Course program
COURSE CONTENTS
The course will be divided in three sections. The first section is dedicated to the study of the properties, structure and function of biological macromolecules. In the second part the main methodologies used in the biochemical laboratory will be examined. The theoretical study of experimental methods will be implemented by exercises in the classroom, with projection and discussion of videos and numerical calculations, and practical experiences in the laboratory. The last part of the course will be devoted to the principles, mechanisms and regulation of cellular metabolism.
PART 1: The biological macromolecules
Protein (8 hours). Water properties. Amino acids and peptide bond. Structure and function of proteins. Structural levels. Fibrous and globular proteins. Protein folding and denaturation. Dynamic properties of proteins.
Myoglobin and hemoglobin (6 hours). Physiological role. Tertiary and quaternary structure. Cooperation of the interaction with oxygen. Concerted and sequential allosteric models. Bohr effect and allosteric effectors. Pathological hemoglobins and molecular diseases.
Enzymology (8 hours). General characteristics of enzymes. General theory of enzymatic catalysis. Enzymatic kinetics. Reversible inhibition mechanisms. Mechanisms of enzymatic catalysis. Role of vitamins and coenzymes in catalysis. Regulation of enzymatic activity.
Lipids (4 hours). Structure and function. Biological membranes. Fat-soluble vitamins.
Sugars (2 hours). Structure and function. Disaccharides and polysaccharides. Glycoproteins.
Nucleic acids (2 hours). Structure of purine and pyrimidine bases, nucleosides and nucleotides.
PART 2: Biochemical methodologies.
Biochemical methods (8 hours). Protein purification strategies. Dosage of proteins. Chromatographic and electrophoretic techniques. Mass spectrometry. Enzymatic assays. Techniques for determining the primary structure and the three-dimensional structure of proteins.
PART 3: Metabolism.
General aspects of metabolism (4 hours). Fundamental principles of thermodynamics applied to biological systems. Role of ATP and high-energy compounds in energy metabolism. Electron transporters. Redox reactions. Mechanisms of metabolic regulation.
Metabolic pathways and their regulation (18 hours). Glycolysis, alcoholic and homolactic fermentation. Pentose phosphate shunt. Gluconeogenesis. Cori cycle. Glycogen metabolism. Pyruvate dehydrogenase. Krebs Cycle. Glyoxylate cycle. Degradation and synthesis of fatty acids. Chetonic bodies. Cholesterol synthesis. Metabolism of protein nitrogen and degradation of amino acids. Glucose-alanine cycle. Urea cycle. Monocarbon units transporters. Electron transport chain. Oxidative phosphorylation. Malate-aspartate and glycerophosphate shuttle systems.
Hormonal regulation and signal transduction (2 hours).
Prerequisites
1) ESSENTIAL: knowledge of the basic concepts of general chemistry and organic chemistry. In particular, it is necessary to know: a) the properties of the main functional groups; b) the mechanism of nucleophilic substitution and addition reactions; c) the concept of acid, base and pH; d) the properties of the buffer solutions.
2) IMPORTANT: knowledge of basic biology and the principles of general and cellular physiology for the understanding of metabolisms in the various organs and organisms.
3) IMPORTANT: knowledge of the molecular biological bases of cell biology for the understanding of cell biochemistry
Books
Nelson, Cox - Lehninger PRINCIPLES OF BIOCHEMISTRY, WH Freeman
Berg, Tymoczko, Stryer – BIOCHEMISTRY, WH Freeman
Garrett, Grisham - BIOCHEMISTRY, Brooks/Cole Pub Co.
Voet-Voet-Pratt - PRINCIPLES OF BIOCHEMISTRY , John Wiley & Sons
Teaching mode
The course will be carried out through theoretical classroom lectures (64 hours), classroom exercises (6 hours) and practical laboratory experiences (6 hours).
Frontal lessons:
1) Anonymous entry test for the evaluation of basic knowledge. Correction and discussion of the test. Explanation of the concepts that make up the prerequisites of the course, at the request of the students and based on the results of the test.
2) Explanation of the topics covered by the program through slides and audio-visual material. This educational model is aimed at providing the theoretical knowledge of Biochemistry.
3) Open discussion of the topics of the lesson, during which the students are called to intervene; this has the purpose of developing communication skills, criticism and judgment.
Theoretical exercises in the classroom:
1) Presentation and discussion of a video on protein purification (2 hours in class)
2) Presentation and discussion of video on electrophoresis (2 hours in class)
3) Practical exercise on the use of molecular models (2 hours in class)
These exercises are intended to deepen the theoretical concepts studied in class and to put them into practice.
Laboratory experiences:
1) Simulation of computer protein purification (2 hours in computer lab)
2) Chromatographic separation of proteins and small molecules (2 hours of practical activity in the laboratory).
3) Enzymatic kinetics measurements (2 hours of practical activity in the laboratory).
The laboratory experiences are designed to put into practice the theoretical concepts studied in class, to develop the ability to plan an experiment and interpret it, to increase critical and judgmental skills.
Frequency
Attendance is optional but strongly recommended, especially with regard to practical exercises
Exam mode
The Biological Chemistry exam takes place at the end of the course and includes a written description of a metabolic pathway, followed by an oral exam. The oral exam consists of three consecutive 10-minute sessions, all held on the same day. Each session consists of an oral interrogation organized around three broad questions, ensuring that all parts of the program are covered: biological macromolecules, biochemical methodologies, and metabolism.
In general, the student’s preparation will be assessed based on their ability to describe biochemical processes clearly and with scientific rigor, and to connect different topics, demonstrating an understanding of the biochemical logic of living organisms. Specifically, the student will be expected to:
Know the structure and function of the main classes of biological macromolecules; Explain the main metabolic pathways in terms of chemical reactions, recognizing and reproducing the structures of metabolites; Explain the principles and applications of the most common biochemical methodologies.
For the overall evaluation of the student’s preparation, communication, critical thinking, and judgment skills will also be taken into account.
A score out of 30 is given for each of the three questions based on the criteria described. The final grade is calculated as the average of the three individual scores.
Bibliography
Not required
Lesson mode
The course will be carried out through theoretical classroom lectures (64 hours), classroom exercises (6 hours) and practical laboratory experiences (6 hours).
Frontal lessons:
1) Anonymous entry test for the evaluation of basic knowledge. Correction and discussion of the test. Explanation of the concepts that make up the prerequisites of the course, at the request of the students and based on the results of the test.
2) Explanation of the topics covered by the program through slides and audio-visual material. This educational model is aimed at providing the theoretical knowledge of Biochemistry.
3) Open discussion of the topics of the lesson, during which the students are called to intervene; this has the purpose of developing communication skills, criticism and judgment.
Theoretical exercises in the classroom:
1) Presentation and discussion of a video on protein purification (2 hours in class)
2) Presentation and discussion of video on electrophoresis (2 hours in class)
3) Practical exercise on the use of molecular models (2 hours in class)
These exercises are intended to deepen the theoretical concepts studied in class and to put them into practice.
Laboratory experiences:
1) Simulation of computer protein purification (2 hours in computer lab)
2) Chromatographic separation of proteins and small molecules (2 hours of practical activity in the laboratory).
3) Enzymatic kinetics measurements (2 hours of practical activity in the laboratory).
The laboratory experiences are designed to put into practice the theoretical concepts studied in class, to develop the ability to plan an experiment and interpret it, to increase critical and judgmental skills.
