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Biological Chemistry II

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  • Course Description

    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.

    About Prof. Joanne Stubbe Prof. Alice Ting

    Alice Y. Ting has been a member of the MIT Chemistry Department faculty since 2002. She has a diverse range of interests, including single molecule microscopy, neurobiology, protein engineering, molecular evolution, and bio-organic chemistry. JoAnne Stubbe, Novartis Professor of Chemistry, Professor of Biology

    Note: Contents for this page are Licensed from under the Creative Commons Attribution Share-Alike license.

    Massachusetts Institute of Technology

    Course Code

    Date Taught
    Spring/Summer 2004

    Undergraduate (First Year)
  • L1-L2 1: Size and Components of Cells and Implications with respect to Regulation Required

    Minton, Allen P. "The Influence of Macromolecular Crowding and Macromolecular Confinement on Biochemical Reactions in Physiological Media." Journal of Biological Chemistry 276, no. 14 (2001): 10577-10580.

    Goodsell, D. S. "Inside a Living Cell." Trends Biochem Sci. 16, no. 6 (June 1991): 203-6.
    L3-L14 2: Fatty Acid Synthases (FAS), Polyketide Synthases (PKS), and Non-ribosomal Polypeptide Synthases (NRPS) Required

    Voet & Voet section on FAS (pp. 682-690) or the equivalent section in your biochemistry text.

    Keating, T. A., and C. T. Walsh. "Initiation, Elongation, and Termination Strategies in Polyketide and Polypeptide Antibiotic Biosynthes." Current Opinion in Chemical Biology 3 (1999): 598-606.

    Ranghan, V. S., A. K. Joshi, and S. Smith. "Mapping the Functional Topology of the Animal Fatty Acid Synthase." Biochemistry 40, no. 36 (2001): 10792-10799.

    Voet & Voet. Biochemistry. pp. 680-704.

    Brown, Michael S., and Joseph L. Goldstein. "A Receptor-mediated Pathway for Cholesterol Homeostasis." Science 232 (1986): 34-47.

    Brown, Michael S., and Joseph L. Goldstein. "Receptor-Mediated Control of Cholesterol Metabolism." Science 191 (1976): 150-4.

    Mazur, Walsh, and Kelleher. Biochemistry 42 (2003): 13393-13400.

    Optional Readings

    Tsuji, S. Y., N. Wu, and C. Khosla. "Intermodular Communication in Polyketide Synthases." Biochemistry 40, no. 8 (2001): 2317-2325.

    Rozwarski, D. A., et al. "Modification of the NADH of the Isoniazid Target (InhA)." Science 279 (1998): 98-102.

    Brown, M. S., and J. L. Goldstein. "Receptor-Mediated Control of Cholesterol Metabolism." Science 191 (1976): 150-154.

    Song, W. S. et al. "Role of Sec61alpha in the Regulated Transfer of the ribosome-nascent chain complex from the signal recognition particle to the translocation channel." Cell 100 (2000): 333-343.

    Suo, Zucai, Huawei Chen, and Christopher T. Walsh. "Acyl-CoA Hydrolysis by the High Molecular Weight Protein 1 Subunit of Yersiniabactin Synthetase: Mutational Evidence for a Cascade of Four Acyl-Enzyme Intermediates during Hydrolytic Editing." PNAS 97 (2000): 14188-14193. (Fidelity in PKS)
    L14-L25 3: Translation: Loading, Initiation, Elongation, and Termination - A Machine in Action; Introduction to G-proteins: Switches or Motors Required

    Voet and Voet. Biochemistry text chapter on Translation. pp. 959-1004.

    Rodnina, M. V., T. Daviter, K. Gromadski, and W. Wintermeyer. "Structural Dynamics of Ribosomal RNA during Decoding on the Ribosome." Biochimie 84, no. 8 (August 2002): 745-754. (Elongation Kinetics) (Review)

    Steitz, and Moore. "The Involvement of RNA in Ribosome Function." Nature 418 (2002): 229-235. (Review)

    Noller. Biochemistry 38 (1999): 945-951. (Methods)

    Pape, Tillmann, Wolfgang Wintermeyer, and Marina V. Rodnina. "Complete Kinetic Mechanism of Elongation Factor Tu-dependent Binding of Aminoacyl-tRNA to the A site of the E.coli Ribosome." EMBO J 17 (1998): 7490-97. (Methods)

    Wang, L, Z Zhang, A Brock, PG Schultz. "Addition of the Keto Functional Group to the Genetic Code of Escherichia coli." Proc Natl Acad Sci 100, no. 1 (January 7, 2003): 56-61. (Methods)

    Additional References

    Voet and Voet. Biochemistry text chapter on Translation. pp. 959-1004.

    Newcomb, and Noller. "Direct Hydroxyl Radical Probing of the 16S Ribosome RNA in the 70S Ribosomes from Internal Positions of RNA." Biochemistry 38 (1999): 945-951.

    Wilson, K. S., H. F. Noller. "Molecular Movement Inside the Translational Engine." Cell 92 (1998): 337-49.

    Ramakrishnan, V. "Ribosome Structure and the Mechanism of Translation." Cell 108 (2002): 557-572.

    Vale, J. "Common Themes of G Proteins and Molecular Motors." Journal of Cell Biology 135 (1996): 291-302.

    Rodnina, et al. "Dynamics of Translation on the ribosome." FEMS Microbiol Reviews 23 (1999) 317-333.

    tRNA Synthetases

    Silvian, et al. "Insights into Editing from an Ile-tRNA Synthetase Structure with tRNAIle with Mupirocin." Science 285 (1999): 77-79.

    Hendrickson, et al. "Errors from Selective Disruption of the Editing Center of a tRNA Synthetase." Biochemistry 39 (2000): 8180-8186.


    These papers provide the details of the mechanisms of GTP-dependent elongation and translocation that will be discussed in class. The TAs will go over these papers in recitation.

    Pape, et al. "Complete Kinetic Mechanism of Elongation Factor Tu-dependent binding." The EMBO Journal 17 (1998): 7490-7497.

    Pape, et al. "Induced fit in initial selection and proofreading of aa-tRNA on the ribosome." The EMBO Journal 18 (1999): 2800-3807.

    Rodnina, et al. "Hydrolysis of GTP by Elongation Factor G drives tRNA movement on the ribosome." Nature 385 (1997): 37-41.

    Peptide Bond Formation

    Niessen, et al. "The Structural Basis of Ribosome Activity in Peptide Bond Synthesis." Science 289 (2000): 920-930.

    Muth, et al. "A single Adenosine with a Neutral pKa in the Ribosome Transferase Center." Science 289 (2000): 947-949.

    Two new papers dispute the mechanism presented in the above two papers.

    Thompson, et al. "Analysis of Mutations at residues A2451 and G2447 of 23S rRNA in the Peptidyltransferase Active Site of the 50S Ribosomal Subunit." Proc. Natl. Acad. Sci. U.S.A. 98 (2001): 9002-7.

    Xiong, L., N. Polacek, P. Sander, E. C. Bottger, and A. Mankin. "pKa of Adenine 2451 in the Ribosomal Peptidyl Transferase Center Remains Elusive." RNA 7, no. 10 (2001): 1365-1369.
    L25-L35 4: Crypts and Chambers: Macromolecular Machines involved in Protein Folding and Degradation Required

    Voet and Voet. Chapter 8, pp. 191-205.

    Hartl, and Hartl. "Molecular Chaperones in the Cytosol: From Nascent Chain to Folded Protein." Science 295 (2002): 1852-1858. (Review)

    Houry, W. A., D. Frishman, C. Eckerskorn, F. Lottspeich, and F. U. Hartl. "Identification of in vivo Substrates of the Chaperonin GroEL." Nature 402 (1999): 147-151. (Methods paper)

    Optional Readings

    V., Daggett, and A. R. Fersht. "Is there a Unifying Mechanism for Protein Folding?" Trends Biochem Sci 28, no. 1 (Jan 2003): 18-25.

    Walter, S., and J. Buchner. "Molecular Chaperones - Cellular Machines for Protein Folding." Angew. Chem. Int. Ed. 41 (2002): 1098-1113.

    Dougan, D. A., A. Mogk, and B. Bukau. "Protein Folding and Degradation in Bacteria: To Degrade or Not to Degrade? That is the Question." Cell: Mol Life Sci 59 (2002): 1607-1616.

    Not Required but Interesting Reading

    Overview of protein misfolding and disease:
    Dobson. "Getting out of Shape: Protein Folding and Disease." Nature 418 (2002): 729-30.

    Stroud, Walter. "Substrate Twinning Activates the Signal Recognition Particle and its Receptor." Nature 427 (2004): 215-220.

    Frank. "Structure of the Signal Recognition Particle Interacting with the Elongation-arrested Ribosome." Nature 427 (2004): 808-814.
  • DescriptionTypeLink
    Problem Set 1DownloadClick
    Problem Set 2DownloadClick
    Problem Set 3DownloadClick
    Problem Set 4DownloadClick
    Problem Set 5DownloadClick
    Problem Set 6DownloadClick
  • DescriptionTypeLink
    Introduction: cell constituents, prokaryotes vs. eukaryotesDownloadClick
    Fatty Acid Synthase: polymerization, biosynthesis, players, chemistry, structure, chemistry as a paradigm for PKS and NRPS, medical interludeDownloadClick
    Experimental methods for elucidating FAS structureDownloadClick
    Chemistry of FAS as paradigm for other molecular machinesDownloadClick
    Secondary metabolism: PKS, NRPSDownloadClick
    Chemistry of PKS and NRPS: post-translational modification, initiation, elongation, decoration, termination, fidelityDownloadClick
    Biosynthesis of yersiniabactin and cholesterolDownloadClick
    Cholesterol biosynthesisDownloadClick
    Cholesterol regulation and homeostasisDownloadClick
    Sensing insoluble moleculesDownloadClick
    Elongation, termination, RNA polymeraseDownloadClick
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