Introduction



Chapter 1  Amino Acids to Proteins



1.1Protein Composition



1.2Protein Conformations



1.2.1Describing Protein Structure



1.2.2Chemical and Physical Basis for Protein Folding



1.3Protein Structure and Function:A Few Examples



1.4The Dynamics of Proteins



1.5Experiments



Summary



Vocabulary



Review Questions



Exploration Questions







Chapter 2  Nucleic Acids



2.1Properties of a Genetic Material



2.2Nucleic Acids and DNA structure



2.2.1Nucleotides



2.2.2General Structure of Nucleic Acids



2.2.3Structure of DNA



2.3DNA as the Genetic Material



2.4DNA in the Cell



2.5RNA (Ribonucleic Acid)



2.6Experiments



Summary



Vocabulary



Review Questions



Exploration Questions







Chapter 3  Transcription in
Prokaryotes:Mechanism and Regulation



3.1Why Use an RNA Intermediate



3.2Mechanism of Transcription



3.2.1Promoters



3.2.2RNA Polymerase



3.2.3Transcription Mechanism in Three Phases



3.3Regulation of Gene Expression in Prokaryotes



3.3.1Coordinate Regulation



3.3.2The Lac Operon



3.3.3The Trp Operon



3.3.4Ara and Gal Operons



3.4Experiments



Summary



Vocabulary



Review Questions



Exploration Questions







Chapter 4  Transcription in
Eukaryotes:Mechanism and Regulation



4.1Eukaryotic RNA Polymerases



4.2Eukaryotic Promoters



4.3General Transcription Factors and Initiation



4.3.1TFⅡD



4.3.2Other TFⅡs



4.3.3General Transcription Factors for RNA Polymerase Ⅰand Ⅲ



4.4Specific Transcription Factors and Transcriptional Regulation



4.4.1Activators



4.4.2Repressors



4.4.3Enhancers and Silencers



4.5Structures of Specific Transcription Factors



4.5.1DNA-Binding Motifs in Prokaryotes



4.5.2DNA-Binding Motifs in Eukaryotes



4.6Experiments



4.6.1RNA Polymerase Targets



4.6.2Modularity of Specific Transcription Factors



Vocabulary



Review Questions



Exploration Questions







Chapter 5  mRNA Modifications in
Eukaryotes



5.1Capping



5.2Polyadenylation



5.3Splicing



5.3.1The Basic Splicing Reaction



5.3.2Proteins Involved in Splicing



5.3.3Self-Splicing



5.3.4Trans-Splicing



5.3.5Reasons for Introns



5.4mRNA Editing



5.5Experiments



Summary



Vocabulary



Review Questions



Exploration Questions







Chapter 6  Translation



6.1The Genetic Code



6.2Mechanism of Translation in Prokaryotes



6.2.1Initiation



6.2.2Elongation



6.2.3Termination



6.3Translation in Eukaryotes



6.4tRNA Structure and Wobble



6.4.1Anti-codons



6.4.2Wobble



6.5Experiments



6.5.1Deciphering the Genetic Code



6.5.2Direction of Translation



Summary



Vocabulary



Review Questions



Exploration Questions







Chapter 7  Regulation of Gene Expression
in Eukaryotes



7.1Histones and Transcriptional Regulation



7.1.1Histones and DNA Organization



7.1.2Histones and Transcription



7.1.3Covalent Modification of Histones



7.1.4Proteins that Recognize and Modify Histones



7.2Post-Transcriptional Regulation



7.3Nuclear Export



7.4RNA Stability



7.4.1mRNA Stability Regulation by Proteins



7.4.2mRNA Stability Regulation by Small RNAs



7.5Translational Control



7.5.1Global Control



7.5.2mRNA-Specific Control



7.6mRNA Localization



7.7Protein Regulation



7.8Experiments



7.8.1Beads-on-a-string Structure



7.8.2Repression of Gene Expression in Heterochromatin



Summary



Vocabulary



Review Questions



Exploration Questions







Chapter 8  DNA Replication



8.1Semi-Conservative Replication



8.2Initiation of Replication



8.3Semi-Discontinuous Replication



8.4Elongation of Replication and its Proteins



8.4.1Helicase and SSBs



8.4.2DNA Polymerases



8.4.3Explanation for 3′→5′Synthesis



8.4.4Primers



8.5DNA Topology



8.6DNA Replication in Eukaryotes



8.6.1Initiation of DNA Replication in Eukaryotes



8.6.2Telomeres



8.7Experiments



Summary



Vocabulary



Review Questions



Exploration Questions







Chapter 9  Mutations and Mutation Repair



9.1DNA Damage and Mutations



9.2Point Mutations



9.2.1Mismatched Base



9.2.2Spontaneous Mutations



9.2.3Induced Mutations



9.3Insertions and Deletions



9.3.1Strand Slippage



9.3.2Transposons



9.3.3Intercalating Agents



9.4Large-Scale DNA Changes



9.5Consequences of DNA Mutations



9.5.1Consequences of Point Mutations



9.5.2Consequences of Insertions and Deletions



9.5.3Consequences of Translocations



9.5.4Mutation Hot Spots



9.6Mutation Repair



9.6.1Direct Reversal



9.6.2Mismatch Repair



9.6.3Nucleotide Excision Repair



9.6.4Base Excision Repair



9.6.5Double-Stranded Break Repair



9.7Experiments



9.7.1Nucleotide Excision Repair and Human Disease



9.7.2The Ames Test



Summary



Vocabulary



Review Questions



Exploration Questions







Chapter 10  Recombination



10.1Homologous Recombination



10.1.1Mechanism for Crossing-Over



10.1.2Mechanism for Double-Stranded Break Repair



10.1.3The RecBCD Pathway



10.1.4Gene Conversion



10.2Non-homologous Recombination



10.2.1Transposons



10.2.2Retrotransposons



10.2.3Bacteriophage λ Integration



Summary



Vocabulary



Review Questions



Exploration Questions







Answers to Review Questions



Index(Chinese)



Index(English)











緒論



第1章從氨基酸到蛋白質



1.1蛋白質的組成



1.2蛋白質的構像



1.2.1描述蛋白質的結構



1.2.2蛋白質折疊的化學和物理基礎



1.3蛋白質的結構與功能：幾個例子



1.4蛋白質動力學



1.5實驗研究



小結



詞彙



習題



思考題







第2章核酸



2.1遺傳物質的性質



2.2核酸與DNA結構



2.2.1核苷酸



2.2.2核酸的一般結構



2.2.3DNA的結構



2.3DNA作為遺傳物質



2.4細胞中的DNA



2.5RNA（核糖核酸）



2.6實驗研究



小結



詞彙



習題



思考題







第3章原核生物轉錄：機理與調控



3.1為什麼使用RNA作為中間物



3.2轉錄機理



3.2.1啟動子



3.2.2RNA聚合酶



3.2.3轉錄機理的三個階段



3.3原核生物基因表達調控



3.3.1協同調控



3.3.2乳糖操縱子



3.3.3色氨酸操縱子



3.3.4阿拉伯糖與半乳糖操縱子



3.4實驗研究



小結



詞彙



習題



思考題







第4章真核生物轉錄：機理與調控



4.1真核生物RNA聚合酶



4.2真核生物啟動子



4.3通用轉錄因子與轉錄起始



4.3.1TFⅡD



4.3.2其他TFⅡs



4.3.3RNA聚合酶Ⅰ和Ⅲ的通用轉錄因子



4.4特異轉錄因子與轉錄調控



4.4.1激活蛋白



4.4.2阻遏蛋白



4.4.3增強子和沉默子



4.5特異轉錄因子的結構



4.5.1原核生物DNA結合基序



4.5.2真核生物DNA結合基序



4.6實驗研究



4.6.1RNA聚合酶的目標



4.6.2特異轉錄因子的模塊化Summary



詞彙



習題



思考題







第5章真核生物mRNA的修飾



5.1加帽



5.2聚腺苷酸化



5.3剪接



5.3.1基本的剪接反應



5.3.2在剪接中發揮作用的蛋白質



5.3.3自我剪接



5.3.4反式剪接



5.3.5內含子存在的原因



5.4mRNA編輯



5.5實驗研究



小結



詞彙



習題



思考題







第6章翻譯



6.1遺傳密碼



6.2原核生物翻譯機理



6.2.1起始



6.2.2延伸



6.2.3終止



6.3真核生物翻譯



6.4tRNA結構與搖擺



6.4.1反密碼子



6.4.2搖擺



6.5實驗研究



6.5.1破譯遺傳密碼



6.5.2翻譯的方向



小結



詞彙



習題



思考題







第7章真核生物基因表達調控



7.1組蛋白與轉錄調控



7.1.1組蛋白與DNA組織



7.1.2組蛋白與轉錄



7.1.3組蛋白的共價修飾



7.1.4識別和修飾組蛋白的蛋白質



7.2轉錄後調控



7.3細胞核輸出



7.4RNA穩定性



7.4.1蛋白質調控mRNA穩定性



7.4.2小RNA調控mRNA穩定性



7.5翻譯調控



7.5.1全局控制



7.5.2mRNA特異性控制



7.6mRNA定位



7.7蛋白質調控



7.8實驗研究



7.8.1線珠結構



7.8.2異染色質中基因表達的阻遏



小結



詞彙



習題



思考題







第8章DNA復制



8.1半保留復制



8.2復制的起始



8.3半不連續復制



8.4復制延伸及其相關蛋白



8.4.1解旋酶與SSB



8.4.2DNA聚合酶



8.4.3關於3′→5′合成



8.4.4引物



8.5DNA拓撲學



8.6真核生物DNA復制



8.6.1真核生物DNA復制起始



8.6.2端粒



8.7實驗研究



小結



詞彙



習題



思考題







第9章突變與突變修復



9.1DNA損傷與突變



9.2點突變



9.2.1錯配的堿基



9.2.2自發突變



9.2.3誘發突變



9.3插入和缺失



9.3.1鏈滑動



9.3.2轉座子



9.3.3嵌入劑



9.4大規模DNA變化



9.5DNA突變的後果



9.5.1點突變的後果



9.5.2插入和缺失的後果



9.5.3易位的後果



9.5.4突變熱點



9.6突變修復



9.6.1直接回復



9.6.2錯配修復



9.6.3核苷酸切除修復



9.6.4堿基切除修復



9.6.5雙鏈斷裂修復



9.7實驗研究



9.7.1核苷酸切除修復與人類疾病



9.7.2埃姆斯測驗法



小結



詞彙



習題



思考題







第10章重組



10.1同源重組



10.1.1交換機理



10.1.2雙鏈斷裂修復機理



10.1.3RecBCD途徑



10.1.4基因轉換



10.2非同源重組



10.2.1轉座子



10.2.2反轉錄轉座子



10.2.3λ噬菌體的整合



小結



詞彙



習題



思考題







習題答案



中文索引



英文索引



參考文獻

Foreword   



Dear Readers,



With this new edition of An Introduction to Molecular Biology with Chinese
Translation we continue our mission that has captivated and motivated us from the
beginning.Firstly, to convey fundamental concepts of how genetic information is
replicated, expressed and modified.Secondly, to assist Chinese readers in
learning words and phrases in the English language used to describe these
processes.We have been honored by the positive feedback of students over the
past decade, and used these comments to maintain and improve the qualities of
this book that students value the most: the native English main text, accurate
translation, clear figures and audio files narrated in American English.



The past decade has witnessed remarkable advancements in biotechnology — the
reduction in cost of DNA sequencing and synthesis, the application of genome
engineering techniques such as CRISPR, the use of transposases for generating
DNA libraries and profiling chromatin, to name just a few.In each case, these
advances would not have been made if not for basic research into genome
structure, stability, and expression.We have an enormous amount still to gain
from the basic study of molecular biology in a variety of organisms, as well as
the innovative application of discoveries to solve challenges in
biotechnology.It is our sincere hope that this new edition will advance the
goal of introducing Chinese and English-speaking students to this exciting
field and fostering global collaboration.



Best wishes,







The Authors



Jan 2018 











前言



親愛的讀者：



在新版《英漢對照分子生物學導論》中，我們繼續努力達成促使與激勵我們編寫本書的初衷——首先，講述遺傳信息是如何進行復制、表達和改變的基本概念；其次，幫助中國讀者學習描述這些生命過程的英語詞彙與短語。我們很榮幸在過去十年裡收到不少學生對本書的積極反饋，這些反饋表明了學生關心本書的以下品質：地道的英語課文，準確的中文翻譯，清晰的圖解以及美式英語音頻文件。在新版《英漢對照分子生物學導論》中，這些品質都得到了維護與提升。



過去十年裡生物技術領域取得了令人矚目的成就——DNA測序與合成成本顯著降低、CRISPR等基因編輯技術的應用、使用轉座酶生成DNA文庫及分析染色質等等，不勝枚舉。具體到某一方面，所有成就的取得都是建立在對基因組結構與穩定性以及基因表達特性的基礎研究之上的。現今，分子生物學基礎研究仍有待在許多不同生物中展開，生物技術領域所面臨的挑戰也需要創造性地應用分子生物學基礎研究成果來應對。我們誠摯希望新版《英漢對照分子生物學導論》能有助於引導中國學生與英語國家學生進入這一令人興奮的領域並培養全球合作精神。



致以良好祝願！







作者



2018年1月











Foreword to the First Edition   



One of the wonderful things about molecular biology is that the field depends
on constant communication.Important questions can only be answered through the
collaboration of researchers from all over the world, who each contribute their
piece of the puzzle and build on each others work.But this lively interaction
also poses challenges, particularly the problem of language.How can scientists
collaborate if they speak and publish in different languages?



As it happens, the language of molecular biology is now English.The vast
majority of published research is in English, as are most international
conferences.The language has become so central because a large number of
scientists and research centers that have made important contributions to
molecular biology were, and still are, based in England and the United
States.The predominance of one language is not necessarily fair, but it is a
reality that most professionals working in the field must face.



For Chinese students, learning biology in English can be very exciting, but
also quite challenging.Chinese and English are very different languages, with
completely different phonetics and writing systems.On top of this, biology
textbooks and articles in English are especially difficult to understand, even
for native English speakers.There is a lot of unique vocabularies, and there
may be sentence structures particular to scientific writing.



In many cases, Chinese students are presented with a giant textbook only in
English and instructors hope for the best.Our experience as teachers of
molecular biology in China is that this approach is unrealistic.Most students
in China at this time, especially those who are on a course of scientific
study, do not have enough training in English to understand textbooks written
for native English speakers.Struggling with the language often comes at the
expense of actually learning the concepts and principles of molecular biology.



We have put together this book with the hope of creating a more realistic, more
sympathetic, and more specialized approach to learn molecular biology in
English.Advanced students can learn by reading the English portion of the book,
and refer to the Chinese translation to check their understanding, or for
reference on individual words.Beginners in English can learn from the Chinese
portion, and refer to the English for an introduction to vocabularies.With both
languages present, students and instructors have more options for how to learn!



An added feature of this book is that all the English texts have been
accompanied by audio files.They are especially helpful for those who intend to
improve their listening comprehension of academic English.Meanwhile,the
elaborately designed figures will enable readers to understand concepts and
principles in molecular terms much more easily.



The book covers the material that we feel an advanced, undergraduate student of
molecular biology should know.Unlike many textbooks used for molecular biology,
this is not meant as a reference book, a large volume where one can look up any
facts about the cell.Those kinds of volumes have their use, but we feel that it
is unproductive to present students with such piles of information.If students
can master all of the information present even in this relatively brief book,
they will already be more informed than most students of the field, and even
some professionals!



It is with great excitement that we invite you to learn molecular biology with
us in English.This is an important age for China and the rest of the world!As
China becomes every day more prosperous, its research centers and companies are
improving and have much to offer scientific communities around the world.At the
same time, the continued development of China depends on the knowledge and
skills that have been developed in the West and continue to flourish there.In
molecular biology, there is much to gain if we can share and communicate with
each other!



Sincerely,







The Authors



October 2007











版前言



關於分子生物學的美好事物之一就是這一領域的發展依賴於不斷的交流。重大問題隻能通過全世界研究人員的合作纔能找到答案，每個研究小組為解答難題貢獻出他們的研究成果，並在他人研究成果的基礎上開展更深入的研究。但是要開展這種密切合作也面臨著許多挑戰，特別是語言問題。如果科學家們說著不同的語言、用不同的語言發表文章，那他們之間怎麼去開展合作呢？



算是一種機緣巧合吧，現在分子生物學所用的語言是英語。絕大多數研究結果都用英語發表，大多數國際會議也用英語發言。由於對分子生物學做出過重大貢獻的許多科學家和研究中心都在英國和美國，現在也仍然是這些國家在發揮著主導作用，因此英語已經成為首要的語言。一種語言起主導作用不一定是公平的，但這是大多數在這一領域工作的專業人員必須面對的現實。



對中國學生來說，用英語學習生物學會是很令人興奮的，但也會是頗具挑戰性的。漢語和英語是很不一樣的語言，具有完全不同的語音和語法體繫。此外，生物學的英語教材和文章特別難以理解，即使對母語為英語的讀者來說也是如此。書中有許多特殊的詞彙，還會有一些特殊的科技寫作方面的慣用句子結構。



許多時候，中國學生拿到手的是一本厚厚的英文教材，教師希望學生從中獲得的收益。我們在中國講授分子生物學的體會是：這樣的做法是不切合實際的。這一階段的大多數中國學生，特別是那些還處於科學研究課程學習階段的學生，並不具備足夠的英語能力去理解為母語是英語的讀者編寫的教材。在語言上的些許進步實際上是以犧牲理解分子生物學概念與原理為代價的。



我們編寫此書的目的是想為用英語學習分子生物學提供一種更實際、更讓人喜歡和更專業的方法。程度好的學生可以閱讀本書的英文部分，並參考中文譯文以檢查他們的理解情況，或參考個別單詞的中文含義。英語程度差一點的學生可以從本書的中文部分學習，並參考英文而開始掌握專業詞彙。使用這樣的英漢對照教材，在如何學習上學生和教師都可以有更多的選擇！



本書的另一個特點是：所有的英語課文都有配套的音頻文件。它們對那些希望提高自身專業英語聽力水平的人特別有幫助。同時，精心設計的插圖能使讀者更容易地從分子水平上理解相關的概念與原理。



本書包括的內容是我們認為一個分子生物學高年級本科生應該掌握的。與許多分子生物學教材不同，它不是一本參考書，不是一本讓人查閱關於細胞各方面內容的大部頭著作。那些大部頭著作自然有它們的用武之地，而我們覺得向學生提供這麼一大堆信息並不是很有成效的做法。如果學生能掌握這本相對來說比較簡單的書中的所有內容，他們就已經是這一領域學生中出類撥萃的了，他們甚至可能比一些專業人員還要強！



能邀請你與我們一道用英語來學習分子生物學讓我們覺得很興奮。中國和世界的其他國家正處於一個重要的時代！隨著中國的日益進步與繁榮，中國的研究中心和公司正在取得更大的進展，它們正在為世界科學共同體提供更多的研究成果。同時，中國的持續發展需要了解西方已經擁有的和即將湧現的知識和技能。在分子生物學領域，如果我們能夠共享知識與技能並互相交流，我們就都可以取得更大的成就！



 



作者  謹識



2007年10月