|
 |  Molecular Biology, 3/e Robert F. Weaver
What's New to this Edition| New to the Third Edition
One of the most obvious changes has been the addition of Analytical Questions to each chapter (except Chap-ter 1). I have always intended the Review Questions to check students’ retention of the material in each chapter, and the answers are readily available in the text and figures. But many users of the book have asked me for questions that require a bit more thought and extrapolation beyond the presented material. That is the purpose of the new Analytical Questions. I thank Marie Pizzorno for her contribution to this new set of questions and welcome further contributions to expand these questions in future editions.
Most of the chapters of this third edition have been updated and include new information. Here are a few highlights:Chapter 6: A considerable amount of new structural information has been added on prokaryotic RNA polymerase, including new x-ray crystal structures of the prokaryotic RNA polymerase holoenzyme and of the holoenzyme bound to DNA.Chapter 7: The x-ray crystal structure of the complex of lac DNA, CAP-cyclic AMP, and the a-CTD of RNA_polymerase shows exactly what part of the CAP protein contacts the a-CTD.Chapter 8: This chapter shows a new insight into how transcription is controlled in bacterial cells infected with l phage, including new evidence that shows how NusA facilitates transcription termination by facilitating the formation of a hairpin at the terminator, and how the l N protein overrides termination by inhibiting hairpin formation. Also, we know how the heat shock s-factor appears so rapidly after heat shock in E. coli: Elevated temperature melts inhibitory secondary structure in the mRNA, rendering it more accessible to ribosomes.Chapter 10: New structural information on RNA_polymerase II and its mechanism is presented in Chapter 10. For example: The structure of yeast polymerase II at atomic resolution reveals a deep cleft that can accept a linear DNA template from one end to the other. The catalytic center, containing a Mg2+ ion, lies at the bottom of the cleft. A highly mobile clamp appears to swing open to allow the DNA template to enter the cleft.Chapter 11: Chapter 11 examines a new class II transcription elongation factor: Sometimes, phosphorylation on serine 2 of the RNA polymerase II CTD is also lost during elongation and that can cause pausing of the polymerase. For elongation to begin again, rephosphorylation of serine 2 of the CTD_must occur.Chapter 12: This chapter presents new information on insulators and insulator regulation, and new insights into how transcription can be controlled by covalent modifications, including ubiquitination and sumoylation of transcription factors.Chapter 13: A_new concept of a histone code is introducted in Chapter 13, with the interferon-b _(INF-b) gene as an example. In principle, each particular combination of methylations, acetylations, phosphorylations, and ubiquitinations can send a different message to the cell about activation or repression of transcription.Chapter 14: A minor class of introns with 5'-splice sites and branchpoints can be spliced with the help of a variant class of snRNAs, including U11, U12, U4atac, and U6atac.Chapter 15: The CTD of the largest subunit of RNA polymerase II serves as a platform for assembly of factors that carry out capping, polyadenylation, and splicing. These factors come and go as needed, and the phosphorylation state of the CTD can change as transcription progresses. Also, new information on the coupling of polyadenylation and transcription termination is presented.Chapter 16: We introduce a more widespread form of RNA editing: Some adenosines in mRNAs of higher eukaryotes, including fruit flies and mammals, must be deaminated to inosine posttranscriptionally for the mRNAs to code for the proper proteins. Enzymes known as adenosine deaminases active on RNAs (ADARs) carry out this kind of RNA editing.Chapter 17: We introduce a new eukaryotic translation initiation factor: This factor, eIF5B, is homologous to the prokaryotic factor IF2. It resembles IF2 in binding GTP and stimulating association of the two ribosomal subunits.Chapter 19: We examine another role for IF1 in prokaryotic translation initiation: preventing aminoacyl tRNAs from binding to the ribosomal A site until the initiation phase is over.Chapter 24: This chapter has seen the greatest change, as befits such a rapidly evolving subdiscipline. The proteomics part of the chapter has been expanded, including new techniques to probe protein–protein interactions. To relfect this expansion, the chapter has been renamed Genomics and Proteomics. We have also designed a short tutorial on the use of the NCBI website including: querying the database for a sequence match; finding information on a gene of interest; and viewing the structure of a protein of interest in three dimensions by rotating the structure on the computer screen.
The genomics part of the chapter has also been extensively revised. For example, the positional cloning of the Huntington disease (HD) gene has been moved to the beginning of the chapter as an introduction to genomics to illustrate how laborious such searches were before the genomics era. We also present a hypothesis to explain why expansion of the polyglutamine tract in huntingtin leads to the deterioration of the central nervous system that characterizes HD. We also show that is is possible to define the essential gene set of a simple organism by mutating one gene at a time to see which genes are required for life. In principle, it is also possible to define the minimal genome—the set of genes that is the minimum required for life. |
|
|
2005 McGraw-Hill Higher Education