Download Name 1 BIO 451 14 December, 1998 FINAL EXAM

Name ______________________ 1
BIO 451
KEY
14 December, 1998
FINAL EXAM
This exam will be taken apart for grading. Please PRINT your name on 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.
Question
Maximum Points
Earned Points
I.
18
__________
II.
12
__________
III.
10
__________
IV.
7
__________
V.
6
__________
VI.
16
__________
VII.
10
__________
VIII.
8
__________
IX.
10
__________
X.
8
__________
XI.
8
__________
XII.
10
__________
XIII.
10
__________
==================================================================
TOTAL 133
Exam I Exam II
Exam III
Final
Total*/3.3 = Course Avg.
Score on :
Total* = Sum of two best scores + points earned on the Final
[COURSE GRADE ON REVERSE SIDE]
Name ______________________ 2
NOTE:
FULL CREDIT WILL BE GIVEN FOR THOSE ANSWERS WHICH CLEARLY ADDRESS ALL RELEVANT ASPECTS OF
THE QUESTION S IN THE CLEAREST AND MOST CONCISE MANNER.
I. [18 points]
Select the statements from the right column that best describe the metabolism of each organ, tissue or
cell in the left column. [2 points for each correct answer; 1 point off for each incorrect guess]
(1) Releases glycerol and fatty acids into the
(a) Brain
______ 2 _________
blood during fasting periods
(b) Muscle
______4, 6 ________
© Adipose
Tissue ______1 __________
(d) Liver
(2) In a normal nutritional state, utilizes glucose
as the exclusive fuel
(3) Synthesizes ketone bodies when the supply
of acetyl-CoA is very high
______3, 5, 7 ______
(4) Can release lactate into the blood
(e) Red blood cell_____ 2, 4 _____
(5) Utilizes " -keto acids from amino acid
degradation as an important fuel
(6) Can store glycogen but cannot release
glucose into the blood
(7) Can synthesize fatty acids, triacylglycerols
and VLDL when fuels are abundant
Name ______________________ 3
II. [12points] (2 points for each correct answer and 1point off for each incorrect guess)
Consider the following examples of metabolic regulation:
1) Fatty acid oxidation in mitochondria is diminished when fatty acid biosynthesis in the
cytosol is active due to the inhibition of carnatine acyltransferase I by malonyl
CoA.
2) The synthesis of HMG CoA reductase in various cells is inhibited by low-density
lipoproteins.
3) Glucose 6-phosphatase is present in the liver and kidneys but not in muscle.
4) Amidophosphoribosyl transferase, the enzyme that catalyses the committed step in the
biosynthesis of purine nucleotides, is inhibited by all purine nucleotides.
5) The enzyme that catalyses the synthesis and degradation of fructose 2,6-bisphosphate is
phosphorylated and dephosphorylated in response to hormonal signals.
Indicate which of the following of these examples apply to each of the following modes of metabolic
regulation:
(a) Allosteric interactions
_______ 1, 4 _______________
(b) Covalent modifications
_________
(c) Enzyme levels
__________ 2 ________________
5 ______________
(d) Compartmentation
___________ 1 _______________
(e) Metabolic specialization of organs
____________3 ______________
Name ______________________ 4
III. [10 Points]
Match the molecules in the left column with their precursors from the right column.
a) Glucerophospholipids ______ 2, 4, 5 _____
1) Tetrahydrofolate
b) Glycogen
_________ 4, 6 _____
2) Acetyl-CoA
c) Cholesterol
_________ 2 _______
3) Ribose-5-phosphate
d) Triacylglycerols
_______ 2, 4 ________
4) Dihydroxyacetone phosphate
e) Nucleic acids
_________ 3, 1 ______
5) CDP-choline
6) UDP-glucose
IV.. [7 points]
Use an “S” to indicate the following metabolic processes that are stimulates and an “I” to indicate those
that are inhibited by the action of insulin.
Gluconeogenesis in liver
Entry of glucose into muscle and adipose cells
__I___
___S__
Glycolysis in the liver
_S ____
Intracellular protein degradation
__I___
Glycogen synthesis in liver and muscle
Uptake of branched-chain amino acids by myscle
Synthesis of triacylglycerols in adipose tissue
__S___
___S__
__S___
Name ______________________ 5
V. [6 points]
For each of the following molecules, indicate whether there is a high group transfer potential (Y for yes,
N for No), AND from the list of choices of )Go’ listed, indicate (by a T) the approximate )Go’ for
hydrolysis of the bond in each compound with the highest group transfer potential.
PLEASE PAY CAREFUL ATTENTION TO SIGNS.
< -7kCal/mol
)Go’
0
~ +5kCal/mol
T
ATP
Y
AMP
N
T
F-6-P
N
T
1,3-bisphosphoglyceric acid
Y
T
Phosphoenolpyruvate
Y
T
Acetyl-CoA
Y
T
Name ______________________ 6
VI. [16 points]
Each of the items listed below is associated with the breakdown of heme from red blood cells.
Illustrate your familiarity with the biochemistry of heme turnover and the physiological significance of the
integration of metabolism, as well as the role of intertissue cooperation associated with heme
degradation by providing a brief but informative statement of the relevance of these items to heme
catabolism. Be sure to read the whole question.
Ferritin
When RBC are degraded in the spleen, the iron is conserved for reuse. It is transported in the
blood, as a complex with the protein transferrin, to the bone marrow, and stored a a complex
with the protein ferritin.
Intestinal bacteria
Bilirubin is delivered to the intestine as the diglucuronide. The intestinal bacteria have
enzymes that catalyze the removal of the sugar residues, producing free bilirubin; it is further
modified and appears as major pigment in the feces.
Carbon monoxide
The first step in heme catabolism in the spleen is to cleave out a bridge carbon to yield
verdoglobin and one molecule of CO.
Spleen
The site of the initial stages in the destruction of senescent red cells. Hb –>amino acids + CO
+ verdoglobin —>bilirubin –> exported to the liver via the blood as a serum albumin complex
Verdoglobin
See above.
Transferrin
See above.
Name ______________________ 7
Bilirubin diglucuronide
A less toxic, more soluble derivative of bilirubin with two redidues of glucuronic acid
attached to side chains of pyrrole groups. It is produced in the liver.
Liver
Site of conversion of bilirubin to the less toxic glucuronide. In the case of liver dysfunction
bilirubin accumulates in the tissues (jaundice) and causes brain damage in the newborn.
VII. [10 points]
What is a signal transduction cascade? (2 points)
This is essentially a biological mechanism for enhancement of a signal. For example, a
hormone binds to a receptor on the surface of a target tissue cell. The binding is
stoichiometric (no catalysis).
This triggers a series of events (usually associated with chemical modification; e.g.,
phosphorylation) that activates an enzyme that catalyzes a conversion that is biologically
relevant (since the result is the activation of a catalyst the signal (e.g., hormone binding) is
enhanced (lots of molecules are modified). There are often several sequential steps, each
involving the activation of yet another catalyst. ---- leading to a physiological response.
Provide a specific example of a well characterized signal transduction cascade and describe it in as
much detail as you are able. For full credit you must be both thorough and specific, and your awareness
of its physiological significance and biochemical mechanism must be reflected in your answer. (8 points)
The activation of phosphorylase (b –>a) is an example — all the kinases should be mentioned
and in proper order. They should also mention the need for a G-protein mediated process
prior to the activation of cAMP-dependent protein kinase but they do NOT need to describe
the details of the G-protein bit.
Name ______________________ 8
VIII. [ 8 points]
Consider the following mechanism for an enzyme-catalyzed reaction.
E
+
NADH
º
E:NADH
Enzyme first forms a complex with NADH.
E:NADH
+
Pyruvate
º
The E:NADH complex then binds pyruvate.
E:NADH:Pyruvate
E
+
Pyruvate
=/=>
Pyruvate will not bind to the free enzyme
E:NADH:Pyruvate
º
E:NAD+:Lactate
The pyruvate is converted to lactate; there is still a ternary complex.
E:NAD+:Lactate
º
E:NAD+
+
Lactate
The ternary complex dissociates to give a binary complex and free lactate
E:NAD+
º
E
+
NAD+
The binary E:NAD+ complex dissociates to give free NAD and free enzyme.
A. What does each line of the mechanism say in words? PLEASE WRITE IN THE SPACE
BELOW EACH LINE OF THE MECHANISM. (3 points total)
B. What does the mechanism say about which substrate binds first? (1 point)
NADH must bind before pyruvate can bind.
Name ______________________ 9
C. Offer a rational explanation as to whether ordered binding of substrate is necessaryand why. (4
points)
The binding of NADH is associated with a conformational change in the enzyme that
‘creates’ a binding site for pyruvate.
IX. [10 points]
A.
Starch is the plant equivalent of glycogen; the linkages among the sugars are identical but starch
is less highly branched. What is the principle reason that marathon runners would be better advised to
eat pasta (high starch content) rather than a meal containing a high amount of sucrose prior to
participation in a competitive event? Explain. (5 points)
The cleavage of sucrose generates a molecule of glucose; this would raise the level of blood
glucose, this would trigger the release of insulin, this would facilitate the storage of glucose
at a time when the runner needs energy.
Breakdown of starch would release glucose more slowly, thus having less of an effect on
blood glucose so that more of the glucose from starch would be available for energy
production.
Name ______________________ 10
B.
Patsteur observed that the rate and extent of glucose consumption by yeast under anaerobic
and aerobic conditions were very different.
Which condition (anaerobic or aerobic) would be associated with the greatest rate of glucose
consumption? (2 point)
The greatest glucose consumption would be under anaerobic conditions.
Explain why ---- in terms of the most relevant metabolic parameters. (3 points)
To obtain an equivalent amount of energy [e.g., ATP] far more glucose must be utilized under
anaerobic conditions. (Ox phos vs glycolysis)
X. [8 points]
A.
Two biochemistry students are about to use mitochondria isolated from rat liver for an experiment on
oxidative phosphorylation. The protocol for the experiment specifies addition of the soluble protein
cytochrome c from any source to the reaction mixture.
Why is the added cytochrome c needed and why does the source not necessarily have to be the same
as that of the mitochondria? (6 points)
Cyt C is loosely bound to the matrix; much of it is removed during the washes required to
isolate the mitochondria.
Cyt C is a highly conserved protein so almost any source will bind properly.
B.
The three-dimensional structure of cytochrome c indicates that one of its surfaces has charged amino
acid residues. What is the role of these charged residues in the reaction mediated by cytochrome c? (2
points)
The integrity of these charged residues is essential for the binding and mobility of the Cyt C
on the surfave of the matrix. They interact with oppositely charged residues on the surface of
the matrix.
Name ______________________ 11
XI. [8 points]
Suppose that the concentration of mitochondrial malic acid increases dramatically in a liver cell. Briefly
describe how this increase would affect each of the pathways below, and justify your answer.
A. Aspartic acid synthesis
MAL W
OAA W Asp [via aminotransferase]
Thus, an increase in malic acid leads to an increase in Asp synthesis.
B. Gluconeogenesis
6
666
MAL W
OAA
PEP
Glucose
Thus, an increase in malic acid leads to an increase in gluconeogenesis.
C. Biosynthesis of cholesterol
MAL W
OAA ; OAA combines with mitochondrial Acetyl-CoA to form mitochondrial
citrate which moves to the cytosol and generates cytosolic Acetyl-CoA, a precursor for both
cholesterol and palimitoyl-CoA.
D. Biosynthesis of Palmitoyl-CoA
See C.
Name ______________________ 12
XII. [10 points]
A. What is )F508? For full credit you must be specific and its physiological significance must be clear.
(3 point)
) F508 is a deletion mutation in the nucleotide binding domain of CFTR (cystic fibrosis
transmembrane conductance regulator; the F (Phe) residue at position 508 is absent. This
deletion is responsible for ~70% of the cases of cystic fibrosis. CFTR is a cAMP-dependent
chloride transporter.
B. Provide a clear statement of the structural and functional distinctions bewteen molecular and
chemical chaperones. (2 points)
Molecular chaperones are proteins (large molecular weight) or complexes of proteins that
interact with folding proteins so as to facilitate trafficking and/or proper folding. Chemical
chaperones are low molecular weight molecules that accumulate under stress and are known
from in vitro studies to stabilize protein structure; they also seem to facilitate protein folding.
C. Describe the effect of eithe r temperature OR osmolytes on the trafficking and function of
)F508. (5 points)
Normally very little ) F508 protein reaches the cell surface and thus cannot transport
chloride. When
) F508- transfected cells are grown at lower temperatures or in the
presence of certain osmolytes, a significant portion is expressed on the cell surface and
transports chloride.
D. For extra credit. [ 3 points]
What experimental parameters are used to assess maturation and function of )F508? Explain in detail..
The fully mature protein is fully glycosylated --- as assessed by lack of digestion with
Name ______________________ 13
proteinase K. It will also transport chloride in a cAMP-dependent manner.
XIII. [10 points] Note: For simplification PrPC = PrPC and PrPSc = PrPSc.
A reasonably well informed relative of an individual diagnosed with the early stages of BSE was very
excited when he/she read the list of titles appearing in the October issue of PNAS. “Inhibition of
Protease-resistant Prion Protein Formation by Porphyrins.” Illustrate your appreciation for the potential
significance of this observation by addressing the following questions.
What is the significance of the PrPC to PrPSc conversion? (1 point)
Certain ultimately-fatal neurodegerative diseases (encephalosophies) are characterized by the
appearance of protein deposits in neural tissue. These deposits are comprised largely of a
polymerized form of the infectious protein (PrPSc). PrpC is the normal (noninfectious)
conformation of prion protein.
How is this conversion assessed biochemically? (1 points)
Immunoprecipitates obtained with " -PrP of PrPC is fully digested by proteinase K and is
soluble in mild nonionic detergents while PrPSc is not.
There are at least two models that are used to explain the process of conversion of PrPC to PrPSc.
Describe one of them.(4 points)
Example: In the nucleation polymerization model, the conversion of monomeric PrPC to
monomeric PrPSc is rapid and reversible, but the conversion PrPSc to the polymer is slow.
Once a nucleus of polymer is formed, this can bind and facilitate the conversion of more
PrPC to PrPSc
Name ______________________ 14
The template model is described in the legend to Fig. 2 of the reference.
Inasmuch as I said in class that you would be asked a question about these models based on
the section of the reference from Cell, it was fair to expect you to describe one of them in your
answer to this question. If you described an alternative model that was not given credit, if you
will provide a proper literature reference for the model you described, I will reconsider your
answer.
Site at least one specific example of a physical precedent for the mechanism.you described. Explain
how this observation supports the mechanism. (2 points)
Example:
In vitro experiments indicate that a minimum stable nucleus of polymer of PrPSc (>300kDa)
must be formed in order for conversion of PrPC to occur. The model predicts the requirement
for such a nucleus from PrPSc.
Several examples of support for these models that are based on independent examples from
studies of other proteins appear in the assigned section.
Provide two fundamentally different examples of evidence that supports the “protein only”
hypothesis for prion diseases. (2 points)
Treatment of infectious particles with reagents that inactivate nucleic acids (e.g., nucleases)
does not affect infectivity, but proteases do.
Reagents known to affect protein folding/stability (e.g., certain chemical chaperones) inhibit
the conversion of C to Sc.
Other valid answers were accepted.