Principles MB

http://bbruner.org/107gi.htm

Principles of Molecular Biology (X107A)

Course syllabus (partial)

I am not currently teaching this course. Therefore, I am showing here only those sections that are likely to be of interest to general readers. I last taught the course in 2001; many of the materials are from that time. The basics are still likely to be of value; I have done some updating.

Introduction. Overview, prerequisites.

What are genes and how do they function? Genes are DNA sequences, and the "Central Dogma of Molecular Biology", simply stated, says that information flows DNA --> RNA --> protein. We will spend most of our time on the structure, function, and synthesis of these three macromolecules. We emphasize those aspects (principles) of molecular biology that are universal.

Prerequisites: college chemistry (preferably including some organic chemistry), general biology. Some background in genetics, especially microbial genetics, is very helpful.

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Textbook

Textbook: R F Weaver, Molecular Biology, 2/e, 2002, WCB/McGraw-Hill. ISBN 0072345179. Course materials posted here are for this edition.Newer editions: 3/e, 2005, is ISBN 0072846119. 4/e, 2008, is ISBN 9780073319940.

There is a web site for this book. with web links and various other materials (which vary with the edition). The web sites listed here for the earlier editions are still available and may still be useful. For the 3rd and 4th editions, the link below is to the "Information Center" for the book; you will most likely want to try the "Student Center", from top toolbar.

4/e: http://highered.mcgraw-hill.com/sites/0072995246/information_center_view0/.

3/e: http://highered.mcgraw-hill.com/sites/0072846119/information_center_view0/

2/e: http://www.mhhe.com/biosci/cellmicro/weaver2/

1/e: http://www.mhhe.com/biosci/cellmicro/weavermolbio/

"Recommended": D P Clark & L D Russell, Molecular Biology made simple and fun, 2/e. Cache River Press, 2000. ISBN 1889899046. This book is intended for both a general audience and a wide range of science students. It presents the basics of molecular biology in a way that is readable and fun, yet scientifically quite sound. It may be helpful as an introduction for some students. Others will just find it fun. (Caution: You cannot use it to replace Weaver.) Third edition, 2005: ISBN 1-889899-07-0.

Buying Books. I encourage you to read this page for information about your options for buying the textbook, at college bookstores or on the Internet.

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Supplementary books

• H Lodish et al, Molecular Cell Biology, 6/e. Freeman, 2008. ISBN 978-0-716-77601-7. Web site: http://www.whfreeman.com/lodish/. (Materials for 4th and 5th editions are also available there.) Useful material, including animations.
• B Alberts et al, Molecular Biology of the Cell. 5/e, 2007. (This edition is also listed as Lewis et al.) ISBN 978-0815341055. The Problems Book (Study guide) by Wilson & Hunt. ISBN 9780815341109.
• G M Cooper & R E Hausman, The Cell - A Molecular Approach. 5/e, 2009. ISBN 978-0-87893-300-6. Web sites, with links keyed to the chapters:
• * 5/e: http://www.sinauer.com/cooper5e/.
• * 4/e: http://www.sinauer.com/cooper/4e/index.html.
• Some web site features require registration. New edition added 4/25/09.
  • The Lodish, Alberts, and Cooper books listed above are among the books now available online -- searchable full text -- at thePubMed Bookshelf: http://www.ncbi.nlm.nih.gov/sites/entrez?db=Books. These online books may not be the most recent edition, but are still useful. Other books of possible relevance there include the Stryer (Berg et al) biochemistry book and the Griffiths et al genetics book. This is from the National Center for Biotechnology, and is part of the Medline/PubMed system. More books are being added. (If you are already at the PubMed site, choose Books.)
• B Alberts et al, Essential Cell Biology: An Introduction to the Molecular Biology of the Cell. 2/e, 2003. ISBN 0-8153-3480-X (with CD-ROM). A short version of the Alberts book listed above.
• J D Watson et al, Molecular Biology of the Gene, 6/e. Benjamin/Cummings, 2007. ISBN 978-080539521-1. (An earlier edition of this book was the course textbook for several years.)
• J D Watson et al, Recombinant DNA: Genes and Genomes -- A Short Course. 3/e. Freeman, 2007. ISBN 978-07167-78158.
• B Lewin, Genes IX. Jones & Bartlett, 2008. ISBN 9780763740634. Web site with supplemental materials, including animations:http://biology.jbpub.com/book/genes/index.cfm.
• G Williams, HyperCELL. 1997. ISBN 0-8153-289-82. CD-ROM, from publisher of Alberts et al, but it is general. Excellent animations.
• B R Glick & J J Pasternak, Molecular Biotechnology -- Principles & Applications of Recombinant DNA. 3/e, 2003. ISBN 1-55581-224-4. 4th edition due late 2009. Posted 8/21/09.
• J J Pasternak, An introduction to human molecular genetics - Mechanisms of inherited diseases. 2/e, 2005. ISBN 978-0471474265.
• A N Glazer & H Nikaido, Microbial Biotechnology -- Fundamentals of Applied Microbiology. 2/e, 2007. ISBN 9780521842105.
• F C Neidhardt et al (ed.), Escherichia coli and Salmonella -- Cellular and Molecular Biology. 2/e, 1996. ISBN 1-55581-084-5. CD-ROM version, 1999; ISBN 1-55581-164-7C. This is now maintained as a web resource, called EcoSal: http://www.ecosal.org/. UC Berkeley provides subscription access.
• R C King et al, A Dictionary of Genetics. 7/e, 2006. ISBN 0-19-530761-5, paperback.
• T A Brown, various books. His books are well written; just check that the content and level are what you want. Introductory books include Gene Cloning and DNA Analysis: An Introduction (2001); Genomes 2 (2002).
• K Drlica, Understanding DNA and Gene Cloning - A guide for the curious. 4/e, 2003. ISBN 978-0471434160.
• L Gonick & M Wheelis, The Cartoon Guide to Genetics. 1991. ISBN 0-06-273099-1.

You may also find it useful to refer to a standard text for such subjects as general biology, genetics or biochemistry. Browse the bookstore for current books.

Also see the page Books: Suggestions for general reading -- some molecular biology, but also a wide range of science.

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Course outline (topics)

One reason for including the outline here is that it might guide you to which of the chapter handouts to look at. A complete set of chapter handouts is at Chapter handouts. These handouts are from 2001, but much of the basics are still quite ok.

The general plan is to establish the basics of all parts of gene structure and function in X107A.

Please read the upcoming chapter before class, and please bring the book to class.

The outline below gives you an idea of my plan, but the details are flexible.

Class 1. Introduction to course. Perspective.

Classes 2-5. Background. Mendel and genes; genetic terminology; genetic mapping. Cells and chromosomes. Discovery of the role of DNA; overview of how it fills that role. DNA structures. Protein structure; role of weak bonds. Mutations, an introduction. Ch 1-3.

Classes 6-8. Transcription. The basics of making RNA, in bacteria; an introduction to regulation. How RNA polymerase recognizes (and distinguishes) genes; promoters, σ (sigma) factors. Interaction of transcription and DNA supercoiling. Elongation and termination. Ch 6.

Classes 9-10. Gene regulation; DNA-protein interactions. Proteins interact with DNA and modulate its structure and function. The Lac operon paradigm, plus a sampling of other regulatory systems. Types of DNA-binding proteins; sequence recognition; DNA-bending. Ch 7-9, excerpts.

Classes 11-12. Transcription in eukaryotes. An introduction to the complexity of the transcriptional apparatus in higher organisms. A focus on Pol II, TFIID and the TBP. Ch 10-13, excerpts.

Classes 13-18. Translation. Formation of initiation complex, prokaryotes and eukaryotes. Genetic code: standard and variations; recoding. The players... mRNA, tRNA, activating enzymes, ribosomes, "factors". Ch 17-19.

Classes 19-21. DNA replication. DNA polymerases. Issues of the replication process: getting started, priming, unwinding the template, working accurately, hanging on, finishing and untangling. The replication apparatus, or replisome. Repair processes; topoisomerases. Ch 20-21.

Class 22. Post-transcriptional processing of RNA. Changes in RNA after synthesis and (usually) before use. Splicing, including alternative splicing; capping; polyadenylation. Trimming. mRNA degradation. Ch 14-16, excerpts.

Class 23. Final exam.

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Chapter handouts (and homework)

A complete set of chapter handouts is at Chapter handouts. These handouts are from 2001, but much of the basics are still quite ok.

The chapter handouts complement, but do not replace, the textbook.

The chapter handouts are informal, and their content may vary. In general, they are likely to contain the following features...

Chapter content. A brief outline of the material, including my emphases.

Further reading (FR). This section serves several purposes. In some cases it provides references for material we discuss beyond the book. In some cases it provides updating of the book material, even though we may not go into it. In some cases it is simply to give an idea of some of the things going on in molecular biology, including applications of material we have covered.

No attempt is made to be comprehensive. Many of the references are to reviews, including minireviews, and "news" items from journals such as Nature and Science. These are efficient ways to guide you to the literature, and they are often very readable and instructive on their own.

If there is material from FR that you are to be responsible for, I will present it in the handouts, including the annotations in the FR section. I do assume that you read the FR section, but you have no obligation to read any of the references themselves.

If you want to explore specific topics, you are encouraged to make use of the computer-assisted searching of recent biomedical literature available in the UC Library - or even from home. Library computers provide access to many databases, including Medline and BIOSIS (and many other databases, in diverse fields, as well as the UC library catalog system, Melvyl). Some resources are freely available to the general public, and you can do searches from home; these include Medline and Melvyl.

For information about using these electronic resources and the UC Libraries, see the Library Matters page at the web site. Major topic areas there include: UC Berkeley library; electronic journals; journal articles; Medline searches; citation searches. You can also ask in the library for assistance, or for informational brochures -- or just jump in. Some of the UC library branches offer training classes.

I encourage you to contribute articles that you think might interest the class. I will make them available in class, and will consider them for next year's FR.

Weaver provides a good reading list in each chapter. Further, he maintains his own updated FR section at the textbook web site, listed above in theTextbook section.

Errata. Many of the errors are reported by students. If you find further errors (in textbooks or handouts), please tell me about them. (Also, please let me know if errors that I list are now ok in the book.)

Homework. Weaver provides an extensive set of questions for each chapter; answers are not available. In the handout I may indicate that certain questions are more or less important. For most chapters, I will add some questions of my own.

Some of the homework will be discussed in class, usually in the period following the primary class on the subject. Your preparation is essential for a good discussion. You are welcome to turn in any work on which you would like written feedback.

Homework serves a variety of purposes, perhaps different for different people. One purpose is to stimulate thinking about how to use class material. Some questions are open-ended, far more so than would be practical on tests. In my questions, I may introduce some new material; the purpose is to get you to think about a situation before providing some new information or ideas. You are responsible for the material in the parts of the homework sets that are explicitly assigned.

For the questions I provide, I may also include partial answers. In class discussion we will skip some of the homework with relatively straightforward factual answers, unless there are questions. In some cases the answer section provides, literally, partial answers to more complex questions, so you can see whether you are on the right track. In no case is this section intended to discourage class discussion of alternative answers.

I do have one suggestion for those who want a way to organize studying "details." Make a "vocabulary" list as you read the chapter. Later, use this as a check list to see if you understand the terms. A nice feature of this approach is that it is very personal: you choose what goes on the list. Emphasize understanding (being able to use the terms), not simply being able to state a definition.

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Last update: August 21, 2009