Biochemistry Topics

Biochemistry Topics List and Learning Tools

for a
Modern Course in Biochemistry
(should fit current full-year texts)

Gale Rhodes
University of Southern Maine

Always under construction. Last revised 2008/05/22

Topic Biochemistry in Context	Learning Tools and Essential Skills	Learning Strategies (with Quizzes) Introduction	Graphics Exercises Introduction	The Well-Read Biochemist A literary supplement to biochemistry Introduction See full list of readings. Connecting Science and Literature
Metabolic setting for biochemistry	Chapter Zero (click to download)	• Basic Strategy • Reviewing Chemistry (includes suggested format for about a quiz for Chapter Zero)		Click an image of a reader to view an entry from The Well-Read Biochemist. •
Setting the scene Neat Web Site: Locating Proteins in the Cell	Essential Skills	• Reviewing Biology • Also see this Goodie: 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 these Goodies: • 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 this Goodie: • Extra Problems: Oxygen Transport Solutions HERE.	Protein Structure Protein Function	• •
Topic	Essential Skills	Learning Strategies (with Quizzes) Introduction	Graphics Exercises Introduction	The Well-Read Biochemist Introduction
Enzyme kinetics	Essential Skills	• Enzymes Also see these Goodies: 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	The Well-Read Biochemist Introduction
Lipids & membranes	Essential Skills	• Lipids Also see this Goodie: •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	The Well-Read Biochemist Introduction
Electron transport & ATP synthesis	Essential Skills	• ET&OP	ET&OP
End of First Semester				A Closing Thought
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	The Well-Read Biochemist 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	• 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	The Well-Read Biochemist 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)	See this Goody: Diffraction Equations 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	•

Biochemistry Topics List and Learning Tools

Gale Rhodes University of Southern Maine

Gale Rhodes
University of Southern Maine