As teachers, we know that undergraduate science education is evolving. Simply conveying facts does not produce a scientifically literate student, a long-held perception now reinforced by numerous studies. Students of science need more: a better window on what science is and how it is done, a clear presentation of key concepts that rises above the recitation of details, an articulation of the philosophical underpinnings of the scientific discipline at hand, exercises that demand analysis of real data, and an appreciation for the contributions of science to the well-being of humans throughout the world. As undergraduate science educators rise to these challenges, we are faced with both higher numbers of students and declining resources. How can we all do more with less?

Textbooks are an important part of the equation. A good textbook must now be more than a guide to the information that defines a discipline. For instructors, a textbook must organize information, incorporate assessment tools, and provide resources to help bring a discipline to life. For students, a textbook must relate science to everyday experience, highlight the key concepts, and show each student the process that generated those key concepts.

This book had its genesis at a meeting of the authors in Napa Valley in January 2006. From the outset, we set ambitious goals designed to address the key challenges we face as teachers.

Students see science as a set of facts rather than an active human endeavor. Molecular biology has a wealth of important stories to tell. We wanted to convey the excitement that drives modern molecular biology, the creativity at the bench, and the genuine wonder that takes hold as the workings of a new biological process are revealed. This theme is set in the first chapter, dedicated in large measure to an introduction to the scientific process. Every chapter then begins with a Moment of Discovery, highlighting a researcher’s own description of a memorable moment in his or her career. After Chapter 1, every chapter ends with a How We Know section, with stories relating the often circuitous path to a new insight. Additional anecdotes—scientists in action—are woven into the text and the accompanying Highlights. As students read the text, the laboratories and the people behind the discoveries will never be far away.

This second edition is an update, and much more. It has allowed us to refine the initial vision we had when we started this project and to augment that vision with unparalleled resources that will bring the subject to life for students and educators alike.

MOMENT OF DISCOVERY

Scientific breakthroughs represent the exhilarating culmination of a lot of hard work. Each chapter opens with a description of a significant breakthrough in molecular biology, told by the scientist who made the discovery. The scientists featured in the Moments of Discovery are David Allis, Norm Arnheim, Bonnie Bassler, Steve Benner, James Berger, Carlos Bustamante, Rose Byrne, Jamie Cate, Joe DeRisi, Roxana Georgescu, Lin He, Tracy Johnson, Melissa Jurica, Judith Kimble, Robert Lehman, Steve Mayo, Harry Noller, Smita Patel, Lorraine Symington, Jack Szostak, Robert Tjian, and Wei Yang.

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HOW WE KNOW

Each chapter ends with a How We Know section that combines fascinating stories of research and researchers with experimental data for students to analyze.

Students often view science as a completed story. The reality is far different. Data can take a researcher in unexpected directions. An experiment designed to test one hypothesis can end up revealing something quite different. The analysis of real data is a fundamental skill to be honed by every student of science. We have tried to address this need aggressively. Each chapter in this text features a challenging set of problems, including at least one requiring the analysis of data from the scientific literature. Many of these are linked to the discoveries described in the How We Know sections. Each chapter also ends with some Unanswered Questions, providing just a sampling of the endless challenges that remain for those with the motivation to tackle them.

UNANSWERED QUESTIONS

A short section at the end of each chapter describes important areas still open to discovery, showing students that even well-covered subjects, such as nucleic acid structure and DNA replication, are far from fully explored.

END-OF-CHAPTER PROBLEMS

Extensive problem sets at the end of each chapter give students the opportunity to think about and work with the chapter’s key ideas. New problems have been added in each chapter for this second edition. Each problem set concludes with a Data Analysis Problem, giving students the critical experience of interpreting real research data. Solutions to all problems can be found at the back of the book.

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Students get lost in the details. Presenting the major concepts clearly, in the text as well as in the illustrations, is crucial to teaching students how science is done. We have worked to use straightforward language and a conversational writing style to draw students in to the material. We have collaborated closely with our illustrator, Adam Steinberg, to create clean, focused figures. Featured Key Conventions highlight the implicit but often unstated conventions used when sequences and structures are displayed and in naming biological molecules.

KEY CONVENTIONS

In brief paragraphs, the Key Conventions clearly lay out for students some fundamental principles often glossed over.

ILLUSTRATIONS

Good figures should speak for themselves. We have worked to keep our figures simple and the figure legends as brief as possible. The illustrations in the text are the product of close collaboration with our colleague Adam Steinberg. Together with the talented artists at Dragonfly Media Group, Adam has helped to hone and implement our vision.

Students see evolution as an abstract theory. Every time a molecular biologist studies a developmental pathway in nematodes, identifies key parts of an enzyme active site by determining what parts are conserved among species, or searches for the gene underlying a human genetic disease, he or she is relying on evolutionary theory. Evolution is a foundational concept, upon which every discipline in the biological sciences is built. In this text, evolution is a theme that pervades every chapter, beginning with a major section in Chapter 1 and continuing as the topic of many Highlights and chapter segments.

HIGHLIGHTS

These discussions are designed to enhance students’ understanding and appreciation of the relevance of each chapter’s material. There are four categories of Highlights:

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EXPERIMENTAL TECHNIQUES

As researchers, we know that it is critical to understand the benefits and limitations of experimental techniques. We strive to give students a sense of how an experiment is designed and what makes the use of a particular technique or model organism appropriate. The techniques covered in this book are:

Ames test 

Chemical modification interference 

Chemical protection footprinting 

Chemical synthesis of nucleic acids 

ChIP-Chip 

ChIP-Seq 

Chromatography

     Affinity chromatography 

           Using terminal tags 

           Using tandem affinity purification (TAP) tags 

     Column chromatography 

     Gel-exclusion chromatography 

     Ion-exchange chromatography 

     Thin-layer chromatography 

CRISPR/Cas 

Detecting A=T-rich segments of DNA by denaturation analysis 

DNA cloning 

DNA cloning with artificial chromosomes (BACs, YACs) 

DNA footprinting 

DNA genotyping (DNA fingerprinting, DNA profiling, STR analysis) 

DNA library creation (cDNA, genomic) 

DNA microarrays 

DNA sequencing

     Automated Sanger sequencing 

     Deep sequencing 

     Genome sequencing techniques 

     Ion torrent 

     Next generation sequencing 

     Pyrosequencing 

     Reversible terminator sequencing 

     Sanger sequencing 

     Single molecule real time (SMRT) sequencing 

Electrophoresis

     Agarose gel electrophoresis 

     Isoelectric focusing 

     Pulsed field gel electrophoresis (PFGE) 

     Sodium dodecyl sulfate–polyacrylamide gel electrophoresis (SDS-PAGE) 

     Two-dimensional gel electrophoresis 

Electrophoretic mobility shift assay (EMSA) 

Electroporation 

Epitope tagging 

Haplotype analysis 

Immunoprecipitation 

Linkage analysis 

Localization of GFP fusion proteins 

Mass spectrometry 

Northern blotting 

Nuclear magnetic resonance (NMR) 

Optical trapping 

Photolithography 

Phylogenetic analysis 

Phylogenetic profiling 

Polymerase chain reaction (PCR) 

     Quantitative PCR (qPCR) 

     Reverse transcriptase PCR (RT-PCR) 

Protein chips 

Protein localization via indirect immunofluorescence 

Recombinant protein expression 

RNA interference (RNAi) 

RNA-Seq 

Selection and screening 

Site-directed mutagenesis 

Somatic cell nuclear transfer (SCNT) 

Southern blotting 

Transformation 

Western blotting 

X-ray crystallography 

Yeast three-hybrid analysis 

Yeast two-hybrid analysis 

NEW AND UPDATED CONTENT

The second edition addresses recent discoveries and advances, corresponding to our ever-changing understanding of molecular biology. In addition to the text updates listed here, there are numerous new figures and photos, along with significantly updated figures in every chapter. There are also new end-of-chapter problems for every chapter and many new Unanswered Questions.

Chapter 1

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Chapter 2

Chapter 3

Chapter 4

Chapter 5

Chapter 6

Chapter 7

Chapter 8

Chapter 10

Chapter 11

Chapter 12

Chapter 13

Chapter 14

Chapter 15

Chapter 16

Chapter 18

Chapter 19

Chapter 22

MEDIA

Simulations

One of our central goals in tackling the revision of this textbook was to provide special resources to engage students (and educators) in molecular biology. New to the second edition are simulations that cover core molecular biology concepts and techniques. Created using the art from the text, the simulations reinforce students’ understanding by allowing them to interact with the structures and processes they have encountered. A gamelike format guides students through the simulations, unlocking them in order, and multiple-choice questions after each simulation ensure that instructors can assess whether students have thoroughly understood each topic. These simulations are the product of many days of meetings among the authors, editors, and media developers. From story-boarding to the finished product, these simulations were one of the most challenging as well as stimulating efforts associated with preparing the second edition. We are excited to present this new approach to learning key concepts.

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Nucleotide Structure (Chapter 3)

DNA/RNA Structure (Chapter 6)

PCR (Chapter 7)

Sanger Sequencing (Chapter 7)

CRISPR (Chapters 7 and 19)

DNA Replication (Chapter 11)

DNA Polymerase (Chapter 11)

Mutation and Repair (Chapter 12)

Transcription (Chapter 15)

mRNA Processing (Chapter 16)

Translation (Chapter 18)

Nature Articles with Assessment

These articles engage students in reading about primary research and encourage critical thinking. Specifically selected for both alignment with the text coverage and exploration of identified difficult topics, the Nature articles include assessment questions that can be automatically graded. Also included are open-ended questions that are suitable for use in flipped classrooms and active learning discussions either in class or online.

The simulations and Nature articles for Molecular Biology: Principles and Practice are available in our LaunchPad system, along with many additional resources.

This dynamic, fully integrated learning environment brings together all of our teaching and learning resources in one place. It also contains the fully interactive e-Book and other newly updated resources for students and instructors, including the following:

New Clicker Questions allow instructors to integrate active learning in the classroom and to assess students’ understanding of key concepts during lectures.

Updated Test Bank contains at least 40 multiple-choice and short-answer questions for each chapter.

allows students to test their comprehension of the chapter concepts. The system adapts to students’ individual level of preparedness by giving them questions at varying levels of difficulty, depending on whether they answer a question without help, or they need help but eventually get the question right, or they are unable to answer the question. Links to the appropriate e-Book section, hints, and feedback help students realize where they need more practice on a topic.

Key Term Flashcards allow students to review the definitions of all the glossary terms and quiz themselves.

Textbook Images and Tables are offered as high-resolution JPEG files. Each image has been fully optimized to increase type size and adjust color saturation. These images have been tested in a large lecture hall to ensure maximum clarity and visibility.

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