CHEM-643 Biochemistry
Mid-term Examination
7:30 – 9:00 am, Friday, 3 November 2006
Name ______________________________
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 errors you encounter.
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; however, the questions can be
answered by applying basic principles and patterns 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.
Breakdown of the examination by sections:
I. Short Answer
II. Natural Product Synthesis
III. Problems
IV. Short Essay
Total
16 Points
27 Points
47 Points
10 Points
100 Points
Exam Statistics
_________ Class Range
_________ Class Mean
_________ Your Rank in class
CHEM-643 Intermediary Metabolism
Mid-term Examination, 3 November 2006
Page 2
Name ______________________________
Part I - Short Answer Questions (1 point each, 16 Points Total)
H
SCoA
H3N C H
C O
CH3
COO
CH3
12
11
1
HO C H
G
CH2
COO
10
COO
C O
8
6
B. __________________________
COO
COO
C OPO3H
CH2
C O
CH2
CHO
CH3
E
1. Identify by name compounds:
CH3
C O
COO
B
4
5
7
HO C H
3
CH3
9
F
2
COO
COO
The diagram at the left was used for an inclass assignment early in the semester. Since
that time we have encountered every reaction
displayed in a metabolic context. All of the
questions in this section refer to this diagram.
A
COO
C
CH2
H C OH
H C OH O
H2C O P O
D
OH
C. __________________________
F. __________________________
G. __________________________
H. __________________________
2. Identify the (or a) pathway associated
with the reactions indicated:
3. Identify a cofactor associated with
each reaction, but don’t use same one
twice.
1. ______________________________
1. ___________________________
4. ______________________________
2. ___________________________
5. ______________________________
7. ___________________________
7. ______________________________
9. ___________________________
10. _____________________________
10. __________________________
12. __________________________
CHEM-643 Intermediary Metabolism
Mid-term Examination, 3 November 2006
Page 3
Name ______________________________
Part II Natural Product Biosynthesis:
1. (13 Points Total) A strain of alfalfa is resistant to feeding damage by the potato
leafhopper due to a homologous series of N-(3-methylbutyl) amides of normal saturated
fatty acids it produces [Ranger et al. (2005) Phytochemistry 66, 529-541]. The structure
of one of these compounds is given below:
A. (2 Points) What fatty acid (give the common name) is a precursor to this
compound?
B. (2 Points) What amino acid is a precursor to this compound?
C. (9 Points) Starting with the compounds you have identified, propose a
biochemically reasonable biosynthetic pathway that includes all intermediates and
necessary cofactors. A retrobiosynthetic approach may help.
H
N
C
O
CHEM-643 Intermediary Metabolism
Mid-term Examination, 3 November 2006
Page 4
Name ______________________________
2. (14 Points Total) Only relatively recently did researchers discover that plants have a
different pathways to generate isopentenylpyrophospate (IPP) than do animals. The plant
pathway, which was not discussed in class, is shown below [Modified from Fellermeier
et al. (2001) Eur. J. Biochem 268, 6302]. The questions that follow refer to the plant
pathway and its comparison to the pathway in us.
COO
A
CH3
O
C
CO2
CH3
CHO
H
OH
C
B
1
CH2OH
C
O
HO
C
H
H
C
OH
H3C
C
OH
H
C
OH 3
2
CH2OPO3H
CH2OPO3H
CH2OPO3H
H2C
CH3
C
CH2
CH2O P P
IPP
CH2OH
NH2
H3C C OH
N
H C OH
CH2O O
O
N
O
P O P O
CH2 O
O
O
H
H
H
H
OH OH
CH2OH
4
O
CH2OH
H3C C O
P
CH2O
O
P
NH2
H C OH
O
O
H C OH
CH2O
H3C C OPO3H
5
O
N
O
O
N
P O P O
CH2 O
O
O
H
H
H
H
OH OH
O
A. (2 Points) Name compounds A and B.
B. (2 Points) What coenzyme would you expect to be involved in step 1?
C. (2 Points) What nucleotide triphosphate is a substrate in step 3?
D. (4 Points) If Compound A were labeled at its carbonyl carbon, where would that
label appear in the product IPP? (Draw a circle around the carbon in IPP.)
E. (4 Points) If carbonyl-labeled Compound A were used as a precursor in the
mammalian synthesis of IPP, where would the label appear in IPP? (Put a box
around the carbon(s) in IPP above.)
CHEM-643 Intermediary Metabolism
Mid-term Examination, 3 November 2006
Page 5
Name ______________________________
Part III Problems
3. (10 Points Total) The US Army Cold Weather Research Laboratory in Natick, Massachusetts
is interested in the well being of American troops in cold climates. Among other things, they
study the responses of small experimental mammals under environmental stress. The data in
the following table report the amount of carnitine in two groups of four rats; one group kept
at 25°C and the other at 5°C for six weeks. The half-life of carnitine in these animals was
also determined. The rats were fed identical standard diets ad libitum (they ate as much as
they wanted whenever they wanted). The diet contained no carnitine.
Environmental Temp
25°C
5°C
Carnitine (mg/100g body wt)
22.5
172
Carnitine half-life (days)
9.7
4.8
Data derived from: Therriault & Mehlman (1965) Can. J. Biochem. 43, 1437-1443.
In a separate and unpublished experiment, two groups of rats raised at warm temperatures
were transferred to a frigid environment. Shortly before the transfer, one group was fed
carnitine. All of the carnitine-fed rats survived the transfer while none of the
unsupplemented rats survived.
A. (6 Points) What are the major implications of these experiments? (Implications are
different than results.) Explain.
B. (4 Points) Generate two substantive questions relating to these experiments, the results,
or the implications.
CHEM-643 Intermediary Metabolism
Mid-term Examination, 3 November 2006
Page 6
Name ______________________________
4. (10 Points Total) The formation of saccharopine and its conversion to lysine in fungi is
shown below. Both reactions involve oxidation-reduction with pyridine nucleotide
coenzymes.
COO+
H3N
C
COO-
COO+
H
+
CH2 NADPH + H
H3N
NADP+
CH2
+
H3N
H
C
NAD+
CH2
NADH + H+
Glu
H2O
H
CH2
CH2
CH2
CH2
C
CH2
H2O
aKG
CH2
-
C
H
COO
H2C
O
N
H
Saccharopine
C
CH2
H
NH3+
CH2
CH2
Lysine
COO-
A.
(5 Points) Explain the metabolic logic that rationalizes the use of NADP in
the first step and NAD in the second.
B.
(5 Points) Pick the first or second reaction and show with chemical
structures what is being oxidized or reduced and how it is formed or broken
down.
CHEM-643 Intermediary Metabolism
Mid-term Examination, 3 November 2006
Name ______________________________
Page 7
5. (12 Points Total) Below are four reactions involving thioesters and their corresponding
carboxylic acids. Reaction 1 is found in the TCA cycle and is an example of a substratelevel phosphorylation. Reaction 2 occurs in mitochondria and shows how acetoacetate, a
ketone body, is converted to acetoacetyl CoA in tissues where ketone bodies are
“burned”. Reaction 3 is the reaction that converts fatty acids to their corresponding
thioesters. Reaction 4 shows the hydrolysis of a thioester to its acid and free CoASH. All
reactions are shown in the direction that carbon would flow metabolically.
O
SCoA
C
O
GTP
GDP + Pi
CH2
1
CH2
COO
CoASH
-
O
COO-
COO-
CH2
CH2
CH2
CH2
COO
SCoA
O
COO-
C
2
CH2
CH2
COO-
R
-
O
COO-
ATP
AMP + PPi
3
SCoA
C
CH2
CH2
CoASH
R
SCoA
C
COO-
H 2O
CoASH
CH2
CH2
CH2
CH2
CH2
COO-
R
R
4
CH2
SCoA
C
CH2
CH2
C
O
C
O
CH3
CH3
A.
(2 Points) Which reaction above has an equilibrium constant closest to 1?
B.
(2 Points) Which reaction above would be metabolically wasteful?
C. (4 Points) From a chemical perspective, the energetics of the isolated Reactions 1
and 3 are not very different other than their directions are reversed. From a
metabolic perspective, explain circumstances where reactions like Reaction 3 that
produce PPi would be preferred over reactions like Reaction 1 (in reverse) that
would produce Pi.
D. (4 Points) In ketone body metabolism, what would be a reasonable explanation for
why reaction 2 is used rather than the type in reaction 3?
CHEM-643 Intermediary Metabolism
Mid-term Examination, 3 November 2006
Page 8
Name ______________________________
6. (15 Points) The figure below depicts the conversion of five molecules of
glyceraldehyde-3-P into three molecules of ribulose-5-P.
CHO
H C OH
CH2O P
CHO
H C OH
CH2O P
1
2
1
CH2OH
CO
CH2O P
4
CH2O P
CO
HO C H
H C OH
H C OH
CH2O P
3
CHO
H C OH
CH2O P
CHO
H C OH
CH2O P
CHO
H C OH
CH2O P
CH2OH
CO
HO C H
H C OH
H C OH
CH2O P
CHO
H C OH
H C OH
CH2O P
CH2OH
CO
CH2O P
5
HO
H
H
H
CH2OH
CO
HO C H
H C OH
CH2O P
7
CH2O P
CO
6
CH
C OH
C OH
C OH
CH2O P
HO
H
H
H
CH2OH
CO
CH
C OH
C OH
C OH
CH2O P
8
CH2OH
CO
HO C H
H C OH
CH2O P
9
9
CH2OH
CO
H C OH
H C OH
CH2O P
CHO
H C OH
H C OH
H C OH
CH2O P
CH2OH
CO
H C OH
H C OH
CH2O P
CH2OH
CO
H C OH
H C OH
CH2O P
a. (5 Points) Starting with [1-14C] glyceraldehyde-3-P, trace the five 14C-labeled
carbon atoms through part of one turn of the cycle into the five carbons of
ribulose-5-P. Maintain the identifying shapes associated with each of the five
carbon atoms.
b. (3 Points) Although the diagram does not indicate easily reversible reactions,
most of the reactions are reversible. Mark with an “X” through the number of the
reaction or reactions that would have the largest -ΔG°´?
c. (2 Points) Aside from enzyme reactions 1 and 9, which are represented twice, all
of the other reactions represent distinct enzymes. What other reaction is
chemically most similar to reaction 1?
d. (5 Points) It takes 6 turns of the Calvin Cycle to fix six carbon atoms—enough to
make one glucose unit in a starch molecule. On the diagram above, indicate with
a dashed arrow where carbon would be removed from the cycle on its way to
starch synthesis. At the end of your dashed arrow, draw the structure of the first
intermediate on the way to starch.
CHEM-643 Intermediary Metabolism
Mid-term Examination, 3 November 2006
Page 9
Name ______________________________
Part IV Essay Questions-Answer only one of the two Questions
Writing reflects how you think. Among the “right answers” I will read for the following
questions, some will be better than others because they show greater depth of understanding,
avoid extraneous or inaccurate information, provide a more logical structure, use appropriate
examples, and choose words with precision. Better quality answers will receive higher marks.
Therefore organize your thoughts before you write. Strive to write not that you may be
understood, but rather that you cannot possibly be misunderstood. Stream of consciousness
answers are rarely well organized or clearly presented.
7. (10 Points) There are a large number of inherited metabolic diseases, none of which are
particularly common. What are the various analytical strategies for detecting and
identifying metabolic diseases? If you were in charge of laboratory screening newborn
children for metabolic diseases, what strategy or strategies would most effective in
identifying the metabolic block?
CHEM-643 Intermediary Metabolism
Mid-term Examination, 3 November 2006
Page 10
Name ______________________________
8. (10 Points) (Do not answer if you have answered question 7 for credit.) Parents of
children with metabolic disease are heterozygous carriers of the disease and yet are
phenotypically normal. In terms of flux analysis, explain the lack of parental symptoms.