Course program
The course will be divided into three parts:
1) Study of the properties, structure, and function of biological macromolecules;
2) Main methodologies used in the biochemical laboratory. The theoretical study of experimental methods will be accompanied by video projections and discussions;
3) Principles of cellular metabolism, metabolic pathways, and their regulation.
PART 1: Biological Macromolecules
Cell architecture.
Overview of the structure of prokaryotic and eukaryotic cells. Differences and similarities between animal and plant cells.
Structure and function of nucleic acids.
Structure of nucleosides and nucleotides, purine and pyrimidine bases. Structure of DNA. Role of DNA as a carrier of genetic information. DNA replication (overview). Transcription (overview). Role of messenger RNA and transfer RNA in protein translation. Genetic code. Overview of DNA sequencing and recombinant DNA technology.
Amino acids and proteins.
Structure, stereochemistry, and acid-base properties of amino acids. Peptide bond. Primary, secondary (α-helix, β-sheets), tertiary, and quaternary structure of proteins. Ramachandran plot. Protein folding. Denaturation and renaturation of proteins. Anfinsen’s experiments.
Myoglobin and hemoglobin.
Structure and function. Structure and role of the prosthetic group. Oxygen binding equilibrium to myoglobin and its equation. Cooperative oxygen binding to hemoglobin. Hill equation. Symmetry model and sequential model of allostery. Bohr effect. Allosteric effectors of hemoglobin (protons, CO2, 2,3-bisphosphoglycerate). Fetal hemoglobin. Overview of antibody structure. Antigen-antibody binding. Catalytic antibodies.
Lipids and biological membranes.
Overview of lipid classification and biological roles. Structure and organization of biological membranes. Membrane proteins. Facilitated passive transport: ionophores and porins. Active transport. Translocation systems: uniport, symport, antiport. ATP-driven active transport: Na⁺/K⁺-ATPase and Ca²⁺-ATPase (Na/K; Ca/H; H/K). Ion gradient-driven active transport: secondary glucose transport in the intestinal epithelium.
Enzymes.
Substrate specificity, stereospecificity, prochiral specificity. Catalytic strategies (acid-base catalysis, covalent catalysis, etc.). Overview of enzyme nomenclature and classification. Enzyme kinetics. Michaelis-Menten equation. Enzyme inhibition: competitive, uncompetitive, and mixed inhibition (equations). Example of catalytic mechanism: serine proteases. Regulation of enzymatic activity: allosteric regulation and covalent modifications.
PART 2: Biochemical Methodologies
Biochemical methodologies.
Protein purification strategies. Source selection. Protein quantification. Main chromatographic and electrophoretic techniques. Overview of mass spectrometry. Primary structure of proteins and molecular evolution. Overview of techniques to determine the three-dimensional structure of proteins (X-ray crystallography, NMR, Cryo-EM).
PART 3: Metabolism
General aspects of metabolism.
Catabolic and anabolic pathways. Experimental approaches to metabolic studies. Coupled reactions. ATP and phosphoryl group transfer potential. Redox reactions and electron carriers (NAD⁺, NADP⁺, FAD, FMN). Redox potential.
Carbohydrate metabolism.
Glycolysis: reactions of the glycolytic pathway. Homolactic and alcoholic fermentation. Gluconeogenesis. Pentose phosphate pathway: oxidative phase reactions and general features of the non-oxidative phase. Coordinated regulation of glycolysis and gluconeogenesis (role of fructose 2,6-bisphosphate and hormonal control). Overview of glycogen metabolism: degradation and synthesis.
Pyruvate dehydrogenase multienzyme complex.
Overview of the structure. Reaction mechanism of pyruvate dehydrogenase.
Citric acid cycle.
Cycle reactions. Amphibolic role and anaplerotic reactions. Overview of regulation.
Lipid metabolism.
Activation and degradation of fatty acids. Overview of ketone bodies, fatty acid biosynthesis, and the glyoxylate cycle.
Amino acid metabolism.
Role and mechanism of transaminases. Oxidative deamination of glutamate. Overview of the urea cycle. Overview of amino acid degradation. Overview of the role and structure of one-carbon unit carriers (tetrahydrofolate and S-adenosylmethionine).
Electron transport and oxidative phosphorylation.
General overview of electron carriers. Overview of complexes I–IV function. Generation of the proton motive force. Structure and mechanism of ATP synthase (rotational catalysis).
IMPORTANT:
For further clarity, it is specified that knowledge of the structural formulas of the following biochemically relevant molecules is required:
The 20 amino acids (GALVIPFYHWKRDENQCSTM) and the peptide bond
Oxy and deoxy-nucleotides and the phosphodiester bond in R(D)NA
ATP and GTP, cAMP and cGMP
Glucose (α and β cyclic forms; α and β glycosidic bonds), fructose
Triacylglycerols, glycerol-3-phosphate, glycerophospholipids, sphingosine, sphingolipids
NAD(P)⁺/NAD(P)H; FAD/FADH₂; FMN; Q/QH₂
Coenzyme A, heme (protoporphyrin IX), pyridoxal-5'-phosphate (PLP)
Intermediates of the following metabolic pathways: glycolysis, homolactic and alcoholic fermentation, gluconeogenesis, oxidative phase of the pentose phosphate pathway, Krebs cycle (including the reaction mechanism of pyruvate dehydrogenase), activation and β-oxidation of fatty acids.
The structures of intermediates in pathways marked as “overview” in the syllabus are not required.
Prerequisites
ESSENTIAL. Knowledge of the basic concepts of general chemistry and organic chemistry. In particular, it is necessary to be familiar with: a) the properties of the main functional groups; b) the nucleophilic substitution mechanism and addition reactions; c) the concept of acid, base and pH; d) the properties of buffer solutions.
Books
“Principi di Biochimica” Voet, Voet, Pratt - Zanichelli
Teaching mode
Normally, lectures are given face-to-face.
However, in the event of specific governmental and regional provisions related to the COVID-19 emergency, in some periods the lectures may take place in a mixed mode (face-to-face and remote).
The course will be carried out through theoretical lectures (44 hours) and theoretical exercises (4 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 audiovisual material. This educational model is aimed at providing the theoretical knowledge of Biochemistry.
3) Open discussion of the topics treated in lessons, during which the students take part, which have the purpose yo develop the skills of communication, criticism and judgment.
Theoretical exercises in the classroom:
1) Projection and discussion of videos on protein purification (2 hours in class)
2) Projection and discussion of videos on electrophoresis (2 hours in class)
Exercises are intended to deepen the previously studied theoretical concepts, also through numerical exercises, and to put them into practice.
Frequency
Attendance is not mandatory but it is strongly recommended.
Exam mode
The Biochemistry exam, which takes place at the end of the course, is oral although it implies the writing of chemical structures, graphs and schemes.
It consists of three phases lasting about 10 minutes each. The three phases of the interrogation concern the parts of the program: the biological macromolecules, the biochemical methodologies and the metabolism.
In general, the student's preparation will be assessed on the basis of his ability to describe biochemical processes in a clear and scientifically rigorous manner and to be able to link the various topics, showing that they understood the biochemical logic of living beings. In particular, the student will be required to have the following skills: the knowledge of the structure and function of the main classes of biological macromolecules; the ability to explain the main metabolic pathways in terms of chemical reactions, recognizing and reproducing the structures of the metabolites; the ability to explain the principles and applications of the most common biochemical methodologies. For the purpose of the overall assessment of the student's preparation, the skills of communication, criticism and judgment will also be taken into consideration.
Bibliography
Not expected
Lesson mode
Normally, lectures are given face-to-face.
However, in the event of specific governmental and regional provisions related to the COVID-19 emergency, in some periods the lectures may take place in a mixed mode (face-to-face and remote).
The course will be carried out through theoretical lectures (44 hours) and theoretical exercises (4 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 audiovisual material. This educational model is aimed at providing the theoretical knowledge of Biochemistry.
3) Open discussion of the topics treated in lessons, during which the students take part, which have the purpose yo develop the skills of communication, criticism and judgment.
Theoretical exercises in the classroom:
1) Projection and discussion of videos on protein purification (2 hours in class)
2) Projection and discussion of videos on electrophoresis (2 hours in class)
Exercises are intended to deepen the previously studied theoretical concepts, also through numerical exercises, and to put them into practice.