Biochemistry Online: An Approach Based on Chemical Logic

Updates 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

A 3 minute video describing my book

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

Preface

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

Interactivity

Homework Problems

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

Chapter 1:  LIPID STRUCTURE

1. Lipid Structure 
2. Lipids in Water
3. Dynamics of Membrane Lipids

• Molecular Mechanics and Dynamics
• Thermodynamics Review

4. Lipids in Water: Thermodynamics
5. Lipid Aggregates from Single and Double Chain Amphiphiles
6. Lipids and Signaling  

Homework Problems - Literature Learning Module:

•  Sphingomyelinase Activity Causes Transbilayer Lipid Translocation

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

Homework Problems - Literature Learning Module:

• Steroidogenic Acute Regulatory Protein

Chapter 3:  CARBOHYDRATES/GLYCANS

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

Homework Problems - Literature Learning Module:

• Trypanosoma brucei Glycoproteins

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

Homework Problems - Literature Learning Module:

• Binding 1:  Severe Acute Respiratory Syndrome Coronavirus 3C-like Proteinase 
• Binding 2:  Conformational Switches in SelB

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

Homework Problems - Literature Learning Modules:

• Enzyme Inhibition 1 - KCAT

Chapter 7:  CATALYSIS

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

Homework Problems - Literature Learning Module:

•  Cas9 RNA-guided Endonuclease 
• Inhibitors of a Transpeptidase

Chapter 8:  OXIDATION/PHOSPHORYLATION

1. The Chemistry of Dioxygen
2. Oxidative Enzymes
3. ATP and Oxidative Phosphorylation    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

Homework Problems - Literature Learning Module:

• Regulation of Oxidative Phosphorylation by Cytochrome C Phosphorylation

Chapter 9:  METABOLIC AND SIGNAL TRANSDUCTION

1. Active Transport
2. Neural Signaling
3. Signaling Proteins 6/14/17 - new section on small G proteins, GAPs and GEFs
4. mTOR and Nutrient Signaling
5. Metabolic Control Analysis and Systems Biology
6. 11/16/17 (just beginning development)  Signaling Math : Graphic Analyses of Input and Outputs 

Homework Problems - Literature Learning Module:

•  Transcription factor Regulation of Protein Phosphatase 2A 

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 11:  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!

It has also been listed in:

May 30, 2003

WeWebWatch: March, 2001

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