Academic Cell Molecular biology-Academic Press (2019) PDF
Preview Academic Cell Molecular biology-Academic Press (2019)
Molecular Biology http://booksite.elsevier.com/9780128132883/index.php Molecular Biology, Third Edition David P. Clark, Nanette J. Pazdernik and Michelle R. McGehee Molecular Biology Third 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 M i c h e l l e R . M c G e h e e AcademicPressisanimprintofElsevier 125LondonWall,LondonEC2Y5AS,UnitedKingdom 525BStreet,Suite1650,SanDiego,CA92101,UnitedStates 50HampshireStreet,5thFloor,Cambridge,MA02139,UnitedStates TheBoulevard,LangfordLane,Kidlington,OxfordOX51GB,UnitedKingdom Copyrightr2019ElsevierInc.Allrightsreserved. Nopartofthispublicationmaybereproducedortransmittedinanyformorbyanymeans,electronic ormechanical,includingphotocopying,recording,oranyinformationstorageandretrievalsystem, withoutpermissioninwritingfromthepublisher.Detailsonhowtoseekpermission,further informationaboutthePublisher’spermissionspoliciesandourarrangementswithorganizations suchastheCopyrightClearanceCenterandtheCopyrightLicensingAgency,canbefoundatour website:www.elsevier.com/permissions. ThisbookandtheindividualcontributionscontainedinitareprotectedundercopyrightbythePublisher (otherthanasmaybenotedherein). Notices Knowledgeandbestpracticeinthisfieldareconstantlychanging.Asnewresearchandexperience broadenourunderstanding,changesinresearchmethods,professionalpractices,ormedicaltreatment maybecomenecessary. Practitionersandresearchersmustalwaysrelyontheirownexperienceandknowledgeinevaluatingand usinganyinformation,methods,compounds,orexperimentsdescribedherein.Inusingsuchinformation ormethodstheyshouldbemindfuloftheirownsafetyandthesafetyofothers,includingpartiesfor whomtheyhaveaprofessionalresponsibility. Tothefullestextentofthelaw,neitherthePublishernortheauthors,contributors,oreditors,assumeany liabilityforanyinjuryand/ordamagetopersonsorpropertyasamatterofproductsliability,negligence orotherwise,orfromanyuseoroperationofanymethods,products,instructions,orideascontainedin thematerialherein. BritishLibraryCataloguing-in-PublicationData AcataloguerecordforthisbookisavailablefromtheBritishLibrary LibraryofCongressCataloging-in-PublicationData AcatalogrecordforthisbookisavailablefromtheLibraryofCongress ISBN:978-0-12-813288-3 ForInformationonallAcademicPresspublications visitourwebsiteathttps://www.elsevier.com/books-and-journals Publisher:AndreWolff AcquisitionEditor:MaryPreap EditorialProjectManager:KathyPadilla ProductionProjectManager:PoulouseJoseph CoverDesigner:MilesHitchen TypesetbyMPSLimited,Chennai,India Dedication This book is dedicatedto Lonnie Russellwho was to have been mycoauthor on thefirst edition. Afew months after we started this projecttogether, inearly July 2001,Lonnie drowned inthe Atlantic Ocean off thecoast ofBrazilin a tragicaccident. DPC To my family, especiallymy husbandand mythree children. They have given me thegiftof time,courage,and strength. Time to actuallywrite, courage to continue even when Iwas tired,and thestrengthto do my verybestwork no matter thecircumstances. NJP This book is dedicated to myparents and brother fortheirencouraging words and unwavering support through it all,andto my special friends,Mark and Dianne, forthe giftof their time and opportunities forbalance. MRM Preface to Third Edition The last few decades have seen major advances in both biology and information technology. Indeed, processing the vast amounts of genetic data generated depends on advanced computer technology. This book reflects this massive surge in under- standing the molecular foundations of genetics. Today we 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 and, more recently, even inliving organisms. Over the next half century our understanding 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. In particular, this will have a major impact in David P. Clark the area of health. Many people are now having their own genomes partly or fully sequenced and it is becoming possible to tailor clinical treatment individually by using the geneticdata of individual patients, an area known as personal genomics. Nonetheless, because molecular biology illuminates an ever-widening array of topics, we have avoided overdoing detail in favor of wider coverage. Molecular biol- ogy applies to far more than just health care and has greatly impacted other areas such asagriculture, animal behavior, evolution, and microbiology. This book is intended for upper division students in a variety of biological disci- plines. In particular it is aimed at final year undergraduates and beginning graduate students. This book does not attempt to be exhaustive in its coverage. There is a companion volume, entitled “Biotechnology,” that emphasizes the more practical aspects of modern genetics. Together we hope that both books effectively survey the foundations and applications of modern molecular genetics. Some students who are using this book will already be well grounded in molecu- lar biology, due to having taken courses in genetics, biochemistry, and cell biology. However, others will not be so well prepared, due to the continued influx into Nanette J. Pazdernik molecular biology of students from biology programs that are not molecular in their orientation. For them we have tried to create a book whose early chapters cover the basics before launchingout into the depths. The book is divided into modules, each of several related chapters. The first module contains introductory material that experienced students can either skip or skim through rapidly. Sections within chapters have been numbered to aid in cross- reference. Review questions and suggestions for further reading are provided at the end of each chapter. Changes in the Third Edition Although much of its basics have remained largely unchanged, several areas of molecular biology have shown spectacular growth in recent years. These include the overwhelming flood of sequence information that is emerging faster than it can be thoroughly analyzed. Many areas, such as molecular evolution and metagenomics Michelle R. McGehee have been stimulated by this plethora of new data. The related area of epigenomics, has recently flourished, largely due to new analytical techniques. This has been cov- ered ina new chapter, Epigenetics and Epigenomics (Chapter 22). The role of RNA is still expanding with the discovery of new classes of noncod- ing RNA most with new regulatory roles. But the most publicized advance has been the emergence of genome editing techniques based on the CRISPR system of bacte- ria.Two new chapters, NoncodingRNA(Chapter 19)and Genome Defense(includ- ing CRISPR and its applications; Chapter 20) have been designed to accommodate these advances. xiii xiv PrefacetoThirdEdition Online Materials The website contains the “Focus on Relevant Research” features. These include dis- cussions of recent papers in the field published by Cell Press and build case studies around the content. The objective is to help students learn how to read and under- stand the primary literature in hopes of preparing them for the scientific world. “Conceptual Questions,” which were previously incorporated in the book are now on thewebsite as well. 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. Professors have access to all of the previously mentioned, including PowerPoint slides of the book and journal articles, and test banksfor thebook and journal articles. Thank you! David P. Clark, NanetteJ. Pazdernik and Michelle R.McGehee Acknowledgments Wewouldliketothank thefollowing individuals fortheirhelpinprovidinginforma- tion, suggestions for improvement, and encouragement: Malikah Abdullah-Israel, Laurie Achenbach, Steven Ackerman, Rubina Ahsan, Kasirajan Ayyanathan, Marilyn Baguinon, Alex Berezow, 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, Ana Medrano, Thomas Mennella, Donna Mueller, Khalil Zaynali 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, HongzhuanWu,and Ding Xue. xv C h1a p t e r Cells and Organisms 1. WhatIsLife?............................2 2. LivingCreaturesAreMade ofCells.......................................4 Before tackling the complex details of biology at the 3. EubacteriaandArchaea AreGeneticallyDistinct........9 molecular level, we need to get familiar with the 4. EukaryoticCellsAre subject of our investigation—the living world. First, we SubdividedInto will consider what it means to be alive and then we shall Compartments........................10 survey a range of cells and organisms that are often 5. TheDiversityof Eukaryotes..............................13 studied by molecular biologists. 6. Haploidy,Diploidy,and Life is impossible to define exactly, but a general idea theEukaryoteCellCycle.....13 is sufficient here. Living things consist of cells—some 7. OrganismsAreClassified....15 consist of a single cell, whereas others are made from 8. SomeWidelyStudied assemblies of many million cells. Whatever the situation, OrganismsServeas Models.....................................16 living cells must grow, divide, and pass on their character- 9. BasicCharacteristics istics to their offspring. Molecular biology focuses on the ofaModelOrganism...........28 details of growth and division. In particular, we are inter- 10. PurifyingDNAFrom ested in how division is arranged so that each descendent ModelOrganisms..................28 can inherit their parents characteristics. 11. VirusesAreNotLiving Cells.........................................30 Scientists have devoted much effort in investigating 12. BacterialVirusesInfect certain favored organisms. In some cases this is a matter Bacteria...................................31 of convenience—bacteria, yeast, and other single-celled 13. HumanViralDiseases microorganisms are relatively easy to investigate. In other AreCommon..........................33 cases it is due to self-interest. Mice—and some other 14. AVarietyofSubcellular GeneticEntitiesExist...........33 animals—reveal much about humans, plants provide our ReviewQuestions.........................36 food, and viruses make us sick. FurtherReading.............................37 MolecularBiology.DOI:https://doi.org/10.1016/B978-0-12-813288-3.00001-X 2 ©2019ElsevierInc.Allrightsreserved.
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