cod. 1007200

Academic year 2023/24
1° year of course - First semester
- Claudio RIVETTI
Academic discipline
Biologia molecolare (BIO/11)
Discipline del settore biomolecolare
Type of training activity
52 hours
of face-to-face activities
6 credits
hub: PARMA
course unit

Learning objectives

The main goal of the course is to provide students with the tools necessary for a detailed and critique analysis of the structure of proteins and their macromolecular complexes. The first part of the course is dedicated to the understanding of the physical-chemical properties of the amino acids and their interaction within a protein. During the second part of the course, students are challenged with practical exercises on the structural analysis of protein models by means of open source software.

The educational objective of the course is to achieve the necessary knowledge for a critical analysis of the structure of proteins and nucleic acids. By the end of the course students will have acquired the skills necessary to deal with the analysis and experimental study of biological macromolecules. They will learn how to retrive protein and nucleic acid coordinates from the PDB database, recognize the fold and use sofware for a detailed analysis of their structure.

The course is aimed at increasing the ability to critically analyze the structure of proteins, nucleic acids and their interactions.

The course includes significant activity of classroom discussion aimed at developing the ability of students to transfer skills acquired in support of their arguments. In the final exam, students must take an oral presentation on the structure and function of an assigned protein.

The many advancements of scientific research, particularly in the field of molecular biology require a continuous updating of skills. For this reason, the course aims to provide the necessary tools to achieve a wider knowledge and to align skills to the advancement in molecular biology research.


Course unit content

The amino acids
Peptide bond
Secondary structure
Tertiary structure
Quaternary structure
Protein Folding
DNA-protein interaction
Membrane proteins
Fibrose proteins
Methods for the determination of protein structure

Full programme

Physicochemical properties of amino acids

Organization of the genetic code

Chemical reactions involved in protein synthesis

Biosynthesis of selenocysteine and pyrrolysine

Peptide bonding, phi and psi rotation angle, Ramachandran diagram.

Secondary structures: alpha, 3.10 and pi helices, beta sheets, loop regions.

Graphical representations of proteins.

Globular proteins, calcium-binding helix-turn-helix motifs, beta hairpins, beta-alpha-beta motif.

Alpha-helix structures: inter-helix contacts and superstructural organization of alpha-helix proteins, edges and grooves, knots and cavities, four-helix bundle, globin folding, leucine hinges.

Alpha-beta structures: TIM barrel structure, Rossmann folding.

Beta structures: "barrels" formed by antiparallel beta filaments; Greek key motif; "jelly roll" (vitamin A-binding proteins; neuraminidase; gamma-crystallin; immunoglobulins, beta helices and antifreeze proteins TmAFP, Green Fluorescent Protein, GFP chromophore formation reaction.

Quaternary structures

Fibrous proteins: alpha keratins, collagen, interchain bonds.

Post-translational modifications of proteins, maturation and proteolytic processing, the inteins, lipidation, glycosylation, phosphorylation, acetylation, methylation, nonenzymatic modifications, ubiquitination.

Protein folding: conformational flexibility, thermodynamic and kinetic factors affecting folding, Weak non-covalent interactions (electrostatic, non-polar interactions, hydrogen bridges, van der Waals interactions), disulfide bridges, hydrophobic effect, foding mechanisms, protein stability and resilience, isomerization of proline residues, disulfide isomerase, structure and function of GroEL/GroES chaperonins. Prion proteins and pathologies related to protein folding. Protein denaturation and adaptation to extreme conditions. Engineered proteins. Intrinsically unstructured proteins.

Membrane proteins: characteristics of the lipid bilayer, membrane protein architecture and general principles. Transport proteins, porins, the potassium channel, aquaporins, active and passive transporters, Cys-loop ion channels.

DNA-protein interaction: determinants of DNA-protein binding, thermodynamic principles of binding, free energy of interaction, saturation fraction and dissociation constant, specificity, binding cooperativity, direct and indirect DNA recognition, specific and non-specific interactions. DNA recognition motifs: helix-turn-helix, zinc-finger, leucine zippers, the TATA binding protein. Lac repressor, tryptophan repressor, allosteric effectors.

Enzyme-substrate interactions; shape and charge complementarity; binding specificity; thermodynamics of catalysis; why enzymes; classification of enzymes; catalysis strategies: proximity and orientation, bond distortion, transition state stabilization, acid-base catalysis, covalent catalysis, catalysis by metal ions; molecular dynamics and catalysis; enzyme cofactors; enzyme inhibition; examples of enzymes: the serine proteases, cysteine proteases, aspartic acid proteases.

Methodologies for determining the three-dimensional structure of proteins: X-ray diffraction; electron cryomicroscopy (CryoEM).


Amit Kessel & Nir Ben-Tal

Branden C., Tooze J.

PRINCIPI DI BIOCHIMICA (Zanichelli Ed. 2017)
Donald Voet, Judith G Voet, Charlotte W Pratt

Teaching methods

The course will be held in the classroom where the main topics of the program will be presented. Exercises will be carried out in the computer room by using open-source software to analyze the structure and the interactions that characterize biological macromolecules. In addition to the textbooks, students will have access to the slides used in class and scientific articles made available by the teacher.

Assessment methods and criteria

The assessment of learning outcomes is based on a written test and an oral report in which students are asked to describe the structure and function of an assigned protein. The oral report can be sustained after passing the written test. The written test to be held in a maximum time of two hours, consists of six questions designed to assess the degree of learning and critical analysis of the topics covered.

Other information

Class schedule, exams dates, slides and other teaching resources can be found at the url: