84898 - General and Molecular Biochemistry

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

Module 1 - Prof. Bergamini

1) Water as a general solvent of biological molecules: Structure and chemical characteristics
2) Protein structure 1: general structure of an amino acid (a.a.), the properties of the different side chains of the 20 essential a.a., peptide bond, and levels of protein structure.
3) Protein structure 2: primary, secondary, tertiary and quaternary structure. Anfinsen's experiment.
4) Protein Structure 3: the structural features of alpha-keratins, silk fibroin, and triple helix of collagen.
5) Hemoglobin and Myoglobin: Structure and function, cooperative effect, allosteric regulators (pH, CO2, BPG), fetal hemoglobin and sickle cell anemia.
6) Lipids and structure of biological membranes
7) Enzymology: definition of catalysis, chemical mechanisms, thermodynamic and kinetic considerations, Michaelis-Menten kinetics, rate vs. [S] graph, Lineweaver-Burk graph, enzymatic inhibition, conserved catalytic mechanisms, the catalytic triads of proteases.
8) Signal Transduction
9) Metabolism: Introduction and definition of metabolic processes (catabolism and anabolism), organization of catabolic metabolism
10) Glycolysis and its regulation
11) Utilization of other sugars (galactose, fructose and mannose)
12) The pentose phosphate pathway. The Warbourg effect
13) Glycogenolysis and glycogen synthesis and their regulation
14) Gluconeogenesis and its regulation
15) The citric acid cycle and its regulation
16) The electron transport chain and oxidative phosphorylation.
17) Oxidative degradation of fatty acids: beta-oxidation.
18) The synthesis of fatty acids and aspects of regulation in relation to energy demands and glucose availability.
19) The synthesis of cholesterol
20) The degradation of the amine group of proteins: urea cycle.

Module 2 - 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.


Hemostasis: role of platelets, coagulation cascade, activation of coagulation factors, role of vitamin K. Conversion of fibrinogen to fibrin. Oral anticoagulants and genetic defects in hemostasis.


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 both modules. The study work based on these books must be integrated by the relative professor's IOL material.

Teaching methods

The course consists of 2 teaching modules, of which 7 CFU of Module 1 (general structure of biomolecules and metabolic part with related regulation) and 3 CFU of Module 2 (structure and metabolism of nucleic acids). The two modules will proceed in parallel. 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

To attend the exam, it is necessary to enroll through the electronic notice board (AlmaEsami), respecting the deadlines. Two dates will be published: one for the written exam on Module 2 and the other (usually the day after) for the oral exam on Module 1. Please note that in order to be admitted to the oral exam of Module 1 it is mandatory to have previously passed the written test on Module 2. Students can choose whether to attend the written and oral exam in the same call (on the following day) or to attend them separately, since the written exam of Module 2 is valid for one calendar year. During this period, students can attend the oral exam in any available call. If the student does not pass the oral exam during the period of validity of the written test, he/she will have to repeat this test to be admitted to the oral exam. Students who are not able to sign up for the oral exam by the due date must communicate the problem to the teacher via e-mail. The teacher will have the faculty to admit them to the test. Students who, for any reason, do not intend to participate in a call for which they had previously enrolled are required to notify the teachers by e-mail.

Module 1
As long as the Coronavirus pandemic persists, verification of learning will be done ONLINE, via Teams platform. The exam will consist of an oral interview. In order to attend the exam, it is necessary to have passed the written exam related to Module 2 not more than one calendar year ago and to have passed and registered the preparatory exams of ANIMAL BIOLOGY and ORGANIC CHEMISTRY.
The student will be asked two questions: one concerning the structure and functions of the main biomolecules (proteins, lipids, membrane structure, etc.); the second concerning the description (with formulas) of 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, paying 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 2/3 on the grade achieved in Module 1 and 1/3 on the grade achieved in Module 2.

Module 2

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. It is mandatory to use a computer.
Each test contains questions related to all topics covered in class, referring to the Program published on Virtual.

The test is organized as follows: 5 multiple-choice questions (each worth 3 points) that admit MORE than 1 answer (among 5 choices); 2 multiple-choice questions (each worth 1.5 points) that admit ONE answer (among 5 choices); 3 open-ended questions (each worth 4 points), which must be answered concisely.


The score is therefore given by 15 (5x3) + 3 (1.5x2) + 12 (4x3) = 30. The wrong answers are not scored. To pass the test it is necessary to have scored a minimum of 18 points.


The time allowed for the test is 32 minutes. The students will be required to share their screen with the teacher's screen. The written test may be recorded.

The results will be available on AlmaEsami. The judgment "Withdrawn" refers to the failure to reach the sufficiency; in this case, is not possible to sustain the oral exam related to Module 1. In this case, it will be necessary to repeat the test.

If passed, the test will be valid for ONE SINGLE YEAR, regardless of how many times the oral test related to Module 1 of Prof. Bergamini will be taken.
To this end, the dates for enrolment will be published on AlmaEsami: each date includes 3 rounds (9.30; 11; 14.30), each reserved for a maximum of 20 students. For each round, two virtual classrooms with 10 students each will be set up, so that each participating student can be supervised.

 

Please also note that:
- Students not admitted to the oral exam, and those who are not satisfied with the grade achieved in the written test, can always repeat the test (usually the day before the date set for the oral exam, registration on AlmaEsami). In this case, the grade obtained in the last test taken will be considered valid.
- Students who are not admitted to the oral exam can write to the teacher asking for an explanation about the correction of their written assignment; the teacher will send an e-mail containing a detailed explanation of the errors made.
At the end of the course related to Module 2, 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 Diana Fiorentini