B2818 - General, Molecular and Metabolic Biochemistry

Learning outcomes

The student acquires basic knowledge of general and molecular biochemistry. In particular, the student is able to: - understand the structure and function of the main molecules of biological interest; - understand the molecular mechanisms underlying metabolic activities and signaling and their regulation, with particular regard to the biochemical basis of drug action, useful for understanding topics covered in subsequent courses; and - understand the biochemical basis of diseases characterized by metabolic alterations.

Course contents

MODULE 2 - Prof. Fiorentini 3 CFUs.

Classification of amino acids. Peptide bond and primary structure of proteins. Secondary structure (alpha-helix, beta structure, beta folding, random coil). Fibrous proteins and globular proteins. Tertiary structure, denaturation, chaperones and misfolding. Quaternary structure.

Structure of myoglobin and hemoglobin, heme structure. Saturation curves and cooperativity. Effect of pH, CO2 and 2,3-bisphosphoglycerate. Fetal hemoglobin and pathological hemoglobins.

Carbohydrates: structures of maltose, lactose, cellobiose and sucrose. Structure and function of starch, glycogen and cellulose. Outline of heteropolysaccharides heparin and hyaluronic acid.

Structure of biological membranes, fluid mosaic model, asymmetry, fluidity and role of cholesterol. Integral and peripheral membrane proteins. Outline of lipid rafts. Movement of molecules across membranes: simple diffusion systems, facilitated diffusion, primary and secondary active transport.

Structure and function of nucleotides, triphosphate nucleosides. ATP as a conserving energy molecule molecule.

General structure of nucleic acids: 5'-3' phosphodiester bond. Basic hydrolysis of RNA. Enzymatic hydrolysis of nucleic acids, restriction endonuclease.

DNA: Watson and Crick model, denaturation, supercoils and their significance. Topoisomerase types I and II.

RNA: structure, mature forms of mRNA, tRNA, eukaryotic rRNAs and their functions.

Human genome, chromatin structure

DNA replication in E. coli: polymerization reaction. Functions and characteristics of DNA polymerases III and I. Mechanism of replication. Proof-reading of DNA polymerases III and I. Outline of DNA replication in eukaryotes.

DNA damage in eukaryotes: purification, deamination. Mutagenic agents, radiation damage. Free radicals and reactive oxygen species (ROS). Fenton and Haber-Weiss reactions. Physiological functions of ROS. Outline of DNA repair systems. Outline of mitochondrial DNA.

Transcription in E. coli: polymerization reaction. Characteristics of RNA polymerase. Mechanism of transcription. Promoters. Alternative sigma subunits. Outline of transcription in eukaryotes. Splicing and significance of alternative splicing. Update of central dogma: retroviruses, reverse transcriptase, cDNA construction.

Aminoacylation: aminoacyl-tRNA synthetase, reaction mechanism, recognition of the correct amino acid and corresponding tRNA.

Genetic codon: definition, description of the complete picture, degeneration, synonymous codons. Silent, sense and nonsense mutations.

Codon/anticodon pairing: mode of pairing, wobbling base hypothesis and wobbling. tRNA for the AUG codon.

Protein synthesis (translation) in E. coli: prokaryotic ribosomes. Initiation phase, Shine-Dalgarno sequence, elongation phase, peptide bond formation, termination. Outline of post-translational modifications.

Regulation of gene expression in eukaryotes: regulation by activators (steroid or peptide hormones); regulation by noncoding RNAs (lncRNA, miRNA, siRNA) and their mechanism of action, interfering RNA, therapeutic applications; regulation by epigenetic modifications: acetylation/deacetylation of histones, DNA methylation and its transmissibility, differences between genotype and phenotype.

Recombinant DNA: construction of chimeric DNA, cloning vectors, construction of genomic library and cDNA library. Modes of insulin production by bacteria.

MODULE 1 - Prof. Bergamini 5 CFUs.

Role of weak interactions in macromolecules. Outline of thermodynamics of biological systems.

Enzymes: Classification of enzymes. Enzyme catalysis. Activation energy. Structure and general properties of enzymes. General mechanisms of catalysis. Cofactors and coenzymes.

Enzyme kinetics: Acquisition and analysis of kinetic data and significance of kinetic parameters (Km, Vmax, Kcat). Michaelis-Menten equation. Effect of pH and temperature on enzyme activity. Irreversible inhibition. Inhibition of enzyme activity: reversible competitive and noncompetitive inhibition. Drugs as inhibitors. Regulation of enzyme activity: allosteric enzymes and cooperativity, positive and negative modulators; reversible and irreversible covalent modifications.

Signal transduction. G-protein-coupled receptors and tyrosine kinase receptors.

Metabolism: Introduction and definition of metabolic processes (catabolism and anabolism), organization of catabolic metabolism

Glycolysis and its regulation

Catabolism of sugars (galactose, fructose and mannose)

The pentose phosphate pathway and its regulation. The Warburg effect

Glycogenolysis and glycogen synthesis and their regulation

Gluconeogenesis and its regulation

The citric acid cycle and its regulation

The electron transport chain and oxidative phosphorylation.

Oxidative degradation of fatty acids: beta-oxidation.

Fatty acid synthesis and aspects of its regulation in relation to energy demands and glucose availability.

Outline of cholesterol synthesis and its functions.

Protein catabolism. Elimination of the amino group of amino acids: urea cycle.

 

Readings/Bibliography

D.L. Nelson, M.M. Cox “Introduzione alla Biochimica di Lehninger” VII edizione, ed. Zanichelli, 2023

D.L. Nelson, M.M. Cox «I principi di Biochimica di Lehninger» VIII edizione, Zanichelli, 2022

Campbell, Farrell, McDougal «Biochimica», V edizione, EdiSES Università, 2019

 

All the suggested book are suitable to cover the programs of the three modules. The study work based on these books must be integrated by the relative professor's IOL material.

Teaching methods

The course consists of two modules for a total of 8 credits, of which 3 CFU for module 2 (structure and function of major macromolecules, structure and metabolism of nucleic acids), 5 CFU for module 1 (Introduction to thermodynamics, introduction to enzymology, metabolic biochemistry and regulation). The lecturers will make use of Power Point presentations and simple educational videos. The teaching does not include laboratories.

Assessment methods

In order to be admitted to the exam, registration via electronic notice board (AlmaEsami) is required, in strict compliance with the deadlines. Please note that in order to be admitted to the oral exam of Module 1 it will be necessary to have previously passed the written test related to Module 2.

If the student fails to pass the oral exam within the validity period of the written test, he/she will have to repeat this test in order to be admitted to the oral exam. Those who fail to register by the scheduled date are required to notify the teacher of the problem promptly (and in any case before the official closing of the registration lists) by e-mail. The teacher will have the faculty to admit them to the test. In order to be fair to the teachers, students who, for any reason, do not intend to attend a call for which they were previously enrolled, must inform the teachers by e-mail.

Please note that for out-of-course students, the call date can be agreed upon by e-mail with the professors.

Module 2

Module 2 knowledge verification is done through a written test. The test contains questions related to all the topics covered in class, referring to the Program published on Virtual.

The test is organized as follows: open-ended questions. A minimum of 18 points must be scored to pass the test. The time allowed for the test is 60 minutes. Results will be visible on AlmaEsami, any "Rejected" grade refers to failure to achieve a sufficiency and consequent NON-admission to the oral exam related to Module 1 by Prof. Bergamini. In this case, it will be necessary to retake the test. If passed, the test will remain VALID FOR ONE SINGLE YEAR, regardless of how many times the oral exam related to Prof. Bergamini's Module 1 is taken. It should also be noted that students who are not admitted to the oral and those who are not satisfied with the grade achieved in the written test can always repeat it and in this case the grade achieved in the last test taken will count. Students not admitted to the oral can write to the teacher asking for explanations related to the correction of their written test.

Module1

The exam is oral. In order to take the exam it is necessary to have passed the Modules 1 not more than one calendar year ago and to have passed and recorded the exams of "Anatomy and Biology (C.I.)" and obtained the frequency signature of the course of "Organic Chemistry". 

 

 

The student will be asked to describe a metabolic pathway and its regulation. In the final evaluation, the Commission will ascertain that the student has achieved the objectives set by the course and will pay particular attention to the ability of the candidate to accurately frame the topic, to have achieved an overall organic vision and the possession of the property of specific language. Knowledge of the structure formulas of the intermediates of the major metabolic pathways is required to pass the exam. The final score will be calculated for 3/8 on the grade achieved in Module 2 and for 5/8 on the grade achieved in Module 1.

 

 

Teaching tools

The textbook recommended by the teacher is the instrument on which the student must achieve his preparation. The remaining didactic material, i.e. the notes taken during the lessons by the student himself, the copy of the Power Point presentations shown during the lessons by the teachers (available on the VIRTUAL platform) and all the other information and detailed information that the teacher considers useful to provide to the students, is not a substitute for the textbook, but constitutes a guide and a basis for the better understanding of the topics to be studied.


The registration to the VIRTUAL platform on which to find a copy of the lessons is done automatically by the Course of Study; if a student does not find his name, he is kindly requested to communicate it to the teacher, who will enroll him manually. The platform also allows direct dialogue teacher/student and the sending of emails to all enrolled students by the teacher, for urgent communications.


The material uploaded by the teachers is in pdf format. As far as possible, the teachers will take care of publishing it in advance of the lessons, but the revision and updating of the lessons could also lead to some delay in publication. In any case, the use of teaching material by students is strictly personal, it is not allowed the disclosure and circulation of printed copies is not authorized.

Office hours

See the website of Christian Bergamini

See the website of Diana Fiorentini