Biological Chemistry II

Lecture & Recitation Videos

For reading material pertaining to the lectures, please see the Readings page.

ses #	videos	RECITATION READINGS AND HANDOUTS
General Background
L1	Lecture 1: Introduction
Module 1: Translation
L2	Lecture 2: Protein Synthesis 1
R1	Recitation 1: Determining, Analyzing, and Understanding Protein Structures	Recitation 1 Handout (PDF) Recitation 1 Packet (PDF) PyMOL Worksheet (PDF)
L3	Lecture 3: Protein Synthesis 2
L4	Lecture 4: Protein Synthesis 3
L5	Lecture 5: Protein Synthesis 4
R2	Recitation 2: Pre-Steady State and Steady-State Kinetic Methods Applied to Translation	Pape, T., W. Wintermeyer, and M. Rodnina. “Induced Fit in Initial Selection and Proofreading of Aminoacyl-tRNA on the Ribosome (PDF)” EMBO J 1999, 18, 3800-3807. Recitation 2 Discussion Questions (PDF) Recitation 2 Pre-Steady-State Kinetics Handout (PDF)
L6	Lecture 6: Protein Synthesis 5
L7	Lecture 7: Protein Synthesis 6
Module 2: Protein Folding
L8	Lecture 8: Protein Folding 1
R3	Recitation 3: Pre-Steady State and Steady-State Kinetic Methods Applied to Translation	Pape, T., W. Wintermeyer, and M. Rodnina. “Induced Fit in Initial Selection and Proofreading of Aminoacyl-tRNA on the Ribosome (PDF)” EMBO J 1999, 18, 3800-3807. Recitation 3 Radioactive Experiments Handout (PDF)
L9	Lecture 9: Protein Folding 2
L10	Lecture 10: Protein Folding 3
L11	Lecture 11: Protein Folding 4
R4	Recitation 4: Purification of Native and Mutant Ribosomes, Protein Purification	Background: Mesa P., A. Deniaud, et al. “Directly From the Source: Endogenous Preparations of Molecular Machines” Curr Opin Struct Biol 2013, 23, 319-325. Case study: Youngman, E.M., R. Green. “Affinity purification of in vivo-assembled ribosomes for in vitro biochemical analysis” Methods 2005, 36, 305-312. Recitation 4 Discussion Questions (PDF) Recitation 4 Ribosome Purification Handout (PDF)
Module 3: Protein Degradation
L12	Lecture 12: Protein Degradation 1
L13	Lecture 13: Protein Degradation 2
L14	Lecture 14: Protein Degradation 3
R5	Recitation 5: Overview of Cross-Linking, Including Photo-Reactive Cross-Linking Methods	Recitation 5 Overview of Cross-Linking (PDF) Recitation 5 Discussion Questions (PDF) Optional Reading "Thermo Scientific Crosslinking Technical Handbook. Easy molecular bonding crosslinking technology: Reactivity chemistries, applications and structure references (PDF)" Thermo Fisher Scientific Inc., 2012. Sinz, A. “Chemical Cross-Linking and Mass Spectrometry to Map Three-Dimensional Protein Structures and Protein-Protein Interactions” Mass Spectrometry Reviews 2006, 25, 663-682.
Module 4: Polyketide and Nonribosomal Peptide Assembly Lines
L15	Lecture 15: PK and NRP Synthases 1
L16	Lecture 16: PK and NRP Synthases 2
R6	Recitation 6: Macromolecular Electron Microscopy Applied to Fatty Acid Synthase (Guest Speaker Ed Brignole)	Background: DeRosier, D. “3D Reconstruction from Electron Micrographs: A Personal Account of its Development” Met Enzymol 481(2010):1-24. Case study: Brignole, E.J., S. Smith, and E.J. Asturias. “Conformational Flexibility of Metazoan Fatty Acid Synthase Enables Catalysis” Nat Struc Mol Biol 16(2009):190-197. Recitation 6 Handout (PDF) Recitation 6 Discussion Questions (PDF)
L17	Lecture 17: PK and NRP Synthases 3
L18	Lecture 18: PK and NRP Synthases 4
Module 5: Cholesterol Biosynthesis and Cholesterol Homeostasis
R7	Recitation 7: Application of Single Molecule Methods to Understand Macromolecular Machines And Protein Degradation (Guest Speaker Reuben Saunders)	Aubin-Tam, M.E., A.O. Olivares, et al. “Single-Molecule Protein Unfolding and Translocation by an ATP-fueled Proteolytic Machine” Cell 2011, 145, 257-267. Cordova, J.C., A.O. Olivares, et al. “Stochastic but Highly Coordinated Protein Unfolding and Translocation by the ClpXP Proteolytic Machine” Cell 158(3), 2014, 647-658. Recitation 7 Discussion Questions (PDF)
L19	Lecture 19: Cholesterol Biosynthesis 1
L20	Lecture 20: Cholesterol Biosynthesis 2
L21	Lecture 21: Cholesterol Biosynthesis 3 & Cholesterol Homeostasis 1
R8	Recitation 8: Application of CRISPR to Study Cholesterol Regulation	Ding, Q., A. Strong, K.M. Patel, et al. “Permanent Alteration of PCSK9 with in Vivo CRISPR-Cas9 Genome Editing” Circulation Research 115, 488-492 2014. Lander, E.S. “The Heroes of CRISPR” Cell 164(2016): 18-28. Peng, R., G. Lin, J. Li. “Potential Pitfalls of CRISPR/Cas9-Mediated Genome editing" The FEBS Journal 283, no.7, 2016, 1218-1231. Recitation 8 CRISPR Reading (PDF)
L22	Lecture 22: Cholesterol Homeostasis 2
L23	Lecture 23: Cholesterol Homeostasis 3
L24	Lecture 24: Cholesterol Homeostasis 4
R9	Recitation 9: Cholesterol Homeostasis and Sensing	Radhakrishnan, A., J.L. Goldstein, et al. “Switch-like Control of SREBP-2 Transport Triggered by Small Changes in ER Cholesterol: A Delicate Balance” Cell Metabolism 2008 8, 512-521. Recitation 9 Cholesterol Homeostasis (PDF)
L25	Lecture 25: Cholesterol Homeostasis 5 & Metal Ion Homeostasis 1
Module 6: Metal Ion Homeostasis
L26	Lecture 26: Metal Ion Homeostasis 2
L27	Lecture 27: Metal Ion Homeostasis 3
R10	Recitation 10: Metal-Binding Studies and Dissociation Constant Determination	Xiao, Z., and A.G. Wedd. “The Challenges of Determining Metal-Protein Affinities.” Nat Prod Rep 27(2010):768-789. Read sections 1 - 3.3.2 (pg. 768-772) Lisher, J.P., and D.P. Giedroc. “Manganese Acquisition and Homeostasis at the Host-Pathogen interface.”  Front Cell Infect Microbiol 3(2013):91. Read sections on entitled “Structural studies of bacterial manganese import systems,” “Host sequestration of transition metal ions,” and “Calprotectin: structural, metal binding and functional properties”(pg. 8-10) Recitation 10 Metal-Binding and Dissociation Constant (PDF)
L28	Lecture 28: Metal Ion Homeostasis 4
L29	Lecture 29: Metal Ion Homeostasis 5
R11	Recitation 11: Mass Spectrometry	Seo, Y.H., and K.S. Carroll. “Quantification of Protein Sulfenic Acid Modifications Using Isotope-Coded Dimedone and Iododimedone.” Angew Chem Int Ed 50(2011):1342-5. C.E. Paulsen et al. “Peroxide-Dependent Sulfenylation of the EFGR Catalytic Site Enhances Kinase Activity.”  Nat Chem Biol 8(2011)_:_57-64. Recitation 11 Mass Spectrometry (PDF)
L30	Lecture 30: Metal Ion Homeostasis 6
L31	Lecture 31: Metal Ion Homeostasis 7 & Reactive Oxygen Species 1
Module 7: Reactive Oxygen Species (ROS)
R12	Recitation 12: Mass Spectrometry of the Cysteine Proteome	Deng, X. et. al. “Steady State Hydrogen Peroxide Induces Glycolysis in Staphylococcus aureus and Pseudomonas aeruginosa.” J Bacteriol 196(2014): 2499-513. Recitation 12 Intracellular Proteome Analysis via MS (PDF)
L32	Lecture 32: Reactive Oxygen Species 2
L33	Lecture 33: Reactive Oxygen Species 3
L34	Lecture 34: Reactive Oxygen Species 4 & Nucleotide Metabolism 1
Module 8: Nucleotide Metabolism
R13	Recitation 13: Fluorescence Methods	A. Zhao, M. Tsechansky, et al. “Revisiting and Revising the Purinosome.” Mol Biosyst 10(2014): 369-74. Critically evaluate: An, S., R. Kumar, et al. “Reversible Compartmentalization of de novo Purine Biosynthetic Complexes in Living Cells.” Science 320(2008): 103-106.
L35	Lecture 35: Nucleotide Metabolism 2
L36	Lecture 36: Nucleotide Metabolism 3