peptide chain

Biochemistry Topics List and Learning Tools

for a
Modern Course in Biochemistry
(compatible with current full-year texts)

Gale Rhodes
Contact Information

Revised 2008/05/22

Topic

Biochemistry in Context

Learning Tools
and
Essential Skills

 

Learning Strategies (with Quizzes)
Introduction
Graphics Exercises
Introduction
Metabolic setting for biochemistry
Chapter Zero
(click to download)

Basic Strategy

Reviewing Chemistry
(includes suggested format for about a quiz for Chapter Zero)

Setting the scene

Neat Web Site: Locating Proteins in the Cell

Life's medium: water

Water

 

Amino acids & protein sequence

Neat Web Site:
Bioinformatics Tutorial

Amino Acids
Protein Sequence

Also see
Sequencing Problem (for class discussion)
Graphical pI Calculator (Excel File)
Get to Know Histidine

Protein structure & function

Neat Web Site:
Protein Data Bank

Protein Structure
Protein Function
Learn to
View in Stereo

Also see
Extra Problems: Oxygen Transport
Solutions HERE.

Topic
Learning Strategies (with Quizzes)
Introduction
Graphics Exercises
Introduction
Enzyme kinetics

Enzymes

Also see
1) Deriving the MM Equation
2) Summary: Effects of Inhibitors
3) Enzyme Kinetics Problem (for class discussion) Try solving the problem using this Nonlinear Least Squares Curve Fitter.
4) More About Bisubstrate Reactions

Enzyme mechanisms
• Enzyme Mechanisms

Coenzymes

Neat Web Site:
HIC-Up
database of ligands in biomolecular models

Various Coenzymes

Carbohydrates

Topic
Learning Strategies (with Quizzes)
Introduction
Graphics Exercises
Introduction
Lipids & membranes
Lipids

Also see
Supplemental Problems in Transmembrane Transport
Solutions will appear HERE.

More detailed model of the Na+/K+ pump HERE.

Metabolism

Bioenergetics
Metabolism

Table: More Free Energies of Hydrolysis

Glycolysis

Essential Skills

HERE is a one-page chart of glycolysis.

Citric acid cycle

Essential Skills

HERE is a one-page chart of the citrate cycle.

Topic
Learning Strategies (with Quizzes)
Introduction
Graphics Exercises
Introduction
Electron transport & ATP synthesis

End of First Semester

 

 
 
Carbohydrate metabolism II
Photosynthesis

• Photosynthesis

Click HERE for a figure depicting excitation transfer among photosynthetic antenna pigments.

Lipid metabolism
Topic
Learning Strategies (with Quizzes)
Introduction
Graphics Exercises
Introduction
Amino-acid metabolism
Chapter 17, all
see Essential Skills
Nucleotide metabolism
Chapter 18, all
see Essential Skills
(a good chapter to skip, unless you are really focusing on metabolism)
Nucleic acids
Chapter 19, all
see Essential Skills

Understanding
Supercoiling
and
Linking Number
of Circular DNA

Replication and DNA repair
Topic
Learning Strategies (with Quizzes)
Introduction
Graphics Exercises
Introduction
Transcription & RNA processing
Translation: protein synthesis
Recombinant DNA technology

HERE are slides for a lecture: Recombinant DNA Project
Lecture Outline

 

Site-Directed Mutagenesis:
A Recombinant DNA Project.
Special Topics  
 
Structure Determination
of
Macromolecules
by X-ray crystallography, NMR spectroscopy, and homology modeling

1) CMCC, 3rd Edition

2) Principles of Protein Structure, Comparative Protein Modelling and Visualisation
(online modeling text)

A useful reference:
Judging the Quality of Macromolecular Models: A Glossary of Terms from Crystallography, NMR, and Homology Modeling

 
Bioinformatics Tutorial: Bioinformatics for Beginners    
The Five Senses

Background reading
The Nervous System (read about nerve cells, nerve impulses, and synapses)
Animations of Nerve Action

Reading: Sensory Systems in Biochemistry, by Stryer, Berg, and Tymoczko

 

• Nerve Action
Molecules of the Nervous and Sensory Systems
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