Biological Chemistry II
This course deals with a more advanced treatment of the biochemical mechanisms that underlie biological processes. Emphasis will be given to the experimental methods used to unravel how these processes fit into the cellular context as well as the coordinated regulation of these processes. Topics include macromolecular machines for energy and force transduction, regulation of biosynthetic and degradative pathways, and the structure and function of nucleic acids.
Lecture Notes
The table below includes an example set of notes taken by a student in the course for each lecture session (L#).| Module 1: Size and Components of Cells and Implications with respect to Regulation | | L1 | Introduction: cell constituents, prokaryotes vs. eukaryotes (PDF) | | L2 | Introduction (cont'd) (PDF) | | 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 (PDF) | | L4 | Experimental methods for elucidating FAS structure (PDF) | | L5 | Chemistry of FAS as paradigm for other molecular machines (PDF) | | L6 | Secondary metabolism: PKS, NRPS (PDF) | | L7 | Chemistry of PKS and NRPS: post-translational modification, initiation, elongation, decoration, termination, fidelity (PDF) | | L8 | Chemistry of PKS and NRPS (cont'd) (PDF) | | L9 | Chemistry of PKS and NRPS (cont'd with specific examples) (PDF) | | L10 | Biosynthesis of yersiniabactin and cholesterol (PDF) | | L11 | Cholesterol biosynthesis (PDF) | | L12 | Cholesterol regulation and homeostasis (PDF) | | L13 | Sensing insoluble molecules (PDF) | | L14 | Module 2: Regulation of the transcription level by insoluble metabolites and Module 3: Translation (PDF) | | Module 3: Translation: Loading, Initiation, Elongation, and Termination - A Machine in Action; Introduction to G-proteins: Switches or Motors | | L15 | Translation (cont'd) (PDF) | | L16 | Elongation, termination, RNA polymerase (PDF) | | L17 | Chemical methods for studying translation and the ribosome (PDF) | | L18 | Chemical methods for studying translation and the ribosome (cont'd) (PDF) | | L19 | Chemical methods for studying translation and the ribosome (cont'd) (PDF) | | L20 | Isoleucine tRNA synthetase (PDF) | | L21 | tRNA synthase editing mechanisms; G proteins (EF-Tu/EF-G) (PDF) | | L22 | G proteins: motors (PDF) | | L23 | G proteins: switches (PDF) | | L24 | Peptide bond formation; new technologies using the ribosome (PDF) | | L25 | Module 3: methods for the incorporation of unnatural amino acids and Module 4: what happens as a protein exits the ribosome? (PDF) | | Module 4: Crypts and Chambers: Macromolecular Machines involved in Protein Folding and Degradation | | L26 | Protein folding in vitro (PDF) | | L27 | Protein folding: in vitro vs. in vivo; degradation (PDF) | | L28 | Protein folding in vivo (PDF) | | L29 | Chaperone proteins (PDF) | | L30 | GroEL/GroES (PDF) | | L31 | Proteases (PDF) | | L32 | Proteosome (PDF) | | L33 | Proteosome (cont'd) (PDF) | | L34 | Role of Ubiquitin in degradation (PDF) | | L35 | Degradation through polyubiquitination (PDF) |
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