Download Final Exam (5/15/14)

Bioc3321 Spring 2014 Final Exam
Name:______________________________________
Biochemistry (Bioc3321 Spring 2014)
Final Exam (5/15/14)
Instructions
1. This exam consists of 12 pages. If a page is missing return the exam immediately.
2. PRINT your name NOW in the spaces at the top of ALL pages
3. The exam is designed to be completed in 100 minutes. However, you have 120 minutes to
finish it. Some advice, save the more difficult problems for the end.
4. Please, show all your work and be certain that all your explanations are given as
complete sentences and that all your calculations contain the right units. No credit is
given to the right answer for the wrong reason.
Good luck!!
Please sign:
Honor code: By the definition of academic integrity, the exam I am handing in is solely my own
work and truthfully represents work I have done. I will not release the contents of this exam to
anyone else until after the official date of the final exam.
___________________________________
Signature
Midterm 1. Biomolecules
Question 1.
Question 2.
Question 3.
Question 4.
Question 5
Total midterm 1
Midterm 2. Catabolism
Question 6.
Question 7.
Question 8.
Question 9.
Question 10.
Total midterm 2
Midterm 3. Biosynthesis and Metabolism
Question 11.
Question 12.
Question 13.
Question 14.
Question 15.
Total midterm 3
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Bioc3321 Spring 2014 Final Exam
Name:______________________________________
1. Answer the questions related to peptide structure
a. Draw the backbone of a tetrapeptide showing all hydrogens (you can use R for
generic side chains) at pH 7.
b. Circle above the bonds of the backbone’s tetrapeptide with limited rotation.
c. Draw a tetrapeptide with real amino acids at pH=7. The tetrapeptide needs to have a
total charge = +2 at pH = 3.5, charge = 0 at pH = 7 and charge = -3 at pH = 12
d. Name the tetrapeptide with the amino acid names and with the three letter codes.
2. State whether the following sentences are true or false. If false, explain in one sentence
what’s wrong with the statement.
a. When in an isoelectric focusing experiment a peptide with a pI = 9 is set in the area
pH = 5, the peptide will move towards higher pH because it has an overall negative
charge.
True/False
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Bioc3321 Spring 2014 Final Exam
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b. In a cation-exchange column (a column that exchanges cations) the peptide Arg-His
will elute earlier than the peptide Asn-Val (at pH = 7)
True/False
c. In a Michaelis-Menten curve, the total concentration of enzyme does not have to be
the same for all points of the curve.
True/False
d. The Ramachandran plot shows the dihedral angles adopted by the amide bonds of
the backbone of the protein.
True/False
e. Unsaturated fatty acids have a higher boiling point because the double bonds are
stronger than single bonds and harder to break.
True/False
3. A protein has a quaternary structure as shown in the following diagram. Each circle
indicates a peptide monomer with its mass, dash lines are intermolecular forces and solid
lines are disulfide bridges
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Bioc3321 Spring 2014 Final Exam
Name:______________________________________
a. On the left draw a schematic result of a gel electrophoresis when the protein is
boiled with SDS (a soap agent). On the right show a schematic result of a gel
electrophoresis when the protein is boiled with SDS and treated with a reducing
agent such as dithiothreitol. Comment on the intensity of each band. Indicate the
exact mass corresponding to each band.
4. Prostaglandins are a class of eicosanoids, fatty acid derivatives with a variety of extremely
potent actions on vertebrate tissues. They are responsible for producing fever and
inflammation and its associated pain. Prostaglandins are derived from the 20-carbon fatty
acid arachidonic acid in a reaction catalyzed by the enzyme prostaglandin endoperoxide
synthase. This enzyme, a cyclooxygenase, uses oxygen to convert arachidonic acid to PGG2,
the immediate precursor of many different prostaglandins. Ibuprofen is an inhibitor of
prostaglandin endoperoxide synthase. By inhibiting the synthesis of prostaglandins,
ibuprofen reduces inflammation and pain.
a. Draw in the axis below two Michaelis-Menten curves that would represent, one the
Vo with no ibuprofen and , two, a Vo with ibuprofen as competitive inhibitor. Label
the axis and indicate the value of Km and Vmax for both curves.
Name of substrate:_______________________________
Name of inhibitor:________________________________
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Bioc3321 Spring 2014 Final Exam
Name:______________________________________
b. Draw in the axis below three Michaelis-Menten curves. Label the axis and indicate
the value of Km and Vmax for both curves
i. With 0.1mM of ibuprofen
ii. With 0.2mM of ibuprofen
iii. Without ibuprofen but with half the concentration of prostaglandin
endoperoxide synthase than in the two previous curves.
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Bioc3321 Spring 2014 Final Exam
Name:______________________________________
5. Each of the carbohydrates shown below are different cyclic forms that can also be
represented in linear forms as Fischer projections.
Molecule A
Molecule B
Molecule C
Molecule D
a. For each Fischer projection below, identify if they are present in cyclic form above.
Circle the correct letter, there may be more than one or none.
A
B
D-Glucose
C
D
None
A
B
D-Fructose
C
D
None
A
B
D-Ribose
C
D
None
A
B
D-Xylose
C
D
None
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Bioc3321 Spring 2014 Final Exam
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6. Glycolysis consists in ten steps. The table below shows for each of those steps the standard
Gibb free energy G’o and the “instant” Gibbs free energy G that depends on the specific
concentrations of the cell:
Step #
G’o (kJ/mol)
G (kJ/mol)
Step 1
-16.7
-33.5
Step 2
+1.7
-2.5
Step 3
-14.2
-22.2
Step 4
23.9
-1.3
Step 5
7.6
+2.5
Step 6
12.6
-3.4
Step 7
-37.6
+2.6
Step 8
+8.8
+1.6
Step 9
+3.4
-6.6
Step 10
-62.8
-33.4
a. The step with the largest equilibrium constant is (explain 1 sentence)
b. List all the product favored reactions at cell conditions.
c. The step with the highest ratio [product]/[reactants] in cell conditions is (explain 1
sentence)
d. The step with the smallest ratio [product]/[reactants] in cell conditions is (explain 1
sentence)
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Bioc3321 Spring 2014 Final Exam
Name:______________________________________
7. Aldolase is the enzyme that has the molecule shown below as substrate.
a. Draw the product of aldolase and number the product using the carbon labels 1 to 6
used in the molecule above.
b. Draw the pyruvate molecule using the labels 1 to 6 used in in the molecule above.
c. Draw the oxaloacetate molecule at the end of the first Krebs cycle using the labels 1
to 6 used in the molecule above. Explain your reasoning.
8. State whether the following sentences are true or false. If false, explain in one sentence
what’s wrong with the statement
a. The complete beta-oxidation of an unsaturated fatty acid will provide the same
number of NADH molecules than the complete beta-oxidation of the corresponding
saturated fatty acid.
True/False
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Bioc3321 Spring 2014 Final Exam
Name:______________________________________
b. Glycerate phosphate is more oxidized than Glyceraldehyde phosphate, however,
phosphoenol pyruvate is as oxidized as glycerate phosphate.
True/False
c. The activity of phosphofructokinase-1 as a function of [ATP] and [F-2,6BP] shown
below shows that since ATP is a reactant, due to Le Chatelier principle too much
ATP decreases the activity of the enzyme.
True/False
9. In some bacteria, the citric acid cycle runs backwards from oxaloacetate to citrate to reduce
CO2. We feed bacteria with oxaloacetate labeled with14-C on the methyl carbon (-CH2-).
a. Draw the citrate molecule indicating where the label is. If only a fraction of
molecules contain that label, indicate what fraction of what carbon contains labels.
b. If we had fed the bacteria with labeled 14-CO2 instead of oxaloacetate, draw the
citrate molecule indicating where the labels would be.
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Bioc3321 Spring 2014 Final Exam
Name:______________________________________
10. The fermentation of glucose is useful because it recycles the NAD+ used in glycolysis.
Keeping this in mind, the molecule of glucose should have the same number of electrons
than two molecules of lactate.
a. Draw the molecule of glucose and lactate (disregard stereochemistry)
b. Calculate the oxidation state on each carbon and show that fermentation does
maintain the number of electrons between glucose and lactate.
11. Draw the products of transamination and name them. In the case where no transamination
is possible write “not possible”
a. Glutamate + Oxaloacetate 
b. Pyruvate + Aspartate 
c. Alanine + -ketoglutarate 
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Bioc3321 Spring 2014 Final Exam
Name:______________________________________
12. In the respiratory chain the electrons flow from one transporter to another in a very specific
sequence. Fill the gaps to show the sequence of flow of electrons in the respiratory chain
using the electron transporters below. All gaps must be filled and none can be repeated.
1) Oxygen
2) Complex I
3) Complex II
4) Complex III
5) Complex IV
6) NADH
7) Succinate
8) FADH2
9) Cyrochrome C
10) Ubuquinone (complex Q)
a. ______  ___8___  ______  ______  ______ ______ ______
b. ______ ____2___  ______  ______  ______  ______ ______
13. Adult rats are only fed with [14C]glucose, all glucose molecules contain two labels, one in the
second carbon and another in the fourth carbon. Their metabolism converts the glucose into
fat.
a. Draw a 10-C saturated fatty acid and circle the carbons that will contain 14C.
b. What fraction of 10-C fatty acid molecules will contain all the labels that you have
identified above?
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Bioc3321 Spring 2014 Final Exam
Name:______________________________________
14. Draw the Cori cycle indicating the following aspects
a.
i. In what steps is NADH a reactant and in what steps is a product
ii. The tissues participating and what species leave each tissue
iii. The ATP produced and consumed on each tissue.
b. Draw the glucose-alanine cycle showing the same aspects as in the Cori Cycle. Show
the main differences between the two cycles.
15. Identify if the secretion of glucagon will activate or deactivate the following processes or
enzymes
a. Carnitine shuttle (transporter of fatty acid into mitochondria) in muscle
activated/deactivated
b.
c.
d.
e.
f.
g.
Glycogen breakdown in liver
Glycolysis in liver
Acetyl-CoA carboxylase
Phosphofructokinase-1 in liver
Pyruvate carboxylase
Glucose uptake in liver
activated/deactivated
activated/deactivated
activated/deactivated
activated/deactivated
activated/deactivated
activated/deactivated
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