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to accompany
Biochemistry, Fifth Edition
Richard I. Gumport
College of Medicine at Urbana-Champaign,
University of Illinois
Frank H. Deis
Rutgers University
Nancy Counts Gerber
San Francisco State University
Expanded Solutions to Text Problems
contributed by
Roger E. Koeppe, II
University of Arkansas at Fayetteville
W. H. Freeman and Company
New York
eISBN: 0-7167-9758-5
© 2002 by W. H. Freeman and Company
No part of this book may be reproduced by any mechanical, photographic, or electronic process, or in the form of a phonographic recording, nor may it be stored in a retrieval system, transmitted, or otherwise
copied for public or private use, without written permission from the
Chapter 1: Prelude
Chapter 2: Biochemical Evolution
Chapter 3: Protein Structure and Function
Chapter 4: Exploring Proteins
Chapter 5: DNA, RNA, and the Flow of Genetic Information
Chapter 6: Exploring Genes
Chapter 7: Exploring Evolution 105
Chapter 8: Enzymes: Basic Concepts and Kinetics
Chapter 9: Catalytic Strategies
Chapter 10: Regulatory Strategies: Enzymes and Hemoglobin
Chapter 11: Carbohydrates
Chapter 12: Lipids and Cell Membranes
Chapter 13: Membrane Channels and Pumps
Chapter 14: Metabolism: Basic Concepts and Design
Chapter 15: Signal-Transduction Pathways: An Introduction to Information Metabolism
Chapter 16: Glycolysis and Gluconeogenesis
Chapter 17: The Citric Acid Cycle
Chapter 18: Oxidative Phosphorylation
Chapter 19: The Light Reactions of Photosynthesis
Chapter 20: The Calvin Cycle and the Pentose Phosphate Pathway
Chapter 21: Glycogen Metabolism
Chapter 22: Fatty Acid Metabolism
Chapter 23: Protein Turnover and Amino Acid Catabolism
Chapter 24: The Biosynthesis of Amino Acids
Chapter 25: Nucleotide Biosynthesis
Chapter 26: The Biosynthesis of Membrane Lipids and Steroids
Chapter 27: DNA Replication, Recombination, and Repair
Chapter 28: RNA Synthesis and Splicing
Chapter 29: Protein Synthesis
Chapter 30: The Integration of Metabolism
Chapter 31: The Control of Gene Expression
Chapter 32: Sensory Systems
Chapter 33: The Immune System
Chapter 34: Molecular Motors
Opening a comprehensive biochemistry text for the first time can be a daunting experience for a neophyte. So much detailed material is presented that it
is natural to wonder if you can possibly master it in one or two semesters of
study. Of course, you can’t learn everything, but experience indicates that you
can, indeed, learn the fundamental concepts in an introductory biochemistry
course. We have written this Student Companion for Biochemistry to ease your
entry into the exciting world of biochemistry.
Your goal is to “know” and “understand” biochemistry. Unfortunately,
awareness of these grand goals offers no practical help in reaching them, because they are such high-level and complex intellectual processes. In addition,
it is difficult for you to know to what extent you have attained them. We have
found that, by subdividing these goals into simpler ones and expressing them
in terms of demonstrable behaviors, you can begin to approach them and, in
addition, can readily assay your progress toward reaching them. Thus, a part
of each chapter consists of Learning Objectives that ask you to do things that
will help you to begin to understand biochemistry. When you can master the
objectives, you are well on your way to learning the material in the chapter.
It is important to add a cautionary note here. Being able to respond to all the
objectives adequately does not mean that you know biochemistry, for they are
a limited sampling of all the possible objectives; more to the point, they do
not explicitly require such higher-level activities as creation, analysis, integration, synthesis, problem-solving, evaluation, application, and appreciation.
These more advanced skills will develop to varying levels as you continue your
studies of biochemistry beyond the introductory stage.
Each chapter in the Companion consists of an introduction, Learning
Objectives, a Self-Test, Answers to Self-Test, Problems, Answers to Problems,
and Expanded Solutions to Text Problems. The introduction sets the scene,
places the chapter material in the context of what you have already learned,
and reminds you of material you may need to review in order to understand
what follows. The Learning Objectives are presented in the order that the information they encompass appears in Biochemistry. Key Words—important
concepts or vocabulary—are italicized in the objectives. Self-Test questions,
requiring primarily information recall, are followed by the answers to the
questions. A Problems section, in which more complex skills are tested, is
followed by answers to the problems. Finally, Expanded Solutions to end-ofchapter problems in the text are presented.
The Companion may be used in many ways, and as you begin your
studies you will develop the “system” that is best for you. Over 30 years of
experience teaching introductory biochemistry to first-year medical students
has suggested one pathway that you should consider. Start by reviewing the
prerequisite chapters mentioned in the introduction and skim the Learning
Objectives to obtain an overview of what you are to learn. Some students like also to skim
the Self-Test questions at this time to form an impression of the levels of difficulty and the
kinds of questions that will be asked. Next, read the chapter in Biochemistry, using the
Learning Objectives to help direct you to the essential concepts. Note the Key Words and look
up those you don’t know. Then attempt to meet the objectives. When you cannot satisfy an
objective, reread the relevant section of the text. You should now take the Self-Test to check
your ability to recall and apply what you have learned. Finally, solve the Problems, which
have been designed to further test your ability to apply the knowledge you have gained. It is
not sufficient simply to read the problems and look at the answers to see if you would have
done them the same way. You must struggle through the solutions yourself to benefit from
the problems. As you are using the Companion, you will, of course, be integrating what you
have learned from your studies and your lectures or laboratory exercises.
Besides helping you to learn biochemistry, you will find the Companion useful in studying for examinations. Go over each of the Learning Objectives in the chapters covered by an
exam to ensure that you can respond to it knowledgeably. Similarly, review the Key Words.
Decide which chapter topics you feel uncertain about and reread them. This protocol, coupled with a review of your lecture and reading notes, will prepare you well for examinations.
It is important to talk about biochemistry with others in order to learn the pronunciation of scientific terms and names and to help crystallize your thinking. Also, realize that although biochemistry has a sound foundation and we understand much about the chemistry
of life, many of our concepts are hypotheses that will require modification or refinement as
more experimental evidence accrues. Alternative and sometimes contradictory explanations
exist for many biochemical observations. You should not regard the material in Biochemistry
or the Companion as dogma, and you should, wherever possible, attempt to read about any
given topic in at least two sources. Try to follow up topics that particularly interest you by
reading about them in the scientific literature. References are given in Biochemistry, and your
instructor can help you locate research and review articles. In this way, you can begin to appreciate the diversity of opinion and emphasis that exists in the field of biochemistry.
The authors welcome readers’ comments, especially those drawing our attention to errors in the text. Comments should be sent to:
Professor Richard I. Gumport
Department of Biochemistry
University of Illinois
600 S. Mathews Avenue
Urbana, Illinois 61801-3792
The Student Companion has its origins in a curriculum guide that was initiated over 30 years ago for first-year medical students studying biochemistry
at the College of Medicine of the University of Illinois at Urbana-Champaign.
A number of colleagues have contributed to the Companion over the years.
We especially wish to thank Ana Jonas, Richard Mintel, and Carl Rhodes, who
were authors on previous editions, for their contributions of concept and content, which we continue to use. We also thank our colleagues Fumio
Matsumura, Gaetano Montelione, and Robert Niederman in the Department
of Molecular Biology and Biochemistry at Rutgers University. We also thank
John Clark, Lowell Hager, Walter Mangel, William McClure, and Robert
Switzer for their efforts in helping to develop the initial curriculum guide.
Special thanks go to George Ordal and James Kaput, our fellow teachers of
biochemistry at the College of Medicine. We thank Gordon Lindberg and
Chad Thomas for their careful reading and insightful contributions to the
book. We also thank William Sorlie for educating us to the value of learning
objectives. Thanks are also due to the many students who took the time to
criticize the Companion. Finally, RIG appreciates the sustained support provided our teaching efforts by the Department of Biochemistry and the College
of Medicine at the University of Illinois.
Richard I. Gumport
Frank H. Deis
Nancy C. Gerber
The woods are lovely, dark, and deep,
But I have promises to keep,
And miles to go before I sleep,
And miles to go before I sleep.
Prelude: Biochemistry
and the Genomic Revolution
he introductory chapter of Biochemistry begins by describing recent advances in
this exciting branch of science. We now know the complete genome sequences
for several species, and have a nearly complete sequence for human DNA. The
implications for biology and medicine are enormous, and they are touched on in this
chapter. The authors begin with a brief explanation of the structures of DNA, RNA,
and proteins. The unity of biochemistry is an important concept. It means that we
can learn about human biochemistry by studying mice, yeast, bacteria, or any living organism. Many biochemical interactions depend on weak noncovalent interactions. Because the great majority of biochemical processes occur in water, the
properties of water and their effects on biomolecules are also described. Then follows a discussion of entropy, energy, and the laws of thermodynamics. This provides
a basis for understanding hydrophobic interactions and protein folding. Then the
authors highlight the impact of biochemistry on modern biology and medicine.
Finally, an appendix presents the most popular molecular models and other representations used by biochemists.
When you have mastered this chapter, you should be able to complete the following objectives.
DNA Illustrates the Relation Between Form and Function (Text Section 1.1)
1. Recognize, name, and draw the four bases used in DNA, and explain the structure of the
sugar phosphate backbone.
2. Discriminate between the larger bases, A and G, and the smaller bases, C and T.
3. Describe how the DNA bases pair with each other. Notice that “larger” always pairs
with “smaller.”
4. Explain how base pairing provides an accurate means for reproducing DNA sequences.
5. Compare the structure of RNA to that of DNA.
6. Define the terms transcribe and translate.
7. Explain how proteins relate the one-dimensional world of sequence information to the
three-dimensional world of biological function.
Biochemical Unity Underlies Biological Diversity (Text Section 1.2)
8. Describe the evidence for the common origin of all life on Earth.
9. Differentiate between Archaea, Eukarya, and Bacteria.
Chemical Bonds in Biochemistry (Text Section 1.3)
10. Define the terms covalent bond, resonance structures, and arrow pushing.
11. List the three kinds of noncovalent bonds that mediate interactions of biomolecules and
describe their characteristics.
12. Describe how the properties of water affect the interactions among biomolecules.
13. Explain the origin of hydrophobic attractions between nonpolar molecules and give examples
of their importance in biochemical interactions.
14. State the first and second laws of thermodynamics. Define the entropy (S) and enthalpy (H)
of a system, and give their mathematical relationship.
15. Explain how protein folding is affected by changes in entropy and free energy.
Biochemistry and Human Biology (Text Section 1.4)
16. Discuss the most important achievements of biochemistry in the elucidation of the molecular
basis of life and in the advancement of modern biology and medicine.
Appendix: Depicting Molecular Structures
17. Explain the uses of different molecular models.
18. Relate the planar Fischer projection to the tetrahedrally arrayed substituents around a carbon atom.
DNA Illustrates the Relation Between Form and Function
1. Which base is NOT found in DNA’s building blocks?
(a) uracil
(d guanine
(b) thymine
(e) adenine
(c) cytosine
2. The DNA sequence AAA would pair with the sequence
(a) AAA.
(c) CCC.
(b) GGG.
(d) TTT.
3. RNA differs from DNA because RNA (select all correct answers)
(a) is usually single stranded.
(b) often base-pairs with itself (intrastrand pairing).
(c) uses deoxyribose instead of ribose.
(d) uses uracil instead of thymine.
(e) forms a triple helix instead of a double helix.
4. In the genetic code, a sequence of how many bases codes for one amino acid?
(a) 2
(c) 5
(b) 3
(d) 7
Biochemical Unity Underlies Biological Diversity
5. Which of the following molecular patterns or processes are common to both bacteria
and humans?
(a) development of tissues
(b) information flow from proteins to DNA
(c) the “energy currency”
(d) genetic information flow
(e) similar biomolecular composition
6. The distinguishing feature of the Eukarya is that
(a) they are all multicellular.
(b) they have tough cell walls around each cell.
(c) they have a well-defined nucleus within each cell.
(d) they are more primitive than the Archaea or the Bacteria.
Chemical Bonds in Biochemistry
7. For the bonds or interactions in the left column, indicate all the characteristics in the
right column that are appropriate.
(a) electrostatic interaction
(1) requires nonpolar species
(b) hydrogen bond
(2) involves charged species only
(c) van der Waals bond
(3) requires polar or charged species
(d) hydrophobic interaction
(4) involves either O and H or N and H
(5) involves polarizable atoms
(6) is also called a salt bridge
(7) exists only in water
(8) is optimal at the van der Waals contact
(9) has an energy between 3 and 7 kcal/mol
(10) has an energy of around 1 kcal/mol
(11) is weakened in water
8. The properties of water include
(a) the ability to form hydrophobic bonds with itself.
(b) a disordered structure in the liquid state.
(c) a low dielectric constant.
(d) being a strong dipole, with the negative end at the O atom.
(e) a diameter of 5 Å.
9. Biological membranes are made up of phospholipids, detergent-like molecules with
long nonpolar chains attached to a polar head group. When isolated phospholipids are
placed in water, they associate spontaneously to form membrane-like structures.
Explain this phenomenon.
10. If two molecules had a tendency to associate with each other because groups on their
surfaces could form hydrogen bonds, what would be the effect of putting these molecules in water? Explain.
11. Which of the following statements is correct? The entropy of a reaction refers to
(a) the heat given off by the reaction.
(b) the tendency of the system to move toward maximal randomness.
(c) the energy of the transition state.
(d) the effect of temperature on the rate of the reaction.
12. What are the three main noncovalent interactions that contribute to the folding of proteins into specific shapes?
Biochemistry and Human Biology
13. According to the chapter, which diseases are understood at a molecular level because of
advances in biochemistry and molecular biology?
(a) sickle-cell anemia
(b) cystic fibrosis
(c) hemophilia
(d) alcoholism
(e) schizophrenia
Appendix: Depicting Molecular Structures
14. Match the types of molecular models in the left column with the appropriate application
in the right column.
(a) space-filling model
(1) shows the bond framework in macro
(b) ball-and-stick model
(2) indicates the volume occupied by a bio(c) skeletal model
(3) shows the bonding arrangement in
small biomolecules
15. Hydrogen atoms are frequently omitted from ball-and-stick models and skeletal models
of biomolecules. Explain why.
1. a
2. d
3. a, b, d
4. b
5. c, d, e
6. c
7. (a) 2, 6, 9, 11 (b) 3, 4, 9, 11 (c) 5, 8, 10 (d) 1, 7. Hydrophobic interactions are
strengthened in water.
8. d
9. When the nonpolar chains of the individual phospholipid molecules are exposed to
water, they form a cavity in the water network and order the water molecules around
themselves. The ordering of the water molecules requires energy. By associating with one
another through hydrophobic interactions, the nonpolar chains of phospholipids release
the ordered water by decreasing the total surface area and hence reduce the energy required to order the water. Such coalescence stabilizes the entire system, and membranelike structures form.
10. Because of the high dielectric constant of water and its ability to form competing hydrogen bonds, the interaction between the molecules would be weakened.
11. b
12. The book mentions the hydrophobic effect, hydrogen bonds, and van der Waals interactions as contributing to protein folding.
13. a, b, c. After many decades of work, the puzzle of human alcoholism and schizophrenia have evaded easy biochemical explanation. There is good evidence of genes
that produce increased alcohol consumption in experimental animals. In humans, free
will gets in the way of clear experimental results. The genetics of alcohol preference
in mice is discussed in an article from Lee M. Silver’s lab in Mamm. Genome 9 (1998):
942 by J. L. Peirce et al., and in Chapter 18 of the excellent book Time, Love, Memory,
by Jonathan Weiner.
14. (a) 2, (b) 3, (c) 1
15. The ball-and-stick model and skeletal model best show the bonding arrangements and
the backbone configurations of biomolecules; the inclusion of the numerous hydrogen
atoms would obscure the very features revealed by these models.
1. Proteins have 20 building blocks (amino acids) and DNA has only four (nucleotides),
yet the “messages” in the two sequences have the same information content and are
translatable. Could there be an informational molecule with even fewer than four
building blocks?
2. The three roles of RNA described in the text all deal with protein synthesis, that is, making chains of amino acids having the correct sequence. Describe the three jobs of RNA
in this process.
3. As will be seen in succeeding chapters, enzymes provide a specific binding site for substrates where one or more chemical steps can be carried out. Often these sites are designed to exclude water. Suppose that at a binding site, a negatively charged substrate
interacts with a positively charged atom of an enzyme.
(a) Using Coulomb’s equation, show how the presence of water might affect the interaction.
What sort of environment might be preferable for an ionic interaction? Note that a numerical answer is not required here.
(b) How would an ionic interaction be affected by the distance between the oppositely
charged atoms?
4. In some proteins the contact distance between an amide hydrogen and a carbonyl oxygen that are participating in hydrogen binding is somewhat less than expected from
adding their respective van der Waals contact distances. What feature of hydrogen bonding allows the two atoms to be closer to each other?
5. Water molecules have an unparalleled ability to form hydrogen bonds with one another.
Water also has an unusually high heat capacity, as measured by the amount of energy required to increase the temperature of a gram of water by 1ºC. How does hydrogen bonding contribute to water’s high heat capacity?
6. The oxygen-carrying protein myoglobin is composed of 153 amino acids, linked by covalent bonds into an unbranched polymeric chain. If all amino acids in the chain assume
a regular and periodic conformation in which each residue is separated from the next by
a distance of 1.5 Å, then the molecule could be as long as 230 Å (153 residues × 1.5 Å
per residue). Analysis of the myoglobin molecule in solution reveals that it is no more
than 45 Å in length. What does this observation tell you about how a linear polymer of
amino acids might behave in solution?
7. The Second Law of Thermodynamics states that the entropy (disorder) of a system and
its surroundings always increases for a spontaneous process. So why do proteins fold up
spontaneously? It is evident that protein folding moves from a disorderly state (randomly
unfolded proteins) to an orderly state (folded proteins). Explain.
8. The text states that genetically engineered bacteria can be used as “factories” to produce
insulin and other valuable proteins. Where did insulin come from for the treatment of
diabetes before genetic engineering was developed?
1. A good analogy is the alphabet (26 letters) versus Morse Code (three symbols—dot, dash,
and space). Any thought that can be expressed in English can be written out using the
26 letters, or can be translated into Morse Code. The Morse Code requires a longer string
of symbols to express the same message as the alphabet, but it works. So we could imagine as few as two symbols—when letters are encoded in a computer, the storage is binary, with each bit being “off” or “on.”
2. RNA provides the “factory” for protein synthesis—the ribosome is about half RNA, and
owes its functionality to ribosomal RNA. It provides the “message” or “blueprint” for
every protein synthesized, in the form of mRNA or messenger RNA. And it “translates”
the mRNA message into amino acids using “adaptor” molecules of transfer RNA, which
bring the amino acids one by one into the ribosome “factory.”
3. (a) The magnitude of the electrostatic attraction would be diminished by the presence of water because D, the dielectric constant, is relatively high for water.
Inspection of Coulomb’s equation shows that higher values of D will reduce the
force of the attraction. Lower values, such as those for hydrophobic molecules
like hexane, allow a higher value for F. We shall see that many enzyme active
sites are lined with hydrophobic residues, creating an environment that enhances
ionic interaction.
(b) Inspection of Coulomb’s equation also reveals that the force between two oppositely
charged atoms will vary inversely with the square of the distance between them.
4. Both atoms have partial charges that attract each other. The single electron of the hydrogen atom is partially shifted to the nitrogen atom to which the hydrogen is covalently
bound. As a result, the distance between the electronic shells of the hydrogen and the
carbonyl oxygen is reduced, allowing them to approach each other more closely.
5. When water is heated, considerable energy is required to break the hydrogen bonds.
Only after a large percentage of bonds are broken are the molecules more mobile and
the temperature raised. This buffering capacity of water is very important to cells,
which can resist changes caused by increases in temperature because of water’s high
heat capacity.
6. Because the length of the myoglobin molecule in solution is much less than its extended length, it is likely that the polymeric chain is folded into a compact structure.
This conclusion was first reached in the 1930s when studies on the radius of gyration of certain proteins showed that they are shorter than their predicted length. The
globular structure of a soluble protein was visualized in detail by John Kendrew in
1957 when he used x-ray analysis to show that myoglobin is an assembly of rodlike
chains with overall dimensions of 45 × 35 × 25 Å. It is now well established that most
soluble proteins fold into globular, compact structures in solution. Discussion of those
folded structures as well as how they undergo folding will be discussed at length in
the text. (Kendrew, J. C. et al., Nature 181[1958]:662 .)
7. As explained in the chapter—folded globular proteins have a hydrophobic interior. The
process of folding releases water molecules, which would have been otherwise kept hydrogen bonded to the protein chain. Thus the “surroundings” have an increased entropy
although the “system”—the protein itself—has a decrease. The negative (favorable) enthalpy changes when weak bonds form as a protein folds correctly also tend to result in
a favorable (negative) free-energy change.
8. Insulin had to be purified from cow, sheep, pig, etc. The pancreatic glands were collected
from slaughter-houses. It was not unusual for people to develop allergies to these foreign types of insulin. Modern methods allow production of the human form of insulin
in large quantities and high purity, a very clear improvement over the old system.
Biochemical Evolution
he authors have used evolution as the unifying theme of this book. The present
chapter is an ambitious attempt to illustrate how all aspects of cellular functioning can be better understood from an evolutionary perspective. Truly mastering
the breadth of information touched on here may be difficult but the reward will be a
more basic, thorough, and intuitive grasp of the whole remainder of the book.
The origin of life is considered in four stages—generation of biomolecules, transition to replicating systems, interconversion of light and chemical energy, and adaptability to change. This discussion is theoretical, since the origins are obscure and hard
data is lacking about actual mechanisms.
Evolution requires three properties: a system must reproduce, there must be variation, and there must be competition in a selective environment. Any system that satisfies these requirements will evolve, whether pure RNA in solution with a replicating
enzyme, or a population of cells or higher plants and animals.
After touching on ribozymes as evidence that life passed through an “RNA
World” stage, the authors illustrate how duplication and variation led to the many
features of modern cells including DNA genes, ATP, lipid membranes, ion pumps, energy transducers, receptors with second messengers, etc. Cells have to move, either
with flagella (procaryotes) or by changing shape using microfilaments, microtubules,
and molecular motors (eucaryotes). Multicellular organisms require cells to differentiate according to developmental programming and signals from neighboring cells.
All life on Earth came from a single progenitor, so we can learn about human biochemistry by studying any species, even simple single-celled organisms.
When you have mastered this chapter, you should be able to complete the following objectives.
Key Organic Molecules Are Used by Living Systems (Text Section 2.1)
1. List the four stages leading from inert chemicals to modern living cells.
2. Explain the Urey-Miller experiment, and diagram the apparatus. Describe the major
products produced by this experiment.
Evolution Requires Reproduction, Variation, and Selective Pressure
(Text Section 2.2)
3. Identify the three principles necessary for evolution to occur.
4. Describe Spiegelman’s experiment with Qb RNA. Understand how the three principles
of evolution are included in this experiment.
5. Most enzymes are composed of protein. Explain how ribozymes differ from more normal enzymes.
6. Describe what is meant by a “hammerhead ribozyme.”
7. Explain how RNA bases are derived from amino acids.
8. Explicate the advantages that polymers of amino acids have over nucleic acid polymers
in providing catalysis for the cell.
9. Describe the roles of mRNA, tRNA, and rRNA in protein synthesis. Know that three
mRNA bases are required to code for a single amino acid.
10. Ribosomal catalysis of peptide bond synthesis is mediated by regions of rRNA, and not
by protein. Understand the implications of this catalysis for the concept of an RNA World.
11. Recall the three principles necessary for evolution as defined in Section 2.2. With these in
mind, explain how the genetic code is ideally suited as a medium for evolutionary change.
12. Transfer RNAs all have very similar structures with minor variations that lead to significant differences in function. This is a common phenomenon in biochemistry. Describe
how this situation would arise.
13. Explain the advantages of DNA compared to RNA for long-term storage of information.
14. The building blocks of DNA are made directly from the building blocks of RNA.
Understand that this leads to the deduction that RNA must be older than DNA.
15. Define transcription and translation.
Energy Transformations Are Necessary to Sustain Living Systems
(Text Section 2.3)
16. Describe the similarities between ATP production and use, and the function of money
in society. You should appreciate the fact that this leads to the description of ATP as
“energy currency” in the cell.
17. Describe the properties of a cell membrane that are responsible for keeping important
cellular constituents (enzymes, nucleic acids, ATP, etc.) inside.
18. Define osmosis, ion pump, and ion gradient.
19 Describe the process of photosynthesis in general terms. Understand why photosynthesis must be membrane-associated.
20. Write the equation for the oxidation of water to oxygen.
21. Understand why oxygen is described as “toxic.”
22. Know how many ATPs are produced per glucose consumed when using oxygen in glucose metabolism.
Cells Can Respond to Changes in Their Environments (Text Section 2.4)
23. Describe how E. coli responds when arabinose is the only source of carbon.
24. Define second messenger and signal transduction. Name two second messengers.
25. Distinguish between flagella, microfilaments, and microtubules.
26. Identify what happens on a molecular level when cells change shape.
27. Define cell differentiation.
28. Describe how the slime mold Dictyostelium uses signaling and changes in cell differentiation to respond to varying conditions. Understand that cAMP acts as a messenger (not
a second messenger) for Dictyostelium.
29. Give a general description of how development is controlled in C. elegans. Notice the total
number of cells in an adult human, and contrast that with the number of cells in C. elegans.
30 Know why understanding enzymes and processes in single-celled organisms like yeast
or E. coli help us understand how human cells work.
31. Examine the time line in Figure 2.27, and explain during what time frame single-celled
anaerobes would have dominated life on Earth.
Key Organic Molecules Are Used by Living Systems
1. A reducing atmosphere as described in this chapter would not contain significant
amounts of
a. CH4
d. H2O
b. CO2
e. H2
c. NH3
Evolution Requires Reproduction, Variation, and Selective Pressure
2. What would happen in Spiegelman’s experiment with Qb RNA if no selective conditions
were imposed (inhibitors, limited time, etc.)? Would a variety of different RNAs still arise?
3. Does RNA self-replicate?
4. Which amino acid is not mentioned in textbook Figure 2.6 as a source for synthesis of
RNA bases?
a. glutamine
d. serine
b. glycine
e. none of the above
c. aspartic acid
5. Are ribozymes (RNA enzymes) theoretical or laboratory constructs, or are they present
in cells today?
6. Which building block helps maintain the informational integrity of DNA?
a. uracil
d. cytosine
b. adenine
e. guanine
c. thymine
Energy Transformations Are Necessary to Sustain Living Systems
7. Osmosis tends to equalize concentrations on both sides of a membrane. Any living cell
will have protein and nucleic acid inside, which “draws” water inward. To prevent bursting, concentration of something inside the cell has to be made lower than the concentration outside. Concentration of what? How is this adjustment made?
8. Would the structure of an ion-driven ATP synthase have to be different from that of an
ATP-driven ion pump?
9. What is the advantage to the use of oxygen in metabolism?
Cells Can Respond to Changes in Their Environments
10. What signal causes aggregation of Dictyostelium slime mold amoebae into mobile slugs?
11. Actin is an important part of human muscle. It is equally important in other species
including amoebas and slime molds. Is it surprising to find the same protein in such
diverse species?
1. b. CO2. Interestingly, modern theories based on observations of atmospheres of other
planets, and observations of the geochemistry of early minerals, hold that there was much
more carbon dioxide (CO2) than hydrogen (H2) in the Earth’s early atmosphere.
2. Yes. Variability should remain constant, but the variant RNAs would presumably remain in low concentrations or disappear, and the original RNA would probably remain
3. No. Despite much work to find a self-replicating RNA, the replication always requires
the presence of protein. Recent work by David P. Bartel at MIT is showing some promise toward finding an RNA replicase ribozyme (Science 292[5520]:1319). The fact that
an RNA replicase may be produced in the laboratory does not, of course, prove that the
ribozyme existed in nature.
4. d. Serine. In modern cells, the glycine plus two of the other carbons of the purine ring
can originate as parts of the amino acid serine.
5. Ribozymes are easy to find in modern cells, and probably the most abundant one is the
ribosome where peptide bonds are formed. Several others exist including certain ribonuclease enzymes.
6. c. Thymine. All of the other building blocks are found in RNA. Uracil is only found in
RNA. Thymine replaces it in DNA.
7. Small ions including sodium and protons (H;) are routinely pumped out of the cell. This
allows the outward osmotic pressure generated by the ions to match the inward pressure generated by cellular macromolecules.
8. No. In fact, textbook Figures 2-16 and 2-17 depict the same system functioning inward
or outward. And in living cells the structures are the same or very similar.
9. While aerobic cells have to have protection against oxygen damage, the rewards for dealing with oxygen are great. As stated in the text, glucose metabolism using oxygen affords
15 times as much ATP as anaerobic glucose metabolism. Thus anaerobes have to ingest
15 times as much sugar to do the same work as aerobes. Use of other fuels also produces
much more ATP in aerobic cells. It is also true that using oxygen as an electron acceptor can aid in maintenance of a proton gradient.
10. Cyclic AMP causes the cells to aggregate into a multicellular organism. cAMP is found
as a kind of “hunger signal” in many different organisms, from procaryotes to man.
11. Considering the “Unity of Biochemistry” perhaps it is more surprising that actin does not
appear to play the same role in procaryotic cells. But actin is found in essentially all eucaryotes in a similar role, often paired with myosin as the contractile apparatus.
1. Stanley Miller’s experiments are called the “Primordial Soup Theory.” There are other
schools of thought not mentioned in the chapter, notably Günter Wächtershäuser’s Pyrite
World. He suggests that early life might have lived in the hot sulfur-rich environment near
deep volcanic vents, and that precellular reactions could have taken place on the surface
of pyrite crystals. One disadvantage is the extreme heat and pressure—over 110ÚC—but
that environment is rich in life today. Can you think of other advantages or disadvantages
of the Pyrite Theory versus the Soup Theory?
2. The RNA from Phage Qb was shown to evolve in an artificial system with no membranes
or cells. Why is it so important that organisms should have had membranes for them to
evolve efficiently? What is the difference?
3. The antibiotic peptide, gramicidin, is assembled (in modern cells) without the use of
RNA. Peptide bonds are formed after the amino acids are activated by attachment to sulfur on the enzyme surface. Does this suggest an alternative, or a precursor, to the RNA
world described in the chapter?
4. RNA bases are built from amino acids. Thus amino acids (which are produced in the
Urey Miller experiment) are older than RNA building blocks (which are not produced
in this experiment). Is it reasonable that the only use to which amino acids were put was
synthesis of RNA building blocks?
5. DNA has a remarkable ability to preserve complex information perfectly intact for millennia. Would it be a favorable situation if DNA could always be reproduced with absolutely no errors, and never had any mutations?
6. Theorists of the RNA World have debated whether the constituents of the cell arose in the
sequence RNA-DNA-Protein or RNA-Protein-DNA. The universal use of ribonucleotide
reductase enzymes provided an answer to this question. Can you see why?
7. If arabinose is the only source of carbon, E. coli cells utilize it for metabolism. The system described in this chapter apparently is driven only by the presence of arabinose.
What if glucose and arabinose are present in equal concentrations? The arabinose
would not be the “sole source.” Is there an implication that the cell also checks for the
absence of glucose?
8. Scientists know that the Earth’s early oceans around three billion years ago were very
rich in dissolved iron salts, including ferrous chloride (FeCl2). Many ferric compounds,
including ferric oxide (Fe2O3), are rather insoluble in water. Given these facts, what kind
of hard evidence would you look for to prove that oxygen entered the atmosphere about
two billion years ago, as shown in textbook Figure 2.27?
1. One major advantage of the “hot deep” origin of life is the fact that at volcanic vents,
one finds metal sulfides that would be insoluble at cooler temperatures, and hydrogen sul fide gas (H 2 S). These can combine to form pyrite or “Fool’s Gold”
(H2S+FeSDFeS2+H2). Thus a deep-sea volcanic vent is a reducing environment (with electrons from hydrogen [H2]), and spontaneous synthesis of both amino
acids and peptides has been observed in laboratory simulations of this environment.
Much of the work and theory has come from the collaboration of Claudia Huber and
Günter Wächtershäuser (recent papers published in Science). It is especially important to identify a terrestrial system with reducing properties now that the Earth’s early
atmosphere is thought to have been a CO2 greenhouse and not reducing at all. The
obvious disadvantage is that organic compounds can be destroyed by the extremely
hot environment. But the fact that there are abundant living organisms at the vents
illustrates that this is a problem that life has solved. (Huber & Wächtershäuser. Science
281[5377]: 670.)
2. Spiegelman’s RNA system with a replicase enzyme is very artificial; there is only one molecule being reproduced. A living cell has many constituents, and part of the competition
in evolution involves which cell has the best mixture of constituents. The whole organism must evolve, with all its parts. This cannot happen in a “soup”; it requires individuals surrounded by a barrier, hence a membrane.
3. Yes, it does. While the thioester method of peptide synthesis used in making gramicidin
is cumbersome compared to RNA-directed peptide synthesis, it does suggest that proteins might be able to self-replicate. Several prominent theoreticians including Graham
Cairns-Smith, Freeman Dyson, Robert Shapiro, and the Nobel laureate Christian de Duve
see a period before the “RNA World” in which proteins are the dominant cellular macromolecule, and many aspects of metabolism would resemble what is seen in modern cells.
The use of ATP and other nucleotides as energy currency in a very primitive system
would lead naturally to an environment where RNA synthesis could occur spontaneously.
This is in contrast to the “Primordial Soup” where nucleotides would be unstable and
probably quite rare.
4. Not really. A system rich in amino acids would have at least some peptides. And there
are many processes that are easily catalyzed by simple proteins but have never been
demonstrated using RNA ribozymes. An example would be the sort of electron transfer
mediated by iron sulfur clusters. Cellular synthesis of purines and pyrimidines must be
very ancient, but it would seem likely that these are merely representatives of many other
processes involving amino acids and peptides.
5. No, it would not be favorable. While some critical genes, such as those for the histone
proteins found in the nuclei of eucaryotes, appear to remain pristine and never change,
in fact there must be variation that is ruthlessly trimmed by selection. A lack of variation, of mutation in the DNA, would lead to an end to evolution. We would be “stuck”
with the species that lived millions of years ago, or more accurately, “we” would never
have come into existence. Considering the fact that DNA must vary, it is quite interesting that some of the earliest microfossils found by J. William Schopf and others appear
to be cyanobacteria, or blue-green algae, which are morphologically almost identical to
pond-scum living today. This is despite the fact that one or two billion years separate the
fossils from the living examples (e.g., Entophysalis, living today, and Eoentophysalis, 2.1
billion years old [see Cradle of Life, Schopf, Princeton 1999, p. 229]).
6. The mere fact that DNA building blocks are made from RNA building blocks shows that
DNA is newer than RNA. But the fact that, universally, DNA building blocks are produced by a protein enzyme proves that protein also came before DNA. Note that it does
not resolve the question of whether the correct sequence is RNA-Protein-DNA or ProteinRNA-DNA. There are several other indications that DNA is a “recent” development, including RNA genomes in some viruses, and inconsistencies in DNA structure and usage.
There are some eucaryotic species (dinoflagellates) which use 5-Hydroxymethyluracil instead of Thymine, for example. The fact that DNA is bound to histones as chromatin in
most eucaryotes is very different from the way DNA is handled in procaryotes.
Freeland, Knight, & Landweber. Science 286(5440): 690.
7. Yes, there is. If there were no mechanism to check for the presence of glucose, then arabinose or other sugars would be utilized whenever they were present, and not only when
they were the “sole source.” In fact a second messenger mentioned in this chapter, cyclic
AMP, is generated when glucose is absent. This “hunger signal” then allows the use of
other sugars.
8. The evidence is as hard as iron! Geologists know that the best iron ore is found in
“banded iron formations,” which are usually in layers that were part of the ocean floor
around two billion years ago. These attractive red-layered formations represent the precipitation of most of the dissolved iron in the world’s oceans as hematite, magnetite, and
other insoluble ferric salts. The age of these layers can be clearly established by isotopic
dating. The emergence of more abundant oxygen is the only possible explanation for this
worldwide chemical reaction.
1. For alanine, the NH2 would come from NH3; CH3, CH, and the other carbon from CH4;
OH and the other oxygen from H2O. (Some hydrogens could also be replaced from H2
if lost in earlier oxidation reactions.)
2. The lone fast-replicating molecule will complete three “generations” for every replication
of the 99 other molecules. After n “generations,” each of 15 minutes duration, therefore,
one population will be (99)(2n), while the other population will be (1)(23n). The results
will be:
# Slow
# Fast
% Slow
% Fast
3. The more tightly bound nucleotide monomers would be more available for RNA replication and could therefore cause a faster rate of replication. This advantage would be
most important if the monomers were in short supply, that is, present only in low concentrations in the solution (environment).
4. Chemical or physical equilibrium between two compartments would require the same
ion concentrations in both compartments (a state of high entropy). To establish a gradient with unequal ion concentrations in the two compartments would require work to
impose more order on the system (and move the system to a state of higher energy and
lower entropy). (Consider also a bag of 100 red marbles and another equivalent bag that
has 100 green marbles. It requires less effort [energy] to allow the marbles to mix together in a single bag than it does to separate the mixture back into the original all-red
and all-green compartments.)
5. If a “gate” is opened to allow protons to flow out of the cell, then energy will be released.
If some of this energy could be captured for useful work, then the energy could be used
for pumping a second type of ion out of the cell? (E.g., a proton ATPase would couple
the synthesis of a high-energy bond in adenosine triphosphate (ATP) to the release of a
proton gradient; the chemical energy stored in the ATP could then be used for another
purpose, such as pumping the second ion.)
6. Eight protons, because the generation of hydroxide ion on one side is equivalent to the
generation of a proton on the other side.
7. Very hydrophobic molecules could cross the cell membrane without the assistance of a transport protein. For these molecules, therefore, only a gene-control protein would be needed.
8. From the early part of the time scale in Figure 2.26, it appears that there are between
five and seven cycles of approximately synchronous division before the respective cell
division rates diverge.
Protein Structure and Function
roteins are macromolecules that play central roles in all the processes of life.
Chapter 3 begins with a discussion of key properties of proteins and continues
with a description of the chemical properties of amino acids—the building
blocks of proteins. It is essential that you learn the names, symbols, and properties
of the 20 common amino acids at this point, as they will recur throughout the text
in connection with protein structures, enzymatic mechanisms, metabolism, protein
synthesis, and the regulation of gene expression. It is also important to review the behavior of weak acids and bases, either in the appendix to Chapter 3 or in an introductory chemistry text. Following the discussion of amino acids, the chapter turns
to peptides and to the linear sequences of amino acid residues in proteins. Next, it
describes the folding of these linear polymers into the specific three-dimensional
structures of proteins. The primary structure (or sequence of amino acids) dictates
the higher orders of structure including secondary (a, b, etc.), tertiary (often globular), and quaternary (with multiple chains). You should note that the majority of functional proteins exist in water and that their structures are stabilized by the forces and
interactions you learned about in Chapter 1. This chapter concludes with a discussion of the theory of how proteins fold, including attempts to predict protein folding
from amino acid sequences.
When you have mastered this chapter, you should be able to complete the following objectives.
1. List the key properties of proteins.
2. Explain how proteins relate one-dimensional gene structure to three-dimensional structure in the cell, and their complex interactions with each other and various substrates.
Proteins Are Built from a Repertoire of 20 Amino Acids (Text Section 3.1)
3. Draw the structure of an amino acid and indicate the following features, which are common to all amino acids: functional groups, side chains, ionic forms, and isomeric forms.
4. Classify each of the 20 amino acids according to the side chain on the a carbon as
aliphatic, aromatic, sulfur-containing, aliphatic hydroxyl, basic, acidic, or amide derivative.
5. Give the name and one-letter and three-letter symbol of each amino acid. Describe each
amino acid in terms of size, charge, hydrogen-bonding capacity, chemical reactivity, and
hydrophilic or hydrophobic nature.
6. Define pH and pKa. Use these concepts to predict the ionization state of any given amino
acid or its side chain in a protein.
7. State Beer’s Law. Understand how it can be used to estimate protein concentration.
Primary Structure: Amino Acids Are Linked by Peptide Bonds
to Form Polypeptide Chains (Text Section 3.2)
8. Draw a peptide bond and describe its conformation and its role in polypeptide sequences.
Indicate the N- and C-terminal residues in peptides.
9. Define main chain, side chains, and disulfide bonds in polypeptides. Give the range of
molecular weights of proteins.
10. Explain the origin and significance of the unique amino acid sequences of proteins.
11. Understand why nearly all peptide bonds are trans.
12. Define the f and y angles used to describe a peptide bond, and be able to read a
Ramachandran plot.
Secondary Structure: Polypeptide Chains Can Fold into Regular Structures
Such as the Alpha Helix, the Beta Sheet, and Turns and Loops (Text Section 3.3)
13. Differentiate between two major periodic structures of proteins: the a helix and the
b pleated sheet. Describe the patterns of hydrogen bonding, the shapes, and the dimensions of these structures.
14. List the types of interactions among amino acid side chains that stabilize the threedimensional structures of proteins. Give examples of hydrogen bond donors and acceptors.
15. Describe a-helical coiled coils in specialized proteins and the role of b turns or hairpin
turns in the structure of common proteins.
Tertiary Structure: Water-Soluble Proteins Fold into Compact Structures
with Nonpolar Cores (Text Section 3.4)
16. Using myoglobin and porin as examples, describe the main characteristics of native folded
protein structures.
Quaternary Structure: Polypeptide Chains Can Assemble
into Multisubunit Structures (Text Section 3.5)
17. Describe the primary, secondary, tertiary, and quaternary structures of proteins. Describe
The Amino Acid Sequence of a Protein Determines
Its Three-Dimensional Structure (Text Section 3.6)
18. Using ribonuclease as an example, describe the evidence for the hypothesis that all of the
information needed to specify the three-dimensional structure of a protein is contained
in its amino acid sequence.
19. Rationalize the conformational preferences of different amino acids in proteins and
20. Give evidence that protein folding appears to be a cooperative transition, and explain
why that means it is an “all or none” process.
21. Explain how protein folding proceeds through stabilization of intermediate states rather
than through a sampling of all possible conformations.
22. Discuss the methods and advances in the prediction of three-dimensional structures
of proteins.
23. List examples of the modification and cleavage of proteins that expand their functional roles.
Proteins Are Built from a Repertoire of 20 Amino Acids
1. (a) Examine the four amino acids given below:
Indicate which of these amino acids are associated with the following properties:
aliphatic side chain
basic side chain
three ionizable groups
charge of ;1 at pH 7.0
pK ~10 in proteins
secondary amino group
designated by the symbol K
in the same class as phenylalanine
most hydrophobic of the four
side chain capable of forming hydrogen bonds
(b) Name the four amino acids.
(c) Name the other amino acids of the same class as D.
2. Draw the structure of cysteine at pH 1.
3. Match the amino acids in the left column with the appropriate side chain types in the
right column.
(a) Lys
(1) nonpolar aliphatic
(b) Glu
(2) nonpolar aromatic
(c) Leu
(3) basic
(d) Cys
(4) acidic
(e) Trp
(5) sulfur-containing
(f) Ser
(6) hydroxyl-containing
4. Which of the following amino acids have side chains that are negatively charged under
physiologic conditions (i.e., near pH 7)?
(a) Asp
(d) Glu
(b) His
(e) Cys
(c) Trp
5. Why does histidine act as a buffer at pH 6.0? What can you say about the buffering capacity of histidine at pH 7.6?
Primary Structure: Amino Acids Are Linked by Peptide Bonds
to Form Polypeptide Chains
6. How many different dipeptides can be made from the 20 L amino acids? What are the
minimum and the maximum number of pK values for any dipeptide?
7. For the pentapeptide Glu-Met-Arg-Thr-Gly,
(a) name the carboxyl-terminal residue.
(b) give the number of charged groups at pH 7.
(c) give the net charge at pH 1.
(d) write the sequence using one-letter symbols.
(e) draw the peptide bond between the Thr and Gly residues, including both side chains.
8. If a polypeptide has 400 amino acid residues, what is its approximate mass?
(a) 11,000 daltons
(c) 44,000 daltons
(b) 22,000 daltons
(d) 88,000 daltons
9. Which amino acid can stabilize protein structures by forming covalent cross-links between polypeptide chains?
(a) Met
(d) Gly
(b) Ser
(e) Cys
(c) Gln
10. Discuss the significance of Ramachandran plots. Contrast the conformational states of Gly
and Pro in proteins compared with other amino acid residues.
Secondary Structure: Polypeptide Chains Can Fold into Regular Structures
Such as the Alpha Helix, the Beta Sheet, and Turns and Loops
11. Which of the following statements about the peptide bond are true?
(a) The peptide bond is planar because of the partial double-bond character of the bond
between the carbonyl carbon and the nitrogen.
(b) There is relative freedom of rotation of the bond between the carbonyl carbon and
the nitrogen.
(c) The hydrogen that is bonded to the nitrogen atom is trans to the oxygen of the carbonyl group.
(d) There is no freedom of rotation around the bond between the a carbon and the carbonyl carbon.
12. Which of the following statements about the a helix structure of proteins is correct?
(a) It is maintained by hydrogen bonding between amino acid side chains.
(b) It makes up about the same percentage of all proteins.
(c) It can serve a mechanical role by forming stiff bundles of fibers in some proteins.
(d) It is stabilized by hydrogen bonds between amide hydrogens and amide oxygens in
polypeptide chains.
(e) It includes all 20 amino acids at equal frequencies.
13. Which of the following properties are common to a-helical and b pleated sheet structures in proteins?
(a) rod shape
(b) hydrogen bonds between main-chain CO and NH groups
(c) axial distance between adjacent amino acids of 3.5 Å
(d) variable numbers of participating amino acid residues
14. Explain why a helix and b pleated sheet structures are often found in the interior of
water-soluble proteins.
Tertiary Structure: Water-Soluble Proteins Fold into Compact Structures
with Nonpolar Cores
15. Which of the following amino acid residues are likely to be found on the inside of a
water-soluble protein?
(a) Val
(d) Arg
(b) His
(e) Asp
(c) Ile
16. Which of the following statements about the structures of water-soluble proteins, exemplified by myoglobin, are not true?
(a) They contain tightly packed amino acids in their interior.
(b) Most of their nonpolar residues face the aqueous solvent.
(c) The main-chain NH and CO groups are often involved in H-bonded secondary
structures in the interior of these proteins.
(d) Polar residues such as His may be found in the interior of these proteins if the
residues have specific functional roles.
(e) All of these proteins contain b sheet structural motifs.
Quaternary Structure: Polypeptide Chains Can Assemble
into Multisubunit Structures
17. Match the levels of protein structures in the left column with the appropriate descriptions in the right column.
(a) primary
(1) association of protein subunits
(b) secondary
(2) overall folding of a single chain, can
(c) tertiary
include a-helical and b sheet structures
(d) quaternary
(3) linear amino acid sequence
(4) repetitive arrangement of amino acids
that are near each other in the linear
The Amino Acid Sequence of a Protein Determines
Its Three-Dimensional Structure
18. Which of the following statements are true?
(a) Ribonuclease (RNase) can be treated with urea and reducing agents to produce a
random coil.
(b) If one oxidizes random-coil RNase in urea, it quickly regains its enzymatic activity.
(c) If one removes the urea and oxidizes RNase slowly, it will renature and regain its
enzymatic activity.
(d) Although renatured RNase has enzymatic activity, it can be readily distinguished
from native RNase.
19. When most proteins are exposed to acidic pH (e.g., pH 2), they lose biological activity.
Explain why.
20. Which one of the following amino acids may alter the direction of polypeptide chains
and interrupt a helices?
(a) Phe
(d) His
(b) Cys
(e) Pro
(c) Trp
21. If we know that a solution of protein is half-folded, what will we find in solution?
(a) 100% half-folded protein
(b) 50% fully folded, 50% unfolded
(c) 33% fully folded, 34% half-folded, and 33% unfolded
22. Several amino acids can be modified after the synthesis of a polypeptide chain to enhance the functional capabilities of the protein. Match the type of modifying group in
the left column with the appropriate amino acid residues in the right column.
(a) phosphate
(1) Glu
(b) hydroxyl
(2) Thr
(c) g-carboxyl
(3) Pro
(d) acetyl
(4) Ser
(5) N-terminal
(6) Tyr
23. How can a protein be modified to make it more hydrophobic?
1. (a) (a) C (b) D (c) B, D (d) D (e) B, D (f) A (g) D (h) B (i) C (j) B, D (k) D.
(b) A is proline, B is tyrosine, C is leucine, and D is lysine.
(c) Histidine and arginine (basic amino acids).
2. See the structure of cysteine. At pH 1, all the ionizable groups are protonated.
3. (a) 3 (b) 4 (c) 1 (d) 5 (e) 2 (f) 6
4. a, d
5. Histidine acts as a buffer at pH 6.0 because this is the pK of the imidazole group. At pH
7.6, histidine is a poor buffer because no one ionizing group is partially protonated and
therefore capable of donating or accepting protons without markedly changing the pH.
6. The 20 L amino acids can form 20¥20=400 dipeptides. The minimum number of
pK values for any dipeptide is two; the maximum is four.
7. (a) glycine
(b) 4, namely the 2 carboxyl groups of glutamate, the R group of arginine, and the alpha
amino group of glycine.
(c) ;2, contributed by the N-terminal amino group and the arginine residue
(d) E-M-R-T-G
(e) See the structure of the peptide bond below.
Peptide bond
8. c
9. e
10. a. A Ramachandran plot gives the possible f and y angles for the main polypeptide chain
containing different amino acid residues. The fact that glycine lacks an R group means
that it is much less constrained than other residues. In Figure 3.31, the left-handed helix
region, which occurs rarely, generally includes several Gly residues. In contrast to glycine,
proline is more highly constrained than most residues because the R group is tied to the
amino group. This fixes f at about :65Ú. In Figure 3.26, the rare cis form of the peptide
bond is shown as occurring about half of the time in X-Pro peptide bonds.
11. a, c
12. c, d
13. b, d
14. In both a-helical and b sheet structures, the polar peptide bonds of the main chain are
involved in internal hydrogen bonding, thereby eliminating potential hydrogen bond
formation with water. Overall the secondary structures are less polar than the corresponding linear amino acid sequences.
15. a, c. Specific charged and polar amino acid residues may be found inside some proteins,
in active sites, but most polar and charged residues are located on the surface of proteins.
16. b, e. Statement (b) is incorrect because globular, water-soluble proteins have most of
their nonpolar residues buried in the interior of the protein. Statement (e) is incorrect
because not all water-soluble proteins contain b sheet secondary structures. For example, myoglobin is mostly a-helical and lacks b sheet structures.
17. (a) 3 (b) 4 (c) 2 (d) 1
18. a, c
19. A low pH (pH 2) will cause the protonation of all ionizable side chains and will change
the charge distribution on the protein; furthermore, it will impart a large net positive
charge to the protein. The resulting repulsion of adjacent positive charges and the disruption of salt bridges often cause unfolding of the protein and loss of biological activity.
20. e
21. b
22. (a) 2, 4, 6 (b) 3 (c) 1 (d) 5
23. The attachment of a fatty acid chain to a protein can increase its hydrophobicity and
promote binding to lipid membranes.
1. The net charge of a polypeptide at a particular pH can be determined by considering the
pK value for each ionizable group in the protein. For a linear polypeptide composed of
10 amino acids, how many a-carboxyl and a-amino groups must be considered?
2. For the formation of a polypeptide composed of 20 amino acids, how many water molecules must be removed when the peptide bonds are formed? Although the hydrolysis
of a peptide bond is energetically favored, the bond is very stable in solution. Why?
3. Where stereoisomers of biomolecules are possible, only one is usually found in most organisms; for example, only the L amino acids occur in proteins. What problems would
occur if, for example, the amino acids in the body proteins of herbivores were in the L
isomer form, whereas the amino acids in a large number of the plants they fed upon were
in the D isomer form?
4. Many types of proteins can be isolated only in quantities that are too small for the direct
determination of a primary amino acid sequence. Recent advances in gene cloning and amplification allow for relatively easy analysis of the gene coding for a particular protein. Why
would an analysis of the gene provide information about the protein’s primary sequences?
Suppose that two research groups, one in New York and the other in Los Angeles, are both
analyzing the same protein from the same type of human cell. Why would you not be surprised if they publish exactly the same primary amino acid sequence for the protein?
5. Each amino acid in a run of several amino acid residues in a polypeptide chain has f
values of approximately :140Ú and y values of approximately ;147. What kind of structure is it likely to be?
6. A survey of the location of reverse turns in soluble proteins shows that most reverse turns
are located at the surface of the protein, rather than within the hydrophobic core of the
folded protein. Can you suggest a reason for this observation?
7. Wool and hair are elastic; both are a-keratins, which contain long polypeptide chains
composed of a helices twisted about each other to form cablelike assemblies with crosslinks involving Cys residues. Si ... zobacz całą notatkę

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