CHM 521/ 522 (BIOCHEMISTRY)
3 Examinations ( dates listed below) 50 points each..................150 points
1 Comprehensive Examination......................................................100 point
Grading ScaleTotal score (%)
90 and above....... A
87,88,89............... A-
84,85,86............... B+
81,82,83............... B
78,79,80............... B-
75,76,77............... C+
72,73,74............... C
69,70,71............... C-
66,67,68............... D+
63,64,65............... D
60, 61,62.............. D-
59 and below.......... E
NOTE: THE 4 EXAMINATIONS WILL DECIDE YOUR FINAL GRADE. THERE IS NO EXTRA CREDIT FOR ANYTHING ELSE !
READING MATERIAL
1. Text (required):PRINCIPLES OF BIOCHEMISTRY 3rd edition by Lehninger/Nelson/Cox
2. Course Pack (optional)
TO DO WELL IN THIS CLASS, IT IS IMPORTANT:
1. NOT TO MISS CLASS LECTURES. IN CLASS, IMPORTANT CONCEPTS (SUMMARIZED IN A COURSE PACK) TO HELP YOU UNDERSTAND YOUR TEXT WILL BE EMPHASIZED.
2. TO LOOK UP THE SYLLABUS BELOW AND READ THE CHAPTER BEFORE THE NEXT CLASS LECTURE. DO NOT PROCRASTINATE OR YOU WILL FIND YOURSELF WITH A LOT OF CATCHING-UP TO DO !
3. TAKE THE WEB QUIZZES— THIS WILL HELP YOU UNDERSTAND CLASS LECTURES AND PREPARE FOR YOUR EXAMINATIONS.
4. FOR CLARIFICATIONS DROP BY DURING MY OFFICE HOURS. SINCE MY OFFICE HOURS ARE FOR ALL STUDENTS IN THIS CLASS AND IN OTHER CLASSES I’M CURRENTLY TEACHING AS WELL AS FOR MAJOR/MINOR SIGNING AND ADVISING, IT WOULD BE IMPOSSIBLE FOR ME TO GO THROUGH THE WHOLE LECTURE IF YOU MISSED ONE !
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LECTURE MATERIAL
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1.Introduction to Biochemistry (Chapters 1-4) Aug 27
Go through the tutorial in your UNDERSTAND! Biochemistry Interactive CD-ROM
BACKGROUND
Chemical Fundamentals I
Chemical Fundamentals II
Fundamentals of Cell Architecture
Try the following quizzes !
2. Proteins 1 (Chapters 5-7) Aug 29
3. Proteins 2 Aug 31
1.Another importance of the Henderson Hasselbach equation is in acid-base physiology of blood.
The main blood buffer is the carbonic acid/bicarbonate system (H2CO3 / HCO3- ) which has a pK of 6.1.
H2CO3 ========== H+ + HCO3 -
Using the Henderson-Hasselbach equation
pH of blood = pK + log [HCO3-] / [H2CO3]
Since the pK=6.1, the pH = 6.1 + log [bicarbonate in blood] / [carbonic acid in blood]
For a healthy person [blood bicarbonate] = 24 mM while [blood carbonic acid] = 1.2 mM
Thus pH = 6.1 + log (24) / 1.2 which is equal to 7.4. The blood pH of a healthy individual is thus 7.4.
4. Proteins 3 Sep 5
Question: A protein has 30 amino acids, ALL of which are asp (such a protein can be called polyaspartic acid).
Will this protein form an alpha-helix at pH 7 ?
Question: Will you find many pro residues in alpha-helices of proteins ?
Question: Will polyleucine form alpha-helices ?
5. Proteins 4 Sep 7
6. Proteins 5 Sep 10
7. Proteins 6 Sep 12
Go through the tutorial in your
UNDERSTAND! Biochemistry Interactive CD-ROM
MOLECULES OF LIFE
8. Proteins 7 Sep 14
a. Recommended practice problems (from Lehninger 3rd ed.)on the above material (Introduction & Proteins).
1. Chapter 5: Problem 2
2. Chapter 5: Problem 4
3. Chapter 5: Problem 6
4. Chapter 5: Problem 13
5. Chapter 5: Problem 15
6. Chapter 6; Problem 4
7. Chapter 6; Problem 5
8. Chapter 6; Problem 6
9. Chapter 6; Problem 10 (this is an internet problem-the database you use may give slightly different results depending on how you input your data (e.g. entering a 30 residue sequence instead of a 50 residue sequence).
In order to make sure that you are reasonably close in your search,
the authors answer is NF-kappa-B transcription factor subunit (HUMAN).
10. Chapter 7: Problem 5
11. Chapter 7: Problem 6
b. View some protein images and properties by going to PROTEIN DATA BANK
and typing in the name of the protein you are interested in.
c. You can also see some protein images in your CD ( MOLECULES OF LIFE-interactive
gallery of protein structures - some images like insulin #32 can be rotated, flipped etc by
manipulating your mouse).
d. Review proteins by going to the worthpublishers website and clicking on the proteins tutorial.
e. Review allosteric/nonallosteric proteins by going to the worthpublishers website and clicking on the oxygen binding proteins tutorial.
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Try these quizzes!
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QUIZ 5
Refer to the polypeptide structure below (Q1-10) and answer the following questions.
1. What is the primary structure of the protein ?
2. What is the NET charge of the protein at pH 7 ?
3. How many peptide bonds are present?
4. Carboxypeptidase treatment will identify the amino acid _____?
5. What is the acidic amino acid present?
6. The R groups on amino acid numbers ___ and ___ are hydrophobic since they are aromatic.
7. Assuming that this protein forms a salt bridge when folded. The salt bridge may be formed between the N-terminal amino group and the amino acid ______.
8. The protein has ___ hydroxyl groups, ______ sulfhydryl group, sand ____ carboxyl groups.
9. Which of the following would you use for selective hydrolysis of the protein?
a. trypsin
b. chymotrypsin
c. thermolysin
d. CNBr
10. Assume that the protein folds into a three dimensional shape. The protein thus has a primary, secondary, tertiary and quaternary structure. TRUE or FALSE?
11. Pro is an imino acid. TRUE or FALSE?
12. Pro has an indole side chain. TRUE or FALSE?
13. When oxygen binds hemoglobin, BPG (formerly called DPG) is expelled. TRUE or FALSE?
14. When oxygen binds hemoglobin, electrostatic bonds are broken. TRUE or FALSE?
15. When oxygen binds hemoglobin, its quaternary structure is altered. TRUE or FALSE?
16. When oxygen binds hemoglobin, the Fe atom moves into the porphyrin's plane. TRUE or FALSE?
17. Val and ile branch at the beta-carbon. TRUE or FALSE?
18. Myoglobin is a fibrous protein. TRUE or FALSE?
19. Polyglutamic acid at pH 7 will exist as an alpha-helix. TRUE or FALSE?
20. PITC is a chemical used in the identification of the N-terminal amino acid. TRUE or FALSE?
QUIZ 5 (answers in blue)
Refer to the polypeptide structure below (Q1-10) and answer the following questions.
1. What is the primary structure of the protein ? gly-asp-asp-asp-phe-phe-ser-ser
2. What is the NET charge of the protein at pH 7 ? 1 positive and 4 negatives makes net charge 3 negative
3. How many peptide bonds are present? SEVEN
4. Carboxypeptidase treatment will identify the amino acid _Ser____?
5. What is the acidic amino acid present? Asp
6. The R groups on amino acid numbers _5_ and _6__ are hydrophobic since they are aromatic.
7. Assuming that this protein forms a salt bridge when folded, at pH 7. The salt bridge may be formed between the N-terminal amino group and the amino acid _asp_____.
8. The protein has _2__ hydroxyl groups, __0____ sulfhydryl group, sand _4___ carboxyl groups.
9. Which of the following would you use for selective hydrolysis of the protein?
a. trypsin
b. chymotrypsin
c. thermolysin
d. CNBr
10. Assume that the protein folds into a three dimensional shape. The protein thus has a primary, secondary, tertiary and quaternary structure. TRUE or FALSE?
11. Pro is an imino acid. TRUE or FALSE?
12. Pro has an indole side chain. TRUE or FALSE?
13. When oxygen binds hemoglobin, BPG (formerly called DPG) is expelled. TRUE or FALSE?
14. When oxygen binds hemoglobin, electrostatic bonds are broken. TRUE or FALSE?
15. When oxygen binds hemoglobin, its quaternary structure is altered. TRUE or FALSE?
16. When oxygen binds hemoglobin, the Fe atom moves into the porphyrin's plane. TRUE or FALSE?
17. Val and ile branch at the beta-carbon. TRUE or FALSE?
18. Myoglobin is a fibrous protein. TRUE or FALSE?
19. Polyglutamic acid at pH 7 will exist as an alpha-helix. TRUE or FALSE?
20. PITC is a chemical used in the identification of the N-terminal amino acid. TRUE or FALSE?
Back to page 3 (beginning of exam 1)
EXAMINATION 1 Sep 27/28
There will be 30 multiple choice questions (1 pt. each for a total of 30 pts.);
2-3 essay questions
worth 15 pts total and 1 take-home question worth 5 pts.
The total for the whole exam is 30 + 15 + 5 = 50 pts.
9. Enzymes 1 (Chapter 8) Sep 17
10. Enzymes 2 Sep 19
11. Enzymes 3 Sep 21
12. Enzymes 4 Sep 24
13. Enzymes 5 Sep 26
14. Enzymes 6 Sep 28
15. Enzymes 7 Oct 1
NOTE: Names of enzymes and Regulation of enzyme function will be covered later at
the end of metabolism.
16. Enzymes review Oct 3
a. Recommended practice problems (from Lehninger 3rd ed.)
on the above material (Enzymes).
1. Chapter 8: Problem 7
2. Chapter 8: Problem 8
3. Chapter 8: Problem 9
4. Chapter 8: Problem 10
5. Using Michaelis-Menten equation, calculate Km when [reactant] = 10 µM, initial velocity
is 0.1 µmol/min and maximal velocity is 0.5 µmol/min.
Answer :Km = 40 µM
b. Go through the tutorial in your UNDERSTAND! Biochemistry
Interactive CD-ROMPROTEINS IN ACTION
Catalysis & Regulation
Nonallosteric enzyme kinetics
Allosteric enzymes
QUIZ 6 (Enzymes) - answers are at the end of the quiz
Are the following statements (1-12) True or False?
1. ALL enzymes are proteins.
2. Enzymes may have one or more polypeptide chains.
3. In order to function, some enzymes require biomolecules which are NOT proteins.
4. Vitamins A,D,E and K function as cofactors for allosteric enzymes.
5. Enzymes do not have disulfide linkages in their chemical structure.
6. Sodium ion (Na +) is a coenzyme for some enzymes.
7. In the reaction A ---------> B, the amount of B formed in one minute is the rate of the reaction.
8. In a reaction X----> Y, the energy of the product (Y) is higher than that of the reactant - this reaction is easily catalyzed
by an appropriate enzyme.
9. Reaction 1 has an activation energy of 11 kcal/mol while reaction 2 has an activation energy of 22 kcal/mol. Reaction 1 therefore is much slower than reaction 2.
10. The graph between velocity and [S] for an allosteric enzyme is hyperbolic.
11. The graph between pH and enzyme function is bell-shaped.
12. Km is the rate at which the substrate concentration is half maximum.
13. Which of the following would be a unit for Km?
(a). mmol / min (b).µmol / sec (c). / min (d) mM (e). kca l/ mol
14. A drug binds to the active site of an enzyme and inhibits the catalytic activity of the enzyme. If the substrate concentration
is high compared to the concentration of the drug, then the inhibition is negligible. This inhibition is called
(a) irreversible inhibition
(b) competitive inhibition
(c) non-competitive inhibition
(d) all of the above are true
15. The following data was obtained in an enzyme experiment:
| Substrate concentration, mM | Reaction velocity mmol / min |
| 1.0 | 205 |
| 2.0 | 320 |
| 4.0 | 435 |
| 6.0 | 490 |
| 1000 | 640 |
| 1300 | 640 |
The Km for this enzyme is approximately
(a) 1 mM
(b) 2 mM
(c) 6 mM
(d) 1000 mM
(e) Greater than 1300 mM
16.The regression equation obtained for a double reciprocal plot was y = 0.37x + 0.008. Determine
Km and Vmax (ignore units in this question!).
17. In an enzyme inhibition study, the double reciprocal plots gave the following equations:
No inhibitor : y = 0.103x + 0.021
With inhibitor : y = 0.188x + 0.02
What is the Km in the absence and presence of inhibitor?
18. What is the Vmax in the presence and absence of inhibitor in question 17?
19. What kind of competition is shown in question 17?
20. If you were to plot the data in question 17, at which axis would the two lines (plus and minus
inhibitor) meet?
QUIZ 6 (Enzymes) ANSWERS
Are the following statements (1-12) True or False?
1. ALL enzymes are proteins.
FALSE-some enzymes are RNA molecules
2. Enzymes may have one or more polypeptide chains.
TRUE
3. In order to function, some enzymes require biomolecules which are NOT proteins.
TRUE - these are the cofactors such as metal ions (eg. Zn++, Mg++) and NAD, FAD
4. Vitamins A,D,E and K function as cofactors for allosteric enzymes.
FALSE - cofactors are usually water soluble vitamins especially the B family
5. Enzymes do not have disulfide linkages in their chemical structure.
False
6. Sodium ion (Na +) is a coenzyme for some enzymes.
False - coenzymes are ORGANIC molecules
7. In the reaction A ---------> B, the amount of B formed in one minute is the rate of the reaction.
True
8. In a reaction X----> Y, the energy of the product (Y) is higher than that of the reactant - this reaction is easily catalyzed by an appropriate enzyme.
False - enzymes do not catalyze non-spontaneous reactions
9. Reaction 1 has an activation energy of 11 kcal/mol while reaction 2 has an activation energy of 22 kcal/mol. Reaction 1 therefore is much slower than reaction 2.
False - lower the Ea (activation energy), faster the reaction
10. The graph between velocity and [S] for an allosteric enzyme is hyperbolic.
False - it is sigmoidal ("S-shaped")
11. The graph between pH and enzyme function is bell-shaped.TRUE
12. Km is the rate at which the substrate concentration is half maximum.
False - Km is the SUBSTRATE concentration at half maximal velocity
13. Which of the following would be a unit for Km?
(a). mmol / min (b).µmol / sec (c). / min (d) mM (e). kca l/ mol
Ans: (d) Km is substrate concentration - it must have concentration units eg. mM
14. A drug binds to the active site of an enzyme and inhibits the catalytic activity of the enzyme. If the substrate concentration is high compared to the concentration of the drug, then the inhibition is negligible.
This inhibition is called
(a) irreversible inhibition
(b) competitive inhibition
(c) non-competitive inhibition
(d) all of the above are true
Ans: (b) competitive - in this reversivle inhibition, if the concentration of substrate is much more than
that of the inhibitor, then most of the active sites of the enzyme would be bound by substrate molecules,
and the inhibition will be negligible.
15. The following data was obtained in an enzyme experiment:
| Substrate concentration, mM | Reaction velocity mmol / min |
| 1.0 | 205 |
| 2.0 | 320 |
| 4.0 | 435 |
| 6.0 | 490 |
| 1000 | 640 |
| 1300 | 640 |
The Km for this enzyme is approximately
(a) 1 mM
(b) 2 mM
(c) 6 mM
(d) 1000 mM
(e) Greater than 1300 mM
Ans: (b) 2.0 mM - the Vmax is 640 mmol/min. Half of 640 is 320 mmol/min. The substrate
concentration at 320 (or half Vmax) is the Km which in this case is 2.0 mM.
16.The regression equation obtained for a double reciprocal plot was y = 0.37x + 0.008. Determine
Km and Vmax (ignore units in this question!)
Vmax = 125 ; Km = 48
17. In an enzyme inhibition study, the double reciprocal plots gave the following equations:
No inhibitor : y = 0.103x + 0.021
With inhibitor : y = 0.188x + 0.02
What is the Km in the absence and presence of inhibitor?
Minus I : Km = 4.9; Plus I : Km = 9.4
18. What is the Vmax in the presence and absence of inhibitor in question 17?
Vmax = 50
19. What kind of competition is shown in question 17?
Competitive since Km is increased with inhibitor and Vmax is unchanged.
20. If you were to plot the data in question 17, at which axis would the two lines (plus and minus
inhibitor) meet?
The two lines will meet at the y-axis (note that the y intercepts of the two equations are the same)
17. Lipids & Membranes 1 (Chapters 11,12) Oct 5
18. Lipids & Membranes 2 Oct 8
Quiz 7
1. Which of the following is true of fatty acids ?
a. They are polar molecules
b. They are aldehydes
c. Lecithin is a fatty acid
d. Prostaglandins are derived from a fatty acid.
2. The following does NOT contain sphingosine:
a. cerebroside b. ganglioside c. ceramide d. phosphatidylcholine
Questions 3-10 : Answer true or false
3. Carbon 1 in palmitic acid is also called the alpha carbon
4. A triglyceride rich in oleic acid is a liquid at room temperature.
5. The "head" of PE is hydrophobic.
6. In a cerebroside, the polar head is a sugar.
7. Cholesterol esters are made up of a steroid and a fatty acid.
8. Sphingomyelin can function as a detergent.
9. When a triglyceride is saponified with potassium hydroxide, soaps are formed.
10.Cholesterol dissolves in water easily.
Quiz 7 (answers in blue)
1. Which of the following is true of fatty acids ?
a. They are polar molecules
b. They are aldehydes
c. Lecithin is a fatty acid
d. Prostaglandins are derived from a fatty acid.
2. The following does NOT contain sphingosine:
a. cerebroside b. ganglioside c. ceramide d. phosphatidylcholine
Questions 3-10 : Answer true or false
3. Carbon 1 in palmitic acid is also called the alpha carbon : F
4. A triglyceride rich in oleic acid is a liquid at room temperature. T
5. The "head" of PE is hydrophobic. F
6. In a cerebroside, the polar head is a sugar.T
7. Cholesterol esters are made up of a steroid and a fatty acid.T
8. Sphingomyelin can function as a detergent. T
9. When a triglyceride is saponified with potassium hydroxide, soaps are formed.T
10.Cholesterol dissolves in water easily.F
Recommended practice problems (from Lehninger 3rd ed.) on the above material (Lipids).
1. Chapter 11: Problem 2
2. Chapter 11: Problem 3
3. Chapter 11: Problem 4
4. Chapter 11: Problem 5
5. Chapter 11: Problem 6
6. Chapter 11: Problem 7
7. Chapter 11: Problem 8
8. Chapter 11: Problem 9
9. Chapter 11: Problem 10
19. Carbohydrates 1 (Chapter 9) Oct 10
20. Carbohydrates 2 Oct 12
21. Carbohydrates 3 Oct 15
22. Carbohydrates 4 Oct 17
a. Recommended practice problems (from Lehninger 3rd ed.) on the above material (Carbohydrates).
1. Chapter 9: Problem 6
2. Chapter 9: Problem 9
3. Chapter 9: Problem 10
4. Chapter 9: Problem 13
5. Chapter 9: Problem 14
6. Chapter 9: Problem 15
Quiz 8 (answers at end of quiz)
Examine the structures below to answer the following questions
Structure
1 
Structure
2
Structure
3
Structure
4
Structure
5
Structure
6
Structure
7
Structure
8
1. Structure ___ is a steroid
A. 1 B. 2 C. 3 D. 4 E. 5
2. A water soluble compound is structure ___
A. 1 B. 2 C. 3 D. 4 E. 5
3. A non-steroidal amphipathic molecule is represented by structure ___
A. 1 B. 2 C. 3 D. 4 E. 5
4. The linkage represented by an arrow in structure 1 is ___
A. glycosidic B. amide C. anhydride D. ester E. acetal
5. Staeric acid is structure
A. 1 B. 2 C. 3 D. 4 E. 5
6. The polar portion of structure 5 contains a phosphate and ___
A. serine B. choline C. alanine D. ethanolamine E. glycerine
7. The fatty acids in structure 5 are saturated fatty acids. True or False?
8. In solution, structure ___ is in equilibrium with a linear ketohexose.
A. 1 B. 3 C. 6 D. 7 E. 8
9. The bond between the two monosaccharides in structure 6 is
A. alpha 1,4 B. beta 1,4 C. alpha 1,1
D. beta 1,1 E. alpha 4,1 F. beta 4,1
10. The anomeric carbon in structure 7 is carbon number __ while that of structure 8 is carbonnumber __
A. 1,1
B. 1,2
C. 2.1
D. 2,2
E. 4,4
11. Pick the TRUE statement
A. Structure 6 is a reducing disaccharide
B. Structure 7 is a non-reducing sugar
C. Structure 8 is reducing disaccharide
D. Structures 6,7,8 are non-reducing sugars
E. Structure 7 is a reducing pentose
Answers to Quiz 8
1. Structure ___ is a steroid
A. 1 B. 2 C. 3 D. 4 E. 5 ans: D
2. A water soluble compound is structure ___
A. 1 B. 2 C. 3 D. 4 E. 5 ans: C
3. A non-steroidal amphipathic molecule is represented by structure ___
A. 1 B. 2 C. 3 D. 4 E. 5 ans:E
4. The linkage represented by an arrow in structure 1 is ___
A. glycosidic B. amide C. anhydride D. ester E. acetal ans:D
5. Stearic acid is structure
A. 1 B. 2 C. 3 D. 4 E. 5 ans: B
6. The polar portion of structure 5 contains a phosphate and ___
A. serine B. choline C. alanine D. ethanolamine E. glycerine
ans: D
7. The fatty acids in structure 5 are saturated fatty acids. True or False? ans: true
8. In solution, structure ___ is in equilibrium with a linear ketohexose.
A. 1 B. 3 C. 6 D. 7 E. 8 ans: D
9. The bond between the two monosaccharides in structure 6 is
A. alpha 1,4
B. beta 1,4
C. alpha 1,1
D. beta 1,1
E. alpha 4,1
F. beta 4,1
ans: B
10. The anomeric carbon in structure 7 is carbon number __ while that of structure 8 is carbonnumber __
A. 1,1
B. 1,2
C. 2.1
D. 2,2
E. 4,4
ans: C
11. Pick the TRUE statement
A. Structure 6 is a reducing disaccharide
B. Structure 7 is a non-reducing sugar
C. Structure 8 is reducing disaccharide
D. Structures 6,7,8 are non-reducing sugars
E. Structure 7 is a reducing pentose
ans: A
Back to page 14 (beginning of material for exam 2)
EXAMINATION 2 (OCT 25 and OCT 26)
There will be 60 multiple-choice questions worth 0.75 point each for a total of 45points (which you will take at CLAS) and
a 2-question take-home worth 5 points.TOTAL = 50 points.
23. Metabolism 1 (chapter 14) Oct 19
24. Metabolism 2 Oct 22
Problems (answers are after Quiz 9 below; answers for text problems
are at the end of the book):
1. For the reaction:
ATP ----> ADP + Pi
the ratio [ADP] [Pi] / [ATP] in the cell is 0.000467. The free energy under
standard conditions is -7.3 kcal/mol. Calculate the
free energy of the reaction at 37 degrees celsius. R is 1.99 cal / mol.K.
2. Given the following information:
S + H ------------> G + F (Free energy under standard conditions = - 29 kJ/mol)
G1P + H --------> G + Pi (Free energy under standard conditions = -21 kJ/mol)
Calculate the free energy under standard conditions for the following reaction:
S + Pi ------------> G1P + F
3. Calculate the Keq for a reaction with a free energy change under standard conditions of -8 kJ/mol. R=8.315 J/mol.K
Answers next page
4.PROBLEM 2 (Ch.14)
5.PROBLEM 3(Ch.14)
6.PROBLEM 4 (Ch.14)
7.PROBLEM 5 (Ch.14)
8.PROBLEM 6(Ch.14)
9.PROBLEM 7(Ch.14)
10.PROBLEM 8(Ch.14)
11.PROBLEM 9 (Ch.14)
12.PROBLEM 14(Ch.14) (molecular weight of ATP is 507 )
25. Metabolism 3 Oct 24
26. Metabolism 4 Oct 26
27. Metabolism 5 Oct 29
28. Metabolism Review Oct 31
____________________________________________________________________________
ANSWERS to problems on page 37:
1. The ÆG' is -12000 cal/mol or -12kcal/mol.
2. -8000 J / mol or -8 kJ/mol
3. Keq = 25
________________________________________________________________________________
QUIZ 9 (answers at the end of the quiz)
Refer to the figure below (fig.1) to answer questions 1-5:
Questions 1-5:Classify reactions 1-5. Choose among the following selections.
Note each selection may be used more than once.
a. decarboxylation
b. redox
c. isomerization
d. addition / elimination
e. group transfer
1. Reaction 1
2. Reaction 2
3.Reaction 3
4. Reaction 4
5. Reaction 5
6. Which of the reactions require niacin ?
a. reaction 1
b. reaction 2
c. reaction 3
d. reaction 4
e. reaction 5
7. Which of the following carbons is the most reduced?
a. carbon with four hydrogens
b. carbon with an alcohol group
c. carbon dioxide
d. carbon of a ketone
e. carbon of a carboxylic acid
8. The enzyme catalyzing the reaction S + ATP ------> S-P + ADP is a
a. carboxylase
b. kinase
c. dehydrogenase
d. isomerase
e. synthetase
9. The following group is NOT found in CoA
a. phosphate
b. sulfhydryl
c. ribose
d. amide
e. pyridine
Answers to quiz 9: (answers in blue)
Questions 1-5:Classify reactions 1-5. Choose among the following selections.
Note each selection may be used more than once.
a. decarboxylation
b. redox
c. isomerization
d. addition / elimination
e. group transfer
1. Reaction 1 (ans: e. group transfer - phosphorylation)
2. Reaction 2 (ans: b.redox)
3.Reaction 3 (ans: a. decarboxylation)
4. Reaction 4 (ans: d. addition/elimination)
5. Reaction 5 (ans: c. isomerization )
6. Which of the reactions require niacin ?
a. reaction 1
b. reaction 2
c. reaction 3
d. reaction 4
e. reaction 5
7. Which of the following carbons is the most reduced?
a. carbon with four hydrogens
b. carbon with an alcohol group
c. carbon dioxide
d. carbon of a ketone
e. carbon of a carboxylic acid
8. The enzyme catalyzing the reaction S + ATP ------> S-P + ADP is a
a. carboxylase
b. kinase
c. dehydrogenase
d. isomerase
e. synthetase
9. The following group is NOT found in CoA
a. phosphate
b. sulfhydryl
c. ribose
d. amide
e. pyridine
29. Glycolysis 1(Chapter 15) Nov 2
30. Glycolysis 2 Nov 5
31. Glycolysis 3 Nov 7
32. Pyruvate dehydrogenase complex 1(Chapter 16) Nov 9
33. Pyruvate dehydrogenase complex 2 Nov 12
Back to page 36 (beginning of exam 3)
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EXAMINATION 3 Nov 29 / Nov 30
There will be 10 multiple choice questions (1 pt. each for a total of 10 pts.); 11 essay questions
including problems involving calculations, worth 40pts. Do not forget your CALCULATOR !
The total for the whole exam is 10 + 40 = 50 pts.
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34.Krebs cycle (Chapter 16) Nov 14
35.Krebs cycle Nov 16
36.Krebs cycle Nov 19
37. Electron transport chain / oxidative phosphorylation 1(Chapter 19) Nov 21
38. Electron transport chain / oxidative phosphorylation 2 Nov 26
39. Electron transport chain / oxidative phosphorylation 3 Nov 28
40. Electron transport chain / oxidative phosphorylation 4 Nov 30
PROBLEMS:
1. In mitochondria, the pH outside the inner membrane is 1.4 units LOWER that that in the matrix. Using the equation:
ÆG = 2.3 RT log [ H+] inside / [H+] outside
calculate the energy available in kcal/mol, from this pH gradient at 25 C, given R = 1.98 cal / mol. K.
(HINT: rearrange the equation in the form of pH rather than H+ ; remember, pH= -log [H+] ).
Answer: -1.9 kcal / mol
2. Determine the equilibrium constant for the reaction:
2 cyt a (Fe 2+) + 1/2 O2 ---------> 2 cyt a (Fe 3+) + H 2 O
(F= 23 kcal / V. mol; R = 1.98 cal / mol. K)
Answer : K eq = 1X 10 EE 18
3. Chapter 14 Question 18.
4. Chapter 14 Question 19.
41. Energetics of the central pathways 1 Dec 3
42. Mechanisms of selected reactions Dec 5
43. Review Dec 7
QUIZ 10
1. One turn of the TCA cycle produces
a. 2 FADH2 molecules
b. requires 3 NADH molecules
c. releases 2 CO2 molecules
d. produces 1 ADP molecule
2. The following is a substrate-level phosphorylation reaction:
a. fructose 1,6-bisphosphate ----------------> DHAP + glyceraldehyde-3 phosphate
b. 1,3 bisphosphoglycerate + ADP <=========> 3-P-glycerate + ATP
c. malate + NAD+ ------------> oxaloacetate + NADH + H+
d. pyruvate + CoA-SH + NAD ---------------> acetyl CoA + NADH + CO2
e. fumarate + H2 O -------------. malate
3. For every glucose oxidized by the central pathways (glycolysis / PDH / TCA cycle),
how many NADH are produced?
a. 5 b. 10 c. 15 d. 20 e. 25
4. For every ONE molecule of acetyl CoA oxidized by the citric acid cycle, how many
ATP (or equivalents)are produced?
a. 6 b. 12 c. 18 d. 24 e. 36
5. The conversion of succinate into fumarate is catalyzed by
a. synthase
b. synthetase
c, dehydrogenase
d. kinase
e. carboxylase
6. The following are electron carriers except:
a. coenzyme A
b. cytochrome a
c. nonheme iron protein
d. Co Q
e. NADH
7. In a RBC, pyruvate is converted into ____ so that glycolysis may continue.
8. The following is a mobile electron carrier in the electron transport chain?
a. complex I
b.. complex II
c. complex III
d. cytochrome c
e. all of the above
9. There are __ irreversible reactions in glycolysis.
a. 1 b. 2 c. 3 d. 4 e. 5
10.As electrons are transferred from NADH or FADH2 to oxygen along the electron transport chain, ___ are pumped from
the matrix into the intermembrane space.
11. There are ____ substrate level phosphorylation reaction(s) in the TCA cycle
a. 1 b. 2 c. 3 d. 4 e. 5
12. The conversion of pyruvate to acetyl CoA, isocitrate to alpha-ketoglutarate and alpha-ketoglutarate to succinyl
CoA have the following in common:
a. they are carboxylation reactions
b. they occur in the cytoplasm
c. they involve oxidation and decarboxylation and are thus called oxidative decarboxylation
d. they are reactions of the TCA cycle
e. they produce ATP
13. The following vitamin is needed for the decarboxylation of an alpha-keto acid
a. thiamine (B1)
b. niacin
c. riboflavin
d. biotin
e. vitamin A
14. The following lipoprotein is predominantly composed of trglycerides and disappears from blood a few hours after a meal:
a. LDL b. HDL c. VLDL d. chylomicrons
15. Glycogen is mostly stored in the
a. liver and red blood cells
b. kidney
c. heart
d. liver and skeletal muscles
e. adipose tissue
16. Which of the following is a catabolic pathway for lipids?
a. glycogenesis
b. gluconeogenesis
c. beta-oxidation
d. urea cycle
e. Embden Meyerhoff pathway
17. Which of the following carbons is the most reduced?
a. carbon with four hydrogens
b. carbon with an alcohol group
c. carbon dioxide
d. carbon of a ketone
e. carbon of a carboxylic acid
18. The enzyme catalyzing the reaction S + ATP ------> S-P + ADP is a
a. carboxylase
b. kinase
c. dehydrogenase
d. isomerase
e. synthetase
19. The following group is NOT found in CoA
a. phosphate
b. sulfhydryl
c. ribose
d. amide
e. pyridine
20. The poison cyanide affects
a. glycolysis
b. TCA cycle
c. electron transport chain
d. substrate level phosphorylation
e. none of the above
Answers to Quiz 10 (answers in blue)
1. One turn of the TCA cycle
a. produces 2 FADH2 molecules
b. requires 3 NADH molecules
c. releases 2 CO2 molecules
d. produces 1 ADP molecule
2. The following is a substrate-level phosphorylation reaction:
a. fructose 1,6-bisphosphate ----------------> DHAP + glyceraldehyde-3 phosphate
b. 1,3 bisphosphoglycerate + ADP <=========> 3-P-glycerate + ATP
c. malate + NAD+ ------------> oxaloacetate + NADH + H+
d. pyruvate + CoA-SH + NAD ---------------> acetyl CoA + NADH + CO2
e. fumarate + H2 O -------------. malate
3. For every glucose oxidized by the central pathways (glycolysis / PDH / TCA cycle), how many NADH are produced?
a. 5 b. 10 c. 15 d. 20 e. 25
4. For every ONE molecule of acetyl CoA oxidized by the citric acid cycle, how many ATP (or equivalents)are produced?
a. 6 b. 12 c. 18 d. 24 e. 36
5. The conversion of succinate into fumarate is catalyzed by
a. synthase
b. synthetase
c. dehydrogenase
d. kinase
e. carboxylase
6. The following are electron carriers except:
a. coenzyme A
b. cytochrome a
c. nonheme iron protein
d. Co Q
e. NADH
7. In a RBC, pyruvate is converted into lactate so that glycolysis may continue.
8. The following is a mobile electron carrier in the electron transport chain?
a. complex I
b.. complex II
c. complex III
d. cytochrome c
e. all of the above
9. There are __ irreversible reactions in glycolysis.
a. 1 b. 2 c. 3 d. 4 e. 5
10.As electrons are transferred from NADH or FADH2 to oxygen along the electron transport chain, protons are pumped from
the matrix into the intermembrane space.
11. There are ____ substrate level phosphorylation reaction(s) in the TCA cycle
a. 1 b. 2 c. 3 d. 4 e. 5
12. The conversion of pyruvate to acetyl CoA, isocitrate to alpha-ketoglutarate and alpha-ketoglutarate to succinyl
CoA have the following in common:
a. they are carboxylation reactions
b. they occur in the cytoplasm
c. they involve oxidation and decarboxylation and are thus called oxidative decarboxylation
d. they are reactions of the TCA cycle
e. they produce ATP
13. The following vitamin is needed for the decarboxylation of an alpha-keto acid
a. thiamine (B1)
b. niacin
c. riboflavin
d. biotin
e. vitamin A
14. The following lipoprotein is predominantly composed of trglycerides and disappears from blood a few hours after
a meal:
a. LDL b. HDL c. VLDL d. chylomicrons
15. Glycogen is mostly stored in the
a. liver and red blood cells
b. kidney
c. heart
d. liver and skeletal muscles
e. adipose tissue
16. Which of the following is a catabolic pathway for lipids?
a. glycogenesis
b. gluconeogenesis
c. beta-oxidation
d. urea cycle
e. Embden Meyerhoff pathway
17. Which of the following carbons is the most reduced?
a. carbon with four hydrogens
b. carbon with an alcohol group
c. carbon dioxide
d. carbon of a ketone
e. carbon of a carboxylic acid
18. The enzyme catalyzing the reaction S + ATP ------> S-P + ADP is a
a. carboxylase
b. kinase
c. dehydrogenase
d. isomerase
e. synthetase
19. The following group is NOT found in CoA
a. phosphate
b. sulfhydryl
c. ribose
d. amide
e. pyridine
20. The poison cyanide affects
a. glycolysis
b. TCA cycle
c. electron transport chain
d. substrate level phosphorylation
e. none of the above
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EXAMINATION 4 (FINAL COMPREHENSIVE) Mon Dec 10 2:00-3:50 p.m.
There will be 50 multiple choice questions (1 pt. each for a total of 50 pts.); 8 essay questions
worth 50pts. Do not forget your CALCULATOR !
The total for the whole exam is 50 + 50 = 100 pts.
Best of luck - see you in CHM 522 !
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BIOCHEMISTRY II (CHM 522)
(continuation of CHM 521)
Do not forget your CD-ROM and publisher's web site for you to clarify key concepts discussed in class!
1. Glycogen metabolism (Chapters 15 & 20) Jan 9-11
Problem:
The phosphorylase reaction at 25 C under standard conditions has a free energy of 0.73 kcal/mol (R=1.98 cal/mol.K).
What is the equilibrium constant for this reaction?
(glucose)n + Pi ---------------> (glucose)n-1 + glucose 1-P
2. Gluconeogenesis (Chapter 20) Jan 14
3. Gluconeogenesis 2 Jan 16
Problem:
1. Problem 2(Chapter 20) of your text.
2. Problem 9(Chapter 20) of your text.
3. Problem 10(Chapter 20) of your text.
4. Pentose Phosphate Pathway (Hexose monophosphate shunt) 1(Chapter 15)
Jan 18
5. Pentose Phosphate Pathway (Hexose monophosphate shunt) 2 Jan 21
QUIZ 11
1. Which of the following statements about glycogen metabolism is FALSE?
a. Unlike the liver, skeletal muscles do not have glucose 6-phosphatase; thus skeletal muscles do not export
their glycogen derived glucose to other tissues.
b. Glycogenolysis occurs at the non-reducing end of the glycogen chain.
c. In glycogenesis, glucose activation is carried out by reaction with a nucleotide, UTP.
d. The alpha 1,4 glycosidic linkages in glycogen is broken down by the enzyme pyrophosphorylase.
e. Glycogen synthesis requires energy.
2. Gluconeogenesis requires:
a. biotin
b. bicarbonate
c. PEP carboxykinase
d. ATP
e. all of the above
3. In humans, glucose can be made from all of the following EXCEPT:
a. lactate
b. pyruvate
c. acetyl CoA
d. glycerol
e. some amino acids (glucogenic amino acids)
4. The oxidative phase of HMS produces
a. FADH2
b. NADH
c. CoA-SH
d. NADPH
e. Glucose
5. Which of the following is a function of the pentose phosphate pathway?
a. it produces ribose 5-P required for DNA, RNA synthesis
b. it produces a reducing agent required to keep red blood cells flexible.
c. it produces sugars with varioust number of carbon atoms
d. it oxidizes glucose
e. all of the above
6. Gluconeogenesis occurs predominantly in the
a. spleen
b. skeletal muscles
c. liver
d. RBC
e. adipose tissue
7. Which of the following atoms is NOT found in biotin?
a. N
b. S
c. P
d. O
e. H
8. One mole of glucose oxidized by HMS produces one mole of CO2, one mole pentose and
two moles NADPH. True or False?
9. One of the substrates for glycogen synthase is glucose. True or False?
10. TPP is required for transaldolase. True or False?
QUIZ 11 (answers in Blue)
1. Which of the following statements about glycogen metabolism is FALSE?
a. Unlike the liver, skeletal muscles do not have glucose 6-phosphatase; thus skeletal muscles do not export
their glycogen derived glucose to other tissues.
b. Glycogenolysis occurs at the non-reducing end of the glycogen chain.
c. In glycogenesis, glucose activation is carried out by reaction with a nucleotide, UTP.
d. The alpha 1,4 glycosidic linkages in glycogen is broken down by the enzyme pyrophosphorylase.
e. Glycogen synthesis requires energy.
2. Gluconeogenesis requires:
a. biotin
b. bicarbonate
c. PEP carboxykinase
d. ATP
e. all of the above
3. In humans, glucose can be made from all of the following EXCEPT:
a. lactate
b. pyruvate
c. acetyl CoA
d. glycerol
e. some amino acids (glucogenic amino acids)
4. The oxidative phase of HMS produces
a. FADH2
b. NADH
c. CoA-SH
d. NADPH
e. Glucose
5. Which of the following is a function of the pentose phosphate pathway?
a. it produces ribose 5-P required for DNA, RNA synthesis
b. it produces a reducing agent required to keep red blood cells flexible.
c. it produces sugars with varioust number of carbon atoms
d. it oxidizes glucose
e. all of the above
6. Gluconeogenesis occurs predominantly in the
a. spleen
b. skeletal muscles
c. liver
d. RBC
e. adipose tissue
7. Which of the following atoms is NOT found in biotin?
a. N
b. S
c. P
d. O
e. H
8. One mole of glucose oxidized by HMS produces one mole of CO2, one mole pentose and
two moles NADPH. True or False?
9. One of the substrates for glycogen synthase is glucose. True or False?
10. TPP is required for transaldolase. True or False?
Review Examination: Jan 23
6. Lipid metabolism -catabolism1 (Chapter 17) Jan 25
7. Lipid metabolism -catabolism 2
8. Lipid metabolism -catabolism 3 Jan 28
9. Lipid metabolism -anabolism 1(Chapter 21) Jan 30
10. Lipid metabolism -anabolism 2 Feb 1
11. Lipid metabolism -anabolism 3 Feb 4
12. Lipid metabolism -anabolism 4 Feb 6-8
RECOGNIZE STRUCTURES OF Progesterone,Pregnenolone,Cortisol, Aldosterone,Testosterone, Estradiol
QUIZ 12
1. The reducing agent used in fatty acid synthesis is:
a. FADH2
b. NADH
c. CoA-SH
d. NADPH
e. Hydrogen
2. The conversion of acetoacetate into acetone during ketone body formation is a _______ reaction.
CH3 CO CH2 COO -----------------> CO2 + CH3 CO CH3
a. redox
b. isomerization
c. carboxylation
d. decarboxylation of alpha-keto acid
e. none of the above
3. In beta-oxidation, fatty acids are converted into their:
a. phosphates
b. esters
c.thioesters
d. anhydrides
e. none of the above
4. Which of the following pathways occur in the mitochondria?
a. glycogenesis
b. glycogenolysis
c. fatty acid synthesis
d. beta-oxidation of fatty acids
e. HMS
5. Fatty acid oxidation produces:
a. FADH2
b. NADH
c. Acetyl CoA
d. all of the above
6. Which of the following is a product when CH3 CH2 CH2 CH2 COO undergoes fatty acid oxidation?
a. butyl CoA
b. propionyl CoA
c. hexyl CoA
d. methane
e. none of the above
7.How many acetyl CoA molecules are produced when
CH3 CH2 CH2 CH2 CH2 COO
undergoes beta-oxidation?
a. 1
b. 2
c. 3
d.4
e. 5
8.How many high energy bonds are hydrolyzed when the fatty acid
CH3 CH2 CH2 CH2 CH2 COO
undergoes beta-oxidation ?
a. 1
b. 2
c. 3
d.4
e. 5
9.How many NET ATPs are produced when the fatty acid
CH3 CH2 CH2 CH2 CH2 COO
undergoes beta-oxidation ?
a. 4
b. 6
c. 36
d. 46
e. 44
10. Fatty acid synthesis requires:
a. biotin
b. malonyl CoA
c. acetyl CoA
d. ATP
e. all of the above
11. The following are ketone bodies EXCEPT:
a. acetyl CoA
b. beta-hydroxybutyrate
c. acetoacetate
d. acetone
12. Acetyl CoA is an important reactant/product or intermediate for the following metabolic pathways EXCEPT:
a. fatty acid synthesis
b. cholesterol synthesis
c. beta-oxidation
d. gluconeogenesis
e. none of the above
13. HMG-CoA is converted into mevalonate during cholesterol synthesis by the enzyme
a. oxidase
b. isomerase
c. reductase
d.phosphorylase
e. kinase
14. Fatty acid transport into mitochondria is carried out by
a. creatine
b. carnitine
c. ornithine
d. creatinine
15. The fatty acid *CH3-CH2-CH2-CH2-CH2-CH2-COOH ( the asterisk * represents a radioactive
label ) is fed to a human. After half-hour where would the label be found?
a. acetyl-CoA
b. propionyl-CoA
c. malonyl-CoA
d. both acetyl and propionyl-CoA
QUIZ 12 (answers in Blue)
1. The reducing agent used in fatty acid synthesis is:
a. FADH2
b. NADH
c. CoA-SH
d. NADPH
e. Hydrogen
2. The conversion of acetoacetate into acetone during ketone body formation is a _______ reaction.
CH3 CO CH2 COO -----------------> CO2 + CH3 CO CH3
a. redox
b. isomerization
c. carboxylation
d. decarboxylation of alpha-keto acid
e. none of the above (it is actually the decarboxylation of a beta-keto acid!)
3. In beta-oxidation, fatty acids are converted into their:
a. phosphates
b. esters
c.thioesters
d. anhydrides
e. none of the above
4. Which of the following pathways occur in the mitochondria?
a. glycogenesis
b. glycogenolysis
c. fatty acid synthesis
d. beta-oxidation of fatty acids
e. HMS
5. Fatty acid oxidation produces:
a. FADH2
b. NADH
c. Acetyl CoA
d. all of the above
6. Which of the following is a product when CH3 CH2 CH2 CH2 COO undergoes fatty acid oxidation?
a. butyl CoA
b. propionyl CoA
c. hexyl CoA
d. methane
e. none of the above
7.How many acetyl CoA molecules are produced when
CH3 CH2 CH2 CH2 CH2 COO
undergoes beta-oxidation?
a. 1
b. 2
c. 3
d.4
e. 5
8.How many high energy bonds are hydrolyzed when the fatty acid
CH3 CH2 CH2 CH2 CH2 COO
undergoes beta-oxidation ?
a. 1
b. 2
c. 3
d.4
e. 5
9.How many NET ATPs are produced when the fatty acid
CH3 CH2 CH2 CH2 CH2 COO
undergoes beta-oxidation ?
a. 4
b. 6
c. 36
d. 46
e. 44
10. Fatty acid synthesis requires:
a. biotin
b. malonyl CoA
c. acetyl CoA
d. ATP
e. all of the above
11. The following are ketone bodies EXCEPT:
a. acetyl CoA
b. beta-hydroxybutyrate
c. acetoacetate
d. acetone
12. Acetyl CoA is an important reactant/product or intermediate for the following metabolic pathways EXCEPT:
a. fatty acid synthesis
b. cholesterol synthesis
c. beta-oxidation
d. gluconeogenesis
e. none of the above
13. HMG-CoA is converted into mevalonate during cholesterol synthesis by the enzyme
a. oxidase
b. isomerase
c. reductase
d.phosphorylase
e. kinase
14. Fatty acid transport into mitochondria is carried out by
a. creatine
b. carnitine
c. ornithine
d. creatinine
15. The fatty acid *CH3-CH2-CH2-CH2-CH2-CH2-COOH ( the asterisk * represents a radioactive
label ) is fed to a human. After half-hour where would the label be found?
a. acetyl-CoA
b. propionyl-CoA
c. malonyl-CoA
d. both acetyl and propionyl-CoA
Go to glycogen metabolism (beginning of material for exam 1)
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EXAMINATION 1 (Feb 20)
There will be 45 multiple choice questions (1 pt. each for a total of 45 pts.); 1 essay question
(5 pts.). The total for the whole exam is 45+ 5= 50 pts.
------------------------------------------------------------------------------------------------------------------------------------------------------------------------
13.Regulation of metabolism 1(Chapters 13 and 23) Feb11
14.Regulation of metabolism 2 Feb13
15.Regulation of metabolism 3 Feb15
16.Regulation of metabolism 4
QUIZ 13
1. Which enzyme in gluconeogenesis is regulated by fructose 2,6-bisphosphate?
a. fructose 1,6-bisphosphatase
b. PEP carboxykinase
c.pyruvate carboxylase.
d. glucose g-phosphatase.
2. Glucagon
1. stimulates glycogenolysis.
b. inhibits glycogenesis.
c. slows down glycolysis.
d. stimulates gluconeogenesis.
e. all of the above.
3. The process whereby the catalytic activity of an enzyme is increased or decreased by the covalent attachment of
a group such as phosphate to the enzyme is called
a. induction
b. allosteric control
c. covalent modification
d. repression
e. feedback inhibition
4. Which of the following is an important intrinsic control of beta-oxidation?
a. AMP
b. ADP
c. acetyl CoA
d. fatty acyl CoA
e. malonyl CoA
5. The intracellular messenger that mediates the action of epinephrine and glucagon is
a. ATP
b. acetyl CoA
c. cyclic AMP
d. AMP
e. Pi
6. The key control point in glycolysis is the enzyme
a. PFK-1
b. PFK-2
c. glucokinase
d. hexokinase
e. isomerase
7. Which of the following regulator inhibits glycolysis and TCA cycle intrinsically?
a. cyclic AMP
b. AMP
c. ATP
d. NADH
e. FAD
8. Which of the following is NOT true in LATE starvation?
a. skeletal proteins are broken down into amino acids, some of which are used by the liver to make glucose
b. most cells resort to fatty acid oxidation to make ATP for their energy needs
c. beta-hydroxybutyrate and acetoacetate concentrations in the blood becomes elevated
d. blood insulin level is low
e. glycogen is broken down to stabilize blood glucose
---------------------------------------
Answers to quiz 13 (in RED)
---------------------------------------
1. Which enzyme in gluconeogenesis is regulated by fructose 2,6-bisphosphate?
a. fructose 1,6-bisphosphatase
b. PEP carboxykinase
c.pyruvate carboxylase.
d. glucose g-phosphatase.
2. Glucagon
1. stimulates glycogenolysis.
b. inhibits glycogenesis.
c. slows down glycolysis.
d. stimulates gluconeogenesis.
e. all of the above.
3. The process whereby the catalytic activity of an enzyme is increased or decreased by the covalent attachment of
a group such as phosphate to the enzyme is called
a. induction
b. allosteric control
c. covalent modification
d. repression
e. feedback inhibition
4. Which of the following is an important intrinsic control of beta-oxidation?
a. AMP
b. ADP
c. acetyl CoA
d. fatty acyl CoA
e. malonyl CoA
5. The intracellular messenger that mediates the action of epinephrine and glucagon is
a. ATP
b. acetyl CoA
c. cyclic AMP
d. AMP
e. Pi
6. The key control point in glycolysis is the enzyme
a. PFK-1
b. PFK-2
c. glucokinase
d. hexokinase
e. isomerase
7. Which of the following regulator inhibits glycolysis and TCA cycle intrinsically?
a. cyclic AMP
b. AMP
c. ATP
d. NADH
e. FAD
8. Which of the following is NOT true in LATE starvation?
a. skeletal proteins are broken down into amino acids, some of which are used by the liver to make glucose
b. most cells resort to fatty acid oxidation to make ATP for their energy needs
c. beta-hydroxybutyrate and acetoacetate concentrations in the blood becomes elevated
d. blood insulin level is low
e. glycogen is broken down to stabilize blood glucose
17.Amino acid metabolism 1 (Chapters 18 & 22) Feb 18
18.Amino acid metabolism 2 Feb 22
19.Amino acid metabolism 3 Feb 25
20.Amino acid metabolism 4 Feb 27
21.Heme & other nitrogen compounds metabolism 1 Mar 1
22.Heme & other nitrogen compounds metabolism 2 Mar 4
23.Heme & other nitrogen compounds metabolism 3 Mar 6
------------------
QUIZ 14
------------------
1.A common reaction in amino acid metabolism between an amino acid and a keto-acid is
a. transamination
b. redox
c. addition/elimination
d. phosphorylation
e. hydrolysis
2.THF is derived from
a.riboflavin
b.pantothenic acid
c.folic acid
d. citric acid
e. ascorbic acid
3. THF carries the following one carbon groups EXCEPT
a. -CH3
b. -CH2
c. -CH=O
d. CO2
4. The nitrogens in urea are derived from aspartic acid and
a. ala
b. gly
c. ammonium
d. citrulline
e. arg
5. In amino acid catabolism, the amino group is carried in the blood as
a. glu
b. gln
c. NH3
d.lys
e. asp
6. The carbon skeletons from glucogenic amino acids are converted into all of the following EXCEPT
a. oxaloacetate
b. fumarate
c. succinyl CoA
d. alpha-ketoglutarate
e. pyruvate
f. acetyl CoA
7. The carbon skeletons required for amino acid synthesis are derived from all of the following except:
a. alpha-ketoglutarate
b. oxaloacetate
c. pyruvate
d. fumarate
e. PEP
8. The following coenzyme is required by transaminases
a. SAM
b. TPP
c. biotin
d. PLP
e. THF
9. What is required for this reaction?
R-NH3 ------------------> R-N(CH3 )3
a. SAM
b. TPP
c. biotin
d. PLP
e. THF
10. Phenylalanine is catabolized to fumarate and acetoacetate and is therefore
a. ketogenic
b. glucogenic
c. ketogenic and glucogenic
d. androgenic
e. none of the above
11.Pyridoxal phosphate has
a. a thiol
b. a quaternary nitrogen
c. a ketone group
d. a carboxyl group
e. none of the above
12. The following are intermediates of the urea cycle EXCEPT:
a. ornithine
b. carbamoyl phosphate
c. citrulline
d. arginine
e. succinate
13.The reaction in which SAM is formed from met and ATP involves the attack of the sulfur atom of
met on the ________ atom of ATP.
a. alpha-phosphorous
b. beta-phosphorous
c. gamma-phosphorous
d. C-1'
e. C-5'
14. In lead poisoning, the heme biosynthesis enzyme __________ is affected.
a. ALA synthase
b. PBG synthase
c. ferrochelatase
d. uroporphyrinogen III synthase
e. none of the above
15. Which of the following about heme metabolism is FALSE?
a. uroporphyrinogen III is a cyclic compound
b. bilirubin is a cyclic, colorless breakdown product of heme
c. The conversion of heme into biliverdin releases CO.
d. ALA synthase requires PLP
16. PLP is derived from vitamin B6. True or False?
17. One of the nitrogen atoms in urea is derived from an amino acid. True or False?
18. One of the first reaction in the breakdown of amino acids is transamination. True or False?
19. Synthesis of glycine from serine requires THF. True or False?
20. Delta-ALA is formed from gly and succinyl-CoA. True or False?
21. THF contains a pteridine ring, PABA and glu. True or False?
22. When THF donates its one-carbon moiety in a reaction, it always becomes oxidized to DHF. True or False?
----------------------------------------
QUIZ 14 (answers)
----------------------------------------
1.A common reaction in amino acid metabolism between an amino acid and a keto-acid is
a. transamination
b. redox
c. addition/elimination
d. phosphorylation
e. hydrolysis
2.THF is derived from
a.riboflavin
b.pantothenic acid
c.folic acid
d. citric acid
e. ascorbic acid
3. THF carries the following one carbon groups EXCEPT
a. -CH3
b. -CH2
c. -CH=O
d. CO2
4. The nitrogens in urea are derived from aspartic acid and
a. ala
b. gly
c. ammonium
d. citrulline
e. arg
5. In amino acid catabolism, the amino group is carried in the blood as
a. glu
b. gln
c. NH3
d.lys
e. asp
6. The carbon skeletons from glucogenic amino acids are converted into all of the following EXCEPT
a. oxaloacetate
b. fumarate
c. succinyl CoA
d. alpha-ketoglutarate
e. pyruvate
f. acetyl CoA
7. The carbon skeletons required for amino acid synthesis are derived from all of the following except:
a. alpha-ketoglutarate
b. oxaloacetate
c. pyruvate
d. fumarate
e. PEP
8. The following coenzyme is required by transaminases
a. SAM
b. TPP
c. biotin
d. PLP
e. THF
9. What is required for this reaction?
R-NH3 ------------------> R-N(CH3 )3
a. SAM
b. TPP
c. biotin
d. PLP
e. THF
10. Phenylalanine is catabolized to fumarate and acetoacetate and is therefore
a. ketogenic
b. glucogenic
c. ketogenic and glucogenic
d. androgenic
e. none of the above
11. Pyridoxal phosphate has
a. a thiol
b. a quaternary nitrogen
c. a ketone group
d. a carboxyl group
e. none of the above
12. The following are intermediates of the urea cycle EXCEPT:
a. ornithine
b. carbamoyl phosphate
c. citrulline
d. arginine
e. succinate
13.The reaction in which SAM is formed from met and ATP involves the attack of the sulfur atom of
met on the ________ atom of ATP.
a. alpha-phosphorous
b. beta-phosphorous
c. gamma-phosphorous
d. C-1'
e. C-5'
14. In lead poisoning, the heme biosynthesis enzyme __________ is affected.
a. ALA synthase
b. PBG synthase
c. ferrochelatase
d. uroporphyrinogen III synthase
e. none of the above
15. Which of the following about heme metabolism is FALSE?
a. uroporphyrinogen III is a cyclic compound
b. bilirubin is a cyclic, colorless breakdown product of heme
c. The conversion of heme into biliverdin releases CO.
d. ALA synthase requires PLP
16. PLP is derived from vitamin B6. True or False?
17. One of the nitrogen atoms in urea is derived from an amino acid. True or False?
18. One of the first reaction in the breakdown of amino acids is transamination. True or False?
19. Synthesis of glycine from serine requires THF. True or False?
20. Delta-ALA is formed from gly and succinyl-CoA. True or False?
21. THF contains a pteridine ring, PABA and glu. True or False?
22. When THF donates its one-carbon moiety in a reaction, it always becomes oxidized to DHF. True or False?
Go to regulation of metabolism (beginning of exam 2)
-----------------------------------------------------------------------------------------------------------------------------------------------------------------------
EXAMINATION 2 (Mar 27)
There will be about 20 multiple choice questions (total of 20 pts.); 4 essay questions,
worth 30 pts. The total for the whole exam is 20+ 30= 50 pts.
------------------------------------------------------------------------------------------------------------------------------------------------------------------------
24.Nucleotide structure (Chapter 10) Mar 8
25.Nucleotide metabolism I(Chapter 22) Mar 11
26.Nucleotide metabolism 2 Mar 13
27.Nucleotide metabolism 3 Mar 15
28.Nucleotide metabolism 4
--------------------
QUIZ 15
--------------------
1. Nucleotides function as
a. precursors of nucleic acids
b. activated intermediates in glycogen synthesis
c. energy carriers
d. intracellular messengers
e. all of the above
2. The difference between uracil and thymine is that thymine has a ____ group
a. carboxyl
b. amino
c. methyl
d. sugar
e. phosphate
3. Which of the following is FALSE of nucleotide metabolism?
a. The activated sugar used in the synthesis of purines and pyrimidines is phosphoribosyl pyrophosphate.
b. pyrimidine nucleotide synthesis is shorter than purine nucleotide synthesis.
c. In UMP synthesis the pyrimidine ring is synthesized first and then attached to the sugar.
d. Carbon dioxide is required as a precursor for synthesis of purine and pyrimidine nucleotide synthesis.
e. Inosine monophosphate (IMP) is a branch point intermediate in synthesis of UMP.
For questions 4-8, match the following:
a. 5' nucleotidase
b.thymidylate synthase
c. APRT
d. nucleoside kinase
e.phosphorylase
4. conversion of deoxy UMP into deoxy TMP
5. nucleosidase
6. remove phosphates from nucleotides
7. salvage pathway synthesis of purine nucleotides
8. interconvert nucleoside mono-, di-, and triphosphates.
9. The end products of amino acid and purine catabolism are
a. pyruvate and acetyl CoA
b. urea and uric acid
c. acetic acid and urea
d. ammonia and alanine
e. SAM and PLP
10. Pyrimidine ring atoms are derived from carbamoyl phosphate and
a. ala
b. gly
c. asp
d. citrulline
e. ammonia
---------------------------------
QUIZ 15 (answers)
---------------------------------
1. Nucleotides function as
a. precursors of nucleic acids
b. activated intermediates in glycogen synthesis
c. energy carriers
d. intracellular messengers
e. all of the above
2. The difference between uracil and thymine is that thymine has a ____ group
a. carboxyl
b. amino
c. methyl
d. sugar
e. phosphate
3. Which of the following is FALSE of nucleotide metabolism?
a. The activated sugar used in the synthesis of purines and pyrimidines is phosphoribosyl pyrophosphate.
b. pyrimidine nucleotide synthesis is shorter than purine nucleotide synthesis.
c. In UMP synthesis the pyrimidine ring is synthesized first and then attached to the sugar.
d. Carbon dioxide is required as a precursor for synthesis of purine and pyrimidine nucleotide synthesis.
e. Inosine monophosphate (IMP) is a branch point intermediate in synthesis of UMP.
For questions 4-8, match the following:
a. 5' nucleotidase
b.thymidylate synthase
c. APRT
d. nucleoside kinase
e.phosphorylase
4. conversion of deoxy UMP into deoxy TMP (b)
5. nucleosidase (e)
6. remove phosphates from nucleotides (a)
7. salvage pathway synthesis of purine nucleotides (c)
8. interconvert nucleoside mono-, di-, and triphosphates. (d)
9. The end products of amino acid and purine catabolism are
a. pyruvate and acetyl CoA
b. urea and uric acid
c. acetic acid and urea
d. ammonia and alanine
e. SAM and PLP
10. Pyrimidine ring atoms are derived from carbamoyl phosphate and
a. ala
b. gly
c. asp
d. citrulline
e. ammonia
---------------------------------------------------------------------------------------------------------------------------
29. DNA/RNA Structure I(Chapter 10 ) Mar 18
30. DNA/RNA Structure 2 Mar 20
31. DNA/RNA Structure 3 Mar 22
32. Genes & Chromosomes (Chapter 24) Mar 25
Problem: Why is negative supercoiling important to DNA structure and function?
answer:
1. makes strands compact for packing into the small nucleus and
2. negative supercoiled structures are equivalent to underwound helices and are thus easier to separate the
two strands (which is required for replication, recombination, transcription etc.)
33. DNA Synthesis 1(replication) & Metabolism 1 (Chapter 25) Mar 29
34. DNA Synthesis 1(replication) & Metabolism 2 Apr 1
35. RNA metabolism 1 (Chapters 26 ) Apr 3
36. RNA metabolism 2 Apr 5
37. RNA Processing 1 (Chapter 26) Apr 8
38. RNA Processing 2 Apr 10
QUIZ 16 (answers at the end)
Pick the BEST selection to the following questions
1. Which compound is NOT usually required in the transcription of DNA?
A.DNA
B.RNA polymerase
C.Sigma factor
D.UTP
2. DNA supercoiling:
A.results in DNA compaction
B.is induced by DNA replication
C.is induced by RNA synthesis
D.all of the above
3. The consensus sequence for a gene which codes for protein, P is (5') TATAAT for the Pribnow box (-10 upstream). Which of the following promoter sequences would yield the highest amount of protein P if all transcriptional and translational conditions are the same.
A.(5') TATACT
B.(5') TATGGT
C.(5') TAGGGT
D.(5') TGGGGT
E.(5') GGGGGT
4. Which of the following are components of a transcription "bubble".
I.DNA coding strand
II.DNA-RNA
III.Nascent-RNA
IV.RNA polymerase
A.I only
B.I, II only
C.I, II, III only
D.None of the above
E.All of the above
5. Write the base sequence of a segment of DNA replicated by DNA polymerase from the following DNA template.
(5') AGCTTGC (3')
A.(5') TCGAACG (3')
B.(5')GCAAGCT (3')
C.(5')UCGAACG (3')
D.(5')GCAAGCU (3')
E.None of the above
6. What is the base sequence of the mRNA transcribed by RNA polymerase from the NEWLY replicated DNA strand in question 5.
A.(5')AGCUUGC (3')
B.(5')CGUUCGA (3')
C.(5')TCGAACG (3')
D.(5')GCAAGCT (3')
E.None of the above
7. Which of the following is a NOT a substrate for RNA polymerase?
A. ATP
B. UTP
C.GTP
D.TTP
E.CTP
8. In the B-DNA molecule of a certain virus, the number of bp is 260 and it has 3 negative supercoils. What is its linking number?
9. Topoisomerases can change the number of bp in a DNA molecule? True or false?
10.Histones are found in bacterial nucleoids? True or false?
11. Histones bind DNA without affecting its supercoiling? True or false?
12. Histones occur at regular intervals along the DNA? True or false?
13. Pentose rings in a nucleotide are in equilibrium between straight chain and ring forms. True or false?
14. Pentoses in a nucleotide are always in the beta-pyranose form? True or false?
15. In a nucleic acid, C-5 of the pentose is joined to a nitrogenous base by a N-glycosidic bond. True or false?
16. The 5' end of a DNA has no nucleotide attached to its 5' end. True or false?
17. Alkaline hydrolysis of RNA produces 2',3'-cAMP and 2'-AMP and 3'-AMP. True or false?
18. Nucleic acid bases absorb best around 260 nm while trp has an absorption peak at 280 nm. True or false?
19. The sequence CATTAC of a DNA is palindromic. True or false?
20. E. coli DNA polymerase III is the primary enzyme for DNA synthesis. True or false?
21. E. coli DNA polymerase III has 5'---->3' exonuclease activity. True or false?
22. E. coli DNA polymerase III has 3'---->5' exonuclease (proofreading) activity. True or false?
23. E. coli DNA polymerase I has 5'---->3' exonuclease activity. True or false?
24. The CORE enzyme of RNA polymerase cannot synthesize RNA unless the sigma subunit is bound. True or false?
25. In E. coli, the 16S, 23S and 5S rRNA is synthesized on separate primary transcripts. True or false?
26. In E. coli, rRNA sequences in primary transcripts are not methylated. True or false?
27. In E. coli, rRNA and tRNA are never found on the same primary transcript. True or false?
28. Eukaryotic transcription factors can bind to RNA polymerase, other transcription factors as well as TATA boxes.
29. There are many copies of the rRNA genes in E. coli. True or false?
30. Splicing of Group I introns require a guanine nucleoside or nucleotide. True or false?
31. The alkaline hydrolysis of RNA does not produce
a. 3',5' - cAMP
b. 2',3' - cAMP
c. 2' - AMP
d. 3' - AMP
32. Prokaryotic DNA pol III
a. contains a 5' -> 3' proofreading activity to improve the fidelity of replication.
b. synthesizes DNA 3'->5'
c. has a beta subunit that acts as a circular clamp that aids in the processitivity of DNA synthesis.
d. synthesizes ONLY the lagging strand, and not the leading strand.
33. The CORE enzyme RNA polymerase from E. coli has the following properties EXCEPT:
a. produces an RNA polymer that begins with a 5'-triphosphate
b. recognizes specific start signals in DNA
c. requires ATP, GTP,CTP and UTP and a DNA template
d. can extend or initiate a RNA chain
e. is required for mRNA, rRNA and tRNA synthesis
34. E.coli RNA polymerase holoenzyme has several subunits - True or FAlse?
35. Rifampicin inhibits RNA synthesis by binding with RNA polymerase and inhibiting it - True or False?
36. mRNA transcripts in eukaryotic cells undergo processing such as addition of cap and tail, intron removal
but not conversion of normal bases to inosine and pseudouridine - True or False?
37. A lariat structure is formed
a.class II intron splicing
b. addition of polyA tail
c. attachment of cap
d. processing of preribosomal transcript
38. In E.coli, rRNA and tRNA may be made from the same primary transcript - True or False?
39. Eukaryotic transcription factors can bind specifically to RNA polymerase II, TATA boxes and other
transcription factors - True or False?
40. Ori C is recognized by the protein DnaA during replication - True or False?
-----------------------------------------------------------------------------------------------------------------------
Answers to quiz 16 (in RED)
-----------------------------------------------------------------------------------------------------------------------
1. Which compound is NOT usually required in the transcription of DNA?
A.DNA
B.RNA polymerase
C.Sigma factor
D.UTP
2. DNA supercoiling:
A.results in DNA compaction
B.is induced by DNA replication
C.is induced by RNA synthesis
D.all of the above
3. The consensus sequence for a gene which codes for protein, P is (5') TATAAT for the Pribnow box (-10 upstream). Which of the following promoter sequences would yield the highest amount of protein P if all transcriptional and translational conditions are the same.
A.(5') TATACT
B.(5') TATGGT
C.(5') TAGGGT
D.(5') TGGGGT
E.(5') GGGGGT
4. Which of the following are components of a transcription "bubble".
I.DNA coding strand
II.DNA-RNA
III.Nascent-RNA
IV.RNA polymerase
A.I only
B.I, II only
C.I, II, III only
D.None of the above
E.All of the above
5. Write the base sequence of a segment of DNA replicated by DNA polymerase from the following DNA template.
(5') AGCTTGC (3')
A.(5') TCGAACG (3')
B.(5')GCAAGCT (3')
C.(5')UCGAACG (3')
D.(5')GCAAGCU (3')
E.None of the above
6. What is the base sequence of the mRNA transcribed by RNA polymerase from the NEWLY replicated DNA strand in question 5.
A.(5')AGCUUGC (3')
B.(5')CGUUCGA (3')
C.(5')TCGAACG (3')
D.(5')GCAAGCT (3')
E.None of the above
7. Which of the following is NOT a substrate for RNA polymerase?
A. ATP
B. UTP
C.GTP
D.TTP
E.CTP
8. In the B-DNA molecule of a certain virus, the number of bp is 260 and it has 3 negative supercoils. What is its linking number?
T=260/10.4=25; linking # = T+W = 25 + (-3) = 22
9. Topoisomerases can change the number of bp in a DNA molecule? True or false?
10.Histones are found in bacterial nucleoids? True or false?
11. Histones bind DNA without affecting its supercoiling? True or false?
12. Histones occur at regular intervals along the DNA? True or false?
13. Pentose rings in a nucleotide are in equilibrium between straight chain and ring forms? True or false?
14. Pentoses in a nucleotide are always in the beta-pyranose form? True or false?
15. In a nucleic acid, C-5 of the pentose is joined to a nitrogenous base by a N-glycosidic bond. True or false?
16. The 5' end of a DNA has no nucleotide attached to its 5' end. True or false?
17. Alkaline hydrolysis of RNA produces 2',3'-cAMP and 2'-AMP and 3'-AMP. True or false?
18. Nucleic acid bases absorb best around 260 nm while trp has an absorption peak at 280 nm. True or false?
19. The sequence CATTAC of a DNA is palindromic. True or false?
20. E. coli DNA polymerase III is the primary enzyme for DNA synthesis. True or false?
21. E. coli DNA polymerase III has 5'---->3' exonuclease activity. True or false?
22. E. coli DNA polymerase III has 3'---->5' exonuclease (proofreading) activity. True or false?
23. E. coli DNA polymerase I has 5'---->3' exonuclease activity. True or false?
24. The CORE enzyme of RNA polymerase cannot synthesize RNA unless the sigma subunit is bound. True or false?
25. In E. coli, the 16S, 23S and 5S rRNA is synthesized on separate primary transcripts. True or false?
26. In E. coli, rRNA sequences in primary transcripts are not methylated. True or false?
27. In E. coli, rRNA and tRNA are never found on the same primary transcript. True or false?
28. Eukaryotic transcription factors can bind to RNA polymerase, other transcription factors as well as TATA boxes. True or false?
29. There are many copies of the rRNA genes in E. coli. True or false?
30. Splicing of Group I introns require a guanine nucleoside or nucleotide. True or false?
31. The alkaline hydrolysis of RNA does not produce
a. 3',5' - cAMP
b. 2',3' - cAMP
c. 2' - AMP
d. 3' - AMP
32. Prokaryotic DNA pol III
a. contains a 5' -> 3' proofreading activity to improve the fidelity of replication.
b. synthesizes DNA 3'->5'
c. has a beta subunit that acts as a circular clamp that aids in the processitivity of DNA synthesis.
d. synthesizes ONLY the lagging strand, and not the leading strand.
33. The CORE enzyme RNA polymerase from E. coli has the following properties EXCEPT:
a. produces an RNA polymer that begins with a 5'-triphosphate
b. recognizes specific start signals in DNA
c. requires ATP, GTP,CTP and UTP and a DNA template
d. can extend or initiate a RNA chain
e. is required for mRNA, rRNA and tRNA synthesis
34. E.coli RNA polymerase holoenzyme has several subunits - True or FAlse?
35. Rifampicin inhibits RNA synthesis by binding with RNA polymerase and inhibiting it - True or False?
36. mRNA transcripts in eukaryotic cells undergo processing such as addition of cap and tail, intron removal
but not conversion of normal bases to inosine and pseudouridine - True or False?
37. A lariat structure is formed during
a.class II intron splicing
b. addition of polyA tail
c. attachment of cap
d. processing of preribosomal transcript
38. In E.coli, rRNA and tRNA may be made from the same primary transcript - True or False?
39. Eukaryotic transcription factors can bind specifically to RNA polymerase II, TATA boxes and other
transcription factors - True or False?
40. Ori C is recognized by the protein DnaA during replication - True or False?
Go to nucleotide structure (beginning of exam 3)
-----------------------------------------------------------------------------------------------------------------------------------------------------------------------
EXAMINATION 3 (Apr 24)
There will be40 multiple choice questions (1 pt. each for a total of 40pts.);
1 essay question, worth 10 pts.
The total for the whole exam is 40+ 10= 50 pts.
------------------------------------------------------------------------------------------------------------------------------------------------------------------------
39. Protein Synthesis 1(Chapter 27) Apr 12
40. Protein Synthesis 2 Apr 15
Major steps in protein synthesis Figs. 27-22, 27-23, 27-24, 27-25, 27-26, 27-27, 27-28, table 27-9
41. Protein Synthesis 3 Apr 17
Major posttranslational modifications in proteins Fig. 27-31
Protein targeting
42. Gene regulation I (Chapter 28) Apr 19
43. Gene regulation II Apr 22
44. Recombinant DNA Technology (Chapter 29) Apr 2
QUIZ 17 (answers at the end)
Pick the BEST selection to the following questions
1. Which compound is NOT usually required in the transcription of DNA?
A.DNA
B.RNA polymerase
C.Sigma factor
D.UTP
2. Which is NOT a characteristic of the genetic code?
A.Commaless
B.Degenerate
C.overlapping
D.triplet
3. Protein synthesis on the ribosome requires the following except
A.DNA.
B.tRNA
C.EF-Tu.
D.GTP.
4. The activation of an amino acid by ATP and its subsequent attachment to the tRNA is mediated by a
A.synthase.
B.dehydrogenase.
C.isomerase.
D.synthetase.
5. DNA supercoiling:
A.results in DNA compaction
B.is induced by DNA replication
C.is induced by RNA synthesis
D.all of the above
6. From the genetic code, what is the anticodon for Trp
A.CCA
B.ACC
C.CAC
D.CCC
E.AAC
7. How many codons can a tRNA with an anticodon sequence IGG recognize?
A.0 B.1 C.2 D.3 E.4
8.Which of the following amino-acids has the most codons?
A.Ala
B.His
C.Glu
D.Tyr
E.Ser
For questions 9-13, match the following terms.
A.30S
B.EF-Tu
C.IF-1
D.EF-G
E.N-formylmethionine
9. Elongation factor which binds incoming tRNA.
10. Protein involved in translocation
11. Initiation factor
12. Ribosomal subunit involved in initiation
13. Initiation amino acid
14. What recognizes the codons UAA, UAG and UGA in protein synthesis?
A.Specific tRNAs
B.Initiation factors
C.Release factors
D.Elongation factors
E.Ribosomal proteins
15. The consensus sequence for a gene which codes for protein, P is (5') TATAAT for the Pribnow box (-10 upstream). Which of the following promoter sequences would yield the highest amount of protein P if all transcriptional and translational conditions are the same.
A.(5') TATACT
B.(5') TATGGT
C.(5') TAGGGT
D.(5') TGGGGT
E.(5') GGGGGT
16. Which of the following are components of a transcription "bubble".
I.DNA coding strand
II.DNA-RNA
III.Nascent-RNA
IV.RNA polymerase
A.I only
B.I, II only
C.I, II, III only
D.None of the above
E.All of the above
17. A human pancreatic enzyme has a polypeptide chain of 200 amino acids. It is coded for by a gene having 1900 base pairs. Based on this finding which of the following is true?
I.The gene for this enzyme has a minimum of 600 nucleotides
II.The introns have more bases than the exons.
III.The 600 nucleotides coding for the amino acids are found in the intron
A.I only
B.I, II, only
C.II, III only
D.All of the above
E.None of the above
18. Write the base sequence of a segment of DNA replicated by DNA polymerase from the following DNA template.
(5') AGCTTGC (3')
A.(5') TCGAACG (3')
B.(5')GCAAGCT (3')
C.(5')UCGAACG (3')
D.(5')GCAAGCU (3')
E.None of the above
19. What is the base sequence of the mRNA transcribed by RNA polymerase from the NEWLY replicated DNA strand in question 18. A.(5')AGCUUGC (3')
B.(5')CGUUCGA (3')
C.(5')TCGAACG (3')
D.(5')GCAAGCT (3')
E.None of the above
20. Which of the following is a NOT a substrate for RNA polymerase?
A. ATP
B. UTP
C.GTP
D.TTP
E.CTP
21. In DNA recombinant technology, plasmids, bacteriophages and BACs are known as ______________________.
22. PCR is a method that can amplify target DNA - it requires the enzyme ________________ and deoxynucleotides.
23. Regulation of the ara operon is performed by the protein _______ which can act either as a repressor or as an activator, when bound to the sugar ______________.
24. The BAD genes are part of
A. The ara operon
B. The trp operon
C. The lac operon
D. A and B are true
E. All of the above are true.
25. Some DNA binding proteins have domains that recognize other proteins. One such domain is
called:
A. lac domain
B. helix-turn-helix
C. Zinc finger
D. Leucine zipper
E. None of the above
-----------------------------------------------------------------------------------------------------------------------
Answers to quiz 17 (in RED)
-----------------------------------------------------------------------------------------------------------------------
1. Which compound is NOT usually required in the transcription of DNA?
A.DNA
B.RNA polymerase
C.Sigma factor
D.UTP
2. Which is NOT a characteristic of the genetic code?
A.Commaless
B.Degenerate
C.overlapping
D.triplet
3. Protein synthesis on the ribosome requires the following except
A.DNA.
B.tRNA
C.EF-Tu.
D.GTP.
4. The activation of an amino acid by ATP and its subsequent attachment to the tRNA is mediated by a
A.synthase.
B.dehydrogenase.
C.isomerase.
D.synthetase.
5. DNA supercoiling:
A.results in DNA compaction
B.is induced by DNA replication
C.is induced by RNA synthesis
D.all of the above
6. From the genetic code, what is the anticodon for Trp
A.CCA
B.ACC
C.CAC
D.CCC
E.AAC
7. How many codons can a tRNA with an anticodon sequence IGG recognize?
A.0 B.1 C.2 D.3 E.4
8.Which of the following amino-acids has the most codons?
A.Ala
B.His
C.Glu
D.Tyr
E.Ser
For questions 9-13, match the following terms.
A.30S
B.EF-Tu
C.IF-1
D.EF-G
E.N-formylmethionine
9. Elongation factor which binds incoming tRNA. B
10. Protein involved in translocation D
11. Initiation factor C
12. Ribosomal subunit involved in initiation A
13. Initiation amino acid E
14. What recognizes the codons UAA, UAG and UGA in protein synthesis?
A.Specific tRNAs
B.Initiation factors
C.Release factors
D.Elongation factors
E.Ribosomal proteins
15. The consensus sequence for a gene which codes for protein, P is (5') TATAAT for the Pribnow box (-10 upstream). Which of the following promoter sequences would yield the highest amount of protein P if all transcriptional and translational conditions are the same.
A.(5') TATACT
B.(5') TATGGT
C.(5') TAGGGT
D.(5') TGGGGT
E.(5') GGGGGT
16. Which of the following are components of a transcription "bubble".
I.DNA coding strand
II.DNA-RNA
III.Nascent-RNA
IV.RNA polymerase
A.I only
B.I, II only
C.I, II, III only
D.None of the above
E.All of the above
17. A human pancreatic enzyme has a polypeptide chain of 200 amino acids. It is coded for by a gene having 1900 base pairs. Based on this finding which of the following is true?
I.The gene for this enzyme has a minimum of 600 nucleotides
II.The introns have more bases than the exons.
III.The 600 nucleotides coding for the amino acids are found in the intron
A.I only
B.I, II, only
C.II, III only
D.All of the above
E.None of the above
18. Write the base sequence of a segment of DNA replicated by DNA polymerase from the following DNA template.
(5') AGCTTGC (3')
A.(5') TCGAACG (3')
B.(5')GCAAGCT (3')
C.(5')UCGAACG (3')
D.(5')GCAAGCU (3')
E.None of the above
19. What is the base sequence of the mRNA transcribed by RNA polymerase from the NEWLY replicated DNA strand in question 18.
A.(5')AGCUUGC (3')
B.(5')CGUUCGA (3')
C.(5')TCGAACG (3')
D.(5')GCAAGCT (3')
E.None of the above
20. Which of the following is NOT a substrate for RNA polymerase?
A. ATP
B. UTP
C.GTP
D.TTP
E.CTP
21. In DNA recombinant technology, plasmids, bacteriophages and BACs are known as vectors.
22. PCR is a method that can amplify target DNA - it requires the enzyme DNA polymerase and deoxynucleotides.
23. Regulation of the ara operon is performed by the protein ara C which can act either as a repressor or as an activator, when bound to the sugar arabinose
24. The BAD genes are part of
A. The ara operon
B. The trp operon
C. The lac operon
D. A and B are true
E. All of the above are true.
25. Some DNA binding proteins have domains that recognize other proteins. One such domain is
called:
A. lac domain
B. helix-turn-helix
C. Zinc finger
D. Leucine zipper
E. None of the above
--------------------------------------------------------------------------------------------------------------------------------------------
Final examination is comprehensive . Wed May 1 12 noon-1:50 p.m.
Questions 1-40 are multiple choice questions (worth total of 40 points), questions
41-70 are essay questions which include structure recognition, mechanisms and
fill in the blanks (worth 60 points). Total points = 100
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