Natural Sciences > Earth, Atmospheric, and Planetary Sciences > Biological Chemistry II

Biological Chemistry II posted by duggu on 2/2/2008

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Courseware/Lectures

Test/Tutorials

Course Highlights

The tools section includes information about various molecular graphics programs used to view three-dimensional structures in this course.

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.

Technical Requirements

RasMol software is required to run the .spt and .pdb files found on this course site.

*Some translations represent previous versions of courses.

Syllabus

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Recommended Textbook

Amazon logo Voet, D., J. Voet. Biochemistry. New York: J. Wiley & Sons, 2003. ISBN: 9780471250906.

This course is divided into four subject area modules as described in the following table.

MODULE #	DESCRIPTION
1	Size and Components of Cells and Implications with respect to Regulation Size of cells and components and implications with respect to regulatory mechanisms. Introduction to macromolecular machines.
2	Fatty Acid Synthases (FAS), Polyketide Synthases (PKS), and Non-ribosomal Polypeptide Synthases (NRPS) Initiation, elongation, termination and implications in human health. A paradigm for thinking about PKS and NRPS. Overview of the macromolecular machines with a common solution to the problems. Specific examples include erythromycin and enterobactin biosynthesis. Cholesterol biosythesis and homeostasis: implications in disease.
3	Translation: Loading, Initiation, Elongation, and Termination - A Machine in Action; Introduction to G-proteins: Switches or Motors An overview of translation: the players and the pacman view of the process. Methods to study macromolecular interactions: reconstitution experiments, crystallography, cryoelectron microscopy, footprinting and crosslinking, presteady state kinetics. Loading: tRNA synthases and their editing mechanisms. G proteins: switches or motors, EF-Tu and EF-G as examples in the elongation process. Molecular mimicry at work. The 50S ribosomal subunit: a view of peptide bond formation using RNA. Is chymotrypsin (a serine protease) a good model? The use of translation equipment to generate proteins containing unnatural amino acids in vitro and in vivo.
4	Crypts and Chambers: Macromolecular Machines involved in Protein Folding and Degradation Protein folding in vitro: Anfinsen's hypothesis. Protein folding in vivo: Hsp70/Hsp40: DNAJ and DNAK as a paradigm. Protein folding in vivo. Hsp6O Family (GroEL and GroES). 26S Proteosome and the role of Ubiquitin in degradation.

Grading

ACTIVITIES	POINTS
Problem Sets	Will not be graded, but will be dicussed in Recitations
Exam I	100
Exam II	100
Exam III	100
Exam IV	100
Final Exam	200 (Comprehensive)
Total	600

Recitations (Techniques and Discussion Sessions)

For one hour each week, Professor Ting will provide an in-depth view of technologies briefly outlined in class and used in the assigned journal papers. These classes will also be used to go over problem sets and to discuss lectures.

Reading

Assigned reading will include sections from your textbook to refresh your memory or to give you a good overview of a specific topic. It will also include a review article on each module to bring you up to date about recent advances in a specific area and an original paper that will highlight the use of a technique to solve a problem covered within the module. Additional background reading will be placed on reserve. Additional references will be given for those so inclined to read about one specific topic in more detail.

Molecular Graphics

In class, we will demonstrate three-dimensional structures using Rasmol, a molecular visualization program. We will provide the pdb files along with Rasmol scripts for the structures discussed per module, so that students can view them at their leisure.

Calendar

The calendar lists both lecture (L#) and recitation (TD#) sessions. Recitations are referred to as the Techniques and Discussion (TD) sessions. See syllabus for a description of the modules.

SES #	TOPICS	KEY DATES
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.)

Readings

This class also requires reading primary research papers and review papers, viewing structural data with molecular graphics programs, and thinking critically about modern topics in biochemistry.

Readings by lecture session (L#) are listed in the table below. Many of the readings are from the required textbook: Amazon logo Voet, D., J. Voet. Biochemistry. New York: J. Wiley & Sons, 2003. ISBN: 9780471250906.

SES #	MODULES	READINGS
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. G-Proteins 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.