Download BIS103-002 (Spring 2008) - UC Davis Plant Sciences

BIS103-002 (Spring 2008)
Final Exam (June 9)
Instructor: Abel
Name_____________________________________
Student ID #
ANSWER KEY
Pls., check appropriate box below.
Undergraduate Student
Completing Incomplete
Open Enrollment Student
Graduate Student
This exam consists of 6 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 re-grading 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
23
3
12
4
12
5
11
6
20 (+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____________________________
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BIS103-002 (Spring 2008)
Final Exam (June 9)
1. (22 pts.)
Name_____________________________________
Questions on fatty acid metabolism.
a) Calculate how many moles of ATP and NADPH are required for the synthesis of lauric acid (a 12:0
fatty acid) from acetyl-CoA. Consider that the acetyl-CoA building blocks need to be exported out of
the mitochondria. You must show your work for full credit. (6 pts)
1. Transport of 6 acetyl-CoA from mitochondria to cytosol (citrate shuttle): 6 ATP
2. Conversion of 5 acetyl-CoA to 5 malonyl-CoA:
5 ATP
3. Five rounds of fatty acid biosynthesis (2 NADPH per round):
10 NADPH
Moles of ATP:
11
Also correct: 11 ATP 4 NADPH
Moles of NADPH:
10
b) Assume that the 12:0 fatty acid is further oxidized to the 12:0(Δ6) desaturated fatty acid using
molecular oxygen as the oxidant. Provide a balanced equation for this desaturation step by filling in the
blanks. (3 pts)
12:0 + O2 + NADPH Î 12:0(Δ6) + 2H2O + NADP+ (+H+)
c) Which major pathway discussed in class provides most of the NADPH needed for fatty acid
biosynthesis? (1 pt)
Pathway:
Pentose Phosphate Pathway (PPP)
d) A minor process of NADPH formation takes place in the cytosol and may convert the NADH from
glycolysis to NADPH for fatty acid synthesis.
First, provide the common name of the enzyme that catalyzes the NADH-producing reaction in
glycolysis. (2 pts) Partial credit for enzyme class (1 pt)
Common name:
Glyceraldehyde-3-P Dehydrogenase ( or G3P Dehydrogenase)
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BIS103-002 (Spring 2008)
Final Exam (June 9)
Name_____________________________________
Second, provide balanced equations for the reactions catalyzed by malate dehydrogenase and
the malic enzyme that can convert NADH produced in glycolysis to NADPH for fatty acid
biosynthesis. Use names or common abbreviations for substrates and products. (4 pts)
Reaction 1:
OAA + NADH Ù Malate + NAD+
Reaction 2:
Malate + NADP+ Î Pyruvate + CO2 + NADPH
e) The conversion of NADH to NADPH in the cytosol by the two enzymes above could provide a way
to regenerate NAD+ for maintaining glycolysis. Why is this alternative not used in tissues or organs
undergoing anaerobic glycolysis to regenerate NAD+? (2 pts)
Tissues that undergo anaerobic glycolysis (e.g., skeletal muscles) are in desperate need of ATP (no
or only very low ATP production by oxidative phosphorylation), which is not used for biosynthetic
processes (requiring NADPH). Tissues would not be regulated so that the PPP pathway is
activated at the same time as anaerobic glycolysis.
f) The synthesis of triacylglycerides involves the formation of ester bonds between glycerol and fatty
acids, an energy-requiring process. What renders the ester bond formation in triacylglycerol synthesis
energetically feasible? (2 pts)
The hydrolysis of the thioester bond of “activated fatty acids”, which are acyl-CoA.
g) Activated fatty acids (acyl-CoA) are produced in the cytosol as the first and last step of fatty acid
degradation and fatty acid synthesis, respectively. How is the transport of newly synthesized acyl-CoA
into the mitochondria for degradation by β-oxidation effectively prevented? (2 pts)
The early intermediate of fatty acid biosynthesis, malonyl-CoA, allosterically inhibits carnitine
acyltransferase I, which imports acyl-CoA from the cytosol into the mitochondria for β-oxidation.
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BIS103-002 (Spring 2008)
Final Exam (June 9)
2. (23 pts.)
Name_____________________________________
Questions related to the metabolism of amino acids
a) The chemical structure in the box depicts an amino acid. Provide
the common name for this amino acid. (1 pt)
COO HC
NH2
CH2OH
Name: Serine
b) Three reactions can produce the amino acid shown above (a) from 3-phosphoglycerate (3-PGA), an
intermediate of glycolysis. Draw the structure of 3-PGA and provide common and simplified names for
each enzyme (e.g., ‘kinase’ or ‘oxidase’). The order of the enzymes is not important. (4 pts)
Draw the structure of 3-PGA into the box:
Enzyme 1:
Dehydrogenase
Enzyme 2:
Phosphatase
Enzyme 3:
Transaminase
c) Several co-factor discussed in class are involved in the transfer of carbon groups. The amino acid
shown in (a) can be converted into glycine. Which co-factor ‘rescues’ the remaining carbon unit? (1 pt)
Circle one!
Biotin
TPP
PLP
SAM
THF
CoA
d) Glycine can be further decomposed to NH3 and CO2. Which co-factor ‘rescues’ the reduced carbon
of glycine? (1 pt) Circle one!
Biotin
TPP
PLP
SAM
THF
CoA
e) The enzyme that catalyzes the initial decarboxylation of glycine (glycine decarboxylase) has a
requirement for which of the co-factors listed below? (1 pt) Circle one!
Biotin
TPP
PLP
SAM
THF
CoA
4
BIS103-002 (Spring 2008)
Final Exam (June 9)
Name_____________________________________
f) Assume that the NH3 derived from glycine decarboxylation is used for the production of urea.
Provide a balanced equation for the reaction that generates carbamoyl-phosphate. Fill in the blanks and
draw the chemical structure of carbamoyl-P into the box. (4 pts)
See booklet
NH3 + HCO3- + 2ATP
Î
Carbamoyl-P
+ 2ADP + 1Pi
g) In addition to urea, fumarate is also produced in the urea cycle of mammals. This fumarate is
converted by three reactions to aspartate, which is a substrate of a previous urea cycle reaction. Sketch
out the reactions for the conversion of fumarate to aspartate. Include co-factors if they are required.
(6 pts)
Reaction 1:
Fumarate + H2O Î Malate
Reaction 2:
Malate + NAD+ Ù Oxaloacetate (OAA) + NADH
Reaction 3:
OAA + Glutamate (Glu) Ù Aspartate (Asp) + α-Ketoglutarate (KGA)
h) Two groups of experimental rats were fed different amino acids as the sole source of carbon for about
one month. Group A was fed with lysine and leucine, and group B received aspartate and glutamate.
Rats of both groups were examined after one month and a striking difference was noticed. One group of
rats was healthy and gained some weight, whereas the other group of animals showed poor health and
lost weight because of a decline in muscle mass.
Which animal group was the healthiest? (1 pt) Circle one!
A
B
Justify your choice by explaining the underlying biochemistry! (4 pts)
Lysine and leucine are ketogenic amino acids, whereas aspartate and glutamate are glucogenic
amino acids.
That means that the animals fed with aspartate and glutatmate can produce glucose and other
carbohydrates to stay reasonably healthy for some time.
On the other hand, the group fed with lysine and leucine cannot produce glucose from this diet as
it will be converted exclusively to acetyl-CoA. Since acetyl-CoA can only be used for lipid
biosynthesis (and ketogenesis), maintenance of blood glucose levels is achieved by degradation of
muscle protein, thus the loss of weight.
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BIS103-002 (Spring 2008)
Final Exam (June 9)
3. (12 pts.)
Name_____________________________________
Short questions on nucleotide metabolism.
a) Draw into the boxes the structures of the aromatic pyrimidine and purine ring system. Do not draw
any R-groups. (4 pts).
Pyrimidine
Purine
b) Briefly describe the difference between “de novo” and “salvage” pathways of nucleotide biosynthesis.
(2 pts)
De novo synthesis assembles the constituents of nucleotides “one-by-one” from simple precursors,
whereas the salvage pathway rescues nucleobases from nucleic acid degradation and converts
them back to nucleotides.
c) How is the ribose unit activated for nucleotide biosynthesis (provide a balanced equation of the
reaction) and briefly point out the major difference between the de novo synthesis of pyrimidine and
purine nucleotides. (4 pts)
Ribose activation:
Ribose-5-P + ATP Î PRPP (5-phospho-ribosyl-1-pyrophosphate) + AMP
Difference: De novo synthesis of pyrimidines first assembles the pyrimidine nucleobase ring and
then attaches it ribose-5-P via activated ribose (PRPP). The opposite occurs in purine nucleobase
synthesis; the purine ring system is assembled on the ribose-5-P scaffold (initially provided by
PRPP).
d) In addition to their role in nucleic acid biosynthesis, the purine ring system can be modified by
“methoxylation”. This modification requires the sequential action of a “monooxygenase” (which inserts
a –OH function) and a methyltransferase (which forms the –OCH3 function). What is the most likely
oxidant for the monooxygenase reaction, and what is the most likely co-factor for the methyltransferase
reaction? (2 pts)
Oxidant (monooxygenase):
Molecular oxygen (O2)
Co-factor (methyltransferase):
S-Adenosylmethionine (SAM)
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BIS103-002 (Spring 2008)
Final Exam (June 9)
4. (12 pts.)
Name_____________________________________
Questions on metabolic regulation.
a) When a dog confronts a “fight-or-flight” situation, the release of epinephrine promotes glycogen
breakdown in the liver and skeletal muscle. The end product of glycogen breakdown in the liver is
glucose; however, the end product in skeletal muscle is pyruvate, which then enters the mitochondria.
What is the biochemical reason for the different end products in the two tissues? (2 pts)
Glucose-6-P phosphatase in the liver produces glucose from G6P, an intermediate of glycogen
degradation. However, this enzyme (G6P phosphatase) is not present in skeletal muscles.
Therefore, in skeletal muscles G6P will enter glycolysis to be converted into 2x pyruvate.
What is the advantage of these two different glycogen breakdown routes? (2 pts)
The liver will export the glucose (derived from glycogen) into the blood where it reaches the
skeletal muscles to supplement their increased fuel requirement for producing ATP.
Degradation of muscle glycogen to pyruvate (and then to CO2 and H2O) provides ATP for
physical activity.
b) Caffeine is an inhibitor of the cyclic nucleotide phosphodiesterase. Predict the effect of a cup of
coffee on the activity of the following key regulatory enzymes. (4 pts) Circle.
Triacylglycerol lipase (adipose)
higher
lower
Glycogen synthase (muscle)
higher
lower
Glycogen phosphorylase (muscle)
higher
lower
Phosphofructokinase-2 (liver)
higher
lower
c) Given below are the names of regulated enzymes. Predict the effect of each of the allosteric effectors
on the activity of the enzymes (write “activator” or “inhibitor” on the line provided). (4 pts)
Phosphofructokinase-1:
ATP:
Inhibitor
H+ (decreasing pH): Inhibitor
Citrate Synthase:
ADP:
Activator
Succinyl-CoA:
Inhibitor
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BIS103-002 (Spring 2008)
Final Exam (June 9)
5. (11 pts.)
Name_____________________________________
Short answer questions.
a) Microorganisms have the ability to convert ethanol into glucose, which, unfortunately, humans can
not do. The blank lines below stand for major biochemical pathways (or segments thereof) that
accomplish this conversion. Write the names of the respective pathways above the lines. (3 pts)
Glyoxylate Cycle
TCA Cycle
Gluconeogenesis (GNG)
Ethanol ÎÎ____________ Î Succinate Î _____________Î OAA Î______________Î Glucose
b) Dihydroxyacetone-P (DHAP), an intermediate of glycolysis, has at least two additional purposes in
metabolism as discussed in class. What are two purposes other than being metabolized in glycoslysis?
(2 pts)
1.
Glycerol-3-P shuttle (transfer of reducing equivalents from cytosol into
mitochondria)
2.
Production of glycerol-3-P for triacylglyceride (lipid) synthesis
c) Vegetarians who do not complement their diet with egg or milk products are highly advised to eat
different types of plant protein. What is the biochemical basis for this recommendation? (2 pts)
Proteins from animal sources contain a balanced set of essential amino acids. However, plant
proteins are often deficient in certain essential amino acids, depending on the source of the plant
diet (crop species; tissues, seeds or fruits consumed).
d) The aromatic amino acids tryptophan and phenylalanine are essential to humans; however, tyrosine is
not. What is the reason? Be specific. (2 pts)
Tyrosine can be produced from phenylalanine in one reaction, which involves the hydroxylation of
the ring system.
e) Leaf cells of plants have particularly high concentrations of antioxidants, such as ascorbic acid or
glutathione, to detoxify reactive oxygen species (ROS). What major metabolic processes generate by
side-reactions ROS in plants? (2 pts)
Mitochondrial electron transport chain (ETC) and light reactions of photosynthesis (PSN)
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BIS103-002 (Spring 2008)
Final Exam (June 9)
Name_____________________________________
6. (20 + 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.
The final product(s) of amino acid catabolism excreted in the urine of humans are:
i
Urea and uric acid
ii
Ammonia and urea
iii
Urea and glutamine
iv
Ammonia and glutamine
v
Uric acid and ammonia
Carbon dioxide derived from carbohydrate catabolism is generated in what cellular
compartment(s)?
i
Cytosol
ii
Mitochondria
iii
Cytosol and Mitochondria
iv
Chloroplasts
v
Cytosol and Mitochondria and Chloroplasts
Excess carbohydrate intake by physically exhausted adults is converted to:
i
Glycogen
ii
Glycogen and protein
iii
Triacylglycerides
iv
Triacylglycerides and glycogen
v
Triacylglycerides and glycogen and protein
Which substance is NOT involved in the production of urea from ammonia via the urea cycle?
i
ATP
ii
Aspartate
iii
Ornithine
iv
Arginine
v
Lysine
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BIS103-002 (Spring 2008)
Final Exam (June 9)
e.
f.
g.
h.
Name_____________________________________
Which one of the following oxygen compounds is the most reactive?
i
Oxygen
ii
Superoxide radical
iii
Hydrogen peroxide
iv
Hydroxyl radical
v
Water
Which one of the following dietary polymers is the least effective source of chemical energy?
i
Starch
ii
Protein
iii
Lipids
iv
Nucleic Acids
v
Glycogen
The methyl cycle serves the following primary purpose:
i
DNA methylation
ii
Regeneration of S-Adenosylmethionine
iii
Regeneration of N5-Methyl THF
iv
Regeneration of pyridoxal-P
v
Synthesis of cysteine from methionine
Which one of the following processes is inhibited by insulin in the muscle?
i
Glycogen degradation
ii
Fatty acid synthesis
iii
Glycolysis
iv
Glycogen synthesis
v
Pentose phosphate pathway
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BIS103-002 (Spring 2008)
Final Exam (June 9)
i.
j.
Name_____________________________________
All of the compounds listed below can be considered “activated” because their hydrolysis is
thermodynamically favored. Which one of the following compounds is “least activated” or has
the lowest ΔGo’ of hydrolysis based on simple chemical principles.
i
Acetyl-CoA
ii
O-Acetylserine
iii
Carbamoyl-phosphate
iv
Creatine-phosphate
v
UDP-Glucose
Homoarginine (a homolog of arginine containing one additional methylene group) is synthesized
by several microorganisms. A major portion of the carbon skeleton of homoarginine is most
likely derived from:
i
Lysine
ii
Ornithine
iii
Asparagine
iv
Glutamine
v
Leucine
Bonus question (2 extra pts). How many moles of ‘reducing equivalents’ and ‘ATP equivalents’ does it
take for bacteria to reduce 1 mole of sulfate (SO42-) to 1 mole sulfhydryl groups (-SH) present in
cysteine?
i
“1 ATP” and 8 Ferredoxin
ii
“2 ATP” and 6 Ferredoxin
iii
“3 ATP” and 6 Ferredoxin
iv
“2 ATP” and 8 Ferredoxin
v
“1 ATP” and 6 Ferredoxin
11
BIS103-002 (Spring 2008)
Final Exam (June 9)
Name_____________________________________
Use as scratch paper, if necessary.
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