Integrated Structural Biology

A.Y. 2020/2021
6
Max ECTS
64
Overall hours
SSD
BIO/10
Language
English
Learning objectives
The theoretical and practical grounds of structural biology, a branch of life sciences spanning different methodological approaches, will be presented. Through the lectures and practical sessions, the students will gain an understanding of the principles through which the interaction of X-rays, or of electrons, with the biological matter can unravel the molecular/atomic organization of molecules and macromolecules (proteins and nucleic acids) that build cells and organisms. The theoretical bases of X-ray crystallography, presented in frontal lectures, will guide the understanding of applicative methods. Students will learn crystallization and X-ray diffraction techniques, use of synchrotron radiation, computational approaches to solving the three-dimensional structure of proteins and nucleic acids. A thorough understanding of the fundamental principles of cryo-electron microscopy will allow students learning the state of the art methods of single particle cryo-electron microscopy to gain access to the three-dimensional structures of large macromolecular complexes. Altogether, the lectures will be integrated by lab and computing practicals. In the end the students will gain a thorough view on the methods and potential of structural biology that provides us with unique views and understanding of the way proteins, DNA, RNA and other biological (macro)molecules act. The course is ideally linked to those dealing with protein engineering and computational biology.
Expected learning outcomes
Students will acquire extended knowledge on the methods of X-ray crystallography and single particle cryo-electron microscopy. Such cultural background will enable them to: i) appreciate the complexity of structural biology experiments and of the physical principles on which they rely; ii) understand the limitations posed by each technique, and learn how to properly plan/execute experiments; iii) understand how three-dimensional structures of macromolecules are achieved, their significance and their standing within the domain of biological research.
Single course

This course cannot be attended as a single course. Please check our list of single courses to find the ones available for enrolment.

Course syllabus and organization

Single session

Lesson period
Second semester
Since this is the first teaching year since the activation of the Course, there are no differences to be singled out relative to the past. All details relative to the teaching activities are described in the following sections of this web page.
Course syllabus
The teaching will cover the main theoretical, technical and software approaches to structural biology analyses by means of X-ray crystallography and single particle cryo-electron microscopy.
- Interaction of X-rays and electrons with matter
- Crystals of biological macromolecules: properties, growth, symmetry, crystal lattices
- X-ray synchrotron sources
- Principles of X-ray diffraction, diffraction experiments for data collection and analysis
- Fourier transform and the phase problem
- Methods for solving crystal structures and their refinement
- Geometry and functioning of electron microscopes
- Sample preparation for single particle cryo-electron microscopy
- Image acquisition techniques in single particle cryo-electron microscopy
- Processing of data and structure solution in single particle cryo-electron microscopy
- Reliability of three-dimensional structures of proteins, data bases
- Integration and complementarity with other structural biology methods
At the end of the lectures and of the practical sessions the students will be able to design and run experiments for crystal growth, electron microscopy sample preparation, processing of data for both techniques. They will also gain a critical view on the design and execution of research experiments in the structural biology context, aiming at understanding structure, function, interactions and modifications that characterize proteins and nucleic acids in living cells.
Prerequisites for admission
Students are expected to have preexisting knowledge on: fundamental properties of electromagnetic radiation: energy, frequency, wavelength, interference; basic mathematics and physics. Basic knowledge on biochemistry of proteins and nucleic acids, related to their structural organization levels. References to basic textbooks and web sites will be provided during lectures, before facing each new argument.
Teaching methods
Frontal lectures, using PowerPoint slides (the exact modality - whether in presence or through the web - will be announced in early 2021 according to the sanitary dispositions), including the theoretical aspects of Structural Biology, will cover about 32 hours of lessons. An equivalent amount of time will be spent in lab (if possible) and computer exercise. These will include protein crystal growth and handling, electron microscopy grid preparation, cryo EM data analysis and collection, crystallographic structure solution procedures. All the computer experiences will be based on the most common software packages present in each field. Practice will be considered a fundamental component of the course.
Teaching Resources
Given the conceptual and practical span of the arguments covered, there is no single textbook covering all the topics. Besides, these fields are rapidly evolving. Materials for study will be provided through lecture slides and addressing to specific textbooks, web sites and scientific review papers.
Assessment methods and Criteria
Assessment of the acquired notions will be carried over through an oral examination and through written reports regarding the practicals. The oral exam will be based on a critical discussion of a selected paper covering arguments that have been presented during the course; this part of the exam will weight 60% for the final score. Description and analysis of the practical experiences developed in the second half of the class (in the form of students' reports) will build 40% of the final exam score. Such reports (four in total) will be produced by the students during the course, after each block of arguments (about 8 hours of practice) is completed.
BIO/10 - BIOCHEMISTRY - University credits: 6
Practicals: 32 hours
Lessons: 32 hours
Professor: Bolognesi Martino