Identifying sequence of nonapeptide and questions about edman degradation.docx

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Identifying sequence of nonapeptide and questions about edman
degradation
𝑝𝑜𝑖𝑛𝑡𝑠 20 𝑝𝑜𝑖𝑛𝑡𝑠 Time Started: _______________ Time Ended: _______________ Time Elapsed (hrs
& mins): _____________ Biochemistry Assessment Part 2E Instructions: Accurately time
yourself as you answer the following 20 comprehensive Biochemistry questions. Consider
this an open book exam, so feel free to use old textbooks, notes, and online resources to
refresh your memory on specific topics/pathways/etc.; however, you will be judged on
accuracy and speed of completion, so try to go for the best combination of both accuracy
and time! Accuracy is more important than time here, so prioritize getting them all right.
Note: This is based on the honor system. Please answer the questions yourself and be
honest with the reporting of your times so that we can make educated decisions on the best
long-term fit for this position. The figure below describes the metabolic sources/fates of
pyruvate. The molecules that can be converted to or converted from pyruvate are labeled A-
E. The cofactors and byproducts of each reaction are labeled 1-5. Use this figure to answer
question 1. 1. A body builder has been consuming large quantities (i.e > 20 per day) of raw
eggs with the hopes of building more muscle mass, however, he has noticed when he has
not eaten in several hours he was becoming more lethargic than normal. You deduce the
patient is suffering from a diet-induced biotin deficiency. Under these conditions, which
molecule above will the patient be unable to make (is it molecule A, B, C, D or E)? 2. A 9-
month old girl presents with a hemolytic anemia. She is found to have a deficiency in the
enzyme responsible for the conversion of molecule B to pyruvate. Shown below is the
oxygen saturation curve for hemoglobin in the erythrocytes of this patient, compared to the
corresponding curve in normal red blood cells (RBCs). Which of the following is the most
likely explanation for the observed oxygen saturation curve in this patient? A. decreased
2,3-diphosphoglycerate B. decreased blood glucose C. increased 2,3-diphosphoglycerate D.
increased blood glucose E. normal levels of pyruvate 3. A 1- year old female patient suffers
from orotic aciduria (elevated level of orotic acid in urine). Which of the following
laboratory tests would be most helpful in distinguishing an orotic aciduria caused by a
defect in one of the urea cycle enzymes (e.g. carbamoyl phosphate synthetase I or ornithine
transcarbamylase) from that caused by a defect in uridine monophosphate synthesis (e.g.
orophosphoribosyl transferase)? A. Blood ammonia level determination B. Blood ascorbate
level determination C. Blood citrate level determination D. Blood folate level determination
E. Blood glucose level determination A patient is to undergo a routine arthroscopic surgery
on her knee and is instructed to fast for 12 hours before reporting to the clinic. With this in
mind, answer questions 4 and 5: 4. During the fast, the patient’s blood glucose level has
decreased from the normal value of about 4 mM to approximately 3 mM. Which of the
following statements describes the most likely activity levels of Glucokinase and/or
Hexokinase given the information below? A. Both enzymes will be maximally active B.
Hexokinase activity will have increased following the starvation period C. Hexokinase will
be at half maximal velocity following the starvation period D. Glucokinase will be at
maximal velocity following the starvation period E. Hexokinase activity will be unchanged
following the starvation period 5. Following the 12 hour fast, which of the following
enzymes will be active in the liver? A. Phosphofructokinase B. Carnitine acyl transferase I C.
Acetyl CoA carboxylase D. Glycogen synthase 6. A patient is brought into the emergency
room near death. You have determined that he has been exposed to a mitochondrial poison.
His life depends on determining to what poison he has been exposed. You quickly determine
that his mitochondria are not making ATP nor utilizing O2. Addition of 2,4-DNP does not
restore oxygen consumption and there appears to be higher than normal concentrations of
reduced cytochrome c. What poison most likely caused the patient’s conditions? A. Amytal
B. Rotenone C. Carbon monoxide D. Antimycin E. Oligomycin 7. A 60-year-old man is
brought to his physician from an institution for severe mental deficiency. The physician
reviews his family history and finds he has an older sister in the same institution. Their
parents are deceased but reportedly had normal intelligence and no chronic diseases. The
man sits in an odd position as though he was sewing. This prompted the experienced
physician to obtain a ferric chloride test on the man’s urine. The ferric chloride test turns
color with aromatic compounds, including certain amino acids and a green color confirms
the physician’s suspicion. Which of the following amino acids was most likely detected in
the man’s urine? A. glutamine B. glycine C. methionine D. phenylalanine E. serine A patient
comes into your clinic suffering from anorexia nervosa. Her mother brought her in
concerned as the patient has not eaten in over 3 days. She has the classic presentation
including low body weight, decreased muscle mass, glycogen, and fat stores, and she is
anemic. With this in mind, answer questions 8, 9 and 10: 8. What would be the expected
phosphorylation state and activity of her liver enzymes glycogen phosphorylase and
pyruvate kinase? 9. What would be the expected rate of nitrogen excretion in this patient?
A. proportional to nitrogen intake B. undetectable due to lack of intake C. constant at about
5 g per day D. increased to greater than 7 g per day due to wasting 10. Why would the
acetyl-CoA generated by this patient not enter the TCA cycle in her liver? A. The liver does
not express the enzyme necessary to utilize acetyl CoA in this way B. The PDH complex will
not run in reverse C. Oxaloacetate is unavailable due to predominance of gluconeogenesis D.
Acetyl CoA is being used to generate glucose E. The high insulin to glucagon ratio in this
patient would inhibit the TCA cycle 11. A patient (7 years old) is brought into the clinic
suffering from ataxia. Upon serum analysis the only abnormalities that were observed were
elevated lactate, alanine, and pyruvate. The patient was partially stabilized by the treatment
of thiamine. What do you think is wrong with the patient? A. Pyruvate kinase deficiency B.
Lactate dehydrogenase deficiency C. Pyruvate carboxylase deficiency D. Pyruvate
dehydrogenase deficiency E. Phosphofructokinase deficiency 12. A 45-year-old man was
rushed to the emergency room from a local restaurant after having “choked” while eating.
On physical examination (temperature, 37.2o C; pulse, 125; blood pressure, 170/110), there
was marked cyanosis and very labored respiration. Lab measurements yielded the
following results: The solubility coefficient for CO2 at 37o C is 0.03 mM/mmHg; the pKa
value for the carbonic acid bicarbonate buffer system is 6.1. Characterize the acid-base
disturbance and physiologic compensation, if any. A. B. C. D. E. Primary Problem Metabolic
acidosis Metabolic alkalosis Respiratory alkalosis Respiratory acidosis Metabolic acidosis
Compensation Respiratory compensation No compensation Metabolic compensation
Metabolic compensation No compensation 13. The glycolytic enzyme, aldolase, catalyzes the
reaction below with a ΔG°’= 5.6 kcal/mol. Given the cellular concentrations [F1,6bisP] = 10
mM, [GAP] = 1 mM, [DHAP] = 1 mM, how would this reaction proceed? A. It would go in
reverse (right to left as written above) B. It would go forward (left to right as written above)
C. It would not proceed (at equilibrium) D. It would go in reverse, but very slowly The next
2 questions deal with the following case study A 38 year old woman comes into the clinic
complaining of feeling tired and physically “drained” for the last 5 days. She has yellow
sclerae and has informed you that her urine is very dark. She has made no foreign trips and
mentions the only thing she did different prior to this bout of fatigue, is she consumed two
meals of broad beans, including fava beans. In both meals, she estimates she consumed
approximately one pound of beans. Her lab reports are detailed in the chart below: 14.
Given the relationship between the appearance of symptoms and the two meals of fava
beans, you suspect she is deficient in erythrocyte glucose 6-phosphate dehydrogenase
(G6PDH) activity. What role does G6PDH play in erythrocytes that render them sensitive to
oxidant-induced lysis in G6PDH deficient patients? A. The NADPH it produces is necessary
to maintain reduced glutathione. B. The lactone it produces is a necessary building block for
cell wall maintenance. C. The NADPH it produces is used to synthesize the steroids
necessary for cell wall biosynthesis D. The lactone it produces can be used to inhibit
phospholipases E. The NADPH it produces is necessary for salvage of partially degraded
phospholipids 15. According to the laboratory data, the patient is suffering from anemia (i.e.
decreased hemoglobin). Given the patient’s decreased oxygen carrying capacity, her muscle
cells might become anoxic, even under non-strenuous activity. Under these conditions (i.e.
anoxic muscle cells) what would you expect the state of glycogen metabolism to be in her
muscle cells? A. High levels of glucose 6-phosphate would stimulate glycogen
phosphorylase. B. High levels of Ca2+ would stimulate glycogen synthase. C. Low levels of
ATP would activate glycogen synthase D. High levels of AMP would activate glycogen
phosphorylase E. High levels glucose 1-phosphate would inhibit glycogen synthase 16.
Suppose you isolated a nonapeptide (9 amino acid residues) from a patient’s blood.
Reaction of the nonapeptide with FDNB followed by acid hydrolysis produces a DNP-
product with a sulfhydryl R-group, indicating that: a) b) c) d) e) C-terminal residue of the
nonapeptide is Cysteine. N-terminal residue of the nonapeptide is Cysteine. N-terminal
residue of the nonapeptide is Tyrosine. C-terminal residue of the nonapeptide is Threonine
C-terminal residue of the nonapeptide is Tyrosine or Glycine. 17. Treatment of the
nonapeptide from the previous problem (21) with CNBr produces a tetrapeptide containing
the Nterminal amino acid and a pentapeptide. After one round of Edman degradation on the
pentapeptide, a product is produced that contained a nonpolar, aliphatic R group, meaning
that the pentapeptide has: a) b) c) d) e) N-terminal I. N-terminal S. C-terminal E. N-terminal
H. N-terminal M. 18. The second and third rounds of Edman degradation on the same
pentapeptide from the problem above (22) produced products with aliphatic alcohol
groups, meaning that the pentapeptide had: a) b) c) d) e) S and H. I and Y. M and C. T and S.
M and Y. 19. Hydrazinolysis of the same pentapeptide from the problems above (22 & 23)
produced modified amino acids & a free αamino acid with an aromatic-alcohol group.
Combining the info from these problems, the pentapeptide is most likely: a) b) c) d) e)
STIRY. HTSMY. TISMY. ISTRY. ISMRY. 20. Deduce the entire sequence of the original
nonapeptide using the following hint and the information from the previous four practice
problems (21 through 24). Hint: The sequence of the nonapeptide using the one-letter
amino acid codes reveals a relevant academic subject. ____-____-____-____-____-____-____-____-____

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Identifying sequence of nonapeptide and questions about edman degradation.docx

  • 1. Identifying sequence of nonapeptide and questions about edman degradation 𝑝𝑜𝑖𝑛𝑡𝑠 20 𝑝𝑜𝑖𝑛𝑡𝑠 Time Started: _______________ Time Ended: _______________ Time Elapsed (hrs & mins): _____________ Biochemistry Assessment Part 2E Instructions: Accurately time yourself as you answer the following 20 comprehensive Biochemistry questions. Consider this an open book exam, so feel free to use old textbooks, notes, and online resources to refresh your memory on specific topics/pathways/etc.; however, you will be judged on accuracy and speed of completion, so try to go for the best combination of both accuracy and time! Accuracy is more important than time here, so prioritize getting them all right. Note: This is based on the honor system. Please answer the questions yourself and be honest with the reporting of your times so that we can make educated decisions on the best long-term fit for this position. The figure below describes the metabolic sources/fates of pyruvate. The molecules that can be converted to or converted from pyruvate are labeled A- E. The cofactors and byproducts of each reaction are labeled 1-5. Use this figure to answer question 1. 1. A body builder has been consuming large quantities (i.e > 20 per day) of raw eggs with the hopes of building more muscle mass, however, he has noticed when he has not eaten in several hours he was becoming more lethargic than normal. You deduce the patient is suffering from a diet-induced biotin deficiency. Under these conditions, which molecule above will the patient be unable to make (is it molecule A, B, C, D or E)? 2. A 9- month old girl presents with a hemolytic anemia. She is found to have a deficiency in the enzyme responsible for the conversion of molecule B to pyruvate. Shown below is the oxygen saturation curve for hemoglobin in the erythrocytes of this patient, compared to the corresponding curve in normal red blood cells (RBCs). Which of the following is the most likely explanation for the observed oxygen saturation curve in this patient? A. decreased 2,3-diphosphoglycerate B. decreased blood glucose C. increased 2,3-diphosphoglycerate D. increased blood glucose E. normal levels of pyruvate 3. A 1- year old female patient suffers from orotic aciduria (elevated level of orotic acid in urine). Which of the following laboratory tests would be most helpful in distinguishing an orotic aciduria caused by a defect in one of the urea cycle enzymes (e.g. carbamoyl phosphate synthetase I or ornithine transcarbamylase) from that caused by a defect in uridine monophosphate synthesis (e.g. orophosphoribosyl transferase)? A. Blood ammonia level determination B. Blood ascorbate level determination C. Blood citrate level determination D. Blood folate level determination E. Blood glucose level determination A patient is to undergo a routine arthroscopic surgery
  • 2. on her knee and is instructed to fast for 12 hours before reporting to the clinic. With this in mind, answer questions 4 and 5: 4. During the fast, the patient’s blood glucose level has decreased from the normal value of about 4 mM to approximately 3 mM. Which of the following statements describes the most likely activity levels of Glucokinase and/or Hexokinase given the information below? A. Both enzymes will be maximally active B. Hexokinase activity will have increased following the starvation period C. Hexokinase will be at half maximal velocity following the starvation period D. Glucokinase will be at maximal velocity following the starvation period E. Hexokinase activity will be unchanged following the starvation period 5. Following the 12 hour fast, which of the following enzymes will be active in the liver? A. Phosphofructokinase B. Carnitine acyl transferase I C. Acetyl CoA carboxylase D. Glycogen synthase 6. A patient is brought into the emergency room near death. You have determined that he has been exposed to a mitochondrial poison. His life depends on determining to what poison he has been exposed. You quickly determine that his mitochondria are not making ATP nor utilizing O2. Addition of 2,4-DNP does not restore oxygen consumption and there appears to be higher than normal concentrations of reduced cytochrome c. What poison most likely caused the patient’s conditions? A. Amytal B. Rotenone C. Carbon monoxide D. Antimycin E. Oligomycin 7. A 60-year-old man is brought to his physician from an institution for severe mental deficiency. The physician reviews his family history and finds he has an older sister in the same institution. Their parents are deceased but reportedly had normal intelligence and no chronic diseases. The man sits in an odd position as though he was sewing. This prompted the experienced physician to obtain a ferric chloride test on the man’s urine. The ferric chloride test turns color with aromatic compounds, including certain amino acids and a green color confirms the physician’s suspicion. Which of the following amino acids was most likely detected in the man’s urine? A. glutamine B. glycine C. methionine D. phenylalanine E. serine A patient comes into your clinic suffering from anorexia nervosa. Her mother brought her in concerned as the patient has not eaten in over 3 days. She has the classic presentation including low body weight, decreased muscle mass, glycogen, and fat stores, and she is anemic. With this in mind, answer questions 8, 9 and 10: 8. What would be the expected phosphorylation state and activity of her liver enzymes glycogen phosphorylase and pyruvate kinase? 9. What would be the expected rate of nitrogen excretion in this patient? A. proportional to nitrogen intake B. undetectable due to lack of intake C. constant at about 5 g per day D. increased to greater than 7 g per day due to wasting 10. Why would the acetyl-CoA generated by this patient not enter the TCA cycle in her liver? A. The liver does not express the enzyme necessary to utilize acetyl CoA in this way B. The PDH complex will not run in reverse C. Oxaloacetate is unavailable due to predominance of gluconeogenesis D. Acetyl CoA is being used to generate glucose E. The high insulin to glucagon ratio in this patient would inhibit the TCA cycle 11. A patient (7 years old) is brought into the clinic suffering from ataxia. Upon serum analysis the only abnormalities that were observed were elevated lactate, alanine, and pyruvate. The patient was partially stabilized by the treatment of thiamine. What do you think is wrong with the patient? A. Pyruvate kinase deficiency B. Lactate dehydrogenase deficiency C. Pyruvate carboxylase deficiency D. Pyruvate dehydrogenase deficiency E. Phosphofructokinase deficiency 12. A 45-year-old man was
  • 3. rushed to the emergency room from a local restaurant after having “choked” while eating. On physical examination (temperature, 37.2o C; pulse, 125; blood pressure, 170/110), there was marked cyanosis and very labored respiration. Lab measurements yielded the following results: The solubility coefficient for CO2 at 37o C is 0.03 mM/mmHg; the pKa value for the carbonic acid bicarbonate buffer system is 6.1. Characterize the acid-base disturbance and physiologic compensation, if any. A. B. C. D. E. Primary Problem Metabolic acidosis Metabolic alkalosis Respiratory alkalosis Respiratory acidosis Metabolic acidosis Compensation Respiratory compensation No compensation Metabolic compensation Metabolic compensation No compensation 13. The glycolytic enzyme, aldolase, catalyzes the reaction below with a ΔG°’= 5.6 kcal/mol. Given the cellular concentrations [F1,6bisP] = 10 mM, [GAP] = 1 mM, [DHAP] = 1 mM, how would this reaction proceed? A. It would go in reverse (right to left as written above) B. It would go forward (left to right as written above) C. It would not proceed (at equilibrium) D. It would go in reverse, but very slowly The next 2 questions deal with the following case study A 38 year old woman comes into the clinic complaining of feeling tired and physically “drained” for the last 5 days. She has yellow sclerae and has informed you that her urine is very dark. She has made no foreign trips and mentions the only thing she did different prior to this bout of fatigue, is she consumed two meals of broad beans, including fava beans. In both meals, she estimates she consumed approximately one pound of beans. Her lab reports are detailed in the chart below: 14. Given the relationship between the appearance of symptoms and the two meals of fava beans, you suspect she is deficient in erythrocyte glucose 6-phosphate dehydrogenase (G6PDH) activity. What role does G6PDH play in erythrocytes that render them sensitive to oxidant-induced lysis in G6PDH deficient patients? A. The NADPH it produces is necessary to maintain reduced glutathione. B. The lactone it produces is a necessary building block for cell wall maintenance. C. The NADPH it produces is used to synthesize the steroids necessary for cell wall biosynthesis D. The lactone it produces can be used to inhibit phospholipases E. The NADPH it produces is necessary for salvage of partially degraded phospholipids 15. According to the laboratory data, the patient is suffering from anemia (i.e. decreased hemoglobin). Given the patient’s decreased oxygen carrying capacity, her muscle cells might become anoxic, even under non-strenuous activity. Under these conditions (i.e. anoxic muscle cells) what would you expect the state of glycogen metabolism to be in her muscle cells? A. High levels of glucose 6-phosphate would stimulate glycogen phosphorylase. B. High levels of Ca2+ would stimulate glycogen synthase. C. Low levels of ATP would activate glycogen synthase D. High levels of AMP would activate glycogen phosphorylase E. High levels glucose 1-phosphate would inhibit glycogen synthase 16. Suppose you isolated a nonapeptide (9 amino acid residues) from a patient’s blood. Reaction of the nonapeptide with FDNB followed by acid hydrolysis produces a DNP- product with a sulfhydryl R-group, indicating that: a) b) c) d) e) C-terminal residue of the nonapeptide is Cysteine. N-terminal residue of the nonapeptide is Cysteine. N-terminal residue of the nonapeptide is Tyrosine. C-terminal residue of the nonapeptide is Threonine C-terminal residue of the nonapeptide is Tyrosine or Glycine. 17. Treatment of the nonapeptide from the previous problem (21) with CNBr produces a tetrapeptide containing the Nterminal amino acid and a pentapeptide. After one round of Edman degradation on the
  • 4. pentapeptide, a product is produced that contained a nonpolar, aliphatic R group, meaning that the pentapeptide has: a) b) c) d) e) N-terminal I. N-terminal S. C-terminal E. N-terminal H. N-terminal M. 18. The second and third rounds of Edman degradation on the same pentapeptide from the problem above (22) produced products with aliphatic alcohol groups, meaning that the pentapeptide had: a) b) c) d) e) S and H. I and Y. M and C. T and S. M and Y. 19. Hydrazinolysis of the same pentapeptide from the problems above (22 & 23) produced modified amino acids & a free αamino acid with an aromatic-alcohol group. Combining the info from these problems, the pentapeptide is most likely: a) b) c) d) e) STIRY. HTSMY. TISMY. ISTRY. ISMRY. 20. Deduce the entire sequence of the original nonapeptide using the following hint and the information from the previous four practice problems (21 through 24). Hint: The sequence of the nonapeptide using the one-letter amino acid codes reveals a relevant academic subject. ____-____-____-____-____-____-____-____-____