Learning objectives
The course is addressed to students from scientific curricula interested to the basic aspects of the biochemistry of proteins and nucleic acids. Lectures will explain the hystorical development, the fundamental concepts and modern techniques in structural biology. Exercises and flipped classrooms stimulate ideas communications and exchange end teach about both individual and group research. At the end of the course students will be able to design a research project to address a question and to verify an hypothesis on the relation between structure and function for bio-macromolecules.
Prerequisites
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Course unit content
The course is an introduction to the preparative chemistry of bio-macromolecules (proteins, nucleic acids), to methods of structural characterization of bio-macromolecules, single crystal bio-crystallography, to transmission electron microscopy for bio-macromolecules.
Full programme
1. Introduction. Structure and function of macromolecules. Hypothesis based research, control experiments, development of experimental based models. Maximum likelihood concepts.
Basics of crystallography
2. historcal and conceptual introduction
3. light-matter interaction, scattering
4. crystallographic and non-crystallographic symmetry; polymorphism
5. X-ray scattering from crystalline materials: diffraction
6. single crystal diffraction data collection
7. single crystal diffraction data processing
8. Patterson function
9. structure solution: diect methods
10. building, refining and validation of structural models
11. structural data deposition: CSD
Bio-macromolecules chemistry
12. hystorical and conceptual introduction
13. production of recombinant proteins
14. DNA point mutation, deletions, insertions
15. chromathography
16. purification of bio-macromolecules from tissues
17. preparation of bio-macormolecular complexes
Biocristallography
18. crystal growth of bio-macromolecules
19. cryo-protection and radiation damage
20. structural determination: isomorphous replacement
21. structural determination: anomalous scattering
22. structural determination: molecular replacement
23. bio-macromelucar model building by molecular graphics
24. Raffinamento e validazione di modelli strutturali bio-macromolecolari
25. deposition of bio-macromolecular structural data: PDB
Trasmission electron microscopy for bio-macromolecules
26. hystorical and conceptual introduction
27. electron scattering
28. Electron microscopy with anionic dyes
29. Electron cryo-miscroscopy
30. single particle structiral reconstruction
31. electron tomography
32. Bio-macromolecular model placement in EM density
Flipped classroom exercises (12 hours)
1. purification strategy for a protein
2. Crystallography on the Iphone: https://www.crystallography.org.uk/crystallography-on-the-iphone/ e Quitztallography App: https://play.google.com/store/apps/details?id=aax.uab.quiztallography&hl=en&rdid=aax.uab.quiztallography
3. Questions and answers after watching Royal Institution: Seeing Things in a Different Light: How X-ray crystallography revealed the structure of everything. https://www.youtube.com/watch?v=gBxZVF3s4cU
4. diffraction data collection strategy
5. structural soluqion and model building (SHELXT)
6. crystallization screening strategy
7. crystal growth: lisozyme
8. Patterson difference map interpretation
9. phase detrminatoin with Harker diagrams
10. graphic bio-macromolecular model building with Coot
11. Building of the EM map of proteosome from noise
12. Use of Cambridge Structural Database (CSD) and of Protein Data Bank (PDB
Bibliography
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Teaching methods
Lectures, group exercises, flipped classrooms. Apps for phones and tablets. https://en.wikipedia.org/wiki/Flipped_classroom.
Assessment methods and criteria
Oral and written exam. Reports of exercises and flipped classrooms.
Other information
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