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ebook download The Cell: A Molecular Approach 7th Edition (eBook PDF) all chapter
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The Cover
The cover image shows the formation of an autophagosome, in which organ-
elles and cytosol are engulfed in cytoplasmic membranes. Original painting
by David S. Goodsell, based on the scientific design of Daniel J. Klionsky.
The Artist
David S. Goodsell is an Associate Professor of Molecular Biology at the
Scripps Research Institute. His illustrated books, The Machinery of Life and
Our Molecular Nature, explore biological molecules and their diverse roles
within living cells, and his new book, Bionanotechnology: Lessons from Nature,
presents the growing connections between biology and nanotechnology.
More information may be found at: http://mgl.scripps.edu/people/goodsell
Address orders and requests for examination copies to: Sinauer Associates
P.O. Box 407, 23 Plumtree Road, Sunderland, MA 01375 U.S.A.
Phone: 413-549-4300
FAX: 413-549-1118
email: orders@sinauer.com
www.sinauer.com
Geoffrey M. Cooper
Brief Table of Contents
PART I
Fundamentals and Foundations 1
Chapter 1 An Overview of Cells and Cell Research 3
Chapter 2 Molecules and Membranes 47
Chapter 3 Bioenergetics and Metabolism 81
Chapter 4 Fundamentals of Molecular Biology 111
Chapter 5 Genomics, Proteomics, and Systems Biology 157
PART II
The Flow of Genetic Information 185
Chapter 6 Genes and Genomes 187
Chapter 7 Replication, Maintenance, and Rearrangements
of Genomic DNA 217
Chapter 8 RNA Synthesis and Processing 259
Chapter 9 Protein Synthesis, Processing, and Regulation 317
PART III
Cell Structure and Function 365
Chapter 10 The Nucleus 367
Chapter 11 Protein Sorting and Transport 397
Chapter 12 Mitochondria, Chloroplasts, and Peroxisomes 447
Chapter 13 The Cytoskeleton and Cell Movement 479
Chapter 14 The Plasma Membrane 531
Chapter 15 Cell Walls, the Extracellular Matrix, and Cell Interactions 571
PART IV
Cell Regulation 599
Chapter 16 Cell Signaling 601
Chapter 17 The Cell Cycle 651
Chapter 18 Cell Death and Cell Renewal 691
Chapter 19 Cancer 723
Contents
PART I
Fundamentals and Foundations 1
Chapter 1 An Overview of Cells and Cell Research 3
The Origin and Evolution of Cells 4 Tools of Cell Biology 23
The first cell 4 Light microscopy 23
The evolution of metabolism 7 Electron microscopy 30
Present-day prokaryotes 8 Super-resolution light microscopy 32
Eukaryotic cells 9 Subcellular fractionation 34
The origin of eukaryotes 11 Growth of animal cells in culture 37
The development of multicellular organisms 13 Key Experiment
HeLa Cells 39
Cells as Experimental Models 17 Culture of plant cells 39
E. coli 17
Viruses 40
Yeasts 18
Molecular Medicine
Caenorhabditis elegans 19 Viruses and Cancer 41
Drosophila melanogaster 20 SUMMARY AND KEY TERMS 43
Arabidopsis thaliana 20 QUESTIONS 44
Vertebrates 20 REFERENCES AND FURTHER READING 45
PART II
The Flow of Genetic Information 185
Chapter 6 Genes and Genomes 187
The Structure of Eukaryotic Genes 187 Repetitive sequences 197
Introns and exons 188 Gene duplication and pseudogenes 201
Key Experiment Chromosomes and Chromatin 203
The Discovery of Introns 190
Chromatin 204
Roles of introns 192 Centromeres 208
Noncoding Sequences 194 Telomeres 213
Key Experiment SUMMARY AND KEY TERMS 214
The ENCODE Project 195 QUESTIONS 215
Noncoding RNAs 196 REFERENCES AND FURTHER READING 215
Protein phosphorylation and other modifications 351 The ubiquitin-proteasome pathway 357
Key Experiment Lysosomal proteolysis 358
The Discovery of Tyrosine Kinases 353 SUMMARY AND KEY TERMS 360
Protein–protein interactions 356 QUESTIONS 361
Protein Degradation 357 REFERENCES AND FURTHER READING 362
PART III
Cell Structure and Function 365
Chapter 10 The Nucleus 367
The Nuclear Envelope and Traffic between the Chromatin localization and transcriptional activity 382
Nucleus and the Cytoplasm 367 Replication and transcription factories 385
Structure of the nuclear envelope 367 Nuclear Bodies 386
Molecular Medicine The nucleolus and rRNA 387
Nuclear Lamina Diseases 371 Polycomb bodies: Centers of transcriptional
The nuclear pore complex 372 repression 391
Selective transport of proteins to and from the Cajal bodies and speckles: Processing and storage of
nucleus 373 snRNPs 391
Key Experiment SUMMARY AND KEY TERMS 392
Identification of Nuclear Localization Signals 374 QUESTIONS 394
Transport of RNAs 378 REFERENCES AND FURTHER READING 394
Regulation of nuclear protein import 380
The Organization of Chromosomes 381
Chromosome territories 381
Chapter 15 Cell Walls, the Extracellular Matrix, and Cell Interactions 571
Cell Walls 571 Cell–Cell Interactions 587
Bacterial cell walls 571 Adhesion junctions 587
Eukaryotic cell walls 573 Tight junctions 590
Gap junctions 591
The Extracellular Matrix and Cell–Matrix
Interactions 577 Molecular Medicine
Gap Junction Diseases 593
Matrix structural proteins 578
Plasmodesmata 594
Matrix polysaccharides 581
SUMMARY AND KEY TERMS 595
Adhesion proteins 582
QUESTIONS 596
Cell–matrix interactions 583
REFERENCES AND FURTHER READING 597
Key Experiment
The Characterization of Integrin 584
PART IV
Cell Regulation 599
Chapter 16 Cell Signaling 601
Signaling Molecules and Their Receptors 601 Eicosanoids 608
Modes of cell–cell signaling 602 Plant hormones 610
Steroid hormones and the nuclear receptor G Proteins and Cyclic AMP Signaling 611
superfamily 603
G proteins and G protein-coupled receptors 612
Nitric oxide and carbon monoxide 605
Key Experiment
Neurotransmitters 606 G Protein-Coupled Receptors and Odor
Peptide hormones and growth factors 607 Detection 613
xiv Contents
The cAMP pathway: Second messengers and protein Phospholipase C and Ca2+ 635
phosphorylation 615
Cyclic GMP 618
Receptors Coupled to Transcription
Factors 637
Tyrosine Kinases and Signaling by MAP Kinase, The TGF-b/Smad pathway 637
PI 3-Kinase, and Phospholipase C/Calcium NF-kB signaling 638
Pathways 619 The Hedgehog, Wnt, and Notch pathways 638
Receptor tyrosine kinases 619
Nonreceptor tyrosine kinases 622
Signaling Dynamics and Networks 641
Feedback loops and signaling dynamics 641
Molecular Medicine
Cancer: Signal Transduction and the Networks and crosstalk 642
ras Oncogenes 625 SUMMARY AND KEY TERMS 644
MAP kinase pathways 626 QUESTIONS 646
The PI 3-kinase/Akt and mTOR pathways 630 REFERENCES AND FURTHER READING 647
Medical applications of adult stem cells 711 Somatic cell nuclear transfer 715
Induced pluripotent stem cells 717
Pluripotent Stem Cells, Cellular
Transdifferentiation of somatic cells 718
Reprogramming, and Regenerative
SUMMARY AND KEY TERMS 719
Medicine 712
QUESTIONS 720
Embryonic stem cells 712
REFERENCES AND FURTHER READING 721
Key Experiment
Culture of Embryonic Stem Cells 713
Acknowledgments
I am particularly grateful to Alexandra Adams for carefully reviewing the
entire text of the Seventh Edition of The Cell. The book has also benefited from
the comments and suggestions of reviewers, colleagues, and instructors who
used the previous edition. I am pleased to thank the following reviewers for
their thoughtful comments and advice:
Organization
The Cell is divided into four parts, each of which is self-contained, so that
the order and emphasis of topics can be easily varied according to the needs
of individual courses.
Part I provides background chapters on the evolution of cells, methods for
studying cells, the chemistry of cells, the fundamentals of modern molecular
biology, and the fields of genomics and systems biology. For those students
who have a strong background from either a comprehensive introductory
biology course or a previous course in molecular biology, various parts of
these chapters can be skipped or used for review.
Part II focuses on the molecular biology of cells and contains chapters
dealing with genome organization and sequences; DNA replication, repair,
and recombination; transcription and RNA processing; and the synthesis,
processing, and regulation of proteins. The order of chapters follows the flow
of genetic information (DNA RNA protein) and provides a concise but
up-to-date overview of these topics.
Part III contains the core block of chapters on cell structure and function,
including chapters on the nucleus, cytoplasmic organelles, the cytoskeleton,
the plasma membrane, and the extracellular matrix. This part of the book
starts with coverage of the nucleus, which puts the molecular biology of Part
II within the context of the eukaryotic cell, and then works outward through
cytoplasmic organelles and the cytoskeleton to the plasma membrane and
the exterior of the cell. These chapters are relatively self-contained, however,
and could be used in a different order should that be more appropriate for
a particular course.
Finally, Part IV focuses on the exciting and fast-moving area of cell
regulation, including coverage of topics such as cell signaling, the cell cycle,
programmed cell death, and stem cells. This part of the book concludes with
a chapter on cancer, which synthesizes the consequences of defects in basic
cell regulatory mechanisms.
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“This demand, which was accompanied by an expression
disapproving any policy of conquest, was repeated when the new
war loan was voted on December 2. On May 29, after Italy had
intervened, the statement was made in the Reichstag in behalf of the
Socialist Party that the desire for peace was increasing and that the
Socialists wanted no policy of conquest. At a meeting in Vienna on
April 12 and 13 representatives of the German and Austro-
Hungarian Socialist Parties again adopted a resolution in favor of
peace. But the German Socialists have not been content with such
measures. In spite of opposition and suspicion, they have striven for
a renewal of international relations with the Social-Democrats of all
countries, and when the executive committee of the international
Socialist organization made a proposal to hold a meeting at The
Hague to discuss the possibility of peace negotiations, the German
Socialist leaders agreed, under condition that the French Socialist
Party participate. All efforts at an international agreement, however,
were thwarted by the attitude of the French Socialists.
“We recognize with satisfaction that in England, as well as in
France, there are Socialists who are working for peace. That cannot
blind us to the deplorable fact that the majority of the Socialists, both
in England and France, favor continuing the war until Germany is
completely conquered.
“The Socialists in the Reichstag and the official leaders of the
Socialist Party have constantly and unitedly fought against a policy
of conquests and annexation. We protest again with all possible
emphasis against all efforts looking to the annexation of foreign
territory and the oppression of other peoples—measures now
demanded by the great business organizations and influential
political leaders. The mere fact that such efforts are being made
tends to postpone the day of peace, which the whole public is now
so earnestly awaiting.
“The people want no conquest of land, they want peace. If the war
is not to go on indefinitely until all the nations are completely
exhausted, some one of the Powers involved must stretch out the
hand of peace. Upon Germany, which has successfully defended
itself against superior forces, and which has frustrated the plan to
bring it to starvation, rests the duty of taking the first steps toward
peace. In the name of humanity and civilization, and recognizing the
favorable military position which our brave troops have won, we urge
the Government to try to end the struggle. We expect of our fellow
Socialists in other belligerent countries that they will make the same
demand upon their own governments.”
I
It is the vital interest of the majority of the Ed. Bernstein.
German nation, that the present war should end by
a peace treaty which, as to the rights and the relations of the nations,
is in conformity with the principles laid down in the program of the
German Social-Democrat Party and in the resolutions adopted by
their party-meetings and by the International Social-Democratic
Congresses.
Only a peace based on these principles will result in renewing the
friendly relations between Germany and the nations she is now at
war with, as soon and as thoroughly as possible.
II
The supreme principle, insisted upon in the program and the
resolutions of the Social-Democratic Party is the right of peoples to
decide their own fate, within the limits of international law.
The German Socialists consider it their duty to defend this
principle by all available means against any attack from any side
whatsoever. No nation or part of a nation having so far enjoyed
national independence, may be deprived of this right or see it
impaired; no territory may be annexed, when the annexation would
deprive the inhabitants of that right.
The Social-Democratic Party do not admit the right of conquest of
one nation over any other.
III
In the case of countries of European civilization, which have lived
under foreign rule, no territorial changes shall take place without a
referendum being taken of the inhabitants. This referendum should
be arranged and supervised by representatives of neutral States, so
as to insure perfect freedom in voting. Any inhabitant, who is of age
and has lived in the country for at least a year before the outbreak of
the war, shall have the right to vote.
In the interests of peace, all peoples of European civilization living
under foreign rule in sufficient numbers to form a community in the
international Concert, shall obtain political independence.
When a sufficient number out of subject peoples incorporated by
force in one State, desire to belong to another, they shall be given
the right to decide by vote as to which State they will belong.
IV
Transfer of territory outside of Europe shall only take place under
such conditions, as guarantee that the legal and material conditions
of such native population shall not be injured.
V
Nations can only be safeguarded against a renewal of war or wars
of retaliation by developing and strengthening international law.
In this respect the following means should be emphasized:
a. Development of the Hague Conference into a Permanent
International Conference for the Codification of International Law and
for International Arbitration. Concentration of the various Hague
institutions into a permanent international court, suitably divided into
branch courts.
b. All States to bring those differences they cannot themselves
peaceably solve, before the Court of Justice to be instituted by the
Hague Conference, where they will be settled either by mutual
agreement, conciliation or arbitration.
c. All signatory States to refrain from war or warlike measures till
the Court of Justice has examined the cause of war and till all
attempts to settle the difference in a peaceful manner, have proved
useless. Any State or Union resorting to hostilities contrary to these
rules to be treated as an enemy by all the others.
d. The Parliaments to decide about war and peace. Secret treaties
to be abolished.
e. Development of International Law relating to the conduct of war
and the protection of the civil population. Abolition of the right of
capture at sea and of the right to levy war-contributions. No hostages
to be taken. Abolition of the system of reprisals against inhabitants of
an invaded country for acts of self-defense or defense of other non-
combatants. Permanent committees to watch the actions of
belligerents in occupied territories and the treatment of prisoners of
war and of civil prisoners interned in the enemy’s country.
f. Internationalization of transcontinental railways and of all
waterways connecting seas or lakes surrounded by different
countries, with the ocean.
g. Adoption of the principle of the Open Door for all Colonies,
Protectorates and for every territory which lies in the sphere of
influence of an European State.
h. These principles to be inserted into the constitutions of the
Powers.
BELGIUM
Whereas, Art. 2 already excludes any forcible annexation of
Belgian territory or any attack on the independence of Belgium by
another State, Germany has moreover invaded Belgium,
overpowered its army and occupied its territory without any
provocation from the side of Belgium and as the Chancellor has
himself admitted violating the neutrality of Belgium in defiance of the
law of nations. Germany having thus made her way into Belgium to
satisfy her own designs, beat down the resistance of the army and
occupied the country by force, Germany is therefore bound in honor
to evacuate Belgium immediately on the conclusion of peace, in
accordance with the solemn declaration, made on August 4, 1914,
by the German Ambassador, Prince Lichnowsky, to the English
Secretary of State, Sir Edward Grey, and to pay a full and ample
indemnity to the people of Belgium for the material and moral injury
which they have suffered.
PEACE PROPOSALS AND PROGRAMS
5. FRANCE
Algeciras, 30.
Alliances, 135 ff, 144, 166;
prohibited, 94, 250, 266.
Alsace-Lorraine, autonomy of, 245, 260.
American School Peace League, program of, 267.
Angell, Norman, 33, 34, 82, 326.
Annexation, 76, 249, 306, 308, 311, 316, 322, 325.
Arbitration, 249, 251, 254, 262, 271, 306, 324;
compulsory, 262, 322, 325.
Armaments, export of, 266;
limitation of, 99, 124, 246, 248, 249, 250, 256, 262, 265,
266, 267, 271, 276, 277, 297, 300, 301, 306, 310, 322,
323, 325;
national manufacture of, 102 ff, 250, 265, 266, 267, 268,
269, 271, 277, 299, 300, 301, 324.
Armed Peace, 121.
Australian Peace Alliance, program of, 300.
Autonomy, 249, 254, 262, 275, 306, 318, 322.