CHEM-643 Biochemistry
Name ______________________________
Final Examination
7:00 – 10:00 PM, Wednesday, 13 December 2006
Dr. H. White – Instructor
There are 10 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.
This is an open-notes examination. You may 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 116. Graded Exams can be picked up Friday after 3 pm.
Exam Statistics:
Class Range 34.5 – 99.5
Class Mean 78.3
Your Score _______
Your Rank in Class _____ out of 35
Course Grade _____
CHEM-643 Intermediary Metabolism
Final Examination, 13 December 2006
Page 2
Name ______________________________
Part I - Short Answer Questions (1 point each)
__________________________ 1.
Another name for AMP.
__________________________ 2.
Organ that is the major site for gluconeogenesis.
__________________________ 3.
Primary source of muscle ATP for a 100 yard dash.
__________________________ 4.
Primary organ consuming glucose in humans.
__________________________ 5.
Reaction associated with β-ketoacids.
__________________________ 6.
Usual target of end-product inhibition.
__________________________ 7.
TCA intermediate that contains Sulfur and Phosphorus.
__________________________ 8. How much 14C will a fossil dinosaur bone contain?
__________________________ 9.
PLP is to vitamin B6 as NAD is to?
__________________________ 10. Atmospheric gas that plants consume at night.
__________________________ 11. Class of macromolecules conserved during prolonged starvation.
__________________________ 12. Coenzyme associated with C-C bond cleavage next to carbonyls.
__________________________ 13. Name for six-membered ring that is part of purine.
__________________________ 14. Name of five-member ring that is part of purine.
CHEM-643 Intermediary Metabolism
Final Examination, 13 December 2006
Name ______________________________
Page 3
15-20 Identify the structures shown.
O
H3C
N
H3C
N
NH
COO
COO
H3N C H
H3C C H
CH3
NH2
16 ______________________
H
H2
C
HS
H3C
N
S
17 _____________________
OH OH
CH3
N
N
O
H2
O
C
OH
H
HCH2
O P O
H
O
OH OH
S S
15 ____________________
N
OH
H2
C
H
N
C
H2
C
O
H
N
C
H2
OH
H
H2
C
C
C
C
O
H3C CH3
OH
H
HO
H
H
18 _____________________
19 ______________________
O
H
OH
OH
20 _____________________
CHEM-643 Intermediary Metabolism
Final Examination, 13 December 2006
Page 4
Name ______________________________
Part II Problems:
1. (10 Points) The October 20 issue of Science this fall included an article in which the
pyridine nucleotide specificity of an E. coli β-isopropylmalate dehydrogenase (IMDH) was
changed from NAD to NADP through genetic engineering. [Miller et al. 314, 458 (2006)].
Kinetic studies showed the following catalytic properties of the wild type and mutated
enzyme.
Kcat/Km for NAD (M-1 s-1)
Kcat/Km for NADP (M-1 s-1)
Wild type IMDH
68 x 103
0.49 x 103
Mutant IMDH
0.2 x 103
34 x 103
IMDH catalyzes a reaction in the leucine biosynthetic pathway, as shown below.
AcCoA
COO-
CoASH
COO-
COO-
CH2
C
O
-
H2O
CH
H3C
OOC
OH
H
C
OH
OOC
C
H
-
C
IMDH
CH
H3C
CH
CH3
H3C
COOO
PLP +H3N
C
CH2
CO2
CH3
a ketovalerate
C
Fe
COO-
NAD+ NADH + H+
Glu
CH2
aKG
CH
CH3
H3C
H
CH
CH3
H3C
CH3
Leucine
a. (1 points) What reaction in the TCA cycle is most like IMDH?
b. (1 point) Transamination of α-ketovalerate yields what amino acid?
c. (3 points) Having engineered a mutant IMDH that was virtually as good with NADP as
the wild type enzyme was with NAD, the authors then replaced the wild type enzyme
with the mutant enzyme and studied the growth characteristics of E. coli.
Will the mutant strain grow better, worse, or indistinguishably from the wild type?
d. (5 points) Provide a well-reasoned explanation for your prediction above.
CHEM-643 Intermediary Metabolism
Final Examination, 13 December 2006
Page 5
Name ______________________________
2. (10 Points) Multiple carboxylase deficiency, also known as biotinidase deficiency, knocks out
biotin-dependent carboxylases. This leads to the accumulation of various carboxylase substrates
that, due to their elevated concentration, begin reacting as substrate analogs in other metabolic
reactions. As a result some unusual metabolites (shown below) appear in the blood and urine of
patients with multiple carboxylase deficiency. Show clearly how one of the unusual molecules
might form by modification of an accumulating carboxylase substrate via well known reactions.
O
H
COO
CH2
CH2OH
3-Hydroxypropionate
CH3 C
OH C
COO
COO
COO
CH2COO
Methylcitrate
H3C
C
H
CH2
C
C
C
OH
CH3
3-Hydroxyisovalerate
CH3
NHCH2COO
CH3
3-Methylcrotonylglycine
CHEM-643 Intermediary Metabolism
Final Examination, 13 December 2006
Name ______________________________
Page 6
3. (23 Points +5) Chorismate, a product of the shikimate pathway, is a biosynthetic precursor of
several important molecules including tryptophan as is shown below.
COOOH OH
COONH2
2
COO-
NH
-
HO3P
C
C
CH H
H
HOC
CH2
O
OH OH
CH2OPO3H-
-
COO-
OOC
COO
H2C
C
COOH 2C
C
HO H
H3N
COO-
C
H2C
B
CH2
C
CH2OPO3H-
O
O
O
H
3
OH OH
1
C
H
N
H
N
H
Anthranilate
C
N
H
COO-
Chorismate
HO H
O
COO-
H2C
A
NH2
C
COO-
C
OH
Fill in the answers to parts a-d & f on the figure above.
a. (2 pt) What is the name of Cofactor A?
b. (2 pt) What are the names of familiar compounds B and C?
c. (2 pt) The reactions forming B and C use same cofactor and additional substrate. What are
they?
d. (2 pt) What reacts with anthranilate in reaction 2 to form the product?
e. (5 pt bonus) Show mechanistically how B or C is formed from the precursor shown.
f. (3 pt) The enzyme catalyzing reaction 3 was a topic in a problem set earlier in the semester.
What familiar three carbon compounds are also substrates and products in this reaction and
what cofactor is involved?
H
CHEM-643 Intermediary Metabolism
Final Examination, 13 December 2006
Page 7
Name ______________________________
g. (6 pt) The following quotation comes from the abstract of an article in Journal of
Experimental Botany [57(12):3069-3078] published this year. It also applies to the preceding
figure.
Metabolic manipulation of plants to improve their nutritional quality is an important goal of plant
biotechnology. Expression in rice (Oryza sativa L.) of a transgene (OASA1D) encoding a feedbackinsensitive subunit of rice anthranilate synthase [Reaction 1] results in the accumulation of tryptophan
(Trp) in calli and leaves. It is shown here that the amount of free Trp in the seeds of such plants is
increased by about two orders of magnitude compared with that in the seeds of wild-type plants. The
total Trp content in the seeds of the transgenic plants was also increased.
Percent maximal activity
How is the mutant anthranilate synthase different than the wild type enzyme? Draw a
graph that would be appropriate for the figure title indicated below. Be sure to identify
which line is which enzyme.
100
0
0
[Tryptophan]
Comparison of the activity of wildtype and mutant antranilate synthase
as a function of tryptophan concentration.
h. (6 pt) Knowing that the transgenic rice plant now produces ~100 fold more free tryptophan in
seeds, what questions would you ask about the resulting rice strain? Provide 3 substantive
questions?
1.
2.
3.
CHEM-643 Intermediary Metabolism
Final Examination, 13 December 2006
Page 8
Name ______________________________
4. (10 pt) There are a number of antifolate drugs including methotrexate, trimethoprim, and
sulfanilamide. Select one of these. Describe how it works. What medical conditions is it
used to treat?
5. (5 points) When Dr. Tadhg Begley visited class, he told several stories in response to
student questions. One was about an ill-fated 1861 British exploration to Australia. 1
Another was about the toxic mechanism of bacimethrin, a natural product shown below. 2
NH2
N
OH
H3C
O
N
In a paragraph or two, with discussion of the relevant chemistry where appropriate,
summarize the important elements of one or the other of these stories.
1
2
Earl, J. W., McCleary, B. V. (1994) Mystery of the poisoned expedition. Nature 368: 683-684.
Reddick, J. J.; Saha, S.; Lee, J.; Melnick, J. S.; Perkins, J.; Begley, T. P.. (2001) The mechanism of action of bacimethrin,
a naturally occurring thiamin antimetabolite. Bioorg. Med. Chem. Lett., 11: 2245-2248.
COO
COO
H3N
O2
H3N
H
C
C
HC
1
C
C
HC
COO
H H2O
H2O +
NADP H3N
O2 +
NADPH
A
H2C
H2C
H
C
C
CH
C
HC
C
H
3
2
C
NH
C
HC
NH2
C
OH
O
Tryptophan
O
C
H
C
C
H
4
C
H
C
O
HC
HC
NH
C
H2C
C
H
C
H HO
2
C
B
D
OOC
O2
H
C
HC
CHO
OOC
5
E
COO
H2O + NAD
H
C
HC
C
6
C
NADH
7
NH2
COO
OOC
G
H2O
CH
NADPH
O
C
NADP
H2C
C
NH2
CH2
9
8
H2C
COO
H
F
I
CoAS
J
FAD
FADH2
C
N
O
SCoA
H2O
O
HC
K
10
11
L
CH
H2C
12
13
CoASH
NAD
C
NADH
2 AcCoA
CH2
HO
CH
14
15
CH3
COO
P
O
6. (23 Points) The figure above shows the catabolic pathway for tryptophan in mammals. Every other intermediate is omitted. Please
deduce and draw the structures of the missing intermediates in the appropriate boxes (2 points for each correct structure.) In the spaces
below, give the common name or abbreviation for the coenzymes and other lettered compounds (1 point each)
M
A. _____________________________
G. _____________________________
K. _______________________________
C. _____________________________
I. _____________________________
L. _______________________________
E. _____________________________
J. _____________________________
N. _______________________________
7. (10 points) Essay. Select one or the other of the following questions to answer clearly. Circle
the letter of the question you intend to answer.
a. ATP is Nature’s dehydrating agent.
b. Clearly explain the following quotation: During human starvation the “high rates of urea
synthesis are simply a consequence of the need for glucose.” 1
1
Watford, M. (2003) The Urea Cycle: Teaching Intermediary Metabolism In a Physiological Setting, Biochem and Mol. Biol. Educ. 31: 289297