Biochemistry Online:

An Approach Based on Chemical Logic

Dr. Henry Jakubowski
Last Update: 06/12/2014

 

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Table of Contents    


Preface

MPO - The Cell:  An Overview from a Chemistry Perspective


6/10/14:  Jmol updated to both Jmol14 and JSmol
Chapter 1:  LIPID STRUCTURE
  1. Lipid Structure 
  2. Lipids in Water : Structure
  3. Dynamics of Membrane Lipids
  1. Lipids in Water: Thermodynamics
  2. Why do Single Chain Amphiphiles form Micelles not Bilayers, and Double Chain Amphiphiles from Bilayers and not Micelles?
  3. Lipids and Signaling  

Lipid Structure:  Literature Learning Module


Chapter 2:  PROTEIN STRUCTURE
  1. The Structure and Property of Amino Acids
  2. Composition, Sequence and Conformational Analysis of Proteins
  3. Understanding Protein Conformation
  4. Proteins Folding - In Vivo and In Vitro
  5. Laboratory Determination of DGo for Protein Folding/Unfolding
  6. Thermodynamics and IMF's in Protein Stability  
  7. Predicting Protein Properties Using Computational Biology and Bioinformatics - Proteomics  
  8. Protein Aggregates - Not Just  Junk

Protein Structure:  Literature Learning Module


Chapter 3:  CARBOHYDRATES/GLYCANS
  1. Monosaccharaides and Disaccharides
  2. Complex Carbohydrates (Glycans/Glycoconjates)
  3. Jeopardy(scrambled list of all Jeopardy answers for which you supply the correct question)
  4. Glycoproteins:  Biosynthesis and Function

Chapter 4:  DNA, GENOMICS, AND PROTEOMICS
  1. The Structure of DNA
  2. The Central Dogma of Biology
  3. The Language of DNA
  4. Genomes and Other Omes (not Gnomes)

Chapter 5:  BINDING (with interactive graphs)
  1. Reversible Binding I: Mathematical Models and Experimental Techniques  
  2. Reversible Binding II: Experimental Binding Curves, Kd, and Error Analysis 
  3. Model Binding Systems   Graphs
  4. Binding and the Control of Gene Transcription  
  5. New Methods in Drug Development
  6. Immune System Recognition (under development)

Binding:   Literature Learning Module


Chapter 6:  TRANSPORT AND KINETICS
  1. Passive and Facilitated Diffusion
  2. Steady State and Rapid Equilibrium Kinetics  
  3. Models of Enzyme Inhibition 4/06/14 Updated with Interactive Graphs
  4. More Complicated Enzymes

Transport and Kinetics:   Literature Learning Module


Chapter 7:  CATALYSIS
REVIEW:  ORGANIC CHEMISTRY 
  1. Methods of catalysis
  2. Mechanisms of enzyme-catalyzed reactions
  3. Cofactors and Electron Pushing: Sources and Sinks
  4. Enzyme catalyzed reactions in organic solvents
  5. Ribozymes and the RNA World

Catalysis:  Literature Learning Module


Chapter 8:  OXIDATION/PHOSPHORYLATION
  1. The Chemistry of Dioxygen
  2. Biological Oxidation Reactions - Dehydrogenases, Mono and Dioxygenases, and Oxidases
  3. ATP and Oxidative Phosphorylation Reactions
  4. Photosynthesis: The Light Reaction

Oxidation/Phosphorylation:  Literature Learning Module


Chapter 9:  SIGNAL TRANSDUCTION
  1. Energy Transduction: Uses of ATP
  2. Signal Transduction: Neurochemistry
  3. Signal Transduction at Cell Membranes: Protein Kinases/Phosphatases
  4. Nutrients and Signaling (to be added) 

Chapter 10:  METABOLIC PATHWAYS (MP)

Capstone: The Origin of Life 


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ęCopyright 2002 Dr. Henry Jakubowski
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