passively through a carrier protein.
e. We need more information.
Answer: a

2. A fungal cell has a potential of -180 mV (negative inside). There is more Ca
2+
inside the cell
than outside the cell. What can we conclude about the movement of Ca
2+
in this case?
a. Ca
2+
will enter the cell through open channels via passive transport.
b. Ca
2+
will exit the cell through open channels via passive transport.
c. Ca
2+
will enter the cell only through active transport.
d. Ca
2+
will exit the cell passively through a carrier protein.
e. We need more information.
Answer: e
Name: ___________________________Lab Section __________________ 3/17/14
2
1oLal olnLs: _____
3. 5 points. Explain your answers to the last two questions.
In the first case both the electrical and concentration gradients favor the movement of Ca ions
into the cell (more negative inside, lower concentration inside). In the second case the
concentration gradient favors the movement outwards (higher concentration inside), but the
electrical gradient favors the movement inwards (more negative inside) so we need to know
which gradient is stronger.

4. Select all that apply: The proton pump in plant cells
a. is considered to be an electrogenic pump
b. moves two + charges into and three + charges out of the cell
c. moves ions down their electrochemical gradient
d. carries out facilitated diffusion of ions across the membrane
e. moves ions against their electrochemical gradient
Answer: a, e

5. Select all that apply: The H
+
-sucrose symporter in plant cells
a. is considered to be an electrogenic pump
b. moves protons down their electrochemical gradient
c. moves sucrose down its concentration gradient
d. moves protons against their electrochemical gradient
e. moves sucrose against its concentration gradient
f. carries out facilitated diffusion of ions across the membrane
Answer: b, e, f

6. The amino acid serine is synthesized from 3-phosphoglycerate through a multi-step pathway
shown below. Each step is catalyzed by an enzyme.

The enzyme that carries out the Iirst reaction is called 3-phosphoglycerate dehydrogenase. It
has a quaternary structure made oI 4 identical polypeptides, each oI which contains an active
site (catalytic site) so that the enzyme can bind 4 substrates at a time. The Iull enzyme also
has two sites where serine can bind: 2 serine molecules bind to each binding site (total oI 4
serine molecules can bind). II 4 serine molecules bind to this enzyme (two serine molecules
to each serine binding site) then the enzyme is rendered Iully inactive.

a. 2 points. In the first reaction carried out by the enzyme 3-phosphoglycerate
dehydrogenase (shown above), what molecule is being oxidized and what molecule is
being reduced?
Oxidized: 3-phosphoglycerate Reduced: NAD
+


3-phosphoglyceraLe
dehydrogenase
Name: ___________________________Lab Section __________________ 3/17/14
3
1oLal olnLs: _____
b. 2 points. What functional group in 3-phosphoglycerate is changed by the first reaction
(shown above)? From what to what? Write the names of the functional groups below.
From: hydroxyl To: carbonyl

c. 8 points. You isolate the enzyme 3-phosphoglycerate dehydrogenase. In a set of test
tubes, you first add a set amount of the enzyme, then add a set amount of the substrate
NAD
+
, then add different amounts of 3-phosphoglycerate to the different test tubes, and
then you measure the rate of reaction as the rate of synthesis of the intermediate 3-
phosphohydroxypyruvate (g/s). You use different concentrations (mM) of 3-
phosphoglycerate from very low levels to very high levels in the different test tubes,
while you keep everything else constant (standardized). In another batch of test tubes,
you first add the same set amount of the enzyme as above, then add a set (constant)
amount of serine to the test tubes, then add the same set amount of the substrate NAD
+
as
above, and then add different amounts of 3-phosphoglycerate as above. You add different
concentrations (mM) of 3-phosphoglycerate from very low levels to very high levels
(same as you added in the first batch) in the different tubes, while you keep everything
else constant (standardized). In the blank graph below draw a line graph to show the
effects of concentration of 3-phosphoglycerate on the rate of the reaction in both the
presence and the absence of serine. Make sure to label the axes and add units where
appropriate. You should have two lines: one for the reactions in the presence of serine,
one for the reactions in the absence of serine.


d. 2 points. What are the independent variables?
Presence of serine and concentration of 3-phosphoglycerate

e. 1 point. What is the dependent variable?
The rate of synthesis of 3-phosphohydroxypyruvate

7. Select all that apply: What kind of inhibition is described in the question above?
a. allosteric
b. competitive
c. non-competitive
d. feedback
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Name: ___________________________Lab Section __________________ 3/17/14
4
1oLal olnLs: _____
e. catalytic
Answer: a, c, d

8. 10 points. Select either experiment a or b, not both. For the one you pick, answer the
following questions:
What is the question being asked?
a. Do membrane proteins move laterally in the membrane?
b. Is proton ATPase needed for synthesis of ATP in the presence of a proton gradient?

What is an alternative hypothesis for this question?
a. Membrane proteins do move laterally in the membrane.
b. Proton ATPase is needed for synthesis of ATP in the presence of a proton gradient.

What is the null hypothesis for the alternative hypothesis you wrote above?
a. Membrane proteins do not move laterally in the membrane.
b. Proton ATPase is not needed for synthesis of ATP in the presence of a proton gradient.

What is the experimental prediction?
a. If we use fluorescent labels to label the membrane proteins in a mouse cell and in a
human cell with different color labels and then fuse the cells and observe the fused cell
under the fluorescent microscope, we will observe the fluorescent colors to mix over
time.
b. If we insert a bacterial proton pump into artificial vesicles and establish a proton gradient
across the membrane and insert ATP synthase in the membrane of half of the vesicles (in
the right orientation) but not the other half and provide ADP and Pi, then we will be able
to measure ATP synthesis outside the vesicles with ATP synthase but not those without
ATP synthase.

Do the results support your alternative hypothesis?
In both cases, yes.




Name: ___________________________Lab Section __________________ 3/17/14
3
1oLal olnLs: _____

Experiment a Experiment b

9. 8 points. Use the letters (a, b, c, d, or e) written to the right of the 5 arrows in the diagram
below to answer the following questions by writing the appropriate letters in the spaces
provided. Note: A letter may be used more than once.
The G for the reaction in the presence of the enzyme: e
The G for the reaction in the absence of the enzyme: e
The activation energy for the reaction in the presence of the enzyme: d
The activation energy for the reaction in the absence of the enzyme: c


a
b
c
d
e
Name: ___________________________Lab Section __________________ 3/17/14
6
1oLal olnLs: _____
10. Select all that apply: The reaction shown in the diagram above is
a. Endergonic
b. Exergonic
c. Spontaneous
d. Non-spontaneous
Answer: a, d

11. As temperature is decreased below the optimal temperature of an enzyme
a. Hydrogen bonds break and the enzyme begins to denature
b. The shape of the enzyme changes and the reaction slows down
c. Fewer reactants have enough activation energy to reach the transition state
d. More reactants have enough activation energy to reach the transition state
e. More hydrogen bonds form and the shape of the enzyme changes
Answer: c

12. Select all that apply: Ethanol fermentation (see figure provided)
a. Recycles NAD+ back to glycolysis
b. Produces additional ATP molecules
c. Happens only in the presence of O
2

d. Produces CO
2
as a byproduct
e. Recycles ADP back to glycolysis
Answer: a, d

13. 6 points. Select either a or b, not both. For your choice (a or b) answer the following
questions.
a. Cyanide attaches to the iron within cytochrome c oxidase and inhibits its activity.
b. Dinitrophenol is an uncoupler.

How would the compound you chose affect electron transport in the mitochondria?
Cyanide: stops electron transport.
Dinitrophenol: does not affect electron transport directly.

How would this compound affect the proton gradient across the inner membrane of
mitochondria?
Cyanide: no electron transport means that no proton gradient will be established (no proton
movement at complexes I, III, and IV, and no reduction of oxygen to make water).
Dinitrophenol: the proton gradient is dissipated = no proton gradient.

How would this compound affect ATP synthesis in the mitochondria?
Cyanide: no proton gradient = no ATP synthesis.
Dinitrophenol: no proton gradient = no ATP synthesis.

14. Lipid-soluble signal molecules, such as testosterone, cross the membranes of all cells but
affect only target cells because
a. only target cells retain the appropriate DNA segments
b. intracellular receptors are present only in target cells
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c. most cells lack the Y chromosome required for the response
d. only target cells have the enzymes that transduce the testosterone
Answer: b

15. In _______ signaling secreting cells discharge a regulator into the blood to affect cells that
are likely to be far away.
a. autocrine
b. paracrine
c. endocrine
d. synaptic
Answer: c

16. Which of the following CANNOT easily cross
the lipid bilayer on its own?
a. N
2

b. CO
2

c. O
2

d. OH
-

Answer: d

17. Select all that apply: Receptor tyrosine
kinases
a. are relay proteins that receive signals from
G-proteins and pass them on to cAMP
b. are membrane receptors that attach
phosphates to specific amino acids in
proteins
c. are a class of GTP G-protein signal
receptors that phosphorylate other proteins
d. dimerize and form a complex when a signal binds to their extracellular domain
e. deactivate their kinase domains when a signal binds to their extracellular domain
Answer: b, d

18. Select all that apply: Review the figures below. Li
+
blocks the activity of phospholipase C
to make IP
3
. This means if the hormone and Li
+
are both present there will be
a. Low Ca
2+
concentration in the cytosol
b. High Ca
2+
concentration in the cytosol
c. Active form of protein kinase C (PKC)
d. Inactive form of protein kinase C (PKC)
e. Active form of the G-protein
f. Inactive form of the G-protein
Answer: a, d, e
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19. Select all that apply:
Review the figures
provided. IP
3
is
a. A primary messenger
b. A secondary
messenger
c. A transducer
d. A ligand
e. A kinase
Answer: b, d

Note: GPCR = G-Protein
Coupled Receptor

20. 5 points. What does the
subunit of the G
protein have to do to help terminate the response?
The alpha subunit has to hydrolyze its GTP back to GDP and reunite with the beta and gamma to
form the inactive G protein.








Name: ___________________________Lab Section __________________ 3/17/14
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Some potentially useful figures:





Glycolysis

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21. 20 points: Please write a short essay in response either a or b, not both. You are expected to write a
logically constructed answer; organization does count. You may wish to outline your answer first.
a. Consider the study done by Patterson and his colleagues in studying autistic mice. They injected a
chemical that mimics viral infection into normal, pregnant mice, which led to the offspring showing
autistic-like symptoms. You want to find out whether the microbiomes (bacteria species living in the
guts) of the mice whose symptoms result from maternal infection (the way they Patterson and his
colleagues did the experiment) differ from those of mice that are genetically pre-disposed to autism-
like symptoms. Briefly describe how you will find this out. If there are any differences, you then
would like to find out whether the difference actually would cause the observed symptoms to change.
How would you do this? Describe the elements of experimental design needed for this experiment
including the null and alternative hypotheses, experimental details including independent and
dependent and standardized variables, levels of treatment, and experimental prediction. Note: you do
not need to specify what the symptoms are.
You need to include 20 of the following points.

4 points. In order to find out whether the microbiomes (bacteria species living in the guts) of
the mice whose symptoms result from maternal infection differ from those of mice that are
genetically pre-disposed to autism-like symptoms we would have to isolate the gut bacteria
from these different mice and compare them to find out whether there are species present in
one group that are absent in the other, or species are present in both but have different
abundance levels.

2 points. After we find such differences we would want to answer the question: Does any
such difference in the microbiome actually cause the observed symptoms to change?

2 points. One alternative hypothesis is that such difference in the microbiome causes the
observed symptoms to change.

2 points. The null hypothesis is that such difference in the microbiome does not cause the
observed symptoms to change.

The experiment would be designed as follows.

1 point. We would want to use several animals as test subjects to have a large sample size.

4 points. We would divide them into two groups, both groups will share the standardized
variables listed below. We take one group of mice with autism-like symptoms (caused by
either with genetic pre-disposition or with maternal infection; pick one) and remove their gut
bacteria (through use of an antibiotic). Then we infect their guts with bacteria from other
mice that are either genetically predisposed to autism-like symptoms or are offspring of
mothers who received the injection during pregnancy. (Alternatively you could just add or
remove the additional or missing bacteria species, or increase or decrease the abundance of
various bacteria species in the gut to match what is observed in the other group; this will
change what you identify as your independent variable below).

1 points. We can repeat the experiment with the other group of mice with autism-like
symptoms as the recipients of gut bacteria.

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2 points. For each experiment, the independent variable is the different microbiomes with
two levels: microbiomes from mice with genetic predisposition and microbiomes from mice
with maternal infection (injection). In effect half receive gut bacteria from animals that are
similar to themselves and half receive gut bacteria from animals that are different.

1 point. Receiving bacteria from animals that are similar to themselves is the control
treatment.

Up to 4 points for listing standardized variables. Examples:
Same species.
Same age animals.
Same diet.
Examined at the same time intervals.
Same environmental stimuli.
Or any other reasonable one you can think of.

3 points. We would examine the autism-like symptoms of the animals before the experiment
begins, and then look for changes in these symptoms after treatment. The dependent variable
is change in autism-like symptoms observed post-treatment compared to what was observed
before the treatment.

1 point. The experiment would have to be replicated multiple times.

2 points. Our experimental prediction is: if we study several mice that are genetically pre-
disposed to showing autism-like symptoms (or are offspring of mice that received an
injection during pregnancy as described), that are the same species, the same age, receive the
same diet and are treated similarly for the same duration of experiment, and we remove their
gut bacteria by antibiotic treatment and replace the gut bacteria of half the mice with those
taken from other mice that are genetically predisposed to showing autism-like symptoms, and
replace the gut bacteria of the other half of the mice with bacteria from the guts of mice that
are offspring of mice that received an injection during pregnancy as above, and we examine
their autism-like symptoms before the treatment and several times after the treatment, we
expect to see changes in the symptoms of mice that received gut bacteria from the opposing
group but not in the mice that received gut bacteria from their own group.

b. Review the diagrams provided for the processes of glycolysis and different steps of aerobic
respiration. We start with a molecule of glucose and end with water and carbon dioxide.
Describe in which steps energy is harvested and in what form it is stored. List the steps in
which the carbon atoms from the original glucose molecule are released as CO
2
. If an
aerobically respiring cell is deprived of oxygen, what will happen to the different steps of
aerobic respiration? Explain.
You need to include 20 of the following points.

2 points. As a molecule of glucose is processed during glycolysis some of the energy stored
in the chemical bonds of glucose is harvested in the form of high energy electrons in NADH
in the reaction that oxidizes glyceraldehyde-3-phosphate to 1,3-bisphosphoglycerate.
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2 points. Some of the remaining energy is harvested in the form of ATP as 1,3-
bisphosphoglycerate is converted to PGA (phosphoglycerate), and as PGA is converted to
pyruvate.

2 points. After pyruvate enters the mitochondria, pyruvate oxidation allows for harvesting
some more energy in the form of high energy electrons in NADH.

1 point. This reaction also leads to a loss of one C atom per pyruvate (2 per glucose) in the
form of CO
2
.

3 points. The remaining 2 C atoms per pyruvate (4 per glucose) enter the Citric Acid Cycle
where some energy is harvested in the form of high energy electrons in NADH as isocitrate is
converted to alpha-ketoglutarate, during the formation of succinyl-CoA, and as malate is
converted to oxaloacetate.

2 points. 1 C per acetyl-CoA (2 per glucose) is lost as CO
2
during the formation of alpha-
ketoglutarate, and 1 C per acetyl-CoA (2 per glucose) is lost as CO
2
during the formation of
succinyl-CoA. (These are the last of the C atoms from glucose).

2 points. Some energy is harvested in the form of high energy electrons in FADH
2
as
succinate is converted to fumarate.

2 points. Some energy is harvested in the form of GTP in the production of succinate from
succinyl-CoA.

1 point. This GTP is then used to make ATP through substrate-level phosphorylation.

2 points. The NADH and FADH2 donate their electrons to the electron transport chain in the
mitochondria where some of the energy released from the movement of electrons is
harvested in the form of a H
+
gradient.

2 points. This happens through the actions of complexes I, III, and IV. As these complexes
accept electrons and then donate the electrons, they pick up protons from the matrix and
move them into the intermembrane space to establish a proton gradient.

2 points. Reduction of the final electron acceptor, oxygen, also takes protons out of the
matrix as oxygen is reduced to water. This also helps with establishing the proton gradient.

2 points. The energy stored in the proton gradient is released as protons move down their
gradient through the ATP synthase. Some of this energy is used to make ATP.

4 points. If the cell is deprived of oxygen, there is no final electron acceptor and so electron
transport comes to a halt. Without electron transport there is no proton gradient and thus no
ATP synthesis. Furthermore, without oxygen, pyruvate will stay in the cytoplasm and will
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not move into the mitochondria, and thus pyruvate oxidation and the citric acid cycle come to
a halt!
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BIO 10100 Exam 2 Version 1
Prior to completing this exam, please read the following statement and sign below to indicate
that you have read and understood the statement. No exam will be graded unless the pledge is
signed.
I pledge that I have neither given nor received unauthorized assistance on this exam. I
understand that if I am charged with cheating, my name will be submitted to the Dean for
disciplinary action.

__________________________________________________ _____________________
Name Date

Please make sure you have all 14 pages of the exam. Please read each question carefully. If you
do not understand the meaning or intention of a question, please ask. Please put away your cell
phones, blackberries, iPods, laptop computers, etc., otherwise you will receive a grade of 0.
Please separate the last sheet from the rest of the exam. Write the answer to only the last
question on the last sheet. The last sheet is graded separately from the rest of the exam.
Note that a correct statement is not necessarily the best answer to a multiple-choice question.
Each multiple-choice question is worth 2 points. If a question states Select all that apply then
select all of the correct choices. For each multiple-choice question write the letter for the best
answer in the space provided. Note: circling your answer, a , or an x wont count. You will
receive ZERO credit for any question for which we cannot tell what your final answer is. If you
cross out an answer, please be clear as to what your final answer is. Please pace yourself and use
your time efficiently; allow time for the essay type questions. If a question states Answer
either a or b, not both: if you answer both, then we will read only the answer to a, regardless
of how much better your answer to b might be. Write your answers using a pen. Answers
written using pencils will not be graded.

2 Bonus Points: Write your name and lab section on all sheets.

1. A cell has a potential of -110 mV (negative inside). There is more NO
3-
outside the cell than
inside the cell. What can we conclude about the movement of NO
3-
in this case?
a. NO
3-
will enter the cell through open channels via passive transport.
b. NO
3-
will exit the cell through open channels via passive transport.
c. NO
3-
can enter the cell only through active transport.
d. NO
3-
can exit the cell only through a carrier protein.
e. We need more information.
Answer: e

2. A cell has a potential of -110 mV (negative inside). There is more NO
3-
inside the cell than
outside the cell. What can we conclude about the movement of NO
3-
in this case?
a. NO
3-
will enter the cell through open channels via passive transport.
b. NO
3-
will exit the cell through open channels via passive transport.
c. NO
3-
can enter the cell only through a carrier protein.
d. NO
3-
can exit the cell only through active transport.
e. We need more information.
Answer: b
Text
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3. Select all that apply: In the
figure to the right, water
molecules are moving:
a. out of the cell
b. into the cell
c. against a gradient
d. down a gradient
e. through active transport
f. through simple diffusion
Answer: a, d

4. Select all that apply: The
sodium/potassium pump in
animal cells
a. is considered to be an
electrogenic pump
b. moves two + charges
into and three + charges
out of the cell
c. moves ions down their electrochemical gradient
d. carries out facilitated diffusion of ions across the membrane
e. is an example of active diffusion across the membrane
Answer: a, b

The enzyme succinate dehydrogenase carries out the reaction depicted below, converting
succinate ions into fumarate ions and FAD into FADH
2
. Malonate ions are structurally similar to
succinate ions and can mimic succinate in the active site of succinate dehydrogenase. However,
malonate is not converted to anything else by this enzyme and is released from the enzyme
without any change.



Succinate FAD FADH
2
Fumarate


Malonate
Succinate dehydrogenase
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5. 10 points. You isolate the enzyme succinate dehydrogenase from mice mitochondria. In a set
of test tubes, you first add a set amount of the enzyme succinate dehydrogenase, then add a
set amount of the substrate FAD, then add different amounts of succinate to the different test
tubes, and then you measure the rate of reaction as the rate of synthesis of fumarate (g/s).
You use different concentrations (mM) of succinate from very low levels to very high levels
in the different test tubes, while you keep everything else constant (standardized). In another
batch of test tubes, you first add the same set amount of the enzyme succinate dehydrogenase
as above, then add a set (constant) amount of malonate to the test tubes, then add the same set
amount of the substrate FAD as above, and then add different amounts of succinate as above.
You add different concentrations (mM) of succinate from very low levels to very high levels
(same as you added in the first batch) in the different tubes, while you keep everything else
constant (standardized).
a. Use a line graph to show the effects of substrate concentration on the rate of the reaction
in both the presence and the absence of malonate. Make sure to label the axes and add
units where appropriate. You should have two lines: one for the reactions in the presence
of malonate, one for the reactions in the absence of malonate.
b. What is the dependent variable? The rate of reaction as the rate of synthesis of fumarate
c. What are the independent variables? Concentration of succinate and presence of malonate
Absence of malonate ____ Presence of malonate ____
















Succinate concentrations (mM)

6. What kind of inhibition is described above?
a. allosteric
b. competitive
c. non-competitive
d. feedback
e. catalytic
Answer: b
R
a
t
e

o
f

s
y
n
t
h
e
s
i
s

o
f

f
u
m
a
r
a
t
e

(

g
/
s
)


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7. 4 points. The diagram above shows the change in the free energy for a reaction converting
the substrates A and B into the products C and D as the reaction progresses in either the
presence or the absence of an enzyme. Use the letters from the diagram above (a, b, c, d, or
e) to answer the following questions by writing the appropriate letters in the spaces provided.
A letter may be used more than once.
The G for the reaction in the presence of the enzyme: d
The G for the reaction in the absence of the enzyme: d
The activation energy for the reaction in the presence of the enzyme: b
The activation energy for the reaction in the absence of the enzyme: c

8. In _______ signaling secreting cells discharge a regulator into the extracellular space to
affect cells nearby.
a. autocrine
b. paracrine
c. endocrine
d. synaptic
Answer: b

9. 10 points. Answer either a or b, not both:
a. As life evolved on the Earth, prokaryotes arose first and eukaryotes arose much later.
Margulis explained the evolution of eukaryotes using the serial endosymbiotic theory (SET).
According to this theory, eurkaryotic cells arose through a series of endosymbiotic events
that involved different prokaryotic species that acted as host cells and endosymbionts. The
following pieces of evidence are generally presented as support for her theory: mitochondria
have their own chromosomes that are more similar to bacterial chromosomes than those in
the nuclei, and mitochondria have ribosomes that are similar to bacterial ribosomes and differ
from the ribosomes in the cytoplasm of the eukaryotic cell. But if both the endosymbiont
and the host cell were prokaryotic, why would there be differences between the ribosomes of
the host cell and those of the mitochondria, or between the chromosomes of the host cell and
Name: ___________________________Lab Section __________________ 10/21/13
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those of the mitochondria? Explain your answer in light of what we now know about eocytes
and the proposed eocyte tree.
Prokaryotes include two major lineages: bacteria and archaea. The eukaryotic cell, the
original prokaryotic host cell, is more closely related to some lineages of archaea than to
other archaea, and more distantly related to bacteria. The organelles such as mitochondria
that evolved through endosymbiosis are more closely related to bacteria and are likely to
have evolved from some bacterial ancestor. This is what the eocyte tree suggests: eocytes are
the archaeal ancestors and closest relatives of eukaryotes, putting eukaryotes in the archaea
lineage. In other words, eukaryotes are just a peculiar kind of archaea. This is the reason
the host cell and the organelles such as mitochondria differ in their chromosome structure
and their ribosomes, even though both came from prokaryotic ancestors: one is a descendent
of an archaeal ancestor while the other is a descendent of a bacterial ancestor.
3 alternative points: if you draw the eocyte tree.

b. According to SET mitochondria evolved first and the fact that almost all eukaryotes have
mitochondria supports this suggestion. However, mitochondria-free eukaryotes have been a
question for the supporters of SET: did the ancestral eukaryotic cell with its nucleus and
other organelles evolve first and then some eukaryotes got mitochondria or did the ancestral
eukaryotic cell have mitochondria? Explain how the discovery of mitosomes in Giardia and
that of hydrogenosomes in some fungi and protozoa have helped answer this question.
5 points. Mitochondria-free eukaryotes have posed a question to the supporters of SET.
Organisms like Giardia that lack mitochondria have been shown to contain proteins very
similar to the proteins that build iron-sulfur clusters in mitochondria. These proteins are
shown to clump together in a tiny sac that is now called a mitosome. Mitosomes are now
thought to be vestigial mitochondria, suggesting that Giardia is not a truly mitochondria-free
organism and that it is a descendent of an organism that contained mitochondria.

5 points. Other groups of organisms without mitochondria are some protozoans and fungi
that make ATP without mitochondria using structures called hydrogenosomes, which
produce hydrogen as waste. These organisms have motochondria-like genes and it is thought
that mitochondria and hydrogenosomes have descended from the same endosymbiont. Thus
these organisms are not exactly mitochondria-free either. Thus all eukaryotes seem to have
descended from an ancestral cell that already had a mitochondria-like endosymbiont.

10. 6 points. Answer either a or b, not both:
a. How does increasing temperature above the optimum temperature of an enzyme affect
the rate of reaction? Why?
It will break the weak hydrogen bonds and cause the shape of the enzyme including that
of the active site to change thus lowering the rate of reaction.
b. How does increasing pH above the optimum pH of an enzyme affect the rate of reaction?
Why?
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The additional hydroxide ions (OH
-
) in the solution will interfere with hydrogen bonds as
the partial positive charges in the hydrogen bond will be attracted to the full negative
charge of the hydroxide ions. This will cause the shape of the enzyme including that of
the active site to change thus lowering the rate of reaction.

11. Caffeine is an inhibitor of phosphodiesterase. Therefore, the cells of a person who has
recently consumed coffee would have increased levels of
a. phosphorylated proteins
b. GTP
c. cAMP
d. adenylyl cyclase
e. activated G proteins
Answer: c

12. Synaptic signaling between adjacent neurons is like hormone signaling in which of the
following ways?
a. It sends its signal molecules through the blood.
b. It sends its signal molecules quite a distance.
c. It requires binding of a signaling molecule to a receptor.
d. It persists over a long period.
Answer: c

13. Select all that apply: In
the diagram to the right,
acetylcholine is
a. the primary messenger
b. the secondary
messenger
c. the ligand
d. the relay protein
Answer: a, c

14. In the diagram to the right,
AChR is a
a. G-protein coupled
receptor
b. ligand-gated ion
channel
c. receptor tyrosine
kinase
d. receptor carrier protein
Answer: b

15. Select all that apply: Receptor tyrosine kinases
a. are membrane receptors that attach phosphates to specific amino acids in proteins
b. are relay proteins that receive signals from G-proteins and pass them on to cAMP
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c. are a class of GTP G-protein signal receptors that phosphorylate other proteins
d. dimerize and form a complex when a signal binds to their extracellular domain
e. deactivate their kinase domains when a signal binds to their extracellular domain
Answer: a, d

16. Select all that apply: A G-protein
a. subunit with GTP attached separates from the and subunits
b. subunit with GTP attached unites with the and subunits
c. is activated when a signal binds to a GPCR and activates it
d. with a GTP attached acts as a kinase
e. with a GDP attached acts as a phosphatase
Answer: a, c

17. Select all that apply. The free energy for the oxidation of glucose to CO
2
and water is -686
kcal/mole and the free energy for the reduction of NAD+ to NADH is +53 kcal/mole. Why
are only two molecules of NADH formed during glycolysis when it appears that as many as a
dozen could be formed?
a. Because most of the energy of glucose oxidation is released as heat.
b. Because most of the energy of the original glucose is stored in ATP.
c. Because glucose is not fully oxidized to CO
2
during glycolysis.
d. Because most of the energy of the original glucose is retained in pyruvate.
Answer: c, d

18. An inhibitor of which of the following could be used to block the release of calcium from the
endoplasmic reticulum?
a. tyrosine kinases
b. serine/threonine kinases
c. phosphodiesterase
d. phospholipase C
e. adenylyl cyclase
Answer: d

19. 6 points. Review the figure below. Circle the steps that contribute to the formation of the
proton gradient across the inner membrane of mitochondria. Identify the steps you circled as
removing protons from matrix at that specific step or adding protons to the
intermembrane space at that specific step.
Adding protons to the intermembrane space
Removing protons from the matrix
Name: ___________________________Lab Section __________________ 10/21/13
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20. 6 points. Review the figure below. List 3 steps that have to be taken to terminate the
response.
The steps needed are:
Epinephrine must be removed. The primary messenger is either broken down or recycled.
The alpha subunit of the G protein must hydrolyze its GTP to GDP. Adenylyl cyclase must be
inhibited.
The relay proteins must be dephosphorylated by a phosphatase to be deactivated.
Glycogen synthase is dephosphorylated by a phosphatase to be activated.



Name: ___________________________Lab Section __________________ 10/21/13
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21. Select all that apply: In the reaction leading to the synthesis of oxaloacetate
a. Malate is oxidized to oxaloacetate
b. Malate is reduced to oxaloacetate
c. NAD
+
is oxidized to NADH
d. NAD
+
is reduced to NADH
Answer: a, d


Name: ___________________________Lab Section __________________ 10/21/13
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22. How many carbon atoms from one glucose molecule are fed into the citric acid cycle?
a. 2
b. 4
c. 6
d. 8
e. 10
Answer: b



23. 6 points. Explain how either a or b (not both) affects electron transport, the proton gradient,
and ATP synthesis through oxidative phosphorylation in mitochndria: a) an uncoupler, or b)
cyanide (binds to cytochrome c oxidase and prevents oxidation of cytochrome c).
a) An uncoupler allows the protons to go down their gradient back into the matrix thus
dissipating the proton gradient. Therefore, the protons will not necessarily go through the
ATP synthase. That means ATP synthesis through oxidative phosphorylation will be
reduced. However, the uncoupler has no direct effect on electron transport.
b) Cyanide will inhibit oxidation of cytochrome c thus stopping electron transport. No
electron transport means no proton gradient. No proton gradient means no ATP synthesis
through oxidative phosphorylation.




Name: ___________________________Lab Section __________________ 10/21/13
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Some potentially useful figures:

Phosphodiesterase
cAMP AMP








Name: ___________________________Lab Section __________________ 10/21/13
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Note: GPCR = G-Protein Coupled Receptor


Glycolysis

24. 20 points: Please write a short essay in response either a or b, not both. You are expected to write a
logically constructed answer; organization does count. You may wish to outline your answer first.
a. What do the bark beetles do to a tree that may kill the tree? What is verbenone? Design a field
experiment to be carried out in forests to answer the following question: Can verbenone in plastic
flakes (like a sandwich with verbenone in the middle releasing verbenone gradually along the edges)
be used effectively in a forest to prevent infestation by the bark beetle? Describe the elements of
experimental design needed for this experiment including the null and alternative hypotheses,
experimental details including independent and dependent and standardized variables, levels of
treatment, and experimental prediction.
You must include 20 of the following points.

Name: ___________________________Lab Section __________________ 10/21/13
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5 points. Bark beetles have become a huge problem in the last 15 years. Adult bark beetles
bore into the trunk and carve out tunnels (galleries) where the females lay eggs. When beetle
larvae emerge, they feed on the trees tissues before flying off to colonize another tree. The
beetles disrupt the flow of water and nutrients between the roots and the rest of the tree thus
killing it.

3 points. Verbenone is a pheromone that repels the beetles. It is like a no-vacancy sign in
an occupied tree. This pheromone overrides the attraction pheromones, and signals outside
beetles to find another tree.

2 points. One alternative hypothesis is that verbenone in plastic flakes can be used
effectively in a forest to prevent infestation by the bark beetle.

2 points. The null hypothesis is that verbenone in plastic flakes cannot be used effectively in
a forest to prevent infestation by the bark beetle.

1 points. We would use several forest plots to have a large sample size.

4 points. We would divide them into two groups, both groups will share the standardized
variables listed below, but one group will additionally have verbenone flakes dispersed over
it while the other group will have plastic flakes without verbenone dispersed over it.
Presence of verbenone in the plastic flakes is the independent variable with two levels of
treatment: present or absent.

Up to 4 points for standardized variables. Examples:
Species composition of the forest plots should be the same.
The age distribution of the trees in the plots should be similar.
They should be on the same soil type.
They should be in the same general location with similar weather/water, etc.
Duration of the experiment before measurements are taken.
Same density of bark beetles initially, or bark beetles added to both groups initially.
Any other reasonable variable you can think of.

2 points. The dependent variable is the level of infestation of the forest: either number of
trees with any bark beetles, or with x number of bark beetles above a certain threshold, or
number of trees that die due to beetle infestation (pick one or more such dependent variable).
Note: infestation has to involve trees, you cannot just count the beetles in the forest.

1 point. The experiment would have to be replicated multiple times.

2 points. Our experimental prediction is: if we have several similar forest plots in a similar
location on similar soil type (etc.) and we disperse plastic flakes with verbenone to one half
and plastic flakes without verbenone to the other half, at the end of the experiment we will
find that more trees are infested with bark beetles (or die due to infestation caused by bark
beetles, etc.) in the plots with plastic flakes without verbenone compared to the plots with
plastic flakes with verbenone.
Name: ___________________________Lab Section __________________ 10/21/13
14
1oLal olnLs: _____
b. Explain how the structure of the phospholipids is important in making a selectively permeable
membrane made of a phospholipid bilayer. What kinds of molecules can cross this bilayer on their
own without any input of energy or help from proteins? You have identified a new protein that has a
structure similar to calcium pumps. We want to know whether this protein is in fact a calcium pump
and can use the energy from ATP hydrolysis to transport calcium ions across the lipid bilayer
membrane of an artificial vesicle actively. Design an experiment to figure this out. You do not need
to describe details of methods. For example, you can simply state we will measure the voltage across
the membrane without explaining how you will do that (if that applied to your experiment). Describe
the elements of experimental design needed for this experiment including the null and alternative
hypotheses, experimental details including independent and dependent and standardized variables,
levels of treatment, and experimental prediction.

You must include 20 of the following points.

4 points. The primary function is to provide separation of what is inside from what is outside
through selective permeability. The hydrophobic fatty acid tails are the barrier that separates
the aqueous solution outside from the aqueous solution inside. The hydrophilic phosphate
heads (charged and polar) allow the lipid bilayer to be stable in the presence of water on both
sides while the hydrophobic tails are packed inside the bilayer forming the barrier.

4 points. Only small non-polar molecules can easily pass through this layer via simple
diffusion down their gradient without the need for any specific passageway. This movement
is passive and does not require any energy as the substances are moving down their gradient.

2 points. Calcium ions are charged so both the electrical gradient and the concentration
gradient have to be considered.

2 points. One alternative hypothesis is that this protein can use the energy from ATP
hydrolysis to transport calcium ions across the lipid bilayer of an artificial vesicle actively
against an electrochemical gradient.

2 points. The null hypothesis is that this protein cannot use the energy from ATP hydrolysis
to transport calcium ions across the lipid bilayer of an artificial vesicle actively against an
electrochemical gradient.

1 points. We would use many vesicles to have a large sample size.

There are different ways you could set up this experiment. For example, you could provide
ATP to one half of the vesicles and not the other half and see which set shows calcium
transport (matters for pumps, but not channels). Or, you could add the protein to the
membrane of all vesicles in the same orientation, provide ATP to all vesicles, divide them
into two groups, set the electrochemical gradients in opposite directions in the two groups of
vesicles, and then see which group shows calcium movement. Or you could come up with
your own, reasonable experiment.

Ill describe the first type of experiment below.

Name: ___________________________Lab Section __________________ 10/21/13
13
1oLal olnLs: _____
4 points. We would divide the artificial vesicles into two groups, both groups will share the
standardized variables listed below, but one group will additionally have ATP added while
the other will not. Presence of ATP is the independent variable with two levels of treatment:
present or absent.

Up to 4 points for standardized variables. Examples:
Same composition lipid bilayer.
Same concentration gradient for calcium.
Same voltage across the vesicle membrane.
Protein inserted into the membrane of all of the vesicles.
Any other reasonable variable you can think of.

2 points. We could measure the amount of ATP left (or amount of ADP produced) and the
concentration of calcium on both sides of the membrane. These are potentially the dependent
variables.

1 point. The experiment would have to be replicated multiple times.

2 points. Our experimental prediction is: if we have several identical, artificial vesicles with
the protein inserted into the vesicle membrane, with the same calcium concentration gradient,
and same membrane potential (etc.), and we add ATP to one half and we do not add ATP to
the other half, if the protein acts as a pump at the end of the experiment we will find that the
amount of ATP has decreased and calcium has moved against its gradient in the vesicles with
ATP but no such changes are observed in the vesicles without ATP.


Ill describe the second type of experiment below.

4 points. We would divide the artificial vesicles into two groups, both groups will share the
standardized variables listed below, but the two groups will have the electrochemical
gradients for calcium set in opposite directions. The direction of the electrochemical gradient
for calcium is the independent variable with two levels of treatment: favoring movement into
the vesicle and favoring movement out of the vesicle.

Up to 3 points for standardized variables. Examples:
Same composition lipid bilayer.
Protein inserted in the membrane of all vesicles in the same orientation.
ATP provided to all vesicles.
Any other reasonable variable you can think of.

2 points. We could measure the concentration of calcium on both sides of the membrane.
The changes in calcium concentration or the direction of movement of calcium is the
dependent variables.

1 point. The experiment would have to be replicated multiple times.

Name: ___________________________Lab Section __________________ 10/21/13
16
1oLal olnLs: _____
2 points. Our experimental prediction is: if we have several identical, artificial vesicles with
the protein inserted into the vesicle membrane in the same orientation, with ATP provided to
all, divided into two groups with opposing calcium gradients, if the protein acts as a pump at
the end of the experiment we will find that calcium has moved against its gradient in one
group of vesicles but no such changes are observed in the vesicles the opposite gradient.

Name: ___________________________Lab Section __________________ 6/21/11
"
BIO 10100 Exam 1 Version 1
Prior to completing this exam, please read the following statement and sign below to indicate
that you have read and understood the statement. No exam will be graded unless the pledge is
signed.
I pledge that I have neither given nor received unauthorized assistance on this exam. I
understand that if I am charged with cheating, my name will be submitted to the Dean for
disciplinary action.

__________________________________________________ _____________________
Name Date


Please make sure you have all 12 pages of the exam. 2 bonus points: Write your name and
lab section on all sheets. Please read each question carefully. If you do not understand the
meaning or intention of a question, please ask. Please pace yourself and use your time
efficiently.
Please put away your cell phones, blackberries, iPods, laptop computers, etc. Write your
answers using a pen. Answers written in pencil will not be accepted.
Each T/F or multiple-choice question is worth 2 points. Note that a correct statement is not
necessarily the best answer to a multiple-choice question. For each multiple-choice question,
circle the best answer (unless the question states select ALL that apply). You will receive
ZERO credit for any question for which we cannot tell what your final answer is. If you cross out
an answer, please make it clear as to which answer is your final answer.
Please pace yourself and use your time efficiently; allow time for the essay type questions. If a
question states answer a or b, not both: if you answer both, then we will read only the answer
to a, regardless of how much better your answer to b might be.
1. Which of the following relationships between cell structures and their respective functions is
correct?
a. cell wall: support, protection
b. chloroplasts: chief sites of cellular respiration
c. chromosomes: cytoskeleton of the nucleus
d. ribosomes: secretion

2. The diagram below shows a solute molecule in the center surrounded by five water
molecules. Based on your knowledge of the polarity of water molecules, the solute molecule
shown below is most likely
a. positively charged.
b. negatively charged.
c. without charge.
d. hydrophobic.
Name: ___________________________Lab Section __________________ 6/21/11
#
e. nonpolar.



3. (6 points) Consider the plant nutrients Ca
2+
and Mg
2+
in the soil. Consider how these ions
are attracted to the negative charges on the surface of clay particles and what happens to
these ions as more nitrate (NO
3
-
) rains down on forests due to pollution and acid rain.
Denitrifying bacteria in wetlands will break down nitrates and clean the water of surface
springs by removing the nitrate. Will this solve the problem the trees in the forests are facing
from acid rain? Explain.
Denitrifying bacteria in wetlands will break down nitrates and clean the water of surface springs.
This will not solve the problem the trees are facing from acid rain for the following reason.
Wetlands are downstream from the forests. The nitrate and nutrients leaching out of the forest
soils enter runoff and reach these wetlands where the bacteria get rid of the nitrate and reduce the
amount of nitrate that would otherwise enter surface springs. However, this does not do anything
for any organism upstream of the wetlands. So, the malnourished forests do not benefit from this
process.
4. The volume enclosed by the plasma membrane of plant cells is often much larger than the
corresponding volume in animal cells. The most reasonable explanation for this observation
is that
a. plant cells are capable of having a much higher surface area-to-volume ratio than animal
cells.
b. plant cells have a much more highly folded plasma membrane than animal cells.
c. plant cells contain a large vacuole that reduces the volume of the cytoplasm.
d. animal cells are more spherical, while plant cells are elongated.
e. the basic functions of plant cells are very different from those of animal cells.

5. (4 points) Answer either a or b, not both:
a. Billions of years ago, life apparently arose from inorganic chemicals, but all life today
apparently arises only by the reproduction of preexisting life. If life could come from
nonlife on the ancient Earth, what is one major reason that this does not continue to
happen today?
The presence of oxygen in the atmosphere, which breaks down the chemical bonds in
organic molecules through oxidation reactions, thus preventing the formation of a critical
mass of simple organic compounds to allow the basic reactions to continue forward
leading to more and more complex compounds.
b. What is the seeding hypothesis?
Name: ___________________________Lab Section __________________ 6/21/11
$
The idea that meteors could have brought the building blocks of life or even
microorganisms to the ancient earth.
The next two questions refer to the figures below. Write the appropriate letter(s) (A, B, C, D, or
E) as your answer.

6. (2 points) Which molecule(s) contain(s) a carbonyl (aldehyde or ketone) functional group?
B and C
7. (2 points) Which molecule(s) contain(s) a carboxyl group?
D

8. (8 points) One of the fundamentals of cell theory is biogenesis. Pasteur carried out
experiments in support of biogenesis. See the figure below. Answer either a or b, not both
(you may use the space next to the figure):
a. What is biogenesis? How do Pasteurs experiments support biogenesis? Explain.
Biogenesis is the hypothesis that all living cells arise from preexisting cells and there is no
spontaneous creation of living cells. Pasteurs experiments showed that all else being equal
when a sterilized broth was exposed to the particles in air there was microbial growth in the
broth, but when a trap prevented the particles from getting to the broth there was no
microbial growth. Therefore, microbial growth resulted from exposure, showing that there
was no spontaneous creation of microbes. Microbes arose from pre-existing microbes, thus
supporting biogenesis.

b. What was the question Pasteur tried to answer? What was the alternative hypothesis?
What was the null hypothesis? What was the experimental prediction?

Question: Can microorganisms be created spontaneously? Or where do microorganisms
come from? You can state it in different ways.
Alternative hypothesis: There is no spontaneous creation of microorganisms. Or
Microorganisms arise from pre-existing microorganisms.
Null hypothesis: There is spontaneous creation of microorganisms. Or microorganisms arise
without any pre-existing microorganisms.
Experimental prediction: If nutrient broths are placed in identical flasks with swan necks to
prevent dust particles and what they carry to be trapped and not be able to enter the flasks,
and the broth is boiled so that there is no living microorganism left, and then the swan neck is
broken off one flask to expose its contents to the outside air, then there will be no microbial
growth in the flask with intact swan neck, while there will be microbial growth in the flask
with the swan neck broken off.
Name: ___________________________Lab Section __________________ 6/21/11
%


Name: ___________________________Lab Section __________________ 6/21/11
&

9. In each of the following scenarios, a scientist has attempted to study whether phosphorus has
an effect on chlorophyll synthesis by photosynthetic organisms in freshwater lakes.
i. The scientist fertilizes one lake with phosphorus and takes 12 water samples 1 month later
to determine the amount of chlorophyll (mg/L) in the lake. At the same time, the scientist
also takes 12 samples from a lake of the same size that did not receive phosphorus. The
average chlorophyll level is much higher in the fertilized samples than in the control
samples, so the scientist concludes that phosphorus has an effect on production of
chlorophyll by photosynthetic organisms.
ii. The scientist takes 12 different lakes and measures their chlorophyll levels in May. The
scientist then fertilizes all the lakes with phosphorus and re-measures chlorophyll levels
in July. Because the average chlorophyll concentration is much greater in July, the
scientist concludes that phosphorus has an effect on production of chlorophyll by
photosynthetic organisms.
iii. Because the scientist has a limited budget to buy fertilizer, s/he fertilizes the 6 smallest
lakes in the area with phosphorus and measures the change in chlorophyll concentration
(mg/L) over time. Because the change in these lakes is significantly greater than the
change in 6 larger lakes that did not receive phosphorus, the scientist concludes that
phosphorus has an effect on production of chlorophyll by photosynthetic organisms.
For each experiment:
a. (3 points) List the control treatment. If there is none, state none.
i. Not adding phosphorus to one lake

ii. None

iii. Not adding phosphorus to 6 large lakes

b. (3 points) List the standardized factors described above. If there is none, state none.
i. Size of lakes, (# of samples)

ii. None mentioned

iii. The size of the lakes within each treatment (but not between!), (# of lakes)

c. (6 points) Explain the problem with the experimental design.
i. Sample size of one per treatment, not replicated, no pre-fertilization measurement, no
statistical analysis,

ii. No control treatment (nothing to compare the results of the treatment!), not repeated,
no statistical analysis (just averages),

iii. Treatments not assigned randomly and size not standardized, not repeated,
presumably statistical analysis was carried out since the problem says significantly
greater
Name: ___________________________Lab Section __________________ 6/21/11
'
d. (8 points) For case iii draw a column graph below showing what the data would
potentially look like. Make sure to label the axes of the graph; include the treatments and
the units where appropriate. Make sure to distinguish the results from the different
treatments.




Change in
[Chl]
(mg/L)
(dependent)




+ phosphorus - phosphorus
Treatment (independent)
If you add error bars, even better!

e. (2 points) Mark the dependent and independent variables on your graph.


10. Charles Lyells theory of uniformity
a. suggested that all life evolved from a common ancestor
b. explained why ostriches, emus, and rheas have similar structures
c. explained why all tetrapods have similar embryonic development
d. suggested that earth was much older than previously thought

11. (9 points) Describe 3 of the four tenets of Darwins theory of descent with modification
through natural selection.
Here are the 4 tenets:
a. Organisms produce more offspring than the environment can support: competition
b. There is variation in a population that could be the basis for adaptation
c. Some variation is heritable and can be passed on from generation to generation
d. There will be differential survival AND reproduction: populations evolve by natural
selection of adaptive traits


12. 4 points. You can ripen your unripe tomatoes if you put them in a paper bag with some apple
peel. Explain the function of the apple peel and the importance of the bag.
a. Apple peel
Produced the hormone ethylene, which is a gas, so it will diffuse through the surrounding air.

b. Paper bag
Name: ___________________________Lab Section __________________ 6/21/11
(
Will help to keep the ethylene concentration high inside the bag where the tomatoes are to
begin the ripening process sooner.

13. True/False. A cell has a potential of -70 mV (negative inside). Therefore, positively charged
ions such as K+ will leave the cell only through pumps via active transport.

14. Testosterone functions inside a cell by
a. acting as a signal receptor that activates ion-channel proteins.
b. binding with a receptor protein that enters the nucleus and activates specific genes.
c. acting as a steroid signal receptor that activates ion-channel proteins.
d. becoming a second messenger that inhibits adenylyl cyclase.
e. coordinating a phosphorylation cascade that increases glycogen metabolism.

15. Caffeine is an inhibitor of phosphodiesterase. Therefore, the cells of a person who has
recently consumed coffee would have increased levels of
a. phosphorylated proteins.
b. GTP.
c. cAMP.
d. adenylyl cyclase.
e. activated G proteins.

16. Which of the following would be inhibited by a drug that specifically blocks the addition of
phosphate groups to proteins?
a. G-protein-linked receptor signaling
b. ligand-gated ion channel signaling
c. adenylyl cyclase activity
d. phosphatase activity
e. receptor tyrosine kinase activity

17. Which of the following is the best explanation for the inability of an animal cell to reduce the
Ca2+ concentration in its cytosol compared with the extracellular fluid?
a. blockage of the synaptic signal
b. loss of transcription factors
c. insufficient ATP levels in the cytoplasm
d. low oxygen concentration around the cell
e. low levels of protein kinase in the cell

18. (2 points) Explain your answer to the last question above.
As shown in the figure on p. 9, ATP is used by Calcium pumps to pump the ion out of the
cytoplasm.

19. Which of the following would likely move through the lipid bilayer of a plasma membrane
most rapidly?
a. An amino acid
b. CO
2

c. Starch
Name: ___________________________Lab Section __________________ 6/21/11
)
d. Glucose

20. What maintains the secondary structure of a protein?
a. peptide bonds
b. hydrogen bonds
c. disulfide bonds
d. ionic bonds
e. phosphodiester bonds

21. Select all that apply: Which of the following is (are) true of natural selection?
a. requires genetic variation
b. results in descent with modification
c. involves differential reproductive success
d. requires sexual reproduction

22. (6 points) Answer either a or b, not both:
a. Carbon deposits from around 3.7 billion years ago have higher C
12
: C
13
ratio than older
deposits. Explain how this finding suggests that there was probably life on earth back
then.
Enzymes discriminate against the heavier isotope. Therefore, this change in the ratio is
indicative of the presence of enzymatic reactions, suggesting there was probably life on
earth back then.

b. RNA is required for protein synthesis while protein-based enzyme complexes are
required for synthesis of RNA. How does Tom Cechs discovery of ribozymes help to
solve this potential problem for the theory of abiogenesis?
Ribozymes are RNA molecules that act as enzymes and can thus potentially act in their
own self replication. Therefore, before complicated protein machinery to replicate nucleic
acids arose, ribozymes could have led to a simple life form that relied on them for
replication of the simpler genetic material.
23. (4 points) The Miller-Urey experiments provided us with evidence for which aspect of
Oparins theory of abiogenesis?
For the first step in abiogenesis: simple inorganic and organic compounds reacting in the
primordial soup in the absence of any living organisms or enzymatic reactions to make
increasingly more and more complex organic molecules, including the basic monomers
needed as the basic blocks of life.

24. A new organism is discovered in the forests of Costa Rica. Scientists there determine that the
polypeptide sequence of hemoglobin from the new organism has 72 amino acid differences
from humans, 65 differences from a gibbon, 49 differences from a rat, and 5 differences from
a frog. These data suggest that the new organism
a. is more closely related to humans than to frogs.
b. is more closely related to frogs than to humans.
c. may have evolved from gibbons but not rats.
d. is more closely related to humans than to rats.
Name: ___________________________Lab Section __________________ 6/21/11
*
e. may have evolved from rats but not from humans and gibbons.

25. Which of the following statements concerning prokaryotic and eukaryotic cells is not
correct?
a. Prokaryotic cells lack a membrane-bound nucleus.
b. Prokaryotic cells contain small membrane-enclosed organelles.
c. Eukaryotic cells contain a membrane-bound nucleus.
d. DNA, or deoxyribonucleic acid, is present in both prokaryotic cells and eukaryotic cells.
e. DNA or deoxyribonucleic acid is present in the nucleus of eukaryotic cells.

26. Select all that apply: Which of the following would be regarded as compounds?
a. H
2

b. H
2
O
c. O
2

d. CH
4


Some potentially useful figures:


Name: ___________________________Lab Section __________________ 6/21/11
"+







Name: ___________________________Lab Section __________________ 6/21/11
""
27. (20 points) Please write a short essay in response to only one (either a or b, but not both)
of the following questions. You are expected to write a logically constructed answer;
organization does count. You may want to outline your answer first.
a. The primary function of the lipid bilayer membrane for any given cell or membrane-
bound organelle is selective permeability. How does the structure of the lipid bilayer
relate to this function? Describe the role of the phosphate heads, the fatty acid tails, and
the transmembrane proteins. In your answer include simple diffusion through the lipid
bilayer, facilitated diffusion through channels and carriers, and active transport through
pumps.
(5 points) The primary function is to provide separation of what is inside from what is outside
through selective permeability. The hydrophobic fatty acid tails are the barrier that separates the
aqueous solution outside from the aqueous solution inside. The hydrophilic phosphate heads (charged
and polar) allow the lipid bilayer to be stable in the presence of water on both sides while the
hydrophobic tails are packed inside the bilayer forming the barrier. The combination of a
hydrophobic barrier and proteins that provide passageways allows the membrane to separate what is
inside from what is outside while allowing for and regulating exchange across the membrane.

(5 points) Only small non-polar molecules can easily pass through this layer via simple diffusion
down their gradient without the need for any specific passageway. This movement is passive and
does not require any energy as the substances are moving down their gradient.

(5 points) The membrane has transmembrane proteins some of which are channels or carrier proteins
that allow for passage of substances that wouldnt normally be able to pass easily through the
membrane (for example charged or polar molecules) down their gradient. These channels and
carriers provide a hydrophilic passageway through the lipid bilayer that allows these substances to
pass through the membrane down their gradient. This is passive movement, but it is facilitated since
a protein is needed to provide the passageway.

(3 alternate points: Carrier proteins change shape to deliver a substance from one side to the other,
while channels just provide a tunnel without the need to change shape. Passage of molecules
through channels could be regulated through opening and closing of the passageways through gates.)

(5 points) Other proteins in the membrane could act as pumps that would allow substances to move
against their gradient via active transport; this requires expenditure of energy to move the substance
against its gradient. This energy is usually supplied through hydrolysis of ATP.

b. In a couple of sentences describe the basic idea proposed by Margulis about how
mitochondria and chloroplasts evolved through serial endosymbiosis. What are the basic
tenets of the theory of autogeny as proposed by Taylor (with regards to the evolution of
eukaryotic cells)? Explain. For the pieces of evidence listed below, explain how each
supports Margulis SET as opposed to Taylors theory of autogeny: i) DNA in
chloroplasts and mitochondria is similar in structure to single circular chromosomes of
bacteria, ii) mitochondria and chloroplasts show sensitivity to inhibitors that affect
bacteria but not eukaryotic cells, iii) mitochondria and chloroplasts reproduce by fission
similar to the way bacteria divide, iv) ribosomes in mitochondria and chloroplasts are
similar to bacterial ribosomes, not ribosomes in the cytoplasm of eukaryotic cells.
(3 points) Margulis basic idea about the evolution of the mitochondria and chloroplasts
involves endosymbiosis. That means that these organelles evolved from free-living bacterial
Name: ___________________________Lab Section __________________ 6/21/11
"#
through a symbiotic relationship with a host cell. As the aerobically respiring or
photosynthetic bacteria were ingested by larger predatory ones, or parasitized these larger
cells, an uneasy relationship developed that eventually lead to the evolution of the organelles
as endosymbionts.
(2 points) Taylors theory of autogeny, on the other hand, does not suggest that these
organelles evolved from free-living bacteria. The tenets of autogeny are
compartmentalization and specialization.
(4 points) According to autogeny, the original ancestor cell was a photosynthetic bacterium
with a complex system of internal membranes leading to increased surface area of
membrane, and had a typical prokaryotic cell wall and flagella. (1 alternate point: There
were several pieces of DNA found in several places in the cell, not just one place).
(2 points) Within this ancestral cell compartmentalization occurred; that means sections of
the internal membranes broke away to form separate compartments. (1 alternate point: As
that happened small pieces of DNA and ribosomes were trapped inside these compartments)
(2 points) Later on, these new compartments became specialized to accomplish specific tasks
(1 alternate point: such as photosynthesis in what became chloroplasts, and aerobic
respiration in what became mitochondria).
(3 points) Eukaryotic cells became larger and lost their prokaryotic walls. More complex
flagella evolved from simpler bacterial flagella. There was loss of chloroplasts in predatory
forms of eukaryotes (2 alternate points: and other cells evolved new protective walls (such as
those in plants, algae, and fungi) that differ from the lost prokaryotic walls).
(4 points)
i) Supports the idea that the chloroplasts and mitochondria are derived from bacteria as
Margulis suggests, but not the idea that the DNA is from the same cell but trapped in the
organelle during compartmentalization as Taylor suggests.
ii) and iii) Supports the idea that the chloroplasts and mitochondria are derived from bacteria
as Margulis suggests, but not the idea that they are derived from the same eukaryotic cell as
the result of compartmentalization and specialization as Taylor suggests.
iv) Supports the idea that the chloroplasts and mitochondria are derived from bacteria as
Margulis suggests, but not the idea that the ribosomes got trapped in these new organelles as
they are derived from the same eukaryotic cell as the result of compartmentalization and
specialization as Taylor suggests.

Name: ___________________________Lab Section __________________ 10/24/11
!

BIO 10100 Exam 2 Version 1
Prior to completing this exam, please read the following statement and sign below to indicate
that you have read and understood the statement. No exam will be graded unless the pledge is
signed.
I pledge that I have neither given nor received unauthorized assistance on this exam. I
understand that if I am charged with cheating, my name will be submitted to the Dean for
disciplinary action.

__________________________________________________ _____________________
Name Date


Please make sure you have all 10 pages of the exam. Write your name and lab section on all
sheets. Please read each question carefully. If you do not understand the meaning or intention
of a question, please ask. Please pace yourself and use your time efficiently. Please put away
your cell phones, blackberries, iPods, laptop computers, etc.

Please separate the last sheet from the rest of the exam. Write the answer to only the last question
on the last sheet. The last sheet is graded separately from the rest of the exam.
Each True/False or multiple-choice question is worth 2 points. Note that a correct statement is
not necessarily the best answer to a multiple-choice question. For each multiple-choice question
write the letter for the best answer in the space provided (circling your answer, a !, or an x
wont count). You will receive ZERO credit for any question for which we cannot tell what your
final answer is. If you cross out an answer, please be clear as to what your final answer is.

Please pace yourself and use your time efficiently; allow time for the essay type questions. If a
question states answer a or b, not both: if you answer both, then we will read only the answer
to a, regardless of how much better your answer to b might be. Write your answers using a pen.
Answers written using pencils will not be graded.

1. Which of the following statements regarding enzymes is true?
a. Enzymes decrease the free energy change of a reaction.
b. Enzymes increase the rate of a reaction.
c. Enzymes increase the activation energy.
d. Enzymes change the direction of chemical reactions.
e. Enzymes are chemically altered by the reactions they catalyze.
Answer: b

2. In bacteria para-aminobenzoic acid (PABA) is converted to folic acid by the enzyme
dihydropteroate synthetase. Folic acid in turn acts as a co-enzyme in the synthesis of several
amino acids the bacteria need. Sulfanilamide is structurally similar to PABA and can bind to
the active site of dihydropteroate synthetase. Sulfanilamide can be used as an antibiotic
Text
Name: ___________________________Lab Section __________________ 10/24/11
#

against these bacteria because it interferes with the production of several amino acids by the
bacteria.
a. 4 points. Based only on the information provided above, what kind of inhibition
(competitive or non-competitive) is occurring when sulfanilamide is used as an antibiotic
against the bacteria mentioned above? How do you know?
Since the antibiotic is structurally similar to PABA and can bind to the active site of the
enzyme and inhibit the activity, it is likely to be a competitive inhibitor and compete with
the substrate (PABA) for the active site.

b. 8 points. On the blank graph provided below, graph the effects of increasing PABA
concentration on the rate of folic acid synthesis by dihydropteroate synthetase in both the
presence and the absence of a constant dose of sulfanilamide. Make sure to label the
axes. Identify the dependent and independent variables on your graph. Make sure the
curves for the presence and absence of sulfanilamide are distinguishable.
c. 2 points. True/False: Sulfanilamide is an example of an allosteric inhibitor.
Answer: False




Rate
of
reaction
(dependent)





!

0 "
Concentration of PABA (independent)

Sulfanilamide absent ______ , Sulfanilamide present (independent)

3. 4 points. Select all that apply: In the graphs below, the reason the reaction rate for each
enzyme drops to zero at certain pH values is because
a. The enzyme is denatured
b. Hydrogen bonds are disrupted
c. The shape of the enzyme changes
d. Secondary structure is disrupted
e. Covalent bonds are disrupted
Answer: a, b, c, d
Name: ___________________________Lab Section __________________ 10/24/11
$


4. 4 points. Fill in the blanks: The pH range for the enzyme with reaction rates depicted in the
curve on the right is from ~6 to ~10 while the pH optimum for this enzyme is ~8.

5. Which of the following is true for catabolic pathways?
a. They do not depend on enzymes as catalysts for reactions.
b. They are usually highly spontaneous chemical reactions.
c. They consume energy to build up polymers from monomers.
d. They are endergonic as they degrade polymers to monomers.
Answer: b

6. 10 points. Using a series of arrows, draw the branched metabolic reaction pathway described
by the following statements, then answer the question at the end.
" A can form either B or C.
" B can form D.
" D can form either E or F.
" C can form G.
" G can form H.
" F inhibits the reaction of A to form B.
" E promotes the reaction of A to form C.
" H inhibits the reaction of C to form G.


What compound would accumulate if there is a high concentration of E and F in the cell?
Answer: C
7. Below is an excerpt from a set of research experiments.
Experiment 1: Mitochondria are isolated from cells and placed in a medium at pH 9. This
results in a low H
+
concentration on both sides of the inner mitochondrial membrane. Half of
the mitochondria are removed quickly to a neutral medium (pH 7) as shown in the figure.
Name: ___________________________Lab Section __________________ 10/24/11
%

ATP is synthesized in these mitochondria. The other half of the mitochondria are kept in a
test tube at pH 9 (not shown in the figure). No ATP is synthesized in these mitochondria.

Experiment 2: A set of artificial vesicles is made and a bacterial proton pump is inserted in
the membrane of the artificial vesicles. The bacterial pump actively transports protons (H
+
)
into the vesicles. This establishes a large proton gradient across the vesicle membrane (more
protons on the inside, fewer protons on the outside). ADP and Pi are provided on the outside
of the vesicle. No ATP is synthesized. The vesicles are divided into two test tubes. ATP
synthase from the mitochondria of a mammal is isolated and then inserted into the membrane
of half of the artificial vesicles in the orientation shown in the figure on the right. These
vesicles are placed in test tube 1. The vesicles that do not have the ATP synthase inserted in
their membrane are in test tube 2 (not shown). There is ATP synthesis in test tube 1. There
is no ATP synthesis in test tube 2.


Experiment 1 Experiment 2

4 points. What is the question being asked for each experiment?
Experiment 1
Is a proton gradient enough for ATP to be synthesized in mitochondria, or is electron
transport required?
Name: ___________________________Lab Section __________________ 10/24/11
&


Experiment 2
Is a proton gradient enough for ATP to be synthesized or is an ATP Synthase required?

4 points. Identify the alternative hypothesis being tested for each experiment:
Experiment 1
A proton gradient is enough in the absence of electron transport for ATP synthesis in
mitochondria.

Experiment 2
The protein ATP synthase is required (or proton gradient is not enough) for ATP
synthesis.

4 points. Identify the null hypothesis for the alternative hypotheses you wrote above:
Experiment 1
The presence of a proton gradient is not enough in the absence of electron transport for
ATP synthesis in mitochondria.

Experiment 2
The protein ATP synthase is not required (or proton gradient is enough) for ATP
synthesis.

4 points. Write the experimental prediction for each experiment based on the alternative
hypotheses you wrote above:
Experiment 1
If isolated mitochondria are incubated in pH 9 solution to equilibrate to pH 9 and then
moved to pH 7 to create a proton gradient across the cristae with more protons on the
outside, then in the absence of electron transport ATP will be synthesized by the
mitochondria. Without the pH gradient (remain in pH 9) there will be no ATP synthesis.

Experiment 2
If a proton gradient is created in an artificial vesicle with the use of a bacterial proton
pump, and an ATP synthase from mitochondria is inserted into the vesicle in the correct
orientation, then ATP will be synthesized in the presence of the substrates ADP and Pi.
If no ATP synthase is added to the vesicle, there will be no ATP synthesis by the vesicle
even with the proton gradient and ADP and Pi.

Bonus: 2 points. What, if anything, is the control treatment in each experiment?
Experiment 1 Keeping the mitochondria in a test tube at pH 9 for the entirety of the
experiment.

Experiment 2 Not adding the ATP synthase to the vesicles in test tube 2.

The Glycolysis figure below illustrates some of the steps (reactions) of glycolysis in their proper
sequence. Each step is lettered. Use these letters to answer the next two questions.
Name: ___________________________Lab Section __________________ 10/24/11
'

8. 2 points. List one step that could be considered part of the energy investment phase. A
9. 2 points. List one step that could be considered part of the energy payoff phase. C, D, or E

10. In liver cells, the inner mitochondrial membranes are about 5 X the area of the outer
mitochondrial membranes, and about 17 X that of the cell's plasma membrane. What purpose
must this serve?
a. It allows for increased rate of glycolysis.
b. It allows for increased rate of the citric acid cycle.
c. It increases the surface for oxidative phosphoryation.
d. It increases the surface for substrate-level phosphorylation.
Answer: c

11. Which of the following processes in eukaryotic cells will proceed normally whether oxygen
(O
2
) is present or absent?
a. chemiosmosis
b. glycolysis
c. electron transport
d. the citric acid cycle
e. oxidative phosphorylation
Answer: b

12. (4 points) Review the structure of pyruvate below. Pyruvate has to enter the mitochondria in
order to enter the citric acid cycle.
a. True/False: pyruvate easily crosses the lipid bilayer membrane on its own. Answer: False.
b. This is because pyruvate is negatively charged (Fill in the blank).


13. 6 points. Fill in the blanks. Ethylene is a plant hormone involved in ripening in fruits such as
tomatoes, bananas, and apples. Ethylene is a gas and diffuses from its point of synthesis
through air. Synthesis of ethylene involves a multi-step pathway of several enzyme-
catalyzed reactions, and requires oxygen and is inhibited by CO
2
. Tomatoes can be picked
green and shipped across the country if the storage area has high concentrations of CO
2
and
low concentrations of O
2
. After arrival at destination, they can be made to ripen quickly if
they are gassed with high concentrations of ethylene.

14. At puberty, an adolescent female body changes in both structure and function of several
organ systems, primarily under the influence of changing concentrations of estrogens and
other steroid hormones. How can one hormone, such as estrogen, mediate so many effects?
a. Estrogen is produced in very large concentration and therefore diffuses widely reaching
every cell.
Name: ___________________________Lab Section __________________ 10/24/11
(

b. Estrogen is kept away from the surface of any cells not able to bind it at the surface.
c. Estrogen has specific antagonists in different cells leading to different responses in the
different cells.
d. Estrogen has specific receptors in different cells leading to different responses in different
cells.
Answer: d
15. See the figures below. Adenylyl cyclase has the opposite effect of which of the following?
a. protein kinase A
b. protein phosphatase
c. phosphodiesterase
d. phospholipase C
Answer: c

16. Based on the figure below, testosterone
a. needs a carrier protein to cross the plasma membrane because it is hydrophilic.
b. binds with a receptor protein that enters the nucleus and activates specific genes.
c. acts as a steroid signal receptor that activates ligand-gated ion-channel proteins.
d. becomes a second messenger that inhibits adenylyl cyclase on the DNA.
Answer: b

17. The process of signal transduction usually begins
a. when the chemical signal is released from the alpha cell.
b. when the signal changes the receptor protein in some way.
c. after the third stage of cell signaling is completed.
d. when the hormone is released from the gland into the blood.
Answer: b

18. An inhibitor of which of the following could be used to block the release of calcium from the
endoplasmic reticulum?
a. phospholipase C
b. tyrosine kinases
c. serine/threonine kinases
d. phosphodiesterase
e. adenylyl cyclase
Answer: a


Name: ___________________________Lab Section __________________ 10/24/11
)


Glycolysis


Name: ___________________________Lab Section __________________ 10/24/11
*


19. a) Consider the single cell amoebas, the cysts, the simple asexual reproduction, the asexual cycle with
facultative multicellularity, and the sexual cycle in the life of Dictyostelium. What evolutionary
sequence do we think might explain the evolution of the complex life cycle of Dictyostelium? What
is the impetus for this? Explain the sequence, how each step relates to the impetus for the evolution
of the complex life cycle of Dictyostelium, and why the sequence goes in the direction you listed.
2 points: Evading the predatory nematodes might have been the evolutionary impetus for the
evolution of the complex life cycle of Dictyostelium.

4 points: We expect the sequence to go from a) single cell amoebas growing and dividing
asexually to b) single cell amoebas that can form a small cyst to c) forming a large and
protected cell through sexual reproduction to d) forming the complicated structure in asexual
reproduction that includes a facultatively multicellular stage. The reason is that this sequence
goes from the simplest structure to the most complex structures and evolutionarily it makes
sense for the most complex steps to have evolved later. Alternative 2 points: Facultative
multicellurity involves several individual organisms coming together to act as a single
multicellular organism.

4 points: Individual Dictyostelium amoeba are vulnerable to predation by nematodes, but
they can turn into isolated cysts covering themselves in a tough cellulose coating, which
allows them a chance to pass through a nematodes gut without being digested. This is the
simplest case.

2 points: However, a better way would be to avoid getting eaten altogether: a larger organism
that is too large for the nematodes to swallow would be the answer.

4 points: In sexual reproduction of Dictyostelium, two amoebas will fuse. They begin
sending out cAMP to their neighbors who then crawl toward the signal. The mating pair then
engulfs the incoming amoebas and digests them. The cell grows very large and coats itself
with cellulose and turns dormant, waiting for the right conditions to germinate. This large
cell is too large for the nematodes to eat (dont expect all of the details; as long as the gist of
the idea is explained). Alternative 2 points: This stage uses the protective layer (cyst-like)
also. By this stage large size, cAMP as a communication signal, and sacrificing some cells
for the benefit of others have evolved

4 points: The asexual life cycle is even more complex, but uses the same signal, cAMP. In
asexual reproduction amoebas come together through the use of the cAMP signal to form a
facultatively multicellular organism that crawls to the surface of the soil where the organism
forms a complicated structure with a stalk and a globe where asexual spores are produced
and are protected by a protective cellulose covering. The facultatively multicellular
organism is also too large for the nematodes to eat. It is much more complicated than the
other stages described above and so expected to have evolved later (dont expect all of the
details; as long as the gist of the idea is explained). Alternative point: for example it can
sense light and heat and direct its movement. Alternative 2 points: The asexual life cycle
builds on the cAMP signal, the protective cyst-like layer, sacrifice of some cells, and large
size.
Name: ___________________________Lab Section __________________ 10/24/11
!+


b. Review the figure below. Explain how the flow of electrons from NADH and FADH
2
to oxygen
leads to the synthesis of ATP. Cyanides attach to the iron within cytochrome c oxidase (Complex IV)
and inhibit its activity. An uncoupler dissipates the proton gradient. Explain how these compounds
could act as metabolic poisons. Explain why an uncoupler would lead to a rise in body temperature.

6 points. As electrons are donated from NADH to complex I, complex I picks up a proton from
the matrix. As complex I donates the electron to ubiquinone, it releases the proton to the
intermembrane space. (1 alternatie point: FADH2 donates its electron at a lower energy level
than NADH, at complex II, and so no complex I is involved and no proton is transported at that
stage.) FADH2 donates its electrons at complex II. Electrons from complex II move to
ubiquinone. As electrons move from ubiquinone to complex III, once again a proton is picked
up from the matrix by complex III. As complex III donates the electron to cytochrome c, the
proton is delivered to the intermembrane space. As cytochrome c donates the electron to
complex IV and then from there the electron moves to reduce oxygen to water on the matrix side,
complex IV moves another proton from the matrix to the intermembrane space. Reduction of
oxygen to make water also removes protons from the matrix. These steps help to establish a
proton gradient with more protons in the intermembrane space than in the matrix.

2 Alternative points: When NADH and FADH2 donate their electrons, they release protons into
the matrix, which reduces the proton gradient across the inner membrane!

4 points: The proton gradient has potential energy that can be used to make ATP. (1 alternative
point: protons are charged and cannot cross the membrane on their own) If the protons are
allowed a passageway, then they will move down their electrochemical gradient. ATP synthase
allows such a passageway and as protons move back into the matrix, they release energy, which
is then used to drive ATP synthesis (2 alternative points: this reaction is endergonic, while
movement of protons down their gradient is exergonic).
Name: ___________________________Lab Section __________________ 10/24/11
!!


4 points. Cyanides inhibit the action of cytochrome c oxidase. This means that in the presence of
cyanide electrons cannot be taken by cytochrome c oxidase from cytochrome c. This stops the
flow of electrons at that point in the electron transport chain, which stops electron flow. If
electrons are not flowing, protons are not moving to the intermembrane space and no proton
gradient is established. Without a proton gradient no ATP is produced through oxidative
phosphorylation. When electron flow stops, then the cell has to rely on glycolysis alone.

4 points. Uncouplers dissipate the proton gradient across a membrane. This means that while
electron flow continues, no usable proton gradient is established. Therefore, no ATP is produced
through oxidative phosphorylation. Glycolysis, the Citric Acid Cycle, and Electron Transport
continue, yet little ATP is made. Every time electrons move from one complex to the next some
of their energy is released as heat. As the cell breaks down more and more glucose and more and
more electrons flow through the ETC to no avail, more and more heat is released and thus body
temperature rises.

2 points. Both uncouplers and cyanides can be metabolic poison because depending on the cell
type, glycolysis alone may not provide enough ATP and the cell could die.


Name: __________________________ Lab Section: ________________ 10/25/10

1
BIO 10100 Exam 2 Version 1 Answer Key
Prior to completing this exam, please read the following statement and sign below to indicate
that vou have read and understood the statement. !" $%&' ()** +$ ,-&.$. /0*$11 23$ 4*$.,$ )1
1),0$.5
I pledge that I have neither given nor received unauthorized assistance on this exam. I
understand that if I am charged with cheating, mv name will be submitted to the Dean for
disciplinary action.

__________________________________________________ _____________________
"#$% &#'%


Please make sure you have all 12 pages of the exam. Write your name and lab section on all
sheets. Please read each question carefully. If you do not understand the meaning or intention
of a question, please ask. Please pace yourself and use your time efficiently. Please put away
your cell phones, blackberries, iPods, etc.

For each multiple choice question please select the best answer. Each multiple choice or
True/False question is worth 2 points.

You will receive ZERO credit for any question for which we cannot tell what your final answer
is. If you erase or cross out an answer, please make it clear as to which answer is your final
answer. Please allow time for the essay type questions.

1. From the perspective of the cell receiving the message, the three stages of cell signaling are
A) signal transduction, local transport, and gene expression.
B) signal reception, signal transduction, and cellular response.
C) signal transduction, nuclear response, and gene expression.
D) signal reception, cellular response, and cell division.

2. (6 points) Ca
2+
is a secondary messenger in some signal transduction pathways. Ca
2+
pumps
actively transport Ca
2+
from the cytosol to either the extracelluar fluid or the cellular
organelles. Explain why it is important for the Ca
2+
pumps to reduce the concentration of
Ca
2+
in the cytosol.
For Ca
2+
to act as a secondary messenger the cytosolic concentration must be kept low so that the
release of calcium in response to a signal is recognized as a secondary messenger. If the
concentration of calcium is high to begin with, addition of a few more ions from the internal
reserves in response to a signal does not lead to a big change in concentration and would not be a
noticeable change in the cell (for example 5% concentration change). But if the internal
concentration is low, addition of a few ions would be a big change in relative concentration (for
example 50%) and that would be a noticeable change in the cell, and could be a useful way to
transmit a signal to cause a cellular response.






Name: __________________________ Lab Section: ________________ 10/25/10

2







3. Lipid-soluble signal molecules, such as testosterone, cross the membranes of all cells but
affect only target cells because
A) only target cells retain the appropriate DNA segments.
B) intracellular receptors are present only in target cells.
C) most cells lack the Y chromosome required.
D) only target cells retain the gene for the intracellular receptors.

4. Review Figure 11.8. A drug designed to inhibit the response of cells to testosterone would
almost certainly result in which of the following?
A) lower cytoplasmic levels of cAMP
B) an increase in receptor tyrosine kinase activity
C) a decrease in transcriptional activity of certain genes
D) an increase in cytosolic calcium concentration
E) a decrease in G-protein activity

5. See Figure 11.11. Phosphodiesterase catalyzes the reaction that turns cAMP into AMP. An
inhibitor of phosphodiesterase activity would have which of the following effects?
A) block the activation of protein kinase A in response to a signal
B) decrease the amount of cAMP in the cytoplasm in response to a signal
C) prolong the activation of G proteins in response to a signal
D) prolong the effect of a signal by maintaining elevated cAMP levels

Name: __________________________ Lab Section: ________________ 10/25/10

3

Figure 11.8 Figure 11.11

6. Which of the following is true for anabolic pathways?
A) They do not depend on enzymes as catalysts for reactions.
B) They are usually highly spontaneous chemical reactions.
C) They consume energy to build up polymers from monomers.
D) They release energy as they degrade polymers to monomers.

7. Which of the following types of reactions would decrease the entropy within a cell?
A) dehydration
B) hydrolysis
C) respiration
D) digestion
E) catabolism

The following questions are based on the reaction A + B C + D shown.

Name: __________________________ Lab Section: ________________ 10/25/10

4


8. Which of the following terms best describes the reaction?
A) endergonic
B) spontaneous
C) anabolic
D) allosteric

9. Which of the following would be the same in an enzyme-catalyzed or noncatalyzed reaction?
A) a
B) b
C) c
D) d
E) e

10. Which of the following represents the activation energy required for a catalyzed reaction?
A) a
B) b
C) c
D) d
E) e

11. Answer either a or b, not both:
a. Succinate dehydrogenase catalyzes the conversion of succinate to fumarate. The reaction is
inhibited by malonic acid, which resembles succinate but cannot be acted upon by succinate
dehydrogenase. Increasing the ratio of succinate to malonic acid (increasing the amount of
succinate for a constant amount of malonic acid) reduces the inhibitory effect of malonic
acid.
A) 2 points: Identify the substrate: Succinate
B) 2 points: Identify the product: Fumarate
C) 6 points. On the next page, graph the effects of substrate concentration on the rate of the
reaction catalyzed by succinate dehydrogenase in the presence of a constant amount of the
inhibitor (increasing ratio of substrate to inhibitor). Make sure to label the axes.
D) 2 points. Identify the dependent variable: Rate of reaction of succinate dehydrogenase
E) 2 points. Identify the independent variable: Substrate concentration (or ratio of substrate
to malonic acid)
F) 6 points. Explain why the inhibitory effect seen here is competitive instead of non-
Name: __________________________ Lab Section: ________________ 10/25/10

5
competitive.





Rate of reaction of
Succinate dehydrogenase








Substrate Concentration

The inhibitory effect is competitive because increasing the ratio of the substrate (succinate) to the
inhibitor (malonic acid) reduces the inhibitory effect of malonic acid. That means the substrate
and the inhibitor are competing for the binding site of the enzyme, and as more substrate is
present for a given amount of inhibitor, there is more chance that the substrate would be able to
successfully bind to the active site of the enzyme: compete more successfully.

b. The muscle M4 LDH enzyme in Fundulus fish has two subtypes (two different forms of
the same protein) produced by two different versions (alleles) of the same gene. One subtype
has an optimal temperature of 20C with a range of 15-25C (zero activity at temperatures
lower than 15 and higher than 25), while the other has an optimal temperature of 30C with a
range of 20-40C (zero activity at temperatures lower than 20 and higher than 40).
A) 8 points. On the next page, graph the temperature range / optima curves for these two enzyme
subtypes. Make sure to label the axes.
B) 2 points. Identify the dependent variable: Activity of M4 LDH
C) 2 points. Identify the independent variable: Temperature
D) 8 points. As you study the subtypes of this enzyme in different fish populations in the US
going from North to South, explain based on natural selection what subtypes you would
expect to find in these populations.
The northernmost population is expected to have the subtype with an optimal temperature of
20C, while the southernmost population is expected to have the subtype with an optimal
temperature of 30 C. As you sample populations going from north to south, you expect to
see a decrease in the prevalence of the 20C subtype in the population and an increase in the
prevalence of the 30C subtype in the population. The reason is that the warmer and warmer
climates select for the 30C subtype in the population. The fish with the 20C subtype will be
less efficient in performing the required tasks and thus their survival and reproductive rates
will suffer compared to the ones with the 30C subtype. Therefore, they will not pass on this
trait to the next generation as successfully as the fish with the 30C subtype and so the
stronger the effect of the environment is, the fewer the individuals in the population with the
incorrect subtype.
Name: __________________________ Lab Section: ________________ 10/25/10

6



Activity of
M4 LDH
Enzyme








15 20 25 30 35 40
Temperature (C)

12. Which of the following statements describes the results of the reaction below?
C
6
H
12
O
6
+ 6 O
2
6 CO
2
+ 6 H
2
O + Energy
A) O
2
is oxidized and H
2
O is reduced.
B) C
6
H
12
O
6
is oxidized and O
2
is reduced.
C) CO
2
is reduced and O
2
is oxidized.
D) C
6
H
12
O
6
is reduced and CO
2
is oxidized.

Refer to the figure below to answer the following questions.
The figure below illustrates some of the steps (reactions) of glycolysis in their proper sequence.
Each step is lettered. Use these letters (A, B, C, D, or E) to answer the questions.

13. 2 points. Which step represents the energy investment phase? A
14. 2 points. In which step is an inorganic phosphate added to the reactant? C
Name: __________________________ Lab Section: ________________ 10/25/10

7
15. 2 points. Which step consists of a phosphorylation reaction in which ATP is the phosphate
source? A

16. During glycolysis, when glucose is catabolized to pyruvate, most of the energy of glucose is
A) transferred to ADP, forming ATP.
B) transferred directly to ATP.
C) retained in the pyruvate.
D) stored in the NADH produced.

17. (4 points) Review the structure of pyruvate below. Pyruvate has to enter the mitochondria in
order to enter the citric acid cycle.
A) Will pyruvate easily cross the lipid bilayer membrane on its own? Yes/No (Circle the
appropriate choice).
B) This is because pyruvate is charged (polar) (Fill in the blank).

18. Review Figure 9.18 for lactic acid fermentation in the absence of oxygen. Fermentation must
be carried out or glycolysis will come to a halt. The reason is that fermentation
A) uses ATP and recycles ADP and Pi
B) uses NADH and recycles NAD+
C) synthesizes more ATP for the cell
D) synthesizes more NADH for the cell

Figure 9.18

Name: __________________________ Lab Section: ________________ 10/25/10

8

Figure 9.12
Review Figure 9.12 for the next two questions.
19. True/False. There is an enzyme inhibitor that blocks step 8 in the cycle. The overall effect
of this inhibitor is that since Oxaloacetate is not available, Acetyl CoA enters the cycle at a
different step.

20. (2 points) Mark the step that involves substrate-level phosphorylation.
Formation of ATP in step 5

21. Answer either a or b, not both.
a. Review figure 9.16 below.
i. (5 points) On the figure, mark the steps that contribute to the formation of the proton gradient
across the membrane.
ii. (5 points) Cyanides attach to the iron within cytochrome c oxidase (Complex IV) and inhibit
its activity. Explain how this could act as a metabolic poison.
iii. (6 points) What would addition of an uncoupler that dissipates the proton gradient do to ATP
synthesis through oxidative phosphorylation? Explain.
Name: __________________________ Lab Section: ________________ 10/25/10

9

Figure 9.16



Cyanides block movement of electrons in the ETC because they block the enzyme that takes an
electron from Cytochrome c. If no electrons are flowing, no protons will be moved to the
intermembrane space by complexes I, III, or IV. And no oxygen is reduced to make water,
which also helps to establish the proton gradient. Without the proton gradient, no ATP is
formed. And so the cell gets very little energy out of pyruvate. (The citric acid cycle comes to a
halt as well as fermentation does not happen in all cells). So, cyanide is a metabolic poison.

Addition of an uncoupler does not stop electron flow, but dissipates the proton gradient. Without
the proton gradient, no ATP is formed. So, while glycolysis and the citric acid cycle continue,
little ATP is formed from Pyruvate through electron transport.

b. Below is an excerpt from a set of research experiments.
i. (8 points) Identify the alternative and null hypotheses being tested.
Alternative hypotheses:
Exp 1: A proton gradient is required for ATP synthesis.

Exp 2: The protein ATP synthase is required for ATP synthesis.

Null hypotheses:
Exp 1: The presence of a proton gradient is not required for ATP synthesis.

Exp 2: The protein ATP synthase is not required for ATP synthesis.


ii. (4 points) What, if anything, is the control treatment in each experiment?
Name: __________________________ Lab Section: ________________ 10/25/10

10
Exp 1: The mitochondria that are kept in a test tube at pH 9 for the entirety of the
experiment.

Exp 2: The vesicles in test tube 2.

iii. (4 points) What are the conclusions for the two experiments?
Exp 1: ATP is synthesized in the presence of a proton gradient, but not in its absence.

Exp 2: ATP is synthesized in the presence of the ATP synthase (in the correct
orientation) but not in its absence.


EXPERIMENT 1:
Mitochondria are isolated from cells and placed in a medium at pH 9. This results in a low H
+

concentration on both sides of the inner mitochondrial membrane. Half of the mitochondria are
removed quickly to a neutral medium (pH 7) as shown in the figure. ATP is synthesized in these
mitochondria. The other half of the mitochondria are kept in a test tube at pH 9 (not shown in
the figure). No ATP is synthesized in these mitochondria.

EXPERIMENT 2:
A set of artificial vesicles is made and a bacterial proton pump is inserted into the membrane of
the artificial vesicles. The bacterial pump actively transports protons (H
+
) into the vesicles. This
establishes a large proton gradient across the vesicle membrane (more protons on the inside,
fewer protons on the outside). ADP and Pi are provided on the outside of the vesicle. No ATP is
synthesized. The vesicles are divided into two test tubes. ATP synthase from the mitochondria
of a mammal is inserted into the membrane of half of the artificial vesicles in the orientation
shown in the figure on the right below. These vesicles are placed in test tube 1. The vesicles
that do not have the ATP synthase inserted in their membrane are in test tube 2 (not shown).
There is ATP synthesis in test tube 1. There is no ATP synthesis in test tube 2.

Name: __________________________ Lab Section: ________________ 10/25/10

11

Experiment 1 Experiment 2


Name: __________________________ Lab Section: ________________ 10/25/10

12
22. 20 points. Answer either a or b, not both:
a. Consider the single cell amoebas, the sexual cycle, and the asexual life cycle of
Dictyostelium. What might be the evolutionary impetus (original drivingforce) for the
complex life cycle of Dictyostelium? What evolutionary sequence do we think might explain
the evolution of the life cycle of Dictyostelium? Explain the sequence and how each step
relates to the original driving force.
2 points: Evading the predatory nematodes might have been the evolutionary impetus for the
evolution of Dictyostelium.
4 points: We expect the sequence to go from a) forming a small cyst to b) forming a large
and protected cell through sexual reproduction to c) forming the complicated structure in
asexual reproduction. The reason is that this sequence goes from the simplest structure to the
most complex structures and evolutionarily it makes sense for the most complex steps to
have evolved later.
4 points: Individual Dictyostelium amoeba can turn into isolated cysts covering themselves in
a tough cellulose coating which allows them a chance to pass through a nematodes gut
without being digested. This is the simplest method.
2 points: However, a better way would be to avoid getting eaten altogether: a larger organism
that is too large for the nematodes to swallow would be the answer.
4 points: In sexual reproduction of Dictyostelium, two amoebas will fuse. They begin
sending out cAMP to their neighbors who then crawl toward the signal. The mating pair then
swallow the incoming amoebas and digest them. The cell grows very large and coats itself
with cellulose and turns dormant, waiting for the right conditions to germinate. This large
cell is too large for the nematodes to eat (dont expect all of the details; as long as the gist of
the idea is explained, give the points).
4 points: The asexual life cycle is even more complex, but uses the same signal, cAMP. In
asexual reproduction amoebas come together through the use of the cAMP signal to form a
facultatively multicellular organism that crawls to the surface of the soil where the organism
forms a complicated structure with a stalk and a globe where asexual spores are produced.
The facultatively multicellular organism is also too large for the nematodes to eat. It is much
more complicated than the other stages described above, and so expected to have evolved
later (dont expect all of the details; as long as the gist of the idea is explained, give the
points).
b. Ethylene is a plant hormone involved in fruit ripening in fruits such as tomatoes, bananas,
and apples. Ethylene is a gas and diffuses from its point of synthesis through air, and thus its
response is not limited to the cell or even the organism that produces it. Synthesis of
ethylene involves a multi-step pathway of several enzyme-catalyzed reactions, and is
promoted by oxygen and inhibited by CO
2
.
i. Explain how you can use apple peel to ripen your bananas.
5 points. Cells in the apple peel produce ethylene. Ethylene is a gas that diffuses
through air. If you keep apple peel and bananas in a semi-closed container so that
Name: __________________________ Lab Section: ________________ 10/25/10

13
ethylene can accumulate near the bananas and the high concentration of ethylene will
then cause ripening in the bananas.
ii. Explain how we can manipulate this enzymatic pathway to store apples for
several months.
5 points. Keep the apples in cold storage to slow down the enzymatic reactions
that normally lead to production of ethylene and ripening. Also, reduce the O2
concentration in the storage area and increase the CO2 concentration in the
storage area. O2 is needed for ethylene production and CO2 inhibits ethylene
production, so reducing O2 and increasing CO2 should lead to lowered ethylene
production and thus preserve the apples for a long time.

iii. Explain how we can manipulate this enzymatic pathway to ship green tomatoes
from CA to NY and buy red tomatoes in the grocery store in NY.
5 points. Tomatoes are picked green before they ripen and shipped from CA to
NY. While in shipment they are kept in cold storage with conditions similar to ii
above to prevent ripening. When they arrive in NY, they are removed from the
inhibitory conditions, and are gassed with ethylene to hasten their ripening.

iv. A genetically engineered tomato was developed that had a mutant gene for the
ethylene receptor in addition to the normal gene for the receptor. The cells of the
tomato fruits had 50% normal receptor proteins and 50% mutant receptor proteins
for the hormone ethylene. The mutant receptor proteins had a slightly modified
shape in their receptor site. Explain why these genetically engineered plants
would produce tomato fruits that would last longer on the grocery shelves before
they began to spoil.
5 points. The fruits have 50% normal receptor and 50% mutant receptor, and the
mutant receptor has a slightly different shape in its receptor site and does not bind
as well to the hormone ethylene because of it. That means that as ethylene is
produced by the fruit cells to begin the ripening process, only half of the ethylene
receptors respond to ethylene. The other half of the receptors do not cause
ripening response. This leads to a longer time required for ripening for the fruit.

Name: ___________________________Lab Section __________________ 10/29/12
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BIO 10100 Exam 2 Version 1
Prior to completing this exam, please read the following statement and sign below to indicate
that you have read and understood the statement. No exam will be graded unless the pledge is
signed.
I pledge that I have neither given nor received unauthorized assistance on this exam. I
understand that if I am charged with cheating, my name will be submitted to the Dean for
disciplinary action.

__________________________________________________ _____________________
Name Date

Please make sure you have all 12 pages of the exam. Please read each question carefully. If you
do not understand the meaning or intention of a question, please ask. Please put away your cell
phones, blackberries, iPods, laptop computers, etc., otherwise you will receive a grade of 0.
Please separate the last sheet from the rest of the exam. Write the answer to only the last
question on the last sheet. The last sheet is graded separately from the rest of the exam.
Each multiple-choice question is worth 2 points. Note that a correct statement is not necessarily
the best answer to a multiple-choice question. If a question states Select all that apply then
select all of the correct choices. For each multiple-choice question write the letter for the best
answer in the space provided (circling your answer, a !, or an x wont count). You will receive
ZERO credit for any question for which we cannot tell what your final answer is. If you cross
out an answer, please be clear as to what your final answer is.
Please pace yourself and use your time efficiently; allow time for the essay type questions. If a
question states Answer either a or b, not both: if you answer both, then we will read only the
answer to a, regardless of how much better your answer to b might be. Write your answers
using a pen. Answers written using pencils will not be graded.
2 Bonus Points: Write your name and lab section on all sheets.

For the next two questions refer to the following: Glycolysis is a multi-step enzymatic
pathway (9 steps) that starts with glucose and ends with pyruvate. The third step of this
pathway is the commitment step and is carried out by the enzyme phosphofructokinase,
which turns F6P into FBP. Pyruvate can then enter the mitochondria, where it is oxidized,
and then some of its carbons enter the citric acid cycle. The first product of the citric acid
cycle is Citrate. If there is excess citrate, meaning citrate is being produced more than it is
being used, then citrate can go to the cytosol where glycolysis occurs, and can bind to
phosphofructokinase at a site other than the active site. When that happens the reaction is
inhibited: the reactant cannot bind to the active site and the reaction cannot go forward. As
Citrate is used in the citric acid cycle, then the inhibition is removed and glycolysis can go
forward again.
1. Select all that apply. What kind of inhibition is described above?
a. Allosteric
b. Competitive
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c. Non-competitive
d. Feed-back
e. Catalytic
Answer: a, c, d
2. 10 points. You isolate phosphofruktokinase. In a test tube, you first add
phosphofruktokinase, then add F6P, and then you measure the rate of reaction as the rate of
synthesis of FBP (in g/s). You do this in multiple test tubes but use different concentrations
(in mM) of F6P from very low levels to very high levels in the different tubes, while you
keep everything else constant (standardized). In another batch of test tubes, you first add
phosphofruktokinase, then add a set (constant) amount of citrate to the test tubes, then add
different concentrations (in mM) of F6P from very low levels to very high levels (same as
you added in the first batch) in the different tubes, while you keep everything else constant
(standardized).
a. Use a line graph to show the effects of substrate concentration on the rate of the reaction
in the presence and absence of citrate. Make sure to label the axes appropriately.
b. What is the dependent variable? Rate of synthesis of FBP
c. What are the independent variables? Concentration of F6P, presence of citrate
















Concentration of F6P (mM)

_____ with citrate
_____ without citrate

3. Select all that apply: During a laboratory experiment, you discover that an enzyme-
catalyzed reaction has a !G of -20 kcal/mol. You double the amount of enzyme in the
reaction. The substrate level is not limiting the reaction rate (there is plenty of substrate
available).
a. The !G for the reaction will be -10 kcal/mol.
b. The !G for the reaction will be -40 kcal/mol.
Rate of
synthesis
of FBP
(g/s)
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c. The reaction will occur at a faster rate.
d. The rate of the reaction will not change.
e. The !G for the reaction will be -20 kcal/mol.
Answer: c, e

4. 8 points. Answer either a or b, not both:
a. Compare and contrast true multicellularity (for example in plants and animals) with
facultative multicellularity in Dictyostelium.
In both Dictyostelium and truly multicellular organisms such as plants and animals there is
division of labor among the cells that make up the multicellular stage and some cells are
sacrificed for the benefit of the others. However, while all of the cells in the truly
multicellular body (in an animal or a plant) derive from a single parent cell (the zygote) and
are genetically identical, the cells that make up the facultatively multicellular stage of
Dictyostelium are not genetically identical and they do not derive from the same parent cell;
each of these cells was a separate amoeba!

b. Explain why in cell-cell communication it is important for the Ca
2+
pumps to reduce the
concentration of Ca
2+
in the cytosol.
For Ca
2+
to act as a secondary messenger the cytosolic concentration must be kept low so that
the release of calcium in response to a signal is recognized as a secondary messenger. If the
concentration of calcium is high to begin with, addition of a few more ions from the internal
reserves in response to a signal does not lead to a big change in concentration and would not
be a noticeable change in the cell (for example 0.5% concentration change). But if the
internal concentration is low, addition of a few ions would be a big change in relative
concentration (for example 10%) and that would be a noticeable change in the cell, and could
be a useful way to transmit a signal to cause a cellular response. Keeping the internal
concentration low also creates a gradient that would allow external Ca
2+
to flow in when
there is a signal and a Ca
2+
channel opens in response to that signal. Also, since Ca
2+
is a
secondary messenger, it has to be removed from the cytoplasm for the response to end
otherwise the pathways turned on by the Ca
2+
would remain activated all the time.

5. Select all that apply: When you add a salt such as NaCl to an aqueous solution, it
dissociates into Na
+
and Cl
-
ions. Adding NaCl to a solution containing an enzyme (a
protein) may
a. Interfere with the peptide bonds
b. Interfere with covalent bonds
c. Change the shape of the enzyme
d. Disrupt its primary structure
e. Interfere with hydrogen bonds
Answer: c, e
6. 4 points. Dictyostelium can go through any of the stages listed below.
A. Facultatively multicellular, asexual life cycle
B. Sexual life cycle
C. Simple amoeba
D. Simple amoeba forming cysts
Name: ___________________________Lab Section __________________ 10/29/12
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In the space below write the order of the letters of the stages above to show the evolutionary
sequence that biologists think might explain the evolution of the life cycle of Dictyostelium.
From C to D to B to A.

The following questions are based on the reaction A + B ! C + D shown in the figure below.


7. The activation energy required for the reaction in the presence of enzymes is shown by __
and that for the same reaction in the absence of enzymes is shown by __.
a. a and e
b. b and c
c. a and b
d. c and e
e. d and d
Answer: b

8. The !G for the reaction in the presence of enzymes is shown by __ and that for the same
reaction in the absence of enzymes is shown by __.
a. a and e
b. b and c
c. a and b
d. c and e
e. d and d
Answer: e

9. Select all that apply: Ethylene is a plant hormone involved in fruit ripening in fruits such as
tomatoes, bananas, and apples. Synthesis of ethylene involves a multi-step pathway of
several enzyme-catalyzed reactions, and requires oxygen and is inhibited by CO
2
. Ethylene
is a gas and diffuses from its point of synthesis through air. Apples can be picked in the fall
and stored for several months without spoilage if
a. The storage area is kept cold
b. The O
2
concentration is kept high
c. The CO
2
concentration is kept high
d. The O
2
concentration is kept low
Name: ___________________________Lab Section __________________ 10/29/12
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e. The CO
2
concentration is kept low
f. The storage area is kept warm
Answer: a, c, d

10. Which of the following would be inhibited by a drug that specifically blocks the addition of
phosphate groups to proteins?
a. G-protein-linked receptor
b. ligand-gated ion channel
c. phosphatase activity
d. receptor tyrosine kinase
Answer: d

11. An inhibitor of which of the following could be used to block the release of calcium from the
endoplasmic reticulum?
a. tyrosine kinases
b. protein kinase C
c. phosphodiesterase
d. phospholipase C
e. adenylyl cyclase
Answer: d

12. In _______ signaling secreting cells act on nearby target cells by discharging a local
regulator.
a. autocrine
b. paracrine
c. endocrine
d. neuroendocrine
Answer: b

13. Below is an excerpt from a set of research experiments. For your answer use either
Experiment 1 or Experiment 2, not both.
Experiment 1: Mitochondria are isolated from cells and placed in a medium at pH 9. This
results in a low H
+
concentration on both sides of the inner mitochondrial membrane. Half of
the mitochondria are removed quickly to a neutral medium (pH 7) as shown in the figure.
ATP is synthesized in these mitochondria. The other half of the mitochondria are moved to a
test tube at pH 9 (not shown in the figure). No ATP is synthesized in these mitochondria.

Experiment 2: A set of artificial vesicles is made and a bacterial proton pump is inserted in
the membrane of the artificial vesicles. The bacterial pump actively transports protons (H
+
)
into the vesicles. This establishes a large proton gradient across the vesicle membrane (more
protons on the inside, fewer protons on the outside). The vesicles are divided into two test
tubes. ATP synthase from the mitochondria of a mammal is isolated and then inserted into
the membrane of half of the artificial vesicles in the orientation shown in the figure on the
right. These vesicles are placed in test tube 1. The vesicles that do not have the ATP
synthase inserted in their membrane are in test tube 2 (not shown). ADP and Pi are provided
Name: ___________________________Lab Section __________________ 10/29/12
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on the outside of the vesicles. There is ATP synthesis in test tube 1. There is no ATP
synthesis in test tube 2.


Experiment 1 Experiment 2
a. 2 points. What is the question being asked?
Exp 1: Is a proton gradient required (or is it enough) for ATP synthesis in mitochondria in the
absence of electron transport?

Exp 2: Is the protein ATP synthase required (or is the proton gradient not enough) for ATP
synthesis?

b. 2 points. What is the alternative hypothesis?
Exp 1: A proton gradient is required (or is enough) in the absence of electron transport for ATP
synthesis in mitochondria.

Exp 2: The protein ATP synthase is required (or proton gradient is not enough) for ATP
synthesis.

c. 2 points. What is the null hypothesis for the alternative hypothesis you wrote above?

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Exp 1: The presence of a proton gradient is not required (or is not enough) in the absence of
electron transport for ATP synthesis.

Exp 2: The protein ATP synthase is not required (or proton gradient is enough) for ATP
synthesis.

d. 2 points. What is the experimental prediction?
Exp 1: If isolated mitochondria are incubated in pH 9 solution to equilibrate to pH 9 and then
half are moved to a test tube at pH 7 to create a proton gradient across the cristae with more
protons on the outside and half are moved to a test tube at pH 9, then in the absence of electron
transport ATP will be synthesized by the mitochondria in the test tube at pH 7 but not by the
mitochondria in the test tube at pH 9.
Exp 2: If a proton gradient is created in artificial vesicles with the use of a bacterial proton pump,
and ATP synthases from mitochondria are inserted into half of the vesicle in the correct
orientation, then in the presence of the substrates ADP and Pi ATP will be synthesized by the
vesicles with ATP synthase (test tube 1) but not by the vesicles without ATP synthase (test tube
2).
e. 2 points. What is the control treatment for this experiment?

Exp 1: Keeping the mitochondria in a test tube at pH 9 for the entirety of the experiment.

Exp 2: Not adding the ATP synthase to the vesicles in test tube 2.


14. 6 points. Answer either a or b, not both:
a. Explain how the reception of a ligand by a G-protein coupled receptor leads to a cellular
response.
Binding of a ligand to the GPCR leads to a change in the shape of this receptor. The
activated receptor causes the associated G-protein to become activated through exchanging
its bound GDP for a GTP. The activated G-protein then dissociates such that the " subunit
with the attached GTP can move to the effector protein to cause it to become activated and
lead to a cellular response.
b. Among enzymes, kinases catalyze phosphorylation, while phosphatases catalyze removal of
phosphate(s). Explain how a cell's use of these enzymes can function as an on-off switch in
signal transduction involving phosphorylation cascades.
Adding phosphate groups with their negative charges changes the overall electrostatic
potential of the protein and leads to a change in the shape of the protein. Removing the
phosphate groups with their negative charges restores the original electrostatic potential and
shape of the protein. This back and forth change in the shape can be the on-off switch for the
proteins involved in the phosphorylation cascade in signal transduction pathways.



Name: ___________________________Lab Section __________________ 10/29/12
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15. Molecular oxygen (O=O) is polar and therefore cannot cross a lipid bilayer on its own.
a. True
b. False
Answer: b

16. A cell has a potential of -70 mV (negative inside). There is more K
+
inside the cell than
outside the cell. What can we conclude about the movement of K
+
in this case?
a. K
+
will enter the cell through channels via passive transport.
b. K
+
will exit the cell through channels via passive transport.
c. K
+
can enter the cell only through active transport.
d. K
+
can exit the cell only through active transport.
e. We need more information.
Answer: e

17. Select all that apply: A cell has a potential of -70 mV (negative inside). There is more NO
3
-

inside the cell than outside the cell. What can we conclude about the movement of NO
3
-
in
this case?
a. NO
3
-
will enter the cell through channels via passive transport.
b. NO
3
-
will exit the cell through channels via passive transport.
c. NO
3
-
can enter the cell only through active transport.
d. NO
3
-
can exit the cell only through active transport.
e. We need more information.
Answer: b and c

18. What do channels and carrier proteins have in common?
a. They require energy to transport solutes across a membrane.
b. They are involved in passive transport across a membrane.
c. They move solutes against a gradient across a membrane.
d. They change their shape as they move solutes across a membrane.
Answer: b

19. Select all that apply: The Na
+
/K
+
pump in animal cells is electrogenic because
a. It requires an ATP to move ions across the membrane.
b. It moves 2 positive charges into the cell and 3 out of the cell.
c. It helps to establish an electrical potential across the membrane.
d. It helps to establish a concentration gradient across the membrane.
Answer: b, c

20. 4 points. In the diagram of the citric acid cycle provided, the steps are numbered 1-8. Which
of the numbered steps involve redox (oxidation/reduction) reactions? List the numbers.
Answer: 3, 4, 6, 8

21. 2 points. In the diagram of glycolysis below, identify one step as the energy investment
phase and one step as the energy payoff phase. Write the appropriate letters below:
Energy investment phase: A
Energy payoff phase: D, E
Name: ___________________________Lab Section __________________ 10/29/12
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22. 4 points. In the diagram below, circle and identify the steps in electron transport that help
to remove protons from the matrix or help to add protons to the intermembrane space. Circle
and label them as add or remove.


23. Select all that apply: What do lactic acid fermentation and ethanol fermentation have in
common?
a. They oxidize glucose to CO
2
.
b. They oxidize NADH to NAD+.
c. They reduce NAD+ to NADH.
d. They allow glycolysis to continue in the absence of O
2
.
e. They produce 2 more ATP molecules than glycolysis alone.
f. They produce 2 more NADH molecules than glycolysis alone.
Answer: b, d

Some potentially useful figures:

hosphodlesLerase
cAM AM

Add
Add
Add
8emove
8emove
8emove
8emove
Name: ___________________________Lab Section __________________ 10/29/12
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12
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Name: ___________________________Lab Section __________________ 10/29/12
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Name: ___________________________Lab Section __________________ 10/29/12
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24. 20 points: Please write a short essay in response either a or b, not both. You are expected to write a
logically constructed answer; organization does count. You may wish to outline your answer first.
a. One of the major problems in the canning industry is the ability of Alicyclobacillus bacteria species to
spoil fruit juices. These bacteria can survive pH levels as low as 2.0 in their environment and inside
their cells. They are found in some soils and in certain springs. Some of their relatives, which also
live in soil or springs, cannot survive pH levels lower than 6.0. These organisms all have similar
enzymes in common (for example DNA polymerase) that perform the same functions. However,
there are small differences in amino acids that allow the enzymes from the different organisms to
function in their respective environments. Explain how changes in pH (both becoming more acidic
and becoming more basic) will affect the structure and function of proteins such as these enzymes and
why any given enzyme would have a pH range and a pH optimum. State the four tenets of Darwins
theory of descent with modification through natural selection and use them to explain how these
related bacteria populations that are thought to have descended from common ancestors have similar
proteins that are different enough to allow them to survive such different pH levels. Remember that
the amino acid sequences are coded for by the DNA, and any change in the amino acid sequence
reflects a change/mutation in the DNA.
3 alternative points. Changes in pH in a solution mean changes in the relative concentration
of hydroxide ions (OH
-
) and protons (H
+
). If the solution is acidic, there are more protons
than hydroxide ions. If the solution is basic, there are fewer protons than hydroxide ions. If
the solution is neutral, there are equal concentrations of both.

2 points. Hydrogen bonds are important in forming the shape of the protein as they are the
reason behind the secondary structure of a protein and are important in forming the tertiary
structure of the protein.
2 alternative points: if you mention alpha helices and beta pleated sheets.

3 points. The higher concentration of protons as a solution becomes more acidic or hydroxide
ions as a solution becomes more basic means that the full charges of these ions can interfere
with hydrogen bonds as a full charge of an ion is more likely to replace the partial charges
involved in a hydrogen bond and thus will disrupt the hydrogen bond.

2 alternative points: if you mention the partial positive charge of a hydrogen (resulting from a
polar covalent bond) in a hydrogen bond and the partial negative charge of an oxygen
(resulting from a polar covalent bond) in a hydrogen bond.

1 point. Therefore, proteins (such as enzymes) have an optimal pH at which the shape of the
protein is in its best form to carry out its function.

2 points. As the pH changes and the shape of the protein gets disrupted due to the interaction
of protons or hydroxide ions with the hydrogen bonds, the effectiveness of these enzymes
decreases until at a certain low pH and at a certain high pH the shape has been compromised
so much that the enzyme is no longer functional. Therefore, each enzyme has a pH range
beyond which it will not be functional.
1 alternative point: if you mention the enzyme is denatured beyond its pH range.

4 points. Here are the four tenets of Darwins theory of descent with modification through
natural selection:
Name: ___________________________Lab Section __________________ 10/29/12
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Living organisms produce more offspring than the environment can support, therefore
there will be competition for resources.
There is variation in the populations that could be the basis for adaptation.
Some variation is heritable and can be passed on from generation to generation
There will be differential survival AND reproduction: populations evolve by natural
selection of adaptive traits.

These 4 tenets help us to explain how these related bacteria populations that are thought to
have descended from common ancestors have similar proteins that are different enough to
allow them to survive such different pH levels.
2 points. All populations, including bacteria, reproduce too much, so the population gets
too big, more than the environment can support, which leads to competition among the
bacteria.
2 points. Some bacteria have proteins (such as the enzymes mentioned) that can
withstand more acidic environments while others do not: there is variation within the
ancestral bacteria population.
2 points. Some of this variation is due to differences in amino acids in the proteins,
which are coded in the DNA sequence due to some kind of mutation in the DNA and thus
heritable so that the bacteria that have the ability to survive acidic environments can pass
on this ability to the next generation.
2 points. The bacteria that have the ability to survive the acidic environments will be
better suited to survive there while the ones that do not will be restricted to less acidic
environments. This means better survival and reproduction and thus more individuals in
the next generation in the acidic environment to have this ability. However, there is no
advantage for the acid tolerant bacteria in the less acidic environments. Thus with each
passing generation the populations become more suited to their environments.

b. Consider the transport of pyruvate from the cytosol into the matrix of a mitochondrion. Explain why
there is a need for transport proteins to bring pyruvate across the membranes. Compare and contrast
the transport of pyruvate from the cytosol into the intermembrane space and that from the
intermembrane space into the matrix. Explain what would happen to the transport of pyruvate and its
concentration in the different compartments (the cytosol, the intermembrane space, and the matrix) if
an uncoupler is added to the matrix. Suppose there is a mutation that makes the outer membrane
channel 80% less efficient (80% fewer pyruvate molecules can enter). What will that mean for the
cell in terms of rates of the citric acid cycle and oxidative phosphorylation and ATP synthesis? How
about the rate of glycolysis? Explain.

2 points. Pyruvate is a negatively charged molecule. Therefore it cannot cross lipid bilayers
on its own. It will need the help of transport proteins.

4 points. Pyruvate is synthesized in glycolysis so there is a high concentration of pyruvate in
the cytosol when glycolysis occurs. (1 alternative point: As pyruvate is moved out of the
intermembrane space by the symporter, there is a low concentration in the intermembrane
space). The intermembrane space has a lot of protons with their positive charges as electron
transport across the cristae leads to movement of protons from the matrix into the
intermembrane space. (1 alternative point: The cytosol is usually negatively charged
Name: ___________________________Lab Section __________________ 10/29/12
16
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compared to the outside or to the intermembrane space). Thus the electrical potential and the
concentration gradient both favor passive transport of pyruvate into the intermembrane space.
This happens through a channel.

4 points. The proton gradient across the cristae (more in the intermembrane space, fewer in
the matrix) that is established through electron transport also means that the electrochemical
gradient for protons favors their movement back into the matrix. The symporter allows the
protons to move back in down their gradient, thus releasing energy, and this is coupled to the
movement of negatively charged pyruvate against its gradient from the intermembrane space
into the matrix.

2 points. If an uncoupler is added to the matrix, then the proton gradient is dissipated. If
there is no proton gradient, then protons will not be moving through the symporter.
Therefore, the symporter can no longer function to bring pyruvate into the matrix.
2 points. Pyruvate with its negative charge will accumulate in the intermembrane space and
fewer positively charged protons will be in the intermembrane space as well.
1 alternative point: This means the gradient for pyruvate from the cytosol into the
intermembrane space will disappear as well, and so pyruvate will not move from the cytosol
into the intermembrane space as easily.

4 points. If there is a mutation that makes the pyruvate channel less efficient, then pyruvate
will accumulate in the cytoplasm and in the matrix it will be used up and not replaced easily.
This means fewer acetyl-coA molecules will be available for the citric acid cycle, so fewer
NADH and FADH2 molecules will be produced and so the rate of electron transport will
drop and fewer ATP molecules will be produced as there will be fewer ATP from oxidative
phosphorylation and from the citric acid cycle.

2 points. The rate of glycolysis has to go up for the cell to produce enough ATP molecules to
survive to make up for what is missing from aerobic respiration.

2 alternative points: if you mention that fermentation has to happen to recycle the NAD+ so
that glycolysis can continue at high rates.



Name: ___________________________Lab Section __________________ 4/7/14
1
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BIO 10100 Exam 3 Answer Key
Prior to completing this exam, please read the following statement and sign below to indicate
that you have read and understood the statement. No exam will be graded unless the pledge is
signed.
I pledge that I have neither given nor received unauthorized assistance on this exam. I
understand that if I am charged with cheating, my name will be submitted to the Dean for
disciplinary action.

__________________________________________________ _____________________
Name Date

Please make sure you answer all 17 questions on the exam. Please read each question carefully.
If you do not understand the meaning or intention of a question, please ask. Please put away
your cell phones, blackberries, iPods, laptop computers, headphones, etc., otherwise you will
receive a grade of 0. Please separate the last sheet from the rest of the exam. Write the answer
to only the last question on the last sheet. The last sheet is graded separately from the rest of
the exam. Note that a correct statement is not necessarily the best answer to a multiple-choice
question. Each multiple-choice question is worth 2 points. If a question states Select all that
apply then select all of the correct choices. For each multiple-choice question write the letter
for the best answer in the space provided. Note: circling your answer, a , or an x wont count.
You will receive ZERO credit for any question for which we cannot tell what your final answer
is. If you cross out an answer, please be clear as to what your final answer is. Please pace
yourself and use your time efficiently; allow time for the essay type questions. If a question
states Answer either a or b, not both: if you answer both, then we will read only the answer
to a, regardless of how much better your answer to b might be. Write your answers using a
pen. Answers written using pencils will not be graded.
2 Bonus Points: Write your name and lab section on all sheets.

1. Review the figure provided. The researchers labeled the microtubules with a fluorescent dye.
They used a laser to remove the fluorescent label from one region to mark it. They
monitored the length of the labeled sections of the microtubules during the course of
anaphase. What is the question being asked? There are multiple alternative hypotheses
possible for this question. Write two logical alternative hypotheses for this experiment.
Write the experimental prediction for each alternative hypothesis. Draw the expected results
for each experimental prediction. Explain why they made a mark only on one side but not
the other.
2 points. Question being asked:
Where do the spindle fiber microtubules depolymerize during anaphase?

2 points. Alternative hypothesis 1:
The spindle fiber microtubules depolymerize at the kinetochores during anaphase.

2 points. Alternative hypothesis 2:
The spindle fiber microtubules depolymerize at the centrosomes during anaphase.
(Another alternative: The spindle fiber microtubules depolymerize at both the centrosome
end and the kinetochore end during anaphase).
Name: ___________________________Lab Section __________________ 4/7/14
2
1oLal olnLs: _____
2 points. Experimental Prediction for alternative hypothesis 1:
If we label the microtubules of the spindle fibers of a cell during anaphase with a fluorescent
dye, use a laser to remove the fluorescent label from one region to mark it, and monitor the
length of the labeled sections of the microtubules during the course of anaphase, we will
observe the labeled section between the mark and the kinetochore will get shorter while the
labeled section between the mark and the centrosome will remain the same length.

2 points. Experimental Prediction for alternative hypothesis 2:
If we label the microtubules of the spindle fibers of a cell during anaphase with a fluorescent
dye, use a laser to remove the fluorescent label from one region to mark it, and monitor the
length of the labeled sections of the microtubules during the course of anaphase, we will
observe the labeled section between the mark and the centrosome will get shorter while the
labeled section between the mark and the kinetochore will remain the same length.

2 points. Why they made a mark only on one side but not the other:
The other side serves as a control to make sure the laser treatment did not affect
depolymerization of the microtubules.

Draw the expected results in the empty boxes.





2 points. Expected results for alternative hypothesis 1


2 points. Expected results for alternative hypothesis 2
In this drawing, the yellow lines should not change in length on the right side of the mark and
should be shorter on the left side of the mark. Something like this:
Name: ___________________________Lab Section __________________ 4/7/14
3
1oLal olnLs: _____


2. Select all that apply: For every two turns of the PCO cycle, the plant
a. Loses two ATP molecules
b. Loses one ATP molecule
c. Loses two C as CO
2
molecules
d. Loses one C as a CO
2
molecule
e. Gains one NADH molecules
f. Loses one NADH molecules
g. Neither gains nor loses NADH
Answer: b, d, g

3. For every two turns of the PCO cycle, the plant
a. Salvages ! of the carbon atoms that would have been otherwise lost.
b. Salvages " of the carbon atoms that would have been otherwise lost.
c. Salvages two 2-C phosphoglycolates that would have been otherwise lost.
d. Salvages two PGA molecules that would have been otherwise lost.
Answer: a

4. Select all that apply: The oxygenation reaction by Rubisco
a. Could lead to a potential loss of 2C per turn
b. Could lead to a potential gain of 2C per turn
c. Is the first step of the Calvin (PCR) cycle
d. Produces a 6-carbon intermediate sugar
e. Splits RuBP into a 2C and a 3C compound
Answer: a, e

5. Select all that apply: The oxygenation reaction by Rubisco
a. Is the reason behind the oxygen evolving complex
b. Is as efficient as the carboxylation reaction by Rubisco
c. Becomes a bigger problem as temperature rises
d. Becomes a bigger problem in a drought
Answer: c, d

6. If a cell in interphase has 2N = 10 chromosomes, how many duplicated chromosomes will it
have during metaphase of mitosis? How many chromosomes will it have during anaphase of
mitosis? How many chromosomes will each daughter nucleus have after telophase?
a. 20, 10, 20
b. 10, 10, 5
c. 10, 10, 20
d. 10, 20, 10
Name: ___________________________Lab Section __________________ 4/7/14
4
1oLal olnLs: _____
e. 20, 20, 10
Answer: d

7. 8 points. In the diagram below, circle and identify where protons are being added to the
lumen or removed from the stroma to help establish a proton gradient. Identify them by
writing next to your circles: adding to the lumen or removing from the stroma.



8. 9 points. You isolate thylakoid membranes from a green plant. You place them in the
appropriate solution in test tubes and provide adequate light to all test tubes. The light
reactions are happening normally. You measure the amount of NADPH produced, the
amount of ATP produced, and the amount of oxygen produced while under constant light for
an hour. You repeat the experiment i) in the presence of DCMU (diuron), which competes
for the binding site of plastoquinone (PQ), ii) in the presence of dinitrophenol, which is an
uncoupler, and iii) with P680 artificially inhibited leading to cyclic electron flow only. In the
graphs below, the results for the first experiment (normal treatment) are shown. Draw the
expected results for the other three treatments.

0
1
2
3
4
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6
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Name: ___________________________Lab Section __________________ 4/7/14
3
1oLal olnLs: _____


9. Where does the Calvin cycle take place?
a. Cytoplasm of mesophyll cell
b. Outer membrane of the chloroplast
c. Stroma of the chloroplast
d. Thylakoid membrane
Answer: c

10. The first chemical reaction in PSII occurs when
a. LHC pigments pass their energy to P680
b. A LHC pigment absorbs light and is excited
c. OEC splits two water molecules
d. OEC donates an electron to P680
e. P680 donates an electron to Pheophytin
Answer: e

11. If photosynthesizing green algae are provided with CO
2
synthesized with heavy oxygen
(
18
O), later analysis will show that all but one of the following compounds produced by the
algae contain the
18
O label. That one is
a. RuBP
b. O
2

c. PGA (phosphoglycerate)
d. PGAL (glyceraldehyde phosphate)
e. Glucose
Answer: b

12. In the thylakoid membranes, what is the main role of the antenna (LHC) pigment molecules?
a. Harvest photons and transfer photons to the reaction-center chlorophyll
b. Harvest photons and transfer electrons to ferredoxin and then NADPH
c. Split water and release oxygen to the reaction-center chlorophyll
d. Harvest photons and transfer energy to the reaction-center chlorophyll
e. Harvest photons and transfer electrons to the reaction-center chlorophyll
normal
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Name: ___________________________Lab Section __________________ 4/7/14
6
1oLal olnLs: _____
Answer: d

13. 6 points. In the figure below circle and label/identify the 3 phases of the PCR (Calvin)
cycle. Each circle must include the reactants and the products for that step (you do not need
to label them as reactants and products).
Carboxylation, Reduction, Regeneration



14. 10 points. Answer either a or b, not both:
a. Review the figure showing the gradual increase in the concentration of carbon dioxide in
the atmosphere as measured in Mauna Loa. Explain why every year the concentration
rises and dips on a seasonal basis. Explain why the northern hemisphere seasons
dominate.
During the winter more fossil fuels are being burnt for heating and rates of photosynthesis
are lower due to dormancy or death of plants while during the summer less fossil fuel is
being burnt and rates of photosynthesis are higher due to more photosynthesis. Therefore the
CO
2
concentration oscillates with a maximum and minimum every year dominated by the
northern hemisphere. Since there are more people and more forests in the northern
hemisphere, the winter of the northern hemisphere dominates over the summer of the
southern hemisphere and so the maximum CO
2
concentrations are reached at the end of the
northern winter. For the same reason, the summer of the northern hemisphere dominates
over the winter of the southern hemisphere and the minimum CO
2
concentrations are reached
at the end of the northern summer.

Name: ___________________________Lab Section __________________ 4/7/14
7
1oLal olnLs: _____
b. Explain why it makes physiological sense for horizontally oriented leaves to have
stomata in the lower epidermis only.
Horizontally oriented leaves receive light from above. The light intensity is highest on the
top surface of the leaf. The palisade mesophyll cells are on the top side and are densely
packed and have a large number of chloroplasts. They have the highest demand for CO
2
.
The spongy mesophyll cells are on the lower side and are more shaded and are widely spaced
and have fewer chloroplasts. They have lower demand for CO
2
. The stomata are located on
the shaded side of the leaf, the lower side, and as they open to let in CO
2
, the gas will diffuse
down its gradient from the highest concentration outside the leaf through the stomata into the
leaf air spaces towards the sunny side of the leaf where the demand is the highest, and thus
all mesophyll cells have access to the incoming CO
2
. Having the stomata on the shaded and
thus cooler side also helps to minimize water loss as temperature affects vapor pressure,
which then drives diffusion of the gas. Therefore, it makes sense to have stomata on the
lower side in terms of both the requirement for CO
2
and the potential loss of water.

15. 10 points. The figure below shows onion root tip cells at various points in the cell cycle. For
each cell identify in which phase of the cell cycle it is by writing the small letters a, b, c, d,
or e designating the phase in the spaces marked as answer:
a. interphase, b. prophase, c. metaphase, d. anaphase, e. telophase / cytokinesis.

Answer: a Answer: c Answer: e Answer: b Answer: d

The data below were obtained from a study of the length of time spent in each phase of the cell
cycle by cells of three eukaryotic organisms designated beta, delta, and gamma.


Minutes Spent in Cell Cycle Phases

16. Of the following, the best conclusion concerning the difference between the S phases for beta
and gamma is that
a. Gamma contains 48 times more DNA than beta.
b. Beta is a plant cell and gamma is an animal cell.
c. Gamma contains more DNA than beta.
d. Beta and gamma contain the same amount of DNA.
e. Beta contains more RNA than gamma.
Answer: c



Name: ___________________________Lab Section __________________ 4/7/14
8
1oLal olnLs: _____
Some potentially useful figures:








8ublsco
1he CC Cycle
Name: ___________________________Lab Section __________________ 4/7/14
9
1oLal olnLs: _____

17. 20 points: Please write a short essay in response to either a or b, not both. You are
expected to write a logically constructed answer; organization does count. You may wish to
outline your answer first.
a. Opening of stomata is affected by various environmental factors. For example, stomata
typically open in response to light and close in darkness. They also open when the
concentration of CO
2
in the intercellular air spaces in the leaf falls, and they close when the
concentration rises. Some have argued that in a typical C3 plant like a bean (Phaseolus
vulgaris) increasing CO
2
concentration would lead to closure of stomata, which might mean
less water loss for the same amount of carbon gain as before. Others have argued that
increasing CO
2
concentration will lead to a higher carboxylation to oxygenation ratio and
thus a higher rate of carbon fixation by the plants for the same amount of water loss as
before. Design an experiment to test this. In your answer include all of the elements of
experimental design we have reviewed in class and lab, including the question being asked,
the two alternative hypotheses and their respective null hypotheses, the experimental details
including independent and dependent and standardized variables, levels of treatment, and
experimental predictions for both alternative hypotheses. You do not need to explain details
of the methods you would use to measure something as long as you mention what variable
will be measured for what purpose.
You need to include 20 of the following the points.

2 points. The question being asked here is what effect increasing CO
2
concentration will
have on the rate of carbon gain versus water loss for C3 plants?

2 points. One alternative hypothesis is that higher CO
2
concentration will lead to stomatal
closure and thus less water loss for the same amount of carbon gain as before.

2 points. The null hypothesis for hypothesis one is that higher CO
2
concentration will not
lead to stomatal closure and thus less water loss for the same amount of carbon gain as
before.
Name: ___________________________Lab Section __________________ 4/7/14
10
1oLal olnLs: _____

2 points. A second alternative hypothesis is that higher CO
2
concentration will lead to a
higher carboxylation to oxygenation ratio and thus a higher rate of carbon fixation by the
plants for the same amount of water loss as before.

2 points. The null hypothesis for hypothesis two is that higher CO
2
concentration will not
lead to a higher carboxylation to oxygenation ratio and thus a higher rate of carbon fixation
by the plants for the same amount of water loss as before.

Experimental procedure:
1 point. We would use several individuals of plant species Phaseolus vulgaris for each
treatment level to have a large sample size.
1 point. The experiment would have to be replicated multiple times.

4 points. We would grow the plants in growth chambers (or different greenhouses) and
divide them into at least two groups, all groups will share the standardized variables listed
below, but one group will be subjected to ambient CO
2
concentration (control = 400 ppm)
while the other group(s) will be subjected to higher CO
2
concentration (for example 600 or
800 ppm). CO
2
concentration is the independent variable with at least two levels of
treatment: ambient and high (or you could have multiple concentration levels).

Up to 4 points for standardized variables. Examples:
Age of plants should be the same.
Pot size should be the same.
Soil type / fertilizer use should be the same.
Light/dark cycle or amount of light should be the same.
Temperature should be the same.
Amount of water received by the plants should be the same.
The measurements are taken at the same time of day by the same person.
Any other reasonable variable you can think of.

2 points. The dependent variables are the amount of C gained and the amount of water lost:
you can measure both CO
2
uptake and water vapor loss by plants in closed chambers.

2 points. The experimental prediction for alternative hypothesis one is that when Phaseolus
vulgaris plants are grown in similar conditions some at ambient CO
2
concentration and
others at higher CO
2
concentration (400 versus 600 versus 800 ppm, for example), the plants
at higher CO
2
concentration will have less water loss for the same amount of carbon gained
compared to the plants grown at ambient CO
2
concentration.

2 points. The experimental prediction for alternative hypothesis two is that when Phaseolus
vulgaris plants are grown in similar conditions some at ambient CO
2
concentration and
others at higher CO
2
concentration (400 versus 600 versus 800 ppm, for example), the plants
at higher CO
2
concentration will have more carbon gain for the same amount of water loss
compared to the plants grown at ambient CO
2
concentration.

Name: ___________________________Lab Section __________________ 4/7/14
11
1oLal olnLs: _____
b. One of the problems with global climate change is the average rise in temperature of bodies
of water where rotifers grow. As temperature rises, solubility of gases such as O
2
changes
also. Gas concentrations in the surface of the body of water will be affected by exchange
with the atmosphere, which is affected by fluctuations in the air temperature. These
fluctuations in air temperature are becoming more and more severe and unpredictable as a
consequence of global climate change! Water temperature and gas concentrations in deeper
waters, however, will be more stable. Recall that rotifer eggs produced sexually are a
different color than eggs produced asexually. You want to find out whether what is
happening with fluctuations in gas concentrations in surface waters versus the stability in
deeper waters would affect the choice between sexual versus asexual reproduction in rotifers
such as Brachionus calyciflorus. Design an experiment to test this. In your answer include
all of the elements of experimental design we have reviewed in class and lab, including the
question being asked, two alternative hypotheses and their respective null hypotheses, the
experimental details including independent and dependent and standardized variables, levels
of treatment, and experimental predictions for each hypothesis.
You need to include 20 of the following the points.

2 points. The question being asked here is would fluctuations in gas concentrations in
surface waters or the stability in deeper waters affect the choice between sexual versus
asexual reproduction in rotifers such as Brachionus calyciflorus?

2 points. One alternative hypothesis is that rotifers living in areas with fluctuations in gas
concentrations will choose sexual reproduction proportionally more than rotifers living in
areas with stable gas concentrations.

2 points. The null hypothesis for alternative hypothesis one is that rotifers living in areas
with fluctuations in gas concentrations will not choose sexual reproduction proportionally
more than rotifers living in areas with stable gas concentrations..

2 points. A second alternative hypothesis is that rotifers living in areas with fluctuations in
gas concentrations will choose asexual reproduction proportionally more than rotifers living
in areas with stable gas concentrations.

2 points. The null hypothesis for alternative hypothesis two is that rotifers living in areas
with fluctuations in gas concentrations will not choose asexual reproduction proportionally
more than rotifers living in areas with stable gas concentrations.

(Another alternative hypothesis is that what is happening with fluctuations in gas
concentrations in surface waters versus the stability in deeper waters would affect the choice
between sexual versus asexual reproduction in rotifers. You would write a corresponding
null hypothesis and an experimental prediction for this hypothesis).

Experimental procedure:
1 point. We would use several populations of Brachionus calyciflorus for each treatment
level to have a large sample size.
1 point. The experiment would have to be replicated multiple times.
Name: ___________________________Lab Section __________________ 4/7/14
12
1oLal olnLs: _____

4 points. We would grow the rotifer species in tanks and divide them into at least two
groups, all groups will share the standardized variables listed below, but one group will be
subjected to stable CO
2
and O
2
concentrations while another group will be subjected to
fluctuating CO
2
and O
2
concentrations; this could be oscillating at certain times, or could be
random. You could further consider two stable groups; one stable at low levels, one stable at
high levels. You could also consider another group that will have access to areas with stable
gas concentrations as well as areas with fluctuating gas concentrations. The stability of the
gas concentration is the independent variable with at least two levels of treatment: fluctuating
and stable. Could have multiple levels, stable high, stable low, fluctuating, part fluctuating
and part stable, etc.

Up to 4 points for standardized variables. Examples:
Age of animals.
Tank size.
Nutrient levels.
Light/dark cycle or amount of light.
Temperature should be the same.
The duration of the experiment.
Any other reasonable variable you can think of.

2 points. The dependent variable is the proportion of eggs produced sexually versus
asexually based on egg color.

2 points. The experimental prediction for alternative hypothesis one is that when we grow
the rotifer species in tanks under similar conditions and we subject one group to stable CO
2

and O
2
concentrations while another group will be subjected to fluctuating CO
2
and O
2

concentrations (whatever you described above) then at the end of the duration of the
experiment there will be proportionally more sexually produced eggs as recognized based on
their color in the population with fluctuating gas concentrations than the other population
(depending on how many different treatment levels you included).

2 points. The experimental prediction for alternative hypothesis two is that when we grow
the rotifer species in tanks under similar conditions and we subject one group to stable CO
2

and O
2
concentrations while another group will be subjected to fluctuating CO
2
and O
2

concentrations (whatever you described above) then at the end of the duration of the
experiment there will be proportionally more asexually produced eggs as recognized based
on their color in the population with fluctuating gas concentrations than the other population
(depending on how many different treatment levels you included).

Name: ___________________________Lab Section __________________ 4/22/13
1
1oLal olnLs: _____
BIO 10100 Exam 3 Version 1
Prior to completing this exam, please read the following statement and sign below to indicate
that you have read and understood the statement. No exam will be graded unless the pledge is
signed.
I pledge that I have neither given nor received unauthorized assistance on this exam. I
understand that if I am charged with cheating, my name will be submitted to the Dean for
disciplinary action.

__________________________________________________ _____________________
Name Date

Please make sure you have all 14 pages of the exam. Please read each question carefully. If you
do not understand the meaning or intention of a question, please ask. Please put away your cell
phones, blackberries, iPods, laptop computers, etc., otherwise you will receive a grade of 0.
Please separate the last sheet from the rest of the exam. Write the answer to only the last
question on the last sheet. The last sheet is graded separately from the rest of the exam.
Note that a correct statement is not necessarily the best answer to a multiple-choice question.
Each multiple-choice question is worth 2 points. If a question states Select all that apply then
select all of the correct choices. For each multiple-choice question write the letter for the best
answer in the space provided. Note: circling your answer, a , or an x wont count. You will
receive ZERO credit for any question for which we cannot tell what your final answer is. If you
cross out an answer, please be clear as to what your final answer is.

Please pace yourself and use your time efficiently; allow time for the essay type questions. If a
question states Answer either a or b, not both: if you answer both, then we will read only the
answer to a, regardless of how much better your answer to b might be. Write your answers
using a pen. Answers written using pencils will not be graded.

2 Bonus Points: Write your name and lab section on all sheets.

1. Review the figure below. A set of artificial vesicles is made and bacterial proton pumps are
inserted in the membrane of the artificial vesicles. A bacterial pump actively transports
protons (H
+
) into the vesicle. This establishes a large proton gradient across the vesicle
membrane (more protons on the inside, fewer protons on the outside). The vesicles are
divided into two sets of test tubes. ADP and Pi are provided on the outside of the vesicles in
both sets. ATP synthase proteins from the mitochondria of a mammal are isolated and then
inserted into the membrane of the artificial vesicles in the orientation shown in the figure.
These vesicles are in test tube set 1. The vesicles in test tube set 2 (not shown in the figure)
do not have the ATP synthase inserted in their membrane. After a set amount of time, ATP
levels are measured in both test tube sets. The measurements are as follows as mean S.D.:

20 5 moles ATP in test tube set 1 but only 1 1 moles ATP in test tube set 2.
The researchers attribute the latter to sensitivity error in the measurements.

Name: ___________________________Lab Section __________________ 4/22/13
2
1oLal olnLs: _____

a. 2 points. What is the question being asked?
Is the ATP synthase needed to make ATP or is the proton gradient enough?
b. 2 points. What is one alternative hypothesis?
The ATP synthase is needed to make ATP; the proton gradient is not enough.

c. 2 points. What is the null hypothesis for the alternative hypothesis you wrote above?
The ATP synthase is not needed to make ATP; the proton gradient is enough.

d. 2 points. What is the experimental prediction based on the alternative hypothesis you
wrote above?
If we take artificial vesicles and insert bacterial proton pumps in the membrane of the
vesicles to create a proton gradient across the membrane and divide them into two sets and
add ADP and Pi to both sets and insert ATP synthases from the mitochondria of a mammal
into the membrane of the vesicles in one set but not the other, then we will observe ATP
synthesis in the set with the ATP synthase but not in the set without the ATP synthase.

e. 6 points. In the blank graph below, draw a column graph showing the results of this
experiment. Make sure to label the axes, including units where appropriate, and to
identify the treatments.




Name: ___________________________Lab Section __________________ 4/22/13
3
1oLal olnLs: _____


Means are represented by columns and standard deviations are represented by error bars.

f. 2 points. List 2 standardized variables in this experiment.
The set amount of time before ATP levels are measured, ADP and Pi provided to both
sets,
g. 2 points. What are the independent and dependent variables?
Independent: ATP synthase in the vesicle membrane
Dependent: Amount of ATP produced

2. 10 points. Match the stage of the cell cycle with the appropriate picture by writing the
corresponding letters in the blank spaces for the answer:
a. Interphase b. prophase c. metaphase d. anaphase e. telophase


Answer: c Answer: e Answer: d

Answer: b Answer: a
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30
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Name: ___________________________Lab Section __________________ 4/22/13
4
1oLal olnLs: _____
3. 8 points. Answer either a or b, not both:
a. Review the figure of the CO
2
concentrations as measured at Mauna Loa. Briefly describe
the reason that what happens in the Northern Hemisphere dominates over the Southern
Hemisphere in terms of the seasonal maxima and minima for the concentration of CO
2

measured.
Since there are more people and more forests in the Northern Hemisphere than in the
Southern Hemisphere, the winter of the Northern Hemisphere dominates over the summer
of the Southern Hemisphere and so the maximum CO
2
concentrations are reached then due
to increased use of fossil fuels and lower rates of photosynthesis by the plants in the north.
For the same reason, the summer of the Northern Hemisphere dominates over the winter
of the Southern Hemisphere and the minimum CO
2
concentrations are reached during the
summer of the Northern Hemisphere when there is less fossil fuel burning and higher rates
of photosynthesis.

b. Under normal conditions the ratio of carboxylation:oxygenation reactions carried out by
Rubisco in typical C3 plants is 3:1. How and why might a rise in the CO
2
concentration in
the atmosphere and the accompanying increases in temperature affect this ratio? Explain.
As the concentration of CO
2
increases in the atmosphere, the concentration in the air
spaces in the leaf and thus the stroma of the chloroplasts could potentially increase. This
would mean that the ratio of CO
2
to O
2
could increase and thus the ratio of carboxylation
to oxygenation could increase as Rubisco would have a better chance of binding with CO
2
than with O
2
. However, any increase in temperature that might accompany the changes in
concentration might negate these effects because as temperatures increase the solubility of
CO
2
decreases more than that of O
2
, and thus less CO
2
would be available in the stroma
compared to O
2
and thus the ratio of carboxylation to oxygenation would go down as
temperature increases. Thus, the two effects go in opposite directions, and the final
outcome is not easy to predict.

4. Consider a cell with 2N = 8 chromosomes. During metaphase of mitosis this cell will have
a. 8 chromosomes, each with 1 chromatid
b. 16 chromosomes, each with 1 chromatid
c. 8 chromosomes, each with 2 sister chromatids
d. 4 chromosomes, each with 2 sister chromatids
Answer: c

5. During anaphase of mitosis
a. Cohesins are cleaved and the centromeres split
b. Kinetochores form on either side of the centromeres
c. Homologous chromosomes find each other and pair up
d. Actin and myosin proteins form the cleavage furrow
Answer: a

Review the figure below. The researchers labeled the microtubules with a fluorescent dye. They
used a laser to remove the fluorescent label from one region to mark it. They monitored the
length of the labeled sections of the microtubules on either side of the mark during the course
of anaphase. Their results are shown.
Name: ___________________________Lab Section __________________ 4/22/13
3
1oLal olnLs: _____

6. 2 points. Fill in the blank: Based on their results they concluded that the microtubules
depolymerize at the kinetochore end.

7. 4 points. In the blank box labeled Expected Results, draw what the expected results would
look like if the microtubules depolymerized at both the centrosome and the kinetochore ends.



The researchers results Expected Results:
Your drawing must show that the microtubules on both sides get shorter and the chromosomes
move closer to the centrosomes, and that in the microtubules in the set on the left the labeled
section between the mark and the kinetochore and the labeled section between the mark and the
centrosome both get shorter.

8. Which process in an animal cell will proceed normally whether oxygen (O
2
) is present or
absent?
a. electron transport
b. glycolysis
c. the citric acid cycle
d. oxidative phosphorylation
e. chemiosmosis
Answer: b

9. Select all that apply: In cyclic electron flow in the thylakoid membranes electrons from
ferredoxin (Fd) move to plastoquinone (PQ). Therefore, cyclic electron flow includes:
a. Reduction of NADP
+
to make NADPH
b. Splitting of water to release molecular oxygen
c. Formation of a proton gradient across the thylakoid
d. Reduction of pheophytin (Pheo) by P680
e. Oxidation of PQH
2
by the Cytochrome complex
Answer: c, e

10. When does the first chemical reaction in a given photosystem occur?
a. When a pigment in the light harvesting complex donates an excited electron to the
reaction center Chl a
Name: ___________________________Lab Section __________________ 4/22/13
6
1oLal olnLs: _____
b. When the reaction center Chl a donates an excited electron to the first electron acceptor
molecule
c. When an excited pigment transfers energy through resonance energy transfer to another
pigment
d. When an electron is excited to a higher energy state and returns to its ground state
releasing energy
Answer: b

11. 6 points. Answer either a or b, not both:
a. Describe the costs and benefits of the salvage operation of the PCO cycle.
The salvage operation takes 2 molecules of phosphoglycolate (4 carbons) and salvages 3 of
the 4 carbons in the form of one molecule of PGA. In this process, one of the 4 carbons is
lost. This was a carbon the plant already had and is now lost. The salvage operation also
requires one ATP molecule, also a loss for the plant as ATP is lost without being used to
make new sugars for the plant. The benefit is that instead of losing 4 carbons, the plant only
loses 1 and salvages 3 of the 4. (Also, under certain conditions in the absence of CO2 and
the Calvin Cycle, recycling the ADP and Pi is beneficial to the plant).

b. Describe the major point of each phase of the PCR (Calvin) Cycle in one sentence.
Carboxylation: Carbon is added to the body of the plant when carbon dioxide is joined with
RuBP by the action of Rubisco.

Reduction: The 3C acid phosphoglycerate is reduced to the useful aldehyde form
glyceraldehyde-3-phosphate.

Regeneration: Five of the 3C aldehydes are used to regenerate 3 molecules of RuBP so that
the cycle can continue.

12. 4 points. It is possible to prepare vesicles from portions of the inner membrane of the
mitochondrial components and keep them in a well-aerated, aqueous solution. For oxidative
phosphorylation to be carried out by this isolated inner membrane with its protein complexes
intact, we must provide additional, required substrates. List these substrates:
a) NADH c) ADP
b) FADH
2
d) Pi

13. Select all that apply. The free energy for the oxidation of glucose to CO
2
and water is -686
kcal/mole and the free energy for the reduction of NAD
+
to NADH is +53 kcal/mole. Why
are only two molecules of NADH formed during glycolysis when it appears that as many as a
dozen could be formed?
a. Because most of the energy of glucose is released as heat.
b. Because glycolysis does not oxidize glucose down to CO
2
.
c. Because most the energy of glucose is retained in pyruvate.
d. Because the rest of the energy is stored in FADH
2
.
Answer: b, c

14. 8 points. Answer either a or b, not both:
Name: ___________________________Lab Section __________________ 4/22/13
7
1oLal olnLs: _____
a. Explain why horizontally oriented leaves have both palisade and spongy mesophyll cells
and have stomata on the lower side.
Horizontally oriented leaves receive light from above. Since light always comes from
above, it makes sense to pack most of the chloroplasts in the palisade mesophyll cells that
are tightly packed and have many chloroplasts and fewer chloroplasts towards the lower
side of the leaf as the light intensity is reduced as light passes through the leaf. The
palisade mesophyll cells have the highest demand for CO
2
while the spongy mesophyll
cells are more shaded and have lower demand for CO
2
. The stomata are on the lower
side and when they open to let in CO
2
, the gas will diffuse down its gradient from the
highest concentration outside the leaf through the stomata into the leaf air spaces towards
the sunny side of the leaf where the demand is the highest, and thus all mesophyll cells
have access to the incoming CO
2
. It is beneficial to have the stomata on the shaded and
thus cooler side to minimize water loss when they are open.

b. Review Engelmanns experiment. What was the big question being asked? What would
be a reasonable alternative hypothesis? What would be the null hypothesis for the
alternative hypothesis? What would be the experimental prediction based on the
alternative hypothesis you wrote?
Question: Is the rate of photosynthesis (or oxygen production due to photosynthesis)
affected by the wavelength of light?
One alternative hypothesis: The rate of photosynthesis (or oxygen production due to
photosynthesis) is affected by the wavelength of light.
Null hypothesis: The rate of photosynthesis (or oxygen production due to photosynthesis)
is not affected by the wavelength of light.
Experimental Prediction: If we illuminate a filament of an alga with light that has passed
through a prism, thus exposing different segments of the alga to different wavelengths of
light and add aerobic bacteria then we will observe that the bacteria will congregate along
certain sections of the alga more than others.

15. In the absence of oxygen, fermentation must be carried out for glycolysis to continue because
fermentation
a. Uses ATP and recycles ADP and Pi
b. Produces more ATP for the cell
c. Oxidizes pyruvate and recycles CO
2

d. Uses NADH and recycles NAD
+

Answer: d

16. Dinitrophenol is an uncoupler. If dinitrophenol is added to mitochondria then
a. The citric acid cycle will slow down
b. Electron transport will slow down
c. The rate of ATP synthesis will slow down
d. Reduction of oxygen to water will slow down
e. Oxidation of NADH to NAD
+
will slow down
Answer: c

Name: ___________________________Lab Section __________________ 4/22/13
8
1oLal olnLs: _____
17. Select all that apply: Cyanides attach to the iron within cytochrome c oxidase and inhibit its
activity. If cyanides are added to the mitochondria then
a. The rate of ATP synthesis will slow down
b. Electron transport will slow down
c. Reduction of oxygen to water will speed up
d. Oxidation of NADH to NAD
+
will speed up
Answer: a, b

18. Review the citric acid cycle. How many carbon atoms are fed into the citric acid cycle from
one molecule of glucose?
a. 2
b. 4
c. 6
d. 8
e. 10
Answer: 4

Some potentially useful figures:


Aerobic Bacteria



Filament of Alga

Blue Green Yellow Red

Theodor W. Engelmann illuminated a filament of an alga with light that passed through a prism,
thus exposing different segments of the alga to different wavelengths of light. He added aerobic
bacteria and then noted in which areas the bacteria congregated. A diagram showing the outcome
of the experiment is shown below.

Name: ___________________________Lab Section __________________ 4/22/13
9
1oLal olnLs: _____




Glycolysis
+ 4 P
+

2
Name: ___________________________Lab Section __________________ 4/22/13
10
1oLal olnLs: _____






Name: ___________________________Lab Section __________________ 4/22/13
11
1oLal olnLs: _____



Calvln Cycle
Name: ___________________________Lab Section __________________ 4/22/13
12
1oLal olnLs: _____


The PCO Cycle


Rubisco
Name: ___________________________Lab Section __________________ 4/22/13
13
1oLal olnLs: _____
19. 20 points: Please write a short essay in response to either a or b, not both. You are
expected to write a logically constructed answer; organization does count. You may wish to
outline your answer first.
a. In a multicellular organism what is beneficial for an individual cell may not be beneficial for
the whole organism. Explain what the major conflict is between individual cells and the
multicellular organism. What are cheater genes and what do they do? There are different
types of conflict mediators in a multicellular organism. What is a conflict mediator?
Describe two general types of conflict mediators and how they work.
You should include 20 of the following points:

5 points. The conflict lies in reproduction. Natural selection acts at the level of the individual
organism and the individual cell. The division of labor between somatic (body) cells and
germ (reproductive) cells works for the benefit of the whole organism. However, it means
that the lineage of somatic cells goes extinct when the whole organism dies, while the lineage
of the germ cells continues in the next generation.

5 points. Cheater genes make a somatic cell become a germ cell. The cheater gene might
bring so much reproductive success that more and more cells become germ cells, until
ultimately a colony or body has too few somatic cells to function. This would defeat the
whole advantage of multicellular organization and lead to a dead end. Another way is for a
cell to replicate madly. Instead of restraining themselves for the good of the colony, these
cheaters exploit their fellow cells for their own benefit, like cancer.

2 points. The conflict between individual cells and the entire body favors the evolution of
conflict mediators: genes that bring the interests of the cells and the body into line.

5 points. They might ensure that an organism develops from a single cell instead of a
package of cells. This would reduce the competition between the organisms cells because
they descend from a single common ancestor and there is no reason to cheat. Cheaters would
pay a higher evolutionary cost for betraying their fellow cells because they would be harming
genetically identical cells rather than strangers in a colony: reproduction of one is the same as
the reproduction of the others.

5 points. In other situations, conflict mediators might enforce the bodily peace by punishing
any cell that mutates into an unruly form. Our own cells are programmed to commit suicide
if they start dividing too rapidly; thanks to this mechanism, we suffer far lower rates of
cancer than we would otherwise. The genes that trigger this cellular suicide may have arisen
as our ancestors adapted to multicellularity.

5 points. If you describe the specific example of the Reg gene in Volvox instead.
The Reg gene prevents somatic cells from giving rise to germ cells. It does this by stopping
the growth and division process by curtailing a cells production of chloroplasts. Unable to
boost its level of photosynthesis, the cell cannot grow. Unable to grow, it cannot divide.
Unable to divide, it cannot give rise to germ cells.

Name: ___________________________Lab Section __________________ 4/22/13
14
1oLal olnLs: _____
b. Explain in your own words how the energy of the photons absorbed by the pigments in the
light harvesting complexes associated with PSI and PSII leads to the synthesis of O
2
, ATP,
and NADPH. In your answer follow the fate of the excited electrons and the protons and the
role of water. Explain what will happen to the processes you described above if an inhibitor
slows down the PCR (Calvin-Benson-Basham) Cycle.
You should include 20 of the following points:
1 point. As a photon of light is absorbed by the pigments in any of the LHCs, the energy of
the excited electron of the pigment is passed to another nearby pigment.
1 point. This is through resonance energy transfer.
1 point. This continues pigment to pigment until the energy reaches one of the Chl a
molecules in the reaction center for that photosystem.

2 points. When the reaction center Chl a in PSII is excited, the electron is passed on to the
first electron acceptor molecule Pheophytin. The Chl a then grabs an electron from the OEC.
2 points. After this process is repeated 4 times, the OEC will split 2 molecules of water and
replace the 4 electrons it has donated away.
2 points. This also leads to the release of oxygen, as well as 4 protons inside the lumen,
which helps establish a proton gradient across the thylakoid membrane.

2 points. As electrons move down the ETC, when PQ accepts electrons and then donates
them to the Cyt complex, it also picks up protons from the stroma and releases them inside
the lumen, which also helps to establish a proton gradient across the thylakoid membrane.

2 points. At the same time, when the Chl a in PSI is excited, it passes its electron down to the
ETC associated with PSI. Chl a then gets an electron from PC.
1 point: PC replaces the lost electron by getting an electron from the Cyt complex.

2 points. Meanwhile the electrons in the ETC associated with PSI go to Fd and eventually are
donated to help reduce NADP+ to NADPH.
1 point. This reaction removes a proton from the stroma, thus helping establish a proton
gradient as well as synthesizing NADPH.

1 point: 2 electrons are needed for this reaction.

2 points. As protons move down their gradient through ATP synthase, that movement
releases energy, which is used to synthesize ATP.

3 points. When an inhibitor slows down the Calvin Cycle, ATP and NADPH are used more
slowly and thus ADP and Pi and NADP+ are recycled back more slowly. This will slow
down electron transport.
3 points. However, since light absorption is not affected, the excited electrons of the
pigments in the LHC either will release more of their energy as heat or fluorescence than
previously, or the excitation energy may lead to damaging effects in the thylakoid
membranes.

Name: ___________________________Lab Section __________________ 7/25/11
"
BIO 10100 Final Exam Version 3
Prior to completing this exam, please read the following statement and sign below to indicate
that you have read and understood the statement. No exam will be graded unless the pledge is
signed.
I pledge that I have neither given nor received unauthorized assistance on this exam. I
understand that if I am charged with cheating, my name will be submitted to the Dean for
disciplinary action.

__________________________________________________ _____________________
Name Date

Please make sure you have all 16 pages of the exam. Please read each question carefully. If you
do not understand the meaning or intention of a question, please ask. Please pace yourself and
use your time efficiently.

Please put away your cell phones, blackberries, iPods, laptop computers, etc. Write your
answers using a pen. Answers written in pencil will not be accepted. Each multiple-choice
or True/False question is worth 2 points. Note that a correct statement is not necessarily the best
answer to a multiple-choice question. For each multiple-choice question, circle the best
answer. You will receive ZERO credit for any question for which we cannot tell what your final
answer is. If you cross out an answer, please make it clear as to which answer is your final
answer.

Please pace yourself and use your time efficiently; allow time for the essay type questions. If a
question states answer either a or b, not both: if you answer both, then we will read only the
answer to a, regardless of how much better your answer to b might be.
2 Bonus Points: Write your name and lab section on all sheets.

1. A geneticist introduces a transgene into yeast cells and isolates five independent cell lines in
which the transgene has integrated into the yeast genome. In four of the lines, the transgene is
expressed strongly, but in the fifth there is no expression at all.
True/False: A likely explanation for the lack of transgene expression in the fifth cell line is
that the transgene integrated into a heterochromatic region of the genome.

2. Skin cells and liver cells in one species of animal owe their differences in structure to
a) having different genes.
b) having different chromosomes.
c) having different genes expressed.
d) using different genetic codes.
e) having unique ribosomes.

3. 5 points. Answer either a or b, not both:
Name: ___________________________Lab Section __________________ 7/25/11
#
a) Review the figure below. Briefly explain how the albumin gene is expressed in the liver
cell and not the lens cell, while the crystalline gene is expressed in the lens cell and not
the liver cell.

Each cell type has only some activators
available. If the activator is the type that can
bind to the control elements in the enhancer,
then the gene is expressed. If the correct
activators that bind to the control elements are
not available in the cell, then the gene is not
expressed in that cell.




b) Review the figure below. Briefly explain how the presence or absence of tryptophan
affects synthesis of enzymes that lead to the production of tryptophan!

If there is no or little
tryptophan, then the
repressor is inactive and
does not bind to the
operator. That means the
RNA polymerase can bind
to the promoter and the
operon is transcribed and
the enzymes needed to
synthesize tryptophan are
produced.
If there is plenty of
tryptophan around, it will
bind to the repressor as a
corepressor and will
activate it. The active
repressor will bind to the operator and will prevent the RNA polymerase from
binding to the promoter. Therefore the operon is not transcribed, more copies of the
enzymes needed to synthesize tryptophan are not produced and tryptophan synthesis
drops.

Name: ___________________________Lab Section __________________ 7/25/11
$
4. Review the figure below. The question being investigated is: where do the microtubules
depolymerize and shorten as the chromosomes move to the opposite poles of the cell during
anaphase? There are several possible alternative hypotheses for this question. Their
hypothesis was that the microtubules depolymerize at the centromere (kinetochore) ends.

Figure 12.8: Gary Borisys lab used pig kidney cells. Labeled microtubules with fluorescent
dye. Used laser to remove label from one region to mark it. Monitored labeled
microtubule length during the course of anaphase.
2 points. What is the experimental prediction for this hypothesis?
If we take pig kidney cells and label the microtubules with fluorescent dye and use a laser
to remove the label from one region, then during anaphase the length of the fluorescently
labeled region between the mark and the centromeres shortens while the length of the
fluorescently labeled region between the aster end and the mark remains the same.

2 points. Did the data support the hypothesis? Explain.
Yes, since the length of the fluorescently labeled section between the mark and the
centromeres shortens (compare the middle to the bottom figures) while that between the
mark and the aster ends remains the same.

2 points. Why did they mark only one set of microtubules?
As a control to make sure the laser treatment did not have any adverse effects on the
movement of the chromosomes.

5. If a cell has 2N = 6 chromosomes at metaphase of mitosis, how many chromosomes will it
have during anaphase? How many chromosomes will each daughter nucleus have after
telophase?
a) 6 and 6
b) 6 and 12
c) 12 and 6
d) 3 and 6
e) 6 and 3

6. (3 points) The figure below shows onion root tip cells at various points in the cell cycle.
Identify and mark one cell in: A. interphase, B. prophase, C. anaphase.
Image source: http://www.microscopy-uk.org.uk/micropolitan/botany/mitosis_onion.jpg
Name: ___________________________Lab Section __________________ 7/25/11
%

Prophase Anaphase Interphase
7. 8 points. Answer either a or b, not both:
a) Use the chromosomes and genes shown below for a hypothetical organism and draw one
chiasma (one crossing over event only) during prophase I of meiosis and the new genetic
combinations that result from that crossing over event. Make sure to label the new
combinations versus the original parental combinations.

Red Brown
gene for eye color

Straight gene for wing shape Curled

Maternal Chromosome 1 Paternal Chromosome 1
First you must show the chromosomes have replicated, and mark the point of the chiasma!

Gene for eye color Red Brown

Centromere
For example
Gene for wing shape Straight Curled

Maternal Chromosome 1 Paternal Chromosome 1
Name: ___________________________Lab Section __________________ 7/25/11
&
New genetic combinations:

Gene for eye color Red Brown



Gene for wing shape Curled Straight

b) Consider independent assortment of chromosomes during Meiosis I. For an organism
with a diploid number of 2n = 6, draw out the 4 possible ways the chromosomes
might align during Metaphase I of Meiosis. Make sure the 3 homologous pairs are
identifiable as separate from each other. Make sure the maternal and paternal copies
are identifiable as such. The metaphase plate is drawn with the dotted line.

Possibility 1 Possibility 2






Pair of homologous chromosomes
(one is paternal, one is maternal)
Name: ___________________________Lab Section __________________ 7/25/11
'

Possibility 3 Possibility 4






8. If a cell has 2N = 6 chromosomes at metaphase I of meiosis, how many chromosomes will it
have during anaphase I of meiosis? How many chromosomes will each daughter cell have
during anaphase II of meiosis?
a) 6 and 6
b) 6 and 12
c) 12 and 6
d) 3 and 6
e) 6 and 3

9. A diploid cell (2N = 8) is going through meiosis. During anaphase 2 there is non-disjunction
for one chromosome in one cell. How many chromosomes will there be in the resulting
gametes?
a) 5, 5, 3, 3
b) 4, 4, 5, 3
c) 5, 5, 4, 4
d) 4, 4, 3, 3
e) 4, 4, 4, 3
f) 4, 4, 4, 5

10. 10 points. Compare and contrast the advantages and disadvantages of sexual versus asexual
reproduction.
Sexual reproduction requires two gametes to come together, which can be a cost: need to find
the other gamete, not always successful, and requires more energy and time than cloning
yourself. It produces genetic variability in the population, which can be a benefit if the
environment is changing as some of the new genetic combinations may have an advantage in
the new environment, but could be a cost if the environment is not changing. Asexual
reproduction does not require finding of a mate, which could be a benefit as it saves time and
energy that could be spent on other processes such as replication. It leads to production of
individuals that are genetically identical to the parent, which would be good if the
environment is not changing and the parent is perfectly well adapted to the environment, but
a bad thing if the environment is changing and the parent is not the best suited to the
environment.
Name: ___________________________Lab Section __________________ 7/25/11
(


11. The nucleotide sequence of a DNA piece being transcribed is
5TATAGGATGTATAGGAGGTGAAGG3
3ATATCCTACATATCC TCC ACTTCC5
A messenger RNA molecule with complementary codons is transcribed from the BOTTOM
strand of this piece of DNA.
a) 4 points. What is the nucleotide sequence of the mRNA corresponding to the sequence
provided?
5UAUAGGAUGUAUAGGAGGUGAAGG3
b) 2 points. Label the 3 and 5 ends on the mRNA.
c) 4 points. What is the Amino Acid sequence of the polypeptide that would be produced
from this mRNA if the ribosome starts translating from the start codon?
Starting with the start codon AUG marked above as the starting point and going to the UGA
stop codon also marked above:
Met-Tyr-Arg-Arg (Stop)


12. Introns are significant to biological evolution because
a) they correct enzymatic alterations of DNA bases.
b) they are translated into essential amino acids.
c) their presence allows exons to be shuffled.
d) they protect the mRNA from degeneration.
e) they maintain the genetic code by preventing incorrect DNA base pairings.

13. Review the figures below. In your own words describe the steps involved in translation.
Name: ___________________________Lab Section __________________ 7/25/11
)
a) 2 points. Initiation: The mRNA binds to the small ribosomal subunit, the first tRNA with
the attached Met comes in with a complementary anticodon for the start codon, the large
subunit attaches so that the initiator tRNA is in the P site.

b) 4 points. Elongation: The next tRNA with an anticodon complementing the codon in the
open A Site comes in, brings the next Amino Acid. The ribosome attaches the new
amino acid to the growing polypeptide and releases the tRNA from the P Site through the
E Site. The tRNA in the A site and the mRNA move to the P Site. There is a new codon
in the open A site. The process repeats as long as there are codons to be read.


c) 2 points. Termination: When a stop codon is present in the A site, a release factor enters
the A site. It helps the ribosome to release the polypeptide from the last tRNA. Then the
ribosome assembly comes apart and the mRNA is released.


Name: ___________________________Lab Section __________________ 7/25/11
*
14. Red-green color blindness is a sex-linked (X-linked) recessive trait in humans. A
male/female couple with normal color vision have a son who is color blind.
a) 4 points. What are the genotypes of the two parents?
Father: X
N
Y (N = normal, n = color blind)
Mother: X
N
X
n

b) 2 points. If this couple were to have a daughter, what would be the probability that the
daughter is a carrier for color-blindness?
The daughter will receive a normal allele from the father (X
N
) and so the egg determines
whether the daughter is a carrier. The chance is 50%.

Gene S controls the sharpness of spines in a type of cactus. Cactuses with the dominant
allele, S, have sharp spines, whereas homozygous recessive ss cactuses have dull spines. At
the same time, a second gene, N, determines whether cactuses have spines. Cactuses with the
dominant allele, N, have spines. Homozygous recessive nn cactuses have no spines at all.
For the nn cactuses, the sharpness gene (allele S or s) is irrelevant.

15. What type of progeny would be produced from a cross between a true-breeding sharp-spined
cactus (SSNN) and a spineless cactus (_ _ nn)?
a) all spineless progeny.
b) all sharp-spined progeny. (At least one S and one N, both dominant).
c) 50% sharp-spined, 50% dull-spined progeny.
d) 25% sharp-spined, 50% dull-spined, 25% spineless progeny
e) It is impossible to determine the phenotypes of the progeny.

16. 6 points. If doubly heterozygous SsNn cactuses were allowed to self-pollinate, what would
be the genotypes in the F2 generation? The phenotypic ratio of the F2 generation? Show
your work using a Punnett Square.

Gametes SN Sn sN sn
SN SSNN: sharp
spined
SSNn: sharp
spined
SsNN: sharp
spined
SsNn: sharp
spined
Sn SSNn: sharp
spined
SSnn: no spines SsNn: sharp
spined
Ssnn: no spines
sN SsNN: sharp
spined
SsNn: sharp
spined
ssNN: dull
spined
ssNn: dull
spined
sn SsNn: sharp
spined
Ssnn: no spines ssNn: dull
spined
Ssnn: no spines

9 Sharp spined : 4 no spines: 3 dull spined

17. 12 points. Answer either a or b, not both.
a) Hershey and Chase wanted to find out what the genetic material was that bacteriophage
viruses used when they infected bacteria. To answer this question, they carried out two
experiments. They cultured the phages with either radioactive sulfur (Exp 1) or
radioactive phosphorus (Exp 2). They mixed the labeled phages with bacteria, allowed
the phages to infect the bacterial cells, then agitated the mixture in a blender to separate
Name: ___________________________Lab Section __________________ 7/25/11
"+
what was left outside the bacteria cells from the bacteria cells, then centrifuged the
mixture so that bacteria formed a pellet at the bottom, and the parts of the phages that had
not entered the bacteria cells were in the supernatant, then measured the radioactivity in
the pellet and the supernatant. What are the alternative hypotheses being tested? What
are the experimental predictions based on these hypotheses?


Exp
1




Exp
2

Alternative hypothesis 1:
DNA is the genetic material used by the bacteriophage viruses.
Experimental prediction for alternative hypothesis 1 for experiment 1:
If the proteins are labeled with radioactive sulfur, and the phages infect bacterial cells
and then the cells are separated from what is left outside through agitation, and the
cells are collected in a pellet through centrifugation, in the final extraction the
radioactive sulfur ends in the supernatant.
Experimental prediction for alternative hypothesis 1 for experiment 2:
If the DNA is labeled with radioactive phosphorus, and the phages infect bacterial
cells and then the cells are separated from what is left outside through agitation, and
the cells are collected in a pellet through centrifugation, in the final extraction the
radioactive phosphorus ends in the pellet.
Alternative hypothesis 2:
Proteins are the genetic material used by the bacteriophage viruses.

Name: ___________________________Lab Section __________________ 7/25/11
""
Experimental prediction for alternative hypothesis 2 for experiment 1:
If the proteins are labeled with radioactive sulfur, and the phages infect bacterial cells
and then the cells are separated from what is left outside through agitation, and the
cells are collected in a pellet through centrifugation, in the final extraction the
radioactive sulfur ends in the pellet.
Experimental prediction for alternative hypothesis 2 for experiment 2
If the DNA is labeled with radioactive phosphorus, and the phages infect bacterial
cells and then the cells are separated from what is left outside through agitation, and
the cells are collected in a pellet through centrifugation, in the final extraction the
radioactive phosphorus ends in the supernatant.
b) Meselson and Stahl wanted to find out whether the conservative, the semi-
conservative, or the dispersive models are the correct way to explain how DNA is
replicated. To answer this question, they cultured E. coli bacteria for many
generations in a medium containing nucleotides labeled with a heavy isotope of
nitrogen. They then transferred the bacteria to a medium with only the light isotope
of nitrogen. Two DNA samples were taken from this culture: one at 20 minutes after
one round of replication by the bacteria, and a second one at 40 minutes after a
second round of replication by the bacteria. They extracted DNA from the bacteria
and centrifuged it and could distinguish the density of the extracted DNA through this
method. For each of the 3 alternative hypotheses, describe the experimental
predictions after both the first and the second rounds of replication. Explain which
model is supported by the data.
Experimental predictions for
Conservative model:
If bacteria are grown in heavy N for many generations and then allowed to grow in
light N for just one generation, then half of the daughter cells will have heavy N DNA
(parental) and half of the daughter cells will have light N DNA (all new), leading to 2
bands in the centrifuge tubes. If the cells are allowed to divide for a second time,
since the original heavy N DNA would always remain heavy and all of the new DNA
would be light, after the second division, following centrifugation again there will be
2 bands in the centrifuge tube.
Semiconservative model:
If bacteria are grown in heavy N for many generations and then allowed to grow in
light N for just one generation, then all of the daughter cells will have DNA that has
one strand made of heavy nucleotides and one strand made of light nucleotides,
leading to 1 band in the centrifuge tube. However, if the bacteria are grown for a
second generation, then half of the daughter cells will have DNA made of only light
DNA while half will have DNA that has one strand made of heavy nucleotides and
one strand made of light nucleotides, leading to 2 bands in the centrifuge tube.
Name: ___________________________Lab Section __________________ 7/25/11
"#
Dispersive model:
If bacteria are grown in heavy N for many generations and then allowed to grow in
light N for just one generation, then all of the daughter cells will have DNA
molecules made of a mixture of heavy and light nucleotides leading to one band in
the centrifuge tube. Every generation in the light N would lead to lighter and lighter
DNA, but always one band in the centrifuge tube.
Correct model? Why?
The results of the first replication eliminate the conservative model (2 bands
predicted, only one observed), and the results of the second replication eliminate the
dispersive model (one band predicted, but two observed). The semi-conservative
model is supported (predictions match observations).

18. If gender determination is based on chromosomal genes alone, then what would be the
gender of the following humans: XO and XXY
a) Female, male
b) Female, hermaphrodite
c) Hermaphrodite, Male
d) Hermaphrodite, hermaphrodite

19. The following is a map of four genes on a chromosome. The units are CentiMorgans.
Between which two genes would you expect the highest frequency of crossing over?
Name: ___________________________Lab Section __________________ 7/25/11
"$

a) A and G
b) A and W
c) W and E
d) E and G
e) A and E

20. Guanine (G) makes up 36% of the nitrogenous bases in a sample of DNA from an organism.
Approximately what percentage of the nitrogenous bases in this sample will be Thymine (T)?
a) 14
b) 28
c) 36
d) 72
e) It cannot be determined from the information provided.

21. The leading and the lagging strands differ in that
a) the lagging strand is synthesized continuously, whereas the leading strand is synthesized
in short fragments that are ultimately stitched together.
b) the leading strand is synthesized in the same direction as the movement of the replication
fork, and the lagging strand is synthesized in the opposite direction.
c) the leading strand is synthesized by adding nucleotides to the 3' end of the growing
strand, and the lagging strand is synthesized by adding nucleotides to the 5' end.
d) the leading strand is synthesized at twice the rate of the lagging strand.

22. A new DNA strand elongates only in the 5' to 3' direction because
a) DNA polymerase can only add nucleotides to the free 3' end.
b) DNA polymerase begins adding nucleotides at the 5' end of the template.
c) Okazaki fragments prevent elongation in the 3' to 5' direction.
d) the polarity of the DNA molecule prevents addition of nucleotides at the 3' end.
Name: ___________________________Lab Section __________________ 7/25/11
"%
e) replication must progress toward the replication fork.

23. What is the role of helicase during DNA replication?
a) stabilize the unwound parental DNA
b) synthesize RNA nucleotides to make a primer
c) catalyze the lengthening of telomeres
d) join Okazaki fragments together
e) unwind the parental double helix



Name: ___________________________Lab Section __________________ 7/25/11
"&

24. 20 points. Answer either a or b, not both. You are expected to write a logically constructed
answer; organization does count. You may want to outline your answer first.
a) Consider the genetic code: on any mRNA molecule that is transcribed from a gene, each
sequence of 3 nucleotides usually codes for one amino acid. See the genetic code table
provided. Describe what is meant by a mutation. Why are some mutations harmless?
Why are some mutations harmful? Why are some more harmful than others? What does
a mutation do to the mRNA? To the final product? Explain your answer and provide
simple examples that illustrate what you describe.
3 points. A mutation is any change in the nucleotide sequence of the DNA.

3 points. Mutations in the DNA sequences may or may not necessarily affect mRNAs. If a mutation
occurs in the non-coding regions of the DNA, then it will have no effect on the mRNA. If it occurs in
coding regions, then it may affect the mRNA. 2 Alternative points: In a Eukaryote, mutations in introns
again will not affect the mRNA, while mutations in exons will change the corresponding nucleotide
sequence in the mRNA (unless they affect the splice site: one more alternative point). 1 more alternative
point: a mutation in the non-coding, but regulatory region of DNA may affect transcription of a gene!

6 points. Mutations that change the nucleotide sequence in the mRNA may or may not necessarily affect
the final product: the polypeptide. If the mutation is a substitution in the third nucleotide of an mRNA
codon, then the chances that it will affect the final product are very low due to the redundancy of the
genetic code. For example, if a mutation changes a codon from CUU to CUC, the translated polypeptide
will still contain the amino acid Leu (Leucine) at this position so there is no effect on the final product.
Such mutations are silent mutations as they cause no changes in the amino acid sequence and they are
harmless. It is possible that a mutation in a codon causes a change in the amino acid without affecting the
function of the protein as the change may not affect the shape and thus the function of the protein. Such a
mutation would be harmless as well. If the change in the amino acid affects the shape of the protein in a
way that it interferes with its function, then that would be a harmful mutation.

4 points. Some mutations have the potential to be much more harmful than others because they affect
more than just one amino acid. For example, if a mutation changes a codon for an amino acid to a stop
codon (for example UAC to UAG), what is called a nonsense mutation (one alternative point if know the
name), then the final polypeptide synthesized from this mutated mRNA will be truncated. This could
have devastating effects on the organism. 1 alternative point: if know the name frame shift.

4 points. Another example of a simple mutation that could have devastating effects is the addition or
deletion of one or two nucleotides in the sequence. This type of frame-shift mutation changes all of the
codons downstream from the point of the mutation and can change the entire sequence of amino acids in
the polypeptide. This could result in a completely different polypeptide with very different properties,
which could have devastating consequences. For example, the coding sequence could change from UUU
UUA CUU (Phe-Leu-Leu- ) to UUA UUU ACU U (Leu-Phe-Thr-) simply by the addition of
one nucleotide (A) after the second U. The shift in the reading frame changes the amino acids
completely. Alternative point: sometimes frameshift mutations are nonsense mutations (stop codon
forms)!

Name: ___________________________Lab Section __________________ 7/25/11
"'
b) What does the organizational concept of sexuality entail? Explain. Why does the
organizational concept fail to explain vertebrate sexuality? Explain. Describe two
different modes of sex determination that illustrate why the organizational concept fails
to explain vertebrate sexuality. Explain what the evolutionary view of sexuality is as
opposed to the organizational concept. Describe one piece of evidence (discussed by
David Crews) in support of the evolutionary view.

4 points: According to the organizational concept, the gender and sexual characteristics of the organism
are ultimately determined by the chromosomes. The animals gonads is determined at the time of
conception by the chromosomes inherited from the parents. The gonads produce sex hormones that sculpt
the sexual features.

2 points. The organizational concept fails to explain vertebrate sexuality because many vertebrates lack
sex chromosomes and depend on non-genetic triggers to determine gender.

4 points. One mode of sex/gender determination that does not rely on sex chromosomes is temperature-
dependent sex/gender determination. In these cases, the temperature at which the embryo develops
governs the animals sex ratio. 1 alternative point: this is an all-or-nothing event; does not lead to
formation of hermaphrodites in intermediate temperatures, for example. 2 Alternative points if an
example is described such as leopard gecko (low and high T produce females, intermediate yields males).

4 points. Another mode of sex/gender determination that does not rely on sex chromosomes is behavior-
dependent sex/gender determination. In most cases, they are hermaphrodites, and the social environment
controls whether the individual takes on a male or female role. Some are sequential hermaphrodites
changing from one sex to another (alternative point: but only expressing one sex at any given time).
Some are simultaneous hermaphrodites. 2 Alternative points if an example is described such as anemone
fish (born male, later develop into females) or certain coral reef fish (start female, later develop into males
in response to disappearing dominant males) or simultaneously hermaphroditic butter hamlet fish
(alternate between male and female behavioral roles during successive matings).

2 points. In the scenario described by the organizational concept males are the organized sex and the
females are the default sex: 2 alternative points: If there are testes, then they produce androgens (male
hormones) that lead to male characteristics. If there are no testes, then ovaries develop, leading to female
hormones, leading to female characteristics.

2 points: In the evolutionary view of sexuality, males are considered to have evolved only after the
evolution of the first self-replicating, female organisms (same as saying the female is the ancestral sex
and the male the derived sex).

2 points: Examples of pieces of evidence in support of the evolutionary view, need to describe one only:
a) Fish species that are born male and become female nevertheless pass through a modified ovarian
stage before developing testes.
b) In some species testosterone is converted to estrogen in the brain, and estrogen activates both
copulatory behaviors in males and sexual receptivity in females.
c) In songbirds, estrogen originates primarily in the brain, suggesting that it transcends gender
boundaries.
d) Male rats and humans show a pronounced daily rhythm in progesterone secretion, peaking at the
onset of night, when copulatory behavior most often occurs.
e) Doses of the female hormone progesterone can induce castrated rats to resume mounting.
f) RU486, which nullifies progesterone (the female hormone) reduces sexual behavior in male rats.
Name: ___________________________Lab Section __________________ 11/21/11
!

BIO 10100 Exam 1 Version 1
Prior to completing this exam, please read the following statement and sign below to indicate
that you have read and understood the statement. No exam will be graded unless the pledge is
signed.
I pledge that I have neither given nor received unauthorized assistance on this exam. I
understand that if I am charged with cheating, my name will be submitted to the Dean for
disciplinary action.

__________________________________________________ _____________________
Name Date


Please make sure you have all 12 pages of the exam. Write your name and lab section on all
sheets. Please read each question carefully. If you do not understand the meaning or intention
of a question, please ask. Please pace yourself and use your time efficiently. Please put away
your cell phones, blackberries, iPods, laptop computers, etc.

Please separate the last sheet from the rest of the exam. Write the answer to only the last question
on the last sheet. The last sheet is graded separately from the rest of the exam.

Each True/False or multiple-choice question is worth 2 points. Note that a correct statement is
not necessarily the best answer to a multiple-choice question. For each multiple-choice question
write the letter for the best answer in the space provided (circling your answer, a !, or an x
wont count). You will receive ZERO credit for any question for which we cannot tell what your
final answer is. If you cross out an answer, please be clear as to what your final answer is.

Please pace yourself and use your time efficiently; allow time for the essay type questions. If a
question states answer a or b, not both: if you answer both, then we will read only the answer
to a, regardless of how much better your answer to b might be. Write your answers using a
pen. Answers written using pencils will not be graded.

1. What is the role of cohesin proteins in cell division?
a. They organize the chromosomes into highly condensed structures
b. They hold the sister chromatids together at the centromere
c. They help the cell to divide into two daughter cells
d. They connect microtubules and chromosomes
Answer: b
2. The kinetochore is a structure that functions to
a. Connect the centromere to microtubules
b. Connect centrioles to microtubules
c. Aid in chromosome condensation
Name: ___________________________Lab Section __________________ 11/21/11
#

d. Aid in chromosomes cohesion
Answer: a
3. Separation of the sister chromatids occurs during which phase of mitosis?
a. Prophase
b. Metaphase
c. Anaphase
d. Telophase
Answer: c
4. Which of the following does not contribute to genetic diversity?
a. Independent assortment
b. Recombination
c. Metaphase of Meiosis II
d. Metaphase of Meiosis I
Answer: c
5. Which phase of meiosis I is most similar to the comparable phase in mitosis?
a. Prophase I
b. Metaphase I
c. Anaphase I
d. Telophase I
Answer: d
6. Crossing over involves all of the following except
a. The activity of the recombination nodule
b. The transfer of DNA between two sister chromatids
c. The formation of a synaptonemal complex
d. The alignment of homologous chromosomes
Answer: b
7. What occurs during anaphase of meiosis II?
a. The homologous chromosomes align
b. Sister chromatids are pulled apart to opposite poles
c. Homologous chromosomes are pulled apart to opposite poles
d. The haploid chromosomes line up
Answer: b
8. Consider a diploid cell with six chromosomes.
a. 4 points. Draw the cell with the homologous pairs of chromosomes during metaphase of
meiosis I showing how these chromosomes would arrange themselves during metaphase
of meiosis I. Distinguish the chromosome pairs (either number them or make sure they
are different lengths, for example). Make sure that each member of the pair is
distinguishable as maternal (M) or paternal (P). Draw only one possibility. How many
other possibilities can you draw? Answer: 3 (dont draw them all!)
Name: ___________________________Lab Section __________________ 11/21/11
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a. Cell going through meiosis: Any of the following would do; blue = paternal, red
= maternal
Possibility 1 Possibility 2






Possibility 3 Possibility 4






b. 4 points. Draw out the final gametes after the cell you drew has completed Meiosis I and
II.
Here are the gametes for Possibility 1







c. 4 points. How would the drawing for a above differ if you were diagramming metaphase
of meiosis II? Draw it.


Name: ___________________________Lab Section __________________ 11/21/11
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These are metaphase II for Possibility 1 above. The order of the chromosomes does not matter












9. 5 points. Explain how Meiosis can explain the idea of segregation as described by Mendel.
Mendels law of segregation states that the two alleles for a heritable character segregate
during gamete formation and end up in different gametes. This corresponds to the
separation of the homologous chromosomes (1 inherited from one parent, and 1 inherited
from the other parent) during meiosis I, which results in each gamete receiving only one
chromosome from each homologous pair.

10. Some commercial varieties of corn (Zea mays) exhibit a purple pigment called anthocyanin
in their seed coats (purple corn kernels) while others do not. Two enzymes are involved in
the synthesis of this purple pigment in the following pathway:
Enzyme A Enzyme B
Precursor (colorless) Intermediate (colorless) Pigment (purple)

The genes for enzymes A and B are on separate chromosomes. The gene for enzyme A has
two alleles. The dominant allele produces a functional enzyme: precursor can be turned into
intermediate. The recessive allele produces a non-functional enzyme: no reaction takes place
and no intermediate is produced; therefore the reaction cannot go forward.

The gene for enzyme B has two alleles. The dominant allele produces a functional enzyme:
the intermediate can be turned into purple pigment. The recessive allele produces a non-
functional enzyme: no reaction takes place and no pigment is produced regardless of how
much intermediate is available.

a) 2 points. What is the genotype of a corn plant that is heterozygous for both genes?
AaBb
b) 2 points. Can this plant produce the pigment? Yes or No? Answer: Yes
c) 8 points. This corn plant is allowed to self-fertilize (sperm and egg produced by the same
plant). Assume there is no crossing over taking place. Write the genotypes of the
Name: ___________________________Lab Section __________________ 11/21/11
&

possible gametes and use a Punnett Square to show the potential genotypes of the
offspring.

Gametes AB Ab aB ab
AB AABB AABb AaBB AaBb
Ab AABb AAbb AaBb Aabb
aB AaBB AaBb aaBB aaBb
ab AaBb Aabb aaBb aabb

d) 2 points. What is the phenotypic ratio of the offspring from this cross?
9 pigmented : 7 unpigmented
Note that only the ones with at least one capital A and one capital B can make the
pigment.
11. What is the probability of obtaining an individual with the genotype CC from a cross
between two individuals with the genotypes Cc and cc?
a. 1/2
b. 1/4
c. 1/8
d. 0
Answer: d
12. 6 points. There are 4 steps or processes in the light reactions that lead to the formation of a
proton gradient across the thylakoid membrane. Mark 3 on the diagram below:

13. If the Calvin Cycle runs through 3 turns
a. All of the fixed carbon will end up in the same PGAL (glyceraldehyde-3-phosphate)
molecule.
b. 6 carbons will be fixed by the process.
Name: ___________________________Lab Section __________________ 11/21/11
'

c. Enough carbon will be fixed to make one PGAL molecule, but they will not all be in
the same molecule.
d. All of the fixed carbon will end up in one RuBP molecule that splits to form two
PGAL molecules.
Answer: c
14. Compound X can compete with NADP
+
to accept electrons from NADP reductase in the
Electron Transport Chain. If you provide a high dose of compound X to the chloroplast, then
the first noticeable effect should be that
a. Electron transport comes to a halt
b. The proton gradient does not form
c. ATP is not synthesized
d. Carbon fixation is inhibited
e. All of the above
f. None of the above
Answer: d
15. 5 points. Review the figure provided below. Based on what you know about the
photochemical (light-dependent) reactions and the reactions in the Calvin cycle, answer
either a or b, not both.
a. Compare the effect of increasing CO
2
between the curve #1 and curve #2 (do not talk
about photorespiration or the oxygenation reaction here) and explain what it means to be
CO
2
limited and why in curve #1 increasing light intensity beyond 500 foot-candles does
not lead to higher rates of photosynthesis.
If CO
2
is limiting, then the first step of the Calvin cycle is limiting the rate of
photosynthesis. So, even if you keep increasing the light levels, photosynthesis wont go
any faster because there is not enough CO
2
for the Calvin cycle to go any faster.
Remember that the light reactions and the Calvin cycle are dependent on each other!

b. Compare the effect of increasing temperature between curve #2 and curve #3 and explain
what it means for the reaction to be temperature limited and why in curve #2 increasing
light intensity beyond about 1200 foot candles does not lead to higher rates of
photosynthesis.
In this case, as temperature increases from 20 to 35 degrees C, the rate of the enzymatic
reactions in the Calvin cycle increase. There is plenty of CO
2
and plenty of light but
cooler temperatures slow down the Calvin cycle, and that limits the whole process.
Name: ___________________________Lab Section __________________ 11/21/11
(


16. Jagendorf wanted to test Mitchells chemiosmosis hypothesis with regards to the process of
photosynthesis. He wanted to find out whether a proton gradient is the way that electron
transport in chloroplasts leads to ATP synthesis. To figure this out, he isolated chloroplasts
from spinach leaves, incubated them in a test tube containing a solution at pH4 in the dark to
allow equilibration across the membranes throughout the chloroplast. Then he moved half of
the chloroplasts into another test tube containing medium at pH 8 still in the dark. He kept
the other half in the test tube at pH 4 (not shown below). He provided ADP and
radioactively labeled inorganic phosphate to both test tubes and measured how much
radioactively labeled ATP was produced by the chloroplasts.

a. 2 points. What is the alternative hypothesis being tested?
In the thylakoids a proton gradient is enough to power ATP synthesis in the absence of
electron transport in the dark.

b. 2 points. What is the null hypothesis for the alternative hypothesis you wrote above?
In the thylakoids a proton gradient is not enough to power ATP synthesis in the absence
of electron transport in the dark.
c. 2 points. What is the experimental prediction for this experiment?
If we isolate chloroplasts and create a proton gradient across the membrane by first
incubating them in pH4 to lower the pH everywhere in the chloroplast including in the
lumen and then moving them to pH 8 so that the stroma is now at pH 8, and provide ADP
#3

#2


#1
Name: ___________________________Lab Section __________________ 11/21/11
)

and radioactively labeled Pi in the absence of electron transport in the dark then the
thylakoids will produce radioactively labeled ATP. In the absence of a proton gradient,
when the chloroplasts are kept in pH 4, there is no radioactively labeled ATP produced.

d. 6 points. On the blank graph below, draw a hypothetical column graph for the data
that would support the alternative hypothesis. Make sure to label the axes and to
distinguish between the treatments. Mark and label the dependent and the
independent variables on your graph.


Amount of
radioactive
ATP produced
(dependent
variable)



with pH gradient without pH gradient
Treatment (independent variable)
If you add error bars to show mean and standard deviation, even better!
Bonus 2 points. What if anything is the control treatment for this experiment?
the chloroplasts kept in pH 4 the whole time

17. True/False: A graph showing the rate of photosynthesis at different wavelengths of light is an
example of an absorption spectrum. Answer: False
18. Select all that apply. The problem with oxygen during photosynthesis is that when Rubisco
reacts with oxygen and RuBP
a. A potentially useless 3C compound is produced
b. A potentially useless 2C compound is produced
c. RuBP is used but no C is fixed in the process
d. ATP is used to add the oxygen to RuBP
Answer: b and c
19. Why is lactic acid fermentation an important metabolic function in your cells when O
2
concentrations are low?
a. Fermentation oxidizes NADH to NAD
+
.
b. Fermentation oxidizes pyruvate.
c. Fermentation produces ATP.
d. Fermentation reduces glucose to pyruvate.
Answer: a

Name: ___________________________Lab Section __________________ 11/21/11
*


Name: ___________________________Lab Section __________________ 11/21/11
!+



Name: ___________________________Lab Section __________________ 11/21/11
!!


20. 20 points. Please write a short essay in response to either a or b, but not both. You are expected to
write a logically constructed answer; organization does count.
a. As the concentration of CO
2
in the atmosphere rises, some have argued that this might actually be
good for plants. However, that may not necessarily be good for agricultural crop yield. Explain
why. In your answer consider the potential effects of increased CO
2
concentration on carbon
fixation and water use, overall growth of the plants, agricultural yield, and quality of the
agricultural products. Recall that stomata open when the concentration of CO
2
in the intercellular
air spaces in the leaf falls, and they close when the concentration rises.
5 points. As the concentration of CO
2
rises in the atmosphere, the stomata would not have to stay
open as long for a given amount of CO
2
to enter the leaf as they did when the atmospheric
concentration of CO
2
was lower. That could mean that for a given amount of CO
2
the leaf would lose
less water. If that were to happen, the plants would conserve water for the same amount of carbon
fixed. This means no increase in agricultural crop yield.

5 points. On the other hand, the higher CO
2
concentration in the air may mean an increase in the
carboxylation to oxygenation ratio to higher than the current average of 3:1 for C3 plants. This means
that for the same duration of stomatal opening, the plant gains more carbon under high CO
2

concentrations than when the CO
2
concentration was lower.

Alternative 2 points: This is due to the potential reaction with oxygen when Rubisco carries a reaction
between RuBP and oxygen, which leads to the formation of a potentially useless 2 carbon compound
(phosphoglycolate).
Alternative 1 point: This is due to the reduction in photorespiration.

4 points. Increased carbon fixation by the plant may mean increased amounts of sugars or other
carbohydrates such as starch in the plant. Or it could mean an increase in formation of structural
carbohydrates such as cellulose.

3 points. The increase could happen in tissues and organs that are harvested and useful to us as
agricultural yield. On the other hand, the increase could happen in tissues and organs that are not
what we harvest for that crop. Alternative 2 points: For example, an increase in biomass of lettuce
leaves or an increase in sugar content of beet roots, or an increase in starch content of potato tubers,
etc., which we may want, as opposed to an increase in leaf mass of potatoes, or an increase in seed
mass of lettuce, or an increase in fiber content of beet roots, etc.

3 points. Additionally, the nutritional balance of the harvested tissue/organ may be affected.
Increasing carbohydrate content might not be the best nutritional modification of what we harvest as
we may wish to have a balance between protein content and carbohydrate content, or prefer a higher
protein content, for example. Increasing carbon fixation does not lead to increases in other nutrient in
the harvested part of the crop necessarily.

Name: ___________________________Lab Section __________________ 11/21/11
!#

b. Describe two possible explanations as to why oxygenation by Rubisco (reaction carried out by
Rubisco between RuBP and O
2
) and photorespiration (the salvage operations to minimize carbon
loss) may have evolved.
2 points. One possible explanation is that the oxygenation reaction is an evolutionary accident.

4 points. When Rubisco first evolved, there was little oxygen in the atmosphere. Rubisco can bind
oxygen because oxygen and CO
2
are structurally somewhat similar. However, the affinity of Rubisco
for oxygen is not as high as its affinity for CO
2
because the structures are not identical. Rubisco
evolved to react with CO
2
and it has 80 times more affinity for CO
2
than it does for oxygen.

2 points. As photosynthetic organisms released oxygen into the atmosphere, oxygen became a bigger
problem for Rubisco.

2 alternative points. Since there is so much more oxygen in the atmosphere now than there is carbon
dioxide, the problem with oxygen is now a serious problem as the carboxylation to oxygenation ratio
is about 3:1 for C2 plants under normal conditions.

2 points. Photorespiration evolved as a mechanism to deal with the potential loss caused by the
oxygenation reaction.

2 points. The second explanation is that the process as a whole allows plants to survive stressful
situations when CO
2
is limiting while light is plentiful.

2 alternative points. For example, if the plant is under high light but water stressed conditions,
stomata will close to conserve water and internal CO
2
concentrations will drop as photosynthesis
continues.

5 points. Under such conditions the Calvin cycle will slow down as CO
2
concentration drops. This
creates a problem as ADP is not recycled back to be used in the light reactions again. This will in
turn slow down electron transport, which in turn will mean that the excited electrons in the pigments
have no place to release their energy. They in turn could potentially damage the photosynthetic
machinery.

3 points. The oxygenation reaction and the photorespiration process allow for ATP to be used and for
ADP to be recycled. This allows electron flow to continue and thus reduces the chance for potential
damage to the photosynthetic machinery.
Name: ___________________________Lab Section __________________ 11/21/11
!$


You may continue the answer to the essay question here.
Name: ___________________________Lab Section __________________ 11/22/10
"
BIO 10100 Exam 3 Version 1
Prior to completing this exam, please read the following statement and sign below to indicate
that you have read and understood the statement. No exam will be graded unless the pledge is
signed.
I pledge that I have neither given nor received unauthorized assistance on this exam. I
understand that if I am charged with cheating, my name will be submitted to the Dean for
disciplinary action.

################################################## #####################
Name Date


Please make sure you have all 12 pages of the exam. Write your name and lab section on all
pages. Please read each question carefully. If you do not understand the meaning or intention of
a question, please ask. Please pace yourself and use your time efficiently.
Please put away your cell phones, blackberries, iPods, laptop computers, etc.
For each multiple-choice question please select the best answer. Each multiple-choice question
is worth 2 points. Allow at least 10 minutes for the final essay question.
You will receive ZERO credit for any question for which we cannot tell what your final answer
is. If you erase or cross out an answer, please make it clear as to what your final answer is.
1. 6 points. Answer either a or b, not both:
a) Define a gene, an allele, and a locus.
A gene is a segment of DNA that codes for something.
Alleles are different versions of a gene that produce distinguishable phenotypes.
A locus is the physical location of a gene on a chromosome.

b) Describe the advantages and disadvantages of sexual versus asexual reproduction.
Sexual reproduction requires two gametes to come together, which can be a cost: need to
find the other gamete, not always successful. It produces genetic variability in the
population, which can be a benefit if the environment is changing as some of the new
genetic combinations may have an advantage in the new environment, but could be a cost
if the environment is not changing. Asexual reproduction does not require finding of a
mate, which could be a benefit. It leads to production of individuals that are genetically
identical to the parent, which would be good if the environment is not changing and the
parent is perfectly well adapted to the environment, but a bad thing if the environment is
changing and the parent is not the best suited to the environment.

2. 12 points. Answer either a or b, not both:
a) Review Figure 12.8 below. The question being investigated is: where do the
microtubules depolymerize and shorten as the chromosomes move to the opposite poles
of the cell during anaphase? There are two possible alternative hypotheses for this
Name: ___________________________Lab Section __________________ 11/22/10
$
question (I am not asking for the null hypothesis). What are the two possible alternative
hypotheses? What would be the experimental prediction for each alternative hypothesis?
What is the conclusion? Why did they mark only one set of microtubules?

Figure 12.8: Gary Borisys lab used pig kidney cells.
Labeled microtubules with fluorescent dye. Used laser
to remove label from one region to mark it.
Monitored labeled microtubule length during the
course of anaphase.








2 points. Alternative Hypothesis 1:
The microtubules depolymerize at the kinetochore ends.

2 points. Alternative Hypothesis 2:
The microtubules depolymerize at the spindle pole ends.

2 points. Experimental Prediction for Hypothesis 1:
When the microtubules are labeled with fluorescent dye and the dye is removed from one
section as a marker, the length of the fluorescently labeled microtubules between the
marker and the chromosomes will shorten as the chromosomes move toward the poles,
while the length of the fluorescently labeled microtubules between the marker and the
poles does not.

2 points. Experimental Prediction for Hypothesis 2:
When the microtubules are labeled with fluorescent dye and the dye is removed from one
section as a marker, the length of the fluorescently labeled microtubules between the
marker and the spindle poles will shorten as the chromosomes move toward the poles,
while the length of the fluorescently labeled microtubules between the marker and the
kinetochores does not.

2 points. Conclusion:
The results supported the first hypothesis: since the length of the fluorescently labeled
microtubules between the marker and the kinetochores shortened, the microtubules must
be depolymerizing at the kinetochore ends.

2 points. Why they marked only one set of microtubules
This was a control to make sure the laser treatment did not have any ill effects.


Name: ___________________________Lab Section __________________ 11/22/10
%

b) Design an experiment to test the following hypothesis: a pH gradient is enough to provide
the force to synthesize ATP in the thylakoids in the absence of electron transport. Since
you are provided with the alternative hypothesis above, state the null hypothesis,
experimental procedure, substrates needed, control treatment(s), and experimental
predictions.
2 points. Null Hypothesis:
A pH gradient is not enough for the thylakoids to synthesize ATP in the absence of
electron transport.

4 points. Experimental procedure:
Isolate thylakoid membranes.
Carry out the rest of the procedures in test tubes kept in the dark.
Incubate them in a low pH (for example 5). Allow the lumen inside to equilibrate to the
low pH.
Then move half of the thylakoids to a new medium at a higher pH, for example 8.
Provide ADP and Pi. Measure rate of ATP synthesis.
Keep the other half of the thylakoids in the low pH. Provide ADP and Pi. Measure rate
of ATP synthesis.

2 points. Substrates needed:
ADP and Pi

2 points. Control treatment(s):
Half of the thylakoids kept in low pH (no pH gradient).

2 points. Experimental predictions:
When the thylakoids are moved to the high pH, there will be a proton gradient across the
thylakoid membranes. That will provide the proton motive force needed for ATP
synthesis in the absence of light. ATP synthase will use the ADP and Pi and synthesize
ATP. No such ATP synthesis will be observed in the control treatment since there is no
pH gradient.

3. Spotted salamanders have been shown
a) To have algae growing inside their embryos cells
b) To have algae growing on the surface of their skin
c) To use algae to supplement cellular respiration
d) To use algae as an alternate food source for embryos
This was from the only article you had to read for this exam, a 2-page article that was
assigned for photosynthesis; see the reading assignments for photosynthesis in the
syllabus.
4. (6 points) The figures below show onion root tip cells at various points in the cell cycle.
Circle and identify one cell in each of the following phases: interphase, prophase, and
metaphase:
Name: ___________________________Lab Section __________________ 11/22/10
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Interphase Prophase Metaphase
Since the pictures didnt show up well on the colored paper, if you got 2 out of 3, youll get
full credit.

The data below were obtained from a study of the length of time spent in each phase of the cell
cycle by cells of three eukaryotic organisms designated beta, delta, and gamma.


Minutes Spent in Cell Cycle Phases

5. Of the following, the best conclusion concerning the difference between the S phases for beta
and gamma is that
a) beta contains more RNA than gamma.
b) gamma contains more DNA than beta.
c) beta and gamma contain the same amount of DNA.
d) gamma contains 48 times more DNA and RNA than beta.
e) beta is a plant cell and gamma is an animal cell.

6. If a cell has 10 chromosomes at metaphase of mitosis, how many chromosomes will it have
during anaphase?
a) 2
b) 1
c) 10
d) 5
e) 20

The following 2 questions are based on the figure below.
Name: ___________________________Lab Section __________________ 11/22/10
'


7. Which number represents DNA synthesis?
a) I
b) II
c) III
d) IV
e) V

8. In the figure above, mitosis is represented by which number?
a) I
b) II
c) III
d) IV
e) V

9. 8 points. Consider independent assortment of chromosomes during Meiosis I. For an
organism with a diploid number of 2n = 6, draw out the 4 possible ways the chromosomes
might align during Metaphase I of Meiosis. Make sure the 3 homologous pairs are
identifiable as separate from each other. Make sure the maternal and paternal copies are
identifiable as such.



Pair of homologous chromosomes
(one from each set)
Name: ___________________________Lab Section __________________ 11/22/10
(
Possibility 1 Possibility 2





Possibility 3 Possibility 4







10. An animal species has 20 homologous pairs (40 chromosomes). Each of its gametes and the
next generation zygote will have how many chromosomes, respectively?
a) gametes: 40 and zygote: 40
c) gametes: 20 and zygote: 40
b) gametes: 20 and zygote: 20
d) gametes: 40 and zygote: 80

11. 6 points. Use the chromosomes and genes shown below for a hypothetical organism and
draw one chiasma (one crossing over event only) during prophase I of meiosis and the new
genetic combinations that result from that crossing over event.

Gene for eye color Red Brown

Centromere
For example
Gene for wing shape Straight Curled

Name: ___________________________Lab Section __________________ 11/22/10
)
Maternal Chromosome 1 Paternal Chromosome 1
New genetic combinations:


Gene for eye color Red Brown



Gene for wing shape Curled Straight


12. Randomly oriented leaves like those of pine (see picture)
a) have only palisade mesophyll
b) have uniform mesophyll cells
c) have palisade and spongy mesophyll
d) have only spongy mesophyll cells


13. In the thylakoid membranes, what is the main role of the antenna pigment molecules?
a) split water and release oxygen to the reaction-center chlorophyll
b) harvest photons and transfer light energy to the reaction-center chlorophyll
c) transfer electrons to ferredoxin and then NADPH
d) concentrate photons within the stroma
e) synthesize ATP from ADP and Pi

14. 6 points. In the figure below identify the 3 steps of the Calvin cycle: carboxylation,
reduction, and regeneration.


Name: ___________________________Lab Section __________________ 11/22/10
*


15. (6 points) Briefly describe two ecological reasons why photosynthesis is important.
Reason 1: Source of oxygen for aerobic organisms

Reason 2: Source of food for heterotrophic organisms

16. 8 points. Review the figure shown below. Mark the individual steps that lead to the formation
of a proton gradient across the thylakoid membrane. Identify them as removing protons or
adding protons.






Name: ___________________________Lab Section __________________ 11/22/10
+
Removes protons from stroma

Adds protons to lumen

17. Which of the following are products of the light reactions of photosynthesis that are utilized
in the Calvin cycle?
a) CO
2
and glucose
b) ATP and NADPH
c) H
2
O and O
2

d)
ADP, P
i
, and NADP
+
e)
electrons and H
+

Theodor W. Engelmann illuminated a filament of algae with light that passed through a prism,
thus exposing different segments of algae to different wavelengths of light. He added aerobic
bacteria and then noted in which areas the bacteria congregated. He noted that the largest groups
were found in the areas illuminated by the red and blue light.

18. An outcome of this experiment was to help determine
a) the relationship between heterotrophic and autotrophic organisms.
b) the relationship between wavelengths of light and the rate of aerobic respiration.
c) the relationship between wavelengths of light and the amount of heat released.
d) the relationship between the concentration of carbon dioxide and the rate of
photosynthesis.
e) the relationship between wavelengths of light and the oxygen released during
photosynthesis.

19. If you ran the same experiment without passing light through a prism, what would you
predict?
a) There would be no difference in results.
Name: ___________________________Lab Section __________________ 11/22/10
",
b) The number of bacteria present would decrease due to an increase in the carbon dioxide
concentration.
c) The bacteria would be relatively evenly distributed along the algal filaments.
d) The number of bacteria present would increase due to an increase in the carbon dioxide
concentration.
e) The number of bacteria would decrease due to a decrease in the temperature of the water.



Image Source:
http://www.esrl.noaa.gov/gmd/obop/mlo/prog
rams/coop/scripps/img/img_scripps_co2_reco
rd.gif






Figure 10.5


Cross section of a pine needle
Name: ___________________________Lab Section __________________ 11/22/10
""


Source: Hopkins (1999) Introduction to Plant Physiology. 2
nd
ed. John Wiley & Sons, Inc. New York, NY
Rubisco
Name: ___________________________Lab Section __________________ 11/22/10
"$

20. 20 points. Please write a short essay in response to only one (either a or b, but not both) of
the following questions. You are expected to write a logically constructed answer;
organization does count. You may want to outline your answer first.
a) Review the figure showing the gradual increase in the concentration of carbon dioxide in
the atmosphere as measured in Mauna Loa in Hawaii. Explain why the concentration has
been increasing over time. Explain why every year the concentration as measured in
Mauna Loa rises and dips on a seasonal basis with a maximum concentration during the
northern hemispheres winter and a minimum concentration during the southern
hemispheres winter.

6 points. The concentration of CO
2
in the atmosphere has been increasing steadily due to
human activity. As human population has grown and our reliance on fossil fuels has
grown, more and more fossil fuels are being burned releasing CO
2
in ever increasing
amounts into the atmosphere. In addition, growing human population has also meant
deforestation to create space for housing and other buildings/roads, etc., as well as
deforestation to replace the forests with agricultural fields that are less productive than
forests, that is they have lower rates of photosynthesis and thus take less CO
2
out of the
atmosphere than forests would.

10 points. In addition to this general increase in CO
2
concentrations, there is a seasonal
effect seen in the data. Every year, the concentration of CO
2
in the atmosphere reaches a
maximum during the winter of the Northern Hemisphere (the summer of the Southern
Hemisphere) and a minimum during the summer of the Northern Hemisphere (the winter
of the Southern Hemisphere). The reason is that there are more land masses in the
Northern Hemisphere and thus both more people and more forests. Therefore, the
Northern Hemisphere dominates the global CO
2
cycle. During the winter more fossil
fuels are being burnt for heating and rates of photosynthesis are lower due to dormancy
or death of plants. Since there are more people and more forests in the Northern
Hemisphere, the winter of the Northern Hemisphere dominates over the summer of the
Southern Hemisphere and so the maximum CO
2
concentrations are reached then. For the
same reason, the summer of the Northern Hemisphere dominates over the winter of the
Southern Hemisphere and the minimum CO
2
concentrations are reached during the
summer of the Northern Hemisphere when there is less fossil fuel burning and higher
rates of photosynthesis.

4 points. The reason that these seasonal effects are measurable even in Hawaii is the
global air circulation patterns that distribute the gases throughout the globe so that even
in Mauna Loa the effects of the rest of the globe can be measured.

Name: ___________________________Lab Section __________________ 11/22/10
"%

b) Why is oxygen a problem in photosynthesis? Why is it more of a problem with warmer
temperatures? What is photorespiration and what does it do to help the plant deal with
the problem with oxygen? What are the costs and benefits of this process? As
concentration of CO
2
rises globally, how might that affect the problem with oxygen?
Why? Explain your answer.

5 points. The first reaction in the Calvin cycle involves the enzyme Rubisco that takes a
molecule of CO
2
and attaches it to the 5-carbon sugar RuBP forming a 6-carbon
compound that then splits to make two 3-carbon compounds (PGA). This is the
carboxylation step that adds a C to the body of the plant. If oxygen is present, it too can
react with the 5 C sugar RuBP through the activity of the enzyme Rubisco. However,
when oxygen reacts with RuBP, no C is added to the body of the plant. Instead, the 5-
carbon compound is split to make a 3-carbon compound (PGA) that can be used by the
plant, and a 2-carbon compound (phosphoglycolate) that is not useful to the plant.
Figure included above. Hence the plant is not gaining any carbon from this reaction,
and could potentially lose 2 carbons it already had. That is a problem.

5 points. This problem becomes more serious as temperatures rise. Higher temperatures
mean lower solubility for gases in an aqueous solution such as the stroma of the
chloroplast. As temperatures rise, the solubility of CO
2
decreases faster than that of O
2

and thus the potential for O
2
to react through Rubisco with RuBP increases. Thus the
carboxylation to oxygenation ratio goes down and the plant could potentially lose a lot
more carbon to the reaction with O
2
.

5 points. Plants have evolved a mechanism to salvage the carbons in the potentially
useless 2-carbon compound that is produced through the oxygenation reaction. This
process involves the chloroplasts, mitochondria, and peroxisomes (Figure included
above) and is called photorespiration because it will lead to the loss of CO
2
. Through
photorespiration, the plant can salvage three quarters of the carbons that would have
otherwise been useless to it. That means, for every 2 molecules of phosphoglycolate that
go through this process, 3 carbons are salvaged as one molecule of useful PGA, and only
1 carbon is lost as CO
2
. This process does cost ATP, however. So, the plant salavages !
of the C it would have lost otherwise, but loses one C it already had without gaining any
new C, and loses some ATP in the process as well.

5 points. As concentrations of CO
2
rise globally, that could help the plants with the
oxygenation reaction. More CO
2
in the atmosphere means more CO
2
in the solution in
the stroma and so a lower chance that Rubisco will react with oxygen; that means a
higher carboxylation to oxygenation ratio, which is good for the plants.

The following is additional but not required: However, the increase in CO
2

concentrations in the atmosphere have other consequences as well, such as a potential
increase in air temperature and prolonged droughts and closure of stomata, etc., so the
benefits are not straight forward.
Name: ___________________________Lab Section __________________ 11/22/10
"&

This page is intentionally left blank.



Name: ___________________________Lab Section __________________ 11/28/12
1
1oLal olnLs: _____
BIO 10100 Exam 3 Version 1
Prior to completing this exam, please read the following statement and sign below to indicate
that you have read and understood the statement. No exam will be graded unless the pledge is
signed.
I pledge that I have neither given nor received unauthorized assistance on this exam. I
understand that if I am charged with cheating, my name will be submitted to the Dean for
disciplinary action.

__________________________________________________ _____________________
Name Date

2 Bonus Points: Write your name and lab section on all sheets.

1. Select all that apply: In slash and burn agriculture
a. The soil nutrients are recycled with every cycle of the crops
b. The ash from the burned trees has concentrated mineral nutrients
c. The carbon released from burning the trees is stored in the crops
d. The nutrient cycle is disrupted as the crops are harvested and removed
Answer: b and d

2. How many times must the Chl a in the PSII reaction center get excited and donate an electron
to pheophytin before OEC (oxygen evolving complex) splits water to release oxygen?
a. 6 times
b. 4 times
c. 2 times
d. 1 time
Answer: b
3. 8 points. Answer either a or b, not both. Review the figure showing the gradual increase in
the concentration of carbon dioxide in the atmosphere as measured in Mauna Loa.
a. Describe 3 reasons for the gradual increase in the concentration of CO
2
over the past few
decades.
Here are several reasons: The concentration of CO
2
in the atmosphere has been increasing
steadily due to human activity. As human population has grown and our reliance on fossil
fuels has grown, more and more fossil fuels are being burned releasing CO
2
in ever
increasing amounts into the atmosphere (more cars, more heating fuel, etc.). In addition, a
growing human population has also meant more deforestation to create space for housing and
other buildings/roads, etc., as well as more deforestation to replace the forests with
agricultural fields that are less productive than forests, that is they have lower rates of
photosynthesis and thus take less CO
2
out of the atmosphere than forests would.

b. Explain why every year the seasonal oscillation is dominated by the northern
hemisphere: a maximum CO
2
concentration during the northern hemispheres winter
(southern hemispheres summer) and a minimum CO
2
concentration during the northern
hemispheres summer (southern hemispheres winter).
Name: ___________________________Lab Section __________________ 11/28/12
2
1oLal olnLs: _____
During the winter more fossil fuels are being burnt for heating and rates of photosynthesis
are lower due to dormancy or death of plants while during the summer less fossil fuel is
being burnt and rates of photosynthesis are higher due to more photosynthesis. The CO
2

concentration oscillates with a maximum and minimum every year dominated by the
northern hemisphere because there are more people and more forests in the northern
hemisphere. The winter of the northern hemisphere dominates over the summer of the
southern hemisphere and so the maximum CO
2
concentrations are reached then. For the
same reason, the summer of the northern hemisphere dominates over the winter of the
southern hemisphere and the minimum CO
2
concentrations are reached during the summer of
the northern hemisphere

4. 8 points. Review the figure below. The researchers labeled the microtubules with a
fluorescent dye. They used a laser to remove the fluorescent label from one region to mark
it. They monitored the length of the labeled sections of the microtubules during the course of
anaphase. Draw the expected results for each alternative hypothesis (a and b) below:
a) The microtubules depolymerize at the kinetochore end.
b) The microtubules depolymerize at the aster (centrosome) end.



Expected results:
Draw as follows:
The yellow labeled section The yellow labeled section
between the mark and between the mark and
kinetochores is shorter while the asters is shorter while
that between the mark and that between the mark and
the asters is the same length. the kinetochores is the same length.
a) b)
5. 4 points. In the figure below, there are 2 steps where protons are being removed from the
stroma, and 2 steps where they are being added to the lumen. Circle these steps and label
as Add or Remove.
Name: ___________________________Lab Section __________________ 11/28/12
3
1oLal olnLs: _____

6. In the thylakoid membranes, what is the main role of the antenna (LHC) pigment molecules?
a. harvest photons and transfer light energy to the reaction-center chlorophyll
b. split water and release oxygen to the reaction-center chlorophyll
c. transfer electrons to ferredoxin and then NADPH
d. concentrate photons within the stroma
e. synthesize ATP from ADP and Pi
Answer: a

7. Select all that apply: During the photorespiratory salvage operations
a. 3 carbons from 2 molecules of phosphoglycolate are salvaged as 1 PGA
b. 4 carbons from 2 molecules of phosphoglycolate are salvaged as 2 PGAs
c. There is a net loss of 1 ATP
d. There is a net loss of 1 NADH
e. There is a net gain of 1 NADH
f. There is a net gain of 1 ATP
Answer: a, c

8. 10 points. Answer either a or b, not both:
a. Explain what the organizational concept of sexuality entails and the reason the
organizational concept fails to explain vertebrate sexuality.
In the organizational concept of sexuality gender is ultimately determined by sex
chromosomes. At the time of formation of the zygote, the sex chromosomes determine
the nature of the gonads in the embryo, the gonads produce the sex steroid hormones, and
the sex hormones produce the sexual characteristics during the early stages of
development. In additional, in this concept, the female is considered to be the default sex
and the male is considered to be the organized sex. The organizational concept fails to
explain vertebrate sexuality because not all vertebrates us sex chromosomes for gender
determination.

Add
Add
8emove
8emove
Name: ___________________________Lab Section __________________ 11/28/12
4
1oLal olnLs: _____
b. Vertically oriented leaves have stomata on both sides. Explain how this makes sense in
terms of the requirement for CO
2
and the potential loss of water.
Vertically oriented leaves receive light from all directions. During some part of the day
one side of the leaf receives more direct light, while during other parts of the day the
other side of the leaf receives more direct light. When one side of the leaf is receiving
the highest intensity light, the mesophyll cells on that side have the highest demand for
CO
2
while the mesophyll cells on the other side are more shaded and have lower demand
for CO
2
. The stomata on the sunny side close and those on the shaded side open to let in
CO
2
, which will diffuse down its gradient from the highest concentration outside the leaf
through the stomata into the leaf air spaces towards the sunny side of the leaf where the
demand is the highest, and thus all mesophyll cells have access to the incoming CO
2
.
When one side is receiving direct light, it would be beneficial to close the stomata on the
lighted and thus warmer side and open the stomata on the shaded and thus cooler side to
minimize water loss. At the other times of the day when the opposite side of the leaf is
now the sunny side, the role of the stomata reverses. Therefore, it makes sense to have
stomata on both sides in terms of both the requirement for CO2 and the potential loss of
water.

9. 6 points. In the spaces provided below, identify and label the 3 major steps of the PCR
(Calvin) Cycle.


Carboxylation Answer
Reduction Answer
Answer Regeneration
Name: ___________________________Lab Section __________________ 11/28/12
3
1oLal olnLs: _____
10. Below is an excerpt from a set of research experiments. For your answer use either
Experiment 1 or Experiment 2, not both.


Experiment 1: Chloroplast thylakoids are isolated and incubated in a medium at pH 4. Then
half are transferred to a pH 8 medium (shown above) and half are transferred to a pH 4
medium (not shown) and in the dark ADP and Pi are added to both sets. ATP is produced in
the first set (moved to pH 8) but not in the second set (moved to pH 4).

Experiment 2: A photosynthetic alga, Spirogyra is used. Light is shone on the alga through a
prism so that different wavelengths of light shine on different sections of the algal filament.
Aerotactic bacteria (aerobic, need oxygen) are added to the culture. As the alga
photosynthesizes, aerotactic bacteria aggregate along the different sections of the alga as
shown above. The same experiment is conducted but white light is shone on the alga (no
prism) so that all sections of the alga receive white light (not shown above). The bacteria
aggregate uniformly along the length of the algal filament (data not shown above).

a. 2 points. What is the question being asked?
Exp 1: In the absence of electron transport, is a proton gradient required for ATP synthesis in
thylakoids?
Exp 2: Do all wavelengths of light lead to equal rates of photosynthesis?

Name: ___________________________Lab Section __________________ 11/28/12
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1oLal olnLs: _____
b. 2 points. What is the alternative hypothesis?
Exp 1: In the absence of electron transport, a proton gradient is required for ATP synthesis in
thylakoids.
Exp 2: Different wavelengths of light lead to different rates of photosynthesis.

c. 2 points. What is the null hypothesis for the alternative hypothesis you wrote above?
Exp 1: In the absence of electron transport, a proton gradient is not required for ATP synthesis in
thylakoids.
Exp 2: Different wavelengths of light do not lead to different rates of photosynthesis.
d. 2 points. What is the experimental prediction?
Exp 1: If we isolate thylakoids from chloroplasts, incubate them in a buffered medium at pH 4,
and then transfer half to a buffered medium at pH 8 and the other half to a buffered medium
at pH 4, and in the dark add ADP and Pi, then there will be ATP synthesis in the thylakoids
at pH 8 but not in the ones at pH 4.
Exp 2: If Spirogyra is provided with different wavelengths of light by passing white light
through a prism, and aerotactic bacteria are present in the medium, then the bacteria will
aggregate in some areas more than others. If Spirogyra is provided with white light and
aerotactic bacteria are present in the medium, then the bacteria will aggregate uniformly
along the length of the alga.

11. 9 points. In the figures below the microtubules and the chromosomes have been stained with
two different dyes. Identify in which phase of the cell cycle the cells are: a) prophase, b)
metaphase, c) anaphase, d) telophase, e) cytokinesis, or f) interphase. Write the letters (a, b,
c, d, e, or f) in the spaces below.
Answers: c a b



12. 1 point. If a cell has 10 chromosomes at prophase of mitosis, how many chromosomes will
the cell have during metaphase? Answer: 10

13. Select all that apply: Cytokinesis in animal cells:
a. forms two daughter cells from the parent cell
b. occurs by formation of a cell plate
c. involves formation of a new cell wall
d. involves formation of a cleavage furrow
Answer: a, d
Name: ___________________________Lab Section __________________ 11/28/12
7
1oLal olnLs: _____

14. During the cell cycle, DNA replication occurs during the ___ phase:
a. G1
b. G2
c. S
d. M
Answer: c

15. Cohesins
a. hold the centromeres of a replicated chromosome together
b. are the monomers that make up microtubule polymers
c. make up the protein units around which DNA is wrapped
d. help to attach the centromeres to the microtubules
Answer: a

16. The beginning of anaphase is signaled by:
a. the arrival of the chromosomes at the spindle poles
b. the splitting of the centromeres of the chromosomes
c. the dissolution of the nuclear membrane
d. the attachment of microtubules to kinetochores
Answer: b








17. 10 points. You have isolated thylakoids from plant chloroplasts. You divide them into 15
test tubes with the appropriate aqueous solution to keep them healthy. All test tubes have a
ready supply of NADP+ and Pi (inorganic phosphate). You subject them to similar light
levels to allow for the pigments to get excited so that electron transport could take place.
You divide the test tubes into three groups of 5 test tubes each. To group 1 you add ADP (+
ADP). To group 2 you add an uncoupler that dissipates the proton gradient (+ uncoupler).
To group 3 you add neither ADP nor uncoupler. You measure the rates of oxygen
production (units: moles/sec) in each test tube, then calculate means and standard deviations
for your measurements for each of the treatment groups: your hypothetical data. For group
3 (neither ADP nor uncoupler added) the means for rates you measure turn out to be
0.50.1 moles/sec. Do you expect the rates for groups 1 and 2 to be higher, lower, or
similar to what you measured for group 3? On the blank graph provided below draw a
hypothetical column graph of showing the effect of the three treatments above on the rate
of oxygen production. Make sure to label the axes properly. Make sure to identify the
treatments on your graph. Make sure to identify the means and standard deviations on your
graphs.

Name: ___________________________Lab Section __________________ 11/28/12
8
1oLal olnLs: _____










1 (+ADP) 2 (+uncoupler) 3 (neither)
Treatment group
Columns represent means, and error bars represent standard deviations.
(The reason the rate is lower for group 3 is that electron transport cannot continue in the absence of
ADP and so little water is split to produce oxygen. The reason the uncoupler works is that even
though there is no ADP, the proton gradient does not build up, and electrons can continue to flow to
NADP+ and so water can continue to be split by OEC to produce oxygen.)






Rate of
oxygen
production
(moles/sec)
Name: ___________________________Lab Section __________________ 11/28/12
9
1oLal olnLs: _____
18. 20 points: Please write a short essay in response either a or b, not both. You are expected to write a
logically constructed answer; organization does count. You may wish to outline your answer first.
a. Sea lettuce (Ulva) and Nori (Porphyra) have different combinations of pigments and absorb light
maximally at different wavelengths. See the figure provided. Sea lettuce is typically found in
shallow coastal waters while Nori is found in deeper waters. As white light penetrates water, water
molecules tend to scatter the blue wavelengths and tend to absorb the red wavelengths while green
light reaches into deeper waters. So, the wavelengths of light available in surface waters are different
than those available in deeper waters. Some have suggested that the reason the above algae are
restricted to their respective depths has to do with the available light and their respective action
spectra due to their pigments. However you also have to consider that this depth restriction might
have to do with nutrient requirements, the intensity of light (not the wavelengths), and maybe even
presence of grazers (animals that eat them). Design an experiment to test whether the available light
wavelengths can explain why these algae survive well at their respective depths. Make sure to
include all of the elements of experimental design we have reviewed in class and lab in your answer.
There are various ways you could answer this question. There are various plausible experimental
designs. Make sure you mention your treatment levels. Make sure you mention what is actually
measured.

2 points. Alternative hypothesis: The availability of different light wavelengths at different water
depths explains why these algae survive well at their respective depths.

2 points. Null hypothesis: The availability of different light wavelengths at different water depths
does not explain why these algae survive well at their respective depths.

14 points. Experimental procedure:
1 point for sample size, Make sure your experimental design mentions a sample size that is large
enough to lend itself to data analysis (minimum of 3 samples per treatment level, preferably 5)
1 point for replications, Make sure you suggest repeating the experiment multiple times.
4 points for control and experimental treatments, positive or negative (depending on experimental
design), what are the treatment levels?
1 point for what is measured (% survival, for example)
2 points for how this is set up and measured
3 points for at least three standardized factors (light intensity, no grazers present, water temperature,
nutrient availability same as what is found naturally, etc.)
2 alternative points: if you include more standardized variables.
2 points: identify the independent and dependent variables as such.

Here is an example:
Use multiple identical sea water chamber systems inside each of which you place one species of
algae, either Ulva or Porphyra. We have one individual per chamber but multiple chambers (large
sample size, 5) and we repeat the experiment 5 times (for example). To standardize other variables:
the algae are placed at the same water depth and are subject to no grazing (no animals in the
chambers), and are growing in optimal nutrient solutions for their species so nutrition is not an issue,
the chambers are at the same temperature, the measurements are taken at the same time of day, by the
same individual, etc.

In half of the chambers for each species we shine light with wavelengths characteristic of surface
waters in which Ulva grows. In the other half of the chambers for each species we shine light with
wavelengths characteristic of water depths in which Porphyra grows. The surface light is the control
for Ulva but the experimental treatment for Porphyra while the deep water light is the control for
Porphyra but the experimental treatment for Ulva. The light wavelength is the independent variable.
Name: ___________________________Lab Section __________________ 11/28/12
10
1oLal olnLs: _____
We allow the algae to grow for a fixed number of days and we measure their % survival (the
dependent variable) throughout the experiment and at the end of a set time period. Alternatively you
could suggest that we grow Ulva and Porphyra at their natural depth levels in these chambers (so not
at the same depth), but we put the light source right next to the algae so that while they are growing at
their natural depths, half of them are receiving light typical of their natural depth, while the other half
are receiving light typical of the opposite depth. For example: Half of the Ulva are growing at
shallow depths and receiving light typical of shallow depths, while the other half are growing at
shallow depths but receiving light wavelengths typical of deep waters. Half of the Porphyra are
growing at their natural depths (deeper waters) and receiving light wavelengths typical of naturally
deep waters, while the other half are growing in deeper waters but receiving light wavelengths typical
of surface waters.

2 points. The experimental prediction: When Ulva and Porphyra are grown in experimental
chambers with light wavelengths characteristic of surface waters where Ulva normally grows, all else
being equal, a higher percentage of Ulva will survive than Porphyra. When Ulva and Porphyra are
grown in experimental chambers with light wavelengths characteristic of deeper waters where
Porphyra normally grows, all else being equal, a higher percentage of Porphyra will survive than
Ulva.

2 alternative points: if you mention that you have to do statistical analysis and figure out the level of
confidence for your claim.

b. In your own words describe the problem that oxygen causes for carbon fixation during photosynthesis
in plants. Explain what the 3:1 carboxylation:oxygenation ratio means. As the concentration of CO
2

in the atmosphere rises, some have argued that this might actually be good for plants. Explain why
that would be the case. However, the rise in CO
2
concentrations may not necessarily be good for
agricultural crop yield and the quality of the crops. Explain why. In your answer consider the
different parts of the different crops we eat: for example, lettuce leaves, wheat and corn grains, and
beet roots, etc. Also consider nutritional values of crops: protein content versus carbohydrate content,
as well as important minerals, and what the increase in CO
2
concentration would mean for the
nutritional value of the crops.
3 points. Oxygen causes a problem for plants as they undergo carbon fixation. Since oxygen
can bind to the active site of Rubisco, it can react with RuBP to split the 5C compound into a
usable 3C PGA and a useless 2C phosphoglycolate. This is a potential loss of 2 carbons the
plant already had without any carbon gain as oxygenation is taking place instead of
carboxylation.

2 points. Under normal conditions for C3 plants, for every 3 times that CO
2
binds to
Rubisco to carry out the first step of the Calvin cycle (carboxylation), one time O
2
binds,
leading to the oxygenation reaction, and the potential loss of Carbon by the plant. This is the
3:1 carboxylatiion:oxygenation ratio typically found in C3 plants.

3 points. As the concentration of CO
2
increases in the atmosphere, the concentration in the
air spaces in the leaf and thus the stroma of the chloroplasts could potentially increase. This
would mean that the ratio of CO
2
to O
2
could increase and thus the ratio of carboxylation to
oxygenation could increase as Rubisco would have a better chance of binding with CO
2
than
with O
2
.

Name: ___________________________Lab Section __________________ 11/28/12
11
1oLal olnLs: _____
2 points. This means that for the same duration of stomatal opening, the plant gains more
carbon under high CO
2
concentrations than when the CO
2
concentration was lower.

Alternative 3 points. As the concentration of CO
2
rises in the atmosphere, that could mean
that the stomata would not have to stay open as long for a given amount of CO
2
to enter the
leaf as they did when the atmospheric concentration of CO
2
was lower. That could mean that
for a given amount of CO
2
the leaf would lose less water. If that were to happen, the plants
would conserve water for the same amount of carbon fixed. This means perhaps no increase
in agricultural crop yield, but saving water, which is a benefit.

3 points. Increased carbon fixation by the plant may mean increased amounts of sugars or
other carbohydrates such as starch in the plant. Or it could mean an increase in formation of
structural carbohydrates such as cellulose.

4 points. The increase could happen in tissues and organs that are harvested and useful to us
as agricultural yield. On the other hand, the increase could happen in tissues and organs that
are not what we harvest for that crop. And, how the carbohydrates are partitioned into starch
or simple sugars or structural cellulose may not be what we desire in our crops either.

Alternative 3 points: For example, an increase in biomass of lettuce leaves or an increase in
sugar content of beet roots, or an increase in starch content of wheat grains, etc., which is
more desirable, as opposed to an increase in leaf mass of wheat, or an increase in seed mass
of lettuce, or an increase in fiber content of beet roots, etc., which is less desirable.

3 points. Additionally, the nutritional balance of the harvested tissue/organ may be affected.
Increasing carbohydrate content might not be the best nutritional modification of what we
harvest as we may wish to have a balance between protein content and carbohydrate content,
or a desired concentration of minerals (e.g., calcium and magnesium) in our edible plants, or
prefer a higher protein content, for example. Increasing carbon fixation does not lead to
increases in other nutrient in the harvested part of the crop.

Alternative 2 points. For example, additional nitrogen fertilizers are needed to help to
increase the protein content.

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