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
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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
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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
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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
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Answers to quiz 9: (answers in blue)
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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