TIGER

Other Resources: 55 results
Biomolecules (Netorials)  Rachel Bain, Mithra Biekmohamadi, Liana Lamont, Mike Miller, Rebecca Ottosen, John Todd, and David Shaw
Biomolecules: this is a resource in the collection "Netorials". This set of modules will provide you with a descriptive overview of the four major classes of biomolecules found in all living organisms: carbohydrates, lipids, proteins, and nucleic acids. The Netorials cover selected topics in first-year chemistry including: Chemical Reactions, Stoichiometry, Thermodynamics, Intermolecular Forces, Acids & Bases, Biomolecules, and Electrochemistry.
Bioorganic Chemistry |
Carbohydrates |
Nucleic Acids / DNA / RNA |
Lipids |
Proteins / Peptides
Netorials  
The Netorials cover selected topics in first-year chemistry including: Chemical Reactions, Stoichiometry, Intermolecular Forces, Acids & Bases, Biomolecules, and Electrochemistry.
Acids / Bases |
Stoichiometry |
Proteins / Peptides |
Enzymes |
Carbohydrates |
Nucleic Acids / DNA / RNA |
Lipids |
Oxidation / Reduction |
Noncovalent Interactions
Molecular Models of DNA  William F. Coleman
The featured molecules this month come from the paper by David T. Crouse on the X-ray determination of the structure of DNA. Given that most students are aware of the double helix, it seems appropriate to back up a little and examine the components that give rise to this structure. Accordingly, the molecule collection includes: Purine and pyrimidine, structural precursors of the four bases found in DNA: cytosine (C), thymine (T), adenine (A), and guanine (G) The four corresponding deoxyribonucleosides The four deoxyribonucleotides (the nucleoside monophosphates) A two-base-pair fragment showing the AT and GC hydrogen-bonded complements Several small 24-base-pair DNA fragments polyAT, polyGC, and a random array of bases. The DNA fragments provide a good opportunity to have students explore features of the Jmol and Chime menus. Using the Jmol menu as an example (right-click on the structure to bring up the menu) students can use the measuring tools to get an idea of the length of a complete turn in the DNA, the relative widths of the major and minor grooves, and the diameter of the helix. They can use the coloring schemes to detect the various base pair combinations, and learn to read the code for the random sequence. In Chime they can use the Shapely coloring scheme for this same purpose. Exploring other aspects of the menu will allow students to present the molecules in the various forms, including ribbon and cartoon views. In RNA, thymine is replaced by uracil, and the sugar moiety has an axial hydroxyl group on the carbon atom adjacent to the base binding site (the 2? carbon). The structures of uracil and of uridine monophosphate are included in the molecule collection. Students can use the Web to download and examine more complex DNAs using a site such as the Nucleic Acid Database at Rutgers University.
Nucleic Acids / DNA / RNA
Molecular Models of DAPI  William F. Coleman
This month's Featured Molecule is DAPI (4′,6-diamidino-2-phenylindole), from the paper by Eamonn F. Healy (1). The utility of DAPI is a consequence of its being a minor-groove binder to DNA. A crystal structure of DAPI binding to the minor groove of a synthetic DNA has been determined, and the structure file made available through the RCSB Protein Data Bank (2, 3). That structure is also included in the Featured Molecules Collection, with the water molecules removed for the sake of clarity. For many students this may be their first encounter with the binding of small molecules to DNA. Another example of such binding is the intercalation of the antibiotic actinomycin into DNA. The Department of Biology at the University of Hamburg maintains an excellent Web site showing both crystal and NMR structures of actinomycin intercalation (4). Observant students will also note in the structure of DAPI a theme that has appeared several times in our Featured Molecules, and that is the non-planarity of adjacent delocalized ring systems. In DAPI, it is a five-membered ring adjacent to a six-membered ring, and the observed departure from planarity is less than that in biphenyl. Students might be asked to explain that difference.
Nucleic Acids / DNA / RNA
Information Storage in Sports, Physiology & Health  Tim Wendorff
A section of ChemPrime, the Chemical Educations Digital Library's free General Chemistry textbook.
Nucleic Acids / DNA / RNA
ChemPaths 104 F Feb 4  John W. Moore
Today in Chem 104: * Lecture: Problem-Solving Session (email questions or topics to Prof. Moore jwmoore@chem.wisc.edu by 9am today) * No reading assigned for today. * Homework #3 due by 11:55 pm Today! * Moodle Tutorials o DNA 1 (including debriefing) o DNA 2 (including debriefing) o DNA 1 and 2 Quiz due M Feb 7, 11:55pm
Nucleic Acids / DNA / RNA
ChemPaths 104 M Feb 7  John W. Moore
Today in Chem 104: Lecture: Biochemistry: DNA; Importance of Molecular Structure * Reading: Kotz: Chemistry of Life (pp. 503-510); Moore:Ch. 3: Sec. 11;Ch. 12: Sec. 7 * Moodle Tutorials o DNA 1 (including debriefing) o DNA 2 (including debriefing) o DNA 1 and 2 Quiz due TODAY 11:55pm * Homework #4 due F Feb 11, 11:55 PM
Nucleic Acids / DNA / RNA
Nucleic Acids  Ed Vitz, John W. Moore
A section of ChemPrime, the Chemical Educations Digital Library's free General Chemistry textbook.
Nucleic Acids / DNA / RNA
Nucleic Acid Structure  Ed Vitz, John W. Moore
A section of ChemPrime, the Chemical Educations Digital Library's free General Chemistry textbook.
Nucleic Acids / DNA / RNA
Information Storage  Ed Vitz, John W. Moore
A section of ChemPrime, the Chemical Educations Digital Library's free General Chemistry textbook.
Nucleic Acids / DNA / RNA
The Double Helix  Ed Vitz, John W. Moore
A section of ChemPrime, the Chemical Educations Digital Library's free General Chemistry textbook.
Nucleic Acids / DNA / RNA
DNA Replication  Ed Vitz, John W. Moore
A section of ChemPrime, the Chemical Educations Digital Library's free General Chemistry textbook.
Nucleic Acids / DNA / RNA
Transcription and Translation  Ed Vitz, John W. Moore
A section of ChemPrime, the Chemical Educations Digital Library's free General Chemistry textbook.
Biosynthesis |
Nucleic Acids / DNA / RNA
The World's Food Supply  
Volume 04, issue 05 of a series of leaflets covering subjects of interest to students of elementary chemistry distributed in 1929 - 1932.
Proteins / Peptides |
Carbohydrates |
Lipids |
Nutrition
The World's Food Supply  
Volume 05, issue 10 of a series of leaflets covering subjects of interest to students of elementary chemistry distributed in 1929 - 1932.
Proteins / Peptides |
Carbohydrates |
Lipids |
Nutrition
Nutrition  American Chemical Society
ACS Science for Kids activities that explore the chemical properties of food and nutrition.
Lipids |
Physical Properties |
Proteins / Peptides |
Nutrition |
Carbohydrates
The World's Food Supply  
Volume 03, issue 09 of a series of leaflets covering subjects of interest to students of elementary chemistry distributed in 1929 - 1932.
Plant Chemistry |
Photosynthesis |
Proteins / Peptides |
Carbohydrates |
Lipids |
Nutrition
Your Body  American Chemical Society
ACS Science for Kids activities explore the chemistry of the human body.
Bioenergetics |
Applications of Chemistry |
Nutrition |
Lipids |
Proteins / Peptides |
Carbohydrates |
Food Science
Characteristics of Materials  American Chemical Society
What makes diapers absorbent? Is peanut butter stickier than syrup or jelly? Strong, stretchy, sticky, or sweet—everything around us has special properties which make them unique. See if you can identify and compare the characteristics of materials.
Industrial Chemistry |
Physical Properties |
Reactions |
Consumer Chemistry |
Gases |
Carbohydrates |
Proteins / Peptides |
Crystals / Crystallography |
Water / Water Chemistry |
Plant Chemistry |
Dyes / Pigments |
Lipids |
Molecular Properties / Structure |
Applications of Chemistry |
Nutrition |
Acids / Bases |
Chromatography |
Magnetic Properties |
Metals |
Polymerization |
Solutions / Solvents |
Descriptive Chemistry |
Food Science
Polysaccharides  Ed Vitz, John W. Moore
A section of ChemPrime, the Chemical Educations Digital Library's free General Chemistry textbook.
Carbohydrates |
Polymerization
Umami and Proteins  Robert Hetue
A section of ChemPrime, the Chemical Educations Digital Library's free General Chemistry textbook.
Proteins / Peptides
ChemPaths 104 M Jan 31  John W. Moore
Today in Chem 104: * Lecture: Biochemistry: Proteins * Reading: Kotz: Chemistry of Life (pp. 496-502); Moore: Ch 3, Sec 11; Ch 12, Sec 7 * Biomolecules Tutorials o Proteins 1 (including debriefing) o Proteins 2 (including debriefing) o Quiz due W Feb. 2, 11:55 PM) * Homework #3 due by 11:55pm F Feb 4.
Proteins / Peptides
Polypeptide Chains  Ed Vitz, John W. Moore
A section of ChemPrime, the Chemical Educations Digital Library's free General Chemistry textbook.
Proteins / Peptides
Primary Protein Structure  Ed Vitz, John W. Moore
A section of ChemPrime, the Chemical Educations Digital Library's free General Chemistry textbook.
Proteins / Peptides
Secondary Protein Structure  Ed Vitz, John W. Moore
A section of ChemPrime, the Chemical Educations Digital Library's free General Chemistry textbook.
Proteins / Peptides
Higher-Order Structure  Ed Vitz, John W. Moore
A section of ChemPrime, the Chemical Educations Digital Library's free General Chemistry textbook.
Proteins / Peptides
Food  American Chemical Society
ACS Science for Kids activities that explore the chemical properties of foods.
Plant Chemistry |
Dyes / Pigments |
Lipids |
Proteins / Peptides |
Carbohydrates |
Molecular Properties / Structure |
Applications of Chemistry |
Nutrition |
Acids / Bases |
Chromatography
Secondary Protein Structure with Cultural Connections  Garrett Schwarzman
A section of ChemPrime, the Chemical Educations Digital Library's free General Chemistry textbook.
Proteins / Peptides |
Consumer Chemistry
ChemPaths 104 W Feb 2  John W. Moore
Today in Chem 104: * Lecture: Biochemistry: Proteins * Reading: Biomolecules Tutorials o Proteins 1 (including debriefing) o Proteins 2 (including debriefing) o Quiz due TODAY, 11:55 PM) * Homework #3 due by 11:55pm F Feb 4.
Proteins / Peptides |
Amino Acids
Proteins  Ed Vitz, John W. Moore
A section of ChemPrime, the Chemical Educations Digital Library's free General Chemistry textbook.
Proteins / Peptides |
Enzymes
Limiting Reagent Protein Nutrition  Ed Vitz
A section of ChemPrime, the Chemical Educations Digital Library's free General Chemistry textbook.
Stoichiometry |
Proteins / Peptides |
Amino Acids
Anthropology and Protein Stoichiometry  Ed Vitz
A section of ChemPrime, the Chemical Educations Digital Library's free General Chemistry textbook.
Stoichiometry |
Proteins / Peptides |
Amino Acids
Addition Polymers  Ed Vitz, John W. Moore
A section of ChemPrime, the Chemical Educations Digital Library's free General Chemistry textbook.
Polymerization
Condensation Polymers  Ed Vitz, John W. Moore
A section of ChemPrime, the Chemical Educations Digital Library's free General Chemistry textbook.
Polymerization
Copoly; A Tool for Understanding Copolymerization and Monomer Sequence Distribution of Copolymers  Massoud Miri, Juan A. Morales-Tirado
The study of the composition and monomer sequence distribution of binary copolymers is often complicated because of the many definitions of representative properties for the sequence distribution, the numerous calculations required, and occasionally the abstract treatment of the statistical processes describing the copolymer formation. Copoly resolves these issues with a user-friendly, highly visual interface to perform all calculations. Using Microsoft Excel and Word, Copoly is compatible with Windows and Mac OS. In Copoly the students enter up to five independent data parameters using the Data Input Window, and immediately see the results. To obtain diagrams for a copolymerization obeying a second-order Markovian process, the fraction of one monomer, A, and the reactivity ratios, rA, rB, rA´ and rB´ need to be entered; for a first-order Markovian process only the first three of these are required. For a Bernoullian- or zeroth-order Markovian process only A and rA are required. The results are displayed on separate sheets labeled: 1. Copolymerization Diagrams, 2. Dyads and Triads, 3. Sequence Length Distribution, 4. Simulated Copolymer Design, and 5. Summary.
Polymerization
The Origin of Nylon  Robert Hetue
A section of ChemPrime, the Chemical Educations Digital Library's free General Chemistry textbook.
Polymerization
ChemPaths 104 F Jan 28  John W. Moore
Today in Chem 104: * Lecture: Polymers; Problem-Solving Session (email questions or topics to Prof. Moore jwmoore@chem.wisc.edu by 9am today) * No reading assigned for today. * Homework #2 due 11:55pm Today!
Polymerization
Slime and Goo  American Chemical Society
ACS Science for Kids activities exploring the properties of polymers.
Polymerization
Polymers-Characteristics of Materials  American Chemical Society
ACS Science for Kids explores the properties of polymers.
Polymerization
Mage; A Tool for Developing Interactive Instructional Graphics  Stephen F. Pavkovic
Mage is a graphics program especially well suited for visualizing three-dimensional structures of proteins and other macromolecules. It is an important tool for biochemists and finds many applications in biochemistry courses. We utilize Mage to create interactive instructional graphics of potential use in a wider range of undergraduate chemistry courses, and present some of those applications here.
Crystals / Crystallography |
Group Theory / Symmetry |
VSEPR Theory |
Molecular Properties / Structure |
Stereochemistry |
Proteins / Peptides
Simple Sugars  Ed Vitz, John W. Moore
A section of ChemPrime, the Chemical Educations Digital Library's free General Chemistry textbook.
Carbohydrates
Disaccharides  Ed Vitz, John W. Moore
A section of ChemPrime, the Chemical Educations Digital Library's free General Chemistry textbook.
Carbohydrates
ChemPaths 104 W Jan 26  John W. Moore
Today in Chem 104: * Lecture: Organic Chemistry; Polymers * Reading: Kotz: Ch. 10, Sec. 5 Moore: Ch 12, Sec 5-6 * Homework #2 due 11:55pm F Jan 28. * Quiz 1 in 2nd Discussion section
Esters |
Polymerization
ChemPaths 104 W Feb 9  John W. Moore
Today in Chem 104: * Lecture: Biochemistry: Carbohydrates and Polysaccharides * Reading: Moodle Tutorials o Carbohydrates (including debriefing) o Lipids (including debriefing) o Carbohydrates and Lipids Quiz due F Feb 11 11:55 pm * Homework #4 due F Feb 11 11:55 pm
Carbohydrates |
Lipids
ChemPaths 104 F Feb 11  John W. Moore
Today in Chem 104: * Lecture: Problem-Solving Session (email questions or topics to Prof. Moore jwmoore@chem.wisc.edu by 9am today) * No assigned reading for today. * Homework #4 due by 11:55pm Today! * Moodle Tutorials o Carbohydrates (including debriefing) o Lipids (including debriefing) o Carbohydrates and Lipids Quiz due TODAY 11:55 pm
Carbohydrates |
Lipids
Balancing Equations for Carbohydrate Reactions  Ed Vitz
A section of ChemPrime, the Chemical Educations Digital Library's free General Chemistry textbook.
Stoichiometry |
Carbohydrates
Synthetic Macromolecules: Some Applied Organic Chemistry  Ed Vitz, John W. Moore
A section of ChemPrime, the Chemical Educations Digital Library's free General Chemistry textbook.
Materials Science |
Polymerization
Cross-Linking  Ed Vitz, John W. Moore
A section of ChemPrime, the Chemical Educations Digital Library's free General Chemistry textbook.
Materials Science |
Polymerization
Molecular Models of Polymers Used in Sports Equipment  William F. Coleman
In keeping with the 2008 National Chemistry Week theme of Having a Ball with Chemistry, the Featured Molecules this month are a number of monomers and their associated polymers taken from a paper by Sandy Van Natta and John P. Williams on polymers used in making equipment for a variety of high-impact sports (1). The molecules provide students with an introduction to an important area of applied chemistry and also enable them to examine complex structures using the models they have seen applied to small molecules.It is certainly instructive for students to build small polymer fragments using molecular model kits. Holding a model of n-decane, for example, and twisting it in various ways, provides real insight into the multiplicity of conformations available to supermolecules of polyethylene. Computer-based 3-dimensional structure drawing and visualization programs make it possible to construct large oligomers of known polymers and to begin to explore structural properties of new systems. Two such programs, free for academic use, are DSVisualizer and ArgusLab (2). DSVisualizer includes a useful set of tools for building and viewing structures and a clean geometry option that applies a Dreiding-like force field. ArgusLab adds the ability to perform both molecular mechanics and semi-empirical geometry optimization and to display various molecular surfaces. Using ArgusLab, or a similar program, students can explore the relative energies of various conformations of the substances they have built electronically. Students who are being introduced to molecular modeling and the use of more sophisticated software can easily explore the effects of the modeling and convergence parameters on the stable structures that are found, and can begin to explore the difference between global and local minima on a molecular potential energy surface. Using the conformational search program in HyperChem 7.5 on a tetramer of vinyl chloride (terminated with H; of SRRS stereochemistry; only CCCC torsions varied), approximately half of the 500 structures examined fell within 6 kcal/mol of the lowest energy structure (3). This number would increase significantly if other torsion angles were included.The use of computational software allows us to introduce students in introductory chemistry to the idea of multiple conformations, which is so important in biochemistry and much of organic chemistry. In teaching ideas behind conformational stability care should be taken when attributing conformational stability solely to non-bonded repulsions between peripheral atoms on adjacent carbon atoms. Weinhold and co-workers have recently presented strong evidence that the stability of the staggered conformer of ethane relative to the eclipsed form arises from more favorable interactions of C-H sigma bonding orbitals on adjacent carbons (4). The multiplicity of such interactions could well be responsible for conformational stability in more complex systems. Any discussion of conformational stability should also introduce students to the ultimate conformational problem, the folding of proteins and to the Folding@home project (5).
Polymerization |
Applications of Chemistry
BIODEGRADABLE PLASTICS  Amperegrine57
A section of ChemPrime, the Chemical Educations Digital Library's free General Chemistry textbook.
Polymerization |
Green Chemistry
Bisphenol A  Rrizor
A section of ChemPrime, the Chemical Educations Digital Library's free General Chemistry textbook.
Polymerization |
Green Chemistry
Fat vs. Sugar Metabolism  Ed Vitz
A section of ChemPrime, the Chemical Educations Digital Library's free General Chemistry textbook.
Calorimetry / Thermochemistry |
Metabolism |
Lipids |
Carbohydrates
Soap and Detergent  American Chemical Society
ACS Science for Kids activities explore the properties of soap in aqueous solutions.
Lipids |
Polymerization |
Water / Water Chemistry |
Solutions / Solvents
Toys-ACS Science for Kids  American Chemical Society
ACS Science for Kids activities explore how chemistry can be used to make toys.
Gases |
Polymerization |
Water / Water Chemistry |
Physical Properties |
Lipids |
Reactions
Connected Chemistry  Mike Stieff
Connected Chemistry, a novel learning environment for teaching chemistry, is appropriate for use in both high school and undergraduate chemistry classrooms. Connected Chemistry comprises several molecular simulations designed to enable instructors to teach chemistry using the perspective of emergent phenomena. That is, it allows students to see observed macro-level chemical phenomena, like many other scientific phenomena, as resultant from the interactions of many individual agents on a micro-level. This perspective is especially appropriate to the study of chemistry where the interactions between multitudes of molecules on the atomic level give rise to the macro-level concepts that students study in the classroom. Connected Chemistry comprises molecular simulations embedded in the NetLogo modeling software (1). The collection contains several predesigned simulations of closed chemical systems to teach specific chemistry concepts. Currently, Connected Chemistry contains models for teaching Brønsted Lowry acid base theory, enzyme kinetics, radical polymerization, buffer chemistry, kinetics, chemical equilibrium, and crystallization. Instructors and students can individually tailor the predesigned simulations or generate new simulations as they are needed in the context of a particular lesson, classroom, or department.
Acids / Bases |
Gases |
Kinetics |
Nuclear / Radiochemistry |
pH |
Titration / Volumetric Analysis |
Polymerization |
Equilibrium |
Catalysis