Name : Gita Tri Anggita

NIM : 4143342013
Class : Bilingual Biology
Education 2014

CHAPTER I
INTRODUCTION

1.1 Book Identity

 Book I
Title book : Fundamental Molecular Biology
Author : Lizabeth A. Allison
Publisher : Blackwell Publishing Ltd
Publication Year : 2007
Printing : Thirteen
Dimensional book : Soft copy
Page the book review : 146-153
No. ISBN : 978-1-4051-0379-4
 Book II

Title book : Molecular Biology

Author : David Clark
Publisher : Elsevier Academic Press
Publication Year : 2005
Dimensional book : Soft copy
Page the book review : 312-386
No. ISBN : 0-12-175551-7

Topic : Transcription on Eukaryotes

1.2 Background
The purpose of critical book report are prepared to fulfill the task of
Molecular Biology subject matter and as routine assigment in department biology
especially. While the other functions of the critical book report is to look at the
shortcomings inherent in the book after it was advised that strengthens the authors
in the study of deficiencies and some critisms contained in the book. However,
critical book was made to make the better writing and required the book related to
the topic (Transcription on Eukaryotes). As we know molecular biology define as
the study of function and organism organization from the structure and the
constituent components. When talking abolut biology molecular, its related to the
others study like cellular biology, genetics, biochemistry, organic chemistry and
biophysics, so its usefull to be discuss. But sometimes there is some different
information that written in some books even in the same topic, thats why we can
observe, critics and compare some books and make report, report being studied by
molecular biology course, written by lecturer teaching subjects and topics of
molecular biology.
 CHAPTER II
SUMMARY
 Book I
The synthesis of tens of thousands of different eukaryotic mRNAs is carried
out by RNA polymerase II (RNA pol II). During the process of transcription,
RNA pol II associates transiently not only with the template DNA but with many
different proteins, including general transcription factors. Transcription factors are
sequence-specific DNA-binding proteins that bind to gene promoters and other
regulatory elements, interpret the information present in these regulatory
elements, and transmit the appropriate response to the RNA pol II transcriptional
machinery. The gene promoter consists of core promoter elements and proximal
promoter elements that are required for the initiation of transcription or that
increase the frequency of initiation only when positioned near the transcriptional
start site. The initiation step alone involves the assembly of dozens of factors to
form a preinitiation complex. The general transcription factor TFIID is
responsible for the recognition of most of the known core promoter elements, the
best characterized of which is the TATA box. Long-range regulatory DNA
elements act over distances of 100 kb or more from the gene promoter. Enhancers
increase gene promoter activity downstream, upstream, or in either orientation
relative to the promoter.
Similar elements that repress gene activity are called silencers. Insulators act
as barriers between regions of heterochromatin and euchromatin and block
enhancer or silencer activity of neighboring genes. Locus control regions (LCRs)
maintain functional, independent domains of active chromatin. They are often
characterized by DNase I hypersensitive sites which are indicative of an “open”
chromatin conformation. The LCR of the β-globin gene cluster is required for
high-level transcription of all genes in the cluster, but chromatin loop formation
controls their developmental expression. Matrix attachment regions (MARs)
organize chromatin into independent loop domains, and localize transcription
factors and actively transcribed genes to the nuclear matrix.
Transcription is mediated by the collective action of sequence-specific
DNA-binding transcription factors along with the general RNA pol II
transcriptional machinery, an assortment of coregulators that bridge the DNA-
binding factors to the transcriptional machinery, a number of chromatin-
remodeling factors that mobilize nucleosomes, and a variety of enzymes that
catalyze covalent modification of histones and other proteins.
RNA pol II is a 12-subunit polymerase, capable of synthesizing RNA and
proofreading nascent transcript. A set of five general transcription factors, denoted
TFIIB, TFIID, TFIIE, TFIIF, and TFIIH, is responsible for promoter recognition
and for unwinding the promoter DNA. RNA pol II is absolutely dependent on
these auxiliary transcription factors for the initiation of transcription. Assembling
the transcription preinitiation complex involves a series of highly ordered steps.
Binding of TFIID (TBP and associated TAFs) to the TATA box provides a
platform to recruit other general transcription factors and RNA pol II to the gene
promoter. In vitro, these proteins assemble at the promoter in the following order:
TFIIB (orients the complex on the promoter), TFIIF together with RNA pol II,
and then TFIIE and TFIIH. TFIIH has both kinase and helicase activity.
Phosphorylation of the C-terminal domain (CTD) of RNA pol II is required for
transcript elongation. For recycling of RNA pol II and reinitiation of transcription,
the CTD must again be dephosphorylated. Mediator is a 20-subunit complex,
which acts as a molecular bridge to transmit regulatory information from activator
and repressor proteins to RNA pol II.
Transcription factors mediate gene-specific transcriptional activation or
repression. They are modular proteins consisting of a number of domains,
including a DNA-binding domain, a transactivation domain that activates
transcription via protein–protein interactions, and a dimerization domain. The
majority of transcription factors bind DNA as homodimers or heterodimers. Some
of the more common DNA-binding domain motifs are the helix-turn-helix, zinc
finger, basic leucine zipper, and basic helix-loop-helix motifs. Despite differences
in overall three-dimensional structure, all these common motifs involve
interaction between an α-helical domain of the protein and about five base pairs
within the major groove of the DNA double helix. The homeodomain is a variant
of the helix-turn-helix motif found in many transcription factors that are important
in development. The zinc finger is formed by interspersed cysteines and/or
histidines that covalently bind a central zinc ion, folding a short length of the
amino acid chain into a compact loop domain, one side of which is an α-helix.
The leucine zipper and helix-loop-helix motifs do not directly contact the DNA,
instead they play an indirect structural role in DNA binding by facilitating
dimerization of two similar transcription factors with basic α-helical DNA-
binding domains.

 Book II

For a start, eukaryotes have three different RNA polymerases, unlike bacteria
which have just one.The three RNA polymerases transcribe different categories of
nuclear genes. In addition, mitochondria and chloroplasts have their own RNA
polymerases, which resemble the bacterial enzyme.
RNA polymerase I transcribes the genes for the two large ribosomal RNA
molecules and RNA polymerase III transcribes the genes for tRNA, 5S rRNA and
a few other small RNA molecules. RNA polymerase II transcribes most
eukaryotic genes that encode proteins and as a result is subject to the most
complex regulation. Since ribosomal RNA and transfer RNA are needed all the
time by all types of cells, RNA polymerases I and III operate constitutively in
most cell types.
A variety of proteins, known as transcription factors are also needed for the
correct functioning of RNA polymerases. Transcription factors may be divided
into general transcription factors and specific transcription factors. General
transcription factors are needed for the transcription of all genes transcribed by a
particular RNA polymerase, and are typically designated TFI, TFII, TFIII
followed by individual letters. The I, II, and III refer to the corresponding RNA
polymerase (see below). Specific transcription factors are needed for transcription
of particular specific gene(s) under specific circumstances. Proteins such as the
sigma subunit of bacterial RNA polymerase may also be regarded as transcription
factors, however, this terminology is usually only used for eukaryotes.
 CHAPTER III
CRITICAL BOOK

Strength of Book
 Book I
After read the Lizabeth books as my first book references and observed,
actually the books linkage between topic discussion has good, its can see from the
arrangement that author made, where the topic are sequential with the figure that
completed the explanation of paragraf before. And said as good one also because
the arragement are start from introduction of the transcription, discuss about the
transcription factors and their DNA-binding motifs, the general transcription
machinery and the mechanism of RNA polymerase II transcription, transcriptional
coactivators and corepressors, including chromatin modification and remodeling
complexes, and signal-mediated nuclear import and export of proteins involved in
regulating gene transcription inside. For the function this books consist five
function that genereally known. The arrangement of words is easy to understand
for readers who want to mastery the molecular about transcription on eukaryotes.
This book is designed for beginners as an introduction book for molecular and the
word selection is truly friendly for beginners. Lizabeth books has the good figures
or picture, and every figures or picture has good and clear explanation to make
easy if we learn of book.

 Book II
David Book too has a good linkage one because the arragement of core
content are appropriate with the molecular generally about protein structure and
function topic. This books start with introduction of genes, Transcription of rRNA
and tRNA in Eukaryotes Transcription of Protein-Encoding Genes in Eukaryotes
Upstream Elements Increase the Efficiency of RNA Polymerase II Binding
Enhancers Control Transcription at a Distance. In this book has use more
complicated word that means we’ll found a bit little terminology and more of
figure and table that support the explanation before. This books actually can
already use for student who want to mastery the molecular with a little bit deeper.
Book Weakness
 Book I
Generally Lizabeth book has good linkage between subtopic, but there are the
weakness according to me, it can be seen in writing the sentence should use the
left right alignment to look neat. in this book its alignment is a mess. And next in
sub-title that discus about the explanation of the mechanism of transcription in
eukaryotes is less clear and how pascatranscription isnot clear. Its make the
readers not easy to understand the meaning every paragraf cause we know that the
matter of this a bit complicated.
 Book II
If we compare with this book (Clark, David. 2005) actually there is no
similar chapter with the topic in the primary book, in this book the explanation is
explain in different chapter, like chapter one is life begin with transcription, so its
discuss about trancription in eukaryotes, transcription protein-encoding genes in
eukaryotes and ect. So its less specifict explanation. The explanation also using a
colorfull figure to make reader easier to understand. The content this book has
lack the explanation about matter for learning or have generally expalanation if
we compare with Lizabeth book, Lizabeth book have specific explanation from
the molecular side. In this book not found explanation about mechanism of
transcription on eukaryotes specifically and how the pascatranscription prosses.
Topic of discussion about transcription on eukaryotes include sub-bab not topic in
bab in this book so that the explanation about the topic just a little not specific.
 CHAPTER IV
CLOSING

Conclusion
Based on the observation in some of book, Over all for this book, especially
for topic “Transcription on Eukaryotes” is good enough for studying biology
molecular, because the matery was explained clearly and accompanied by some
figures and graphics to make it more clear. So this book is recommended for use
in learning molecular biology. From the content, the Book of Alizabeth more
spesific than book of David and from the language book of david more easy to
understand than book of alizabeth.

Suggestion
For the suggestion, to make it easier to understand, its good if it use a
simpler language and not using the old-language style, so its not be a
misconceptions and also its better if the figure in 3D and colorfull cause it makes
reader more interest to read it. Its important to study it more and compare it with
many several books so we can know which one is the best to be our reference.
Maybe Lizabeth book can make the specific and more expalanation about
transcription on eukaryotes especially in molecular biologi course, then addd
more figure and table explanation about the topic as david do in their books.
 REFERENCES

Clark, D. (2005). Molecular Biology Understanding the Genetic Revolution.

China: Elsevier Academic Press.

Lizabeth A. Allison. 2007. Fundamental Molecular Biology. USA: Blackwell

Publishing Ltd