| Module 1: Size and Components of Cells and Implications with respect to Regulation |
| L1 | Introduction: cell constituents, prokaryotes vs. eukaryotes | |
| L2 | Introduction (cont.) | |
| Module 2: Fatty Acid Synthases (FAS), Polyketide Synthases (PKS), and Non-ribosomal Polypeptide Synthases (NRPS) |
| L3 | Fatty Acid Synthase: polymerization, biosynthesis, players, chemistry, structure, chemistry as a paradigm for PKS and NRPS, medical interlude | |
| L4 | Experimental methods for elucidating FAS structure | |
| TD1 | Beta-ketoacyl-ACP Synthase I (FabB) | |
| L5 | Chemistry of FAS as paradigm for other molecular machines | |
| L6 | Secondary metabolism: PKS, NRPS | |
| L7 | Chemistry of PKS and NRPS: post-translational modification, initiation, elongation, decoration, termination, fidelity | Problem set 1 due |
| TD2 | Smith Paper | |
| L8 | Chemistry of PKS and NRPS (cont.) | |
| L9 | Chemistry of PKS and NRPS (cont. with specific examples) | Problem set 2 due |
| L10 | Biosynthesis of yersiniabactin and cholesterol | Exam 1 |
| TD3 | Walsh Paper | |
| L11 | Cholesterol biosynthesis | |
| L12 | Cholesterol regulation and homeostasis | |
| L13 | Sensing insoluble molecules | |
| TD4 | Endocytosis of LDL and Radioactivity Techniques | |
| L14 | Module 2: Regulation of the transcription level by insoluble metabolites and Module 3: Translation | |
| Module 3: Translation: Loading, Initiation, Elongation, and Termination - A Machine in Action; Introduction to G-proteins: Switches or Motors |
| L15 | Translation (cont.) | Problem set 3 due |
| L16 | Elongation, termination, RNA polymerase | |
| TD5 | Structure | |
| L17 | Chemical methods for studying translation and the ribosome | |
| L18 | Chemical methods for studying translation and the ribosome (cont.) | |
| L19 | Chemical methods for studying translation and the ribosome (cont.) | Problem set 4 due |
| TD6 | Hydroxyl Radical Footprinting | Exam 2 |
| L20 | Isoleucine tRNA synthetase | |
| TD7 | Gel Electrophoresis; Photoaffinity Probes | |
| L21 | tRNA synthase editing mechanisms; G proteins (EF-Tu/EF-G) | |
| L22 | G proteins: motors | |
| TD8 | Rodnina Paper | |
| L23 | G proteins: switches | |
| L24 | Peptide bond formation; new technologies using the ribosome | Problem set 5 due |
| L25 | Module 3: methods for the incorporation of unnatural amino acids and Module 4: what happens as a protein exits the ribosome? | Exam 3 |
| Module 4: Crypts and Chambers: Macromolecular Machines involved in Protein Folding and Degradation |
| TD9 | FRET, Steady State | |
| L26 | Protein folding in vitro | |
| TD10 | Exam 3 Answers and Discussion | |
| L27 | Protein folding: in vitro vs. in vivo; degradation | |
| L28 | Protein folding in vivo | |
| L29 | Chaperone proteins | |
| TD11 | GroEl / GroES | |
| L30 | GroEL/GroES | |
| L31 | Proteases | Problem set 6 due |
| L32 | Proteosome | Exam 4 |
| TD12 | DnaJ specificity | |
| L33 | Proteosome (cont.) | |
| L34 | Role of Ubiquitin in degradation | |
| L35 | Degradation through polyubiquitination | |
| | Final Exam (3 hours. The first 30 minutes will cover the information since the last exam. The remaining two and a half hours will cover the entire semester.) |