Learning outcomes of the course unit
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 the multiple functions of proteins, with an emphasis on the fundamental role of these macromolecules in the cellular processes. Moreover, the students are expected to be familiar with the main classes of small biomolecules (sugars, lipids, amino acids, nucleotides) and will 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 their knowledge in an experimental setting, will be assessed through written exams.
Basic courses in general and organic chemistry
Course contents summary
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. 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.
Basic biochemical methods:
Cell fractionation. Protein extraction and purification. Electrophoretic and chromatographic techniques.Immunochemical techniques and their applications. Use of radioisotopesin biochemical research. Enzyme assays and units of activity.
General concepts in proteomics. Systematic proteomics and methodological basis of proteomics research: two- dimensional electrophoresis; mass spectrometry coupled to the analysis of databases. Proteomic studies of post-translational modifications. Differential andfunctional proteomics: detailed analysis of some examples of proteomics approaches aimed at addressing biological problems.
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
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.
The course will be based on formal classroom lectures and will also include (if funding allows) laboratory practices. Formal classes will focus on the properties of proteins and enzymes, as well as on the description of the main metabolic pathways. During laboratory practices, the students will be exposed to the main biochemical methods for the identification, isolation and characterization of proteins.
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 written texts. The tests will encompass both multiple-choice quizzes and open questions. The multiple-choice quizzes will mainly serve to assess the acquired knowledge and understanding. As for open questions, the student will be required to write a text concerning a specific topic or problem; this will serve to assess the ability to apply knowledge and understanding, as well as the capacity of making judgments and of communicating ideas and concepts with clarity and property of language. Student will have to take two written tests, at different times. The first written test will focus on the Biochemistry part of the course (protein structure and function, metabolism) whereas the second test will concern the Applied Biochemistry and Proteomics topics (basic laboratory methods, proteomics techniques). For each of the two written texts, performance in the multiple-choices section and performance in the open questions section will contribute similarly to the overall grade (scale 0-30). The student will be admitted to the second written test only after successfully passing the first one. The final grade will represent the arithmetic average of the grades for the two written texts. The 'cum laude' honor is assigned when both written texts achieve a score of 30 and the candidate shows fluency in the lexicon of the discipline.