THREE-DIMENSIONAL MODELING

Course objectives

General Skills At the end of the course the students will know the main biochemical and biophysical principles applied to investigation techniques for the study of folding, structure/function and interactions of biological macromolecules. Given a specific biological problem, they will be able to identify which of the techniques covered during the course is more suitable to provide the expected information. Finally, students will be able to understand the meaning of the experimental data obtained with the different techniques within a scientific context. The course is divided into three sections: Folding; Structure; Interactions. The three sections aim at achieving the following common specific skills. Specific Skills a) knowledge and understanding: Knowledge and understanding of the structure-function relationships in biological macromolecules; Knowledge and understanding of the physical principle underlying the various techniques; Knowledge of the main components of the instruments used to perform the different techniques; Knowledge of the main fields of application of the techniques studied and their complementarity; Understanding of the data analysis principles of the studied methodologies; b) ability to apply knowledge and understanding: Ability to perform, under the supervision of an expert, some of the techniques object of the laboratory classes; Ability to interpret and understand the data obtained through the techniques covered by the course; c) autonomy of judgment: Being able to autonomously understand the results of a study (article, presentation) that is based on the techniques studied in the course. This skill will be reinforced by the analysis, through flipped classrooms, of recently published scientific works; Ability to select, with respect to a specific biological problem, the most appropriate experimental techniques to tackle the problem; Ability to solve autonomously the principal experimental problems that may arise using the methodologies described in the course; Ability to design an experiment based on one of the techniques object of the laboratory classes; d) communication skills: Be able to describe the meaning and the working principles of the techniques analysed in the course; Knowing how to illustrate the data and results obtained using the studied techniques. This skill will be achieved through flipped classroom and laboratory activities; e) learning ability: Acquisition of the fundamentals and cognitive tools to continue autonomously in the study of one or more of the techniques illustrated in the course; Acquisition of the cognitive tools necessary to be trained in the autonomous use of one or more of the techniques studied in the course, in the field of public or private research; Ability to quickly learn new experimental techniques; Ability to dynamically adapt to the evolution of methodologies and scientific instruments characterising the biotechnology R&D laboratories.

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MARCO D'ABRAMO Lecturers' profile

Program - Frequency - Exams

Course program
Molecular Interactions: Theory and techniques (SAXS, Calorimetry, Fluorescence and CD) For each technique the following topics will be addressed: theory, instrumentation, data collection and data analysis. The course may include laboratory classes - computational and/or experimental - on the above techniques..
Prerequisites
Basic knowledge of thermodynamics, kinetics, protein biochemistry and molecular biology, basic notions of electromagnetic waves and properties of electric fields
Books
Cantor e Schimmel Biophysical Chemistry II Mike Williamson, How proteins work; Garland Science Gale Rhodes, Crystallography Made Crystal Clear Academic Press; 3° edition Mike Williamson - How proteins work; Garland Science James A. Goodrich, Jennifer F. Kugel – Binding and kinetics for molecular biologists; Cold Spring Harbor Laboratory Press, CSH, New York
Teaching mode
Lectures and flipped classroom lessons. Laboratory lessons on selected topics, as indicated above in the program and concerning some parts of the study program
Frequency
In person
Exam mode
The student will be evaluated by an oral exam where the student should discuss the physical-chemical properties of biological systems, the related models, and the experimental methods and techniques used for their investigation (principles of techniques and applications). The capability of analysis, making judgment and communication will be also evaluated. Simple and exemplary systems will be discussed to evaluate the student skills to frame the chemical problem in the correct context and choose the most suitable methodologies of investigation. In addition, the student should be capable of discussing the possible applications of the investigated systems in the most advanced fields of biological interest.
Lesson mode
Lectures and flipped classroom lessons. Laboratory lessons on selected topics, as indicated above in the program and concerning some parts of the study program
  • Academic year2025/2026
  • CourseBiochemistry
  • CurriculumSingle curriculum
  • Year1st year
  • Semester1st semester
  • SSDCHIM/02
  • CFU3