Download Islamic University of Gaza Advanced Biochemistry Faculty of

Islamic University of Gaza
Faculty of Science
Biological Sciences Department
Advanced Biochemistry
Midterm Exam
30. 11.2010
Time: 2 hours
A. Each of the following questions has (0.5 point):
(total points: 10)
1. Which of the following terms are used to describe the tendency of a reaction to occur when the
substrates and products of the reaction are at any concentration?
A. ΔG
B. ΔGo
C. ΔGo'
D. -TΔS
E. ΔH
Answer: A
2. Which of the following is not a function of the citric acid cycle?
A.
B.
C.
D.
E.
Catabolism of carbon structures of some amino acids
Catabolism of acetate groups from acetyl CoA
The production of GTP
The production of NADPH
The production of carbon structures for the synthesis of some amino acids
Answer: D
3. In the citric acid cycle, a substrate level phosphorylation is catalyzed by:
A.
B.
C.
D.
E.
Citrate synthase
Succinyl CoA synthetase
Fumarase
Isocitrate dehydrogenase
Citrate lyase
Answer: B
4. In contrast to NADH, FAD(2H):
A.
B.
C.
D.
E.
Can donate electrons, but only two at a time, in a chemical reaction
Has a low affinity for its apoenzyme
Is very reactive in solution
Is an excellent feedback inhibitor
Is derived from a vitamin
Answer: C
5. The anaplerotic reaction that links glycolysis to the TCA cycle:
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A.
B.
C.
D.
E.
Uses thiamin as a cofactor
Is called phosphoenolpyruvate carboxykinase
Produces oxaloacetate
Is activated by malonyl CoA
Is dependent upon vitamin B12
Answer: C
6. Which of the following two enzymes are thought to be the major control enzymes of the TCA
cycle?
A.
B.
C.
D.
E.
Malate dehydrogenase and fumarase
Succinate dehydrogenase and fumarase
Succinyl CoA synthetase and succinate dehydrogenase
Succinyl CoA synthetase and alpha-ketoglutarate dehydrogenase
α-ketoglutarate dehydrogenase and isocitrate dehydrogenase
Answer: E
7. The phosphorylation of glucose to glucose-6-phosphate has a Delta Go'of +3.3 kcal/mol. So
why does the reaction occur in almost every cell of our body?
A.
B.
C.
D.
E.
Glucose becomes unstable intracellularly
Hexokinase is present
ATP hydrolysis
High concentration of glucose in the blood compared to cell
This reaction is coupled to another that has a much higher positive Delta Go
Answer: C
8. Which of the following statements regarding electron-accepting coenzymes is INCORRECT?
A.
B.
C.
D.
E.
FAD accepts electrons as the hydrogen atom
NADH is the reduced form of the coenzyme
FAD(H2) is synthesized from the vitamin riboflavin
The Delta Go' for the oxidation of NADH by the electron transport chain is negative
The electrons donated to these coenzymes are subsequently removed by the enzymes of
the TCA cycle
Answer: E
9. Which of the following statements regarding the TCA cycle is CORRECT?
A. The rate-limiting step involves the enzyme malate dehydrogenase
B. For each acetyl CoA entering the cycle, two molecules of CO2 are produced
C. For each acetyl CoA entering the cycle, 24 high-energy phosphate bonds are produced
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Islamic University of Gaza
Faculty of Science
Biological Sciences Department
Advanced Biochemistry
Midterm Exam
30. 11.2010
Time: 2 hours
D. The cycle will not function unless glutamate is present
E. The TCA cycle occurs in the rough endoplasmic reticulum of virtually every cell in the
body
Answer: B
10. Which of the following statements regarding the alpha-ketoglutarate dehydrogenase complex
is INCORRECT?
A.
B.
C.
D.
E.
One of its coenzymes - lipoic acid - comes from the vitamin B-carotene
It requires FAD as a coenzyme
Carbon dioxide is produced by this complex
One of its coenzymes - CoASH - comes from the vitamin pantothenate
It catalyzes the reaction converting a-ketoglutarate into succinyl CoA
Answer: A
11. Which enzyme complex in the TCA cycle requires the cofactors thiamine pyrophosphate,
lipoic acid, CoA, FAD and NAD+?
A.
B.
C.
D.
E.
Citrate synthase
a-ketoglutarate dehydrogenase
Succiny-CoA synthetase (succinate thiokinase)
Malate dehydrogenase
Fumarase
Answer: B
12. Which of the following statements about the coenzyme FAD is INCORRECT?
A. It accepts single electrons
B. The TCA cycle enzyme that transfers electrons to FAD is found in the inner
mitochondrial membrane
C. It is very reactive in solution
D. It remains tightly bound to the holoenzyme
E. FADH2 is an important allosteric inhibitor of the TCA cycle
Answer: E
13. Which of the following statements about the TCA cycle is CORRECT?
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A. Citrate is frequently used for gluconeogenesis in the liver
B. The production of oxaloacetate by pyruvate carboxylase is one of several anaplerotic
reactions for the TCA cycle
C. Succinyl CoA is used to create a neurotransmitter in the brain
D. Pyruvate dehydrogenase helps convert pyruvate into malate
E. Pyruvate carboxylase is only found in RBCs
Answer: B
14. Which of the following statements regarding the pyruvate dehydrogenase complex is
INCORRECT?
A.
B.
C.
D.
E.
When the complex is phosphorylated, it is inactive
Binding of pyruvate to the enzyme complex decreases the activity of the kinase
High [ADP] stimulates the conversion of pyruvate to acetyl CoA
The phosphatase which activates the complex is itself inhibited by Ca2+
The kinase associated with the pyruvate dehydrogenase complex is an enzyme that adds
phosphate groups
Answer: D
15. Assume standard biological conditions and that all the enzymes are present to catalyze the
reactions. Given the following data:
Glucose + Pi = glucose-6-P + H2O, ΔGo′ = +3.3 kcal/mol
ATP + H2O = Pi + ADP,
ΔGo′ = -7.0 kcal/mole
Calculate the ΔGo′ for the following reaction and determine whether the reaction is spontaneous
Glucose + ATP --> Glucose-6-P + ADP
A.
B.
C.
D.
E.
–10.3 kcal/mol and spontaneous
+10.3 kcal/mol and not spontaneous
–3.7 kcal/mol and not spontaneous
+3.7 kcal/mol and not spontaneous
–3.7 kcal/mol and spontaneous
Answer: E
16. During fasting, all of the following would tend to increase the flux through gluconeogenesis
EXCEPT:
A.
B.
C.
D.
E.
The concentration of free amino acids increases
The concentration of glycerol increases
The concentration of cyclic-AMP rises
The concentration of fructose-2,6-bisphosphate rises
The enzyme phosphoenolpyruvate carboxykinase is induced
Answer: D
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Islamic University of Gaza
Faculty of Science
Biological Sciences Department
Advanced Biochemistry
Midterm Exam
30. 11.2010
Time: 2 hours
17. The enzyme phosphofructokinase-2/fructose-2,6-bisphosphatase plays a key role in the
control of glycolysis exerted by the insulin to glucagon ratio. If the insulin to glucagon ratio
increases, phosphofructokinase-2/fructose-2,6-bisphosphatase in the liver would:
A.
B.
C.
D.
E.
Become more phosphorylated and phosphofructokinase-2 would become more active
Become less phosphorylated and phosphofructokinase-2 would become less active
Become more phosphorylated and phosphofructokinase-1 would become more active
Become less phosphorylated and phosphofructokinase-2 would become more active
Become less phosphorylated and fructose-2,6-bisphosphatase would become more active
Answer: D
18. During a fast, the liver enzyme pyruvate kinase becomes:
A.
B.
C.
D.
More active and more phosphorylated
More active and less phosphorylated
Less active and more phosphorylated
Less active and less phosphorylated
Answer: C
19. How many ATP molecules are generated from the energy of complete anaerobic oxidation of
a molecule of glucose?
a. 4
b. 3
c. 2
d. 35
Answer: A
20. Which of the following enzymes catalyzes a reaction that involves a decarboxylation
reaction?
a. pyruvate dehydrogenase
b. isocitrate dehydrogenase
c. à-keto glutarate dehydrogenase
d. all of the above
e. only a and c
Answer: E
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B. What two enzymes in gluconeogenesis catalyze the reversal of the pyruvate kinase
reaction? What cofactor is essential in the first of these reactions? Name a tissue
besides the liver in which gluconeogenesis occurs.
(3 points)
Answer:
1. Pyruvate Carboxylase: essential cofactor Biotin
2. Phosphoenolpyruvate carboxykinase
Kidney, brain, muscle (heart and skeletal)
C. The citrate synthase reaction is strongly exergonic. Why is this essential to maintaining flux
through the TCA cycle?
(2 points)
Answer:
The first reaction of the cycle is condensation of the methyl carbon of acetyl-CoA with the keto
carbon (C-2) of oxaloacetate. The standard free energy of the reaction, -8.0 kcal/mol, drives it
strongly in the forward direction. Since the formation of oxaloacetate from its precursor is
thermodynamically unfavorable, the highly exergonic nature of the citrate synthase reaction is of
central importance in keeping the entire cycle going in the forward direction, since it drives
oxaloacetate formation.
When the cellular energy charge increases the rate of flux through the citric acid cycle will
decline leading to a build-up of citrate. Excess citrate is used to transport acetyl-CoA carbons
from the mitochondrion to the cytoplasm where they can be used for fatty acid and cholesterol
biosynthesis. Additionally, the increased levels of citrate in the cytoplasm activate the key
regulatory enzyme of fatty acid biosynthesis, acetyl-CoA carboxylase and inhibit PFK-1.
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Islamic University of Gaza
Faculty of Science
Biological Sciences Department
Advanced Biochemistry
Midterm Exam
30. 11.2010
Time: 2 hours
D. Pyruvate is a key intermediate between different metabolic pathways. Describe how pyruvate
is formed (1 point) and the four metabolic fates of pyruvate (2 points). Include enzymes
responsible for these reactions, required cofactors, and additional products formed for each of
these reactions (2 points).
(total points: 5)
Answer:
Glycolysis is the catabolic process in which glucose is broken down to pyruvate
with formation of ATP.
1. Ethanol
2. Oxaloacetate
3. Acetyl CoA
4. Lactate
1. Ethanol synthesis occurs in yeast and some bacteria
Pyruvate decarboxylase (PDC) reaction: This enzyme is Mg++-dependent and
requires an enzyme-bound cofactor, thiamine pyrophosphate (TPP). In this
reaction a molecule of CO2 is released producing acetaldehyde.
Alcohol dehydrogenase reaction: Acetaldehyde is reduced to ethanol using
NADH as reducing power, thus regenerating NAD+.
2. Oxaloacetate synthesis:
Pyruvate carboxylate is activated by acetyl coA Replenishes intermediates of
the TCA cycle. Provides substrates for gluconeogenesis
3. Acetyl CoA synthesis
pyruvate dehydrogenase complex is inhibited by acetyl coA. Source of acetyl
coA for TCA and fatty acid synthesis.
Catalytic cofactors: Thiamine pyrophosphate (TPP), Lipoic acid, FAD.
Stoichiometric cofactor: CoA, NAD+
4. Lactate synthesis
Lactate dehydrogenase
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E. Why does citric acid cycle only operate when there is oxygen present? Be sure to include the
regulatory mechanisms of the cycle in your discussion.
(2 points)
Answer:
Although the Krebs cycle does not directly require oxygen, it can only take place when oxygen is
present because it relies on by-products from the electron transport chain, which requires oxygen.
The Krebs cycle is therefore an aerobic process.
Regulation mechanism of citric acid cycle:
The citric acid cycle must be carefully regulated by the cell. If the citric acid cycle were
permitted to run unchecked, large amounts of metabolic energy would be wasted in the over
production of reduced coenzymes and ATP. Conversely if the citric acid cycle ran too slowly,
ATP would not be generated fast enough to sustain the cell. By looking at the changes in free
energy of the reactions of the citric acid cycle, it is clear that there are three irreversible steps.
These three reactions of the cycle, citrate synthase, isocitrate dehydrogenase and á-ketoglutarate
dehydrogenase operate with large negative free energy changes under the concentrations of
products and reactants in the matrix of the mitochondria. Because the citric acid cycle is linked
to oxygen consumption to regenerate NAD+, the citric acid cycle is regulated primarily by
product feedback inhibition. Glycolysis and glycogen metabolism are under complex systems of
allosteric and hormonal control. The citric acid cycle in contrast is regulated by three simple
mechanisms.
1. Substrate availability
2. Product inhibition
3. Competitive feedback inhibition.
The principle signals are acetyl-CoA, succinyl-CoA, ATP,ADP, AMP, NAD+ and NADH.
All of the regulatory enzymes of the citric acid cycle including pyruvate dehyrogenase are
allosterically inhibited by NADH. The combination of the electron transport chain and oxidative
phosphorylation produce ATP form NADH, consequently ATP is an allosteric inhibitor of
pyruvate dehydrogenase and isocitrate dehydrogenase. The TCA cycle is turned on however by
high ratios of either ADP/ATP or NAD+/NADH which indicate that the cell has run low of
NADH or ATP.
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Islamic University of Gaza
Faculty of Science
Biological Sciences Department
Advanced Biochemistry
Midterm Exam
30. 11.2010
Time: 2 hours
F. Although Enzymes differ widely in structure, specificity, & mode of catalysis, yet their active
sites have common features. What are these features?
(2 points)
 The active site is a 3-D cleft formed by groups that come from different parts of the amino
acid sequence
 Water is usually excluded unless it is a reactant.
 Substrates bind to enzymes by multiple weak attractions (electrostatic interactions,
hydrogen bonds, hydrophobic interactions, etc.
 The specificity of binding depends on the precisely defined arrangement of atoms at the
active site
------------------------------------------------------------------------------------------------------------------F. Give the name of the following cycle appearing in the graphic. What do you know about
this cycle?
(2 points)
Answer:
This is the ATP/ADP cycle
 Only 100g of ATP in the body, turnover is very high.
 This amount must be constantly recycled every day. The ultimate source of energy for
constructing ATP is food; ATP is simply the carrier and regulation-storage unit of
energy. The average daily intake of 2,500 food calories translates into a turnover of a 180
kg of ATP
 Resting human consumes 40 kg of ATP in 24 hours.
 Strenuous exertion: 0.5 kg / minute.
 2hr run: 60kg utilized
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H. Key reactions are reoccurring throughout metabolism. Give 6 examples of such reactions.
Highlight the main task of each reaction.
(4 points)
1. Oxidation-reduction: Electron transfer
2. Ligation requiring ATP cleavage: Formation of covalent bonds.
3. Isomerization: Rearrangement of atoms to form isomers.
4. Group transfer: Transfer of a functional group from one molecule to another.
5. Hydrolytic: Cleavage of bonds by the addition of water
6. Additional or removal of functional groups: Addition of functional groups to double bonds
-----The End----Dr. Tarek M. Zaida
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