Biochemistry Topics

Biochemistry Topics List and Learning Tools

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

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	Essential Skills	• Reviewing Biology Also see • Rubber-Band Thermodynamics	Sample Biomolecules
Life's medium: water	Essential Skills	• Water
Amino acids & protein sequence Neat Web Site: Bioinformatics Tutorial	Essential Skills	• Amino Acids • Protein Sequence Also see • Sequencing Problem (for class discussion) • Graphical pI Calculator (Excel File) • Get to Know Histidine	Amino Acids & Peptides
Protein structure & function Neat Web Site: Protein Data Bank	Essential Skills	• Protein Structure • Protein Function • Learn to View in Stereo Also see • Extra Problems: Oxygen Transport Solutions HERE.	Protein Structure Protein Function
Topic	Essential Skills	Learning Strategies (with Quizzes) Introduction	Graphics Exercises Introduction
Enzyme kinetics	Essential Skills	• 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	Essential Skills	• Enzyme Mechanisms	Enzyme Action
Coenzymes Neat Web Site: HIC-Up database of ligands in biomolecular models	Essential Skills	• Coenzymes	Nucleotide Coenzymes Various Coenzymes
Carbohydrates	Essential Skills	• Carbohydrates
Topic	Essential Skills	Learning Strategies (with Quizzes) Introduction	Graphics Exercises Introduction
Lipids & membranes	Essential Skills	• Lipids Also see •Supplemental Problems in Transmembrane Transport Solutions will appear HERE. More detailed model of the Na⁺/K⁺ pump HERE.	Lipids and Membranes Signal Transduction
Metabolism	Essential Skills	• Bioenergetics • Metabolism Table: More Free Energies of Hydrolysis	Bioenergetics
Glycolysis	Essential Skills HERE is a one-page chart of glycolysis.	• Glycolysis	Glycolysis
Citric acid cycle	Essential Skills HERE is a one-page chart of the citrate cycle.	• TCA Cycle	TCA Cycle
Topic	Essential Skills	Learning Strategies (with Quizzes) Introduction	Graphics Exercises Introduction
Electron transport & ATP synthesis	Essential Skills	• ET&OP	ET&OP
End of First Semester
Carbohydrate metabolism II	Essential Skills	• Pentose Pathway; Starches	Glycogen Metabolism
Photosynthesis	Essential Skills	• Photosynthesis Click HERE for a figure depicting excitation transfer among photosynthetic antenna pigments.	Photosynthesis
Lipid metabolism	Essential Skills	• Fatty-Acid Catabolism	Fatty-Acid Metabolism
Topic	Essential Skills	Learning Strategies (with Quizzes) Introduction	Graphics Exercises Introduction
Amino-acid metabolism	Chapter 17, all see Essential Skills	• Amino-Acid Catabolism	Amino-Acid Metabolism
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	• Nucleic Acids	Nucleotides and Nucleic Acids
Replication and DNA repair	Essential Skills	• Replication	Replication
Topic	Essential Skills	Learning Strategies (with Quizzes) Introduction	Graphics Exercises Introduction
Transcription & RNA processing	Essential Skills	• Transcription	Gene Regulation
Translation: protein synthesis	Essential Skills	• Translation	Translation
Recombinant DNA technology	Essential Skills 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