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Exam 3 backtest
Biochemistry (Johns Hopkins University)
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Biochemistry Exam 3 Practice Problems
WARNING- Do not look at the answers until after you have tried to answer the questions on the
blank version!!! Reviewing the answer key is not effective practice for answering questions on
the exam.
1. TCA cycle
A. What is the most important purpose of the TCA cycle in terms of cellular energy and
biomolecules? Select the best answer.
a. regenerate NAD+ for use in glycolysis
b. synthesis of ATP by succinyl dehydrogenase
c. generate CO2
d. move protons across a membrane
e. generate oxaloacetate
f. reduce electron carriers
B. Which statement is true about NADP+/NADPH? Select one answer.
a. NADPH is used in gluconeogenesis
b. NADP+ and NAD+ can both be reduced by pyruvate dehydrogenase
c. NADPH can donate electrons for oxidative phosphorylation
d. NADPH is consumed by fatty acid synthesis
e. NADPH is generated by fatty acid breakdown
2. Fatty Acid Metabolism
A. Complete metabolic breakdown of a fatty acid to carbon dioxide (CO2) generates lots of
ATP. Which of the following processes or reactions directly generate ATP (ATP is a product
of the process or reaction) during complete fatty acid breakdown to CO2? Select all that
apply.
a. conversion of a fatty acid to acyl CoA
b. conversion of pyruvate to acetyl CoA
c. conversion of acetyl CoA to acyl ACP
d. conversion of acyl ACP to acetyl CoA
e. conversion of acetyl CoA to CO2
FADH2 is generated during fatty acid breakdown.
B. What is true about the FADH2 produced during fatty acid breakdown? Select one answer.
a. is a one electron carrier
b. is generated in the mitochondrial matrix
c. is a product of succinate dehydrogenase
d. is transported across a membrane
e. is generated by oxidation of FAD
C. How many molecules of FADH2 are generated during the breakdown of a fatty acid with
18 carbons? _____8_______
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Biochemistry Exam 3 Practice Problems
The electrons from FADH2 are used for oxidative phosphorylation.
D. See the diagram of the mitochondria. For each of the following, indicate the one letter
that best corresponds to the location
described.
B
D
E
a. Location of ATP when it is first released
by ATP synthase _______ A
C
b. Location in which pH is lowest in cells
undergoing respiration ________C
c. Location of coenzyme Q _______B
A
E. The electrons from FADH2 from fatty
acid breakdown enter the electron
transport chain by a different process than used for FADH2 generated by the TCA cycle.
Electrons from FADH2 generated during fatty acid breakdown are transferred to Coenzyme
Q. Which electron transport components are used when electrons from FADH2 generated
by fatty acid breakdown enter and completely move through the electron transport chain?
Select all that apply.
a. Complex I
b. Complex II
c. Complex III
d. Complex IV
e. cytochrome C
Calculation of the theoretical maximum number of ATP generated by FADH2 requires
consideration of the structure and function of the electron transport chain and ATP
synthase.
F. Explain what aspects of the structure and function of the electron transport chain you
must know to calculate the theoretical maximum number of ATP generated by FADH2.
Which complexes the electrons from FADH2 travel through (III and IV) and how many
protons are pumped by each complex
G. Explain what aspects of the structure and function of the ATP synthase Fo subunit (the
subunit in the membrane) you must know to calculate the theoretical maximum number
of ATP generated by FADH2.
How many c-subunits are present in the c-ring
H. Explain what aspects of the structure and function of the ATP synthase F1 subunit (the
subunit not in the membrane) you must know to calculate the theoretical maximum
number of ATP generated by FADH2.
How many beta subunits are present.
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Biochemistry Exam 3 Practice Problems
I. The gamma subunit connects the Fo and F1 subunits of ATP synthase. Explain the role of
the gamma subunit in the function of ATP synthase.
Gamma subunit rotates when c-ring rotates and changes the conformation of the beta
subunits
J. Explain why the actual estimated amount of ATP generated for every molecule of FADH2
is lower than the theoretical maximum (under normal circumstances). Be sure to provide
one example of how this occurs.
H+ are lost from gradient because they are used for some specific process like a
transporter; or they move out of the intermembrane space through “leak” processes; or
they move into the matrix through an uncoupling protein
3. Metabolism in Physiology and Disease
A. Which of the following enzymes do you think will be activated in a liver cell in the
presence of glucagon signaling and inhibited in the presence of insulin signaling? Select all
that apply.
a. Glucose 6-phosphatase
b. Glycogen phosphorylase
c. Phosphofructokinase-2
d. Phosphofructokinase-1
e. PEP carboxykinase
B. Consider an adipocyte under the fasted state. What do you expect to be happening in that
specific type of cell? Select the best answer.
a. export of ATP into the blood
b. synthesis of ketone bodies
c. synthesis of fatty acids
d. breakdown of triacylglycerols
e. gluconeogenesis
f. breakdown of glycogen
4. Which pathways would you predict are generally stimulated by insulin signaling? Select
all that apply.
i. glycolysis
ii. gluconeogenesis
iii. breakdown of glycogen
iv. synthesis of glycogen
v. fatty acid breakdown
vi. fatty acid synthesis
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Biochemistry Exam 3 Practice Problems
5. Below is a diagram of the electron transport pathway from mitochondria.
a) Which connections diagrammed above represent paths on which electrons flow between
complexes in the Electron Transport Chain (ETC)? (Circle all that apply)
a
b
c
d
e
f
b) In the electron transport chain, water is (circle one)
created/consumed
c) What is the terminal electron acceptor of electron transport?
Oxygen
d) Electron transport is initiated by reduced electron carriers in mitochondria. Describe the
process for the start of electron transport in mitochondria. Include the source of the
electrons that are passed through the chain.
NADH donates electrons to Complex I or FADH2 donates electrons to Complex II (or Q if
from fatty acid breakdown)
6. In the presence of oxygen, pyruvate produced from glycolysis is converted to acetyl
coenzyme A for cellular respiration. Consider one molecule of glucose that goes through
glycolysis and cellular respiration. How many molecules of mitochondrial NADH will be
produced from one molecule of glucose? ____8__
(3 from each acetyl CoA x 2 acetyl CoA + 1 from each pyruvate dehydrogenase reaction x 2
= 8).
7. Fermentation and Respiration. Pyruvate produced from glycolysis can be used for
fermentation or for cellular respiration. When oxygen is supplied, pyruvate produced from
glycolysis is converted to acetyl coenzyme A for cellular respiration.
A. When pyruvate produced from glycolysis is used for cellular respiration, how many
molecules of ATP will be produced per each pyruvate consumed? Assume that NADH and
FADH2 are equivalent to 2.5 and 1.5 molecules of ATP, respectively. _______
Answer: 4 NADH + 1 FADH2 + 1 ATP = 10 + 1.5 +1 = 12.5 ATP.
When oxygen is absent, pyruvate produced from glycolysis is used for fermentation.
B. How many molecules of ATP will be produced by conversion of pyruvate to produce
lactate (part of fermentation)? Assume that mitochondrial NADH and FADH2 are equivalent
to 2.5 and 1.5 molecules of ATP, respectively. _____0
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Biochemistry Exam 3 Practice Problems
8. ETC and ATP synthase
A. The above diagram depicts electron transport chain (ETC). SELECT ALL CORRECT
statements.
a. Mitochondrial NADH can enter ETC through complex I.
b. Mitochondrial FADH2 can enter ETC through complex II
c. Complex II pumps protons into the intermembrane space.
d. The molecule labeled ‘C’ above can carry only one electron at a time.
e. Complex III pumps protons into the intermembrane space.
f. One molecule of ‘D’ is needed to oxidize ‘C’ completely.
g. In complex IV, electrons from cytochrome c proteins reduce water to oxygen.
B. On the diagram of the electron transport chain above, what molecule is represented
by “D”? ________________Cytochrome C
The table lists 3 inhibitors of the electron transport chain.
Inhibitor
Step inhibited
Demerol
complex I
Carboxin
complex II
Antimycin A Complex III
C. Compare the effects of three drugs on the delivery of electrons by NADH and FADH2, the
proton, gradient, and ATP synthesis by ATP synthase. Assume each inhibitor is able to
induce complete inhibition and only consider oxidative phosphorylation (not other
metabolic processes).
Delivery of electrons from NADH and FADH2:
Demerol only inhibits delivery of electrons from NADH which enter through complex I, but
electrons from FADH2 do not use complex I.
Carboxin inhibits delivery of electrons from FADH2 generated by TCA cycle in complex II,
but electrons from NADH and FADH2 from fatty acid breakdown can still enter the chain.
Antimycin A inhibits both because movement of electrons through complex III is required
for all electron movement.
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Biochemistry Exam 3 Practice Problems
Proton Gradient:
Demerol suppress all proton gradient generated by NADH but not from FADH2
Carboxin inhibits all proton movement from FADH2 generated by the TCA cycle (which
includes the protons normally moved from complexes III and IV) but not from NADH
Antimycin A inhibits proton movement from both NADH and FADH2 because electrons
can’t move through the chain.
Synthesis of ATP by ATP synthase: All three reduce ATP synthesis. Antimycin A results in
no protons moved, so reduces ATP synthesis completely. Demerol causes a moderate
decrease in ATP synthesis, and carboxin has the smallest effect because there is generally
less typically less FADH2 present than NADH (because TCA generates 3 NADH for each
FADH2). These effects are directly related to the number of protons that can be moved in
the presence of each drug.
9. Which statement is INCORRECT about the
following diagram? Select one answer.
a. A represents NADH
b. B represents FADH2
c. C is a small molecule that carries two
electrons each time
d. D is a lipid soluble protein that carries
two electrons each time
e. E is a gas molecule
10. NADH
A. When a molecule of glucose is consumed through glycolysis and citric acid cycle,
__2___ molecule(s) of cytosolic and ___8____ molecule(s) of mitochondrial NADH are
produced.
B. Select ALL possible ways that cytosolic NADH molecules can be oxidized.
a. Gluconeogenesis
b. Fermentation
c. Carnitine shuttle
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Biochemistry Exam 3 Practice Problems
11. When one molecule of myristic CoA (myristic acid: C14H28O2) is consumed through fatty
acid breakdown in mitochondria, ___7__ molecules of acetyl CoA, ____6___ molecules of
NADH, and ___6___ molecules of FADH2 are produced.
12. Select ALL metabolic pathways that use NADPH as reductant (substrate).
a. Glycolysis
b. Fermentation
c. Citric acid cycle
d. Electron transport chain
e. Fatty acid biosynthesis
13. Lactate.
Lactate is a primary source of pyruvate in liver cells undergoing gluconeogenesis.
A. What tissue is the most likely source of the lactate used in this reaction? (circle one)
i) brain
ii) adipocytes
iii) muscle
iv) pancreas
B. In the tissue you chose in b), lactate is a product of what pathway(s)? Circle all that
apply.
i) oxidative phosphorylation
ii) electron transport
iii) fermentation
iv) glycogen synthesis
v) fatty acid breakdown
14. Metabolic Pathways in Brain
A. What molecules are used by the brain for energy? Select all that apply.
a. glucose stored as glycogen in brain cells
b. glucose exported into the blood by liver cells
c. fatty acids stored as triacylglycerols in brain cells
d. fatty acids exported into the blood by liver cells
e. fatty acids exported into the blood by adipose/fat cells
B. The brain can also use ketone bodies as a source of energy. How are ketone bodies
converted to energy in the brain? Select the best answer.
a. ketone bodies ---> pyruvate --->glucose
b. ketone bodies--->pyruvate--->lactate
c. ketone bodies ---> pyruvate --->acetyl CoA---->CO2
d. ketone bodies--->acetyl CoA--->CO2
e. ketone bodies--->acetyl CoA--->fatty acid
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Biochemistry Exam 3 Practice Problems
15. Citrate.
A. List two metabolic intermediates that can be generated from citrate by a single reaction.
Indicate the location in the cell where each reaction occurs.
1.
2.
Fate
isocitrate
acetyl CoA
oxaloacetate (OAA)
Cellular Location
mitochondrial matrix
cytosol
B. Which metabolic pathways would be most likely to be active in liver cells during the
FED state? Select the best answer.
a. Glycolysis and fatty acid breakdown
b. Glycolysis and fatty acid synthesis
c. Gluconeogenesis and fatty acid breakdown
d. Gluconeogenesis and fatty acid synthesis
Citrate is a ligand of (binds to) Acetyl CoA carboxylase (ACC), an enzyme that generates
malonyl CoA.
C. What is the metabolic role of malonyl CoA? Select all that apply.
A. intermediate in TCA cycle
B. intermediate in fatty acid synthesis
C. intermediate in fatty acid breakdown
D. inhibitor of TCA cycle
E. inhibitor of fatty acid synthesis
F. inhibitor of fatty acid breakdown
D. What best describes the role of citrate binding to ACC? Select the best answer.
A. Substrate
B. Competitive inhibitor
C. Allosteric inhibitor (negative feedback inhibition)
D. Allosteric inhibitor (not negative feedback inhibition)
E. Allosteric activator (feed forward activation)
F. Allosteric activator (not feed forward activation)
E. For the following three pairs of conditions, circle the condition in which you would
expect ACC to be more likely to be active.
Circle one: Low fatty acid levels or high fatty acid levels
Circle one: Low cellular energy levels or high cellular energy levels
Circle one: High insulin levels or high glucagon levels
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Biochemistry Exam 3 Practice Problems
16. Acyl-carnitine
A. Which statements are true about acyl-carnitine formation (under normal conditions)?
Select all that apply.
a. occurs during fatty acid synthesis
b. occurs during fatty acid breakdown
c. occurs in the cytosol
d. occurs in the mitochondrial matrix
B. Explain the purpose of acyl-carnitine formation in fatty acid metabolism.
Transport acyl group into the mitochondrial matrix through the carnitine transporter in
the inner mitochondrial membrane. Fatty acid breakdown occurs in the mitochondrial
matrix.
17. ATP Synthase.
ATP synthase is comprised of multiple subunits including a, c, gamma and beta each with
distinct structures and functions. Select one of the subunits (a, c, gamma or beta to answer
the following question.
Selection: _______
Describe how key structural features and function of the subunit you selected contribute to
the overall activity of ATP synthase. Your answer must mention H+ (protons) and
specifically address the synthesis of ATP.
The A subunit has two hydrophilic half-channels open to the matrix and intermembrane
space. Protons from the intermembrane space bind to an aspartic acid on a c-subunit. The
c-subunit is deprotonated when it reaches the half-channel open to the matrix which
causes the c-subunits to rotate. The c-ring moves in one direction because it is unfavorable
for the deprotonated subunit to move into the hydrophobic membrane. The spinning of the
c-subunits in the c-ring causes the gamma subunit to rotate. The asymmetry of the gamma
subunit affects the conformation of the beta subunits which have three possible
conformations: open (low affinity for ADP and ATP and Pi), loose (high affinity for ADP and
Pi) and tight (high affinity for ATP). The tight state stabilizes ATP (lowers the energy)
allowing synthesis. (Answer does not need to include all details for full credit, but a
substantial and correct description including discussion of protons and ATP synthesis is
necessary).
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Biochemistry Exam 3 Practice Problems
18. Fatty acid metabolism.
A. Consider the overall process of fatty acid breakdown (fatty acid to acetyl-CoA) and the
overall process fatty acid synthesis (acetyl-CoA to fatty acid). Do not consider any
connecting pathways or reactions. Which statement(s) is/are true? Select all that apply.
a. ATP is a product of fatty acid breakdown and a substrate for fatty acid synthesis
b. NADPH is a product of fatty acid breakdown and substrate for fatty acid synthesis
c. Acyl-CoA with more than 3 carbons is an intermediate in fatty acid breakdown
and fatty acid synthesis
d. Acyl-carnitine is an intermediate in fatty acid synthesis and fatty acid breakdown
e. Malonyl-CoA is an intermediate in fatty acid synthesis and an inhibitor of fatty
acid breakdown
Briefly describe one similarity and one difference between Acetyl-CoA and Acetyl-ACP.
Please focus on characteristics mentioned in this course and relevant to metabolism. For
the difference, please be sure to fully address the characteristics of both molecules. (Stating
that one molecule has one characteristic and one molecule doesn’t is not sufficient.)
Similarity: both are intermediates in fatty acid synthesis; both are attached through
thioester bond, the linker region is similar, both are acyl carriers; both are substrates of
enzymes that are part of fatty acid synthase
Difference: acetyl-ACP is present in cytosol only, acetyl-CoA is present in cytosol and
mitochondrial matrix; ACP is a protein and CoA is similar to a nucleotide; acyl-ACP is part
of fatty acid synthase complex and CoA is used by different many enzymes; Acetyl-CoA is an
intermediate in fatty acid synthesis and fatty acid breakdown; Acetyl-CoA is also part of
other pathways, acetyl-ACP is only part of fatty acid metabolism; Acetyl-CoA is turned into
malonyl-CoA and Acetyl-ACP combines with malonyl-CoA
19. Citrate.
Citrate is an intermediate in the TCA cycle and fatty acid metabolism.
A. How would you predict that citrate would affect the activity of pyruvate dehydrogenase?
Please write inhibit or activate. inhibit
Explain your reasoning. Be sure to name any metabolic pathways or reactions that are
relevant to the connection between citrate and the enzyme.
PDH catalyzes the conversion of pyruvate to acetyl-CoA and acetyl-CoA is converted to
citrate in the first step of the TCA cycle. High levels of citrate would indicated that less
acetyl-CoA is needed so citrate would be predicted to inhibit PDH to reduce the amount of
acetyl-CoA made. This would be negative feedback.
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Biochemistry Exam 3 Practice Problems
B. Some reactions (labeled 1-4) relevant to the metabolic
pathways involving citrate are shown (right). Which of these
reactions occur in the cytosol? Select all that apply. 2,3,4
CoA
Acetyl-CoA
+ Oxaloacetate
CoA
ATP
Citrate
1
ADP
2
HCO3ATP
Acetyl-CoA
CoA
Acetyl-CoA
+ Oxaloacetate
ADP
3
Malonyl-CoA
2Pi
ATP
Fatty Acid
Citrate
AMP
4
Acyl-CoA
20. Fed, Fasted, and Exercise.
A. For each of the following pairs of pathways, select ONE state and tissue (a-f) from the
right column in which you would expect both pathways to be active. Answers may be used
more than once. There may be more than one correct answer, but please select only one.
Write the letter of your selection on the line provided.
Gluconeogenesis and Glycogen breakdown____ D or E
Glycolysis and Glycogen breakdown_____ F
Fatty acid breakdown and Triacylglycerol synthesis____ B
Glycolysis and Fatty Acid synthesis _____A
a. Fed state in liver
b. Fed state in
adipose
c. Fasted state in
brain
d. Fasted state in liver
e. Exercise in liver
f. Exercise in muscle
B. Under what conditions and in which tissues are ketones and lactate synthesized? For
each molecule, select all that apply. Please write the letter(s) of your answers on the
corresponding line. Answers may be used more than once.
Ketones________________ A,B Lactate ______________ C
a. in the liver during exercise
b. in the liver during the fasted state
c. in the muscle during exercise
d. in the muscle during the fasted state
e. in the brain during exercise
f. in the brain during the fasted state
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Biochemistry Exam 3 Practice Problems
21. Transport Across Membranes.
A. What would you predict is true about transport of fatty acids and glucose across the
plasma membrane of cells? Base your answer on the content of the course. Select all that
apply.
a. fat/adipose cells export fatty acids in the fed state
b. brain cells uptake glucose in the fasted state
c. muscle cells export glucose in the fasted state
d. liver cells export glucose in the fasted state
e. liver cells uptake fatty acids during the fasted state
f. brain cells uptake fatty acids in the fed state
B. Both diabetes and cancer affect glucose uptake and export by cells. Pick one of these
diseases and briefly explain how you would expect glucose transport across the plasma
membrane of cells to be affected compared to unaffected cells.
Selection:________________
Explain:
Diabetes- decreased uptake of glucose into cells (because insulin can’t signal increased
import, use, and storage of glucose) and/or increased export out of liver cells (because
gluconeogenesis is increased)
Cancer- increased uptake of glucose into cells (because glycolysis is increased
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C. Choose one metabolic intermediate that is transported across the mitochondrial
membrane and answer the following questions. Be sure to name a molecule that crosses
the membrane itself, was discussed in this class, and is not directly involved in oxidative
phosphorylation.
Name of molecule that is transported across the membrane: __________________
pyruvate, malate, acyl-carnitine, citrate
not correct: fatty acid, acyl-CoA, oxaloacetate, carnitine
Draw a diagram (with arrows and names of metabolites) representing the transport of the
molecule across the mitochondrial membranes through transporters. Include on the
diagram:
1) the molecule in both the cytosol and the mitochondrial matrix with an arrow
representing the direction of transport
2) a representation of a specific reaction that will generate the molecule before
transport
3) a representation of a specific reaction that will consume the molecule after transport
4) a pathway showing ONE likely eventual fate (CO2, lactate, glucose, fatty acid, ketone) of
the molecule after transport including any key intermediates and connections between
pathways.
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22. Oxygen and Oxidative Phosphorylation.
A. When oxygen levels are low, the activity of the TCA cycle and fatty acid breakdown often
decreases, but glycolysis does not. Explain why this observation makes sense based on the
characteristics and connections between the metabolic pathways. Be sure to specifically
explain the nature of the connection between oxygen and the metabolic pathways.
Reduced electron carriers generated must be regenerated to continue. NADH generated
from glycolysis can be conerted to NAD+ by fermentation instead of electron transport, but
NADH and FADH2 generated in TCA and fatty acid breakdown must be converted to NAD+
and FAD by ETC.
B. Consider an experiment measuring the O2 consumption
rates in isolated mitochondria. Assume oxygen, ADP, and Pi
are sufficiently abundant. The observed rates of oxygen
consumption are shown in the table. What types of molecules
do you think X, Y, and Z might be? Select all that apply for each
molecule (X,Y,Z) and write the letters of your choices (a-f) on
the appropriate line.
X _______ a
Y_______ c, d, or e
Z _________ b
a. Inhibitor of Complex I
b. Inhibitor of Complex II
c. Inhibitor of Complex III
d. Inhibitor of Complex IV
e. Inhibitor of ATP synthase
f. Uncoupling agent
Molecules
Added
None
Oxygen
Consumption
Rate
(relative)
0
NADH
100
NADH + X
0
NADH + Y
0
NADH + Z
100
FADH2
100
FADH2 + X
100
FADH2 + Y
0
FADH2 + Z
0
Explain your reasoning:
Molecule X affects exclusively NADH and molecule Z affects exclusively FADH2. Only electrons
from NADH pass through complex I and only electrons from FADH2 pass through complex II so
these are the complexes that must be inhibited by X and Y. Molecule X affects electron
transport when NADH or FADH2 are the electron source. Electrons from both pass through
complexes III and IV so inhibition of these complexes would affect both substrates. Inhibition of
ATP synthase would also decrease oxygen consumption because the electron transport chain
could not continue to move protons across the membrane if the gradient was too big. The
oxygen consumption rate in this case might not be zero due to proton leak so both “c and d”
and “c, d, e” were accepted as correct answers.
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C. How would you expect a reduction in the amount of coenzyme Q to affect oxidative
phosphorylation? Select all that apply.
a. Decrease the rate of electron flow through complex I
b. Decrease the rate of electron flow through complex II
c. Decrease rate of protons moved across the membrane by complex I
d. Decrease rate of protons moved across the membrane by complex II
e. Decrease the number of protons moved across the membrane for each NADH
molecule oxidized
f. Decrease the number of protons moved across the membrane for each FADH2
molecule oxidized
Explain your reasoning:
Coenzyme Q transfers electrons from complex I and II to complex III so electrons donated by
both NADH through complex I and FADH2 through Complex II would be affected. If coenzyme Q
is decreased, the rate of electron flow would be decreased because electrons must be passed
to coenzyme Q for more electrons to enter the complexes. The rate of protons moved across
the membrane by Complex I will also be affected because the proton movement is a result of
electron movement. Complex II does not move any protons so there will be no effect on rate.
The number of protons moved for NADH or FADH2 will not change if the electrons for each
molecule reach complex IV and are donated to water.
23. Fatty Acid Metabolism.
A. Which of the following is directly required as substrates for the process of fatty acid
synthesis (acetyl-CoA --->fatty acid)? Select all that apply.
a. carnitine
b. glycerol
c. acyl-carrier protein (ACP)
d. acyl-CoA (>2 carbons in the acyl)
e. NADH
f. ATP
g. Coenzyme A (CoA)
h. NADPH
B. Fatty acid synthesis and fatty acid breakdown do not occur in the same cell at the same
time. Briefly explain the mechanism of reciprocal regulation.
Malonyl CoA is an intermediate in fatty acid synthesis and inhibits carnitine transferase
which is important step in fatty acid breakdown. ACC activity regulates the production of
malonyl-CoA so activity of ACC inhibits fatty acid breakdown and promotes fatty acid
synthesis.
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24. Regulation of Metabolism.
A. Would you expect each of the following metabolic enzyme to be more likely to be active
in the liver during the fed state or fasted state?
glycogen synthase ______________ fed
carnitine transferase ______________ fasted
acetyl CoA carboxylase ______________ fed
phosphofructokinase 1 ______________ fed
glycogen phosphorylase ______________ fasted
fructose 1,6-bisphosphatase ______________ fasted
25. Muscle Metabolism.
A. During periods of rest, muscle cells tend to use fatty acids as a source of energy. Which other
metabolic processes do you think might also be active during rest (not exercise) in muscle cells
under conditions in which only fatty acids are being used for energy? Consider any possible
answers that would apply if the organism is fed or fasted states (or anywhere in between)
under normal oxygen levels. Please base your answer on the content covered in class. Select all
that apply.
a. gluconeogenesis
b. fatty acid synthesis
b. triacylglycerol breakdown
c. triacylglycerol synthesis
d. pyruvate to acetyl-CoA
e. ketone body synthesis
f. TCA cycle
g. oxidative phosphorylation
Answer: _________________
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During periods of exercise, muscle cells can switch to using glucose for energy. Some muscle
types mainly convert glucose to lactate and other muscle types mainly convert glucose to
acetyl-CoA. In both types of muscle, the fate of the carbons in lactate and acetyl-CoA is release
from the muscle cells into the blood.
B. The most likely fate of the carbons in lactate generated in the muscle during exercise is
__________ (metabolic pathway/reaction) in the ___________ (type of tissue). Assume
exercise is still occurring. Select the best answers from the lists below and write the
corresponding letter in each blank space. A, C
Metabolic Pathways/Reactions
a. Gluconeogenesis
b. TCA cycle
c. Ketone body synthesis
d. Glycogen synthesis
e. Fatty acid synthesis
Types of tissue
a. muscle
b. brain
c. liver
d. adipose
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C. The most likely fate of the carbons in acetyl-CoA generated in the muscle during exercise is
__________ (metabolic pathway/reaction) in the ___________ (type of tissue). Assume
exercise is still occurring. Select the best answers from the lists above (same as previous
question) and write the corresponding letter in each blank space. B, A
D. Which type of muscle cells do you think likely have more mitochondria?
a. cells that convert glucose to lactate
b. cells that convert glucose to acetyl-CoA
Answer: ______________
Explain your reasoning: Be sure to fully explain the connection between the metabolic
characteristics of the cells and the relevant metabolic reactions that occur in the mitochondria.
Conversion of glucose to acetyl-CoA (b) because the conversion of pyruvate to acetyl-CoA
occurs in mitochondria where pyruvate dehydrogenase is located. Also, when glucose is
converted to acetyl-CoA, then TCA and oxidative phosphorylation are likely used which also are
located in the mitochondria. Conversion of glucose to lactate occurs in the cytosol.
E. Carnitine supplements are sold and claim to increase cellular levels of carnitine. Explain why
increased carnitine levels might help increase muscle performance by affecting metabolism.
Please be sure to specifically and sufficiently explain the role of carnitine in metabolism based
on the content covered in this class.
Transport of acyl-CoA into mitochondria during fatty acid breakdown requires transfer of the
acyl from CoA to carnitine in the cytosol, transport through the carnitine transporter in the
inner mitochondrial membrane, and conversion back to acyl-CoA in the mitochondria
(carntitine shuttle). Increasing the amount of carnitine available might increase the rate of
transport of fatty acids into the mitochondria for fatty acid breakdown (it’s the rate limiting
step for fatty acid breakdown).
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26. Oxidative Phosphorylation.
A. NADH and FADH2 are both substrates of oxidative phosphorylation. For each statement
below, indicated whether it applies to oxidative phosphorylation starting with NADH, FADH2,
neither, or both. Write your answer on the line provided.
a. involves movement of electrons through complex I __________ NADH
b. involves movement of protons through complex IV __________ both
c. involves movement of protons through cytochrome C __________ neither
d. involves reduction of coenzyme Q__________ both
Consider an experiment that measures O2 consumption and ATP synthesis in isolated
mitochondria. Sufficient substrates of oxidative phosphorylation are available.
B. The graphs show the rate of
oxygen consumption and ATP
synthesis by the mitochondria
when the samples are
switched to conditions with no
oxygen. Explain how/why the
lack of oxygen affects the rate
of ATP synthesis. Be sure to
fully and specifically address the relevant characteristics, components, and process of oxidative
phosphorylation.
ATP synthesis in mitochondria mostly is from ATP synthase (some from TCA, but TCA is
inhibited in absence of Oxygen because mitochondrial NAD+ can’t be regenerated and NADH
inhibits regulated enzymes). ATP synthase uses proton gradient generated by ETC. Protons are
moved to the intermembrane when electrons move through the electron transport chain. O2 is
the final electron acceptor. If there is no O2 to accept electrons, no electrons will move and no
protons will be moved so there is no gradient for ATP synthase to use to make ATP.
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27. Fatty acid metabolism
A. Acyl-CoA and acetyl-ACP are both intermediates in fatty acid metabolism. Which statement is
true about the synthesis of acyl-CoA and acetyl-ACP? Select the best answer.
a. Acyl-CoA and acetyl-ACP will both be generated under conditions when malonyl-CoA
levels are high
b. Acyl-CoA and acetyl-ACP will both be generated under conditions when malonyl-CoA
levels are low
c. Acyl-CoA will be generated under conditions when malonyl-CoA levels are high
and acetyl-ACP will be generated under conditions when malonyl-CoA levels are low
d. Acyl-CoA will be generated under conditions when malonyl-CoA levels are low
and acetyl-ACP will be generated under conditions when malonyl-CoA levels are high
B. Briefly explain the relationship between malonyl CoA and the relevant factors in the
synthesis of acyl-CoA and acetyl-ACP.
Acyl-CoA is generated in the cytosol during fatty acid breakdown. Malonyl-CoA inhibits
carnitine transferase which is required to transport acyl-CoA into the mitochondrial matrix. If
addition of carnitine and therefore transport of acyl-CoA is inhibited by malonyl-CoA, synthesis
of acyl-CoA will also decrease.
Acetyl-ACP is a substrate for fatty acid synthesis. Malonyl-CoA is another substrate for fatty acid
synthesis so if malonyl-CoA is low, synthesis of acetyl-ACP would also be decreased because
fatty acid synthesis would not be active.
28. Oxidative Phosphorylation.
A. Consider a solution of isolated mitochondria in which oxidative phosphorylation is actively
occurring. If you add an inhibitor of complex II or complex III, could complex I still accept
electrons and move protons across the membrane? Assume complete inhibition of complex II
or III. Consider only oxidative phosphorylation and not potential effects of other metabolic
processes.
Complex II
inhibitor
Complex III
inhibitor
a
Yes
Yes
b
No
No
c
Yes
No
d
No
Yes
If complex II is inhibited, electrons can still enter through complex I (or coenzyme Q in some
cases) and be passed through the electron transport chain because movement through
complex II is not required. If complex III is inhibited in an actively working electron transport
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chain, all electron holding components will be reduced. No more electrons can enter the chain
unless the electrons can exit the chain. All electrons must move through complex III so
complete inhibition would prevent any movement of electrons in any of the components of the
electron transport chain. Protons are only moved across the membrane if electrons can move
through the complexes.
Consider a solution of isolated mitochondria in
which oxidative phosphorylation is actively
occurring. You are testing the effects of three
different molecules (A, B, and C) on oxidative
phosphorylation. You measure the rate of oxygen
consumption and ATP synthesis by oxidative
phosphorylation over time. In experiment 1, you
add molecule A first and then molecule C later. In
experiment 2, you add molecule B first and then
molecule C.
B. What do you think is the most likely identity of
molecule A based on the data? Select the best
answer.
a. inhibitor of complex I
b. inhibitor of complex III
c. inhibitor of ATP synthase
d. an uncoupling molecule
ATP synthesis is reduced completely, oxygen consumption is reduced, but not completely,
affected by uncoupling molecule
C. What do you think is the most likely identity of molecule B based on the data? Select the best
answer.
a. inhibitor of complex I
b. inhibitor of complex III
c. inhibitor of ATP synthase
d. an uncoupling molecule
ATP synthesis and oxygen consumption both reduced completely, unaffected by uncoupling
molecule
D. What do you think is the most likely identity of molecule C based on the data? Select the
best answer.
a. inhibitor of complex I
b. inhibitor of complex III
c. inhibitor of ATP synthase
d. an uncoupling molecule
Increases oxygen consumption independently of ATP synthesis
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E. Why is the effect of molecule C on oxygen consumption different in experiment 1 and
experiment 2? Be sure your answer addresses key relevant aspects of oxidative
phosphorylation.
Oxygen is consumed when electron transport is active. When complex III is inhibited
(experiment 2), there can’t be any electrons moved through the electron transport chain or
protons moved into the intermembrane space (or oxygen consumed or ATP synthesized). The
uncoupling molecule, which moves protons across the membrane, has no effect if electron
transport is blocked. When ATP synthase is inhibited (experiment 1), oxygen consumption
decreases because the H+ gradient is large and only reduced slowly by existing regulated or
unregulated proton leak. The uncoupling molecule allows more the protons accumulated in the
intermembrane space to move to the matrix (increases leak) so electron transport (which
consumes oxygen) can continue.
F. Explain how/why the number of c-subunits in ATP synthase is related to the amount of ATP
generated through oxidative phosphorylation by reduced electron carriers. Be sure your answer
addresses the connection between reduced electron carriers and ATP synthase, the role of the
structure and function of the c-subunits, and the connection to the generation of ATP.
The oxidation of reduced electron carriers results in the accumulation of protons in the
intermembrane space. Protons bind to aspartic acid residue on the c-subunits. The number of csubunits is equal to the number of protons required to turn the c-ring. The turning of the c-ring
causes turning of the gamma subunit. The turning of the gamma subunit changes the
conformation of beta subunits which generate ATP.
29. Exercise.
A. Consider a muscle cell in the body of someone who is running a marathon. Which of the
following metabolic processes do you think may be occurring in the skeletal muscle cells at any
point during the marathon? Select all that apply. Please base your answer on the class material.
a. glycogen synthesis
b. glycogen breakdown
c. glycolysis
d. fermentation
e. ketone body synthesis
f. gluconeogenesis
g. TCA cycle
h. fatty acid synthesis
i. fatty acid breakdown
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After the marathon ends, the person eats a large amount of glucose (so there is a lot of glucose
available in the blood) and there is still lactate circulating through the blood. The muscle cells
can take up both lactate and glucose from the blood. What do you think are the most likely
fates of the carbon atoms in lactate and glucose in the muscle cells? Do not consider any
changes in the conditions.
B. Fate of Glucose:
A. Glycogen
B. CO2
C. Fatty acid/Triacylglycerol
D. Ketone bodies
E. Lactate
Briefly explain your reasoning. Be sure to address the relevant pathways or reactions that are
active and why it makes sense that those pathways and not other relevant pathways would be
active under the conditions described in muscle cells.
Glycogen stores are low because they were used up during exercise. Glucose will be stored as
glycogen though glycogen synthesis. Glucose likely won’t be used for glycolysis/TCA because
fatty acids and lactate can be used for energy (ATP) so CO2 is not the most likely fate. Fatty acid
synthesis and ketone body formation do not occur in muscle cells. Fermentation is not likely to
occur in the rested state when O2 is present.
C. Fate of Lactate:
A. Glycogen
B. CO2
C. Fatty acid/Triacylglycerol
D. Ketone bodies
E. Lactate
Briefly explain your reasoning. Be sure to address the relevant pathways or reactions that are
active and why it makes sense that those pathways and not other relevant pathways would be
active under the conditions described in muscle cells.
Lactate will be converted to pyruvate by lactate dehydrogenase. This reaction is reversible so if
lactate levels are high and pyruvate levels are low, lactate will be turned into pyruvate. The
most likely fate of pyruvate is acetyl-CoA which can enter the citric acid cycle producing CO2.
The reduced electron carriers will be used in oxidative phosphorylation. Using pyruvate for
gluconeogenesis won’t happen because it doesn’t happen (mostly) in muscle cells and there is
plenty of glucose available. Fatty acid synthesis and ketone body formation also do not occur in
muscle cells.
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30. Consider molecule “X” which is a 6-carbon chain that is similar
to, but not exactly a fatty acid. Molecule X can be broken down to
CO2 using some of the same reactions used in conversion of a fatty
acid to CO2. Part of the pathway is represented in the diagram.
How many molecules (net) will be generated by the breakdown of
one molecule X to CO2? Important: Consider any relevant
reactions of the TCA cycle, but do not consider oxidative
phosphorylation or the addition of any additional acetyl-CoA
molecules that are not derived from one molecule X. Please show
sufficient work to show the reasoning for your answer.
CO2 ______
NADH ______
FADH2 _____
Oxaloacetate ______ ATP/GTP_____
Show your work:
Molecule X (6C) to succinyl-CoA (4C)+ acetyl-CoA (2C): 0 CO2, 1 NADH, 1 FADH2, 0
oxaloacetate, -1ATP
• Acetyl-CoA (2C) to CO2: 2CO2, 3 NADH, 1 FADH2, 0 oxaloacetate (-1, +1), 1 GTP
• Succinyl-CoA(4C) to OAA: 0CO2, 1 NADH, 1FADH2, 1 oxaloacetate (OAA is product, but
not substrate in this case), 1 GTP
Total: +2 CO2, +5 NADH, +3 FADH2, +1 oxaloacetate, +1 GTP/ATP
•
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31. Each arrow on the diagram is labeled with a number and a letter and represents one
step catalyzed by one enzyme or one enzyme complex (not many steps).
For the following questions (A, B, C, D), write the number and letter corresponding to one
arrow (for example, 5A for conversion of acetyl-CoA to Malonyl-CoA) in each blank space.
Base your answer on the content covered in class. There may be more than three answers,
but you should only list three.
A. List three steps that occur in the cytosol: ______
________
________
1B, 2B, 5A, 6A, 7B, 8B
B. List three steps that occur in the mitochondrial matrix: ______
3A, 4A, 8A, 7A
C. List three steps that do not occur in human cells: ______
1A, 2A, 3B, 4B, 5B, 6B
_______
_______
D. List three steps that do occur in human “brain” cells: ______
8A
_______
______
_______
______ 2B, 4A, 7A,
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32. Indicate which ATP synthase subunit(s) (labeled
1-4 on the diagram) best fits each of the following
descriptions. Select one answer. Each number may
be used more than once or not at all.
A. Moves protons (H+) across the membrane _______
1- c subunits
B. Binds ADP _________ 4- beta subunits
C. Forms a half-channel in the membrane _________ a subunit
D. Briefly describe how the rotation of specific ATP synthase subunits (labeled 1-4 on the
diagram) contribute to ATP synthesis. Be sure to address the changes that occur in all
relevant subunits during ATP synthesis.
Rotation of C-subunits (1) due to protonation causes the gamma subunit (3) to rotate. The
position of the gamma subunits relative to beta subunits (4) changes incudes 3 different
conformations in an order that leads to ATP synthesis in the tight state.
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