CHAPTER I

INTRODUCTION
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 : 85-107
No. ISBN : 978-1-4051-0379-4
Book II

Title book : Molecular Biology of the Cell Fifth Edition

Author : Bruce Alberts, Alexander Johnson, Julian Lewis, Martin
Raff, Keith Roberts, Peter Walter.
Publisher : Garland Sience, Taylor & Francis Group and etc in the
United States America
Publication Year : 2008
Printing : fifteen
Dimensional book : Soft copy
Page the book review : 81-150
No. ISBN : 978-0-8153-4105-5
Book III

Title book : Molecular Cell Biology Seventh Edition

Author : Harvey Lodish, Arnold Berk, Chris A. Kaiser, Monty
Krieger, Anthony Bretscher, Hidde Ploegh, Angelika
Amon, Matthew P. Scott.
Publisher : Katherine Ahr Parker
Publication Year : 2013
Printing : First
Dimensional book : Soft copy
Page the book review : 59-114
No. ISBN : 978-1-4292-3413-9

The critical book report or actually called as critical sub-bab of book

report becouse for this section just focus to one topic there are protein structure
and function, so that the purpose is for prepared to fulfill the task subjects
Molecular Biology and as obligation assigment in department biology especially
in Molecular Biology on Protein Structure and Function topic. While the function
of this report is fulfillment of obligation assigment, this report also highly
expected to make writer or reader that read easy to understand and know where
the better book using to improve their self. Critical of this book report does not
intend to demonize or degrading treatment or research of the author. The critical
will critized the core complated, where the topic will consist of introducting of
protein, the structure that divided into four types as primary, secondary, tertiary
and quarternary structure and function of protein around cell or body human.

Proteins are probably the most important class of biochemical molecules,

although of course lipids and carbohydrates are also essential for life. Proteins are
the basis for the major structural components of animal and human tissue. Protein
function can be understood in terms of its structure. Indeed, the three-dimensional
structure of a protein is closely related to its biological function. Proteins that
perform similar functions tend to show a significant degree of structural
homology.
 CHAPTER II
SUMMARY
Book I
Proteins, like nucleic acids, are chain-like polymers of small subunits. The
links of the chain are nucleotides. Some proteins contain an abundance of one
amino acid, Each amino acid has an amino group (NH3 + ), and a carboxyl group
(COO-) attached to a central carbon called the a-carbon. The remaining groups
attached to the a-carbon are a hydrogen atom (H) and the side chain or R group.
It is the arrangement of amino acids, with their distinct side chains, that gives each
protein its characteristic structure and function there are Primary, Secondary,
Tertiary and Quaternary structure. Primary Structure; Amino acids joined together
by peptide bonds. The amino group of one molecule reacts with the carboxyl
group of the other in a condensation reaction resulting in the elimination of water
and the formation of a dipeptide. Protein primary structure is divided into two
main components, the polypeptide backbone that has the same composition in all
proteins, and the variable side chain groups. A polypeptide chain has polarity and
by convention is depicted with the free amino group at its left end. This is termed
the amino terminus, or N-terminus. The polypeptide chain also has a free carboxyl
group at its right end which is the carboxyl terminus, or C-terminus. The
explanation more clearly if we look at the figure inside the books. Secondary
structure; Interactions of amino acids with their neighbors. These interactions are
primarily stabilized by hydrogen bonds, but also depend on disulfide bridges, van
der Waals interactions, hydrophobic contacts, hydrogen bonds between
nonbackbone groups, and electrostatic interactions. The three basic elements of
protein secondary structure are the a-helix, the b-pleated sheet, and the
unstructured turns that connect these elements. All other structures represent
variations on one of these basic themes. The right-handed a-helix is the most
common structural motif found in proteins. These a-helices are stabilized by
hydrogen bonding among near neighbor amino acids with each residue being
hydrogen bonded to two other residues. Another common secondary structure
found in proteins is the b-pleated sheet or b-strand. The structure involves
extended amino acid chains in a protein that interact by hydrogen bonding. Two
segments of a polypeptide chain (or two individual polypeptide chains) can form
two different types of b-structures. If both segments are aligned in the N-terminal
to C-terminal direction, or in the C-terminal to N-terminal direction, the b-
structure is said to be parallel. If one segment is N-terminal to C-terminal and the
other is C-terminal to N-terminal, the b-structure is termed antiparallel.
Connecting the a-helices and b-pleated sheets elements in protein are turns.
Turns are relatively short loops of amino acids that do not exhibit a defined
secondary structure themselves, but are essential for the overall folding of a
protein. Other disordered or irregular structures in proteins are normally confined
to the N- and C-terminals or more rarely to loop regions within a protein or linker
region connecting one or more domains. Tertiary structure; The folded three-
dimensional shape of a polypeptide. This spatial arrangement of amino acid
residues that are widely separated in the primary sequence is stabilized by
covalent and noncovalent bonds. Most interactions are noncovalent. The principal
covalent bonds within and between polypeptides are disulfide (S-S) bonds or
bridges between cysteines. The noncovalent bonds are primarily hydrophobic
and hydrogen bonds. The three main categories of tertiary structure are illustrated
by globular, fibrous, and membrane proteins. Queternary structure; The stabilizing
interactions namely disulfide bonds, hydrophobic interactions, charge-pair
interactions, and hydrogen bonds, with the exception that they occur between one
or more polypeptide chains. The protein contains two a- and two b-subunits in its
tetrameric state, and is usually written as a 2b2. Similarly, antibodies contain two
heavy and two light chains, with the antigen-binding site formed by the
interaction of the two chains.

Protein Function; Of particular significance for molecular biologists are

the suites of proteins that mediate the activities of genes at all points in the flow of
genetic information from replication to transcription to translation. The functional
activity of enzymes and other proteins can be regulated at several different levels,
including at the level of gene transcription and protein synthesis. Of importance
for our discussion of protein structure and function here are the roles of post-
translational modifications and allosteric regulation in controlling protein activity.
After translation, proteins are joined covalently and noncovalently with other
molecules, form the lipoproteins, those protein and carbohydrate attachre called
glycoprotein and soon. Many steps in gene expression and cell signaling pathways
involve posttranslational modification of proteins by phosphorylation. The
binding of a ligand to a protein at one site on a protein can cause a substantial
change in the conformation of that protein.

Book II
Protein constitue most of cells dry mass. They are not only the cell
building block; they also execute nearly all the cells functions, Thus, enzymes
provide the intricate moleculer surface in cell that promote its many chemical
reaction. From a chemical point of view, protein are by far the most structurelly
complex and functionally sophisticated moleccules known. There are 20 types of
amino acids in protein, each with different chemical properties. A protein
molecules is made from a long chain of those amino acids that linked together to
neighbor through covalent peptide bond. The repeating sequence of atoms along
the core of polypeptide chain reffered to as the polypeptide backbone, attached the
amino acids side chains.

A protein molecule's amino acid sequence determines its three-

dimensional conformation. Noncovalent interactions between dffirent parts of the
polypeptide chain stabilize its folded structure. The amino acids with hydrophobic
side chains tend to cluster in the interior of the molecule, and local hydrogen-bond
interactions between neighboring peptide bonds giue rise to helices and -
sheets.

Globular regions, known as domains, are the modular units from which
many proteins are constructed; such domains generally contain 40-350 amino
acids. small proteins typically consist of only a single domain, while large
proteins are formed from several domains linked together by various lengths of
polypeptide chain, some of which can be relatively disordered. As proteins have
evolved, domains have been modified and combined with other domains to
construct new proteins. Thus far, about 800 different ways of folding up a domain
have been observed, among more than 20,000 known protein structures.
 Proteins are brought together into larger structures by the same
noncovalent forces that determine protein folding. Proteins with binding sites for
their own surface can assemble into dimers, closed rings, spherical shells, or
helical polymers. Although mixtures of proteins and nucleic acids can assemble
spontaneously into complex structures in a test tube, many biological assembly
processes involve irreversible steps. Consequently, not all structures in the cell are
capable of spontaneous reassembly after they haue been dissociated into their
component parts.

Proteins can form enormously sophisticated chemical device, whose

functions largely depend on the detailed chemical properties of their surfaces.
Binding sites for ligands are formed as surface cavities in which precisely
positioned amino acid side chains are brought together by protein folding. In this
way, normally unreactive amino acid side chains can be activated to make and
break covalent bonds. Enzymes are catalytic proteins that greatly speed up
reaction rates by binding the high-energy transition states for a specific reaction
path; they also perform acid catalysis and base catalysis simultaneously. The rates
of enzyme reactions are often so fast that they are limited only by diffusion; rates
can be further increased if enzymes that act sequentially on a substrate are joined
into a single multienzyme complex, or if the enzymes and their substrates are
confined to the same compartment of the cell.

Proteins reversibly change their shape when ligands bind to their surface.
The allosteric changes in protein conformation produced by one ligand affect the
binding of a second ligand, and this linkage between two ligand-binding sites
provides a crucial mechanism for regulating cell processes. Metabolic pathways,
for example, are controlled by feedback regulation: some small molecules inhibit
and other small molecules activate enzymes early in a pathway. Enzymes
controlled in this way generally form symmetric assemblies, allowing cooperetive
conformational changes to create a steep response to changes in the concentrations
of the ligands that regulate them.

The expenditure of chemical energy can drive unidirectional changes in

protein shape. By coupling allosteric shape changes to ATP hydrolysis, for
example, proteins can do useful work, such as generating a mechanical force or
moving for long distances in a single direction. The three-dimensional structures
of proteins, determined by x-ray crystallography, have revealed how a small local
change caused by nucleoside triphosphate hydrolysis is amplified to create major
changes elsewhere in the protein. By such means, these proteins can serve as
input-output devices that transmit information, as assemblyf actors, as motors, or
as membrane-bound pumps. Highly efficient protein machines are formed by
incorporating many different protein molecules into larger assemblies that
coordinate the allosteric movements of the individual components. Such machines
are now known to perform many of the most important reactions in cells.

Proteins are subjected to many reversible post-translational modifications,

such as the covalent addition of a phosphate or an acetyl group to a specific amino
acid side chain. The addition of these modifying groups is used to regulate the
activity of a protein, changing its conformation, its binding to other proteins and
its location inside the cell. A typical protein in a cell will interact with more than
five different partners. Using the new technologies of proteomics, biologists can
analyze thousands of proteins in one set of experiments. One important result is
the production of detailed protein interaction maps, which aim at describing all of
the binding interactions between the thousands of distinct proteins in a cell.

Book III
Proteins are linear polymers of amino acids linked together by peptide
bonds. A protein can have a single polypeptide chain or multiple polypeptide
chains. Protein are polymers constructed out of 20 different types of amino acids.
Individual amino acids are linked together in linear, unbranched chains by
covalent amino bonds called peptide bonds. Peptide bonds formation between the
amino group of one amino acid and the carboxyl group of another results in the
net release of water molecules and thus is a form of dehydration reaction. The
primary structure of a polypeptide chain is the sequence of covalently linked
amino acids that compose the chain. Various, mosrly noncovalent interactions
between amino acids in the linear sequence stabilize a protein's specific folded
three-dimensional structure, or conformation.
 The helix, strand and sheet, and 13 turn are the most prevalent
elements of protein secondary structure. Secondary structures are stabilized by
hydrogen bonds between atoms of the peptide backbone. Protein tertiary structure
results from hydrophobic interactions between nonpolar side groups and hydrogen
bonds and ionic interactions involving polar side groups and the polypeptide
backbone. These interactiom; rabilize folding of the protein, including its
secondary structural elements, into an overall three-dimensional arrangement.
Certain combinations of secondary structures give rise to different structural
motifs, which are found in a variety of proteins and are often associated with
specific functions.

Proteins often contain distinct domains, independently folded regions with

characteristic structural, functional, and topological properties (see Figure 3-10 in
texbooks). The incorporation of domains as modules in different proteins in the
course of evolution has generated diversity in protein structure and function. The
number and organization of individual polypeptide subunits in multimeric proteins
define their quaternary structure. Cells contain large supramolecular assemblies,
sometimes called molecular machines, in which all the necessary participants in
complex cellular processes (e.g., DNA, RNA, and protein synthesis;
photosynthesis; signal transduction) are bound together. Homologous proteins are
proteins that evolved from a common ancestor and thus have similar sequences,
structures, and functions. They can be classified into families and superfamilies.
 CHAPTER III
CRITICAL BOOK
Book Strength
a. Linkage between chapters

After read the Lizabeth books as my first book references and

observed, actually the books linkage between subtopic 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 becouse the arragement are start from introduction
of the protein, discuss about the central dogma and genetic code inside,
complete protein struture such as primary, secondary, tertiary and queternary
structure, then author adding inside the discussion about protein contain
multiple functional domains and prediction of how the ways protein structure
form. 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 protein structure and function. This book is
designed for beginners as an introduction book for molecular and the word
selection is truly friendly for beginners.

Albert Books too has a good linkage one becouse the arragement of
core content are appropriate with the molecular generally about protein
structure and function topic. This books start with introduction of protein,
shape and structure of proteins, the shape of a protein is specified by its
amino acid sequence, proteins fold into a conformation lowest energy, the
helix and sheet as component of structure, protein domains, protein
classified, summary and function with clearly explanation in every function.
In this book has use more complicated word that means well found a bit little
terminology or latin greek 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.

Lodish books too has a good linkage becouse like the lizabeth and
alberts books the arragement composistion of contant are appropriate with
 the standart generally. There are start with the introduction of protein,
hierachical structure of proteins, protein folding, protein binding and enzyme
catalysis, regulating protein function, purifying, and characterizing protein
and last is proteonimcs. Explanation of this book are more better than 2 book
before becouse the contant completed, proved of the statement based on
experience and experiment, in this book consist more greek latin than alberts
and elizabeth and all of sub topic linkage so we need higher order thinking to
understand clearly about concept or theory inside.

b. Curretness
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.
Example for explanation of the structure protein and component inside the
structure are clearly and easy to understand for beginners with a complete
description bellow the figure.
Alberts books has the better good than lizabeth content of figure or
anything else. When we read this book then compared to many journal
international had been publish, the content has verify.
Lodish books has the more better good than alberts and lizabeth books
becouse this book write based on experiment or journal publishing. And
word selection are suitable for thinking more by her-self or independent
learner. So that this books really responsibility for author or reader.
Book Weakness
a. Linkage between chapter
Generally Lizabeth book has good linkage between subtopic, but there are
the weakness, it can be seen when this book explain about the quaternary struture
of protein, the figure are present but its not enough to make reader imanging how
the form of this struture, then figure of the componet of queternary structure also
lack. And next in sub-title that discus about protein contain multiple functional
domain author also not using the figure to clear the explanation. Its make the
readers not easy to understand the meaning every paragraf cause we know that the
matter of this a bit complicated. As long as i read the books of albert and lodish i
cant found the weakness linkage becouse the linkage are complated based on
standar composition of this topic. Author has arranged with good one.
b. Currentness
The content this book has lack the explanation about materi for
learning or have generally expalanation if we compare with Alberts and
lodish book, Alberts and lodish book have specific explanation from the
molecular side
Implication
a. Implication to the theory/concepts
The three books has the good theory/concepts about the protein
structure and function becouse each book start with the introduction the
protein, meaning of protein, characteristic generally, component
arrangement inside, structure of protein: primary structure, seccondary
structure, tertiary structure, and quarternary structure, summary, function
of protein with details explanation every function, and if we compare one
each other actually right well found the different of them but just a little
bit. The completed one of explanation or arragement theory and concepts
actually found in Lodish books beccouse in this book after theories author
put down the experiment observation to prove it. But its not to said that
other book is bad, Lodish book is relevant to people that want to mastery
olecular protein with deeper. and for lizabeth and alberts books are suitable
for student or people that want to learn about molecular protein in
generally.
b. The developments program in Indonesia
If we compare the three books with indonesian books of course its
was different, becouse in the painful fact that indonesian book mostly
copy paste from one to another one and most of them has lack of figure to
complete the explanation. Then rarely use any journal as the reference of
the statement inside the book or put down the experiment to prove that.
But maybe thislizabeth, Lodish and Albert books can make references for
indonesia book to introducced the protein structure and function topic and
maked easy to know the protein topic.
 Protein chapter that dicuss in the three books are correctly same
with journal international that publishing so that its means the content has
verify and its can help student or people in indonesia who want to learn
about protein as molecular object in completed, coordinates, and easy
ways with them-self or independent ways. The book should be as students
source to look for information related to the protein from molecular view
aspect for their study as well as Indonesian curriculum.

c. Analysis of the student (student critical position)

After read all of books there are lizabeth book, Lodish book and
Albert book we can compare one each other and found a little bit different,
that right becouse every mind and opinion of author has different too. But i
can conclude that if we want mastery the protein especially for protein
structure and function subject with deeper so Lodish is the book that
suitable for. If the student just to know the generally molecular protein can
read the Lizabeth and Alberts book becouse there are complete content one
but using the generally statetment and simple word and figure to make
student or people needed understand.
 CHAPTER IV
CONCLUSION AND SUGGESTION
Conclusion
Based on the reult of my observation in this books, i found that the core
content composition of the three books while it albeth, lizabeth or lodish books
almost same. Where there are starting with the introduction of protein, the the
shape or structure of protein, the component of every structure and function with
completed explanation. In every book consist of figure or table as helping to
imanging the form of protein with independent or self ways. But the three books
actually exist an different packing this topic, where the lodish books as the better
one to student using for mastery the molecular biology subject especially about
protein structure and function.

Suggestion
Maybe Lizabeth book can make the specific and more expalanation about
protein function and structure especially in molecular biologi course, then addd
more figure and table explanation about the topic as albert and lodish do in their
books.
 REFERENCES

Anil Kumar Mandle, Pranita Jain, And Shailendra Kumar Shrivastava. 2012.
Protein Structure Prediction Using Support Vector Machine. India:
International Journal On Soft Computing (Ijsc) Vol. 3

Bruce Alberts, Alexander Johnson, Julian Lewis, Martin Raff, Keith Roberts,
Peter Walter. 2008. Molecular Biology of the Cell Fifth Edition.
United States America: Garland Sience, Taylor & Francis Group and
etc, 81-150.

Harvey Lodish, Arnold Berk, Chris A. Kaiser, Monty Krieger, Anthony Bretscher,
Hidde Ploegh, Angelika Amon, Matthew P. Scott. 2013. Molecular
Cell Biology Seventh Edition. New York: Katherine Ahr Parker, 59-
114.

Khaddouja Boujenfa, Mohamed Limam. 2012. Consensus Decision For

Protein Structure Classification. Tunisia: Journal Of Intelligent
Learning Systems And Applications, 216-222.

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

Publishing Ltd

Steve Fairchild, Ruth Pachter, And Ronald Perri.2017. Protein Structure Analysis
And Prediction. New York: Wright Laboratory, J. Mol. Bio.