• Introduction
• 26 min
  1. From DNA to proteins: the multiple levels of regulation

  • Prof. Panagiotis Tsonis
• Chromatin and DNA
• 44 min
  2. Chromatin architecture and alterations in the control of gene regulation

  • Prof. Jeffrey Hansen
• 43 min
  3. Nucleosome dynamics and remodeling

  • Prof. Jonathan Widom
• 25 min
  4. DNA replication

  • Prof. Smita Patel
• Transcription
• 47 min
  5. Nucleotide dependent functioning of bacterial enhancer binding proteins, activators of sigma54 RNA polymerase

  • Prof. Martin Buck
• 44 min
  6. Mechanisms of transcription: the eukaryotic pre-initiation complex

  • Prof. Michael Hampsey
• RNA (I)
• 38 min
  7. Pre-mRNA splicing

  • Prof. Timothy Nilsen
• 60 min
  8. Self-splicing intron RNAs: ribozymes, parasites and agents of genomic change

  • Prof. Anna Marie Pyle
• 47 min
  9. Polyadenylation of mRNA precursors: mechanism, regulation and connections with other cellular processes

  • Prof. James Manley
• 46 min
  10. mRNA capping

  • Prof. Aaron Shatkin
• RNA (II)
• 40 min
  11. Nonsense-mediated and Staufen1-mediated mRNA decay: related pathways of post-transcriptional control in mammalian cells

  • Prof. Lynne Maquat
• 40 min
  12. The silent revolution: an introduction to gene regulation by microRNAs

  • Dr. Frank Slack
• 50 min
  13. RNA editing: changing the code in plants, animals and parasites

  • Prof. Stephen Hajduk
• Proteins
• 18 min
  14. The principle of translation

  • Prof. Joachim Frank
• 17 min
  15. Translation initiation

  • Prof. Patrick Linder
• 47 min
  16. Elongation of protein synthesis: structural basis of the process of decoding

  • Prof. Marina Rodnina
• 40 min
  17. Elongation of protein synthesis: structural basis of the peptide bond

  • Prof. Marina Rodnina
• 44 min
  18. How do proteins fold and why?

  • Prof. Walter Englander
• 55 min
  19. Protein degradation

  • Prof. Alfred Goldberg
• Understanding Global Gene Expression
• 33 min
  20. Comparing transcriptomes of distant organisms: the comparative ENCODE resource 1

  • Prof. Mark Gerstein
• 22 min
  21. Comparing transcriptomes of distant organisms: models of gene expression 2

  • Prof. Mark Gerstein
• 47 min
  22. Protein networks and analysis of global gene expression

  • Dr. Trey Ideker
• Archived Lectures *These may not cover the latest advances in the field
• 42 min
  23. Chromatin and transcription

  • Prof. Roger Kornberg
• 40 min
  24. Nuclear organization and gene expression

  • Prof. David Spector
• 35 min
  25. Gene and protein microarrays: tools for gene discovery and function

  • Prof. Craig R. Tomlinson

Printable Handouts

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Navigable Slide Index

1. Introduction
2. 70S Ribosome (5.5 angstrom)
3. Chemistry of the peptide bond formation
4. Peptide bond formation is catalyzed by RNA
5. Proteins within 30 angstrom of the PTC
6. tRNA binding in the PTC
7. C-Pmn as model substrate for binding at the A-site
8. CC-Pmn as substrate for binding at the A-site
9. Conformational changes folowing substrate binding
10. Water exclusion keeps peptidyl-tRNA uninduced
11. The 50S subunit with the transition state analogs
12. Potential strategies of catalysis
13. Enthalpic or entropic catalysis
14. Studying the mechanism of peptide bond formation
15. Characteristics of uncatalyzed reaction
16. Reaction pathway on the 50S subunit
17. Measuring kinetics of peptide bond formation
18. pH dependence of reaction with Pmn
19. Contribution of pH-dependent catalysis
20. Aminoacyl-tRNA as A-site substrate
21. Reaction with full-size substrate
22. Entropic effects in ribosome catalysis
23. Role of active-site residues: A2451
24. Conservation of peptidyl transferase mechanism
25. pH-dependent changes in ribosome structure
26. Mutations of inner shell residues
27. Replacement of 2' OH of A76 of the P-site tRNA
28. Roles of 2' OH of A76 of the P-site tRNA
29. Conclusions
30. Literature

Topics Covered

• The ribosome
• Chemistry of peptide bond formation
• Structure of the peptidyl transferase center of the ribosome
• Structures of the catalytic subunit with reaction substrates and transition state analogs
• Induced fit in peptide bond formation and peptidyl-tRNA hydrolysis
• Reaction pathways of catalyzed and uncatalyzed reactions
• pH dependence of catalysis
• Entropic catalysis
• Role of active site residues
• Importance of 2' OH of A76 of the tRNA in the P site
• The mechanism of peptide bond formation

Links

Series:

• From DNA to Proteins

Categories:

• Biochemistry
• Cell Biology

Talk Citation

Publication History

• Published on October 1, 2007

Financial Disclosures

• Prof. Marina Rodnina has not informed HSTalks of any commercial/financial relationship that it is appropriate to disclose.