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CHEM-643 Biochemistry
Name ______________________________
Final Examination
3:30 – 6:30 PM, Thursday, 13 December 2007
Dr. H. White – Instructor
There are 12 pages to this examination including this page. Write your name on each new
page. Read every question so that you understand what is being asked. If you feel any
question is unclear or ambiguous, clearly explain your answer or interpretation. Please
call my attention to any suspected errors you encounter.
The first hour of this examination is with closed notes. You can use your notes thereafter.
You may then refer to your assignments and your lecture notes, but not textbooks. You may
also refer to the metabolic pathway sheets printed from the course website.
This examination will assess your learning, problem-solving skills, and ability to
communicate clearly. It is intended to be challenging even to the best students in the class.
Some of the questions will deal with material you have not seen before and is not in your
text; however, the questions can be answered by applying basic principles discussed in the
course.
Do not expose your answers to the scrutiny of your neighbors. Please fold under each page
before you go on to the next. You may use the backs of pages, if you need more space.
The maximum possible score is 120. Graded Exams can be picked up starting Monday and
will be held until Spring Semester.
Exam Statistics:
Class Range _43.5-107.5/120__
Class Mean ____75.3/120____
Your Score _______
Your Rank in Class _____ out of 28
Course Grade _____
CHEM-643 Intermediary Metabolism
Final Examination, 13 December 2007
Page 2
Name ___________________________
Part I - Short Answer Questions (1 point each)
__________________________ 1.
Avidin, a protein in chicken egg white, binds this
vitamin tightly.
__________________________ 2. Instead of creatine, insects use this compound in their
muscles.
__________________________ 3.
Analog of PABA used as an antibiotic
__________________________ 4.
Vegetarians may need to supplement their diet with this
vitamin.
__________________________ 5.
Antitumor drug that inhibits dihydrofolate reductase.
__________________________ 6.
Amino acid that serves as a major source of carbon for
folate-dependent reactions.
__________________________ 7.
Urea in mammals serves the same purpose as ______ in
birds.
__________________________ 8.
Glyphosate (aka Roundup) inhibits this pathway.
__________________________ 9.
How long can an average human survive without food?
__________________________ 10. Primary source of energy for a 100 meter race.
__________________________ 11. The urea cycle occurs primarily in this organ.
__________________________ 12. Product of transamination of oxaloacetate.
__________________________ 13. Within an order of magnitude, how long does the
average ATP molecule exist in your body before it is
used?
__________________________ 14. The prosthetic group of fatty acid synthase is also part
CHEM-643 Intermediary Metabolism
Final Examination, 13 December 2007
Page 3
Name ___________________________
of this coenzyme.
15-20 Identify the structures shown.
O
O
NH2
N
H2
C
H
O
H
O
OH
O P
O
O
O
O P
O
H2C
H3N
H
O
OH
H3 C
N
C
H3 C
N
N
CH2
H
H
H
OH
NH2
N
N
N
H
COO
N
CH2
CH
H3C
CH3
H
H
OH
NH
O
H C OH
H C OH
H C OH O
CH2 O P OH
O
15 __________________
16 _________________
17 ____________________
CH3
COO
H3N
C
H
H2C
N
H
18 _____________________
H3C
N
NH2
CH3
CH2
CHOH
CH2
COO
19 _______________
N
N
H
N
N
20 _____________________
CHEM-643 Intermediary Metabolism
Final Examination, 13 December 2007
Name ___________________________
Page 4
Part II Problems:
1. (8 Points) Thermodynamics strips away mechanism and tells us that the energy difference
between initial and finals states is independent of the path taken. There is nothing in
biochemistry that violates that principle. However, the rate at which a reaction goes from
starting materials to products is dependent on the mechanism (path). Consider the three
enzymatic steps that convert 3-phosphoglycerate to serine as shown below.
COOH
C
NAD+
NADH + H+
OH
COO-
CH2
H3N
OPO3H-
+
H3N
PLP
O
+
OPO3H-
COO-
Pi
H2O
C
1
CH2
COO-
COO-
C
H
2
COOC
C
+
H
CH2
H3N
3
C
H
CH2
O
CH2
CH2
CH2
CH2
COO-
COO-
OPO3H-
OH
A. (4 points) Why must the dehydrogenation of Step 1 precede the transamination of
Step 2?
B.
(4 points) One might think that it wouldn’t matter where the hydrolysis of
phosphate (Step 3) occurs in the sequence. However, there is a good explanation
for Step 2 (transamination) to precede step 3. Provide a sensible explanation for
the order of Steps 2 and 3. (Hint; Consider the consequences of reversing the
order.)
CHEM-643 Intermediary Metabolism
Final Examination, 13 December 2007
Page 5
Name ___________________________
2. (8 Points) An article in Science [231, 1134-1136 (1986)] entitled, “Long-chain diols: A
new class of membrane lipids from a thermophilic bacterium,” reports the structures of
the lipids shown below. There was no glycerol among the hydrolysis products of the
membranes of Thermomicrobium roseum, an organism that grows at 75°C, but there were
fatty acids and phosphate. Stearic acid and 12 methylstearic acid together account for
84% of the fatty acids.
Examine the structures and considering the structure of typical glycerophospholipids,
postulate the structure of membrane lipids of this organism. How does your structure
differ from a typical glycerophospholipid?
CHEM-643 Intermediary Metabolism
Final Examination, 13 December 2007
Page 6
Name ___________________________
3. (16 Points) In 1906 very little was known about glycolysis. The structures of most of the
intermediates in the pathway displayed below were unknown. In a classic experiment,
Harden and Young broke open yeast cells in buffer and removed the cell debris to make a
cell-free yeast extract. They added glucose to fuel the fermentation pathway and reported
the following observations.
•
Inorganic phosphate added to the extract stimulated the production of CO2.
•
The extra CO2 evolved was stoichiometric with the amount of phosphate added and,
•
The phosphate became organically bound during this process.
P
H CH2O-P
HO
HO
HO
H
H
P
P-OH2C
OH
OH
H
H
O
H
OH
H
HO
H
CH2OH
P-OH2C
P
H OH
HO
HO
H
H
OH
H
H
HO
OH
ATP
ADP
Glucose
O-P
P
O
C
COO
COO
P
H C O-P
P
CH2O-P
CH2O-P
P
CH2OH
H
CH2O-P
P
O
CH2OH
C O
H C OH
P
CH2O-P
P
CH2O-P
NADH+H+ NAD+
H2O
COO
COO
C O-P
P
C O
CH2
OH
HC
H C OH
H C OH
Pi
H
O
H
HO
ADP
ATP
CH3
TPP
HC
O
CH3
CO2
CH2OH
CH3
Ethanol
A. (8 points) Examine the glycolytic fermentation pathway above and explain why
there is a burst of CO2 production with the addition of phosphate and why there
should be or could be a one to one stoichiometric relationship between added
phosphate and CO2 produced.
B. (8 points) Assume these experiments were done today with 32P-labeled phosphate,
trace the fate of the labeled phosphate in the yeast extract giving the order in
which the first few compounds become labeled showing their structures and the
position of the label.
32
Pi →
→
→
CHEM-643 Intermediary Metabolism
Final Examination, 13 December 2007
Name ___________________________
Page 7
4. (25 Points) The pathway from aspartate semialdehyde to lysine as it occurs in E. coli is
depicted below without cofactors, entering substrates, or departing products. Please
answer the questions that follow. (2 points each except for part K)
COOCOOH3N 14C
+
1
+
H3N
H
C
H
3
2
CH2
-
OOC
CH2
HC
C
H
H
COO-
N
OH
-
OOC
H
COO-
N
4
CH2
H2
C
O
C
O
H2C
COO-
CH2
C
-
OOC
C
HN
O
COO+
H3N
C
CH2
COO+
H
H3N
8
+
H3N
7
C
H
6
CH2
H2C
H3N
CH2
CH2
CH2
+
H3N
C
C
H
COO-
COO-
C
C
HN
C
O
H
C
H2
COO-
CH2
CH2
H
C
O
H2
C
+
CH2
NH3+
5
COOH
CH2
CH2
CH2
C
H
COOH2
C
NH3+
C
H2
H
COOH2
C
COO-
COO-
A. What three carbon compound is added in Step 1?
B. What type of reaction occurs in Step 1?
C. The product of Step 2 has a carbon-nitrogen double bond known as a:
D. What would be a likely cofactor for Step 3?
E. What type of reaction is Step 3?
F. What is the source of the four carbon unit added in Step 4?
G. What is expected coenzyme for Step 5?
H. The four carbon unit added in Step 4 departs in Step 6. What role did it serve?
I. What type of reaction is Step 7?
J. What is the expected coenzyme for Step 8?
K. (5 points) Consider the fate of the α-carbon in aspartate semialdehyde as it gets
converted to lysine. On the above pathway, indicate clearly which carbon(s) of lysine
would be 14C labeled?
CHEM-643 Intermediary Metabolism
Final Examination, 13 December 2007
Page 8
Name ___________________________
5. (10 Points) There are two formylation reactions in the biosynthesis of purines that involve
folate coenzymes (see below). When these reactions were worked out originally by
Buchanan, N5N10 methenyl FH4 was thought to be the donor form of the coenzyme. Later
work suggested that N5N10 methenyl FH4 was converted to N10 formyl FH4 by a separate
enzyme in a multienzyme complex before transfer occurred.
O
H 2N
H
N
HN
OHC
HN
O
-
O
GAR Tfase
O P O
O-
H
H
O
OH
-
O-
H
OH
O
N
N
H
N
COO
N5N10 Methenyl FH4
CH2
COO
N
N deaza folate
Enzyme
Substrate
GAR Tfase
N10 formyl FH4
N10 formyl dideazafolate
N10 formyl N5deazafolate
AICAR Tfase
N10 formyl FH4
N10 formyl dideazafolate
N10 formyl N5deazafolate
H
H
OH
H
OH
O
O
O
HN
H2N
N
HC
N
H
N
CH2
COO
N10 formyl FH4
N
H
O
O
COO
N C H
H
CH2
HN
CH2
HN
H2N
COO
N C H
H
CH2
COO
5
N
OH
N C H
H
CH2
HN
H
COO
N
N5N8 dideaza folate
Relative Vmax
Km (μM)
1
0.77
0.002
8.9
1.9
-
1
0.0007
0.47
68
102
O
N
NH2
NH2
AICAR Tfase
O
O-
H
OH
CH2
HN
H2 N
O P O
H
N C H
H
CH2
O
O
O
COO
N
HN
H2N
HC
H
H
O
N
O
-
O P O
H
N
N
O
-
O P O
O-
H
H
O
OH
NH2
N
H
CHO
H
H
OH
Smith et al. [Biochemistry 20,
1241 (1981)] formylated (at
the N10 position) the two
deaza folate analogs shown
below at the left and used
them in place of N10 formyl
FH4 in assays of the GAR and
AICAR transferases. Please
examine the relative maximal
velocities and Km values in
the table below. What
observations and conclusions
can you make?
CHEM-643 Intermediary Metabolism
Final Examination, 13 December 2007
Page 9
Name ___________________________
6. (13 Points) Biotinidase deficiency disrupts the normal recycling of biotin. As a
consequence, the activities of biotin-dependent carboxylase enzymes are greatly reduced
which in turn causes the accumulation of their substrates. These metabolites then become
substrates for enzymes in other pathways and ultimately show up in the urine as unusual
organic acids. Methylcitrate and 3-hydroxypropionate are two such unusual organic acids
that derive from the same carboxylase substrate.
A. (10 points) Select either one of these unusual acids. Show and describe how it is
formed metabolically.
B.
(3 points) Biotinidase deficiency is incurable, but it is treatable. What would you
recommend as a rational treatment of this metabolic disease?
CHEM-643 Intermediary Metabolism
Final Examination, 13 December 2007
Page 10
Name ___________________________
Part III Short Essays. Answer two of the three questions.
1. (10 Points) By having two copies of genes encoding each enzyme, diploid organisms like
us are cushioned from the effects of mutations that generate non-functional enzymes.
Interestingly, genetic carriers for devastating metabolic diseases (persons heterozygous
for a recessive detrimental mutation) produce about half the normal amount of the
affected enzyme and yet rarely show any detrimental effects. Basically they are normal.
In terms of metabolic flux in pathways, how can this be rationalized? Please feel free to
illustrate your answer.
CHEM-643 Intermediary Metabolism
Final Examination, 13 December 2007
Page 11
Name ___________________________
2.
(10 Points) Living organisms do not violate the laws of
thermodynamics. Within terrestrial and shallow water ecosystems,
the energy that maintains the living organisms can be directly
attributed to photosynthetic organisms, the primary producers. It
was a great surprise in the late 1970’s when a whole communities
of organisms were found on the ocean floor where no light
penetrates [Natl. Geog. 156, 680 (1979)] The energy input for
these organisms apparently comes from H2S which comes out of
nearby hydrothermal springs. One rather large organism there is Riftia pachyptila
(Image from www.unbsj.ca.), a type of worm several inches in diameter and up to 10 feet
long. These worms lack a mouth, digestive tract, and anus. Certain parts of their body
contain high densities of endosymbiotic bacteria presumed to be capable of coupling the
aerobic oxidation of sulfide to sulfate to the fixation of CO2 via the Calvin Cycle
[Nature 293, 616 (1981), TIBS 7, 201 (1982), and Science 219, 297 (1983)].
Based on your knowledge of metabolism and the information above, suggest at least
two specific pieces of biochemical information that you would want to know before you
would accept the above hypothesis as possibly valid and not just a science fiction story.
Indicate why this additional information would help your evaluation.
CHEM-643 Intermediary Metabolism
Final Examination, 13 December 2007
Page 12
Name ___________________________
3. (10 Points) The following are descriptions of human metabolic defects in creatine
metabolism as it relates to the brain in particular. Based on these descriptions, draw a
diagram for creatine metabolism in the body showing showing the location of each
defect.
A. This infant boy had extremely low creatine concentrations in serum and urine as well as in muscle.
In vivo magnetic resonance spectroscopy analysis showed a generalized depletion of creatine in
his brain as well. Feeding arginine resulted in an increase in brain guanidinoacetate, but not
creatine. Dietary creatine resulted in increased creatine and decreased guanidinoacetate in the
brain, Stöckler et al. (1994) [Pediatric Research 36, 409-413]. A four year old girl with similar
symptoms excreted large amounts of guanidinoacetate (~10X normal) in her urine, Schulze et al.
(1997) [Journal of Pediatrics 131, 626-631].
B. These two young mentally retarded sisters had severe language delay. Magnetic resonance showed
no detectable creatine or guanidinoacetate in their brains and an intracellular pH of 7.24 compared
to 7.07 in normal brain cells. They had normal levels of creatine in their serum and in muscles.
They excreted normal amounts of creatine and very low amounts of guanidinoacetate. Feeding
large amounts of creatine eventually resulted in near normal brain creatine levels, Bianchi et al.
(2000) [Annals of Neurology 47, 511-513].
C. This male child had elevated serum creatine levels (75 μmol/L vs 15-44 μmol/L) and elevated
excretion of creatine but no detectable creatine in his brain. Creatinine excretion was normal.
Dietary supplementation with creatine had no effect on brain creatine levels, Cecil et al. (2001)
[Annals of Neurology 49, 401-404].