Molecular Biology and Biotechnology By John M. Walker, Ralph Rapley

Molecular Biology and Biotechnology By John M. Walker, Ralph Rapley

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Molecular Biology and Biotechnology By John M. Walker, Ralph Rapley

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Book Description

This popular textbook has been completely revised and updated to provide a comprehensive overview and to reflect all the latest developments in this rapidly expanding area. Chapters on the impact of molecular biology in the development of biotechnology have been fully updated and include the applications of molecular biology in the areas of drug design and diseases. There are also completely new chapters in developing areas such as genome technology, nanobiotechnology, regenerative medicine and biofuels. By presenting information in an easily assimilated form, this book makes an ideal undergraduate text.

From the Back Cover

One of the exciting aspects of being involved in the field of molecular biology is the ever-accelerating rate of progress, both in the development of new methodologies and the practical applications of these methodologies. This popular textbook has been completely revised and updated to provide a comprehensive overview and to reflect all the latest developments in this rapidly expanding area. Chapters on the impact of molecular biology in the development of biotechnology have been fully updated and include the applications of molecular biology in the areas of drug design and diseases. The first six chapters deal with the technology used in current molecular biology and biotechnology. These primarily deal with core nucleic acid techniques and protein expression through microbial and genetic detection methods. Further chapters address the huge advances made in gene and genome analysis and updates the rapid advances into yeast analysis, which is providing very exciting insights into molecular pathways. There are also completely new chapters in developing areas such as genome technology, nanobiotechnology, regenerative medicine and biofuels. In addition, the authors continue to ensure that biotechnology is not just considered at the gene level and full consideration continues to be given to applications and manufacturing, with chapters on downstream processing, biosensors, the applications of immobilised biocatalysts, and a new chapter on the developing area of biofuels. By presenting information in an easily assimilated form, this book makes an ideal undergraduate text. Molecular Biology and Biotechnology 5th Edition will be of particular interest to students of biology and chemistry, as well as to postgraduates and other scientific workers who need a sound introduction to this ever rapidly advancing and expanding area.

Molecular Biology and Biotechnology By John M. Walker, Ralph Rapley

Biochemistry and Molecular Biology Compendium

Biochemistry and Molecular Biology Compendium

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Biochemistry and Molecular Biology Compendium

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Book Description

While biomedical investigation has greatly advanced, investigators have lost touch with and inadvertently corrupted significant nomenclature at the foundation of their science. Nowadays, one has to be an insider to even understand the titles of journals, as modern biochemists have a tendency to invent new terms to describe old phenomena and apply acronyms in a haphazard way. In addition, while the use of kits now saves time, by taking shortcuts, many have lost touch with the principles that lie behind the processes they employ. Assembled by Roger Lundblad, the Biochemistry and Molecular Biology Compendium provides both academic and industrial researchers with an exceptionally accessible resource that offers a plethora of practical information not found in more database-oriented resources. A renowned scientist and author who bridges the old school of protein research and current proteomics, Dr. Lundblad is uniquely qualified to bring forth this handy resource.

With great respect for the roots of the science, Dr. Lundblad provides a list of commonly used acronyms with definitions, as well as a glossary of terms and subjects used in biochemistry, molecular biology, biotechnology, proteomics, genomics, and systems biology. He also provides a chapter on those chemicals commonly employed in biochemistry and molecular biology, complete with properties and structure drawings, as well as a detailed accounting of protease inhibitors and protease inhibitor cocktails. A list of organic name reactions used in biochemistry is also included, as is a list of buffers with references to specific uses and unwanted side reactions.

Until now, this information could only be garnered from older books and Internet searches convoluted by uncertain nomenclature. Biochemistry and Molecular Biology Compendium may not provide all the answers, but researchers will find it to be a valuable tool that will save them time, as well as provide essential links to the roots of their science.

Biochemistry and Molecular Biology Compendium

Cell Biology, Genetics, Molecular Biology, Evolution and Ecology by Verma, Agarwal

Cell Biology, Genetics, Molecular Biology, Evolution and Ecology by Verma, Agarwal

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Cell Biology, Genetics, Molecular Biology, Evolution and Ecology by Verma, Agarwal

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The multicoloured edition of the textbook of Cell Biology, Genetics, Molecular Biology, Evolution and Ecology is the outcome of sincere and combined efforts of the authors and editors (namely Shishir Bhatnagar, Shubha Pradhan, Malini Kothiyal) and young but talented persons of DTP of S.Chand & Company Ltd. Their main motive remained to provide relevant coloured photographs explaining various intricate biological
topics. Multicoloured figures and photographs of this edition would help our target readers to understand and fully appreciate the very gist of the subject matter. Authors and editors have remained quite choosy and vigilant regarding relevance and authenticity of each and every illustration/picture finding its place in this textbook.

Authors earnestly hope that this multicoloured edition of the textbook of Cell Biology, Genetics, Molecular Biology, Evolution and Ecology will enhance the curiosity of our target readers to know more and more about the subject. It will arm them with latest information for facing any type of exam quite adequately.

This book is meant for students of B.Sc., B.Sc. (Hons.) and M.Sc. of biological group. Students appearing in entrance exams of C.P.M.T., I.F.S., P.C.S. and I.A.S., etc, may be immensely benefited by this book.

Cell Biology, Genetics, Molecular Biology, Evolution and Ecology by Verma, Agarwal

Biochemistry, The Molecular Basis of Life

Biochemistry, The Molecular Basis of Life

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Biochemistry, The Molecular Basis of Life

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Book Description

Biochemistry: The Molecular Basis of Life is the ideal text for students who do not specialize in biochemistry but who require a strong grasp of biochemical principles. The goal of this edition has been to enrich the coverage of chemistry while better highlighting the biological context. Once concepts and problem-solving skills have been mastered, students are prepared to tackle the complexities of science, modern life, and their chosen professions.

DISTINCTIVE FEATURES

A Review of Basic Principles. To ensure that all students are sufficiently prepared for acquiring a meaningful understanding of biochemistry, the first four chapters–now streamlined for easier coverage and self-study assessment–review the principles of relevant topics such as organic functional groups, noncovalent bonding, thermodynamics, and cell structure.

Chemical and Biological Principles in Balance. Comprehensive coverage offers each instructor the flexibility to decide how much chemistry or biology he/she would like to present. Chemical mechanisms are always presented within the physiological context of the organism.

Real-World Relevance. Because students who take the survey of biochemistry course come from a range of backgrounds and have diverse career goals, the updated fifth edition consistently demonstrates the fascinating connections between biochemical principles and the fields of medicine, nutrition, agriculture, bioengineering, and forensics.

The Most Robust Problem-Solving Program Available.
* In-chapter “Worked Problems” illustrate how quantitative problems are solved and provide students with opportunities to put their knowledge into action right when new concepts are introduced.
* Dozens of “Questions” are interspersed throughout the chapters, getting students critically thinking about high-interest topics.
* Finally, hundreds of multiple-choice and short-answer questions at the end of the chapters test students’ knowledge, develop their conceptual understanding, and encourage them to apply what they have learned.

Simple, Clear Illustrations. Biochemical concepts often require a high degree of visualization, and the McKee and McKee art program brings complex processes to life. The book includes 700+ full-color figures, many newly enhanced for a more vivid presentation in three dimensions and consistent scale and color for chemical structures.

Biochemistry, The Molecular Basis of Life

Principle of Basic Molecular Bacteriology

Principle of Basic Molecular Bacteriology

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Principle of Basic Molecular 

Bacteriology

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This book briefly describes the basic molecular bacteriology including bacterial Chromosome, molecular techniques used in bacteriology, quorum sensing, Bacterial signal transduction, gene transfer among bacteria in the natural environment, mitochondrial DNA, Index and References.

ISBN1449542832
EAN‐139781449542832
Primary Category: Science / General
Publication Date: October 4 2009
Language: English
Author: Dr Mohammad Reza Shakibaie Ph.D.

Chapter 1	Bacterial chromosome
Chapter 2	Bacterial gene expression
Chapter 3	Molecular techniques in bacteriology
Chapter 4	Genetic exchange among bacteria in the environment
Chapter 5	Quorum sensing
Chapter 6	Bacterial signal transduction
Chapter 7	Mitochondrial DNA
Chapter 8	References

Principle of Basic Molecular Bacteriology

ROTATIONAL CATALYSIS MODEL

Binding-change model

Mechanism of ATP synthase. ATP is shown in red, ADP and phosphate in pink, and the rotating γ subunit in black.

Depiction of ATP synthase using the chemiosmotic proton gradient to power ATP synthesis through oxidative phosphorylation.

In the 1960s through the 1970s, Paul Boyer developed the binding change, or flip-flop, mechanism, which postulated that ATP synthesis is coupled with a conformational change in the ATP synthase generated by rotation of the gamma subunit. The research group of John E. Walker, then at the MRC Laboratory of Molecular Biology in Cambridge, crystallized the F1 catalytic-domain of ATP synthase. The structure, at the time the largest asymmetric protein structure known, indicated that Boyer's rotary-catalysis model was, in essence, correct. For elucidating this, Boyer and Walker shared half of the 1997 Nobel Prize in Chemistry. Jens Christian Skou received the other half of the Chemistry prize that year "for the first discovery of an ion-transporting enzyme, Na+

, K+

 -ATPase."

The crystal structure of the F1 showed alternating alpha and beta subunits (3 of each), arranged like segments of an orange around an asymmetrical gamma subunit. According to the current model of ATP synthesis (known as the alternating catalytic model), the proton-motive force across the inner mitochondrial membrane, generated by the electron transport chain, drives the passage of protons through the membrane via the FO region of ATP synthase. A portion of the FO (the ring of c-subunits) rotates as the protons pass through the membrane. The c-ring is tightly attached to the asymmetric central stalk (consisting primarily of the gamma subunit), which rotates within the alpha3beta3 of F1 causing the 3 catalytic nucleotide binding sites to go through a series of conformational changes that leads to ATP synthesis. The major F1 subunits are prevented from rotating in sympathy with the central stalk rotor by a peripheral stalk that joins the alpha3beta3 to the non-rotating portion of FO. The structure of the intact ATP synthase is currently known at low-resolution from electron cryo-microscopy (cryo-EM) studies of the complex. The cryo-EM model of ATP synthase suggests that the peripheral stalk is a flexible structure that wraps around the complex as it joins F1 to FO. Under the right conditions, the enzyme reaction can also be carried out in reverse, with ATP hydrolysis driving proton pumping across the membrane.

The binding change mechanism involves the active site of a β subunit's cycling between three states. In the "open" state, ADP and phosphate enter the active site; in the diagram to the right, this is shown in red. The protein then closes up around the molecules and binds them loosely — the "loose" state (shown in orange). The enzyme then undergoes another change in shape and forces these molecules together, with the active site in the resulting "tight" state (shown in pink) binding the newly produced ATP molecule with very high affinity. Finally, the active site cycles back to the open state, releasing ATP and binding more ADP and phosphate, ready for the next cycle of ATP production.

T-CELL MATURATION AND SELECTION

PART 1

 PART 2

 PART 3

Interesting facts about Ebola Virus

Interesting facts about Ebola Virus

1. EBOV carries a negative-sense RNA genome in virions that are cylindrical/tubular, and contain viral envelope, matrix, and nucleocapsid components.
2. Ebola first appeared in 1976 in 2 simultaneous outbreaks, in Sudan, and in Democratic Republic of Congo with 151 and 280 deaths respectively.
3. Ebola Virus Disease (EVD) outbreaks have a case fatality rate of up to 90%.
4. Ebola Virus is not transmitted through air. The virus is transmitted to people from wild animals and spreads in the human population through human-to-human transmission.
5. First picture of Ebola Virus was made in 1976 with the magnification of 160,000X
6. There are 5 strains of Ebola virus
   a. Ebola Gabon
   b. Ebola Reston
   c. Ebola Zaire
   d. Ebola Sudan
   e. Ebola Ivory Coast
   Four of the strains can cause severe illness in humans and animals. Reston virus, has caused illness in some animals, but not in humans. Ebola Zaire was discovered first among five of these strains.
7. Typically, symptoms appear 8-10 days after exposure to the virus, but the incubation period can span two to 21 days.
8. Because of its high mortality rate, EBOV is also listed a select agent, World Health Organization Risk Group 4 Pathogen (requiring Biosafety Level 4-equivalent containment).

West Africa 2014 Outbreak

1. The outbreak began in Guinea in December 2013 but was not detected until March 2014.
2. The first suspect was a 2-year-old boy who died on Dec. 6, just a few days after falling ill in a village in Guéckédou, in southeastern Guinea.

Interesting facts about Ebola Virus

OXIDATIVE PHOSPHORYLATION

oxidative phosphorylation

Oxidative phosphorylation (or OXPHOS in short) is the metabolic pathway in which the mitochondria in cells use their structure, enzymes, and energy released by the oxidation of nutrients to reform ATP. Although the many forms of life on earth use a range of different nutrients, ATP is the molecule that supplies energy to metabolism. Almost all aerobic organisms carry out oxidative phosphorylation. This pathway is probably so pervasive because it is a highly efficient way of releasing energy, compared to alternative fermentation processes such as anaerobic glycolysis.

During oxidative phosphorylation, electrons are transferred from electron donors to electron acceptors such as oxygen, in redox reactions. These redox reactions release energy, which is used to form ATP. In eukaryotes, these redox reactions are carried out by a series of protein complexes within the cell's intermembrane wall mitochondria, whereas, in prokaryotes, these proteins are located in the cells' intermembrane space. These linked sets of proteins are called electron transport chains. In eukaryotes, five main protein complexes are involved, whereas in prokaryotes many different enzymes are present, using a variety of electron donors and acceptors.

The energy released by electrons flowing through this electron transport chain is used to transport protons across the inner mitochondrial membrane, in a process called electron transport. This generates potential energy in the form of a pH gradient and an electrical potential across this membrane. This store of energy is tapped by allowing protons to flow back across the membrane and down this gradient, through a large enzyme called ATP synthase; this process is known as chemiosmosis. This enzyme uses this energy to generate ATP from adenosine diphosphate (ADP), in a phosphorylation reaction. This reaction is driven by the proton flow, which forces the rotation of a part of the enzyme; the ATP synthase is a rotary mechanical motor.

Although oxidative phosphorylation is a vital part of metabolism, it produces reactive oxygen species such as superoxide and hydrogen peroxide, which lead to propagation of free radicals, damaging cells and contributing to disease and, possibly, aging (senescence). The enzymes carrying out this metabolic pathway are also the target of many drugs and poisons that inhibit their activities.

Signs and Symptoms of Ebola Virus Disease

Signs and Symptoms of Ebola Virus Disease

Symptoms may appear anywhere from 2 to 21 days after exposure to Ebola, but the average is 8 to 10 days.Ebola Zaire kills people quickly, typically 7 to 14 days after symptoms appear. A person can have the virus but not show any symptoms for as long as 3 weeks. People who survive can still have the virus in their system for weeks afterward. The virus has been detected in semen up to 7 weeks after recovery, according to the WHO. Humans are not infectious until they develop symptoms. A person infected with Ebola virus will typically develop a fever, headache, joint and muscle pain, a sore throat, and intense muscle weakness.

Signs and Symptoms of Ebola Virus Disease are as follows:

• High fever (usually higher than 38.3 °C (100.9 °F))
• Muscle and Joint aches
• Headache
• Sore throat  and Shortness of breath
• Chest pain and cough
• Red eyes
• Weakness
• Swelling
• Severe weight loss
• Chills
• Confusion
• Fatigue
• Nausea and Vomiting
• Diarrhea (may be bloody)
• Internal and External bleeding
• Bleeding, usually from the eyes
• Stomach Pain
• Hiccups
• Raised Rash
• Kidneys and Liver Failure

Recovery from Ebola depends on good supportive clinical care and the patient’s immune response. People who recover from Ebola infection develop antibodies that last for at least 10 years. Ebola virus disease is fatal in 50-90% of cases. The sooner a person is given care, the better the chances that they will survive.

Signs and Symptoms of Ebola Virus Disease

Genome of Ebola Virus

Genome of Ebola Virus

1. Ebola Virus have a negative-sense, non-segmented single stranded linear RNA genome about 18-19 kb in size.
2. The 3′ terminus is not polyadenylated and the 5′ end is not capped.
3. It contains approximately 19,000 base pairs.
4. It encodes seven structural proteins: nucleoprotein (NP), polymerase cofactor (VP35), (VP40), GP, transcription activator (VP30), VP24, and RNA polymerase (L).

Genome of Ebola Virus

Replication of Ebola Virus

Replication of Ebola Virus

Ebola Virus do not replicate through any kind of cell division; rather, they use a combination of host and virally encoded enzymes, alongside host cell structures, to produce multiple copies of viruses. These then self-assemble into viral macromolecular structures in the host cell. The virus completes a set of steps when infecting each individual cell.

Following are the steps during the replication of Ebola Virus:

1. Attachment

First of all, there is attachment of virus to host receptors through GP glycoprotein which is endocytosed into vesicles in the host cell. Host DC-SIGN and DC-SIGNR play a role in virion attachment.

2. Viral Entry (Penetration)

The virion enters early endosomes by Macropinocytosis or clathrin-mediated endocytosis. 

A. Macropinocytosis

 In this process, ruffled segments of the host’s plasma membrane protrude outward from the cell and form invaginations where the virus utilizes glycoproteins in order to attach to the surface of the plasma membrane. Macropinocytosis is a process in which the Eukaryotic host cells form macropinosomes, segments of plasma membranes that extend out from the cell approximately 0.2-10 µm, in order to incorporate the virus into the cell. The formation of macropinosomes occurs spontaneously, as a result of the activation of various growth factors, or simultaneously with the intake of cellular molecules or extracellular fluid.

B. Clathrin-mediated endocytosis

Clathrin-mediated endocytosis is the other means by which Ebolavirus enters the host cell. This process is very similar to macropinocytosis in that the plasma membrane forms invaginations that engulf the cell. However, clathrin-mediated endocytosis is different in that proteins on the surface of the host’s surface, and in particular clathrin, facilitate the attachment of the virus to the host’s cell surface. Glycoproteins are still used to attach the virus to the cell surface, and the NP-C1 cholesterol transporter still facilitates the fusion of the virus with endosomes and lysosomes and still allows the virus to escape into the cytoplasm. Without the NPC1 cholesterol transporter, Ebolavirus cannot leave the vesicle in order to replicate and cause infection in other cells.

To penetrate the cell, the viral membrane fuses with vesicle membrane, and the nucleocapsid is released into the cytoplasm.

In some culture cells, GP glycoprotein can be processed by host Cathepsin L andCathepsin B into 19kDa GP1. But this processing is not happening in all cells or for all ebolavirus. 19kDA GP1 interacts with host NPC1, which is highly expressed in dendritic cells.

Fusion of virus membrane with the vesicle membrane is triggered by either low pH orNPC1 binding.

3. Sequential Transcription

During transcription, the RNA genome is transcribed into seven monocistronic mRNAs whose length is determined by highly conserved start and stop signals.

The transcription process begins with the binding of the polymerase complex to a single binding site located within the leader region of the genome. The complex then slides along the RNA template and sequentially transcribes the individual genes in their 3’ to 5’ order. Encapsidated, negative-sense genomic ssRNA is used as a template for the synthesis (3′-5′) of polyadenylated, monocistronic mRNAs and, using the host cell’s ribosomes, tRNA molecules, etc., the mRNA is translated into individual viral proteins.

4. Replication

As viral protein levels rise, a switch occurs from translation to replication. Using the negative-sense genomic RNA as a template, a complementary +ssRNA is synthesized; this is then used as a template for the synthesis of new genomic (-)ssRNA, which is rapidly encapsidated

Replication presumably starts when enough nucleoprotein is present to encapsidate neo-synthetized antigenomes and genomes.

5. Budding

The newly formed nucleocapsids and envelope proteins associate at the host cell’s plasma membrane; budding occurs, destroying the cell.

These viruses recruit components of the cellular ESCRT (endosomal sorting complex required for transport) system to mediate host-assisted viral budding. SCRT complexes are normally used by the cell for biological functions involving membrane remodeling, such as intraluminal vesicle formation, autophagy or terminal stages of cytokinesis. The ESCRT family consists of ESCRT-0, ESCRT-I, ESCRT-II which are primarily involved in cargo sorting and membrane deformation, and ESCRT-III which cleaves the bud neck from its cytosolic face . In the last step, vps4 disassembles the complex. The budding reaction catalyzed by the ESCRT machinery has reversed topology when compared with most other budding processes in the cell, such as endocytosis and formation of transport vesicles.

6. Release

Finally, the virion is released.

Replication of Ebola Virus