Proteopedia:Biochemistry in 3D

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Biochemistry in 3D was a supplement to the textbook Lehninger Principles of Biochemistry (fourth edition, published in 2000). The supplement was created by Timothy Driscoll and Frieda Reichsman (Worth Publishers). It used a technology called Chime browser plug-in that is no longer easy to access. Inspired by this supplement, the following are topics that students in their first course of biochemistry are likely to encounter. For each topic, some links to relevant Proteopedia articles are given. For logistical support and more suggestions, see Help:Teaching with Proteopedia.

Contents

Introduction to this collection

Proteopedia contains comprehensive content that can be used as a 3D supplement throughout the first semester in a biochemistry course. This page gives suggestions of which pages might match a first semester biochemistry course particularly well. For example, during the section on protein structure, Proteopedia can be used to introduce the ‘levels’ of structure (i.e., primary, secondary, etc.) in both 2D and 3D (Introduction_to_protein_structure). This page, developed by Ann Taylor, includes a number of leading questions and is leveraged to ‘flip’ the classroom and provide motivation to the student for learning structure. The questions embedded in the page serve to spark a conversation about protein structure. Two tutorials on the Ramachandran plot illustrate constraints on the protein main chain geometry that are difficult to teach without 3D visualization and difficult to learn without being able to manipulate a protein backbone to experience the clashes for certain phi/psi angle combinations Tutorial:Ramachandran principle and phi psi angles Tutorial:Ramachandran Plot Inspection. Hemoglobin illustrates protein function, ligand binding, and allostery ([Hemoglobin], Ann_Taylor/Hemoglobin). Glucokinase is another example (The_Structure_and_Mechanism_of_Hexokinase). These models and their Proteopedia pages visually illustrate the conformational changes that occur upon ligand binding and on regulator binding. A page on citrate synthase (Citrate_Synthase, started as student-authored page) can be used during the citric acid cycle; it features an instructive morph of open to closed conformation to teach the concept of protein dynamics. This is a difficult concept to convey with static images, but on Proteopedia, Jmol can visualize the motion, making it easier to grasp.


Biomolecules

Metabolism

Genetic information processing

Proteopedia Page Contributors and Editors (what is this?)

Karsten Theis

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