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:  11/19/2017

Important Notice:  I have replaced this book with a much more comprehensive, updated, and interactive book, Fundamentals of Biochemistry, a BioLibre text book,  that is now avaialble. It cover a full year of biochemistry and is also free. I am no longer updating this book.

2D Cluster Map of FOB TOC

2017 VideoShowCase A 3 minute video describing my book

Also available at Biology LibreText, part of the UC Davis LibreTexts libraries

Hit Counter visitors to this Table of Content page since 8/6/06  


  1. Why Chemical Logic?
  2. Updates
  3. Introduction to Biochemistry  
  4. Biochemistry and Molecular Biology Dictionaries
  5. Permissions


MathematicaLogoInteractive Mathematica graphs:  requires free plugin, CDF player (Wolfram) to play downloadable files. The web-imbedded inteactive Mathematica graph are longer supported by most browsers which no longer allow plugins.
SageMathLogoInteractive SageMath graphs: no plug in required.  Works on Firefox, Chrome and Edge, IE11.
JsmolLogoInteractive Jsmol molecular models: no plugins required.  Based on Javascript; works on all browsers

homework - literature learning moduleHomework Problems

Literature Learning Modules:  Questions (with answers) based on the research literature (added from 2/8/17 on)


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
  6. Review:  The Cell


  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  

homeworkHomework Problems - Literature Learning Module:


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

homeworkHomework Problems - Literature Learning Module:


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

homeworkHomework Problems - Literature Learning Module:


  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 new update on intracellular droplets
  4. Binding and the Control of Gene Transcription  newupdate on chromatin structure and phase transitions
  5. New Methods in Drug Development
  6. Immune System Recognition new - new section on Inflammasomes

homeworkHomework Problems - Literature Learning Module:


  1. Passive and Facilitated Diffusion
  2. Kinetics of Simple and Enzyme-Catalyzed Reactions   
  3. Enzyme Inhibition
  4. More Complicated Enzymes

homeworkHomework Problems - Literature Learning Modules:

Chapter 7:  CATALYSIS

Review: Organic Chemistry
  1. Methods of Catalysis
  2. Mechanisms of enzyme-catalyzed reactions newNew section on CRISPR
  3. Cofactors and Electron Pushing: Sources and Sinks
  4. Enzyme catalyzed reactions in organic solvents
  5. Ribozymes and the RNA World

homeworkHomework Problems - Literature Learning Module:



  1. The Chemistry of Dioxygen
  2. Oxidative Enzymes
  3. ATP and Oxidative Phosphorylation new   New Jmo/Jsmols for Complex I, III, IV, and ATP synthase; New section on Complex III
  4. Photosynthesis: The Light Reaction
  5. Nitrogenase: A Reductive Use of Metal Clusters

homeworkHomework Problems - Literature Learning Module:


  1. Active Transport
  2. Neural Signaling
  3. Signaling Proteins new6/14/17 - new section on small G proteins, GAPs and GEFs
  4. mTOR and Nutrient Signaling
  5. Metabolic Control Analysis and Systems Biology
  6. new11/16/17 (just beginning development)  Signaling Math : Graphic Analyses of Input and Outputs 

homeworkHomework Problems - Literature Learning Module:



  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 11:  ORIGIN OF LIFE

  1. The Origin of Life 


  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!


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.