Molecular Biology. Academic Cell Update Edition

1056 Pages·2013·154.16 MB·English

by  Clark

Molecular
Biology
Clark1570247 978-0-12-378594-7 X0001
http://booksite.elsevier.com/9780123785947/index.php
Molecular Biology, Second Edition
David P. Clark and Nanette J. Pazdernik
Resources for Students:
Online Academic Cell Study Guide features complete Cell Press journal articles with tie-ins to the
book chapters to show students how to read and understand primary literature to prepare them for
the scientific world
Animations that illustrate topics in protein purification, transcription, splicing reactions, cell division
and DNA replication and SDS-PAGE
Flash cards, test prep questions and PPT slides with images from the text
Resources for Professors:
Solutions Manual
Testbank Questions
Molecular
Biology
Second Edition
D a v i d P . C l a r k
N a n e t t e J . P a z d e r n i k
AMSTERDAM • BOSTON • HEIDELBERG • LONDON
NEW YORK • OXFORD • PARIS • SAN DIEGO
SAN FRANCISCO • SINGAPORE • SYDNEY • TOKYO
Academic Press is an imprint of Elsevier
Clark1570247 978-0-12-378594-7 X0001
Academic Press is an imprint of Elsevier
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Notices
Knowledge and best practice in this field are constantly changing. As new research and experience
broaden our understanding, changes in research methods, professional practices, or medical treatment
may become necessary.
Practitioners and researchers must always rely on their own experience and knowledge in evaluating
and using any information, methods, compounds, or experiments described herein. In using such
information or methods they should be mindful of their own safety and the safety of others, including
parties for whom they have a professional responsibility.
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ligence or otherwise, or from any use or operation of any methods, products, instructions, or ideas con-
tained in the material herein.
Library of Congress Cataloging-in-Publication Data
Clark, David P.
Molecular biology / David Clark, Nan Pazdernik. – 2nd ed.
p. cm.
Includes bibliographical references and index.
ISBN 978-0-12-378594-7 (alk. paper)
1. Molecular biology. 2. Molecular genetics. I. Pazdernik, Nanette Jean. II. Title.
QH506.C533 2013
572.8–dc23 2011038218
British Library Cataloguing-in-Publication Data
A catalogue record for this book is available from the British Library
For information on all Academic Press publications
visit our website at www.elsevierdirect.com
Printed in the United States of America
12 13 14 15 10 9 8 7 6 5 4 3 2 1
Dedication
This book is dedicated to Lonnie Russell who was to have been my coauthor
on the first edition. A few months after we started this project together, in early
July 2001, Lonnie drowned in the Atlantic Ocean off the coast of Brazil in
a tragic accident.
DPC
To my family, especially my husband and my three children. They have given
me the gift of time, courage, and strength. Time to actually write, courage to
continue even when I was tired, and the strength to do my very best work no
matter the circumstances.
NJP
Preface to second edition
The last quarter of the 20th century saw major scientific revolutions in genetics and
computer technology. Indeed, handling the vast amounts of genetic information gen-
erated nowadays depends on advanced computer technology. This book reflects this
massive surge in our understanding of the molecular foundations of genetics. Today,
we now know that genes are much more than the abstract entities proposed over a
century ago by Mendel. Genes are segments of DNA molecules, carrying encoded
information. Indeed, genes have now become chemical reagents to be manipulated in
the test tube in ever more complex ways. Over the next half century our understand-
ing of how living organisms function at the molecular level, together with our ability
to intervene, will expand in ways we are only just beginning to perceive.
A full understanding of how living organisms function includes an appreciation
of how cells operate at the molecular level. This is of vital importance to all of us as it
becomes ever more clear that molecular factors underlie many health problems and
diseases. While cancer is the “classic” case of a disease that only became understand-
able when its genetic basis was revealed, it is not the only one by any means. Today,
the molecular aspects of medicine are expanding rapidly and it is becoming possible
to tailor clinical treatment personally by taking into account the genetic make-up of
individual patients, an area known as personal genomics.
This book is intended as a survey-oriented textbook for upper-division students
in a variety of biological subdisciplines. In particular, it is aimed at final-year under-
graduates and beginning graduate students. This book does not attempt to be exhaus-
tive in its coverage, even as a textbook. There is a second book in this series, entitled
“Biotechnology,” which emphasizes the more practical applications of modern genet-
ics. We hope that both books together effectively survey the foundations and applica-
tions of modern molecular genetics.
Some of the students using this book will be well-versed in the basics of mod-
ern molecular biology, having taken courses in genetics, biochemistry, and cell biol-
ogy. However, others will not be so well-prepared, in part due to the continuing influx
of students into molecular biology from biology programs that are not oriented in a
molecular direction. For them we have tried to create a book whose early chapters
cover the basics before launching out into the depths. The first unit of five chapters
covers basic cell structure and genetics. This is followed by a survey of DNA, RNA,
and proteins and how they interact to provide the cell with genetic information.
Because of the continuing interest in applying molecular biology to an ever-
widening array of topics, we have tried to avoid overdoing detail (depth) in favor
of breadth. Molecular biology is applicable to more than just human medicine and
health. The genetic revolution has also greatly impacted other important areas such
as agriculture, veterinary medicine, animal behavior, evolution, and microbiology.
Students of these, and related disciplines, will all benefit from an improved under-
standing of molecular biology.
Changes in the Second Edition
This edition includes significant changes in comparison to the first edition of
Molecular Biology.
The flood of new sequence information has necessitated updates to many areas
of the book, especially Genomics and Systems Biology (Ch. 9), Proteomics (Ch. 15)
Bacterial Genetics (Ch. 25), and Molecular Evolution (Ch. 26). Perhaps the most
rapidly-changing area of molecular biology at present is the ever-expanding role of
RNA. Although scattered items occur throughout the book, particularly in Unit 4,
most of the major novel RNA topics, such as CRISPR and long-non-coding RNA, are
grouped together in Chapter 18, Regulation at the RNA level. vii
viii Preface
In this second edition we have re-ordered some of the chapters in a more logical
order. In particular, chapters on DNA technology and genomics that were toward the
end of the book have been moved far forward. This reflects the much greater role that
sequence analysis and genomics have come to play in the last two or three years.
We have also divided the book into modules, each of several related chapters. The
first module contains introductory material that experienced students can either skip
or skim through rapidly for the reasons cited above. Sections within chapters have
been numbered to aid in cross-reference. Review questions and conceptual problems
are now provided at the end of each chapter.
A new text element, “Focus on Relevant Research,” now appears throughout the
book. These feature discussions of recent papers in the field published by Cell Press.
The content focuses on helping the student learn how to read and understand primary
literature in hopes of preparing them for the scientific world. The complete articles
are also provided on the accompanying website for easy reference by students and
instructors.
The website also includes access to the Focus on Relevant Research Case Studies
that discuss the main topics of each chapter and build case studies around the content
to help students understand the basics of primary literature while allowing them to
make the appropriate connections to the text.
Other online materials to supplement the text include flashcards, animations,
quizzes to prepare for tests, and PowerPoint® slides with images for note-taking.
Students also have access to online references as they can then be directly linked to
Internet databases, such as PubMed® or ScienceDirect®.
Instructors also have access to the images from the book and test banks based on
the text and accompanying journal articles.
We look forward to hearing about your experiences, whether you use our
book for teaching or studying. Please send your comments, criticisms, and advice to
[email protected]. Thank you!
David Clark and Nan Pazdernik,
Carbondale, Illinois, April 2011
Acknowledgements
We would like to thank the following individuals for their help in providing infor-
mation, suggestions for improvement and encouragement: Malikah Abdullah-Israel,
Laurie Achenbach, Steven Ackerman, Rubina Ahsan, Kasirajan Ayyanathan, Marilyn
Baguinon, Joan Betz, Blake Bextine, Gail Breen, Douglas Burks, Mehmet Candas,
Jung-ren Chen, Helen Cronenberger, Phil Cunningham, Dennis Deluca, Linda
DeVeaux, Elizabeth De Stasio, Justin DiAngelo, Susan DiBartolomeis, Brian Downes,
Ioannis Eleftherianos, Robert Farrell, Elizabeth Blinstrup Good, Joyce Hardy, David
L. Herrin, Walter M. Holmes, Karen Jackson, Mark Kainz, Nemat Keyhani, Rebecca
Landsberg, Richard LeBaron, Richard Londraville, Larry Lowe, Charles Mallery,
Boriana Marintcheva, Stu Maxwell, Michelle McGehee, Ana Medrano, Thomas
Mennella, Donna Mueller, Khalil Nezhad , Dan Nickrent, Monica Oblinger, Rekha
Patel, Marianna Patrauchan, Neena Philips, Wanda Reygaert, Veronica Riha, Phillip
Ryals, Donald Seto, Dan Simmons, Joan Slonczewski, Malgosia Wilk-Blaszczak,
Hongzhuan Wu and Ding Xue.
ix
C h a p t e r
Cells and
1
Organisms
1. What Is Life?.............................3
2. Living Creatures Are Made
of Cells .......................................4
Before tackling the complex details of biology at the
3. Eubacteria and Archaea
molecular level, we need to get familiar with the sub-
Are Genetically Distinct .........8
ject of our investigation—the living world. First, we will
4. Eukaryotic Cells Are
consider what it means to be alive and then we shall sur-
Subdivided into
Compartments ..........................9 vey a range of cells and organisms that are often studied
by molecular biologists.
5. The Diversity
of Eukaryotes ..........................13 Life is impossible to define exactly, but a general idea
6. Haploidy, Diploidy, and is sufficient here. Living things consist of cells—some con-
the Eukaryote Cell Cycle ......14 sist of a single cell, whereas others are made from assem-
7. Organisms Are Classified .....15 blies of many million cells. Whatever the situation, living
8. Some Widely-Studied cells must grow, divide, and pass on their characteristics to
Organisms Serve their offspring. Molecular biology focuses on the details of
as Models ...............................16
growth and division. In particular, we are interested in how
9. Basic Characteristics
division is arranged so that each descendent can inherit
of a Model Organism ............27
their parents characteristics.
10. Purifying DNA from Model
Scientists have devoted much effort in investigating
Organisms ...............................27
certain favored organisms. In some cases this is a matter
11. Viruses Are Not
of convenience—bacteria, yeast, and other single-celled
Living Cells ..............................29
microorganisms are relatively easy to investigate. In other
12. Bacterial Viruses Infect
cases it is due to self-interest. Mice—and some other ani-
Bacteria ..................................30
mals—reveal much about humans, plants provide our food,
13. Human Viral Diseases
Are Common ...........................32 and viruses make us sick.
14. A Variety of Subcellular
Genetic Entities Exist ............32
Molecular Biology.
2 © 22001133 Elsevier Inc. All rights reserved.
1. What Is Life? 3
1. What Is Life?
Although there is no definition of life that suits all people, everyone has an idea of
what being alive means. Generally, it is accepted that something is alive if it can grow
and reproduce, at least during some stage of its existence. Thus, we still regard adults No satisfactory technical
who are no longer growing and those individuals beyond reproductive age as being definition of life exists. Despite
this we understand what
alive. We also regard sterile individuals, such as mules or worker bees as being alive,
life entails. In particular, life
even though they lack the ability to reproduce. Part of the difficulty in defining life
involves a dynamic balance
is the complication introduced by multicellular organisms. Although a multicellular
between duplication and
organism as a whole may not grow or reproduce some of its cells may still retain these
alteration.
abilities.
The basic ingredients needed to sustain life include the following:
l Genetic information Biological information is carried by the nucleic acid
molecules, deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). The
units of genetic information are known as genes, and each consists physically
of a segment of a nucleic acid molecule. DNA is used for long-term storage
of large amounts of genetic information (except by some viruses—see Ch. 21).
Whenever genetic information is actually used, working copies of the genes
are carried on RNA. The total genetic information possessed by an organism is
known as its genome. DNA genomes are maintained by replication, a process
where a copy of the DNA is produced by enzymes and then passed on to the
daughter cells.
l Mechanism for energy generation By itself, information is useless. Energy is
needed to put the genetic information to use. Living creatures must all obtain
energy for growth and reproduction. Metabolism is the set of processes in
which energy is acquired, liberated, and used for biosynthesis of cell compo-
nents, then catabolized and recycled. Living organisms use raw material from
the environment to grow and reproduce.
l Machinery for making more living matter Synthesis of new cell compo-
nents requires chemical machinery. In particular, the ribosomes are needed for
making proteins, the macromolecules that make up the bulk of all living tis-
sue. These tiny subcellular machines allow the organism to grow and maintain
itself.
l A characteristic outward physical form Living creatures all have a material
body that is characteristic for each type of life-form. This structure contains all
the metabolic and biosynthetic machinery for generating energy and making
new living matter. It also contains the DNA molecules that carry the genome.
The form has levels of organization from single cells to tissues, organs, and
organ systems of multicellular life-forms.
l Identity or Self All living organisms have what one might call an identity. The
term self-replication implies that an organism knows to make a copy of itself—
not merely to assemble random organic material. This concept of “self” versus
“non-self” is very evident in the immune systems that protect higher animals
against disease. But even primitive creatures attempt to preserve their own
existence.
deoxyribonucleic acid (DNA) The nucleic acid polymer of which the genes are made
gene A unit of genetic information
genome The entire genetic information from an individual
macromolecule Large polymeric molecule; in living cells especially DNA, RNA, protein, or polysaccharide
metabolism The processes by which nutrient molecules are transported and transformed within the cell to release energy and to provide new cell
material
nucleic acid Polymer made of nucleotides that carries genetic information
replication Duplication of DNA prior to cell division
ribonucleic acid (RNA) Nucleic acid that differs from DNA in having ribose in place of deoxyribose and having uracil in place of thymine
ribosome The cell’s machinery for making proteins