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Molecular Cell Biology (4th edition)

Article in Biochemistry and Molecular Biology Education December 2001
DOI: 10.1016/S1470-8175(01)00023-6

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80

BAMBED, Vol. 35, No. 1, pp. 79 82, 2007

coalescence of pre-formed chunks of secondary structure, but this topic is surprisingly absent from the book.
Other potentially important observations that bear on
the protein folding problem are only briefly mentioned,
including the observations that normal cells contain large
percentages of intrinsically disordered proteins [2] and the
observations that many native proteins undergo slow,
spontaneous unfolding events under physiological conditions, often leading to the formation of larger polymers or
aggregates such as amyloid fibers [3]. Such observations
suggest that the same amino acid sequence can adopt
different conformations under physiological conditions
that differ in fundamental ways. Again, the inconvenient
truth about such phenomena is that they are not understood well enough to be factored into the algorithms used
for predicting 3-D structures.
Judging from the many examples of successful protein predictions presented in this book (e.g. Figs. 3.11,
4.24, 5.5, and 6.2), one is forced to conclude that only
marginal progress has been made toward accurate protein
structure predictions, notwithstanding the authors attempt to paint a rosier picture with the Applications and
Examples presented in Chapter 9. Most of these examples illustrate just how far the field has yet to go considering that biologically active structures depend on interactions and distances scaling to less than an Angstrom, well
below the resolution of these examples. Given that many
human diseases result from protein instability and unfolding [4], the problem of understanding what makes folded
proteins unstable seems equally important to the daunting
task of predicting a proteins native conformation ab initio
(the topic of Chapter 3), but this problem was not addressed, even though it would seem to be far more tractable, theoretically. In any case, those who may be contemplating using this book as a teaching resource will
appreciate how well it summarizes the current methodology even though supplemental resources will likely be
required for more detailed explanations of these methods
in terms of their real-life applications and mathematical
foundations.
REFERENCES
[1] D. A. Dolgikh, R. I. Gilmanshin, E. V. Brazhnikov, V. E. Bychkova, G. V.
Semisotnov, S. Yu. Venyaminov, O. B. Ptitsyn (1981) -Lactalbumin:
compact state with fluctuating tertiary structure? FEBS Lett. 136,
311313.
[2] P. Tompa (2002) Intrinsically unstructured proteins, Trends Biochem.
Sci. 27, 527533.
[3] G. G. Glenner (1980) Amyloid deposits and amyloidosisthe -fibrilloses, I. N. Engl. J. Med. 302, 12831292.
[4] C. M. Dobson (2006) An accidental breach of a proteins natural
defenses, Nat. Struct. Mol. Biol. 13, 295297.

Duane Sears
Department of Molecular, Cellular and
Developmental Biology
University of California, Santa Barbara, CA 93106
E-mail: sears@lifesci.ucsb.edu
DOI 10.1002/bmb.8

Molecular Biology
Robert Weaver, 3rd Ed., McGraw-Hill, New York, 2005,
894 pp., ISBN 0-072-84611-9, $138.13
The explosion of biochemical information in the past 20
years has made it difficult to determine what content to
cover in an upper division course in molecular biology.
Lewins Genes texts have increased in thickness steadily
during this time such that it has become another one
volume encyclopedia akin to the massive texts of Alberts
et al. and Lodish et al. for cell biology.
The first edition of Weavers text Molecular Biology in
1999 represented a significant departure in pedagogic
approach to the presentation of molecular biology, and to
date there is no textbook like it. Molecular Biology is not a
compendium of facts but an 894-page discourse on the
experiments that reveal our current understanding of the
biochemical mechanisms underlying the many processes
of the central dogma of molecular biology. Molecular Biology is extraordinarily rich in experimental detail and so is
an outstanding text with which to teach experimental analysis to seniors or first year graduate students. On the other
hand, if one wishes to teach a survey course in molecular
biology, then Genes VIII by Benjamin Lewin, Molecular
Biology of the Gene Fifth Edition by James Watson et al.,
or Genomes 3 by Terry Brown is better. Malacinskis Essentials of Molecular Biology is also suitable for those
offering a sophomore-level course focusing on prokaryotic
molecular biology.
Molecular Biology is divided into eight parts: Introduction, Methods of Molecular Biology, Transcription in Prokaryotes, Transcription in Eukaryotes, Posttranscriptional
Events, Translation, Replication, Recombination and
Transposition, and Genomes. The focus throughout the
text is how specific experiments reveal specific knowledge. The canonical experiments of molecular biology of
which everyone is familiar are here along with many, many
others ranging from experiments demonstrating promoter
clearance, order of RNA edition, identification of branched
nucleotide formation during RNA splicing, editing in protein synthesis, and many others less familiar to most outside of molecular biology. Most of the chapters have at
least nine experiments analyzed in detail, and a few chapters contain as many as 13 experiments. The experimental
data presented come directly from the original published
work and are not idealized data as one often finds in the
more popular texts in molecular and cell biology. Supplementing the real data are diagrams that provide a clear
conceptual framework from which to understand the experiments discussed. There is also a nice blend of structural biochemistry integrated into the discussion to illustrate the molecular details of several reactions in
transcription, translation, RNA processing, and DNA replication. A surprising omission is that the topological analysis of DNA supercoiling is absent. Indeed, there are elegant experiments from Wang and Crick as well as
Cozzarelli and his colleagues that are important to the
canon of molecular biology but are absent in this book.
While the chapters in the Methods of Molecular Biology

81
(Chapters 4 and 5) present most of the key experimental
tools of the trade, numerous other methods are also presented throughout the text. One of my favorite features of
this text is that after the detailed table of contents is a two
page index of over 90 molecular techniques presented in
the book (!), most of them integrated into the discussion of
material outside of Chapters 4 and 5.
The single chapter in the Genomes section (Chapter
24, Genomics and Proteomics) is comparatively terse
and lacks the depth of the rest of the book. Still, the
experimental approach is evident here. What the content
lacks is the conceptual background in bioinformatics to
bring this material to the same level of sophistication as
the rest of the text. This is an understandable omission to
some extent since this material strays from the central
purpose of the text, which is a sophisticated presentation of the mechanisms operating in the reactions of DNA
replication and recombination, transcription, and RNA
processing and translation. This purpose also reveals
another absence in the text, a broader presentation of
the role of differential gene expression in biology, the
prominent reason molecular biology holds a strong interest for most biologists. Hence, if an instructor wants
to delve into gene regulation, there is too little in Molecular Biology that really satisfies beyond the life history
strategies of bacteriophage lambda. Promoter regions of
several eukaryotic genes have been analyzed in spectacular detail such that the brief mention of the sea
urchin endo16 gene is disappointing. While the author
does not completely omit regulatory phenomena, little
attention is paid to the significance of regulation in a
larger context. For instance, the role of PHAS-I is discussed briefly in the context of the regulation of eukaryotic initiation factor-4E, but the importance of this regulation to the biochemistry of the cell is given scant
attention such that students are left with an isolated
regulatory mechanism with no integration into a larger
biological context. What a future edition of Molecular
Biology needs is a chapter devoted to transcriptional
regulation with the same rigor and detail Professor
Weaver brings to the mechanisms of the transcriptional
apparatus discussed in Chapters 11, 12, and 13. Another
weakness is the inattention paid to quantitative parameters of replication, transcription, and translation. Most
of the discussion is focused on experiments revealing a
qualitative description of these biochemical processes.
Indeed, there is important quantitative work that reveals
important regulatory features of transcription in prokaryotic operons, eukaryotic RNA processing, and
translation.
The end of each chapter has an extensive list of review
questions and references. The references include seminal
research papers along with relatively recent reviews. The
review questions walk the students through the experimental evidence and key ideas. Surprisingly, there are only
3 4 analytical questions at the end of most of the chapters. With three editions of this text produced across the
last seven years, I am surprised that McGraw-Hill has not
been able to entice someone to assemble a problems

book to Molecular Biology or develop more analytical

questions for this text. A CD-ROM is available that contains PowerPoint images of the diagrams but not the experimental data; for that you need to go to the instructor
resources website where you can download PowerPoint
presentations for each chapter that contain most of the
experimental data present in the book.
Molecular Biology can be a challenging book from which
to teach; the shear density of experimental discussions
can overwhelm undergraduate students, and the writing
style is often dry and turgid. Fortunately, Molecular Biology
is remarkably free of obvious errors or confusions. For any
instructor wishing to integrate analytical approaches to the
presentation molecular biology, Weavers Molecular Biology is an outstanding one-of-a-kind source of material for
developing problem-based exercises or teaching a course
in molecular biology that goes beyond the typical descriptive survey of the biochemistry of the central dogma.
Akif Uzman
Department of Natural Sciences
University of HoustonDowntown, Houston, TX 77002
E-mail: uzmana@uhd.edu
DOI 10.1002/bmb.9

Practical Guide to Medical Student Assessment

Z. Amin, Y. S. Chong, and H. E. Khoo, World Scientific,
Singapore, 2006, 120 pp., ISBN 981-256-808-5, $38
Assessment has a number of uses and is often regarded
as a necessary evil in the curriculum. We often say that
assessment, typically summative assessment, drives student behavior, but in a more sophisticated way it can be
said that formative assessment with appropriate and
timely feedback stimulates productive and successful
learning. The authors of this Guide point out that assessment is not a process that should be undertaken in isolation; assessment is, and should be, tightly linked to other
components of the curriculum such as learning outcomes
and instructional methods. They also point out that this is
a guide; they present a selection of methods and caution
that no assessment instrument is perfect, not only intrinsically but also dependent on faculty training and curriculum planning.
Both student and teacher need to have an assessment
of how they are doing. Is the student learning; is the
teacher teaching successfully? Assessment also fills in
gaps in instruction (and this is particularly important in the
complex system of training clinicians). Institutions need
assessment grades for deciding on progression and graduation, and most importantly for medical training. The
licensing bodies need an assessment of whether graduates are fit for purpose; in other words are fit to be
unleashed on the public! This is a question of competency
and certification. In the case of medical students both
knowledge and skills need to be assessed, and good
assessment will address the issues of validity, reliability,