BIOCHEMICAL AND PROTEOMICS METHODS
Learning outcomes of the course unit
KNOWLEDGE AND UNDERSTANDING
At the end of the course, the student is expected to have acquired a systematic knowledge of the main research techniques in biochemistry, including the principles on which these techniques are based. Furthermore, the student must be familiar with the issues covered by proteomics, and the main strategies and techniques employed within this discipline.
CAPACITY TO APPLY KNOWLEDGE AND UNDERSTANDING, AUTONOMY AND COMMUNICATION SKILLS
Besides knowing, understanding and being able to describe the methodologies for the identification, isolation, and structural and functional study of proteins, at the end of the course the student must possess the intellectual tools necessary for the analysis of the results and for their description. For example, in the face of an experimental technique (among those illustrated in the course) that produces a certain piece of data, the student should be able (a) to describe the technique and the data that emerges in appropriate language and (b) analyze critically the experimental data and hypothesize one or more possible interpretations.
The level of understanding of the subject, the mastery of the specific language and the ability to use the acquired knowledge by applying them autonomously in some experimental setting are verified by means of written exams.
The continuous evolution of scientific research and, in particular, of biochemical and proteomic methodologies requires a constant updating of skills. For this reason, the course aims to provide the theoretical basis and the autonomy necessary for the continuous alignment of skills with the progress of research in the field.
Course contents summary
Biochemical buffers. Extraction and purification of proteins. Chromatographic techniques: gel filtration chromatography, ion exchange, hydrophobic exchange and affinity chromatography. Protein electrophoresis: native, SDS-PAGE, isoelectrofocusing, 2D-PAGE. Immunochemical techniques: immunoprecipitation, ELISA, Western blotting. Optical spectroscopy techniques and their applications: absorption, spectrofluorometry and circular dichroism. Basic notions of nuclear magnetic resonance spectroscopy (NMR). Basic notions on the use of radioisotopes. Enzymatic assay methods. Continuous and discontinuous assays. Methods based on coupled reactions. Activity Units. Mass spectrometry: ionization systems and analytical methods (magnetic deflection detectors, quadrupole, flight time, orbitrap, tandem detectors). Proteomics, general concepts. Systemic proteomics and methodological basics of the proteomic approach: mono- and bi-dimensional proteins of electrophoresis; Mass spectrometry coupled with the analysis of databases. Proteomic study of post-translational modifications. Differential proteomics and functional proteomics: detailed analysis of some significant examples of proteomic approaches to the study of biological problems. Basic notions of enzymomics and metabolomics.
Notions about the biochemical methods described in the course can be obtained from recent textbooxs such as:
Bonaccorsi, Contestabile, Di Salvo, Metodologie Biochimiche, Casa Editrice Ambrosiana; Reed, Holmes, Weyers & Jones, Metodologie di base per le scienze biomolecolari,
The lectures on proteomics will be based on scientific papers (in English) directly provided by the teacher.
The course will be based on formal classroom lectures, in which the students will be exposed to the main biochemical methods used in protein biochemistry and proteomics.
Assessment methods and criteria
The knowledge and understanding acquired by the student, as well as her/his ability to apply such a knowledge in practice, will be assessed through a written test. The test will encompass a section with 15 multiple-choice quizzes and a section including two open questions. The multiple-choice quizzes will mainly serve to assess the acquired knowledge and understanding. As for open questions, the student will be asked to describe specific techniques in detail and above all to recognize how and when to employ such techniques . This will serve to assess the ability to apply knowledge and understanding, as well as the capacity of making judgements and of communicating ideas and concepts with clarity and property of language.
In the multiple-choices section, students will be awarded one point for each exact answer (maximum score in the section: 15). As for the open questions, each of them will be attributed a score between 0 and 7.5 (maximum score in the section: 15).
The final grade (scale 0-30) will represent the sum of the scores for the two sections. The 'cum laude' honor is assigned when both sections achieve maximum score and the candidate shows fluency the lexicon of the disicpline.