Download Answer Key 2 - UC Davis Plant Sciences

BIS103-001 (Winter 2007)
Midterm #2 (February 27)
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 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 regarding 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
21
2
21
3
12
4
25
5
7
6
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
ΔGo’ = – RTlnKeq
ΔG = ΔGo’ + RTln[Prod.]/[React.]
ΔG = ΔGo’ + 2.303RTΔpH + ZFΔΨ
ΔGo’ = – nFΔEo’
ΔEo’ = Eo’Oxidant – Eo’Reductant
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1
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1
BIS103-001 (Winter 2007)
Midterm #2 (February 27)
1. (21 pts)
Name_____________________________________
Questions on the ETC and proton gradient-dependent ATP synthesis.
a) Some processes of the mitochondrial electron transport chain and of the “light reactions” in photosynthesis are strikingly similar. Which components in chloroplasts and mitochondria are analogous?
Fill in the blanks. (6 pts)
Component in Mitochondria
Component in Chloroplasts
1. Inner membrane
1. Thylakoid Membrane
2. Matrix
2. Stroma
3. Intermembrane Space
3. Thylakoid Lumen
4. Cytochrome c
4. Plastocyanin (PC)
5. Coenzyme Q
5. Plastoquinone
6. Complex III
6. Cytochrome b6f complex
b) Inhibition of the ATP/ADP translocator in the inner mitochondrial membrane of mice by gene knockout technology causes reduced mitochondrial import of ADP in exchange for ATP. Metabolic
consequences are the accumulation of NADH in the mitochondria and the accumulation of lactate in the
blood of the “knock-out” mice. Provide a brief explanation for both observations. (6 pts)
High levels of mitochondrial NADH
Accumulation of mitochondrial ATP (or a concomitant decrease of ADP) will inhibit the ATP
synthase, which in turn will result in a build-up of the proton gradient. Since the proton gradient
(proton motive force) can be considered the “product” of the mitochondrial ETC, an increasing
proton gradient will eventually inhibit mitochondrial electron transport and consequently NADH
oxidation to NAD+. Therefore, NADH will accumulate.
High levels of lactate
Since ATP cannot be exported from the mitochondria in exchange for ADP, the cytosolic ATP
concentration drops. The need for ATP is met by increased glycolysis. The NADH produced in
glycolyis cannot be efficiently transported into the mitochondria because of high mitochondrial
NADH levels. Therefore, cytosolic NAD+ is regenerated by reduction of pyruvate to lactate
(anaerobic glycolysis).
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BIS103-001 (Winter 2007)
Midterm #2 (February 27)
Name_____________________________________
c) An inhibitor is added to isolated mitochondria that are supplied with plenty of pyruvate and oxygen.
You observe that all the cytochrome c is in the oxidized state, but that all the other diffusible electron
carriers are in their reduced states (i.e., CoQH2, NADH, and FADH2). Which complex is inhibited?
Write the name of the complex and write the balanced reaction catalyzed by this complex. (3 pts)
Name:
Complex III
Reaction:
CoQH2 + 2 Cytc (oxidized) Î CoQ + 2 Cytc (reduced) + 2H+
d) A difference in the concentration of protons (ΔpH) and a difference in the membrane potential (ΔΨ)
contribute to the electrochemical gradient of protons, or the so-called proton motive force (PMF).
The following values have been measured for mitochondria and chloroplasts:
o
Mitochondria (at 37 C):
Chloroplasts (at 22oC):
ΔpH
0.76
3.55
ΔΨ
161 mV
0 mV
Calculate the PMF (ΔG) for both organelles at the given physiological temperatures (watch out, there are
no ‘typos’). For full credit you must show your work. (6 pts)
ΔG = ΔGo’ + 2.303RTΔpH + ZFΔΨ
Mitochondria
ΔG = (2.303 x 8.315 J mol-1 K-1 x 310 K x 0.76) + (1 x 96.5 kJ mol-1 V-1 x 0.161 V)
ΔG = 4.5 kJ mol-1 + 15.5 kJ mol-1
ΔG = 20.0 kJ mol-1
Chloroplasts
ΔG = (2.303 x 8.315 J mol-1 K-1 x 295 K x 3.55)
ΔG = 20.0 kJ mol-1
PMF (Mitochondria): ΔG = 20.0 kJ mol-1
PMF (Chloroplasts): ΔG = 20.0 kJ mol-1
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BIS103-001 (Winter 2007)
Midterm #2 (February 27)
2. (21 pts)
Name_____________________________________
Questions on gluconeogenesis/glycolysis. The concentration of lactate in the blood of a
resting adult is typically between 1-3 mM, whereas blood lactate concentrations of 10-20
mM are measured after intense physical work or athletic activity. Answer the following
questions:
a) Draw the structure of lactate into the provided box. (2 pts)
See booklet for structure.
b) Why is it not necessary to phosphorylate lactate in the cell? (1 pt) Be short!
Lactate is a carboxylic acid. At physiological pH, lactate is dissociated (a carboxylate anion),
which prevents its diffusion across the plasma membrane.
c) What cell type, tissue or organ is the major source of lactate in the blood of a resting adult? (1 pt)
Circle only one!
Heart Muscle
Skeletal Muscle
Brain
Liver
Erythrocytes
Macrophages
d) What cell type, tissue or organ is the major source of the additional lactate in the blood after heavy
exercise? (1 pt) Circle only one!
Heart Muscle
Skeletal Muscle
Brain
Liver
Erythrocytes
Macrophages
e) What cell type, tissue or organ converts most of the lactate into glucose? (1 pt) Circle only one!
Heart Muscle
Skeletal Muscle
Brain
Liver
Erythrocytes
Macrophages
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BIS103-001 (Winter 2007)
Midterm #2 (February 27)
Name_____________________________________
f) Formation of glucose from lactate is also energy-dependent. How many moles of ATP equivalents
are required per mole lactate? For full credit you must identify the reactions that consume ATP
equivalents! Name the reactants/products or give the names of the respective enzymes. (7 pts)
ATP/GTP-consuming reactions or enzymes:
1.
Pyruvate Carboxylase
Pyr + ATP + HCO3- Î OAA + ADP + Pi
2.
Phosphoenolpyruvate (PEP) Carboxykinase
OAA + GTP(=ATP) Î PEP + GDP(=ADP) + CO2
3.
Phosphoglycerate Kinase
3-Phosphoglycerate + ATP Î 1,3-Bisphosphoglycerate + ADP
Moles of ATP equivalents required per mole lactate:
3 moles
g) A major control point of gluconeogenesis and glycolysis involves “substrate cycling”, which is also
referred to as “futile cycling”. Two reactions participate in this phenomenon (provide the names of
reactants and products) and briefly describe two reasons why such “futile cycling” is beneficial. (8 pts)
Reaction 1:
Fru-6-P + ATP Î Fru-1,6-BP + ADP
Reaction 2:
Fru-1,6-BP + H2O Î Fru-6-P + Pi
Reason 1:
“Futile cycling” generates heat (hydrolysis of ATP) and contributes to the
maintenance of body temperature.
Reason 2:
Reciprocal regulation of both reactions by allosteric effectors allows for
dynamic flux control.
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BIS103-001 (Winter 2007)
Midterm #2 (February 27)
3. (12 pts)
Name_____________________________________
Questions on the pentose phosphate pathway (or hexose-monophosphate shunt).
a) The pentose phosphate pathway consists of three phases: the oxidation phase (I), the isomerization
phase (II) and the rearrangement phase (III). Which of these three phases will be active during the
following conditions? Circle appropriate phases. (3 pts)
Cells that respond exclusively to oxidative stress:
I
II
III
Cells that require both NADPH and ribose:
I
II
III
Cells that generate ribose from glycogen and do
not need NADPH:
I
II
III
b) Transketolase is an enzyme of the rearrangement phase. Draw the chemical structures of reactants
and products of one transketolase-catalyzed reaction of the pentose phosphate pathway in the boxes
below. (4 pts)
See booklet for structures.
+
Ù
+
c) The transketolase enzyme requires thiamine pyrophosphate (TPP) as a cofactor. Why? (2 pts)
Transketolase catalyzes the cleavage of a C-C bond next to a carbonyl group. This reaction is
similar to the decarboxylation of an α-keto acid (e.g., pyruvate), which requires TPP to weaken
the bond to be cleaved by placing an electrophilic center in β-position to the leaving group (CO2 in
the case of α-ketoacids; GA3P in the case of transketolase).
d) What is the general purpose of the Calvin cycle? (1 pt)
To convert (or assimilate) CO2 into carbohydrates.
e) What is the purpose of the Calvin cycle reactions that are similar to the pentose phosphate pathway?
(2 pts)
Regeneration of the acceptor molecule, ribulose-1,5-bisphosphate, for CO2 fixation by the enzyme
ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco).
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BIS103-001 (Winter 2007)
Midterm #2 (February 27)
4. (25 pts)
Name_____________________________________
Questions on lipid metabolism (β-oxidation and synthesis of fatty acids).
a) Draw the structure of palmitoleic acid, which can be abbreviated as a “16:1 (Δ9)” fatty acid. (2pts)
O
OH
Palmitoleic Acid
b) How many net ATPs are produced when palmitoleic acid is completely oxidized to CO2 and H2O?
For full credit you must show your work (assume that 1NADH = 3ATP and 1FADH2 = 2ATP). (8 pts)
1. Activation of Palmitoleic Acid: Requirement of 2 ATP (–2ATP)
2. 7 Rounds of β-oxidation yield:
7 NADH
6 FADH2 (only 6FADH2 are produced because of the double
bond at C-9)
8 Acetyl-CoA
3. Oxidation of 8 Acetyl-CoA
by TCA cycle yield:
4. Oxidation of NADH and
FADH2 in ETC yield:
5. Total ATP balance:
24 NADH
8 FADH2
8 GTP (=ATP)
31 NADH
14 FADH2
Î
Î
93 ATP
28 ATP
==========
121 ATP
121 ATP
+ 8 ATP (from 8 GTP)
– 2 ATP (“fatty acid activation”)
================================================
Net total of 127 ATP
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BIS103-001 (Winter 2007)
Midterm #2 (February 27)
Name_____________________________________
c) Two groups of experimental rats were fed two different fatty acids as the sole source of carbon for
about one month. The first group was fed with heptanoic acid (a “7:0 fatty acid”), and the second group
received octanoic acid (an “8:0 fatty acid”). After the experiment, rats of both groups were examined
and a striking difference was noticed. While the animals of the first group were healthy and had gained
weight, the rats of the second group were weak and had lost weight because of a decline in muscle mass.
Why were rats fed with heptanoic acid (7:0) relatively healthy? (3 pts)
Heptanoic acid is an odd-numbered fatty acid, which is degraded by β-oxidation into acetyl-CoA
and propionyl-CoA. Unlike acetyl-CoA, propionyl-CoA can be converted to oxaloacetate (OAA),
which is a precursor in gluconeogenesis and carbohydrate synthesis. Thus, rats fed with
heptanoic acid appear to be relatively normal.
Why did muscle mass decline in rats fed with octanoic acid (8:0)? (3 pts)
On the other hand, the animals fed with octanoic acid are unable to synthesize glucose because
acetyl-CoA cannot be converted to pyruvate or OAA. In order to maintain blood glucose levels,
glucogenic amino acids derived from non-essential proteins (skeletal muscle) are used as
substrates for gluconeogenesis. Therefore, these rats are loosing weight.
d) Draw the structure of one “ketone body” and briefly explain circumstances under which you would
expect to find high concentrations of this compound in the blood or urine of a human. (3 pts)
See booklet for structures of ketone bodies (acetoacetate, acetone, β-hydroxy butyrate).
High concentrations of ketone bodies in the blood or urine would be found after prolonged fasting
or starvation as well as in diabetics.
e) A reduced flux through glycolysis is an indirect consequence when the ATP-Citrate Lyase enzyme is
inactivated by chemical inhibitors. Why? (3 pts)
ATP-Citrate Lyase cleaves cytosolic citrate into OAA and acetyl-CoA (used for fatty acid
synthesis). If this enzyme is inhibited, citrate accumulates in the cytosol, which allosterically
inhibits phosphofructokinase-1 (PFK-1) and consequently glycolysis.
8
BIS103-001 (Winter 2007)
Midterm #2 (February 27)
Name_____________________________________
Question 4 continued.
f) Palmitoyl-CoA is an end product of fatty acid biosynthesis and a substrate for β-oxidation. How is
the degradation of newly synthesized palmitoyl-CoA prevented? (3 pts)
Malonyl-CoA, the activated precursor in fatty acid synthesis, inhibits the transport of acyl-CoA
(e.g., palmitoyl-CoA) from the cytosol into the mitochondria (inhibition of carnitine acyl
transferase I).
5. (7 pts)
Two short answer questions.
a) If glycolysis and the TCA cycle do not operate, can the liver still produce ATP? Answer yes or no,
and briefly explain the reason for your answer. (3 pts)
Yes.
ATP can still be produced by β-oxidation of fatty acids, which yields 1 NADH and 1 FADH2, and 1
acetyl-CoA per round. Although the acetyl-CoA cannot be further degraded (the TCA cycle has
stopped its catabolic function), the NADH and FADH2 can be oxidized by the mitochondrial ETC.
b) Fructose is a common monosaccharide found in many fruits. Briefly sketch out a pathway that
converts fructose into glycogen. Fill in the blanks by using common abbreviations for intermediates
(e.g., Xu5P). Do not provide enzyme names or cofactors. (4 pts)
Fructose Î Fru-6-P Ù Glc-6-P Ù Glc-1-P Î UDP-Glc Î Glycogen
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BIS103-001 (Winter 2007)
Midterm #2 (February 27)
Name_____________________________________
6. (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 enzymes does NOT catalyze a decarboxylation reaction?
i
6-Phosphogluconate dehydrogenase
ii
Pyruvate dehydrogenase
iii
Isocitrate dehydrogenase
iv
Glucose-6-P dehydrogenase
v
α−Ketoglutarate dehydrogenase
Which of the following compounds cannot serve as a precursor for glucose synthesis in humans?
i
Glycerol
ii
Lactate
iii
Acetate
iv
Oxaloacetate
v
Succinate
A major function of the pentose phosphate pathway is:
i
to oxidize excess alcohol to carbon dioxide
ii
to produce additional NADH for ATP production
iii
to provide intermediates for the TCA cycle
iv
to produce glycogen from glucose-6-P
v
to generate NADPH for biosynthetic reactions
Which one of the following compounds is NOT an electron carrier of the mitochondrial ETC?
i
Cytochromes
ii
Iron-sulfur clusters (Fe-S centers)
iii
FADH2
iv
NADH
v
NADPH
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BIS103-001 (Winter 2007)
Midterm #2 (February 27)
e.
f.
g.
h.
Name_____________________________________
The relative concentrations of ATP and ADP control the cellular rates of:
i
glycolysis
ii
pyruvate dehydrogenase
iii
the TCA cycle
iv
all of the above
v
none of the above
Cells that utilize “ketone bodies” as fuel degrade those to:
i
Acetyl-CoA
ii
Propionyl-CoA
iii
Butyryl-CoA
iv
Succinyl-CoA
v
Pyruvate
Which of the following is not required in the synthesis of fatty acids from acetyl-CoA present in
mitochondria?
i
Oxaloacetate
ii
FADH2
iii
ATP
iv
Malonyl-CoA
v
Biotin
Bonus question (2 extra points)! The rates of fatty acid β-oxidation can be experimentally
determined by feeding tritium-labeled palmitic acid ([3H]-palmitate) to cultured cells and by
measuring a [3H]-labeled degradation product in the cell culture medium. What product is
measured?
i
[3H]-NADH
ii
[3H]-FADH2
iii
[3H]-Acetyl-CoA
iv
[3H]-H2O
v
[3H]-Palmitate
11
BIS103-001 (Winter 2007)
Midterm #2 (February 27)
Name_____________________________________
Use blank sheet as scratch paper, if needed.
12