Biochemistry seeks to understand biological phenomena through the chemical and physical principles governing biomolecules. This course introduces the fundamental concepts of biochemistry with particular emphasis on the relationship between molecular structure, biochemical function, and biological mechanism.

Students will learn the chemical properties, structures, and functions of proteins, nucleic acids, lipids, and carbohydrates; the principles of enzyme catalysis and regulation; biological membranes and membrane proteins; bioenergetics and central metabolism; and cellular signaling. Rather than focusing primarily on memorization of individual pathways, the course emphasizes the chemical logic underlying biochemical reactions and how molecular interactions and conformational changes give rise to biological function.

Throughout the course, classical biochemical concepts will be connected to modern experimental approaches, including protein purification, structural biology, and structure-based analysis of biological mechanisms. By the end of the course, students should be able to interpret biochemical data, explain biological processes at the molecular level, and integrate concepts of structure, function, energetics, and regulation.

Required prerequisite: None

Recommended background: General Chemistry, Organic Chemistry, and basic knowledge of General Biology or Molecular Biology.

Students are not expected to have extensive prior knowledge of biochemistry. Essential chemical and biological concepts will be reviewed when necessary.

Required Textbook
David L. Nelson, Michael M. Cox, and Aaron A. Hoskins, Lehninger Principles of Biochemistry, 8th ed., W. H. Freeman/Macmillan Learning, 2021.

Supplementary Materials
Selected research articles, structural data, and other supplementary materials will be provided when appropriate. Public biological databases, including the Protein Data Bank (PDB) and UniProt, may be used for class activities and assignments.

Week 1. Foundations of Biochemistry and Water
Lehninger Ch. 1–2
Introduction to biochemistry; cellular and chemical foundations of life; biomolecules; water; noncovalent interactions; hydrophobic effect

Week 2. Amino Acids and Protein Structure
Lehninger Ch. 3–4
Amino acids and peptides; primary, secondary, tertiary, and quaternary protein structures; protein folding and stability

Week 3. Protein Function and Experimental Biochemistry
Lehninger Ch. 5 and selected supplementary materials
Protein–ligand interactions; molecular recognition; protein purification and characterization; introduction to structural biology

Week 4. Enzymes: Catalysis, Kinetics, and Regulation
Lehninger Ch. 6
Enzyme catalysis; Michaelis–Menten kinetics; enzyme inhibition; catalytic mechanisms; allostery and enzyme regulation

Week 5. Lipids, Biological Membranes, and Membrane Proteins
Lehninger Ch. 10–11
Lipid structure; membrane organization; membrane proteins; membrane transport; ion channels and transporters

Week 6. Nucleotides, Nucleic Acids, and the Flow of Genetic Information
Lehninger Ch. 8 and selected topics from Ch. 24–27
DNA and RNA structure; DNA replication; transcription; translation; relationship between sequence, structure, and function

Week 7. DNA-Based Technologies and Modern Structural Biochemistry
Lehninger Ch. 9 and selected supplementary materials
Recombinant DNA technology; protein engineering; mutagenesis; modern approaches to protein structure and function; selected current topics

Week 8. Midterm Examination

Week 9. Bioenergetics and the Chemical Logic of Metabolism
Lehninger Ch. 7 and Ch. 13
Carbohydrates; thermodynamics; free energy; ATP and phosphoryl-group transfer; biological oxidation–reduction reactions; organization of metabolic pathways

Week 10. Glycolysis, Gluconeogenesis, and Glycogen Metabolism
Lehninger Ch. 14–15
Glycolysis; fates of pyruvate; gluconeogenesis; reciprocal regulation; pentose phosphate pathway; glycogen metabolism

Week 11. Citric Acid Cycle and Oxidative Phosphorylation
Lehninger Ch. 16 and Ch. 19
Citric acid cycle; electron transport; proton gradients; membrane potential; ATP synthase; chemiosmotic coupling

Week 12. Lipid and Amino Acid Metabolism
Lehninger Ch. 17–18 and selected topics from Ch. 21
Fatty acid oxidation; ketone bodies; amino acid catabolism; nitrogen metabolism; overview of lipid biosynthesis

Week 13. Integration and Hormonal Regulation of Metabolism
Lehninger Ch. 23
Tissue-specific metabolism; fed and fasting states; hormonal regulation; metabolic homeostasis and integration

Week 14. Biochemical Signaling
Lehninger Ch. 12
Principles of signal transduction; GPCRs; second messengers; receptor tyrosine kinases; protein phosphorylation; amplification and feedback

Week 15. From Molecular Structure to Cellular Function: Modern Biochemistry
Lehninger Ch. 11–12 and selected supplementary materials
Membrane signaling; ion channels and molecular machines; conformational changes and allostery; modern structural biology; structure-based drug discovery; selected research topics and student presentations

Week 16. Final Examination

Course format: Lectures, problem solving, discussion, structural/biochemical data analysis, and student presentations

The first half of the course will emphasize lectures and fundamental concepts. As the course progresses, increasing emphasis will be placed on problem solving, interpretation of biochemical and structural data, and class discussion. Selected research examples will be used to connect fundamental biochemical principles with modern biological research.

Lecture notes and related materials will be uploaded to e-Class before each class. Students are encouraged to review the lecture materials in advance. Selected biochemical problems, molecular structures, and research figures may be discussed during class. Active participation and scientific discussion are encouraged.