84898 - General and Molecular Biochemistry

Course Unit Page

Academic Year 2021/2022

Learning outcomes

The aim of the course is to acknowledge the students on the basis of general biochemistry and molecular biology. In particular to know the structure and the function of the biological molecules, the significance and the molecular mechanisms of the principal metabolic paths.

Course contents

Section: Biochemistry 1 (3 ECTS) Prof. Silvana Hrelia

- The molecules of life: properties of biomolecules. Energy and living systems. Covalent and non covalent bonds. Role of weak bonds in biological molecules.

- Amino acids and proteins: Structure and properties of amino acids. Peptide bonds and protein sequence. Secondary structure. Motifs and structural and functional domains in the tertiary structure. Quaternary structure. Protein folding and degradation. Fibrous proteins.

- Physiological activities of proteins: Structure of myoglobin and haemoglobin. The heme group. Oxygen binding and cooperativity. Competitive inhibitors and allosteric ligands. Hemoglobin variants (embryonic, fetal and pathologic mutant forms).

- Enzymes: Classification and general properties of enzymes. Activation energy. Catalytic mechanisms. Cofactors and prosthetic groups.

- Kinetics of enzymatic reactions: Significance of kinetic data and kinetic parameters (Km, Vmax, kcat). The Michaelis-Menten equation. pH and temperature effect on enzyme activity. Enzyme inhibitors. Drugs as enzyme inhibitors. Control of enzyme activity: allosteric control and covalent modifications.

- Lipids and biomembranes: Fatty acids, triacylglycerols, glycerophospholipids, sphingolipids and steroids. Bilayers. Membrane integral and peripheral proteins. Structural organization and basic functions of biomembranes. Fluidity of membranes. The fluid mosaic model and lipid rafts. Transport across cell membranes, kinetics and thermodynamics of transport. Passive diffusion, uniporter catalyzed transport, active transport by ATP-powered pumps, cotransport by simporters and antiporters.

 

Section: Biochemistry 2 (4 ECTS) Prof.Christian Bergamini

 

  1. Signal Transduction
  2. Metabolism: Introduction and definition of metabolic processes (catabolism and anabolism), organization of catabolic metabolism
  3. Glycolysis and its regulation
  4. Utilization of other sugars (galactose, fructose and mannose)
  5. The pentose phosphate pathway. The Warbourg effect
  6. Glycogenolysis and glycogen synthesis and their regulation
  7. Gluconeogenesis and its regulation
  8. The citric acid cycle and its regulation
  9. The electron transport chain and oxidative phosphorylation.
  10. Oxidative degradation of fatty acids: beta-oxidation.
  11. The synthesis of fatty acids and aspects of regulation in relation to energy demands and glucose availability.
  12. The synthesis of cholesterol
  13. The degradation of the amine group of proteins: urea cycle.

Section: Biochemistry 3 (3ECTS)  - Prof. Fiorentini

Carbohydrates: D isomers, cyclization, mutarotation. Structures of glucose, galactose, fructose, ribose, deoxyribose. O-glycosidic bond. Structures of maltose, lactose, cellobiose, and sucrose. Structure and function of starch, glycogen and cellulose. Heteropolysaccharides: heparin and hyaluronic acid.
Nucleotides: structures of nitrogenous bases. Structure and function of nucleotides, triphosphate nucleosides. Anhydride bonds and ester bonds. ATP as a molecule in which chemical energy is conserved. AMPc and GMPc.

General structure of nucleic acids: 5'-3' phosphodiester bond. Basic hydrolysis of RNA. Enzymatic hydrolysis of nucleic acids, restriction endonucleases. DNA: Watson and Crick model, denaturation, supercoils and their significance. Topoisomerase type I and II. RNA: structure, mature forms of mRNA, tRNA, eukaryotic rRNA and their functions.
Genomes: prokaryotic and eukaryotic. Human genome, chromatin structure
DNA replication in E. coli: polymerization reaction. Functions and characteristics of DNA polymerase III. OriC. Mechanism of replication. Functions and characteristics of DNA polymerase I. Proof-reading of DNA polymerase III and I. DNA replication in eukaryotes.
DNA damage in eukaryotes: depurination, deamination. Mutagens, radiation damage. Free radicals and reactive oxygen species (ROS). Fenton and Haber-Weiss reactions. Physiological functions of ROS. DNA repair systems. Mitochondrial DNA.
Transcription in E. Coli: polymerization reaction. Characteristics of RNA polymerase. Mechanism of transcription. Promoters. Alternative sigma subunits. 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, degeneracy, synonymous codons. Recognition of selenocysteine. Silent, sense and nonsense mutations.
Codon/anticodon pairing: mode of pairing, wobbling base hypothesis. tRNA for the AUG codon.
Protein synthesis (translation) in E. coli: prokaryotic ribosomes. Initiation phase, Shine-Dalgarno sequence, elongation phase, peptide bond formation, termination. Post-translational modifications.
Regulation of gene expression in eukaryotes: regulation by activators (steroid or peptide hormones); regulation by non-coding RNAs (lncRNA, miRNA, siRNA) and their mechanism of action, RNA interfering, therapeutic applications; regulation by epigenetic modifications: histone acetylation/deacetylation, DNA methylation and its transmissibility, differences between genotype and phenotype.
Recombinant DNA: construction of a chimeric DNA, cloning vectors, construction of a genomic library and a cDNA library. Modes of insulin production by bacteria.


 



Readings/Bibliography

- J. Berg, J.L. Tymoczko, L. Stryer “Biochimica” settima edizione, Zanichelli, 2012

- D.L. Nelson, M.M. Cox "I principi di Biochimica di Lehninger", VII edizione, Zanichelli, 2018.

- D. Voet, J.G. Voet, C. W. Pratt “Fondamenti di Biochimica” IV edizione, Zanichelli, 2018

- T.M. Devlin “Biochimica con aspetti clinico-farmaceutici”, EdiSES, 2013

- Bassi, Boffi, de Curtis et al. "Biochimica" Edi.Ermes 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 3 teaching modules, of which 3 CFU of Module 1 (general structure of biomolecules and enzymology), 4CFU of Module 2 (metabolic part with related regulation) and 3 CFU of Module 3 (structure and metabolism of nucleic acids). Throughout the duration of the Coronavirus pandemic, the lectures will be held in mixed mode (lecturer in the classroom, students booked through the application "Present", students connected online) or remotely (lecturer and students connected online). The teachers will use Power Point presentations and videos. The course does not include laboratories.

 

Assessment methods

In order to be admitted to the exam, it is necessary to register through the electronic notice board (AlmaEsami), in compliance with the deadlines. Please note that, in order to be admitted to the oral exam of Module 2, it is mandatory to have previously passed the written tests of Modules 1 and 3.
If the student does not pass the oral exam during the period of validity of the written tests, he/she will have to repeat these tests to be admitted to the oral exam. Students who are not able to enroll by the due date must promptly (and in any case before the official closing of the enrollment lists) communicate the problem to the teacher 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.

Module 1

The examination at the end of the course aims to assess the achievement of learning objectives

- to know the structure and function of the main biological macromolecules and the basis of enzymology.

The verification test is a written test on the structure and function of biomolecules consisting of two open-ended questions that if overcome with positive vote will count as the acquisition of knowledge and will contribute for 3/10 to the final vote.

Module 2


The exam is oral. In order to take the exam it is necessary to have passed the  Modules 1 and 3 not more than one calendar year ago and to have passed and recorded the propaedeutic exams of ANIMAL BIOLOGY and ORGANIC CHEMISTRY. The student will be asked to decribe a metabolic pathway (with structures) 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. The final score will be calculated for 4/10 on the grade achieved in Module 2, for 3/10 on the grade achieved in Module 1 and for 3/10 on the grade achieved in Module 3.

Module 3

 

As long as the Coronavirus pandemic persists, the learning verification will be conducted ONLINE, using the Zoom platform. To have access to the written test, you must install Zoom (https://zoom.us/download ) on your PC. It is not possible to use a cell phone or a tablet. The use of a computer is mandatory. This test must be passed to be admitted to the oral test related to Module 2.

The test is organized as follows: 7 multiple-choice questions and 3 open-ended questions and the time allowed for the test is 32 minutes. To pass the test it is necessary to have scored a minimum of 18 points. If passed, the test will be valid for ONE SINGLE YEAR, regardless of how many times the oral test related to Module 2 of Prof. Bergamini will be taken. At the end of the course related to Module 3, students enrolled in the second year (and not those enrolled in subsequent years) can take a written test, formulated in the same way as above and with the same validity.

 

 

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 Silvana Hrelia

See the website of Diana Fiorentini