BIOCHEMICAL AND PROTEOMICS METHODS
cod. 1007408

Academic year 2024/25
1° year of course - First semester
Professor
Alessio PERACCHI
Academic discipline
Biochimica (BIO/10)
Field
Discipline del settore biomolecolare
Type of training activity
Characterising
52 hours
of face-to-face activities
6 credits
hub: PARMA
course unit
in ITALIAN

Learning objectives


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 upon which these techniques are based.Furthermore, the student must be familiar with the topics of proteome research, and with the main strategies and techniques employed in
proteomics.
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 experimental results and for their description. For example, in the face of
an experimental technique (among those illustrated in the course) that produces a certain result, 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 language of the discipline and the ability to use the acquired knowledge by applying them autonomously in some experimental setting are verified by means of a written exam.
The level of understanding of the subject, the mastery of the specific language and the ability to use the knowledge acquired by applying them autonomously in some experimental setting are verified by means of a written exam (in the classroom). It is understood that, in case of need (resurgence of the pandemic) it may be necessary to convert the test into an oral online exam.
LEARNING ABILITY
The continuous evolution of scientific research and, in particular, of the biochemical and proteomic methodologies requires a constant update of the pertinent skills. For this reason, the course aims at providing the theoretical basis and the autonomy needed by the students for the continuous upgrade of their know-how as research in the field progresses.

Prerequisites

- - -

Course unit content


Biochemical buffers. Cell homogenization.
Centrifugation: differential precipitation and gradient centrifugation.
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, immunohistochemistry.
Optical spectroscopy techniques and their applications:absorption spectroscopy and spectrofluorometry.
Basic notions of nuclear magnetic resonance spectroscopy (NMR).
Flow cytometry (Fluorescent-Activated Cell Sorting).
Basic notions on the use of radioisotopes in biochemistry.
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 (SILAC, ICAT and iTRAQ approaches) and functional proteomics: detailed analysis of some significant examples of
proteomic approaches to the study of biological problems.
Basic notions of enzymomics and metabolomics.

Full programme

- - -

Bibliography


Notions about the biochemical methods described in the course can be obtained from recent textbooxs such as:
Bonaccorsi di Patti, Contestabile, Di Salvo (2019), Metodologie Biochimiche, Zanichelli
Regarding proteomics, an available text in italian is: Alberio, Fasano, Roncada (2021) Proteomica, EdiSES.

Teaching methods


For this academic year, the course will consist of classroom lectures. The slides used for these lectures will be made available to students on the Elly platform. These lectures will illustrate the main methodologies employed in the fields of protein biochemistry and of proteomics. If conditions allow, the classroom lectures will be supplemented by visits to university laboratories.

Assessment methods and criteria


For the current academic year the knowledge acquired by the students, as well as their ability to use this knowledge in practice, will be assessed through a written test. During this test, the student will have to answer at least two open-ended questions, in which he will be asked to describe in detail some specific techniques covered in the course and above all to recognize how and when to use these techniques. Additionally, the test will include some multiple choice quizzes, always on topics of Biochemical and Proteomic Methodologies.
This will serve to assess the ability of the students to apply knowledge and understanding, as well as their autonomy of judgment and ability to communicate ideas and concepts with clarity and property of language.
The final grade (scale 0-30) will derive from a balanced evaluation of the various aspects mentioned. The ‘cum laude’ honor will be awarded in the case of students who show excellent knowledge and understanding of the subject, excellent ability to apply them, good independent judgment and fluency in the lexicon of the discipline.

Other information

- - -