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

BIS103-002 (Spring 2008)
Midterm #2 (May 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 6 questions. A maximum of 100 points can be earned. Partial credit will be given.
There are a total of 13 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 2-12. 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
10
3
24
4
12
5
10
6
22+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
ΔGo’ = – RTlnKeq
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)
Midterm #2 (May 20)
1. (22 pts)
Name_____________________________________
Questions related to the Tricarboxylic Acid (TCA) or Citric Acid cycle.
a) The TCA cycle is sometimes referred to as an “amphibolic” pathway. Briefly explain why. (2 pts)
The TCA cycle simultaneously serves two major functions: In its catabolic mode, products of
carbohydrate, lipid or amino acid degradation, most prominently acetyl-CoA, are completely
degraded to CO2 and NADH/FADH2. At the same time, the TCA cycle also provides the starting
building blocks (also called ‘precursors’) for a number of anabolic (or biosynthetic) pathways and
reactions.
b) Briefly explain the purpose of the “anaplerotic reactions”. (2 pts)
The purpose of the anaplerotic reactions is to maintain a minimal concentration of the TCA cycle
intermediate oxaloacetate (OAA) to enable its catabolic function (degradation of acetyl-CoA)
when other intermediates, including OAA, are withdrawn from TCA cycle reactions for
biosynthetic purposes (e.g. OAA Î glucose or citrate Î fatty acids).
c) Provide complete equations for the reactions catalyzed by pyruvate carboxylase and citrate synthase.
(Name all substrates and products or use common abbreviations). (6 pts)
Pyruvate Carboxylase: Pyruvate (Pyr) + ATP + HCO3- Î Oxaloacetate (OAA) + ADP + Pi
Citrate Synthase: Oxaloacetate (OAA) + Acetyl-CoA + H2O Î Citric acid + Coenzyme A
d) One of the two reactions above requires a covalently bound cofactor. Name the reaction and the
required cofactor? (2 pt)
Reaction:
Pyruvate Carboxylase
Name of co-factor:
Biotin
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BIS103-002 (Spring 2008)
Midterm #2 (May 20)
Name_____________________________________
e) Draw the structure of citric acid into the box. (2 pts)
See booklet or text for structure.
f) If 14CO2 is incorporated into the TCA cycle via the
pyruvate carboxylase reaction, which one of the carbons
of citric acid would be radioactively labeled?
Encircle the carbon. (2 pts)
One of the ‘flanking’ carboxylate groups, not the
‘central’ one.
g) Although oxygen does not participate directly in the TCA cycle, the cycle operates only under aerobic
conditions. Briefly explain why? (2 pts)
The TCA cycle produces NADH and FADH2, which need to be regenerated to NAD+ and FAD in
order to keep the TCA cycle operational. However, in the mitochondria, the regeneration of
NAD+ and FAD is only possible by the ETC, which requires oxygen (aerobic conditions).
h) Two reactions in glycolysis and one reaction of the TCA cycle generate ATP by substrate-level
phosphorylation. The way ATP is produced in the TCA cycle by substrate-level phosphorylation is
conceptually very similar to one of the two ATP-generating reactions in glycolysis. Briefly describe the
common strategy that is used to capture chemical energy released during an oxidation step for the
formation of ATP in glycolysis and the TCA cycle. (4 pts)
The oxidation of an aldehyde to a carboxylate function yields enough energy to form an ATP from
ADP by substrate level phosphorylation in glycoslysis (the combination of the reactions catalyzed
by glyceraldehyde-3-P dehydrogenase and 3-phosphoglycerate kinase) and in the TCA cycle (the
combination of the reactions catalyzed by α-ketoglutarate dehydrogenase and succinyl-CoA
synthetase).
Initially, the energy released during the oxidation step is captured to form a thioester (covalently
linked to glyceraldehyde-3-P dehydrogenase in glycolysis; succinyl-CoA in the TCA cycle). This
thioester is then converted into a high-energy acyl phosphate (1,3-bisP-glycerate in glycolysis;
succinyl-P which remains tightly bound to succinyl-CoA synthetase). In both cases, the high
phosphoryl group transfer potential of the acyl-phosphates allows the subsequent formation of
ATP (GTP) from ADP (GDP).
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BIS103-002 (Spring 2008)
Midterm #2 (May 20)
2. (10 pts)
Name_____________________________________
A recently discovered bacterium, Sulfospirillum arsenophilum, uses arsenate, AsO43- or
As(V), as a respiratory oxidant for the oxidation of a variety of organic compounds,
including acetate. Some components of its electron transfer chain are listed below with
their standard reduction potentials Eo’.
As(V) + 2e- Î As(III)
Acetate + 2e- Î Acetaldehyde
NAD+ + 2H+ + 2e- Î NADH + H+
CoQ + 2H+ + 2e- Î CoQH2
Flavoprotein cox (FPc) + 2H+ + 2e- Î FPcred
Flavoprotein box (FPb) + 2H+ + 2e- Î FPbred
Eo’ =
Eo’ =
Eo’ =
Eo’ =
Eo’ =
Eo’ =
+ 0.16 V
– 0.59 V
– 0.32 V
+ 0.06 V
– 0.19 V
+ 0.10 V
a) Order the electron carriers listed above in such away that would allow spontaneous electron flow from
the initial electron donor to the terminal electron acceptor. Write the appropriate compounds into the
boxes given below (use the abbreviations underlined above). (4 pts)
Initial e- donor
Acetate
Î Carrier 1
NAD+
Î Carrier 2 Î Carrier 3 Î Carrier 4 Î Terminal e- acceptor
FPc
CoQ
FPb
Arsenate, As(V)
b) Calculate the maximum number of ATP molecules that could theoretically be synthesized under
standard conditions per pair of electrons transferred from acetate to the terminal electron acceptor?
Assume ΔGo’ = 30.5 kJ mol-1 for the reaction ADP + Pi Î ATP + H2O, and a coupling efficiency of
85%.
For full credit you must show your work. (6 pts)
ΔEo’ = Eo’(ox) - Eo’ (red) = +0.16V – (–0.59 V)
ΔEo’ (ETC) = + 0.75 V
ΔGo’ = – nF ΔEo’ = –2 x 96,500 Jmol-1 V-1 x 0.75 V
ΔGo’ (ETC) = – 144,750 Jmol-1 or – 144.75 kJmol-1
ΔGo’(ETC) / ΔGo’(ATP) x 0.85
Number of ATPs: 4 ATP
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BIS103-002 (Spring 2008)
Midterm #2 (May 20)
3. (24 pts.)
Name_____________________________________
Lactate, the product of anaerobic glycolysis in skeletal muscles, is converted in the liver
to glucose by gluconeogenesis. In addition, some of the lactate from the muscles is
diverted and used as a “fuel” molecule to meet the ATP demand of gluconeogenesis.
Answer the following questions:
a) Draw the structure of lactate into the provided box. (2 pts)
See booklet or text for structure.
b) Three reactions in gluconeogenesis have a requirement for ATP (or GTP). Name the enzymes
(common name only) that catalyze these reactions. (3 pts)
1. Pyruvate Carboxylase (lyase)
2. Phosphoenolpyruvate (PEP) Carboxykinase (lyase)
3. Phosphoglycerate Kinase (transferase, kinase)
c) In order to provide the 3 moles of ATP required per mole of lactate in gluconeogenesis, a portion of
the recycled lactate from the blood can also be completely degraded to CO2 and H2O by “biological
oxidation”. Below, give the common names of the enzymes (1. and 2.) and the names of the
biochemical pathways (3. and 4.) that catalyze the complete oxidation of lactate in the liver. Do not use
abbreviations, provide the full (common) names. (4 pts)
1. Lactate Î Pyruvate
Lactate Dehydrogenase (oxidoreductase)
2. Pyruvate Î Acetyl-CoA
Pyruvate Dehydrogenase (oxidoreductase)
3. Acetyl-CoA Î 2CO2
Tricarboxylic Acid (or citric acid) Cycle (TCA)
4. NADH or FADH2 Î H2O
Electron Transport Chain (ETC)
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BIS103-002 (Spring 2008)
Midterm #2 (May 20)
Name_____________________________________
d) Calculate how many moles of ATP can be generated per mole lactate during this oxidation process.
Assume the following: NADH = 3 ATP; FADH2 = 2 ATP; and only the malate-oxaloacetate shuttle is
operating. For full credit you must show your work. (8 pts)
1.
Lactate Î Pyruvate:
Yields 1 NADH
2.
Pyruvate Î Acetyl-CoA:
Yields 1 NADH
3.
Acetyl-CoA Î 2CO2 :
Yields 3 NADH
1 FADH2
1 GTP(=ATP)
4.
ETC and ATP synthase:
Yields 15 ATP (from 5 NADH)
2 ATP (from 1 FADH2)
(indirectly transported to mitochondria
via malate-OAA shuttle)
========================================================================
Total:
17 ATP + 1 GTP( or ATP) = 18 ATP
Moles ATP produced per mole lactate: 18 moles ATP per mole lactate
e) The complete oxidation of 1 mole lactate to CO2 generates enough energy (ATP) for how many moles
of glucose to be formed from lactate by gluconeogenesis? (1 pt)
Answer:
3 moles of glucose per mole lactate
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BIS103-002 (Spring 2008)
Midterm #2 (May 20)
Name_____________________________________
f) After gluconeogenesis, glucose is transported from the liver to skeletal muscles where it is converted
into glycogen by four reactions. Provide the names or commonly used abbreviations for the two missing
glucose derivatives (write into the boxes below). Give the balanced equation for reaction 3, and explain
how reaction 3 becomes essentially irreversible. (6 pts)
Glucose
Glc-1-P
1.
2.
Glycogen
3.
Glc-6-P
4.
UDP-Glc
Balanced equation for reaction 3:
Glc-1-P + UTP Ù UDP-Glucose + PPi
What renders reaction 3 irreversible?
The subsequent hydrolysis of PPi to 2x Pi.
4. (12 pts)
Questions related to the pentose phosphate pathway.
a) Two major pathways in metabolism catalyze the “biological oxidation” of one mole glucose into six
moles of CO2. These are: (i) the pentose phosphate pathway, and (ii) glycolysis followed by the PDH
reaction and the TCA cycle. Compare both major metabolic routes as outlined below. (4 pts)
Pentose-P Pathway
GlycolysisÎPDHÎTCA
Cellular compartment(s) of
CO2 formation.
Cytosol
Mitochondria
Cellular compartment(s) of
ATP generation.
None
Cytosol and Mitochondria
Which of the following reducing
equivalents are formed? (FADH2,
FMNH2, NADH, NADPH)
NADPH
NADH and FADH2
What is the major purpose of the
reducing equivalents generated?
Biosynthesis
Production of ATP (ETC)
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BIS103-002 (Spring 2008)
Midterm #2 (May 20)
Name_____________________________________
b) Mannoheptulose is a 7-carbon sugar found in high concentrations in avocado fruit, which can be can
be converted to glucose by humans after avocado consumption via the pentose phosphate pathway and
gluconeogenesis. Which phase(s) of the pentose phosphate pathway transform mannoheptulose into
intermediates of gluconeogenesis (give their names, not numbers)? Give the names (or abbreviations) of
the two initial intermediates of gluconeogenesis into which mannoheptulose is converted. (3 pts)
Phase(s):
Rearrangement phase (or carbon transfer reactions)
Intermediate 1:
Fructose-6-phosphate (F6P)
Intermediate 2:
Glyceraldehyde-3-phosphate (GA3P)
c) Which phase of the Calvin cycle (CO2 assimilation in photosynthesis) is most similar to the pentose
phosphate pathway? (1 pt)
Phase:
Regeneration phase (III. phase)
d) The pentose phosphate pathway is particularly active in the erythrocytes. Briefly explain why? (2pts)
Erythrocytes are exposed to high levels of oxygen, which generates toxic ‘reactive oxygen species’
(or ROS). NADPH, a major product of the pentose phosphate pathway, is used to fully reduce (or
detoxify) those ROS.
e) The pentose phosphate pathway is also very active in tumor cells. Metabolic labeling studies with
14
C-labeled glucose showed that more than 70% of the ribose in DNA is derived from this pathway. The
ribose of DNA will be radioactively labeled if the C-6 position of administered glucose carries the 14Cisotope, but the ribose will not be labeled if the C-1 carbon is radioactive. How do you explain this
observation? (2 pts)
During the oxidation phase of the pentose phosphate pathway, the carbon-1 of glucose is lost as
CO2.
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BIS103-002 (Spring 2008)
Midterm #2 (May 20)
5. (10 pts)
Name_____________________________________
Questions related to the catabolism of lipids.
a) Draw the common structure of a triacylglyceride. (2 pts)
Something like this.
b) What is the biological function of bile acids or bile salts? (1 pt)
Bile salts are ‘biological detergents’ released from the gall bladder to emulsify lipid droplets in the
intestine.
c) Free fatty acids are activated by coenzyme A before their degradation by β-oxidation. You add a
fatty acid and radioactively labeled [14C]coenzyme A to a rat liver homogenate. After an incubation
period you isolate the cytoplasmic and mitochondrial fraction. A subsequent analysis reveals that both
fractions contain the acyl-CoA product; however, the [14C]-label is only present in one of the two
fractions. Which fraction contains acyl-[14C]CoA and why? (4 pts)
Fraction:
Cytosol
Reason:
The pools of CoA in the cytosol and mitochondria are separated and do not
exchange.
d) What is meant by the term “ketogenesis” and list two conditions under which it occurs. (3 pts)
Ketogenesis is the formation of ketone bodies (acetoacetate, acetone, β-hydroxybutyrate) from
acetyl-CoA during prolonged starvation or Diabetes mellitus.
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BIS103-002 (Spring 2008)
Midterm #2 (May 20)
6. (22 pts)
a.
b.
c.
d.
Name_____________________________________
Multiple-choice questions. Circle the best answer. There is only one best answer per
question. Each question is worth 2 pts.
Which one of the following compounds is NOT an intermediate of the TCA cycle?
i
Acetyl-CoA
ii
Citrate
iii
Oxaloacetate
iv
Succinyl-CoA
v
Succinate
Which one of the following substrates cannot be oxidized by isolated mitochondria (i.e. purified
mitochondria that are incubated in buffer and substrate)?
i
Pyruvate
ii
Lactate
iii
Succinate
iv
Fumarate
v
Malate
Vitamine B1 (or thiamine) is the precursor to the coenzyme thiamine pyrophosphate (TPP).
Thiamine deficiency would decrease which one of the following enzyme activities?
i
Fumarase
ii
Isocitrate dehydrogenase
iii
Malate dehydrogenase
iv
Succinate dehydrogenase
v
α-Ketoglutarate dehydrogenase
Which one of the following enzymes of the pentose-P pathway requires TPP as a coenzyme?
i
Transaldolase
ii
Transketolase
iii
Phosphopentose isomerase
iv
Phosphopentose epimerase
v
Glucose-6-P dehydrogenase
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BIS103-002 (Spring 2008)
Midterm #2 (May 20)
e.
f.
g.
h.
Name_____________________________________
Biotin is a cofactor necessary for what type of enzymes?
i
Enzymes catalyzing the transfer of one carbon atom
ii
Enzymes catalyzing the transfer of two carbon atoms
iii
Enzymes catalyzing the transfer of three carbon atom
iv
Enzymes catalyzing oxidoreduction reactions
v
Enzymes catalyzing isomerization reactions
During “oxidative phosphorylation” or “photophosphorylation” the proton motive force that is
generated by electron transport is used to:
i
oxidize NADH to NAD+
ii
induce a conformational change in the ATP synthase
iii
oxidize coenzyme QH2 to coenzyme Q
iv
provide ADP and Pi for ATP synthesis
v
to detoxify reactive oxygen species
The relative concentrations of ATP and ADP control the cellular rates of:
i
the TCA cycle
ii
pyruvate dehydrogenase
iii
the electron transport chain
iv
gluconeogenesis
v
all of the above
The cytochrome b6f complex of the ETC in chloroplasts is analogous to what complex of the
mitochondrial ETC?
i
Complex I
ii
Complex II
iii
Complex III
iv
Complex IV
v
Complex V
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BIS103-002 (Spring 2008)
Midterm #2 (May 20)
i.
j.
k.
Name_____________________________________
What one is the most likely source of propionyl-CoA in metabolism (as discussed in class)?
i
a product of glycolysis
ii
a product of the PDH reaction
iii
a product of fatty acid degradation
iv
a product of ketone body degradation
v
a product of the pentose phosphate pathway
Which one of the following enzymes does NOT catalyze a decarboxylation reaction?
i
6-Phosphogluconate dehydrogenase
ii
α−Ketoglutarate dehydrogenase
iii
Pyruvate dehydrogenase
iv
Succinate dehydrogenase
v
Isocitrate dehydrogenase
After drinking a pint of beer at Sudwerk’s, the ethanol in the blood is taken up by liver cells and
converted into acetate, which is then activated like a fatty acid to form acetyl-CoA. The
conversion of one mole ethanol into one mole acetyl-CoA requires one of the following:
i
1 mole NAD+ and 1 mole ATP
ii
2 moles NADP+ and 1 mole AMP
iii
1 mole FAD and 1 mole ATP
iv
2 moles NAD+ and 1 mole ATP
v
1 mole NADP+ and 1 mole AMP
Bonus Question (2 extra pts): The intermediates of glycolysis are phosphorylated, but those of the
TCA cycle are not. Why? Justify your answer.
All intermediates of the TCA cycles are carboxylic acids and thus negatively charged, which
increases their recognition and binding by enzymes and minimizes diffusion across a membrane.
The addition of a phosphate group to intermediates in glycolysis serves the same functions as the
initial intermediates of glycolysis would not carry a negative charge if unphosphorylated, and
prepares glycolytic intermediates for substrate-level phosphorylation.
12
BIS103-002 (Spring 2008)
Midterm #2 (May 20)
Name_____________________________________
Use blank sheet as scratch paper, if needed.
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