Sitografia
Per ogni capitolo del libro, un'ampia raccolta delle risorse multimediali online sviluppate da enti di ricerca e università di tutto il mondo.
Capitolo 1
This page highlights career opportunities in biotechnology. It describes a long list of entry-level jobs along with their typical requirements in both education and experience. It also includes a brief history of the field. From Access Excellence by Genentech.
Molecules from Chemistry at Okanagan University College
A huge number of images of various chemical compounds, from alcohols to chiral molecules. Includes a searchable index. Requires the free plug-in Chime from MDLI. Maintained by Dave Woodcock.
This four-part series is an excellent introduction to the introductory concepts of biochemistry, especially chemical bonding and the properties of water. Part of The Biology Project from the University of Arizona.
Capitolo 2
National Human Genome Research Institute
The National Institutes of Health’s official Human Genome Project Site.
A collection of links to news articles relating to molecular evolution.
Capitolo 3
Amino Acids
This quiz is the companion to William McClure's Amino Acid Viewer (Side-by Side Images of Amino Acids). It uses JavaScript to keep track of a user's answers, providing hints if needed and randomized questions. Chime structures combined with JavaScript make this one of the best amino acid quiz pages on the Web.
A simple page that lists the 20 standard amino acids, their abbreviations and chemical structures (2D). Includes links to more detailed information for each amino acid, and 3D models are available. From the Institute of Chemistry, Free University of Berlin.
(Still under development) This site allows a user to enter an amino acid number or range of numbers in an entry box next to a Chime protein structure. Pressing Enter zooms in on the selected residue(s) in the protein and highlights them. No information about amino acid properties yet, but the Quizzer does present them in the context of a real protein. From Eric Martz, University of Massachusetts at Amherst, and Brian White, University of Massachusetts at Boston.
A compilation of all things related to amino acids: side-chain characteristics, protecting groups for polypeptide synthesis, solvent accessibility, molecular volumes, hydrophobicities, hydrogen bonding potentials, pKa values, genetic code, mutation strategies for molecular replacement, and much more. From Ronald Beavis, at Proteometrics.
Uses Chime and frames to introduce amino acid structures together with their properties. Part of a large Web project on proteins that you should check out. From Naomi Boxall and John Tweedie, at Massey University in New Zealand.
High Order Structure Tutorials
Start with the Protein Overview for best results. This is a wonderfully complete discussion of all aspects of protein shape and structure, from amino acids to quaternary structure and the biological relevance of structure. Requires the Chime plug-in. From Naomi Boxall and John Tweedie, at Massey University in New Zealand.
Biochemistry in 3D (Biochemistry Tutorials and Lecture Aids)
A good site on protein secondary structure. Designed to accompany an introductory biochemistry course, the self-guided tutorial format allows users to proceed at their own pace; the lecture-aid format lends itself well to presentation. Uses the simple B1 domain of protein G and requires the Chime plug-in. From Frieda Reichsman, at the University of Massachusetts at Amherst.
Macromolecular Geometry
A more advanced site concerning protein geometry-packing, folding, solvent accessibility, etc. Includes a Hypertalk tutorial as well as information from the literature and some cool pictures (Pictures of Packing). From Mark Gerstein, at Yale.
Other Tools
Enzyme Structures Database
Once you know a bit about protein structure, how does it relate to function? Here's an exhaustive index to the experimentally determined structures of many enzymes; all of them can be viewed online as images or downloaded and viewed in RasMol.
Raines Lab
The Raines Lab at the University of Wisconsin at Madison investigates many aspects of protein structure, including folding, function, stability, and interaction with other proteins. Here they present an overview of their research and provide good examples of questions that interest many research labs across the world: how do protein structures form, and how do they relate to function?
Simulating Water and the Molecules
Proteins do not exist in isolation; they live in an aqueous environment. Water plays a pivotal role in determining the structure, shape, and function of proteins. Here is an excellent article from the November 1998 issue of Scientific American magazine that outlines how the computer modeling of water and its effect on proteins can provide clues to how proteins function. Provided by authors Mark Gerstein and Michael Levine and reprinted with permission from Scientific American.
About Linus Pauling
Linus Pauling can be considered the father of structural biology. He was instrumental in introducing X-ray crystallography and electron diffraction to the study of biological molecules, two techniques that helped revolutionize the study of structure. This and Pauling's many other contributions to science are summarized in this brief biography by Robert Paradowski, Rochester Institute of Technology.
The RCSB Protein Data Bank
The worldwide source for macromolecule structure files solved experimentally or by computer modeling. Previously hosted by the PDB at BNL (Brookhaven National Laboratory), now run by the Research Collaboratory for Structural Bioinformatics, this is THE database to find 3D protein structures. It requires some knowledge of protein biochemistry, and it provides links to a comprehensive array of specific information and visualization tools.
Capitolo 4
Molecular Visualization
The Protein Data Bank (PDB) is the single international source for 3D structure files-not only proteins but also nucleic acids and macromolecular complexes. These are experimentally determined structures (solved by X-ray crystallography or nuclear magnetic resonance spectroscopy) or theoretical models. Structure files are contributed by research labs from around the world and available for viewing or downloading free of charge. Since taking over the PDB from Brookhaven National Labs in 1998, the Research Collaboratory for Structural Bioinformatics (RCSB) has redesigned the site, adding powerful new search features, viewing and display options, ftp access, and much more.
This site from Eric Martz at the University of Massachusetts, Amherst, is an invaluable resource for anyone interested in molecular visualization of protein structures. Find it all here-basic information; links to molecular visualization software and structure files; a world index of biomolecular tutorials, both on-line and downloadable; novel web-based utilities for exploring protein structure; and much more. Oriented to the academic community.
A companion to the RasMol Home Page, this site contains everything you need to know about Chime, a free plug-in from MDL Information Systems, Inc. (MDLI) that allows you to view and interact with 3D molecules right in your web browser. Like the RasMol Home Page, this site is comprehensive and full of great resources. Oriented to the academic community.
One of Eric Martz's more powerful software packages, the site allows you to explore a protein's many features in an enhanced RasMol-like interface, right from your web browser. Beginners can follow a comprehensive tutorial; advanced users can use the Chime menu or RasMol command language to manipulate the structure. Included with the Explorer is the Protein Comparator, which can load two molecules at the same time for comparison. Advanced students of protein structure will find these hands-on utilities extremely useful. Requires the Chime plug-in v2.0 and a Java-enabled browser.
Another of Eric Martz's creations, the Bond Finder is a Chime-based web resource that allows you to load a molecule or complex of molecules, choose a target (i.e., a ligand), and easily view the parts of the protein that interact with the target. With too many features to list here, it must be seen to be believed! Requires Chime v2.0 and a Java-enabled browser. WARNING! Follow the instructions carefully!
The National Center for Biotechnology Information (NCBI) provides this free helper application that lets you view structures of molecules downloaded from their Entrez database. Unlike other freeware programs, the latest version of Cn3D simultaneously displays structure, sequence, and alignment.
X-Ray Crystallography
The Department of Crystallography, Birkbeck College
A beautiful web site with wonderful images and a friendly organization. If you are curious what lies in store for crystallography in the future, or if you're interested in further studies in the field, check out this site. But be prepared to be persistent-this site can often take a few tries to access.
Capitolo 5
A Visit with Dr. Francis Crick
A narrated essay by Dr. Crick, co-discoverer of the structure of DNA and winner of the 1962 Nobel Prize in Medicine. This "discussion" is presented at a level understandable by the general public. It focuses on the thought processes that led up to the discovery and on the state of the field of science at the time, as seen by one of the foremost scientists of his generation. A captivating look at the big picture, courtesy of Genentech’s Access Excellence program and the Carolina Biological Supply Company. Also includes some worthwhile links at the bottom of the page.
Nucleotides for Modern Biology
A simple yet powerful look at the nucleotides that make up DNA, from the triphosphate forms to the nonphosphorylated forms. Uses 3D molecular visualization software and includes a number of interactive buttons as well. Created by William McClure, at Carnegie Mellon University, this site requires Netscape 3.x and the Chemscape Chime plug-in.
The RNA World
There is a developing theory among biologists that, sometime in our distant evolutionary past, RNA was the central molecule of life-holding genetic information before the evolution of DNA and carrying on enzymatic catalysis before the advent of proteins. This site by the IMB Jena Biocomputing Group contains hyperlinks to everything you need to know about RNA, its modern-day role, and the RNA-world hypothesis.
The Central Dogma of Molecular Biology
A very nice graphic showing the flow of genetic information from DNA to RNA to protein. From Genentech’s Access Excellence program Graphics Gallery, a great site for a lot of other useful images.
Codon
Also from the Access Excellence Graphics Gallery, an image of how a three-base sequence of RNA codes for a single amino acid of a protein.
Capitolo 6
General Resources
Dr. James Watson, PhD
A narrated essay by James Watson, co-discoverer of the structure of DNA and winner of the 1962 Nobel Prize in Medicine. This "discussion" is presented at a level understandable by the general public. In it, Dr. Watson presents his view of how a good scientist develops, as well some of his own personal history. Courtesy of Genentech's Access Excellence program and the Carolina Biological Supply Company.
Genome Glossary
A glossary of scientific terms to accompany the Human Genome Project Web site (above). Fairly brief and not hyperlinked, but the definitions are concise and clear. A useful resource for beginning students.
Databases
The National Center for Biotechnology Information
There is a staggering amount of information available from the internet on DNA, genes, and heredity. The NCBI does a remarkable job of organizing this information and making it easily accessible. On their site, find links to a numerous databases, including GenBank, dbEST, Molecular Modeling Database (MMDB), Entrez, Medline, Basic Local Alignment Search Tool (BLAST), and more. Also find online newsletters, email servers, etc. This site is the place to start exploring genomics on the internet. A product of the U.S. government.
BLAST
BLAST (Basic Local Alignment Search Tool) is a very popular search engine designed to retrieve information on genes or proteins from a large array of databases. The engine takes a user-entered sequence and looks through the databases for regions of local sequence alignment. It returns a list of related genes, with the closeness of each match indicated. An invaluable tool in many modern research labs. Provided by the National Center for Biotechnology Information.
GenomeNet WWW Server
From Kyoto, Japan, GenomeNet provides links to many popular nucleic acid databases. Researchers use such databases primarily to search for similar (homologous) DNA sequences, which can help assign a function to a newly isolated gene. Web site available in English or Japanese.
Structure Finder
This site provides an interface for searching the Nucleic Acids Database of 3D structures that include nucleic acids. This includes DNA, RNA, DNA:RNA hybrids, proteins bound to DNA or RNA or both, and more. Part of The Nucleic Acid Database Project at Rutgers, The State University of New Jersey.
BodyMap Home Page
The BodyMap is a database of human gene expression levels in various cell and tissue types. It is the product of Kousaku Okubo and Kenichi Matsubara, who have been working since 1991 to collect gene sequences and expression levels and compile them here. BodyMap is a searchable database and includes a helpful introduction to how the data is gathered.
REBASE-Help
Restriction enzymes are one of the most powerful and ubiquitous tools of the modern biochemist. These enzymes recognize and cut very specific sequences of DNA, and they are used in numerous ways in the lab; in addition, they are all naturally occurring enzymes used by microorganisms in their defense mechanisms. REBASE is a comprehensive database of restriction enzymes, including their recognition sites in the genome, potential commercial suppliers, relevant publications, source organisms, and even the corresponding methylases. It is the premier electronic source for this information.
EBI, the European Bioinformatics Institute
The EBI is part of the European Molecular Biology Lab (EMBL) and is a prominent player in bioinformatics services on the Internet. The EBI administers biological databases, including gene sequences, protein sequences, and macromolecular structures. Their site provides access to a number of related databases, and is fairly well documented with helpful introductory materials. The group is headed by Geoff Barton and hosted at the Wellcome Trust Genome Campus, in Cambridge, U.K.
DOGS-Database of Genome Sizes
Every organism has its own genome, unique in sequence and size. This Web site from the Center for Biological Sequence Analysis is a growing compilation of known genome sizes. It is instructive to see the vast differences in genome size between organisms. Thanks to Nikolaj Blom and Kristoffer Rapacki for creating this database.
GeneCards: Human Genes, Proteins and Diseases (Weizmann)
Genes make proteins, and proteins carry out functions in the cell. Sometimes, these proteins do not work properly, if at all, and disease can result. GeneCards is a database of known genes, the proteins they make, and the potential harm that mistakes in these genes can do to humans. It is searchable in many different ways-take the guided tour for a helpful introduction. A wonderful site maintained by Liorra Yaar, at the Weizmann Institute of Science in Israel.
Molecular Tools and Protocols
Nucleic Acid Dot Plots
One way to analyze nucleic acid sequences is called the dot plot, which reveals whether two regions of DNA have enough complementarity in sequence to pair together. This site offers a Java-based online tool for analyzing two user-entered DNA sequences for similarities (an online dot plot). Read the background information and the Help sections for more information on how to use the plotter.
The Molecular Toolkit
A helpful set of online tools for analyzing nucleic acids and proteins. Maintained by R. A. Bowen, at Colorado State University.
ASU Biological Mass Spectrometry Laboratory
Mass Spectrometry (MS) is a sensitive and rapid method that has long been used to determine the identity of small molecules. The Biological Mass Spec Lab at Arizona State University is investigating the use of MS to determine the sequence of bases in a DNA molecule. Check out this site for an example of this technique at work, showing its promise as a revolutionary way to sequence genes.
Recombinant DNA Technology Problem Set
The Biology Project (University of Arizona) brings us this Web site to test our knowledge of basic recombinant DNA technology. The questions are all multiple choice. If a question is answered incorrectly, a detailed tutorial is presented explaining the concept behind the question. A powerful learning tool, especially for review purposes.
Capitolo 7
National Human Genome Research Institute
The National Institutes of Health’s official Human Genome Project Site.
The Institute for Genomic Research
A not-for-profit organization specializing in the mapping of the Human Genome.
GenomeWeb
A collection of links to news articles relating to molecular evolution.
Capitolo 8
ENZYME: Enzyme Nomenclature Database (ExPASy)
The definitive database of enzyme names and descriptions. Includes a link to the Boehringer Mannheim Biochemical PathwaysÐan interactive map of all known pathways in the cell, including the relevant enzymes. Part of the popular ExPASy Molecular Biology Server, from the Swiss Institute of Bioinformatics.
Enzyme Structures Database
The definitive database of enzymes for which 3D structures are known. Arranged by class (see the above link to ExPASy¹s ENZYME database)-a very thorough and helpful arrangement. Each enzyme includes sequence, secondary structure map, PDB ID code for access to the 3D structure file, active site details, various still images, topology cartoons, and sequence alignment with related proteins. A truly amazing repository of information. From Roman Laskowski and Andrew Wallace, University College in London.
Energy, Enzymes, and Catalysis Problem Set
A set of 16 multiple-choice questions pertaining to energy, enzymes, and catalysis. Includes an extensive tutorial with each question. A very nice site for students ready to review concepts in enzymology. Part of The Biology Project at the University of Arizona.
The G6PD Deficiency Homepage
What happens when an enzyme does not work right? A deficiency in the enzyme glucose-6-phosphate dehydrogenase (G6PD) is the most common human enzyme deficiency in the world. This enzyme normally catalyzes the regeneration of NADPH, a crucial energy molecule like ATP. Check out this site to find out the consequences of this deficiency, as well as why the disease arises and what is being done to combat it. Maintained by Ramez Ethnasios.
Virtual Chemistry Lab: Equilibrium and the LeChatelier Principle
This demonstration experiment should be helpful for students struggling to understand enzyme kinetics (which follow similar principles). It begins with a thorough background on equilibrium reactions in chemical systems. The centerpiece of the site is a virtual online experiment, where a student can alter various reaction conditions and view the consequences. A novel interactive lesson in equilibrium, by David Clarke and part of the Virtual Chemistry Lab. This utility is still under development, but many other interesting experiments are planned. Check out the short descriptions that are given at the site.
Symbolism and Terminology in Enzyme Kinetics
Ever wonder how enzymes are named and categorized? This site holds the official recommendations for enzyme nomenclature set forth by the International Union of Biochemistry. It is the definitive guide for enzymology research labs around the world. Web version maintained by G. P Moss.
Ligand Chemical Database for Enzyme Reactions (LIGAND)
A huge searchable database that holds all known enzyme-catalyzed reactions, including detailed information about the enzymes themselves, reactants, and products, as well as other relevant uncatalyzed reactions. This site also includes biochemical pathways, corresponding gene sequences, known genetic diseases linked to specific pathways or enzymes, and more. Hosted by Kyoto University and part of GenomeNet.
Capitolo 9
Carboxypeptidase A
Carboxypeptidase A is a well-studied example of enzyme catalysis. This site contains two in-depth tutorials that address the 3D structure of this enzyme and how it relates to its biological function. The free program RasMol is required to view the tutorials, but help is provided for configuring it properly. Hosted by Curtin University of Technology.
Interactive Biochemistry
Follow the "Enzyme Mechanisms" link from the Table of Contents page of this site to find the Aspartate Protease Mechanism Tutorial. This clever Java-based interactive tutorial takes you through the exact chemical steps in the proteolytic cleavage of a peptide bond. Great for students with some basic knowledge of enzyme-mediated cleavages. Created by Edward O'Neil and Charles Grisham, University of Virginia.
Capitolo 10
An Overview of Pancreatic Development
It is always important to remember that biochemical reactions occur in the context of cells, tissues, and organs. This site, although heavily anatomical, discusses the regulation of chymotrypsin, trypsin, ribonucleases, and carboxypeptidases in the human pancreas. Check out the EXOCRINE section, about a quarter of the way down the page. Hosted by the University of Edinburgh, Anatomy Section.
Capitolo 11
Neose
The home page of a company involved in developing carbohydrates for nutritional and medical purposes. Click on the "carbohydrates as natural anti-infectives" link for a brief summary of their research in this area.
Capitolo 12
Lipid Structure PDB Files
Popular lipids in the CHIME format!
Lipids Online
Maintained by the Center for Collaborative and Interactive Technologies of the Baylor College of Medicine, Lipids Online is an online cardiovascular resource for clinicians, researchers and educators. Includes slides, presentations and a virtual meeting room.
A Graphic Introduction to Lipid Structure
One glance at this Web site reveals how small differences in the composition of a lipid molecule can have dramatic effects on structure. Just compare palmitic acid (no double bonds), oleic acid (one double bond), and linoleic acid (two double bonds). View them as 2D static images, as they first appear, or use the links to view the 3D structures in either VRML (requires the free plug-in WorldView from Intervista) or PDB format (requires either RasMol or the free plug-in Chemscape Chime). Part of the New York University online Library of 3D Molecular Structures.
Capitolo 13
Per questo capitolo non è disponibile nessun link.
Capitolo 14
Metabolism Problem Set
This Web site is a great online quizzing interface for reviewing general concepts in metabolism. If a multiple-choice question is answered incorrectly, an extensive tutorial appears, explaining the concept being tested and giving the correct answer. Part of the Biology Project at the University of Arizona.
Capitolo 15
Peptide Hormones
This site is a nice resource on the structure and function of various families of hormones, which induce many important signal-transduction cascades in the human body. Also included are a summary table of structures and functions, as well as descriptions of hormone receptors, second-messenger molecules, and related diseases. Written for students interested in medical applications, this site is part of the Medical Biochemistry Page of the Terre Haute Center for Medical Education.
Steroid Hormones
A companion to Peptide Hormones above, this site covers the important characteristics of steroids such as testosterone and cortisol and their role in signal transduction. Part of the Medical Biochemistry Page of the Terre Haute Center for Medical Education.
CHIMEView: PKA Signal Transduction
This Web site presents protein kinase A (PKA), an important player in signal-transduction pathways, in an interactive 3D environment called CHIMEView (developed by Craig Martin, at the University of Massachusetts at Amherst). The site requires the free plug-in Chemscape Chime. It offers the 3D structure of PKA with accompanying text and clickable buttons for exploring details of the structure. For advanced students who are familiar with Chime and Rasmol, there is also a command line (located below the structure) to enter Rasmol commands and view the results. The PKA tutorial was authored by Honor Glenn, at the University of Massachusetts at Amherst.
Capitolo 16
ExPASy-Biochemical Pathways
This exPasy search result links the user to the glycolysis section of the popular "Biochemical Pathways" maps from Boehringer-Mannheim. Good for seeing details of the pathways, but does not provide any overview.
Capitolo 17
Structural Look at the TCA Cycle
A terrific Web site detailing the entire citric acid (TCA) cycle, from the entry of carbon as acetyl CoA to the generation of malic acid. Click on a reaction number in the cycle overview (top left corner) to reveal the reaction pathway, a short text description, and 3D structures of the relevant compounds (including any cofactors). Most 3D structures also include interactive buttons that can be pressed to highlight important features. This site uses JavaScript and the Chemscape Chime plug-in. Created and maintained by Wil McClure, at Carnegie Mellon University.
Details of the TCA Cycle
An exhaustive description of the citric acid cycle, including a wealth of information on the activity and regulation of pyruvate dehydrogenase (catalyzes the so-called "step 0" conversion of pyruvate to acetyl-CoA). Each subsequent reaction step is discussed in detail, with focus on the enzyme that catalyzes it. The page ends with a good section on the over-all regulation of the citric acid cycle. Clear, attractive illustrations and extensive hyperlinking to other metabolic pathways make this Web site a great resource for students who want to learn more about this aspect of metabolism. Created by Michael King, at the Terre Haute Center for Medical Education.
Capitolo 18
Details of Oxidative Phosphorylation
An exhaustive description of oxidative phosphorylation, including an introduction to reduction/oxidation reaction chemistry, regulation and inhibition of oxidative phosphorylation, and a summary of other biologically important oxidative pathways. The illustrations are few but clear and useful, and hyperlinks connect this section to pages that detail other metabolic pathways. Created by Michael King, at the Terre Haute Center for Medical Education.
Capitolo 19
Photosynthetic Pigments
Visit this site for a decent description of the major pigment types found in photosynthetic organisms. This Web site covers the different chlorophylls, phycobilins, and carotenoids both from plants and from photosynthetic bacteria. The text is written for beginning students of biochemistry; it provides a good introduction to pigments without a lot of detail. From the University of California Museum of Paleontology, Berkeley.
Photosynthesis Problem Set I
and
Photosynthesis Problem Set II
A pair of excellent Web sites that offer quiz questions covering major concepts in photosynthesis. Questions are multiple choice, and each comes with a thorough tutorial that can be accessed before or after answering the question. A correct answer is accompanied by a short explanation; an incorrect answer brings up the tutorial. This is a wonderful online quiz system for reviewing important concepts, and these Web sites are highly recommended for all students of biochemistry. Part of The Biology Project at the University of Arizona.
Capitolo 20
Per questo capitolo non è disponibile nessun link.
Capitolo 21
Glycogen Metabolism
How does a cell spend energy to convert glucose to glycogen? Why is activation of glucose by uridine diphosphate a necessary step? How does a cell know when to convert glucose to glycogen for storage, and when to break down glycogen into glucose for energy? What happens when something goes wrong in this complex metabolic system? The answers to these and other questions can be found at this comprehensive Web site. It uses text, color figures, and extensive hyperlinks to present a detailed discussion of glycogen metabolism. It covers such topics as glycogen breakdown and synthesis, regulation of both pathways, and the role of glycogen in disease. A highly recommended site for all students of biochemistry. Created by Michael King, at the Terre Haute Center for Medical Education.
Capitolo 22
Per questo capitolo non è disponibile nessun link.
Capitolo 23
Details of Amino Acid Metabolism
Another great site from Michael King, at the Terre Haute Center for Medical Education. This Web site thoroughly addresses the biosynthesis and breakdown of amino acids, taking each one in turn. It also includes a large and illustrative section on the effects of genetic defects in amino acid metabolic enzymes. This site is highly recommended for biochemistry students learning the metabolic pathways.
Details of the Urea Cycle
Everything you need to know about the urea cycle is at this comprehensive Web site. It includes an overview of nitrogen metabolism and the urea cycle, as well as the differences between essential and nonessential amino acids and how nitrogen is removed from an amino acid. Especially interesting is the section on the toxicity of ammonia. Created by Michael King, at the Terre Haute Center for Medical Education.
Capitolo 24
Standard Metabolic Pathways-Amino Acids
Amino Acid-General
Amino Acid Derivatives
Besides their primary role in comprising proteins, amino acids are also the precursors of a number of other important molecules. This Web site details the synthesis of some of these molecules, including various neurotransmitters, creatine, polyamines, glutathione, and nitric oxide. This is a very good Web site for gaining an appreciation of the complexity and interrelated nature of the metabolic pathways. From Michael King, at the Terre Haute Center for Medical Education.
Heme
Heme and Porphyrin Biosynthesis
A comprehensive Web site that covers the intricacies of heme biosynthesis in great detail. The general information at this site will be useful to students of all levels, but it is mostly written for advanced biochemistry students, especially those interested in medicine. From Michael King, at the Terre Haute Center for Medical Education.
Capitolo 25
Details of Nucleotide Metabolism
A comprehensive Web site that addresses all aspects of nucleotide metabolism, written for biochemistry students with an interest in medicine. The combination of text and graphics covers just about everything about nucleotides in great detail, including synthesis and degradation, regulation, interconversion, and clinical significance. There is also an informative section highlighting tetrahydrofolate, an important metabolic intermediate in this and other pathways. This Web site is highly recommended for advanced students of biochemistry who want to know everything about nucleotide metabolism. From Michael King, at the Terre Haute Center for Medical Education.
Details of DNA Synthesis
This Web site discusses all aspects of DNA, including organization in the genome, structure inside the cell, role in the cell cycle, replication, modification, recombination, and repair. A great overview of DNA from a cellular perspective, written for biochemistry students with an interest in medicine. From Michael King, at the Terre Haute Center for Medical Education.
Details of RNA Synthesis
Another comprehensive Web site from Michael King, at the Terre Haute Center for Medical Education. This one addresses the synthesis of RNA, including the different types of RNA in the cell, the mechanism of RNA polymerases, and transcription of DNA into RNA. Most of the content focuses on post-transcriptional events, especially the splicing-out of introns and the clinical significance of errors in splicing.
Capitolo 26
A Graphic Introduction to Lipid Structure
One glance at this Web site reveals how small differences in the composition of a lipid molecule can have dramatic effects on structure. Just compare palmitic acid (no double bonds), oleic acid (one double bond), and linoleic acid (two double bonds). View them as 2D static images, as they first appear, or use the links to view the 3D structures in either VRML (requires the free plug-in WorldView from Intervista) or PDB format (requires either RasMol or the free plug-in Chemscape Chime). Part of the New York University online Library of 3D Molecular Structures.
Details of Phospholipid Metabolism
This Web site presents a comprehensive and well-written description of phospholipids, including structure, synthesis, and significance of each of their major classes. It also covers sphingolipids and glycosphingolipids, including an excellent table summarizing the disorders associated with errors in sphingolipid metabolism. The last section is a detailed look at eicosanoids (steroids), their structure, synthesis, and clinical significance, which is especially related to their role in signal transduction. The section ends with a great table summarizing the important properties of the major eicosanoids. Created by Michael King, at the Terre Haute Center for Medical Education.
Details of Cholesterol and Bile Metabolism
Cholesterol plays a central role in metabolism, both as the precursor of steroid hormones as well as an important determinant of membrane fluidity and structure. This Web site provides a thorough description of cholesterol synthesis and catabolism. It includes a section on regulation of cholesterol metabolism, as well as an introduction to the synthesis, structure, and significance of bile acids. This Web site is highly recommended for all students of biochemistry. Created by Michael King, at the Terre Haute Center for Medical Education.
Capitolo 27
DNA Structure
An interactive, nonlinear tutorial on DNA structure and base pairing using the Chemscape Chime plug-in. This site takes a nonstandard approach to presenting DNA structure, allowing a user to explore the double helix with very little guidance or restrictions. Excellent for students already familiar with DNA basics. From Eric Martz, at the University of Massachusetts at Amherst. This site requires Netscape Navigator 3.x or higher and Chemscape Chime 1.0, and the tutorial can also be downloaded for use off-line.
Nucleic Aids Problem Set
A series of multiple choice questions on nucleic acids, DNA, and the hstory of DNA as the genetic material. Incorrect answers result in impressive review tutorials on the subject of the question. Beginning and advanced students of biochemistry can benefit from this online quiz, which is part of The Biology Project at the University of Arizona.
Capitolo 28
The RNase P Database
tRNA molecules transport amino acids to the ribosome to be incorporated into newly synthesized proteins. RNase P is a ribonucleoprotein (RNA and protein combined) that generates mature tRNA from its precursor by cleaving nucleotides from the tRNA 5' terminus. It is a crucial step in the preparation of tRNA and in protein synthesis in general. This Web site is the premier online resource for RNase P information. It includes RNase P sequences from many different organisms, sequence alignments, secondary structure, 3D models, and more. Entries are extensively hyperlinked to related resources such as the National Center for Biotechnology Information (NCBI) and the Protein Data Bank (PDB). A good resource for advanced students of biochemistry interested in protein synthesis or RNA in general. Maintained by James Brown and hosted at North Carolina State University.
The RNA World
This Web site is the ultimate RNA resource on the Web. Here you will find databases of sequences, maps of secondary structure, 3D structures, structure prediction tools, and more. RNA enthusiasts can download various software packages to use in the lab, access online resources like MFOLD or tRNAscan, learn about RNA meetings, or access tutorials, book reviews, or scientific journals. This is a phenomenal resource for researchers, but it is also a great place for students to see firsthand the cutting edge of RNA research. Hosted by the Institut für Molekulare Biotechnologie (IMB) Jena.
Eukaryotic Gene Expression Problem Set
A great Web site for quizzing students on the basic concepts of RNA synthesis and processing, including splicing and self-catalytic RNAs (ribozymes). Questions are multiple choice, and each comes with a thorough tutorial that can be accessed before or after answering the question. A correct answer is accompanied by a short explanation; an incorrect answer brings up the tutorial. This is a wonderful online review of important concepts and is highly recommended for all students of biochemistry. Part of The Biology Project at the University of Arizona.
Capitolo 29
Details of Protein Synthesis
A phenomenal Web site that details all aspects of protein synthesis. It begins by introducing the revolutionary experiments that led to deciphering the genetic code, and goes on to cover the three steps in protein synthesis. The final section is a wonderful discussion of regulatory processes, including the roles of heme, interferons, and antibiotic inhibitors of protein synthesis. This Web site is highly recommended for students of biochemistry who are interested in medicine. From Michael King, at the Terre Haute Center for Medical Education.
Post-Translational Modification of Proteins
Many important things happen to a protein after it has been translated on the ribosome. One of the most common events is the addition of carbohydrates to the newly-synthesized protein, a process called glycosylation. This comprehensive Web site discusses glycosylation in great detail, as well other post-translational modifications such as proteolytic cleavage, phosphorylation, and more. It is highly recommended for biochemistry students with an interest in medicine. From Michael King, at the Terre Haute Center for Medical Education.
Translate Nucleotides to Protein at ExPASy
A neat tool that allows a user to input a nucleotide sequence (type or paste) and retrieve the corresponding protein translation. Some control over the format of the output sequence is also possible (i.e., three-letter amino acid code or one-letter code). Hosted by the ExPASy (Expert Protein Analysis System) Molecular Biology Server at the Swiss Institute of Bioinformatics.
From Gene to Protein
This Web site contains a simple but beautiful illustration comparing protein synthesis in eukaryotes and prokaryotes. It summarizes the entire process from gene to protein, and includes a well-written and concise legend describing the major differences between cells with a nucleus and cells without. A printable version (PDF) is also available for download, but as always be aware of the copyright restrictions. Part of the Graphics Gallery of Access Excellence, at the National Health Museum.
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Inborn Errors in Metabolism
Errors in metabolism can have disastrous consequences. This comprehensive Web site details many of the metabolic errors that arise from genetic defects, including defects in various metabolic pathways as well as transport processes and even DNA repair. A thorough discussion of inborn errors, geared to students interested in medicine, from Michael King, at the Terre Haute Center for Medical Education.
Diabetes
This Web site defines and describes the many forms of diabetes, one of the best-known metabolic diseases. It includes a thorough discussion of the clinical aspects of the disease, as well as its biochemical and physiological characteristics. Written for students of biochemistry with an interest in medicine. Created by Michael King, at the Terre Haute Center for Medical Education.
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DNA Structure
An interactive, nonlinear tutorial on DNA structure and base pairing using the Chemscape Chime plug-in. This site takes a nonstandard approach to presenting DNA structure, allowing a user to explore the double helix with very little guidance or restrictions. Excellent for students already familiar with DNA basics. From Eric Martz, at the University of Massachusetts at Amherst. This site requires Netscape Navigator 3.x or higher and Chemscape Chime 1.0, and the tutorial can also be downloaded for use off-line.
Nucleic Aids Problem Set
A series of multiple choice questions on nucleic acids, DNA, and the hstory of DNA as the genetic material. Incorrect answers result in impressive review tutorials on the subject of the question. Beginning and advanced students of biochemistry can benefit from this online quiz, which is part of The Biology Project at the University of Arizona.
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National Eye Institute
A link to the National Eye Institute page of the National Institutes of Health. Provides an extensive list of clinical studies supported by the National Eye Institute, as well as information related to vision.
American Pain Society
An organization dealing with pain-related issues
The Glaucoma Research Foundation
Learn about glaucoma, its causes, effects and research being done to combat the disease.
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The Myosin Home Page
THE Web source for information about the crucial motor protein myosin. Advanced students and instructors interested in myosin will find this an invaluable resource. The site contains links to myosin research lab pages around the world, myosin 3D crystal structures, sequence alignments and evolutionary trees, and text descriptions of various aspects of myosin function. Though still incomplete, this Web site is already an important Web-based resource for biochemists interested in motor proteins. Hosted by the Medical Research Council (MRC) Laboratory of Molecular Biology in Cambridge, U.K.
The Cytoskeleton
An excellent Web site outlining the various protein fibers that compose the cytoskeleton-the scaffold that motor proteins use to move around the cell-and also bacterial flagella and cilia. The text is clear and well-written with many hyperlinks. This site also includes a number of very nice electron micrographs of cells, and a few illustrative figures. A recommended site for beginning students to learn the basics of the cytoskeleton. From Kimball's Biology Pages.
The Kinesin Home Page
A valuable Web resource for information about kinesins, similar to the Myosin Home Page (above). This site includes 3D structures of kinesins, evolutionary trees, and thorough text descriptions of kinesin function in various cellular events. The highlight of this excellent site may be the numerous movies available for viewing or download. Most require the QuickTime plug-in. This Web site is hosted at the Fred Hutchinson Cancer Research Center.
Science News Online: Bacterial Flagella
Unicellular bacteria use tiny "propellers" called flagella to navigate in their environment. A flagellum is a complex assortment of proteins that form a molecular motor. Recent evidence has revealed the 3D structure of a flagellum and provides insight into how the proteins function. The article at this Web site presents this evidence to a general audience; it also includes relevant references to the scientific literature for more advanced readers. From Science News Online, companion to the popular weekly Science News.
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Immunology Link
This site is a wonderful general resource for immunology on the Web. On this home page you can find links to online journals, literature search engines, immunology books, research labs and immunology associations, graduate programs, fellowships, and funding opportunities. You can look through job listings or browse online databases for genes, immune molecules, and transgenic mice. Log on to see what else this site has to offer. The best place to start your exploration of immunology on the Web is right here.
The Biology Project: Immunology
This is a great site for learning the basics of immunology quickly and painlessly. Follow the "Introduction to Immunology" for clear descriptions of concepts, including a short self-quiz feature. Case studies are available for more advanced students. Guided tutorials (with accompanying self-quizzes) introduce students to the fundamental laboratory techniques of the ELISA and the Western blot. This is a wonderful resource and is recommended for students at all levels. Part of The Biology Project at the University of Arizona.
Kuby's Immunology Home Page
W. H. Freeman and Company bring us this Web site to accompany Kuby's Immunology, one of the premier textbooks in the field. Follow the "Chapter Resources" link to access material supplemental to the text. Organized by chapter, this material is a combination of well-written text and high-quality images. Some of the chapters allow you to view various immune system molecules in 3D (requires the free plug-in Chemscape Chime). 3D tours written by Duane Sears, at the University of California at Santa Barbara.
Centers for Disease Control and Prevention
Home page of the U.S. agency dedicated to wiping out infectious disease, this Web site is a comprehensive resource for any student of immunology. If it's related to disease and it's on the Web, then it has a link on the CDC home page. Also find here the goals of the CDC, the latest news and announcements, funding, budgets, and more.
Mike Clark's Immunoglobin Structures
A nice set of still images of various antibody (immunoglobin) molecules and models. Also includes some downloadable structure files (PDB format) and a list of Web sites related to immunology. Created by Mike Clark, at Cambridge University.
An Antibody in 3D and Major Histocompatibility Complex in 3D
A wonderful pair of tutorials on the structure and function of these two important immune-system proteins. Both tutorials offer in-depth discussion of detailed structural points, and the images are beautiful. They require the free plug-in Chemscape Chime and are the creation of Eric Martz, at the University of Massachusetts at Amherst.
CHIMEView: MHC Molecules in the Immune Response
This Web site presents HLA-A2, a major histocompatibility complex (MHC) molecule on the surface of a cell that displays peptides for recognition by immune cells. HLA-A2 is shown in an interactive 3D environment called CHIMEView (developed by Craig Martin, at the University of Massachusetts at Amherst). The site requires the free plug-in Chemscape Chime. It offers the 3D structure of the molecule with accompanying text and clickable buttons for exploring details of the structure. For advanced students who are familiar with Chime and RasMol, there is also a command line (located below the structure) to enter RasMol commands and view the results. The HLA-A2 tutorial was authored by Timothy Driscoll, at the University of Massachusetts at Amherst.
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