Download Final Key - UC Davis Plant Sciences

BIS103-001 (Winter 2007)
Final Exam (March 20)
Name_____________________________________
Instructor: Abel
Student ID #
ANSWER KEY
Pls., check appropriate box below.
Undergraduate Student
Completing Incomplete
Open Enrollment Student
Graduate Student
This exam consists of 8 questions. A maximum of 100 points can be earned. Partial credit will be given.
There are a total of 12 pages, including the cover page and one blank sheet at the end for notes.
However, do not use the blank sheet for your final answers. If you need more space, use the back of
pages 2-11. Write your name on top of each page! Petitions for regrading will be considered only if
you have used permanent ink, unless an addition error has occurred.
*IT IS YOUR RESPONSIBILITY TO WRITE LEGIBLE!
No extra effort will be made to decipher your handwriting.
Question
Value
1
22
2
12
3
12
4
12
5
9
6
7
7
12
8
14+2
TOTAL
100 (+2)
Score
T = 25 oC (298 K)
T = 37 oC (310 K)
R = 8.315 J mol-1 K-1
F = 96.5 kJ mol-1 V-1
n = equivalents of electrons
Z = charge of proton
ΔG = ΔGo’ + RTln[Prod.]/[React.]
ΔG = ΔGo’ + 2.303RTΔpH + ZFΔΨ
ΔGo’ = – nFΔEo’
ΔEo’ = Eo’Oxidant – Eo’Reductant
I,_______________________________________, authorize the University to distribute publicly this
graded exam (e.g., handed out in class or left in a bin for pick up).
I am aware of the fact that violations of the Academic Code of Conduct1 may be reported to UC Davis
Student Judicial Affairs.
1
Examples of academic misconduct include: receiving or providing unauthorized assistance on examinations, using
unauthorized materials during an examination, altering an exam and submitting it for re-grading, or using false excuses to
obtain extensions of time (http://sja.ucdavis.edu/cac.htm).
Signature________________________________________ Date____________________________
1
BIS103-001 (Winter 2007)
Final Exam (March 20)
1. (22 pts.)
Name_____________________________________
Short answer warm-up questions.
a) Triglycerides are synthesized from glycerol-3-P and from activated fatty acids. How is glycerol-3-P
produced from an intermediate of glycolysis? How are fatty acids activated? (4 pts)
Balanced reaction generating glycerol-P from a glycolysis intermediate:
Dihydroxyacetone-P (DHAP) + NADH Ù Glycerol-3-P + NAD+
Reaction that activates fatty acids for triacylglyceride synthesis:
Fatty Acid + ATP + CoA-SH Î Acyl-CoA + AMP + PPi (Î 2Pi)
b) Humans do not have the glyoxylate cycle. Describe in one sentence its purpose in plants and
microorganisms. Give the structure of glyoxylate. Give the reaction catalyzed by malate synthase
(names of reactants and products only) (4 pts)
Purpose: To convert lipids (fatty acids) into carbohydrates.
Glyoxylate structure:
See booklet
Malate synthase reaction: Acetyl-CoA + Glyoxylate + H2O Î Malate
c) Draw the structure of urea and indicate the two precursor molecules from which the N and C atoms
are derived. (3 pts)
See booklet for structure.
1) Carbamoyl-P (made from ammonia and bicarbonate)
2) Aspartate
d) Describe in one sentence the role of the “Methyl cycle”. (1 pts)
To regenerate S-Adenosylmethionine (SAM).
2
BIS103-001 (Winter 2007)
Final Exam (March 20)
Name_____________________________________
e) Describe in one sentence the difference between oxidases and oxygenases. (2 pts)
Oxidases use molecular oxygen as electron acceptor and do not incorporate the “O” into the
substrate, whereas oxygenases introduce one or both O atoms into the substrate.
f) Acetyl-CoA (or “activated acetate”) is a central intermediate in metabolism. There is a chemical
reason why each carbon of acetyl-CoA is considered to be “activated” (or reactive). (2 pts)
Reason 1: Hydrolysis of the CoA-thioester bond.
Reason 2: The C-H bonds of the methyl group are more polarized (acidic).
g) Given below are the names of three “activated” precursor molecules. For each precursor, indicate
one biochemical pathway that utilizes it. Give also the reason why the initial reaction (in which the
activated precursor is a reactant) is driven into the direction of product formation. (6 pts)
AMP-Sulfate (APS)
Pathway:
Sulfate assimilation
Reaction driven by:
Release of AMP
UDP-Glucose
Pathway:
Synthesis of carbohydrates (disaccharides, polysaccharides, glycogen)
Reaction driven by: Release of UDP
5-Phosphoribosyl-1-pyrophosphate (PRPP)
Pathway:
Synthesis of nucleotides (salvage pathway, de novo synthesis)
Reaction driven by: Release and hydrolysis of pyrophosphate (PPi)
3
BIS103-001 (Winter 2007)
Final Exam (March 20)
2. (12 pts)
Name_____________________________________
Shown below are several reactions discussed in class. Give the names for the provided
chemical structures of substrate and product, for any missing co-factor that would be
part of the written reaction or for covalently-bound co-factors if required by the enzyme,
and the name of the enzyme catalyzing the reaction (enzyme class is sufficient).
COO-
a)
O
C
H
C
COO-
+
H
C
NH2
H
C
H
Glu
H
H
+ α-KGA
H
Substrate: Pyruvate
Product: Alanine
Co-factor: PLP (pyridoxal-P)
Enzyme: (Ala) Transaminase/
Transferase
b)
NO 3-
N O 2-
Substrate: Nitrate
Product: Nitrite
Co-factor: NAD(P)H
Enzyme: Nitrate reductase
(Oxidoreductase)
COO-
c)
C
CH2
S-CoA
O
C
+
CoA-SH
O
CH2
CH2
CH2
COO-
COO-
+
CO2
Substrate: α-KGA
Product: Succinyl-CoA
Co-factors: NAD+, TPP,
Lipoic acid, FAD
Enzyme: α-KGA Dehydrogenase
(Oxidoreductase)
4
BIS103-001 (Winter 2007)
Final Exam (March 20)
3. (12 pts)
Name_____________________________________
The metabolic pathways and enzymes discussed this quarter are not all localized in the
same subcellular compartment in eukaryotes. Indicate the subcellular location for the
pathways or enzymes listed below (disregard transporters and shuttles). If a pathway
occurs in more than one location, indicate all subcellular compartments. Each
compartment may also be used more than once. Do not guess! You will loose 0.5 point
for each wrong additional answer.
A.
B.
C.
D.
E.
Nucleus
Cytosol
Mitochondrial matrix
Inner Mitochondrial Membrane
Lysosome
F.
G.
H.
I.
J.
Chloroplast (thylakoid lumen)
Chloroplast (stroma)
Glyoxysome
Peroxisome
Secretory vesicles
C, D
TCA Cycle
C
β-oxidation of fatty acids
F
Oxygen evolution
B, C
Substrate level phosphorylation
H
Glyoxylate cycle (plants)
B
Pentose phosphate pathway (animals)
B
Anaerobic glycolysis
G
Calvin cycle
B
Fatty acid synthesis
F
Plastocyanin
D
Cytochrome c oxidase
B, C
Urea cycle
4. (12 pts)
Fretting over a cup of coffee…
a) Caffeine (see structure below) belongs to which class of compounds? Circle only one! (1 pt)
H 3C
O
H 3C
Amino Acids
Pyrimidines
Nucleotides
Purines
Nucleosides
Peptides
N
N
N
N
O
CH 3
5
BIS103-001 (Winter 2007)
Final Exam (March 20)
Name_____________________________________
b) Which co-factor is the most likely the donor of the three methyl groups of caffeine? (1 pts)
Full name of co-factor: S-Adenosylmethionine (SAM)
c) Caffeine is an inhibitor of the enzyme cyclic nucleotide phosphodiesterase that participates in the
adrenaline-mediated regulation of protein kinase A activity. Give the balanced reaction catalyzed by
cyclic nucleotide phosphodiesterase. (2 pts)
Reaction: 3’:5’-cyclic-AMP + H2O Î 5’-AMP
d) What will be the consequence of increased coffee (caffeine) consumption on protein kinase A
activity? Briefly explain your answer. (3 pts)
Protein kinase A activity will be (circle):
Brief explanation:
increased
decreased
Since caffeine inhibits the cyclic nucleotide phosphodiesterase,
3’:5’-cyclic-AMP levels will remain elevated, which in turn leads to a
prolonged activation of protein kinase A.
e) A Google search for “coffee and antioxidants” indicates that coffee is an excellent source of
antioxidants that help to detoxify “reactive oxygen species (ROS)”. What major metabolic process
generates ROS in the cell? (1 pt)
Mitochondrial ETC
f) Diagram the process of ROS detoxification that involves glutathione. (4 pts)
See p. 109 of booklet.
6
BIS103-001 (Winter 2007)
Final Exam (March 20)
5. (9 pts)
Name_____________________________________
Arginine can be synthesized from ornithine in the urea cycle. Therefore, arginine is an
essential amino acid only under certain circumstances when the metabolic demand for
arginine is exceedingly high, such as during childhood, pregnancy, or recovery from
illnesses. Ornithine (see below, compound on the right) can be synthesized in three
reactions from the compound shown on the left.
NH2
-
COO
CH2
CH2
I.
CH2
H
C
CH2
II.
COO -
CH2
H
NH3+
C
COO-
NH3+
Ornithine
a) Name the precursor of ornithine shown on the left (1 pts)
Name of ornithine precursor:
Glutamate
b) How does the synthesis of ornithine proceed, taking into consideration that one reaction requires
NAD+, another is catalyzed by a transaminase, and yet another produces ADP as one of its products
(Note: all reactions have been discussed in class in a different context)?
Draw the structures of the intermediates in the boxes below, write all co-factors and their products above
each arrow, and give the enzyme class below each arrow. (8 pts)
Kinase
(Transferase)
Dehydrogenase
(Oxidoreductase)
Acyl-phosphate
Precursor
Glu Î α-KGA
PLP
NAD+ Î NADH
ATP Î ADP
Intermediate I
Transaminase
(Transferase)
(Semi)-Aldehyde
Intermediate II
Ornithine
7
BIS103-001 (Winter 2007)
Final Exam (March 20)
6. (7 pts)
Name_____________________________________
Questions on the tetrahydrofolate (THF) co-factor.
a) Name the dietary precursor to THF? (1 pt): Folic Acid
b) N5, N10-methylene-THF can be generated from serine. How is serine produced from an intermediate
of glycolysis? Give the chemical structures of the precursor, intermediates and serine in the boxes
below (co-factors or other substrates that are required in the written direction are give above each
arrow). (4 pts)
NAD+
Glu
H2O
Precursor
Serine
3-Phosphoglycerate 3-Phosphohydroxy pyruvate 3-Phospho serine
See Booklet for structures
c) The formation of dTMP from dUMP requires a methylation step. Draw the form of THF on the frame
below that participates in this conversion? (2 pt)
N10
N5
CH2
N5, N10-Methylene-THF
8
BIS103-001 (Winter 2007)
Final Exam (March 20)
Name_____________________________________
7. (12 pts) Questions on regulation.
a) It was recently discovered that xylulose-5-P is an allosteric activator of the phosphoprotein
phosphatase that is responsible for the dephosphorylation of the bifunctional enzyme PFK-2/F2,6BPase.
Dephosphorylation of the PFK-2/F2,6BPase isoenzyme in the liver results in the activation of its kinase
activity. Briefly explain the logic of this regulatory loop with respect to the degradation of excess
dietary xylulose in the liver. (4 pts)
Activation of PFK-2 will lead to the increased formation of F2,6P, which is an allosteric activator
of PFK-1 (phosphofructo kinase 1) and consequently of glycolysis. Xylulose will be converted to
F6P and GA3P by the pentose phosphate pathway. Thus, activation of glycolysis by xylulose via
PFK-2 will metabolize excess dietary xylulose.
b) Why is the hormonal regulation of glycolysis and gluconeogenesis different between the skeletal
muscles and the liver? On the other hand, why is it similar for glycogen synthesis and breakdown?
Mention the metabolic roles of both organs in carbohydrate metabolism. (4 pts)
These two organs have different metabolic roles. One of the major tasks of the liver is to produce
glucose that can be used as a fuel by the other cells of the body. On the other hand, the skeletal
muscles are specialized for energy production (ATP).
Thus, if glycolysis is activated in the muscles (ATP production), gluconeogenesis will be activated
in the liver to produce glucose for the muscles and to recycle the lactate produced during
anaerobic glycolysis (muscles). Glycogen breakdown will be activated in both organs to feed
glycolysis in the muscles and to export glucose from the liver to the muscles.
c) ATP, AMP, and NAD(P)H often act as allosteric regulators of key enzymes in metabolism. Predict
the effect of each regulator of the activities of the following enzymes (use “+” for activation and “-“ for
inhibition). (4 pts)
ATP
AMP
NAD(P)H
Citrate Synthase
-
+
-
Fructose-1,6,-bisphosphatase
+
-
+
ATP:Citrate Lyase
+
-
+
-
+
-
Pyruvate Dehydrogenase
9
BIS103-001 (Winter 2007)
Final Exam (March 20)
Name_____________________________________
8. (14 + 2 pts) Multiple-choice questions. Circle the best answer. There is only one best answer per
question. Each question is worth 2 pts.
a.
b.
c.
d.
Which of the following enzyme is NOT part of the glyoxylate cycle?
i
Isocitrate Dehydrogenase
ii
Malate Dehydrogenase
iii
Malate Synthase
iv
Citrate Synthase
v
Isocitrate Lyase
Which of the following metabolites is NOT an intermediate of the urea cycle?
i
Ornithine
ii
Arginine
iii
Alanine
iv
Fumarate
v
Citrulline
Which of the following C1-groups cannot be transferred by tetrahydrofolate?
i
–CH2–
ii
–CH3
iii
–CHO
iv
–COOH
v
=CH–
Which of the following processes in the liver is inhibited by insulin?
i
Glucose uptake
ii
Glycolysis
iii
Glycogen synthesis
iv
Fatty acid synthesis
v
Glycogen degradation
10
BIS103-001 (Winter 2007)
Final Exam (March 20)
e.
f.
g.
h.
Name_____________________________________
Which of the following carboxylases occurs ONLY in photosynthetic organisms?
i
Pyruvate carboxylase
ii
Ribulose-1,5-bisphosphate carboxylase
iii
Acetyl-CoA carboxylase
iv
Propionyl CoA carboxylase
v
Phosphoenolpyruvate carboxylase
Which of the following enzyme-catalyzed reactions generates urea as a product?
i
Asparaginase
ii
Glutaminase
iii
Argininosuccinase
iv
Arginase
v
Urease
Pyridoxal phosphate is a cofactor in this class of reactions:
i
methylation
ii
acetylation
iii
decarboxylation
iv
phosphorylation
v
adenylylation
Bonus question (2 extra points)! The acceptor molecule for incorporating reduced sulfur
provided by the reduced carrier molecule (carrier-S-S-) is formed by the combination of:
i
Cysteine + Homoserine
ii
Homoserine + Methionine
iii
Serine + Cysteine
iv
Acetate + Serine
v
None of the above
11
BIS103-001 (Winter 2007)
Final Exam (March 20)
Name_____________________________________
12