Biochemistry Topics

Biochemistry Topics and Learning Tools

Biochemistry I and II
University of Southern Maine

Topics List and Assignments
for
Principles of Biochemistry
Horton et al.
4th Edition 2006
TEXT WEBSITE provides additional learning resources.
Click here for a list of ERRORS in this text.

Always under construction. Last revised 200710/22

For dates of coverage, see
Biochemistry I Calendar, Fall 2007
Biochemistry II Calendar, Spring 2008

Chapter	Topic Biochemistry in Context	Assignments & Essential Skills In Horton, the entire chapter and all problems are assigned, unless otherwise specified.	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
Zero	Metabolic setting for biochemistry	Chapter Zero (click to download)	• Basic Strategy • Reviewing Chemistry, including info about QUIZ on Chapter Zero.		Click an image of a reader to view an entry from The Well-Read Biochemist. •
1	Setting the scene Neat Web Site: Locating Proteins in the Cell	Chapter 1, all see Essential Skills	• Reviewing Biology • Also see this Goodie: Rubber-Band Thermodynamics	Sample Biomolecules	•
2	Life's medium: water	Chapter 2, all see Essential Skills	• Water		•
3	Amino acids & protein sequence Neat Web Site: Bioinformatics Tutorial	Chapter 3, all see 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	•
4	Protein structure & function Neat Web Site: Protein Data Bank	Chapter 4, all see Essential Skills	• Protein Structure • Protein Function • Learn to View in Stereo Also see this Goodie: • Extra Problems: Oxygen Transport Solutions will appear HERE.	Protein Structure Protein Function	• •
Chapter	Topic	Assignments & Essential Skills	Learning Strategies (with Quizzes) Introduction	Graphics Exercises Introduction	The Well-Read Biochemist Introduction
5	Enzyme kinetics	Chapter 5, all see 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		•
6	Enzyme mechanisms	Chapter 6, all see Essential Skills	• Enzyme Mechanisms (none yet)	Enzyme Action	•
7	Coenzymes Neat Web Site: HIC-Up database of ligands in biomolecular models	Chapter 7, all see Essential Skills	• Coenzymes	Nucleotide Coenzymes Various Coenzymes	•
8	Carbohydrates	Chapter 8, all see Essential Skills	• Carbohydrates
Chapter	Topic	Assignments & Essential Skills	Learning Strategies (with Quizzes) Introduction	Graphics Exercises Introduction	The Well-Read Biochemist Introduction
9	Lipids & membranes	Chapter 9, all see 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
10	Metabolism	Chapter 10, Sections 1-8, 10, and p. 322, Box 10.1 (Omit problems 12, 14-16) see Essential Skills	• Bioenergetics • Metabolism Table: More Free Energies of Hydrolysis	Bioenergetics	•
11	Glycolysis	Chapter 11, all see Essential Skills HERE is a one-page chart of glycolysis.	• Glycolysis	Glycolysis	•
13	Citric acid cycle	Chapter 13, all see Essential Skills HERE is a one-page chart of the citrate cycle.	• TCA Cycle	TCA Cycle
Chapter	Topic	Assignments & Essential Skills	Learning Strategies (with Quizzes) Introduction	Graphics Exercises Introduction	The Well-Read Biochemist Introduction
14	Electron transport & ATP synthesis	First, Chapter 10, Section 10.9 (and problems, #12, 14-16); then Chapter 14, all see Essential Skills	• ET&OP	ET&OP
	End of First Semester				A Closing Thought
12	Carbohydrate metabolism II	Chapter 12, all see Essential Skills	• Pentose Pathway; Starches	Glycogen Metabolism
15	Photosynthesis	Chapter 15, all see Essential Skills	• Photosynthesis Click HERE for a figure depicting excitation transfer among photosynthetic antenna pigments.	Photosynthesis
16	Lipid metabolism	Chapter 16, all see Essential Skills	• Fatty-Acid Catabolism	Fatty-Acid Metabolism
Chapter	Topic	Assignments & Essential Skills	Learning Strategies (with Quizzes) Introduction	Graphics Exercises Introduction	The Well-Read Biochemist Introduction
17	Amino-acid metabolism	Chapter 17, all see Essential Skills	• Amino-Acid Catabolism	Amino-Acid Metabolism
18	Nucleotide metabolism	Chapter 18, all see Essential Skills	We might skip this.
19	Nucleic acids	Chapter 19, all see Essential Skills	• Nucleic Acids	Nucleotides and Nucleic Acids
20	Replication and DNA repair	Chapter 20, all see Essential Skills	• Replication GR: Needs a quiz!	Replication
Chapter	Topic	Assignments & Essential Skills	Learning Strategies (with Quizzes) Introduction	Graphics Exercises Introduction	The Well-Read Biochemist Introduction
21	Transcription & RNA processing	Chapter 21, all see Essential Skills	• Transcription GR: Needs a quiz!	Gene Regulation
22	Translation: protein synthesis	Chapter 22, all see Essential Skills	• Translation (incomplete) GR: Needs a quiz!	Translation
23	Recombinant DNA technology	Chapter 23, all see Essential Skills HERE are slides for the lecture: Recombinant DNA Project Lecture Outline		Site-Directed Mutagenesis: A Recombinant DNA Project.
	Special Topics (perhaps)
	Structure Determination of Macromolecules by X-ray crystallography, NMR spectroscopy, and homology modeling	CMCC, 3rd Edition (readings provided) and 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 Main reading provided by email.	• Nerve Action (coming)	Molecules of the Nervous and Sensory Systems	•