Biochemistry Online:

An Approach Based on Chemical Logic

Dr. Henry Jakubowski
Last Update: 01/22/2012

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Table of Contents    

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 (New: Lipid Droplets, 1/22/12)
3. Dynamics of Membrane Lipids

• SUPPLEMENT: MOLECULAR MECHANICS AND DYNAMICS
• REVIEW  THERMODYNAMICS

4. Lipids in Water: Thermodynamics
5. Why do Single Chain Amphiphiles form Micelles not Bilayers, and Double Chain Amphiphiles from Bilayers and not Micelles?
6. Lipids as Biological Signals

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 DG^o 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

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. Genomes and Other Omes (not Gnomes)

Chapter 5:  BINDING

1. Reversible Binding I: Equations and Curves
2. Reversible Binding II: Experimental Binding Curves, Kd, and Error Analysis
3. Model Binding Systems
4. Binding and the Control of Gene Transcription  
5. New Methods in Drug 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. More Complicated Enzymes

Transport and Kinetics:   Literature Learning Module

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 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  

Chapter 10:  METABOLIC PATHWAYS (MP) NEW JANUARY 10, 2012

• MP1:  An Overview of Metabolic Pathways - Catabolism
• MP2:  An Overview of Metabolic Pathways - Anabolism
• MP3: Metabolic Maps Home Page
• MP4:  Regulation of Metabolic Pathways A - How is Enzyme Activity Regulated?
• MP5: Regulation of Metabolic Pathways B - Which Enzymes Are Optimal for Regulation?

Capstone: The Origin of Life 

Appendices

• List of Figures

• List of Tables

• List of Moodle Quizzes

• Chime and Jmol Files

• Experimental Techniques

Additional Web Links

• Biochemistry, 2nd Edition. Garret and Grisham
• Lehninger's rinciples of Biochemistry - 4th ed. Cox/Nelson
• Biochemistry by Matthews, van Holde, and Ahern
• Biochemistry, 5th Edition, by Berg, Tymoczko and Stryer
• Searchable Biochemistry/Molecular Biology Books from the NCBI
• Useful Reference:  Molecular Cell Biology by Lodish, et. al.  5th Edition  Free Web Version.
• Martindale's Biochemistry
• Biophysical Resources
• Medical Biochemistry
• Common mistakes found in Biochemistry textbooks!
• Physical Chem/Life Sciences:  Atkins et al.
• Searchable Biochemistry concepts from Mathews, van Holde, and Ahern
• EverythingBio Resource
• A link to all Biochemistry books from the Journal of Chemical Education

• Archived Clustr Map from 1/15/09

• Archived Clustr Map from 1/15/10

Search Engines

• Quertle
• NCBI: National Center for Biotechnology Information
• PubMed

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