Biochemistry Online: An Approach Based on Chemical Logic

Biochemistry Online

Biochemistry Online: An Approach Based on Chemical Logic

NSF logoUpdates from October 2015 are supported in part by NSF DUE 1525021 - Last update:  4/15/16
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Preface

  1. Why Chemical Logic?
  2. Updates
  3. Introduction to Biochemistry  
  4. Biochemistry and Molecular Biology Dictionaries
  5. Review:  The Cell
  6. Permissions

Review: The Cell

  1. MPO - The Cell:  An Overview from a Chemistry Perspective
  2. MP0 - L. The Cell: Lipids
  3. MP0 - P. The Cell:  Proteins
  4. MP0 - N. The Cell:  Nucleic Acids
  5. MP0 - C. The Cell:  Carbohydrates

Chapter 1:  LIPID STRUCTURE

  1. Lipid Structure 
  2. Lipids in Water
  3. Dynamics of Membrane Lipids
  1. Lipids in Water: Thermodynamics
  2. Lipid Aggregates from Single and Double Chain Amphiphiles
  3. Lipids and Signaling  

Lipid Structure:  Literature Learning Module


Chapter 2:  PROTEIN STRUCTURE

  1. 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 Delta G0 of Protein Unfolding
  6. Thermodynamics and IMF's in Protein Stability  
  7. Predicting Protein Properties From Sequences  
  8. Protein Aggregates and Disease

Protein Structure:  Literature Learning Module


Chapter 3:  CARBOHYDRATES/GLYCANS

  1. Monosaccharaides and Disaccharides
  2. More Complex Carbohydrates
  3. Jeopardy
  4. Glycoproteins Biosynthesis and Function

Chapter 4:  DNA AND THE CENTRAL DOGMA OF BIOLOGY

  1. DNA Structure
  2. The Central Dogma of Biology
  3. The Language of DNA

Chapter 5:  BINDING

  1. Introduction to Reversible Binding  
  2. Mathematical Analyses of Binding Graphs 
  3. Model Binding Systems
  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. Kinetics of Simple and Enzyme-Catalyzed Reactions   
  3. Enzyme Inhibition
  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. Oxidative Enzymes
  3. ATP and Oxidative Phosphorylation
  4. Photosynthesis: The Light Reaction

Oxidation/Phosphorylation:  Literature Learning Module


Chapter 9:  METABOLIC AND SIGNAL TRANSDUCTION

  1. Active Transport
  2. Neural Signaling
  3. Signaling Proteins
  4. Nutrients and Signaling (to be added)
  5. Metabolic Control Analysis and Systems Biology (to be added)

Chapter 10:  METABOLIC PATHWAYS (MP)

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

Chapter 10:  ORIGIN OF LIFE

  1. The Origin of Life 

Appendices

  1. List of Figures
  2. List of Tables
  3. List of Moodle Quizzes
  4. Jmol Files
  5. Experimental Techniques

Additional Web Links:

  1. NCBI Biochemistry Texts  -search for biochemistry texts
  2. Biochemistry, 5th edition Jeremy M Berg, John L Tymoczko, and Lubert Stryer - searchable but not broweable, from the NCBI.
  3. Martindale's Biochemistry
  4. Molecular Movies
  5. Biophysical Society:  National Lectures   |    Resources on selected topics
  6. Medical Biochemistry
  7. Common mistakes found in Biochemistry textbooks!

Analytics: (see top hit counter)

  1. My Clustr Map 11/20/15
  2. Archived Clustr Map from 1/15/09
  3. Archived Clustr Map from 1/15/10

Search Engines:

Search BC Online

  1. Quetzal: search engine for the biomedical literature
  2. NCBI: National Center for Biotechnology Information
  3. PubMed

Biochemistry Online can also be found in the following digital libraries!

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It has also been listed in:

May 30, 2003

WeWebWatch: March, 2001

Creative Commons License
Biochemistry Online by Henry Jakubowski is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License.

©Copyright 2002 Dr. Henry Jakubowski
Please send comments to Dr. Henry Jakubowski.