Biochemistry Online:

An Approach Based on Chemical Logic

Dr. Henry Jakubowski
Last Update: 06/17/2005

[ Biochemistry at CSB/SJU ]

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May 30, 2003

Table of Contents

Update - June 17, 2005:  Figures are now being imbedded in text.

Preface

• WHY CHEMICAL LOGIC?
• UPDATES
• INTRODUCTION TO BIOCHEMISTRY  
• BIOCHEMISTRY/MOLECULAR BIOLOGY DICTIONARIES
• REVIEW:  THE CELL
• PERMISSIONS

Chapter 1:  LIPID STRUCTURE

1. Lipid Structure
2. Lipids in Water : Structure
3. Dynamics of Membrane Lipids
4. Review:  Thermodynamics
5. Lipids in Water: Thermodynamics
6. Why do Single Chain Amphiphiles form Micelles not Bilayers, and Double Chain Amphiphiles from Bilayers and not Micelles?
7. What's New in Lipid Biochemistry

Chapter 2:  PROTEIN STRUCTURE

1. The Structure and Property of Amino Acids
2. Composition, Sequence and Conformational Analyis of Proteins;
3. Understanding Protein Conformation
4. Proteins Folding - In Vivo and In Vitro
5. Laboratory Determination of DG^o for Protein Folding/Unfolding
6. Thermodynamics and IMF's in Protein Stability
7. Prediction of Secondary and Tertiary Structure From the Primary Sequence
8. What's New in Protein Chemistry: Protein Aggregates - Not Just  Junk
9. SUPPLEMENT: MOLECULAR MECHANICS AND DYNAMICS

Chapter 3:  CARBOHYDRATES

1. Monosaccharides and Disssacharides
2. Complex Oligosaccharides
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. Proteomics
5. Human Genome Review

Chapter 5:  BINDING

1. Reversible Binding I: Equations and Curves
2. Reversible Binding II: Experimental Binding Curves, Kd, and Error Analysis
3. A Model Binding System: Myoglobin. Hemoglobin, and Dioxygen
4. Binding and the Control of Gene Transcription:  
5. New Methods in Drug Development

Chapter 6:  TRANSPORT AND KINETICS

1. Passive and Facilitated Diffusion
2. Steady State and Rapid Equilbirum Kinetics
3. Models of Enzyme Inhibition
4. More Complicated Enzymes

Chapter 7:  CATALYSIS

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

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

Chapter 9:  SIGNAL TRANSDUCTION

1. Energy Transduction: Uses of ATP
2. Signal Transduction: Neurochemistry
3. Signal Transduction at Cell Membranes: Protein Kinases/Phosphatases
4. Apoptosis - Programmed Cell Death  and Signal Transduction
5. Memory and Learning in Apylsis 

Appendices

• List of Figures
• List of Tables

• Chime Files

Additional Web Links

• Biochemistry, 2nd Edition. Garret and Grisham:  Web Materials
• Web companion for Lehninger's  Principles of Biochemistry
• Searchable Biochemistry/Molecular Biology Books from the NCBI
• Useful Reference:  Molecular Cell Biology by Lodish, et. al.  (1999) Free Web Version.
• Medical Biochemistry
• Common mistakes found in Biochemistry textbooks!
• Searchable Biochemistry concepts from Mathews, van Holde, and Ahern
• Web Companion for Biochemistry, 5th Edition, by Berg, Tymoczko and Stryer

©Copyright 2002 Dr. Henry Jakubowski
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