Download 3 hours - The University of Winnipeg

April 11, 2007
08.3503/3
Intermediate Biochemistry II
UNIVERSITY OF WINNIPEG
Department of Chemistry
FINAL EXAM
Starting Time: 9:00 AM
Duration: 3 hours
Examiner: D. Craig
Student’s Name:
THIS TEST IS FOR STUDENTS IN D CRAIG’S SECTION. IF YOU ARE IN D
VANDERWEL’S SECTION, THIS IS NOT YOUR TEST.
Special instructions
1. Please put your name on all pages in case they become detached.
2. Point value for each question is given with each question.
3. The exam is worth 50% of your final grade.
4. There are 2 parts to this exam. For Part I, fill out the attached "bubble sheet" with your answers.
Answer the questions in Part II in the space provided following each question.
5. There is an extra page at the end of the exam to finish any unfinished question. Please be sure to
indicate which question you are completing.
6. Please be neat. IF I CAN'T READ YOUR ANSWER I CAN'T MARK IT.
Question
Part 1
Part 2 Question 1
Question 2
Question 3
Question 4
Question 5
Question 6
Question 7
total
points
/40
/4
/6
/3
/4
/13
/6
/4
/80
Possibly Useful Information:
? G = ? Go' + RTlnQ + ZFE
? G = ? Go' + RTlnQ
E = Eo' - (RT/nF)lnQ
? G = -nFE
R = 8.3145 J/molK
F = 96480 J/Vmol
N = 6.02x1023 /mol
0 K = -273.15oC
Page 1 of 22
Part I: Answer all questions using the bubble sheets provided. Only the bubble sheets will be
graded. Choose the best answer. Each question is worth 1 point.
Question 1. What is the second product in the following transamination reaction:
O
C
O
O
O
C
O
+
H3N CH C O
CH3
H3N
CH C
CH2
CH2
CH2
CH2
C
C
O
O
O
+
?
O
O
a. oxaloacetate
b. malate
c. pyruvate
d. succinate
e. fumarate
Question 2. The reduction of fumarate produces...
a. oxaloacetate
b. malate
c. succinate
d. citrate
e. glyoxylate
Question 3. In which subcellular location of a hepatocyte does the following reaction predominantly
occur:
O
H3 N
O
CH C O
H3N
CH2
CH2
O
O
CH2
+
H2 O
CH2
NH
C
CH C
NH2
CH2
CH2
NH3
NH2
a. cytosol
b. mitochondrial matrix
c. mitochondrial intermembrane space
d. inner mitochondrial membrane
e. none of the above answers are correct
Page 2 of 22
+
C
H2N
NH2
Question 4. Consider the ß-oxidation of 16:0-CoA (palmitoyl-CoA) into acetyl-CoA. How many
molecules of O2 are consumed by the respiratory chain per molecule of 16:0 converted completely into
acetyl-CoA?
a. 3.5
b. 7
c. 14
d. 8
e. 16
Question 5. Consider the fermentation of glucose into ethanol. The glucose is enriched with 14C in
carbon-1. In which carbon will the ethanol produced be enriched in 14C?
a. carbon-1 only
b. carbon-2 only
c. carbon-3 only
d. in all of the carbons
e. in none of the carbons
Question 6. Removal of the amino group of the following molecule by transamination to aketoglutarate followed by decarboxylation of the resultant product yields...
O
H3N CH C
O
CH2
C
O
O
a. malate
b. pyruvate
c. oxaloacetate
d. citrate
e. fumarate
Question 7. The conversion of malate into oxaloacetate, as catalyzed by malate dehydrogenase,
occurs along with the...
a. oxidation of NAD+
b. oxidation of FAD
c. reduction of NADH
d. reduction of FADH2
e. none of the above
Page 3 of 22
Question 8. The transportation of ATP out of the mitochondrial matrix and ADP into the mitochondrial
matrix is energetically ‘driven’ by...
a. the mitochondrial electochemical proton gradient
b. the Na+ gradient
c. the hydrolysis of ATP into ADP and Pi
d. the hydrolysis of ATP into AMP and PPi
e. none of the above
Question 9. Consider the following redox reaction...
ß-hydroxy-acyl-CoA + NAD+ ? ß-keto-acyl-CoA + NADH + H+
Which of the following statements is false?
a. Eo’ for this reaction is the value of the standard reduction potential for the reduction of NAD+ minus
the value of the standard reduction potential for the reduction of ß-keto-acyl-CoA.
b. Eo’ for this reaction is the value of the standard reduction potential for the reduction of NAD+ plus
the standard oxidation potential for the oxidation of ß-hydroxy-acyl-CoA.
c. At equilibrium, the value of E for the reduction of NAD+ is greater than the value of E for the
reduction of ß-keto-acyl-CoA.
d. Under conditions where the value of E for the overall reaction is positive, the reaction is spontaneous
in the absence of a suitable enzyme.
e. Under conditions where the value of E for the overall reaction is positive, the reaction is spontaneous
in the presence of a suitable enzyme.
Question 10. Consider the oxidation of NADH in the mitochondrial respiratory chain. Electrons are
transferred from...
a. NADH to complex I to complex II to complex III to complex IV to O2
b. NADH to complex II to complex III to complex IV to O2
c. NADH to complex I to complex II to complex IV to O2
d. NADH to complex I to complex III to complex IV to O2
e. NADH to complex I to complex II to complex IV to O2
Question 11. Consider only one cycle of the Kreb’s cycle. Acetyl-CoA is merged with oxaloacetate
which is enriched with 14C in carbon-3. The citrate formed is eventually converted to malate. Which
carbon on malate will be enriched with 14C?
a. carbon-1 only
b. carbon-2 only
c. carbon-3 only
d. carbon-4 only
e. none of the above answers are correct
Page 4 of 22
Question 12. Consider the fatty acid 20:1? 9 and the fatty acid 18:0. How many more ATP will the
complete catabolism of 20:1? 9 into CO2 and water yield than the complete catabolism of 18:0 yield.
Assume each NADH and FADH2 formed are ‘worth’ 3 and 2 ATP respectively.
a. 10
b. 12
c. 14
d. 16
e. none of the above answers are correct
Question 13. The double bonds of fatty acids are normally in the __________ configuration. During
ß-oxidation the double bond formed is usually ____________.
a. cis, cis
b. trans, trans
c. cis, trans
d. trans, cis
e. none of the above answers are correct
Question 14. How many moles of NADH are consumed in the conversion of lactate into glucose (via
gluconeogenesis) in a liver cell?
a. 1
b. 2
c. 3
d. 4
e. none of the above answers are correct
Question 15. The desaturation of a fatty acid in a cell occurs along with the...
a. reduction of NAD+
b. reduction of NADP +
c. oxidation of NADH
d. oxidation of NADPH
e. none of the above answers are correct
Question 16. How many net ATP equivalents does it “cost” for a liver cell to attach a glucose onto a
glycogen chain (not making a branch point)?
a. zero
b. 1
c. 2
d. 3
e. 4
Page 5 of 22
Question 17. Following are 5 sets of molecules. Consider the net sustainable conversion of the first
molecule of each set into the second molecule of each set. In which of the following sets is the net
conversion not possible in a liver cell?
COO
COO
a.
O
C
O
into
C
H 2C
CH3
COO
2-
COO
b.
O
C
O3PO
H
CH 3
c.
OH
H2
OOC CH C COO
OH
O
into
H
H
OH
H
OH
COO
C
into
OPO 32-
H 2C
COO
COO
d.
C
OPO 32-
into
HO CH
H2 C
H 2C
COO
COO
e.
into
OH
H2
OOC CH C COO
Page 6 of 22
Question 18. Under what conditions is muscle glycogen degraded into glucose and released to the
blood?
a. in the presence of a glucagon signal
b. in the presence of an insulin signal
c. in the presence of an adrenalin (epinephrine) signal
d. during a period of starvation which exceeds 3 days
e. none of the above answers are correct
Question 19. Which of the following components of the respiratory chain diffuses the most rapidly?
a. complex I
b. complex II
c. complex III
d. complex IV
e. cytochrome c
Question 20. The matrix of the mitochondria is ________ relative to the cytosol. The electrical
potential of the membrane is about 100 mV, inside _________.
a. basic, negative
b. acidic, positive
c. basic, positive
d. acidic, negative
e. none of the above answers are correct.
Question 21. Increased levels of epinephrine in the blood will:
a. activate adenylate cyclase in liver and muscle cells.
b. stimulate glycogen synthesis.
c. inhibit glycolysis in the muscle cell.
d. stimulate gluconeogenesis in the muscle cell.
e. inhibit the formation of cAMP.
Question 22. Which of the following statements about glycogen and glucose metabolism in skeletal
muscle is correct?
a. Glycogen is hydrolyzed to free glucose that can then enter the glycolytic pathway.
b. Glucose residues from glycogen yield a net of 3 ATP when converted to lactate in skeletal muscle.
c. No nucleotide is required to convert glucose to glycogen.
d. Phosphorylase a is the only enzyme required to totally degrade glycogen to glucose-6-phosphate.
e. ATP is directly required for the conversion of glycogen to glucose-1-phosphate.
Page 7 of 22
Question 23. In skeletal muscle cells, the NADH that is produced by glycolysis under anaerobic
conditions (vigorous exercise) is regenerated to NAD+ by the conversion of:
a. acetaldehyde ? ethanol.
b. lactate ? pyruvate.
c. phosphoenolpyruvate ? pyruvate.
d. pyruvate ? lactate.
e. glyceraldehyde-3-phosphate ? 1,3-bisphosphoglycerate.
Question 24. Which of the following metabolic conversions is considered to be the major control point
of glycolysis?
a. Fructose-1,6-bisphosphate ? dihydroxyacetone phosphate + glyceraldehyde-3-phosphate
b. Glucose ? glucose-6-phosphate
c. 2-phosphoglyerate ? phosphoenolpyruvate
d. Fructose-6-phosphate ? fructose-1,6-bisphosphate
e. pyruvate ? lactate
Question 25. Which of the following is at a higher level of oxidation than CH3CHO?
a. CH3CH2OH
b. CH3CH3
c. CH2=CH2
d. CH3CO2H
e. none of the above
Question 26. Consider the following metabolic reaction:
Succinyl-CoA + Acetoacetate ? Acetoacetyl-CoA + Succinate ? G°' = –1.25 kJ/mol
The ? G°' for the hydrolysis of Succinyl-CoA is –33.9 kJ/mol. What is the ? G°' for the hydrolysis of
Acetoacetyl-CoA (Acetoacetyl-CoA + H2O ? Acetoacetate + CoA)?
a. –35.2 kJ/mol
b. –32.7 kJ/mol
c. +32.7 kJ/mol
d. +35.2 kJ/mole
e. none of the above
Page 8 of 22
Question 27. Which of the numbered arrows in the figure to the right points toward a “high-energy”
phosphoanhydride bond?
O
-
O
-
1
4
5
O
-
NH2
N
-
O
P O
P O
P O CH2
O
O
O
N
O
N
N
2
3
HO
OH
a. 1
b. 2
c. 3
d. 4
e. 5
Question 28. The central pathways for fuel metabolism in mammals converge on the molecules:
a. DNA and RNA.
b. pyruvate and acetyl-CoA.
c. cAMP and ATP.
d. lipids and glucose.
e. none of the above
Question 29. The metabolic fate(s) of glucose-6-phosphate include:
a. glycogen and glucose.
b. ribose-5-phosphate and acetyl-CoA.
c. DNA and RNA.
d. a and b
e. a, b, and c
Question 30. When glutamate is oxidatively deaminated by glutamate dehydrogenase (GDH), the
products include______.
a. NADH, ? -iminoglutarate, and NH3
b. NAD(P)H + H+, NH4+, and ? -ketoglutarate
c. NADH, glutamine, and NH3
d. NAD(P)H, H2O, and ? -ketoglutarate
e. none of the above
Page 9 of 22
Question 31. The electrons formed from the oxidation of glucose are:
a. directly transferred to O2 during the citric acid cycle.
b. transferred to the coenzymes NAD+ and FAD.
c. transferred to succinate and arachidonic acid.
d. a and b
e. none of the above
Question 32. Which of the following statements about the mitochondrial inner membrane is (are) not
true?
a. The inner membrane is permeable to CO2, H2O, and small ions.
b. The inner membrane contains about 75% protein.
c. The inner membrane contains many respiratory proteins.
d. The inner membrane is highly invaginated.
e. all of the above are true
Question 33. How many electrons do (does) the prosthetic group(s) in cytochrome c accept?
a. none
b. two
c. one
d. one or two
e. none of the above
Question 34. The Glucose-Alanine cycle involves:
a. the conversion of the gluconeogenic precursor alanine to glucose.
b. the synthesis of pyruvate from alanine in skeletal muscle and the synthesis of alanine from pyruvate in
liver.
c. the synthesis of alanine from pyruvate in skeletal muscle and the synthesis of pyruvate from alanine in
liver.
d. the synthesis of urea in liver and degradation of urea to carbon dioxide and ammonia by bacteria in
the gut.
e. the production of lactate from glucose in peripheral tissues with the resynthesis of glucose from
lactate in liver.
Question 35. The largest energy store in a well-nourished human is:
a. muscle glycogen.
b. liver glycogen.
c. blood glucose.
d. triacylglycerols in adipose tissue.
e. ATP in all tissues.
Page 10 of 22
Question 36. Almost all of the oxygen (O2) one consumes in breathing is converted to:
a. carbon dioxide (CO2).
b. carbon monoxide and then to carbon dioxide.
c. water.
d. acetyl-CoA.
e. none of the above.
Question 37. A new compound is isolated from mitochondria and a claim is made that it represents a
previously unrecognized carrier in the electron transfer chain, and it is given the name of coenzyme Z.
Which line of evidence do you feel is the least conclusive in assigning this compound a position in the
electron transfer chain?
a. When added to a mitochondrial suspension, coenzyme Z very rapidly and specifically is taken up by
the mitochondria.
b. Removal of coenzyme Z from the mitochondria results in a decreased rate of oxygen consumption.
c. Alternate oxidation and reduction of the mitochondrion-bound coenzyme Z can be readily
demonstrated.
d. The rate of oxidation and reduction of mitochondrion-bound coenzyme is of the same order of
magnitude as the overall rate of electron transfer in mitochondria as measured by oxygen consumption.
e. All of the above provide definitive proof that coenzyme Z is in the electron transfer chain.
Question 38. For which of the following compounds does the inner mitochondrial membrane have a
transporter (i.e., which of the compounds CAN cross the inner mitochondrial membrane)?
a. oxaloacetate
b. acetyl-CoA
c. protons
d. NADH
e. none of the above.
Question 39. In the majority of cases, the a-amino group of an a-amino acid is removed by a(n)
__________ reaction.
a. Carboxylation
b. Hydrolysis
c. Dehydrogenation
d. Allergic
e. Transamination
Page 11 of 22
Question 40. Ketogenic amino acids are broken down to acetoacetate or ______.
a. ? -hydroxybutyrate
b. acetone
c. fatty acids
d. acetyl-CoA
e. pyruvate
Page 12 of 22
Part II. Answer all questions in the space provided following them.
Question 1 (4 points). You discover a new electron transport chain-type pathway in some obscure
bacteria that you discovered somewhere. NADH is oxidized into NAD+ and its electrons are
transferred through a series of redox proteins and finally used to reduce nitrate into nitrite. The relevant
half reactions are as follows:
NAD+ + H+ + 2e- ? NADH
Eo' = -315 mV
cytochrome X3+ + 2e- ? cytochrome X+
Eo' = +256 mV
3+
+
cytochrome Y + 2e ? cytochrome Y
Eo' = +286 mV
cytochrome Z23+ + e- ? cytochrome Z2+
Eo' = +390mV
NO3- + 2H+ + 2e- ? NO2- + H2O
Eo' = +420 mV
Which step in this electron transport chain-type pathway occurs with the largest amount of free energy
if [NADH]/[NAD+] = 23, [cytochrome X+]/[cytochrome X3+] = 1.8,
[cytochrome Y+]/[cytochrome Y3+] = 2.6, [cytochrome Z2+]/[cytochrome Z3+] = 3.0 and
[NO2-]/[NO3-] = 1.1. Calculate ? G at a temperature of 25oC.
Page 13 of 22
Question 2 (6 points): Draw a sequence of reactions that allows for the complete sustainable
catabolism of oxaloacetate into CO2. Use only reactions seen in class and show complete reactions.
Chemical structures are not required.
Page 14 of 22
Question 3 (3 points): Consider a liver cell that is converting glucose into fatty acids. Draw a
sequence of reactions which allows for the sustainable net transportation of acetyl-CoA equivalents out
of the mitochondrial matrix and into the cytosol. Draw complete reactions. Chemical structures are not
required.
Page 15 of 22
Question 4 (4 points): A cell contains inhibitors for pyruvate kinase (PEP ? pyruvate) and
glyceraldehyde-3-phosphate dehydrogenase (glyceraldehyde-3-P ? 1,3-bisphosphoglycerate). These
inhibitors completely inhibit these enzymes. The cell is fed 2-phosphoglycerate enriched with 14C in
carbon-1. The cell is incubated for a few hours. Draw the structure of the glycolytic intermediates that
will be enriched with 14C and indicated which carbons will be enriched. Assume the cell remains viable
during the experiment.
Page 16 of 22
Question 5 (13 points). Following are a series of sets of two molecules. Name what pathway(s)/
processes are required for the net sustainable (don’t worry about how inorganic species and
nucleotides are regenerated) conversion of the first molecule of each set into the second molecule of
each set. There is not necessarily a 1:1 molar ratio. For each answer, indicate a cell type seen in class
that can undergo this process and in which subcellular location(s) this process predominantly occurs.
Not all parts of this question are of equal value.
Question 5a.
HO CH 2
O
O
OH
into
-O
O
O
OH
O-
OH
OH
P
OH
OH
OH
Question 5b.
O
H 3N
CH C
CH2
O
O
H3N
into
CH C
CH2
CH2
C
C
O
O
O
O
O
Page 17 of 22
Question 5c.
HO
CH 2
O
H 3N
O
CH C
O
OH
into
CH3
OH
OH
OH
Question 5d.
HO
CH2
O
OH
into
H2C
H
C
CH2
O
O
O
O C O C O
C
OH
OH
OH
Page 18 of 22
Question 6 (6points). Draw the structures of the following molecules and answer any associated
questions.
Question 6a. Dihydroxyacetone phosphate. What is the class of enzyme that converts this molecule
into glyceraldehyde-3-phosphate (ie it is not a ‘kinase’ but rather a ...)
Question 6b. Open chain form of ribulose-5-phosphate. If a liver cell was ‘fed’ ribulose-5-phosphate,
would it be possible for the cell to catabolize it for the purpose of reducing NADP +?
Question 6c. A liver cell is fed galactose. The first thing that happens is it gets phosphorylated. Draw
the phosphorylated form of galactose (in the pyranose form) that is first formed. How many ATP can
be produced from the complete catabolism of a molecule of galactose (as seen in class with the usual
assumptions).
Page 19 of 22
Question 7 (4 points). A liver cell is well fed with alanine. It requires glutamate. How many ATP are
consumed/produced in the net sustainable conversion of alanine into glutamate. Determine your answer
per molecule of glutamate produced. You are not required to show the reactions nor structures but you
are required to show enough of you work to demonstrate that you did not just make a lucky guess.
Page 20 of 22
Extra pages to finish any unfinished questions. Please indicate which question it is that you
are finishing.
Page 21 of 22
Page 22 of 22