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. “This resource may not render correctly in a screen reader.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. “This resource may not render correctly in a screen reader.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

"This resource may not render correctly in a screen reader.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