BIOCHEMISTRY 9TH EDITION

CAMPBELL
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Contents
Chapter 1: Biochemistry and the Organization of Cells……………………………..………..1
Chapter 2: Water: The Solvent for Biochemical Reactions………………………………….11
Chapter 3: Amino Acids and Peptides………………………………………………………...23
Chapter 4: The Three-Dimensional Structure of Proteins…………………………………..34
Chapter 5: Protein Purification and Characterization Techniques…………………………44
Chapter 6: The Behavior of Proteins: Enzymes………………………………………………55
Chapter 7: The Behavior of Proteins: Enzymes, Mechanisms, and Control……………….67
Chapter 8: Lipids and Proteins Are Associated in Biological Membranes…………………77
Chapter 9: Nucleic Acids: How Structure Conveys Information……………………………86
Chapter 10: Biosynthesis of Nucleic Acids: Replication……………………………………..96
Chapter 11: Transcription of the Genetic Code: The Biosynthesis of RNA………………105
Chapter 12: Protein Synthesis: Translation of the Genetic Message………………………120
Chapter 13: Nucleic Acid Biotechnology Techniques……………………………………….132
Chapter 14: Viruses, Cancer, and Immunology…………………………………………….142
Chapter 15: The Importance of Energy Changes and Electron Transfer in Metabolism..151
Chapter 16: Carbohydrates…………………………………………………………………..159
Chapter 17: Glycolysis………………………………………………………………………...171
Chapter 18: Storage Mechanisms and Control in Carbohydrate Metabolism……………181
Chapter 19: The Citric Acid Cycle…………………………………………………………...189
Chapter 20: Electron Transport and Oxidative Phosphorylation…………………………200
Chapter 21: Lipid Metabolism……………………………………………………………….210
Chapter 22: Photosynthesis…………………………………………………………………...220
Chapter 23: The Metabolism of Nitrogen……………………………………………………228
Chapter 24: Integration of Metabolism: Cellular Signaling………………………………..239
 1
Chapter 1: Biochemistry and the Organization of Cells

Chapter 1
Biochemistry and the Organization of Cells

SUMMARY
Section 1.1
• Biochemistry describes the molecular nature of life processes. In living cells, many
chemical reactions take place simultaneously.
• Cells of all types have so many fundamental features in common that it is reasonable to
say that they all had a common origin.
Section 1.2
• Life is based on compounds of carbon. This is the subject matter of organic chemistry.
• The basic building blocks that make up the molecules of biochemistry can be grouped
into carbohydrates, amino acids, nucleotides, and lipids.
• The reactions of organic compounds are those of their functional groups, which are
specifically linked atoms that react in similar ways under many different conditions.
Section 1.3
• Our solar system, including the Earth, is postulated to have been formed from chemical
elements produced by first-generation stars. The early Earth had an atmosphere that
consisted of simple chemical compounds.
• The atmospheric conditions of the early Earth allowed the formation of molecules, such
as amino acids, that play a role in life processes.
• Several theories describe the origin of living cells from component molecules. All require
explanations for coding and for catalytic activity, and all assign an important role to
RNA.
Section 1.4
• All cells contain DNA and are separated from their environment by a cell membrane.
Prokaryotic cells do not have significant internal membranes, but the larger cells of
eukaryotes have an extensive membrane system. The internal membranes mark off the
organelles, portions of the cell with a specific function.
• Prokaryotes have a nuclear region, which contains DNA, and ribosomes, the site of
protein synthesis, as their main features. They have a cell membrane, but do not have an
internal membrane system.
• Three of the most important organelles in eukaryotic cells are the nucleus, the
mitochondrion, and the chloroplast. Each is separated from the rest of the cell by a double
membrane. The nucleus contains most of the DNA of the cell and is the site of RNA
synthesis. The mitochondria contain enzymes that catalyze important energy-yielding
 2
Chapter 1: Biochemistry and the Organization of Cells

reactions. Chloroplasts, which are found in green plants and green algae, are the sites of
photosynthesis. Both mitochondria and chloroplasts contain DNA that differs from that
found in the nucleus, and both carry out transcription and protein synthesis distinct from
that directed by the nucleus.
• Other organelles play specific roles. They include the Golgi apparatus, lysosomes, and
peroxisomes.
Section 1.5
• In the five-kingdom classification scheme, prokaryotes have a kingdom to themselves
(Monera). The remaining four kingdoms—protists, fungi, plants, and animals—consist of
eukaryotes.
• In the three-domain classification schemes, eukaryotes have a domain to themselves.
Two domains consist of prokaryotes. Eubacteria are the commonly encountered
prokaryotes. Archaea are organisms that live in extreme environments such as those that
were found on the early Earth.
• Many theories about the rise of eukaryotes from prokaryotes focus on a possible role for
symbiosis.
• The idea of endosymbiosis, in which a larger cell engulfs a smaller one, plays a large role
in scenarios for the development of organelles in eukaryotic cells.
Section 1.6
• The Sun is the source of energy for all life on Earth. It provides the energy for
photosynthesis, which produces carbohydrates as well as oxygen.
• Carbohydrates can be processed in chemical reactions that release energy.
• Reactions that release energy are favored and thus are likely to occur. Thermodynamics is
the branch of science that predicts the likelihood of reactions.
• A spontaneous reaction is one that will take place without outside intervention. This point
does not specify reaction rate. Some spontaneous processes can take a long time to occur.
• The change in free energy (∆G) that accompanies a reaction determines whether that
reaction is spontaneous at a given temperature and pressure.
• A negative free energy change (∆G<0) is characteristic of a spontaneous reaction. A
positive free energy change (∆G>0) indicates that the reaction is not spontaneous, but the
reverse process is spontaneous. When the free energy change is zero (∆G = 0), the
reaction is at equilibrium.
• Living things are ordered assemblies of molecules. They represent a local decrease in
entropy. Because the entropy of the universe increases in spontaneous processes, this
local decrease in entropy is offset by a larger increase in the entropy of the surroundings.
There is an increase in total entropy.
 3
Chapter 1: Biochemistry and the Organization of Cells

LECTURE NOTES
As an introduction, this should not take more than one lecture. Students should be made aware of
some unifying themes and background information. Biochemistry is intimately related to other
physical sciences, most especially organic chemistry. Living things may be seen as hierarchical
structures, and as such, the properties of functional groups on molecules lead, ultimately, to the
complexity of cells and multicellular organisms. A very brief introduction to thermodynamics is
included here as well.

LECTURE OUTLINE
I. Basic themes
A. Interconnections among physical sciences
B. Structural hierarchy in living systems
C. Review of functional groups in biomolecules

II. Origins of life

A. Big Bang—elements, comparison of abundances in living organisms vs.
universe at large
B. Origin of biomolecules, abiotic synthesis
C. Polymeric structure of biomolecules
D. Molecules to cells
1. Importance of catalysts
2. RNA world and other theories

III. Prokaryotes vs. eukaryotes—structural comparisons

A. Prokaryotes
1. No membrane-bound nuclei, but a nuclear region
2. Ribosomes—protein synthesis
3. Cell membrane
4. Cell wall
B. Eukaryotes
1. Many membrane-bound organelles
2. Structures and functions: nucleus, mitochondria, ER (± ribosomes),
chloroplasts, Golgi, lysosomes, peroxisomes, cytoskeleton, vacuoles

IV. Biological classification systems

A. Five kingdoms
1. Fungi, plants, animals—mostly multicellular, all eukaryotes
2. Protists—mostly unicellular, all eukaryotes
3. Monera—prokaryotes
B. Three domains
1. Archaebacteria
2. Eubacteria
3. Eukarya
C. Endosymbiotic theory
 4
Chapter 1: Biochemistry and the Organization of Cells

V. Energy use
A. Sun as ultimate source
B. Thermodynamics, favorability of processes, release of energy

ANSWERS TO PROBLEMS
1.1 Basic Themes
1. A polymer is a very large molecule formed by linking smaller units (monomers) together.
A protein is a polymer formed by linking amino acids together. A nucleic acid is a polymer
formed by linking nucleotides together. Catalysis is the process that increases the rate of
chemical reactions compared with the rate of the uncatalyzed reaction. Biological catalysts are
proteins in almost all cases; the only exceptions are a few types of RNA, which can catalyze
some of the reactions of their own metabolism. The genetic code is the means by which the
information for the structure and function of all living things is passed from one generation to the
next. The sequence of purines and pyrimidines in DNA carries the genetic code. (RNA is the
coding material in some viruses.)

1.2 Chemical Foundations of Biochemistry

2. The correct match of functional groups and the compounds containing those functional
groups is given in the following list:
Amino group CH3CH2NH2
Carbonyl group (ketone) CH3COCH3
Hydroxyl group CH3OH
Carboxyl group CH3COOH
Carbonyl group (aldehyde) CH3CH2CHO
Thiol group CH3SH
Ester linkage CH3COOCH2CH3
Double bond CH3CH=CHCH3
Amide linkage CH3CON(CH3)2
Ether
CH3CH2OCH2CH3
 5
Chapter 1: Biochemistry and the Organization of Cells

3. The functional groups in the compounds follow:

4. Before 1828, the concept of vitalism held that organic compounds could be made only by
living systems and were beyond the realm of laboratory investigations.
 6
Chapter 1: Biochemistry and the Organization of Cells

Wöhler’s synthesis showed that organic compounds, like inorganic ones, did not require a
vitalistic explanation, but that, rather, they obeyed the laws of chemistry and physics and thus
were subject to laboratory investigation. Subsequently, the concept was extended to the much
more complex, but still testable, discipline of biochemistry.
5. Urea, like all organic compounds, has the same molecular structure, whether it is
produced by a living organism or not.
6.
Item Organic Biochemical
Solvent Varies (smelly) Water (usually)
Concentrations High Low (mM, M, nM)
Use catalyst? Usually not Almost always (enzymes)
Speed Min, hr, day sec, nsec
Temp Varies (high) Isothermal, ambient temp
Yield Poor–good (90%) High (can be 100%)
Side reactions Often* No
Internal control Little Very high**—choices
Polymers (product) Usually not Commonly (proteins, nucleic
acids, saccharides)
Bond strength High (covalent) High, weak (in polymers)
Bond distances Not critical Critical (close fit)
Compartmented No Yes (esp. eukaryotes)
Emphasis One reaction Pathways, interconnected
(control** choices)†
System Closed or open Open (overcome +G)
*Example of side reactions: Glucose → G6P or G1P or G2P.
**Control levels: enzyme, hormone, gene.
†Example of choices:

1.3 The Beginnings of Biology

7. It is generally believed that carbon is the likely basis for all life forms, terrestrial or
extraterrestrial.
 7
Chapter 1: Biochemistry and the Organization of Cells

8. Eighteen residues would give 2018 possibilities, or 2.6 × 1023 possibilities. Thus,
19 residues would be necessary to have at least Avogadro’s number (6.022 × 1023) of
possibilities.
9. The number is 440 or 1.2 x 1024, which is twice Avogadro’s number.
10. RNA is capable of both coding and catalysis.
11. Catalysis allows living organisms to carry out chemical reactions much more efficiently
than without catalysts.
12. Two of the most obvious advantages are speed and specificity; they also work at constant
temperature or produce little heat.
13. Coding allows for reproduction of cells.
14. With respect to coding, RNA-type polynucleotides have been produced from monomers
in the absence of either a preexisting RNA to be copied or an enzyme to catalyze the process.
The observation that some existing RNA molecules can catalyze their own processing suggests a
role for RNA in catalysis. With this dual role, RNA may have been the original informational
macromolecule in the origin of life.
15. It is unlikely that cells could have arisen as bare cytoplasm without a plasma membrane.
The presence of the membrane protects cellular components from the environment and prevents
them from diffusing away from each other. The molecules within a cell can react more easily if
they are closer to each other.

1.4 The Biggest Biological Distinction—Prokaryotes and Eukaryotes

16. Five differences between prokaryotes and eukaryotes are as follows: (1) Prokaryotes do
not have a well-defined nucleus, but eukaryotes have a nucleus marked off from the rest of the
cell by a double membrane. (2) Prokaryotes have only a plasma (cell) membrane; eukaryotes
have an extensive internal membrane system. (3) Eukaryotic cells contain membrane-bounded
organelles, while prokaryotic cells do not. (4) Eukaryotic cells are normally larger than those of
prokaryotes. (5) Prokaryotes are single-celled organisms, while eukaryotes can be either single-
celled or multicellular.
17. Protein synthesis takes place on ribosomes both in prokaryotes and in eukaryotes. In
eukaryotes, ribosomes may be bound to the endoplasmic reticulum or found free in the
cytoplasm; in prokaryotes, ribosomes are only found free in the cytoplasm.
18. It is unlikely that mitochondria would be found in bacteria. These eukaryotic organelles
are enclosed by a double membrane, and bacteria do not have an internal membrane system. The
mitochondria found in eukaryotic cells are about the same size as most bacteria.
19. See Section 1-4 for the functions of the parts of an animal cell, which are shown in Figure
1.18.
 8
Chapter 1: Biochemistry and the Organization of Cells

20. See Section 1-4 for the functions of the parts of a plant cell, which are shown in Figure
1.18.
21. In green plants photosynthesis takes place in the membrane system of chloroplasts, which
are large membrane-enclosed organelles. Photosynthetic bacteria have extensions of the plasma
membrane into the interior of the cell called chromatophores, which are the sites of
photosynthesis.
22. Nuclei, mitochondria, and chloroplasts are all enclosed by a double membrane.
23. Nuclei, mitochondria, and chloroplasts all contain DNA. The DNA found in mitochondria
and in chloroplasts differs from that found in the nucleus.
24. Mitochondria carry out a high percentage of the oxidation (energy-releasing) reactions of the
cell. They are the primary sites of ATP synthesis.
25. The Golgi apparatus is involved in binding carbohydrates to proteins and in exporting
substances from the cell. Lysosomes contain hydrolytic enzymes, peroxisomes contain catalase
(needed for the metabolism of peroxides), and glyoxysomes contain enzymes needed by plants
for the glyoxylate cycle. All of these organelles have the appearance of flattened sacs, and each
is enclosed by a single membrane.

1.5 How We Classify Eukaryotes and Prokaryotes

26. Monera includes bacteria (e.g., E. coli) and cyanobacteria. Protista includes such
organisms as Euglena, Volvox, Amoeba, and Paramecium. Fungi includes molds and
mushrooms. Plantae includes club mosses and oak trees. Animalia includes spiders, earthworms,
salmon, rattlesnakes, robins, and dogs.
27. The kingdom Monera consists of prokaryotes. Each of the other four kingdoms consists
of eukaryotes.
28. The five-kingdom classification takes into account the fact that bacteria, fungi, and
protists do not fit the plant/animal divide.
29. The major advantage of being eukaryotic is that of having compartments (organelles)
with specialized functions (and thus division of labor). Another advantage is that cells can be
much larger without surface area-to-volume considerations being critical because of
compartmentalization.
30. See the discussion of the endosymbiotic theory in Section 1-5.
31. See Question 30. The division of labor in cells gives rise to greater efficiency and a larger
number of individuals. This in turn allows more opportunity for evolution and speciation.
 9
Chapter 1: Biochemistry and the Organization of Cells

1.6 Biochemical Energetics

32. Processes that release energy are favored.
33. The term spontaneous means energetically favored. It does not necessarily mean fast.
34. The system consists of the nonpolar solute and water, which become more disordered
when a solution is formed; ∆Ssys is positive but comparatively small. ∆Ssurr is negative and
comparatively large because it is a reflection of the unfavorable enthalpy change for forming the
solution (∆Hsys).
35. Processes (a) and (b) are spontaneous, whereas processes (c) and (d) are not. The
spontaneous processes represent an increase in disorder (increase in the entropy of the Universe)
and have a negative ∆G° at constant temperature and pressure, while the opposite is true of the
nonspontaneous processes.
36. In all cases, there is an increase in entropy, and the final state has more possible random
arrangements than the initial state.
37. Since the equation involves multiplication of ∆S by T, the value of ∆G is temperature-
dependent.
38. If one considers entropy a measure of dispersion of energy, then at higher temperatures, it
is logical that molecules would have more possible arrangements due to increased molecular
motion.
39. Assuming the value of ∆S is positive, an increase in temperature increases the −∆G
contribution of the entropy component to the overall energy change.
40. The heat exchange, getting colder, reflects only the enthalpy or ∆H component of the
total energy change. The entropy change must be high enough to offset the enthalpy component
and to add up to an overall −∆G.
41. Entropy would increase. Two molecules, ADP and Pi, can be randomized in more ways
than a single molecule, ATP, can.
42. The lowering of entropy needed to give rise to organelles leads to higher entropy in the
surroundings, thus increasing the entropy of the Universe as a whole.
43. Compartmentalization in organelles brings components of reactions into proximity with
one another. The energy change of the reaction is not affected, but the availability of components
allows it to proceed more readily.
44. DNA would have higher entropy with the strands separated. There are two single strands
instead of one double strand, and the single strands have more conformational mobility.
45. See the answer to Question 43. It is still unlikely that cells could have arisen as bare
cytoplasm, but the question of proximity of reactants is more to the point here than the energy
change of a given reaction.
 10
Chapter 1: Biochemistry and the Organization of Cells

46. It would be unlikely that cells of the kind we know would have evolved on a gas giant.
The lack of solids and liquids on which aggregates could form would make a large difference.
47. The available materials differ from those that would have been found on Earth, and
conditions of temperature and pressure are very different.
48. Mars, because of conditions more like those on Earth.
49. A number of energetically favorable interactions drive the process of protein folding,
ultimately increasing the entropy of the Universe.
50. Photosynthesis is endergonic, requiring light energy from the Sun. The complete aerobic
oxidation of glucose is exergonic and is a source of energy for many organisms, including
humans. It would be reasonable to expect the two processes to take place differently in order to
provide energy for the endergonic one.
 11
Chapter 1: Biochemistry and the Organization of Cells
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