Dr. Henry Jakubowski
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Table of Contents
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Preface
WHY CHEMICAL LOGIC?
UPDATES
INTRODUCTION TO BIOCHEMISTRY
BIOCHEMISTRY/MOLECULAR BIOLOGY DICTIONARIES
REVIEW: THE CELL
PERMISSIONS
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Chapter 1: LIPID STRUCTURE
Lipid Structure
Lipids in Water : Structure
Dynamics of Membrane Lipids
SUPPLEMENT: MOLECULAR MECHANICS AND DYNAMICS
REVIEW THERMODYNAMICS
Lipids in Water: Thermodynamics
Why do Single Chain Amphiphiles form Micelles not Bilayers, and Double Chain Amphiphiles from Bilayers and not Micelles?
Lipids as Biological Signals
Lipid Structure: Literature Learning Module
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Chapter 2: PROTEIN STRUCTURE
The Structure and Property of Amino Acids
Composition, Sequence and Conformational Analyis of Proteins;
Understanding Protein Conformation
Proteins Folding - In Vivo and In Vitro
Laboratory Determination of DGo for Protein Folding/Unfolding
Thermodynamics and IMF's in Protein Stability
Predicting Protein Properties Using Computational Biology and Bioinformatics - Proteomics
Protein Aggregates - Not Just Junk
Protein Structure: Literature Learning Module
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Chapter 3: CARBOHYDRATES
Monosaccharides and Disssacharides
Complex Oligosaccharides
Jeopardy | (scrambled list of all Jeopardy answers for which you supply the correct question)
Glycoproteins: Biosynthesis and Function
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Chapter 4: DNA, GENOMICS, AND PROTEOMICS
The Structure of DNA
The Central Dogma of Biology
The Language of DNA
Genomes and Other Omes (not Gnomes)
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Chapter 5: BINDING
Reversible Binding I: Equations and Curves
Reversible Binding II: Experimental Binding Curves, Kd, and Error Analysis
A Model Binding System: Myoglobin. Hemoglobin, and Dioxygen
Binding and the Control of Gene Transcription:
New Methods in Drug Development
Binding: Literature Learning Module
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Chapter 6: TRANSPORT AND KINETICS
Passive and Facilitated Diffusion
Steady State and Rapid Equilibrium Kinetics
Models of Enzyme Inhibition
More Complicated Enzymes
Transport and Kinetics: Literature Learning Module
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Chapter 7: CATALYSIS
REVIEW: ORGANIC CHEMISTRY
Methods of catalysis
Mechanisms of enzyme-catalyzed reactions
Cofactors and Electron Pushing: Sources and Sinks
Enzyme catalyzed reactions in organic solvents
Ribozymes and the RNA World
Catalysis: Literature Learning Module
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Chapter 8: OXIDATION/PHOSPHORYLATION
The Chemistry of Dioxygen
Biological Oxidation Reactions - Dehydrogenases, Mono and Dioxygenases, and Oxidases
ATP and Oxidative Phosphorylation Reactions
Photosynthesis: The Light Reaction
Oxidation/Phosphorylation: Literature Learning Module
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Chapter 9: SIGNAL TRANSDUCTION
Energy Transduction: Uses of ATP
Signal Transduction: Neurochemistry
Signal Transduction at Cell Membranes: Protein Kinases/Phosphatases
Apoptosis - Programmed Cell Death and Signal Transduction
Memory and Learning in Apylsis
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Capstone: The Origin of Life
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Appendices
List of Figures
List of Tables
List of Moodle Quizzes
Chime and Jmol Files
Experimental Techniques
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