| Module 1: Size and Components of Cells and Implications with respect to Regulation |
| L1 |
Introduction: cell constituents, prokaryotes vs. eukaryotes |
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| L2 |
Introduction (cont.) |
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| 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 |
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| L4 |
Experimental methods for elucidating FAS structure |
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| TD1 |
Beta-ketoacyl-ACP Synthase I (FabB) |
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| L5 |
Chemistry of FAS as paradigm for other molecular machines |
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| L6 |
Secondary metabolism: PKS, NRPS |
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| L7 |
Chemistry of PKS and NRPS: post-translational modification, initiation, elongation, decoration, termination, fidelity |
Problem set 1 due |
| TD2 |
Smith Paper |
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| L8 |
Chemistry of PKS and NRPS (cont.) |
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| 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 |
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| L11 |
Cholesterol biosynthesis |
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| L12 |
Cholesterol regulation and homeostasis |
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| L13 |
Sensing insoluble molecules |
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| TD4 |
Endocytosis of LDL and Radioactivity Techniques |
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| L14 |
Module 2: Regulation of the transcription level by insoluble metabolites and Module 3: Translation |
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| 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 |
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| TD5 |
Structure |
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| L17 |
Chemical methods for studying translation and the ribosome |
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| L18 |
Chemical methods for studying translation and the ribosome (cont.) |
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| L19 |
Chemical methods for studying translation and the ribosome (cont.) |
Problem set 4 due |
| TD6 |
Hydroxyl Radical Footprinting |
Exam 2 |
| L20 |
Isoleucine tRNA synthetase |
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| TD7 |
Gel Electrophoresis; Photoaffinity Probes |
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| L21 |
tRNA synthase editing mechanisms; G proteins (EF-Tu/EF-G) |
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| L22 |
G proteins: motors |
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| TD8 |
Rodnina Paper |
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| L23 |
G proteins: switches |
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| 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 |
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| L26 |
Protein folding in vitro |
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| TD10 |
Exam 3 Answers and Discussion |
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| L27 |
Protein folding: in vitro vs. in vivo; degradation |
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| L28 |
Protein folding in vivo |
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| L29 |
Chaperone proteins |
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| TD11 |
GroEl / GroES |
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| L30 |
GroEL/GroES |
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| L31 |
Proteases |
Problem set 6 due |
| L32 |
Proteosome |
Exam 4 |
| TD12 |
DnaJ specificity |
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| L33 |
Proteosome (cont.) |
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| L34 |
Role of Ubiquitin in degradation |
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| L35 |
Degradation through polyubiquitination |
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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.) |