Biochemical Goodies

This page is originally authored by Gale Rhodes (© Jan 2000) and is still under continuous update.
The page has been modified with permission and supplemented with new material by Claude Aflalo (© Jan 2000).

Introduction

Here is (or will be...) a catch-all of illustrations, handouts, class problems, and demonstration outlines from biochemistry classes.

Goodies marked CA (or ca) were contributed (or modified) by Claude Aflalo.
BGU STUDENTS: Using these pages may turn to be useful for succeeding in your studies. They are provided in English (as are your textbooks) on purpose: most the biochemical literature is. Make sure to fully understand both the spirit and the text itself.
PC users may download the Babylon program (an on-line English-Hebrew dictionary) here.
Goodies marked OPG are links to Other People's Goodies that might be useful, and by all means highly recommended.
TEACHERS: Please download and use anything that looks useful. Please request permission from the copyright owners Gale Rhodes or Claude Aflalo (items marked accordingly) to use these resources in your teaching. Here's why.

Attention STUDENTS and TEACHERS: for detailed learning tips, a visit to the

Learning Strategies in Biochemistry,
Lab Tips, and
Student Led Discussion, as well as
Other general Learning and Teaching Resources pages is highly recommended for deeper and more efficient learning.
Last, but not least, don't miss the Biochemistry howlers depicting the most common misconceptions in the field, fed and propagated by your textbooks!!! (compiled, explained and rectified by Athel Cornish-Bowden).

List of Goodies, by Topics

Water and Biomolecules

OPG Foundations first! This crash summary of basic organic chemistry will certainly help if kept both in mind and in an accessible drawer...
OPG Confusion about the D- and L- prefixes in Stereochemistry.
OPG Confusion about the ionic state of amino acids.

Basics of Bioinformatics

OPG An anglo-brazilian cooperation yielding a substantial package on Molecular Systematics. Includes a glossary, and extensive teaching/learning materials (lectures outline, tutorials, and slides.)
A Protein Sequencing Problem For Classroom Discussion

Protein Structure

Graphics Tutorials and workshops. For beginners in macromolecular modeling. Learn to use these powerful programs by working through self-guiding tutorials that teach you modeling while reviewing the essentials of protein structure. Start with simple operations, but progress to advanced structural analysis. Thoroughly tested by students and researchers around the world.
- SwissPdbViewer Tutorial. Learn about and get SwissPdbViewer.
- Rasmol Tutorial. Learn about and get RasMol. At the same site, learn about and get Chime, a Netscape plug-in version of RasMol.
- OPG Protein Explorer, an extremely versatile and powerful protein vizualization tool.
- OPG Kinemage a scientific illustration of protein structures presented as an interactive computer display, allowing manipulation, measurements and much more (Jane and David Richardson).
Learn to View Stereo Pairs
OPG How To Grow Protein Crystals
OPG Pictures of Protein Crystals
OPG Fourier Transforms -- Relationship Between Diffraction Pattern and Molecular Structure.
Strengths and Limitations of Crystallographic Models

Enzyme Kinetics & Mechanism

Clear, Step-By-Step Derivation of the Michaelis-Menten Equation (ca)
Summary of Inhibition Types and Their Kinetic Effects
Hill Plots for Myoglobin and Hemoglobin
OPG Dynafit: a powerful enzyme kinetics modeling and simulation program (PC and Mac)
OPG Confusion about bad representation of the Vmax asymptote in the Michaelis-Menten plot.
OPG Misconception about the specificity and properties of liver hexokinase (glucokinase).

Bioenergetics: Oxidative Phosphorylation and Photophosphorylation

DEMONSTRATION: Thermodynamics of Rubber-Band Contraction
Concentration and Activity Plugging the Right Numbers Into Energy Calculations (ca)
OPG The Myth of Catalytic (thermodynamic) Efficiency.
Summary of DG calculations for Redox Reactions and Proton Gradients (ca)
CA Respiratory electron transport chain: summary, details, and redox molecules (iron clusters).
CA Oxidative phosphorylation: energetics, energy transduction, uncoupling, and Respiratory Control.
CA Mitochondrial microcompartmentation.
OPG More mitochondrial resources (structure, function, regulation) for download (PC users).
CA Photosynthesis: harvesting light. Hill reaction in membranes of chloroplast, or photosynthetic bacteria.
CA The quinones cycle.
CA The binding change mechanism of ATP synthase.
CA Bioenergetics in action:
- a molecular motor and its mechanism in bacteria.
- bacterial motility and the mechanism of chemotaxis (signal transduction).

Carbohydrate Metabolism (see also the Metab. Pathw. Biochem. site)

CA Degradation and formation of glucose.
OPG Misconception about Phosphofructokinase control of glycolysis, or control of any metabolic pathway by a single enzyme.
CA Glycogen: degradation, formation, and regulation (but see below).
OPG Correction about the structure of glycogen.
CA The pentoses phosphate pathway: a metabolic scrambler.
CA Sugar biosynthesis in plants. The Calvin cycle: overview and details.

Metabolism: Regulation and Integration

OPG Excellent pages can be also found in a project to develop web-based educational materials for teaching biochemistry of metabolism in studio format. By Joyce Diwan.

CA A general map for Metabolism.
CA Signal transduction pathways
- the adenylate cyclase-protein kinase A route.
- the phospholipase C-protein kinase C route.
- the activation of protein kinases.
- the activation of generic gated channels.
CA Humoral (hormonal) control of carbohydrate metabolism and its physiological effects in different organs.
CA A glossary of unusual terms emerging in (organized) cellular metabolism.
OPG Beyond individual enzymes and their linear gathering: Metabolic Control Analysis (MCA or how 1 + 1 differs from 2)

From DNA to organized Cell

OPG The Great Experiments are short essays explaining many of the classic experiments of the 20th century that have contributed most significantly to our understanding of biology at the molecular and cellular level. A powerful, empowering experience providing first hand historical perspective. The project initiated and continuously developed by Ergito, a new company dedicated to propagate web-based educational materials for Molecular and Cell Biology, was founded by Benjamin Lewin, a former editor of Cell.

DEMONSTRATION: Using Rubber Tubing to Demonstrate DNA Supercoiling and the Action of Topoisomerases (Article from The Chemical Educator)

modified: Sep 2000- Claude Aflalo

Suggestions are welcome...