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.
In the first part of this course, students will be introduced to the structure and the multiple functions of proteins, emphasizing the fundamental role of these macromolecules in the cellular processes.
Moreover, the students will become 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 synthetized.
In the second part of the course, the students will receive a systematic preparation on the main techniques used in the biochemistry laboratory for the identification, isolation and characterization of biological macromolecules.
Finally, they will be informed about the themes, the strategies and major techniques employed in the field of proteomics.
The acquired knowledge and understanding will be assessed through written exams.
Basic courseses in general and organic chemistry
Course contents summary
Structure and function of proteins.
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 model of Michaelis-Menten. Inhibition of the enzymatic activity. A model enzyme: chymotrypsin. Regulatory strategies of enzyme activity.
Foundations of bioenergetics: DG0 and DG0'. 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 radioisotopes in biochemical research. Enzyme assays and units of activity.
Proteomics - general concepts.
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 and functional proteomics: detailed analysis of some examples of proteomics approaches aimed at addressing biological problems.
David L. Nelson e Michael M. Cox I Principi di Biochimica di Lehninger (V edizione) Zanichelli, Bologna, 2010
Mary K. Campbell, Shawn O. Farrell Biochimica (III edizione) EdiSES, Napoli, 2009
Reed, Holmes, Weyers & Jones, Metodologie di base per le scienze biomolecolari, Zanichelli, 2002
The classes on proteomics will be based on scientific papers (in english) directly provided by the teacher.
The course will be based on formal classroom lessons 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 the 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 the ability to apply such a knowledge in practice, will be assessed through written texts. The tests will encompass both a section with multiple-choice quizzes and a section with 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 judgements 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 (structure and function of the proteins, metabolism) whereas the second test will concern the Applied Biochemistry and Proteomics topics (basic laboratory methods, proteomics techniques).
The student will be admitted to the second written test only after successfully passing the first one.