CHM 421 (SURVEY OF BIOCHEMISTRY)
THIS CLASS IS DESIGNED FOR STUDENTS WITH ONLY ONE SEMESTER OF INORGANIC (e.g. CHM 120)
AND ONE SEMESTER OF ORGANIC CHEMISTRY (e.g. CHM 342). IF YOU HAVE TAKEN TWO SEMESTERS
OF INORGANIC ( e.g. CHM 131/132) AND ORGANIC CHEMISTRY( e.g. CHM 345/346), THEN YOU SHOULD
CONSIDER TAKING CHM 425 OR CHM 521/522.
Grading
2 Tests-50 minutes( Oct 17 and Dec 3) at 16.6% each.....................................................33 %
Unannounced Quizzes...............................................................................................................33 %
1 Comprehensive-60 minutes(ACS Standardized) Examination ......................................33 %
TOTAL ...........................................................................................................................................100 %
Grading Scale
Total 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 3 TESTS AND QUIZZES WILL DECIDE YOUR FINAL GRADE. THERE IS NO EXTRA CREDIT FOR ANYTHING ELSE !
READING MATERIAL
1. Text (required): Biochemistry and Molecular Biology by WH Elliott & DC Elliott 2nd ed.
2. Course Pack (optional)
TO DO WELL IN THIS CLASS, IT IS IMPORTANT:
1. NOT TO MISS CLASS. IMPORTANT CONCEPTS (SUMMARIZED IN A COURSE PACK) TO HELP
YOU UNDERSTAND YOUR TEXT WILL BE EMPHASIZED IN CLASS.
2. TO LOOK UP THE SYLLABUS BELOW AND READ THE CHAPTER UNDER "READINGS" 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 ....................Aug 25
a. How do biomolecules associate with one another to form larger and larger structures leading to a cell, the basic unit of life?
b. What are the major biomolecules and macromolecules and their relative sizes
(in Angstrom and the nanometer units) ?
c. What is the solvent in which the biomolecules are dissolved or suspended?
d. What are the major elements of life and why were they chosen?
e. Do you have to memorize the chemical structure of a complex biomolecule? Focus on its functional groups, polarity and shape!
f. What are the forces involved in folding a biomolecule into its unique 3D shape and what are the forces that make this 3D shape so stable?
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2. Proteins 1 (Chapter 3).............................Aug 27
a. What is the basic structure of a typical protein?
b. What are primary, secondary, tertiary and quaternary structures (Fig. 2.2)?
c. What is a peptide bond?
d. How are amino acids numbered?
e. How is the sequence of amino acids in a polypeptide chain written?
f. What is the C and N-terminal?
g. What is an alpha-helix (Fig. 3.4), beta sheet (Fig.3.5) and random coil and what forces hold these shapes intact (Fig 3.6)?
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3. Proteins 2............................................Aug 29
a. What is the chemical structure of a typical amino acid and how do the 20 standard amino acids differ from one another?
YOU MUST BE ABLE TO RECOGNIZE THE 20 AMINO ACID STRUCTURES (shown on pages36 and 37)
AND THEIR 3-LETTER ABBREVIATIONS
(e.g. isoleucine = ile; tryptophan = trp; asparagine = asn; glutamine = gln)
b. What is a chiral molecule, enantiomers, stereoisomers?
c. What are some common polar (or hydrophilic) and non-polar or hydrophobic groups in biology ?
Answer - commonly found polar groups include -NH2 , -OH, -COOH and positively or negatively charged groups. Common non-polar groups include aliphatic hydrocarbons and aromatic rings.
d.Why is it important to know whether a chemical structure is polar or non-polar?
Labor day- Sep 1
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4. Proteins 3.....................Sep 3
a. How does the structure of an amino acid change with pH?
List of pKs for the 20 amino acids (you do not have to memorize these numbers!)
Amino acid-------------------alpha-COOH-----------------alpha-NH2--------------------other (R group)
Glycine (gly)---------------------------2.3-----------------------------9.6
Alanine (ala)--------------------------2.3------------------------------9.7
Valine (val)----------------------------2.3------------------------------9.6
Leucine (leu)-------------------------2.4------------------------------9.6
Isoleucine (ile)------------------------2.4-----------------------------9.7
Methionine (met)---------------------2.3-----------------------------9.2
Phenylalanine (phe)-----------------1.8-----------------------------9.1
Tyrosine (tyr)---------------------------2.2-----------------------------9.1-------------------------------10.1
Tryptophan (trp)-----------------------2.4-----------------------------9.4
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List of pKs for the 20 amino acids (you do not have to memorize these numbers!)
...continuedAmino acid--------------------alpha-COOH---------------------alpha-NH2------------------------other (R group)
Serine (ser)---------------------------2.2----------------------------9.2
Proline (pro)--------------------------2.0-----------------------------11Threonine (thr)-----------------------2.1----------------------------9.6
Cysteine ( cys)-----------------------2.0----------------------------10.3---------------------------------8.2
Asparagine (asn)--------------------2.0-----------------------------8.8
Glutamine (gln)----------------------2.2-----------------------------9.1
Lysine (lys)----------------------------2.2-----------------------------9.0---------------------------------10.5
Histidine (his)------------------------1.8-----------------------------9.2----------------------------------6.0
Arginine (arg)-------------------------2.2-----------------------------9.0----------------------------------12.5
Aspartic acid (asp)------------------1.9-----------------------------9.6----------------------------------3.7
Glutamic acid (glu)------------------2.2-----------------------------9.7----------------------------------4.3
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b. What is the isoelectric point?
c. What is the Henderson-Hasselbach equation and what is its importance?
Answer :
1. One importance is that it can be used to calculate how much of a ionizable group (such as COOH, NH2 ) exists
as the protonated or unprotonated form.
You can use this equation to show that when the pH = pK, then exactly 50% of a group will be protonated (which means
the remaining 50% is unprotonated)
i.e. the pK is that pH where the concentrations of protonated and unprotonated forms are EQUAL.
2. Another importance 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.
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5. Proteins 5....................Sep 5
a. How do two or more amino acids link together to form peptides, polypeptides and proteins?
See Figure 3.7 for structures of various proteins
b. Problems on protein structure
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QUIZ 5
Refer to the polypeptide structure below 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. What is the C-terminal amino acid?
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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. The smallest amino acid in the protein is ___.
10. Assume that the protein folds into a three dimensional shape. The protein thus has a primary, secondary, tertiary and quaternary structure. TRUE / FALSE
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Answers to quiz 5.
1. What is the primary structure of the protein ?
Ans: gly-asp-asp-asp-phe-phe-ser-ser
2. What is the NET charge of the protein at pH 7 ?
Ans: net charge at pH 7 is 3 negative
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3. How many peptide bonds are present?
Ans: there are 7 peptide bonds
4. What is the C-terminal amino acid?
Ans: C-terminal is ser
5. What is the acidic amino acid present?
Ans: acidic amino acid is 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. The salt bridge may be formed between the N-terminal amino group
and the amino acid asp.
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8. The protein has 2 hydroxyl groups, 0 (zero) sulfhydryl group, and 4 carboxyl groups.
9. The smallest amino acid in the protein is gly.
10. Assume that the protein folds into a three dimensional shape. The protein thus has a primary, secondary, tertiary and quaternary structure. TRUE / FALSE
Ans: False - the protein will not have a quaternary structure since it has only one
polypeptide chain.
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6. Enzymes 1 (Chapters 1 & 2)......................Sep 8
a. What are enzymes and what do they do?
b. What are coenzymes?
7. Enzymes 2......................Sep 10
a. Why does a chemical reaction occur? Why do some reactions occur very fast while others so slow?
b. What is activation energy?c. How does an enzyme increase the speed or velocity or rate of a chemical reaction?
8. Enzymes 3.....................Sep 12
a. How does an enzyme work?
b. What is the effect of pH and temperature on the catalytic function of an enzyme?
9. Enzymes 4.....................Sep 15
a. What is enzyme kinetics and what information does it provide?
b. What is the Michaelis-Menten equation?
c. How are the catalytic activities of an enzyme affected by "inhibitors"?
d. Types of enzymes - we will learn some common names of enzymes later in metabolism.
e. Regulation of enzyme function will be covered later at the end of metabolism.
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QUIZ 6 (Enzymes) - the answers are at the end of this 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.
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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
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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. What is v if [S ]=10 Km ?
(a) 1% Vmax (b) 5% Vmax (c) 50% Vmax (d) 91% Vmax (e) 100% Vmax
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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
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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
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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.
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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. What is v if [S ]=10 Km ?
(a) 1% Vmax (b) 5% Vmax (c) 50% Vmax (d) 91% Vmax (e) 100% Vmax
Answer: (d) 91% Vmax (Substitute S=10Km in the Michaelis Menten equation and you get v=0.91Vmax (or 91% Vmax)
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10. Lipids & Membranes 1 (Chapter 4)....................Sep 17
a. What are the chemical structures of common fatty acids?
b. What is an amphiphilic structure? What are soaps ? What is saponification?
c. How are the carbons of a fatty acid labeled?
d. Can you recognize the structure of a mono-, di-, or triglyceride?
e. Can you recognize the structure of a phospholipid (eg. PC); a sphingomyelin; a glycolipid, a steroid such as cholesterol and
an eicosanoid such as a prostaglandin ?
c. What are the key features of a biomembrane?
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d. How are biomolecules transported across membranes? (summarized in the diagram below)
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.
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Quiz 7 (answers)
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. False
4. A triglyceride rich in oleic acid is a liquid at room temperature. True
5. The "head" of PE is hydrophobic. False
6. In a cerebroside, the polar head is a sugar. True
7. Cholesterol esters are made up of a steroid and a fatty acid.True
8. Sphingomyelin can function as a detergent.True
9. When a triglyceride is saponified with potassium hydroxide, soaps are formed.True
10.Cholesterol dissolves in water easily. False
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11. Carbohydrate Structure 1.......Sep 19
a. What is the chemical structure of glucose, fructose and ribose?
b. What are enantiomers?
Answer - two mirror image forms of a chiral molecule eg. D-glucose and L glucose.
c. What are epimers?
Answer - compounds that differ in configuration at one carbon eg. glucose and galactose
b. What are common terms used in describing sugars (eg. hexose, aldose, ketose) ?
c. What is the anomeric carbon?
d. What is the difference between alpha and beta glucose or fructose?
e. What is a hemiacetal?
f. What is a reducing sugar? a non-reducing sugar?
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12. Carbohydrate Structure 2..............Sep 22
a. How are two or more monosaccharides linked together to form disaccharides or polysaccharides?
b. What is an acetal?
c. What are the common disaccharides found in nature?
c. What are the common polysaccharides found in nature ?
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Quiz 8
Examine the structures below to answer the following questions (answers are at the end of the quiz)
Structure
1
Structure
2
Structure
3
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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. Stearic 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
13. Metabolism 1 (Chapters 1, 5,6,7,8)........ Sep 26
a. What is the basic design of metabolic pathways in a typical cell?
b. What are the central pathways?
c. What are the two major biomolecules used for the energy needs of a cell under normal conditions and where are they stored?
Answer - the two major energy suppliers are carbohydrates (especially glucose which is stored as glycogen mainly in the liver and skeletal muscles) and triglycerides (which is store in cells called adipocytes located in the adipose tissue scattered all over the body).
14. Metabolism 2..................Sep 29
a. How are carbohydrates, proteins and lipids digested and absorbed into the blood?
b. What are the major organs involved in metabolism?
15. Glycolysis (Chapter 9).........Oct 1
a. What are the main functions of glycolysis?
b. Why is a phosphate group added to glucose in the very first reaction?
c. What kind of reacitons do the enzymes "kinases" catalyze?
d. Why is the enzyme catalyzing the conversion of glucose-6-P to fructose-6-P called an isomerase?
e. Why is glucose-6-P converted to fructose-6-P (reaction 2 in course pack) ?
f. What is the name of the reaction which breaks the C-C bond between C3 and C4 forming two three-carbon fragments?
g. Does glycolysis require NAD+ ?
h. How many ATPs are used up and how many are formed when one molecule of glucose is broken down to two molecules of
pyruvate in glycolysis?
i. Are all steps in glycolysis reversible?
j. What happens to the NADH that is formed in glycolysis?
k. Which cells rely mostly on glycolysis for their energy (ATPs)?
l. What are the other names for glycolysis? Answer - Embden Meyerhoff pathway; anaerobic respiration
m. In which part of the cell does this pathway occur?
16. Pyruvate dehydrogenase complex (conversion of pyruvate to acetyl CoA)
(Chapter 9)...................Oct 3
a. What is the pyruvate dehydrogenase complex and in which part of the cell is it found?
b. What are the vitamins needed to convert pyruvate to acetyl CoA?
c. What is thiamine pyrophosphate or TPP and what vitamin is it derived from?
d. What is NAD and which vitamin is it derived from?
e. What is FAD and which vitamin is it derived from?
f. What is coenzyme A (CoA-SH) and which vitamin is it derived from?
17.Krebs cycle (Chapter 9)...............Oct 6
a. What are the main functions of the Kreb's cycle (TCA cycle, citric acid cycle)and in which part of the cell does it occur?
b. What happens to the two carbons of acetyl CoA when it enters the TCA cycle ?
c. How many redox reactions are there in the TCA cycle?
d. How many NADH are produced when one molecule of acetyl CoA is oxidized by the TCA cycle?
f. How many FADH are produced when one molecule of acetyl CoA is oxidized by the TCA cycle?
g. How many ATP (or equivalents such as GTP) are produced when one molecule of acetyl CoA is oxidized by the TCA cycle?
h. Why is the anaplerotic reaction whereby pyruvate is converted to oxaloacetate important to the cell?
i. What are the sources of acetyl CoA ?
j. Are the intermediates of the Krebs cycle used or produced from other metabolic pathways?
18. Electron transport chain / oxidative phosphorylation (Chapter 9)........Oct 8
a. What are the major components of the electron transport chainand whre are they located?
b. What are cytochromes and non-heme iron proteins?
c. How are electrons transported from FADH2 and NADH to oxygen along the electron transport chain?
d. What is the chemiosmotic hypothesis?
e. How is the energy obtained when electrons transported from one component to another (ie. redox reactions)in the electron
transport chain coupled to the synthesis of ATP from ADP and Pi (which would not occur unless energy is supplied!)?
19. Energetics of the central pathways (Chapter 9)................F-Oct 10
a. Can you account for all the ATPs used up or produced from a molecule of glucose being oxidized by the central pathways?
QUIZ 9 (answers at the end of the quiz)
Refer to the figure below (fig.1) to answer questions 1-10:
1. Reaction 1is equivalent to the following reaction in metabolism:
a. conversion of glucose-6P into fructose-6-P in glycolysis
b. converison of glucose into glucose-6P in glycolysis
c. conversion of pyruvate into acetyl CoA catalyzed by pyruvate dehydrogenase complex
d. converison of succinate into fumarate in TCA cycle
e. conversion of oxaloacetate into citric acid in the citric acid cycle.
2. Reaction 5 is equivalent to the following reaction in metabolism:
a. conversion of glucose-6P into fructose-6-P in glycolysis
b. converison of glucose into glucose-6P in glycolysis
c. conversion of pyruvate into acetyl CoA catalyzed by pyruvate dehydrogenase complex
d. converison of succinate into fumarate in TCA cycle
e. conversion of oxaloacetate into citric acid in the citric acid cycle.
3. Reaction 3 is equivalent to the following reaction in metabolism:
a. conversion of glucose-6P into fructose-6-P in glycolysis
b. converison of glucose into glucose-6P in glycolysis
c. conversion of pyruvate into acetyl CoA catalyzed by pyruvate dehydrogenase complex
d. converison of succinate into fumarate in TCA cycle
e. conversion of oxaloacetate into citrate in the citric acid cycle.
4.Reaction 6 occurs in:
a. TCA cycle
b. Embden-Meyerhof pathway
c. Glycolysis
d.Eelectron transport chain
e. TCA cycle
Questions 5-9: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. phosphorylation
5. Reaction 1
6. Reaction 2
7.Reaction 3
8. Reaction 4
9. Reaction 5
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10. Which of the reactions require niacin ?
a. reaction 1
b. reaction 2
c. reaction 3
d. reaction 4
e. reaction 5
11. 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
12. 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
13. 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
14. 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
15. The conversion of succinate into fumarate is catalyzed by
a. synthase
b. synthetase
c, dehydrogenase
d. kinase
e. carboxylase
16. The following are electron carriers except:
a. coenzyme A
b. cytochrome a
c. nonheme iron protein
d. Co Q
e. NADH
Page 52
17. In a RBC, pyruvate is converted into ____ so that glycolysis may continue.
18. 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
19. There are __ irreversible reactions in glycolysis.
a. 1 b. 2 c. 3 d. 4 e. 5
Page 53
20.As electrons are transferred from NADH or FADH2 to oxygen along the electron transport chain, ___ are pumped from
the matrix into the intermembrane space.
21. There are ____ substrate level phosphorylation reaction(s) in the TCA cycle
a. 1 b. 2 c. 3 d. 4 e. 5
22. 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
Page 54
23. 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
24. 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
25. Glycogen is mostly stored in the
a. liver and red blood cells
b. kidney
c. heart
d. liver and skeletal muscles
e. adipose tissue
26. Which of the following is a catabolic pathway for lipids?
a. glycogenesis
b. gluconeogenesis
c. beta-oxidation
d. urea cycle
e. Embden Meyerhoff pathway
27. 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
28. The enzyme catalyzing the reaction S + ATP ------> S-P + ADP is a
a. carboxylase
b. kinase
c. dehydrogenase
d. isomerase
e. synthetase
29. The following group is NOT found in CoA
a. phosphate
b. sulfhydryl
c. ribose
d. amide
e. pyridine
30. 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 9: (answers in blue)
----------------------------------------------------
1. Reaction 1is equivalent to the following reaction in metabolism:
a. conversion of glucose-6P into fructose-6-P in glycolysis
b. converison of glucose into glucose-6P in glycolysis
c. conversion of pyruvate into acetyl CoA catalyzed by pyruvate dehydrogenase complex
d. converison of succinate into fumarate in TCA cycle
e. conversion of oxaloacetate into citric acid in the citric acid cycle.
2. Reaction 5 is equivalent to the following reaction in metabolism:
a. conversion of glucose-6P into fructose-6-P in glycolysis
b. converison of glucose into glucose-6P in glycolysis
c. conversion of pyruvate into acetyl CoA catalyzed by pyruvate dehydrogenase complex
d. converison of succinate into fumarate in TCA cycle
e. conversion of oxaloacetate into citric acid in the citric acid cycle.
3. Reaction 3 is equivalent to the following reaction in metabolism:
a. conversion of glucose-6P into fructose-6-P in glycolysis
b. converison of glucose into glucose-6P in glycolysis
c. conversion of pyruvate into acetyl CoA catalyzed by pyruvate dehydrogenase complex
d. converison of succinate into fumarate in TCA cycle
e. conversion of oxaloacetate into citrate in the citric acid cycle.
4.Reaction 6 occurs in:
a. TCA cycle
b. Embden-Meyerhof pathway
c. Glycolysis
d.Eelectron transport chain
e. TCA cycle
Questions 5-9: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. phosphorylation
5. Reaction 1 (ans: e. phosphorylation)
6. Reaction 2 (ans: b.redox)
7.Reaction 3 (ans: a. decarboxylation)
8. Reaction 4 (ans: d. addition/elimination)
9. Reaction 5 (ans: c. isomerization )
10. Which of the reactions require niacin ?
a. reaction 1
b. reaction 2
c. reaction 3
d. reaction 4
e. reaction 5
11. 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
12. 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
13. 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
14. 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
15. The conversion of succinate into fumarate is catalyzed by
a. synthase
b. synthetase
c. dehydrogenase
d. kinase
e. carboxylase
16. The following are electron carriers except:
a. coenzyme A
b. cytochrome a
c. nonheme iron protein
d. Co Q
e. NADH
17. In a RBC, pyruvate is converted into lactate so that glycolysis may continue.
18. 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
19. There are __ irreversible reactions in glycolysis.
a. 1 b. 2 c. 3 d. 4 e. 5
20.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.
21. There are ____ substrate level phosphorylation reaction(s) in the TCA cycle
a. 1 b. 2 c. 3 d. 4 e. 5
22. 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
23. 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
24. 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
25. Glycogen is mostly stored in the
a. liver and red blood cells
b. kidney
c. heart
d. liver and skeletal muscles
e. adipose tissue
26. Which of the following is a catabolic pathway for lipids?
a. glycogenesis
b. gluconeogenesis
c. beta-oxidation
d. urea cycle
e. Embden Meyerhoff pathway
27. 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
28. The enzyme catalyzing the reaction S + ATP ------> S-P + ADP is a
a. carboxylase
b. kinase
c. dehydrogenase
d. isomerase
e. synthetase
29. The following group is NOT found in CoA
a. phosphate
b. sulfhydryl
c. ribose
d. amide
e. pyridine
30. The poison cyanide affects
a. glycolysis
b. TCA cycle
c. electron transport chain
d. substrate level phosphorylation
e. none of the above
Hi! Hope all is going well with this class! From lecture 1 to this point
is the material for exam 1. Best of luck!
20. Glycogen metabolism (Chapter 9)..................Oct 13
a. What is the key enzyme in glycogen synthesis (glycogenesis)?
b. How is glucose activated (made more chemically reactive) in glycogen synthesis?
c. What is the key enzyme in glycogenolysis?
d. How does glycogen metabolism in the liver differ from that in skeletal muscle?
21. Gluconeogenesis (Chapter 12)................Oct 15
a. Whatare the glycolytic reactions that need to be bypassed in order for glucose to be synthesized?
b. What are the precursors of glucose?
c. What is the location of this pathway?
d. What is the function of biotin?
EXAM I : 30 multiple choice questions (50 minutes; covers 1-19-upto energetics of the central pathways)........Oct 17
22. Pentose Phosphate Pathway (Hexose monophosphate shunt) (Chapter 14).....Oct 20
a. What are the functions of this pathway?
b. What is the key enzyme of the oxidative pahse?
c. What are the key enzymes of the non-oxidative phase?
23. Lipid metabolism 1 (Chapters 10, 11)...............Oct 22
a. How is energy derived from the breakdown of fatty acids?
b. Which part of the cell does beta-oxidation occur?
c. What is the "beta" in beta oxidation?
24. Lipid metabolism 2.................Oct 24
a. How much energy is derived from the beta oxidation of a 16carbon fatty acid (eg. palmitic acid)?
25. Lipid metabolism 3................Oct 27
a. How is a 16carbon fatty acid (eg. palmitic acid) made from acetyl Co A?
b. What are ketone bodies and why are they formed?
c. What is the key step in cholesterol biosynthesis?
QUIZ 10
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 reducing agent used in fatty acid synthesis is:
a. FADH2
b. NADH
c. CoA-SH
d. NADPH
e. Hydrogen
5. 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
6. The oxidative phase of HMS produces
a. FADH2
b. NADH
c. CoA-SH
d. NADPH
e. Glucose
7. 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
8. In beta-oxidation, fatty acids are converted into their:
a. phosphates
b. esters
c.thioesters
d. anhydrides
e. none of the above
9. 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
10. Fatty acid oxidation produces:
a. FADH2
b. NADH
c. Acetyl CoA
d. all of the above
11. 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
12.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
12.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
13.12.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
14. Fatty acid synthesis requires:
a. biotin
b. malonyl CoA
c. acetyl CoA
d. ATP
e. all of the above
15. The following are ketone bodies EXCEPT:
a. acetyl CoA
b. beta-hydroxybutyrate
c. acetoacetate
d. acetone
16. 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
17. HMG-CoA is converted into mevalonate during cholesterol synthesis by the enzyme
a. oxidase
b. isomerase
c. reductase
d.phosphorylase
e. kinase
18. Fatty acid transport into mitochondria is carried out by
a. creatine
b. carnitine
c. ornithine
d. creatinine
19. Gluconeogenesis occurs predominantly in the
a. spleen
b. skeletal muscles
c. liver
d. RBC
e. adipose tissue
20. Which of the following atoms is NOT found in biotin?
a. N
b. S
c. P
d. O
e. H
QUIZ 10 (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 reducing agent used in fatty acid synthesis is:
a. FADH2
b. NADH
c. CoA-SH
d. NADPH
e. Hydrogen
5. 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!)
6. The oxidative phase of HMS produces
a. FADH2
b. NADH
c. CoA-SH
d. NADPH
e. Glucose
7. 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
8. In beta-oxidation, fatty acids are converted into their:
a. phosphates
b. esters
c.thioesters
d. anhydrides
e. none of the above
9. 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
10. Fatty acid oxidation produces:
a. FADH2
b. NADH
c. Acetyl CoA
d. all of the above
11. 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
12.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
12.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
13.12.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
14. Fatty acid synthesis requires:
a. biotin
b. malonyl CoA
c. acetyl CoA
d. ATP
e. all of the above
15. The following are ketone bodies EXCEPT:
a. acetyl CoA
b. beta-hydroxybutyrate
c. acetoacetate
d. acetone
16. 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
17. HMG-CoA is converted into mevalonate during cholesterol synthesis by the enzyme
a. oxidase
b. isomerase
c. reductase
d.phosphorylase
e. kinase
18. Fatty acid transport into mitochondria is carried out by
a. creatine
b. carnitine
c. ornithine
d. creatinine
19. Gluconeogenesis occurs predominantly in the
a. spleen
b. skeletal muscles
c. liver
d. RBC
e. adipose tissue
20. Which of the following atoms is NOT found in biotin?
a. N
b. S
c. P
d. O
e. H
26.Regulation of metabolism 1 (Chapter 13)................Oct 29
a.How are enzymes regulated?
27.Regulation of metabolism 2.....................Oct 31
a.What are the main intrinsic controls in metabolism?
b.What are the main extrinsic controls in metabolism?
c. Recognize the structure of cyclic AMP and know its role in extrinsic control of metabolism.
28.Regulation of metabolism 3 .....................Nov 3
a.How does metabolism change as one goes from a well fed state to early and then late starvation?
29.Amino acid metabolism 1 (Chapter 16).....................Nov 5
a.What are the main products of amino acid catabolism?
b.What are the main precursors for the synthesis of amino acids?
30.Amino acid metabolism 2.....................Nov 7
a.Whatis the faith of the amino group in amino acid catabolism?
31.Amino acid metabolism 3.....................Nov 10
a.What are the key features of the urea cycle?
b.What are the structures and functions of PLP, THF and SAM?
32.Nucleotide structure (Chapter 19) .....................Nov 12
a.What are the structures of the major nucleotides?
33.Nucleotide metabolism (Chapter 19).....................F-Nov 14
a.What are thekey features of nucleotide metabolism?
QUIZ 11
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
9.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
10.THF is derived from
a.riboflavin
b.pantothenic acid
c.folic acid
d. citric acid
e. ascorbic acid
11. THF carries the following one carbon groups EXCEPT
a. -CH3
b. -CH2
c. -CH=O
d. CO2
12. The nitrogens in urea are derived from aspartic acid and
a. ala
b. gly
c. ammonium
d. citrulline
e. arg
13. In amino acid catabolism, the amino group is carried in the blood as
a. glu
b. gln
c. NH3
d.lys
e. asp
14. 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
15. The carbon skeletons required for amino acid synthesis are derived from all of the following except:
a. alpha-ketoglutarate
b. oxaloacetate
c. pyruvate
d. urea
e. PEP
16. The following coenzyme is required by transaminases
a. SAM
b. TPP
c. biotin
d. PLP
e. THF
17. What is required for this reaction?
R-NH3 ------------------> R-N(CH3 )3
a. SAM
b. TPP
c. biotin
d. PLP
e. NADH
18. Phenylalanine is catabolized to fumarate and acetoacetate (which is basically acetyl CoA)and is therefore
a. ketogenic
b. glucogenic
c. ketogenic and glucogenic
d. androgenic
e. none of the above
19. 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
20. The difference between uracil and thymine is that thymine has a ____ group
a. carboxyl
b. amino
c. methyl
d. sugar
e. phosphate
21. 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 22- 26, match the following:
a. 5' nucleotidase
b.thymidylate synthase
c. APRT
d. nucleoside kinase
e.phosphorylase
22. conversion of deoxy UMP into deoxy TMP
23. nucleosidase
24. remove phosphates from nucleotides
25. salvage pathway synthesis of purine nucleotides
26. interconvert nucleoside mono-, di-, and triphosphates.
27. 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
28. Pyrimidine ring atoms are derived from carbamoyl phosphate and
(a) ala (b) gly (c) asp (d) citrulline (e) ammonia
29. The following are intermediates of the urea cycle EXCEPT:
(a) ornithine (b) carbamoyl phosphate (c) citrulline (d) arginine (e) succinate
30. Pyridoxal phosphate has
(a) a thiol (b) a quaternary nitrogen (c) a ketone group (d) a carboxyl group (e) none of the above
----------------------------------------
Answers to quiz 11 (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
9.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
10.THF is derived from
a.riboflavin
b.pantothenic acid
c.folic acid
d. citric acid
e. ascorbic acid
11. THF carries the following one carbon groups EXCEPT
a. -CH3
b. -CH2
c. -CH=O
d. CO2
12. The nitrogens in urea are derived from aspartic acid and
a. ala
b. gly
c. ammonium
d. citrulline
e. arg
13. In amino acid catabolism, the amino group is carried in the blood as
a. glu
b. gln
c. NH3
d.lys
e. asp
14. 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
15. The carbon skeletons required for amino acid synthesis are derived from all of the following except:
a. alpha-ketoglutarate
b. oxaloacetate
c. pyruvate
d. urea
e. PEP
16. The following coenzyme is required by transaminases
a. SAM
b. TPP
c. biotin
d. PLP
e. THF
17. What is required for this reaction?
R-NH3 ------------------> R-N(CH3 )3
NOTE THAT THIS IS A METHYLATION REACTION.
a. SAM
b. TPP
c. biotin
d. PLP
e. NADH
18. Phenylalanine is catabolized to fumarate and acetoacetate (which is basically acetyl CoA) and is therefore
a. ketogenic
b. glucogenic
c. ketogenic and glucogenic
d. androgenic
e. none of the above
19. 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
20. The difference between uracil and thymine is that thymine has a ____ group
a. carboxyl
b. amino
c. methyl
d. sugar
e. phosphate
21. 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 22- 26, match the following:
a. 5' nucleotidase
b.thymidylate synthase
c. APRT
d. nucleoside kinase
e.phosphorylase
22. conversion of deoxy UMP into deoxy TMP (b)
23. nucleosidase (e)
24. remove phosphates from nucleotides (a)
25. salvage pathway synthesis of purine nucl
eotides (c)
26. interconvert nucleoside mono-, di-, and triphosphates. (d)
27. 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
28. Pyrimidine ring atoms are derived from carbamoyl phosphate and
a. ala
b. gly
c. asp
d. citrulline
e. ammonia
29. The following are intermediates of the urea cycle EXCEPT:
a. ornithine
b. carbamoyl phosphate
c. citrulline
d. arginine
e. succinate
30. Pyridoxal phosphate has
a. a thiol
b. a quaternary nitrogen
c. a ketone group
d. a carboxyl group
e. none of the above
Hi! Hope all is going well with this class! From lecture 20 to this point
is the material for exam 2. Best of luck!
34.DNA & RNA Structure 1 (Chapter 20).....................Nov 17
a.What are the main features of DNA structure?
b.How is DNA organized in a bacterium and a human cell?
c.How does the structure of RNA differ from that of DNA?
35. DNA Synthesis (replication) (Chapter 21).....................Nov 19
a.What are the mainsteps in the synthesis of DNA?
b.What is the reaction catalyzed by DNA polymerase?
36. RNA Synthesis (transcription) (Chapter 22)....................Nov 24
a.What are the mainsteps in the synthesis of RNA?
b.What is the reaction catalyzed by DNA polymerase?
c.Why are some genes copied so rapidly while others so slow?
d. What happens to RNA after it is synthesized (RNA processing)?
37. Protein Synthesis 1(translation) (Chapter 24).....................Nov 26
a.What are the major requirements for protein synthesis?
Nov 28 ; Thanksgiving recess
38. Protein Synthesis 2.....................Dec 1
a.How are amino acids activated?
b.What are the main steps in protein synthesis?
QUIZ 12 (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 (ie. one amino acid may have more than one codon)
C.overlapping
D.triplet
3. Protein synthesis on the ribosome requires the following except
A.DNA.
B.tRNA
C.EF
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 unwinding in replication is catalyzed by the enzyme:
A..DNA polymerase
B. RNA polymearse
C. primase
D. ligase
E. helicase
6. From the genetic code, what is the anticodon for Trp
A.CCA
B.ACC
C.CAC
D.CCC
E.AAC
7. 7. How many bases in an anticodon?
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 (small ribosomal subunit)
B. EF-Tu
C.IF
D. ligase
E.N-formylmethionine
9. Elongation factor which binds incoming tRNA. B
10. Protein involved in replication 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. Sites that are recognized by RNA polymerase (sigma subunit) which regulate the rate of transcription are called
A.anticodons
B.introns
C.exons
D.codons
E.promoters
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
Answers to quiz 11 (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 (ie. one amino acid may have more than one codon)
C.overlapping
D.triplet
3. Protein synthesis on the ribosome requires the following except
A.DNA.
B.tRNA
C.EF
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 unwinding in replication is catalyzed by the enzyme:
A..DNA polymerase
B. RNA polymearse
C. primase
D. ligase
E. helicase
6. From the genetic code, what is the anticodon for Trp
A.CCA
B.ACC
C.CAC
D.CCC
E.AAC
7. How many bases in an anticodon?
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 (small ribosomal subunit)
B. EF-Tu
C.IF
D. ligase
E.N-formylmethionine
9. Elongation factor which binds incoming tRNA. B
10. Protein involved in replication 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. Sites that are recognized by RNA polymerase (sigma subunit) which regulate the rate of transcription are called
A.anticodons
B.introns
C.exons
D.codons
E.promoters
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
39. EXAM 2: 30 multiple choice questions (50 minutes;lectures 20-33)........Dec 3
40. Review....................Dec 5
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MONDAY DEC 8/12 Noon-1:00 p.m.
Final ACS (American Chemical Society) examination is comprehensive .
In the past, there were 60 questions in this examinaiton.
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