cod. 1004367

Academic year 2020/21
2° year of course - First semester
- Alessio PERACCHI
Academic discipline
Biochimica (BIO/10)
Discipline biologiche
Type of training activity
84 hours
of face-to-face activities
9 credits
hub: PARMA
course unit

Learning objectives

In this course, students will be provided with the basic knowledge and understanding needed to perform experimental analyses in biochemistry and to properly interpret the results of such analyses.
At the end of the first part of this course, students are expected to possess a robust general understanding of the structure and of the manifold functions of proteins, with an emphasis on the fundamental role of these macromolecules in the cellular processes. Moreover, the students are expected to become familiar with the main classes of small biomolecules (sugars, lipids, amino acids, nucleotides) and to learn the basic metabolic pathways through which these molecules are degraded and synthesized. The students should also be able to express their knowledge of biochemistry in proper scientific language.
At the end of the second part of the course, the students are expected to have acquired a systematic preparation on the main techniques used in the biochemistry laboratory for the identification, isolation and characterization of biological macromolecules. They are also expected to possess competences regarding the analysis and interpretation of the experimental results. Finally, the students are also expected to know and understand the themes, strategies and major approaches employed in the field of proteomics. The acquired knowledge and understanding, as well as the capacity to apply such a knowledge in an experimental setting, will be assessed through a written exam (on part I) and an oral exam (on part II). As long as the COVID-19 emergency continues, the tests will be carried out online.


Basic courses in general and organic chemistry

Course unit content

Part I
Protein structure and function. The amino acids. The peptide bond. The three-dimensional structure of proteins: primary, secondary, tertiary and quaternary structures. Function and evolution of proteins. Hemoglobin: a model allosteric protein. Enzymes: basic concepts and kinetics. The Michaelis-Menten model. Inhibition of the enzyme activity. A model enzyme: chymotrypsin. Regulatory strategies of enzyme activity.
Foundations of bioenergetics: deltaG0 and deltaG0’. ATP, a molecule for the storage of (bio)chemical energy. Other key molecules of metabolism: NADH, FADH2, coenzymes and vitamins. The carbohydrates: properties and general concepts. Glicolysis and fermentations; citric acid cycle; pentose-phosphate pathway and gluconeogenesis; glycogen metabolism. Oxidative phosphorylation: the mitocondrial chain of electron transporters; proton gradients and the biosynthesis of ATP. The metabolism of lipids and its regulation: fatty acids degradation (beta- oxidation) and fatty acids biosynthesis. Synthesis and utilization of ketone bodies. Degradation of the amino acids and the urea cycle. Biosynthesis of amino acids and nucleotides.

Part II
Basic biochemical methods:
Cell fractionation. Protein extraction and purification. Electrophoretic and chromatographic techniques. Immunochemical techniques and their applications. Use of radioisotopes in biochemical research. Enzyme assays and units of activity.
General concepts in proteomics. Systematic proteomics and methodological basis of proteome research: two- dimensional electrophoresis; mass spectrometry coupled to the analysis of databases. Proteomic studies of post-translational modifications. Differential and functional proteomics: detailed analysis of some examples of proteomics approaches aimed at addressing biological problems.

Full programme

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Part I
Biochimica: David L. Nelson e Michael M. Cox, (2017) I Principi di Biochimica di Lehninger (VII ed.) Zanichelli.
Mary K. Campbell, Shawn O. Farrell (IV Ed.) Biochimica EdiSES
Part II
Bonaccorsi, Contestabile, Di Salvo (2019) Metodologie Biochimiche II ed, Zanichelli.
The lectures on proteomics will be based on scientific papers (in English) directly provided by the teacher.

Teaching methods

For this academic year, the course will mainly consist of online lessons. Classes will be given in live streaming (i.e. the teacher will present his lectures on the Teams platform at the times and dates specified by the course calendar), and the videos of these classes will remain available to students on the Elly platform (or on another platform indicated by the university) for at least 15 days. In the lessons of the first part of the course, the properties of proteins and enzymes will be illustrated, as well as the fundamental metabolic pathways. The second part of the course will examine the main biochemical techniques for the identification, isolation, and structural and functional study of proteins. For some of these techniques (if the sanitary and funding conditions allow) laboratory practices will also be possible.

Assessment methods and criteria

For the current academic year, the knowledge acquired by the student, as well as the ability to use such knowledge in practice, will be assessed through two distinct tests: a written and an oral test, to be taken at different times. As long as the COVID-19 emergency persists, both tests will be carried out online. The written test will cover the Biochemistry program and the oral test will cover the Applied Biochemistry and Proteomics program. During the written test (first partial), the student will have to write a relatively extensive text on some (indicatively three) topics or problems concerning the structure and function of proteins and the metabolism; this will serve to evaluate the acquired knowledge and understanding of the subject as well as the student's clarity.
At the oral exam (second partial), the student will be asked to describe in detail some biochemical and proteomic techniques covered during the course and, above all, to recognize how and when to use these techniques. This will serve to assess the capacity to apply the acquired knowledge and understanding, the autonomy of judgment and the ability to expose concepts properly and precisely.
Only after successfully passing the first written test will the student be able to access the second partial. The final grade (scale 0-30) will reflect the arithmetic average of the grades achieved in the two partial. The ‘cum laude’ honor will be awarded if the candidate achieves the maximum score in each of the two tests, and shows fluency in the lexicon of the discipline.

Other information

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