BIOCHEMISTRY
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 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 two written exams (on part I and part II, respectively).Barring unforeseen circumstances, the exams will take place in person. In the event of a resurgence of the pandemic, the exams could adopt an online format, and the second written test could be replaced by an oral exam.
Prerequisites
Basic courses in general and organic chemistry
Course contents summary
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.
Metabolism:
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.
Proteomics:
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.
Recommended readings
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 consist of classroom lectures, with the exception of the lectures presented by the visiting professor, which will be delivered online. The videos of all the classroom lectures will remain available to the students on the Elly platform (or on another platform indicated by the university) for at least 15 days. The classes of the first part of the course will focus on the properties of proteins and enzymes, as well as on the fundamental metabolic pathways. The second part of the course will deal with the main biochemical techniques for the identification, isolation, and structural and functional study of proteins. For some of these techniques (if conditions allow) laboratory practices will be also conducted.
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 two written classroom tests. The first test will cover the Biochemistry topics and the second test will cover the Applied Biochemistry and Proteomics topics. During the first written test, the student will have to answer some (indicatively three) open-ended questions concerning the structure and function of proteins and metabolism; furthermore, the test will include some (approximately twelve) multiple choice quizzes, again on these topics. This will serve to evaluate the student’s acquired knowledge and understanding of the subject, as well as his/her clarity of presentation.
During the second test, the student will be invited to describe in detail some biochemical and proteomic techniques covered in the course and, above all, to recognize how and when to use these techniques. This written test will also include some multiple choice quizzes. This format will serve to assess the ability to apply the acquired knowledge and understanding, the autonomy of judgment and the ability to present concepts with precision and properties.
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 tests. 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.
It is understood that, in case of need (resurgence of the pandemic) it may be necessary to convert the two tests to online mode; in this instance the first test will be a written one with only open-ended questions, while the second test will consist of an oral examination.
