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.
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.
Prerequisites
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.
Metabolism.
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.
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.
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.
Full programme
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Bibliography
Parte I
Biochimica: David L. Nelson e Michael M. Cox, I Principi di Biochimica di Lehninger Zanichelli,.
Mary K. Campbell, Shawn O. Farrell Biochimica EdiSES
Parte II
Bonaccorsi, Contestabile, Di Salvo, Metodologie Biochimiche, Casa Editrice Ambrosiana;
Reed, Holmes, Weyers & Jones, Metodologie di base per le scienze biomolecolari,
Zanichelli.
The lectures on proteomics will be based on scientific papers (in english) directly
provided by the teacher.
Teaching methods
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 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 (protein structure and function, 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.
Other information
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