OVERVIEW

The course is structured in two modules: Structural Biology and Nanotechnologies

The structural Biology module is aimed at students of the postgraduate courses of Biotechnology, Biological Sciences, Chemistry, Materials Sciences.

The Structural Biology module aims to provide the basis for understanding the three-dimensional structure of macromolecules of biochemical and biotechnological interest such as proteins and nucleic acids.  The functional aspects to structural ones will be discussed through various examples present in the  literature.

The Nanotechnology module aims to provide the information about the advanced methods of nanotechnology, useful for structural biology, as well as on appropriate instrumentation, both laboratory and international facilities as synchrotrons and X-ray free electron lasers (XFELs).

AIMS AND CONTENT

LEARNING OUTCOMES

The course consist of two modules: Structural Biology and Nanotechnology. The Structural Biology module aims to provide the basis for understanding the three-dimensional structure of macromolecules of biochemical and biotechnological interest such as proteins and nucleic acids. The functional aspects to structural ones will be discussed through various examples present in the literature. The Nanotechnology module aims to provide students with an overview of the latest and most advanced nanobiotechnologies and nanobiomaterials. In particular, the two aspects of nanobioscience and nanobiotechnology application take place: structural proteomics and functional proteomics. In the first case, the novel method of protein nanocrystallography and the advanced synchrotron radiation techniques, including micro and nano-focussed high intense synchrotron radiation and the new trends in radiation damage reduction are presented. In the second case, the most innovative technologies of protein microarrays NAPPA (Nucleic Acid Programmable protein Array) and their fluorescent-label as well as label-free technology of are demonstrated. In the both cases the application to the regenerative medicine are underlined.

AIMS AND LEARNING OUTCOMES

Attendance and participation in the planned educational activities (lectures and laboratory experiences) will allow the student to acquire the necessary knowledge to study, at the molecular level, the structural and functional aspects of biological macromolecules.
Specifically, the student will be able to understand, learn and describe the methodological approaches for the study and prediction of the three-dimensional structures of macromolecules of biological interest.

PREREQUISITES

Fundamental requirements for the study of the subject are the knowledge of general and organic chemistry and biochemistry.
In particular, the student will have to know in detail subjects such as pH and chemical equilibrium. the main functional groups and their reactivity. the main reactions of biochemical interest.

TEACHING METHODS

The teaching consists of lectures completed by laboratory activities. Activities aimed at applying the knowledge acquired in the classroom during the lectures are foreseen.
Lectures in the classroom are delivered through the use of multimedia presentations and the constant use of the blackboard for the writing of molecular structures and the description of instruments and methods.

SYLLABUS/CONTENT

Chemical bonds that stabilize polypeptides: covalent bonds (peptide bond and its properties), hydrogen bonds, salt bridges, hydrophobic bonds, and weak electrostatic interactions. Molecular structures, and their stability. Main classes of organic organic molecules and basis of nucleic acids and proteins structures. Structure of nucleic acids. Primary and secondary structure of DNA and RNA and their integration into the genome. Tertiary structure of tRNA and rRNA. Methods for the definition of the primary structure of nucleic acids. Quaternary structure of the ribosome (rRNA protein integration). Structure of human chromosomes. Protein structure and function. Methods for studing the primary protein structure; Edman degradation, electrospray mass spectrometry, and single or multiple analyzers (MS / MS) MALDI. Levels of structural organization of proteins (primary, secondary, tertiary and quaternary structures). Motifs and domains. Dynamic and thermodynamic folding processes. Molecular evolution, conservation of the three-dimensional fold (divergent evolution, convergent evolution) and protein topologies. Classification of protein structure in structural hierarchies with increasing detail. Correlation of structures with the biological activity of proteins (examples of literature). Principles of crystallization and analysis of crystals of biological macromolecules. Hydrodynamic principles and models for the study of low resolution proteins. Protein Representative Graphing Methods: Lesk & Hardman, RIBBON, TOPS. Van der Waals surfaces. Protein surfaces and interactions with other proteins, ligands and nucleic acids. Criteria for the recognition of binding sites and catalysis. Catalysis and enzymatic kinetics: mechanisms of action of some classes of enzymes of biotechnological and biomedical interest.

Nanotechnology definition. Passive and active Nanostructures, nanoprobes and nanotechniques. Langmuir-Blodgett nanotechnolology for protein assembly. Protein organization in highly ordered mono- and multilayers. Quartz crystal microbalance with dissipation factor. AFM characterization of protein nanofilms and nanocrystals. Basis of protein X-ray crystallography. Synchrotron radiation sources, X-ray data collection, micro and nano-focussed beamlines, radiation damage. Protein crystallization with nanotemplates, nanobiocrystallography. X-ray free electron laser (XFEL) and serial femtosecond crystallography. Protein structures of scientific and industrial relevance.

RECOMMENDED READING/BIBLIOGRAPHY

All slides used during the lessons and other teaching material will be available on AulaWeb before the beginning of the lessons together with other bibliographic material in pdf format.

The books indicated are suggested as a supporting text and are available and can be consulted together with other books for further information by the teacher.

Texts advised for further information:                                                                                              Ringe-Petsko- Structure and function of proteins – Zanichelli

Pechkova, E., Riekel, C., Structural Proteomics and Synchrotron Radiation, Pan Stanford Series on Nanobiotechnology Volume 3, pp. 1-447, (ISBN, Singapore, New Jersey and London) 2012.
Introduction to Protein Structure - Branden C., Tooze J. - Garland Pub

TEACHERS AND EXAM BOARD

Exam Board

GIANLUCA DAMONTE (President)

ALBERTO DIASPRO

EVGENIYA PESHKOVA

LESSONS

LESSONS START

The second semester lessons will start from the beginning of March 2022

Class schedule

The timetable for this course is available here: Portale EasyAcademy

EXAMS

EXAM DESCRIPTION

The oral exam lasts about 30 minutes / student on the topics covered in class.
The student is asked three questions of increasing difficulty aimed at assessing the degree of study of the subject and preparation of the student.

As for the part of nanotechnology (Prof.Peshkova) the examination will be carried out in written form with multiple choice tests.

ASSESSMENT METHODS

Details on how to prepare for the exam and the degree of detail required for each topic will be provided at the beginning of the course and confirmed during lectures and exercises.

The oral exam will focus on the topics covered during the lectures and will aim to assess the achievement of the appropriate level of knowledge, the ability to use the theoretical notions to integrate the different concepts addressed in class and developed in the laboratory. The ability to present the topics clearly and with correct terminology will also be evaluated.

Exam schedule

FURTHER INFORMATION

Attendance at lectures is  mandatory.