Molecular Biology, 2nd Edition
David P. Clark and Nanette J. Pazdernik, Academic Press-Cell, 2012, 928 pp., ISBN 978-0-1237-8594-7, $135.00 (hardback).
This is a handsome looking, well-written text aimed at survey courses in molecular biology for senior level undergraduates and beginning graduate students. The authors recognize that not all such students will have the necessary prerequisites for such a course and provide a few chapters of introduction to the material in the first unit in the book. These chapters actually make for good reading as they incorporate many gee-whiz type figures and facts. One is a colorful figure of a larval zebrafish brain; another is the fact that Lederberg was fortunate in choosing E. coli K-12 for his work, as it is one of the few bacterial strains that undergoes mating. It was also gratifying to see mention of Gosling's work in the first X-ray studies on DNA. Unfortunately, their description of X-ray crystallography is rather scant and they spend more words describing how to get protein crystals than how to get protein structures.
Some competing texts put their methods chapters near the end of the book reasoning that students may not grasp the details of the methods if they have not had the relevant biology. They may not understand replicating recombinant DNA if they have not been exposed to replication of cellular DNA. The presence of the fairly detailed introductory chapters in this text allows the authors to present Unit 2 (somewhat oddly titled as “The Genome”) as four good chapters on molecular biological methods. They begin with polymerase chain reaction and end with systems biology. As an instructor, I prefer this approach as the students will now have the ability to follow the logic of the experiments that have provided the deluge of information that is to come. They include two other excellent methods chapters; one is on “Proteomics” and is after the Unit on the Central Dogma, the other is called “Analysis of Gene Expression” and is found after the Unit on regulation of gene expression. These authors have also written a much more detailed text on applied molecular biology titled BIOTECHNOLOGY.
The authors are clear about their overall approach to the material. They “…tried to avoid overdoing detail (depth) in favor of breath.” Nevertheless, they seem to be selective as to where they do provide more depth. For example, there is an entire section on rolling circle replication but no mention of sugar pucker and its relevance to DNA and RNA. There is a long section on the biological origin of vaccinia virus but nothing on the origins of introns.
I believe the authors have made a decision to set their work apart from much of the competition by using a more biological approach as opposed to a biochemical one. There is an entire unit devoted to subcellular life forms (this seems to be an odd title for chapters devoted to plasmids, viruses, and mobile DNA). There is less emphasis on exact molecular structures and more on good schematic representations of molecules and complexes.
Although some chapters and sections seem to avoid depth a little too much (DNA replication seems thin and there is essentially nothing on the cell cycle), other parts show real strength and provide excellent material for students at this level. Good examples are the discussion of alternate sigma factors and the mechanisms of heat shock in E. coli, the biological detail on the lac operon and why glyceryl-galactose may be the actual target for this operon, and the various mechanisms of transposition. The chapters of Unit 4 dealing with regulation of gene expression, the chapter on RNA processing, and the chapter on mobile DNA elements are the strongest ones in the text and among the best I have seen in books targeted at this audience.
I have some philosophical quibbles with the authors and also need to point out some obvious errors. I find the term “junk DNA” to be of little use but it is prominent in a couple of places in the book. The Encyclopedia of DNA Elements (ENCODE) project (to be fair, these results date from 2012 and the book cites a date of early 2011 as its closing date) has shown that over 80% of the human genome may be functional and over 75% of noncoding DNA is transcribed. Although not accepted by all, these results do cast doubt on the concept of “junk.” They use the terms eubacteria and archaebacteria. The originator of these terms, Carl Woese, revised his nomenclature in 1990 to bacteria and archaea. Most texts have followed his lead. They indicate that there are over 100,000 copies of LINE-1 (over 5%) in the human genome. The actual genome sequence shows 500,000 copies (almost 17% of the genome). On page 387, they state that the ribosome binding site in prokaryotes is near the 5′ end of the mRNA. They correctly contradict this limitation on page 394 when talking about polycistronic mRNAs.
The book provides broadening information for students via boxed “Focus on Relevant Research” passages interspersed throughout the chapters. These give brief descriptions of research or review articles (published in Cell Press only) available to students at the book's website. The website also has the usual animations and quiz material. Most pages in the text have small blue boxes at the bottom that show definitions for key terms highlighted in the text on that page. This is a neat way for students to quickly review the material.
If the more biological approach is appropriate for a particular class, this could be a useful text book. If particular areas seem a bit sparsely presented, there is probably sufficient material from various sources to use as a supplement. The sections that are well-done are indeed useful and the methods chapters could also be helpful for a class.
Department of Biochemistry and Molecular Biology Mississippi State University Mississippi, 39762