Download Name 1 Bio 451 17th November 2000 EXAM III KEY

1
Name ____________________________
17th November 2000
Bio 451
EXAM III
KEY
This exam will be taken apart for grading. If you expect to receive proper credit for your
answers it is essential that you PRINT your name clearly at the top of EACH page. If you do
not have sufficient room for your answer in the space provided, please continue on the back of the page
on which the question appears.
NOTE: FULL CREDIT WILL BE GIVEN FOR THOSE ANSWERS THAT CLEARLY
ADDRESS ALL RELEVANT ASPECTS OF THE QUESTIONS IN THE CLEAREST AND
MOST CONCISE MANNER.
QUESTION
MAXIMUM POINTS
EARNED POINTS
I
6
II
12
III
6
IV
7
V
5
VI
6
VII
4
VIII
5
IX
6
X
6
XI
6
XII
5
XIII
6
XIV
10
XV
10
EXTRA POINT
10
TOTAL SCORE
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Name ____________________________
I. [ 6 points]
There are two shuttle systems by which NADH reducing equivalents (produced in the cytosol) can be
transferred into the matrix of the mitochondrion and enter the electron transport system.
How is it that NADH that participates in the glycerophosphate shuttle ultimately produces less ATP
than NADH that participates in the malate-aspartate shuttle. Note: You are not required to describe the
two systems in detail, but for full credit you should provide sufficient specific information to explain the
distinction.
SEE ANSWER TO 17-2 IN TEXT.
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Name ____________________________
II. [12 points]
The time course of O2-consumption for a well-buffered suspension of mitochondria containing an
excess of ADP and Pi is illustrated below.
SEE ANSWER TO 17-4 IN TEXT
Sketch the curves that would be expected if:
a) amytal is added at t = 1
b) amytal is added at t = 1 and succinate is added at t = 2.
c) CN! is added at t = 1 and succinate is added at t = 2.
d) oligomycin is added at t = 1 and DNP is added at t = 2.
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Name ____________________________
III
[6 points]
What is the advantage of hormones activating a lipase to stimulate nonshivering thermogenesis in brown
fat rather than activating UCP?
SEE ANSWER TO 17-8 IN TEXT.
IV
[7 points]
Sonication of mitochondria produces submitochondrial particles derived from the inner mitochondrial
membrane. The membranous vesicles seal inside out, so that the inter-membrane space of the
mitchondrion becomes the lumen of the submitochondrial particle.
a)
Diagram the process of electron transfer and oxidative phosphorylation in these particles.
SEE ANSWER TO 17-6 IN TEXT, EXCEPT PLEASE ACCEPT THAT THEY MAY
CHOOSE TO SHOW ONLY ONE OF THE FOUR COMPLEXES PLUS ATP SYNTHASE.
b) Assuming all the substrates for oxidative phosphorylation are present in excess, does ATP synthesis
increase or decrease with an increase in the pH of the fluid in which the submitochondrial particles are
suspended? Explain.
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Name ____________________________
V. [5 points] Answer A OR B, but not both. Only your first answer will be graded.
A. Explain why individuals with a hereditary deficiency of carnitine palmitoyl transferase I have muscle
weakness. Why are these symptoms more severe during fasting?
This enzyme is required for transport of fatty acids into the mitochondrion so that they can
yield energy. FA are particularly important to muscle during fasting because there is less
glucose for energy.
B. What would be the major metabolic consequence if the gene for the enzyme that catalyzes the
reaction indicated below was introduced into the liver of an animal (assuming that the gene is expressed
and that the protein for which it codes is fully functional)? Your rational must be very clear.
Acetoacetate + Succinyl-CoA
W
Acetoacetyl-CoA
+
Succinate
Normally liver cannot catalyze this reaction; it converts acetoacetate to ketone bodies
so that they can provide important energy sources to peripheral tissues. If the enzyme is
introduced into liver there would be less export of these energy producing substrates to
peripheral tissues.
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Name ____________________________
VI. [6 points]
Answer A or B but not both. Only your first answer will be graded.
A. On what carbon atoms does the 14CO2 used to synthesize malonyl-CoA from acetyl-CoA appear
in palmitate? Explain
NONE the CO2 that is used to make malonyl-CoA is lost due to the action of
condensing enzyme.
B. Consider an experiment in which acetyl-CoA, malonyl-CoA, and all appropriate cofactors were
incubated with purified fatty acid synthase from avian liver. Palmitic acid [16:0] was the
final product.
The only radiolabeled compound added to the reaction mixture was malonyl-CoA
(radiolabeled with tritium [T] atoms at both positions of the methylene group [ - CT2-]. Where
[including how many] would the tritium label appear in the palmitic acid?
You do not need to show ALL intermediate steps, but in order to receive full credit your
answer must clearly demonstrate that you know the principal steps which lead to incorporation
and retention of label. Your answer must be consistent with known metabolic processes.
7 malonyl-CoA’s are required each brings in two tritium atoms but one is lost in each
cycle when the unsaturated intermediate is formed. So there would be 7 tritium atoms
on C’s 2,4,6,8,1 and 12.
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Name ____________________________
VII. [ 4 points]
Match the term on the left with its function in the short-term regulation of fatty acid metabolism.
_A____ Citrate
__C___ cAMP-dependent
phosphorylation
__D___ Palmitate
__B___ Malonyl-CoA
A. Activates acetyl-CoA carboxylase
B. Inhibits carnitine acyl transferase I
C. Activates hormone-sensitive lipase
D. Inhibits acetyl-CoA carboxylase
VIII. [6 points]
Which of the following statements is(are) correct?
A. In the $-xidation of fatty acids,
1) The activation of fatty acids by acyl-CoA synthetase is driven by the hydrolysis of
T
pyrophosphate.
2) The reaction catalyzed by acyl-CoA dehydrogenase uses FAD as an electron
T
receptor.
3) The reaction catalyzed by acyl-CoA dehydrogenase is analogous to malate
dehydrogenase of the citric acid cycle.
B. The transport of acetyl-CoA from the mitochondrial matrix to the cytosol for fatty acid
biosynthesis:
T1) is necessary because the inner mitochondrial membrane is impermeable to acetylCoA
2) uses the tricarboxylic acid transporter, which operates in both directions
3) can generate equal numbers of acetyl-CoA and NADPH molecules in the cytosol
T
C. Inhibitors of HMG-CoA reductase are used to decrease serum
cholesterol levels. Such inhibitors would also:
T1) reduce the intracellular level of mevalonate
2) reduce the synthesis of $-hydroxybutyrate
3) reduce the synthesis of palmitoyl-CoA
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Name ____________________________
IX. [6 points]
Place the following intermediates in cholesterol biosynthesis in the correct order
starting with the first: [USE NUMBERS, NOT ARROWS]
____5__ squalene
___4___ farnesyl pyrophosphate
___1___ HMG-CoA
___6___ lanosterol
___2___ mevalonate
___3___ geranyl pyrophosphate.
X. [6 points]
Indicate [by number or letters NOT BY ARROWS] the order of the events involving lipoproteinmediated transport of cholesterol.
__4__ Clusters of LDL particles and LDL receptors are internalized
__2__ VLDL are are converted to IDL and then LDL by the action of lipoprotein lipase and
other processes that occur in the blood
_5___ B100 is degraded , LDL receptors are recycled, and cholesterol is released into the cell
by the action of lysosomal enzymes.
__1__ VLDL are synthesized in and exported by the liver
_3___ Recognition of B100 on LDL particles by LDL receptors on cells of extra hepatic
tissues
__6__ ACAT activity
8 ; HMG-CoA Reductase 9; LDL-receptor synthesis 9
____ Normally, fully functional LDL receptors are released into the blood and recycled to the
liver.
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Name ____________________________
XI.
[6 points]
Explain why protein degradation by proteasomes requires ATP even though proteolysis is an
exergonic process.
SEE 20-1 OF TEXT.
XII. [5 points]
Some forms of maple syrup urine disease are amenable to treatment with large doses of dietary
thiamine. What metabolic [NOT NUTRITIONAL] defect is being treated in these cases? Explain.
THIS DISEASE DERIVES FROM A DEFECT IN THE BRANCHED-CHAIN
KETO ACID DEHYDROGENASE COMPLEX. THIS COMPLEX, LIKE
PDH, REQUIRES THIAMINE PYROPHOSPHATE. PERHAPS THE
DEFECT MAY REFLECT DIMINISHED CAPACITY TO CONVERT
THIAMINE TO THPP, OR IN THE AFFINITY FOR THPP.
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Name ____________________________
XIII [6 points]
Answer A or B but not both. Only your first answer will be graded.
(a)
Many of the most widely used herbicides inhibit the synthesis of aromatic amino acids. Explain
why these compounds are regarded as safe to use near animals.
BECAUSE PLANTS MAKE AROMATIC AMINO ACIDS AND WE DO NOT.
(b)
One of the symptoms of kwashiorkor, the dietary protein deficiency disease in children is the
depigmentation of the skin and hair. Explain the biochemical basis of this symptom.
A PROTEIN DEFICIENT DIET WILL GENERALLY BE DEFICIENT IN PHE/TYR
THAT ARE REQUIRED FOR MELANIN PRODUCTION.
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Name ____________________________
XIV [10 points]
Illustrate your familiarity with relevant aspects of nitrogen, lipid, or heme metabolism, including relevant
genetic defects (where appropriate) by identifying and describing the significance of the following items.
While your answer should be concise, for full credit you must be very specific. Choose 5; only your
first five answers will be graded. (Please continue on the back of this page.)
See class notes and text. Any reasonable answer that is factually accurate and which
also addresses the question asked should be accepted.
a) Acute intermittent porphyria - a painful but not life threatening condition that is due to
a defect in PBG deaminase; )-ALA and porphobilinogen
accumulate
b. Porphobilinogen- precursor to the pyrrole rings in heme; produced by condensation of 2
molecules of )-ALA
c. SAM - carrier of a C1 unit at the level of a methyl group
d.Glutamate dehydrogenase.- catalyzes oxidative deamination of Glu; located in the
mitochodrion
e. Hemin. – oxidized heme; regulates heme synthesis; inhibits the committed step in heme
synthesis [)-ALA synthase] and the translocation of the enzyme into the
mitochondrion.
f. Pyridoxal phosphate — cofactor involved in aminotransferase (transaminase) reactions
g. Uro'gen I — a tetrapyrrole that cannot be converted to heme; accumulates when
urogen III cosynthase is defective; associated with porphyria of
erythropoietic origin.
h. )-Aminolevulinic acid [ )-ALA] synthase — committed step in heme synthesis
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Name ____________________________
i. FH individuals— individuals that suffer from familial hypercholesterolemia; associated
with a defect in the LDL receptor
j. Serine-Glycine hydroxymethyltransferase – catalyzes the interconversion of glycine and
serine; requires N5,N10-Methylene- THF as a
C1 carrier
k. Ferrocheletase — adds iron atom to protoporphyrin IX to produce heme
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Name ____________________________
XV [10 points]
A. What are lipid rafts composed of?
Sphingolipids, cholesterol, and certain proteins that have saturated lipid modifications
(myristilations, palmitoilations and GPI anchors).
B. What are the two main functions that lipid rafts are believed to have in mammalian
1. Apical sorting: help targeting proteins to apical membranes by
association with rafts.
2. Signaling platforms: enhance signaling pathways by
colocalizing receptors and downstream partners in the membrane.
cells?
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Name ____________________________
EXTRA POINT
[10 POINTS] ANSWER A OR B BUT NOT BOTH. ONLY
YOUR FIRST ANSWER WILL BE GRADED.
A. Noji et al (1997) performed an elegant experiment that allowed the direct observation of the rotation
of the ((gamma) subunit of F1-ATPase relative to " 3$3. [A b/w figure illustrating the experimental
setup was included in Handout 12 and one of the links provided in the announcement of this question
provided a color illustration of this figure.]
In a subsequent report they perfomed a similar experiment in which " 3$3 was linked to a bead
via a His tag instead of directly the cover slip, and a lower ATP concentration was used to
drive the roatation, otherwise the experimental setup was essentially the same. The following
paragraph is taken from this second paper.
A single molecule of F1-ATPase, a portion of ATP synthase, is by itself a rotary motor in
which a central ( subunit rotates against a surrounding cylinder made up of " 3$3
subunits. Driven by three catalytic $'s, each fueled by ATP hydrolysis, the ( subunit
makes discrete 120o steps. The work done in each step is constant over a broad range of
imposed load and is close to the free energy of hydrolysis of one ATP molecule.
How do these observations relate to the binding-change mechanism for ATP synthase?
The model and experiment are in excellent agreement. The stepwise 120o rotation is
consistent with the proposed L –> T --> O conformational changes of the model.
Please continue on the revers side.
B. The attached figure provides a view of the experimental setup employed by Sambongi et al. (1999)
[one of the links provided in the announcement of this extra point question].
Compare and contrast this experimental system with the one used by Noji et al.(1997).
The attachment of the F1 fragment to the cover slip is the same in the two experiments.
However, in the setup of Sambongi et al, the C subunits of Fo was included as well ---- along
with the a and b [NOT ALPHA AND BETA] subunits of Fo. [This adds recent detail that is
missing in your text’s model of Fo.]. In the latter experiment the actin filament was attached
to a c subunit of Fo, whereas it was attached to the ( subunit in the experiment reported by
Noji, et al.
What new information were they able to obtain?
The results indicate that the c subunit oligomer rotates with the ( subunit during ATP
hydrolysis by the intact FoF1. In the reverse direction, proton transport should may drive
rotation of the c subunit oligomer, which in turn would drive rotation of the ( subunit to
promote ATP synthesis. The study demonstrates that the mechanical rotation of the ( and c
subunit complex is an essential feature for the energy coupling between proton transport
through the Fo sector and ATP hydrolysis or synthesis in the F1 sector.
Please continue on the reverse side.