CHEM-643 Biochemistry
Mid-term Examination
8:00 – 10:00, Friday, 2 November 2007
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 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 available 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.
Breakdown of the examination by sections:
I. Short Answer
II. Problems
III. Short Essays
Total
15 Points
83 Points
12 Points
110 Points
Exam Statistics
__31-100__ Class Range
___65.2___ Class Mean
__________ Your Rank in class
CHEM-643 Intermediary Metabolism
Mid-term Examination, 2 November 2007
Page 2
Name ______________________________
Part I - Short Answer Questions (1 point each)
__________________________ 1.
A coenzyme in which a pterin ring is found.
__________________________ 2.
Nucleotide from which pterin is synthesized.
__________________________ 3.
Coenzyme associated with reductive biosynthetic reactions.
__________________________ 4. Coenzyme associated with C-C bond cleavage next to
carbonyls.
__________________________ 5.
Vitamin D is derived from this class of compounds.
__________________________ 6.
Isoprenoid compounds containing 15 carbon atoms.
__________________________ 7.
Virtually exclusive metabolic fuel for your brain.
__________________________ 8.
Aspirin inhibits the synthesis of this class of compounds.
__________________________ 9.
Class of enzymes in which ATP is used to generate a
phosphorylated product.
__________________________ 10. Enzyme in E. coli that is feedback inhibited by histidine,
AMP, GMP, glycine, alanine, and glucosamine-6-P.
___________________________11. Defining thermodynamic characteristic of the first
committed step in a metabolic pathway.
__________________________ 12. Metal atom other than Fe associated with nitrogen fixation.
__________________________ 13. Industrial process that globally exceeds natural biological
nitrogen fixation.
__________________________ 14. Structurally, glutamate is to aspartate as lysine is to
______?
__________________________ 15. δ13C value for carbon in the Peedee belemnite.
CHEM-643 Intermediary Metabolism
Mid-term Examination, 2 November 2007
Name ______________________________
Page 3
Part II: Problems
1. Four enzymes with similar reactions are laid out for comparison in a way that I had
hoped students would have portrayed them in their answer to Question 3 on Problem Set
4.
HMGCoA Synthase (E.C. 2.3.3.10)
Citrate Synthase (E.C. 2.3.3.1)
CH3
COO
CH2
SCoA
C
O
+
C
CH2
CH3
O
OOC
C
CH2
SCoA
C
OH
C
O
O
H3C
+
C
CH2
H2O
CoASH
CH2
H2O
CH3
COO
OAA
OH
CH2
CoASH
C
AcCoA
COO
AcCoA
COO
COO
Citrate
C
SCoA
O
AcAcCoA
O
SCoA
HMG CoA
Citrate Cleavage Enzyme (E.C. 2.3.3.8)
HMGCoA Lyase (E.C. 4.1.3.4)
COO
COO
CH3
COO
C
C
CH2
CoASH
SCoA
O
C
OOC
C
OH
C
O
H3C
O +
+
C
CH2
CH2
CH3
AcCoA
O
CH2
SCoA
COO
OAA
ADP+Pi
ATP
CH2
COO
Citrate
CH2
CH3
AcCoA
OH
COO
C
AcAc
O
SCoA
HMG CoA
A. (9 points) The standard free energy, ΔGº´, for the citrate synthase reaction as
displayed above is -32.2 kJ/mol. The ΔGº´ for hydrolysis of ATP and CoA
thioesters are -30.5 kJ/mol and -31.4 kJ/mol, respectively. From this information,
estimate the ΔGº´ values for the other three enzymes in the direction of flux in
metabolism (direction of the reaction arrows). Please show your work and any
assumptions you make.
Page 4
CHEM-643 Intermediary Metabolism
Mid-term Examination, 2 November 2007
Name ______________________________
2. (10 points) Pyridoxal phosphate (PLP) participates as a coenzyme in a variety of
metabolic reactions involving amino acids. In addition to the well-known transamination
reactions, it is a coenzyme for the decarboxylation of certain amino acids such as
histidine. The structure of PLP is shown below. Draw out the mechanism by which PLP
would facilitate the decarboxylation of histidine to form histamine.
O
H2
O P
C
O
O
H
C
O
OH
N
H
CH3
3. (5 points) Camphor is a terpene sometimes used for mothballs. It is derived
biosynthetically from geranyl pyrophosphate. Indicate in both structures below, which
carbon-carbon bonds form in the cyclization.
H3C
CH3
C
HC
CH3
H3C
CH2
C
CH3
H2C
CH3
C
H2C
H2C
HC
CH2OP2O6H=
Geranyl Pyrophosphate
C
CH
Camphor
C
CH2
O
Name ______________________________
Page 5
CHEM-643 Intermediary Metabolism
Mid-term Examination, 2 November 2007
4. Anthranilate is an intermediate in the biosynthesis of tryptophan after it branches from
chorismate (not shown). The conversion of anthranilate to tryptophan occurs in four
enzymatic steps as shown below. The amounts of each of these enzymes in yeast cells
can be manipulated separately by introducing additional gene copies on plasmids.
Mutants with decreased activities for one of the four enzymes can also be created. If one
measures the flux of anthranilate to tryptophan in these various strains [Biochem. J. 287,
473 (1992)], only strains with less than 20% of the wild type enzyme activity have any
significant effect on flux.
COOCOO-
PRPP
PPi
NH2
-
HO3P
COO-
N
H
OH OH
C
C
CH H
H
HOC
CH2
O
Anthranilate
COO
OH OH
NH
CH2OPO3H-
CO2
N
H
C
C
H
H
CH2OPO3H-
H3N
C
H2C
PLP
GAP
Ser
OH OH
a. (6 points) Draw and label the axes for a graph depicting the in vivo rate of tryptophan
synthesis as a function of the activity of any one of the four enzymes in the pathway.
b. (4 points) Provide a reasonable explanation for the relative insensitivity of flux to the
enzyme activity described.
N
H
H
Name ______________________________
Page 6
CHEM-643 Intermediary Metabolism
Mid-term Examination, 2 November 2007
5. The biosynthesis of phosphatidyl choline as it may occur in human liver is depicted
below. The questions that follow refer to this figure.
CoASH
CoASH
ATP
ATP
AMP + PPi
AMP + PPi
Stearoyl CoA
CH2OH
C O
CH2OPO3H-
Linoleoyl CoA
H2C O
1
R1
C O
CH2OPO3H-
H2C O
2
CH3
R1
HO C H
CH2OPO3H-
H2C O
R2
3
R1
O C H
CH2OPO3H-
R
H2C O 1 H3C N CH2
R2
CH2
O C H OCH2O P O CH2
4
O
Phosphatidyl Choline
CH3
CH2
CH2
OH
Choline
CH3
CH3
H3C N CH3
H3C N CH3
H3C N CH3
5
CH2
CH2
OPO3H-
CH2
6
NH2
CH2
O
O
O
O
P - P
O O
O
N
N
O
CH2 O
H
H
H
H
OH OH
a. (4 points) Draw the structures of stearic acid and linoleic acid in the appropriate
boxes.
b. (2 points) Identify by name or common abbreviation the three-carbon substrate
for reaction 1.
c. (4 points) Fill in the missing coenzymes or substrate/products in reaction 2.
d. (2 points) Identify the missing product in reaction 4
e. (2 points) In the box provided, give another name for phosphatidyl choline.
f. (4 points) Fill in the missing coenzymes or substrate/products in reaction 5.
g. (4 points) Fill in the missing coenzymes or substrate/products in reaction 6.
h. (9 points) Propose a reasonable short pathway for the biosynthesis of choline
from serine and methionine.
Name ______________________________
Page 7
CHEM-643 Intermediary Metabolism
Mid-term Examination, 2 November 2007
6. Phenylketonuria (PKU) gets its name from the phenylketones that accumulate and
appear in the urine of people who, due to a mutation in the gene for phenylalanine
hydroxylase, cannot convert phenylalanine to tyrosine.
COO
H3N
C
CH2
COO
H
H3N
X
PKU
C
CH2
COO
H
?
C
COO
O
+
CH2
CH2
OH
a.
(4 points) Based on common reactions in intermediary metabolism, how is
phenylpyruvate formed from phenylalanine? Show the reactions involved and
indicate which, if any, coenzymes are needed.
b.
(6 points) Based on common reactions in intermediary metabolism, how is
phenylacetate formed from phenylpyruvate? Show the reactions involved and
indicate which, if any, coenzymes are needed.
CHEM-643 Intermediary Metabolism
Mid-term Examination, 2 November 2007
7.
Name ______________________________
Page 8
(8 points) When tadpoles undergo metamorphosis to become frogs the obvious
morphological changes are also accompanied by significant metabolic changes as
shown in the figure and data below. These data come from an article by Philip P. Cohen
entitled, “Biochemical differentiation during amphibian metamorphosis” Science 168,
533 (1970). Cohen measured the activity of a number of enzymes in the liver of adult
frogs and premetamorphic tadpoles and expressed them as a ratio.
Liver Enzyme Activity
Carbamyl phosphate synthetase
Ornithine transcarbamylase
Argininosuccinate synthase
Argininosuccinase
Arginase
Glutamate dehydrogenase
Lactate dehydrogenase
Glucose 6-P dehydrogenase
Malate dehydrogenase
Glutamate-oxaloacetate transaminase
Frog/Tadpole
Activity
Ratio
30
8
35
20
30
10
0.4
0.5
1.4
5
Image http://dj003.k12.sd.us/SCHOOL%20NOTES/chapter_12.htm
Based on the enzyme activity ratios reported, what conclusions can you make about the
metabolic changes that occur during amphibian metamorphosis?
CHEM-643 Intermediary Metabolism
Mid-term Examination, 2 November 2007
Page 9
Name ______________________________
Part III Essay Question
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. Answer only one of the two questions
that follow.
1. (12 points) The figure below depicts the incorporation of 14C from carbon dioxide and 32P
from phosphate into 3-phosphoglycerate in the transition from light to dark in a photosynthetic
algae. Explain in your own words, what is going on here. Include how the flux changes in
different pathways.
CHEM-643 Intermediary Metabolism
Mid-term Examination, 2 November 2007
Page 10
Name ______________________________
2. (12 Points) Fix your attention on a particular carbon atom in a glucose molecule (identify it)
that you consumed at your last meal. In a narrative (no structures), generate a reasonable story
of the fate of that carbon atom involving several tissues and at least three different metabolic
pathways before exiting as carbon dioxide.