Biochemistry

Educational objectives

General skills

The issues developed in this course concern the physico-chemical properties of biological systems and the spectroscopic and structural techniques, theoretical and experimental, that allow their characterization. Theoretical models and related proofs regarding such complex systems will be treated.

Specific Skills

As regards essential knowledge, the student should acquire skills on physico-chemical properties of biological systems and the experimental and theoretical methodologies more used to investigate them. In this respect, the student should know the main thermodynamic and kinetics processes concerning biological systems, the involved quantities and functions and their macroscopic and microscopic physical meaning. It should be clearly understood the approximations and the hypothesis at the base of the models used. It is expected that the student will show the capacity of choosing formulations and equations suitable to solve quantitative problems and methods proper to investigate the proposed systems (first and second Dublin descriptors).
The capability of analyzing the problems of synthesis and logical coherence will be evaluated as well as the ability to adopt a correct language (third and fourth Dublin descriptors).
Finally, considering that the course belongs to the graduate degree (second cycle), competence on applications of techniques to solve biological relevant problems from a chemical-physical point of view will be appreciated.

Educational objectives

General skills

The purpose of this course is to provide the students with the fundamental intellectual tools required to carry out measurements, analyses and interpretation of enzyme kinetics. At the end of the course, the students will be confident with the elementary concepts of chemical kinetics, will understand the theoretical basis of steady state and rapid equilibrium enzyme kinetics, and will be able to derive the relevant rate equations. They will also be familiar with the practical aspects of enzyme kinetics, such as enzyme assay methods and the use of computer software to analyse kinetics data. The understanding and analytical skills of the students will include enzyme reactions with more than one substrate, enzyme inhibition and activation. Concerning the transient phase of enzyme reactions, students will understand the theoretical basis of rapid kinetics and the main experimental techniques used for their measurement; they will also be able to analyse and interpret rapid kinetics.

Specific skills

At the end of the course the student will acquire

a) knowledge and understanding of:
 theoretical principles of single substrate and multisubstrate steady-state and rapid equilibrium kinetics;
 practical aspects linked to the measurement and analysis of enzyme kinetics, which include the various enzyme assay methods but also the correct determination of reaction velocity from a progress curve, the strategies for determination of kinetic and equilibrium constants using graphical methods and computer software, the determination of active site concentration and the statistical analysis of enzyme kinetics data;
 the effect of pH and temperature on enzyme activity and kinetic parameters;
 the main types of enzyme inhibition and activation, including complex mechanisms deriving from allosteric and non-allosteric interactions with small molecules; students will also know and understand irreversible, mechanism-based inhibition; in this context, students will appreciate how enzymes are regulated in the metabolism and how enzyme inhibition can be used as a means of control of cell metabolism in medicine;
 theoretical principles of pre-steady state kinetics and also the main experimental techniques and instruments used for the measurement of rapid kinetics, including continuous-flow, stopped-flow, laser and relaxation methods.

b) ability to apply knowledge and understanding:
 apply the principles of steady-state and rapid equilibrium kinetics to derive equations describing the behaviour of single substrate and multisubstrate reactions;
 apply these equations to the analysis of kinetic data, using graphical methods and computer software, in order to estimate kinetic and equilibrium parameters;
 apply knowledge on practical aspects of enzyme kinetics to carry out correct experimental measurements and analysis of kinetic data;
 derive rate equations that describe simple and complex activation and inhibition systems, and apply such equations to analyse kinetics data and estimate kinetic and equilibrium constants;
 apply knowledge on the transient phase of enzyme reactions to derive rate equations describing pre-steady state kinetics; apply these equation, using computer software, to estimate kinetic parameters.
 at the end of the course, students will understand how enzyme kinetics data can be used in the study of structure-function relationships of proteins.

c) autonomy of judgment:
 for a specific enzyme kinetics study, choose the most appropriate experimental set up and measurement method;
 judge the goodness of the experimental results in terms of reproducibility and replicability;
 recognize the main features of the system under study, so as to derive or identify in the literature the equations required for data analysis; use these equations to analyse the experimental data in quantitative terms, using appropriate computer software;
 interpret the outcome of kinetic analyses, so as to propose the most appropriate theoretical model describing the behaviour of the experimental system under study.

d) communication skills:
 produce PowerPoint presentations with experimental data, equations and graphs;
 for a specific enzyme kinetics system, explain the analysis of experimental data and their interpretation, present a theoretical model that explains experimental data;
 trace the chosen theoretical model back to structure-function relationships.

e) learning ability:
 autonomously face and solve novel enzyme kinetics problems;
 independently continue and make progress in the study of enzyme kinetics;
 learn independently, or with limited supervision, how to apply the skills acquired in this course to the experimental laboratory work.

Educational objectives

General Skills.

The teaching course will be held with lectures and supplemented by thematic seminars coordinated by the teacher for highly specific topics.
The course aims to develop the following skills:
-Knowledge of the structure and function of the main classes of nanovectors, the limitation on the formulations and of the production of nanovectors;
-Knowledge of the relationship between physical-chemical properties and applications of the nanocarrier;
-Knowledge and understanding of the various methodologies to properly characterize the physical-chemical properties of the nanocarrier;
-Knowledge and understanding of the various active substances used to functionalize the nanocarrier surface to perform active and passive targeting;
-Knowledge and understanding of the most appropriate nanocarrier to select on the basis of the nature of active loaded molecules and the field of application.

Specific skills.

a) knowledge and understanding:
- Knowledge and understanding of the relationship between structure and function of the main classes of nanocarriers and their physical-chemical properties;
- knowledge of the main techniques for their characterization;
- knowledge of the active compounds and their surface functionalization for the targeted delivery by using active or passive strategy;
- knowledge of the limits depending on the biochemical structure of the active ingredient regarding to its field of application underlying the main properties influencing the choice of the nanocarrier;

b) applying knowledge and understanding:
- ability to select and explain the proper formulation of the nanocarrier depending on the nature of the substance and its field of application;
- ability to select appropriate techniques for nanocarrier characterization;

c) making judgments:
- be able to solve delivery problems;
- be able to identify biological and biomedical barriers related to the administration route or the field of application and therefore to select the most appropriate carrier;

d) communication skills:
- be able to illustrate and explain the main nanocarriers with appropriate terms and with logical rigor;
- be able to explain the main methodologies of characterization in general;
- be able to describe targeting strategies and the field of application of the nanocarrier;

e) learning skills:
- acquisition of the fundamentals and cognitive tools to continue independently in the study of nanotechnologies;
- acquisition of the basic knowledge necessary to progress autonomously in other biological and technological disciplines;
- ability to learn quickly and apply nanobiotechnology techniques in various working environments.

Educational objectives

General Skills.

The teaching course will be held with lectures and supplemented by thematic seminars coordinated by the teacher for highly specific topics.
The course aims to develop the following skills:
-Knowledge of the structure and function of the main classes of nanovectors, the limitation on the formulations and of the production of nanovectors;
-Knowledge of the relationship between physical-chemical properties and applications of the nanocarrier;
-Knowledge and understanding of the various methodologies to properly characterize the physical-chemical properties of the nanocarrier;
-Knowledge and understanding of the various active substances used to functionalize the nanocarrier surface to perform active and passive targeting;
-Knowledge and understanding of the most appropriate nanocarrier to select on the basis of the nature of active loaded molecules and the field of application.

Specific skills.

a) knowledge and understanding:
- Knowledge and understanding of the relationship between structure and function of the main classes of nanocarriers and their physical-chemical properties;
- knowledge of the main techniques for their characterization;
- knowledge of the active compounds and their surface functionalization for the targeted delivery by using active or passive strategy;
- knowledge of the limits depending on the biochemical structure of the active ingredient regarding to its field of application underlying the main properties influencing the choice of the nanocarrier;

b) applying knowledge and understanding:
- ability to select and explain the proper formulation of the nanocarrier depending on the nature of the substance and its field of application;
- ability to select appropriate techniques for nanocarrier characterization;

c) making judgments:
- be able to solve delivery problems;
- be able to identify biological and biomedical barriers related to the administration route or the field of application and therefore to select the most appropriate carrier;

d) communication skills:
- be able to illustrate and explain the main nanocarriers with appropriate terms and with logical rigor;
- be able to explain the main methodologies of characterization in general;
- be able to describe targeting strategies and the field of application of the nanocarrier;

e) learning skills:
- acquisition of the fundamentals and cognitive tools to continue independently in the study of nanotechnologies;
- acquisition of the basic knowledge necessary to progress autonomously in other biological and technological disciplines;
- ability to learn quickly and apply nanobiotechnology techniques in various working environments.

Educational objectives

General Skills.

The teaching course will be held with lectures and supplemented by thematic seminars coordinated by the teacher for highly specific topics.
The course aims to develop the following skills:
-Knowledge of the structure and function of the main classes of nanovectors, the limitation on the formulations and of the production of nanovectors;
-Knowledge of the relationship between physical-chemical properties and applications of the nanocarrier;
-Knowledge and understanding of the various methodologies to properly characterize the physical-chemical properties of the nanocarrier;
-Knowledge and understanding of the various active substances used to functionalize the nanocarrier surface to perform active and passive targeting;
-Knowledge and understanding of the most appropriate nanocarrier to select on the basis of the nature of active loaded molecules and the field of application.

Specific skills.

a) knowledge and understanding:
- Knowledge and understanding of the relationship between structure and function of the main classes of nanocarriers and their physical-chemical properties;
- knowledge of the main techniques for their characterization;
- knowledge of the active compounds and their surface functionalization for the targeted delivery by using active or passive strategy;
- knowledge of the limits depending on the biochemical structure of the active ingredient regarding to its field of application underlying the main properties influencing the choice of the nanocarrier;

b) applying knowledge and understanding:
- ability to select and explain the proper formulation of the nanocarrier depending on the nature of the substance and its field of application;
- ability to select appropriate techniques for nanocarrier characterization;

c) making judgments:
- be able to solve delivery problems;
- be able to identify biological and biomedical barriers related to the administration route or the field of application and therefore to select the most appropriate carrier;

d) communication skills:
- be able to illustrate and explain the main nanocarriers with appropriate terms and with logical rigor;
- be able to explain the main methodologies of characterization in general;
- be able to describe targeting strategies and the field of application of the nanocarrier;

e) learning skills:
- acquisition of the fundamentals and cognitive tools to continue independently in the study of nanotechnologies;
- acquisition of the basic knowledge necessary to progress autonomously in other biological and technological disciplines;
- ability to learn quickly and apply nanobiotechnology techniques in various working environments.

Educational objectives

General skills

At the end of the course, the student will have acquired the main basic notions regarding medicinal chemistry by a biochemical approach. In particular, he will know the physical and chemical principles of the action of drugs, the classes of receptors on which the drugs act and the action of the main classes of drugs on their receptors.

Specific skills

a) knowledge and understanding
- knowledge of the main classes of receptors involved in the action of drugs
- knowledge of the chemical structure of drugs

b) applying knowledge and understanding
- explain the mechanism of action of drugs by a biochemical approach
- explain the binding of the drugs on their receptors

c) making judgments
- identify the biochemical mechanisms of the drug action
- suggest the potential action of drugs on different receptors

d) communication skills
- draw the chemical structures of drugs
- describe the interaction of drugs on their receptors by a biochemical approach

e) learning skills
- acquisition of the basics of medicinal chemistry to carry out in-depth study of the subject
- apply the knowledge acquired in medicinal chemistry working conditions

Educational objectives

General skills.

The student will be able to fully describe the execution of a diagnostic test, starting from the phase of collection/preparation of biological materials, to the detection of the main macromolecules (proteins, lipids, carbohydrates) or metabolites of clinical relevance, up to the interpretation of the variations in their levels or their chemical-physical properties in the context of the physiology or pathology of different organs and tissues.

Specific skills.

a) knowledge and understanding:
- theoretical knowledge of the main techniques used for the preparation and analysis of biological samples in biochemical diagnostics;
- knowledge of the biological role of the main markers used in biochemical diagnostics;
- understanding the significance of the variations in the levels and/or in the chemical-physical properties of the main markers used in biochemical diagnostics;

b) applying knowledge and understanding:
- ability to critically evaluate the adequacy and limits of a given experimental procedure to address specific questions in the biochemical diagnostic field;
- ability to evaluate the diagnostic significance of the current and potential new markers in the context of biochemical diagnostics;

c) making judgments:
- ability to critically evaluate the results of the diagnostic tests presented in the course;
- ability to critically analyse the scientific literature in the field of clinical biochemistry;

d) communication skills:
- ability to illustrate and describe the main analytical techniques with scientific rigor and properties of language;
- ability to explain the results of the main diagnostic tests, linking them with the physiology and pathology of the apparatus, organ or tissue under examination;

e) learning skills:
- knowledge of the appropriate terminology used in the field;
- acquisition of the basic knowledge to adequately support working in the biochemical diagnostics field.

Educational objectives

General skills.

At the end of the course, students will acquire the theoretical/practical principles of the most frequently used methodologies in Molecular Diagnostics and will be able to critically evaluate and interpret the experimental procedures and the result of the tests used for the diagnosis of some of the main pathologies. In particular, students will be able to fully describe the execution of a diagnostic test, starting from the phase of collection/preparation of biological materials (such as plasma, serum, urine or tissues or cellular preparations), to the detection of the main macromolecules (proteins, lipids, carbohydrates) or metabolites of clinical relevance, up to the interpretation of the results of the diagnostic study.

Specific skills.

a) knowledge and understanding
- knowledge of the techniques of Molecular Biology and Molecular Genetics used in Molecular Diagnostics, including their theoretical basis;
- knowledge of the fundaments of Molecular Biology and Molecular Genetics needed to interpret the results of molecular diagnostic;

b) applying knowledge and understanding
- ability to critically evaluate the adequacy and limits of the different methodologies of Molecular Diagnostics;
- ability to choose the appropriate molecular methodology to address a specific diagnostic issue;

c) making judgments
- be able to critically evaluate the results of the diagnostic tests presented in the course;
- be able to critically analyse the scientific literature in the field of Molecular Diagnostics;

d) communication skills
- be able to illustrate and describe the main analytical techniques with scientific rigor and property of language;
- be able to explain and interpret the results of the main diagnostic tests, in relation with the pathological issues under examination;

e) learning skills
- knowledge of the correct terminology used in the field;
- acquisition of the basic knowledge needed to work in a Molecular Diagnostic lab.

Educational objectives

General skills.

The student will be able to fully describe the execution of a diagnostic test, starting from the phase of collection/preparation of biological materials, to the detection of the main macromolecules (proteins, lipids, carbohydrates) or metabolites of clinical relevance, up to the interpretation of the variations in their levels or their chemical-physical properties in the context of the physiology or pathology of different organs and tissues.

Specific skills.

a) knowledge and understanding:
- theoretical knowledge of the main techniques used for the preparation and analysis of biological samples in biochemical diagnostics;
- knowledge of the biological role of the main markers used in biochemical diagnostics;
- understanding the significance of the variations in the levels and/or in the chemical-physical properties of the main markers used in biochemical diagnostics;

b) applying knowledge and understanding:
- ability to critically evaluate the adequacy and limits of a given experimental procedure to address specific questions in the biochemical diagnostic field;
- ability to evaluate the diagnostic significance of the current and potential new markers in the context of biochemical diagnostics;

c) making judgments:
- ability to critically evaluate the results of the diagnostic tests presented in the course;
- ability to critically analyse the scientific literature in the field of clinical biochemistry;

d) communication skills:
- ability to illustrate and describe the main analytical techniques with scientific rigor and properties of language;
- ability to explain the results of the main diagnostic tests, linking them with the physiology and pathology of the apparatus, organ or tissue under examination;

e) learning skills:
- knowledge of the appropriate terminology used in the field;
- acquisition of the basic knowledge to adequately support working in the biochemical diagnostics field.

Educational objectives

General skills.

At the end of the course and upon passing the exam, the student will acquire the knowledge and skills in the areas listed below.
In general, the student will be able to:
- describe the main causes of diseases in terms of plant pathology;
- explain the main metabolic pathways underlying the communication between plant and pathogen;
- describe the constitutive and inducible ways of defense of the plant;
- explain the biochemical mechanisms during plant-environment-biome (phytobiome) communication to improve the sustainable strategies for containing plant diseases;
- describe the metagenomic and bioinformatics approach to control and contain the plant diseases exploiting the natural abilities of the agrobiomes;
- describe the mechanisms of action of the main agrochemicals to contain the plant diseases;

Conceptual tools will be provided to carry out laboratory experiences, which will be supported by facilities made available by the University (e.g. Smart Phytotrones). Communication skills will be explored during some lessons, in fact the course provide the use bibliographic resources and to clearly present scientific contents relating to the aspects covered by the program.

Specific skills.

a) knowledge and understanding:
- knowledge and understanding of the plant-pathogen-biome-environment interaction (pathobiome);
- knowledge of phytopathogens;
- knowledge and understanding of the concept of disease and the pathobiome;
- knowledge of the main metabolic pathways underlying plant-pathogen communication.
- knowledge of biostimulants and bio-protectors of crops.
- knowledge of investigation techniques in the study of plant-pathogen relationships (e.g. metagenomics and bioinformatics);
- understanding of the more correct and sustainable use of products for the plant protection with the purpose of protecting human health and environment.

b) applying knowledge and understanding:
- ability to use specific terminology;
- ability to interpret and explain the biological phenomena underlying the plant-pathogen interaction;
- ability to outline the classic and integrated strategies to control the plant diseases;
- ability to use bibliographic resources and software available on the Web to address and interpret specific problems relating to the topics being taught;
- ability to search in the main databases for the metagenomic characterization of complex communities.

c) making judgments:
- be able to identify the biological mechanisms underlying plant-pathogen interactions;
- be able to identify new strategies for protection of the main crops of food interest;
- be able to acquire the ability of critical judgment, through the study of scientific articles on key aspects and through in-depth collective discussions.

d) communication skills:
- be able to describe the metabolic pathways involved during the interaction among plants, organisms and the environment;
- be able to illustrate a scientific work through discussions and seminars;
- be able to illustrate the results of the research and experimentation carried out in the context of the exercises.

e) learning skills:
- learning the specific terminology;
- acquisition of an autonomous and flexible study method, to allow to conduct research and personal insights in the field of scientific research;
- acquisition of skills in the use of bioinformatics tools.

Educational objectives

General skills.
The course is designed to provide an understanding of the principles of food microbiology and food biotechnology (6 credits).
The main focus is a detailed analysis of the quality of raw materials and the biotechnological processes involving the use of microorganisms. The course will cover the ecophysiology and control of food microorganisms.
It will also explore the influence of fermentation processes—whether spontaneous or using selected starter cultures—on the nutritional, functional, technological, and sensory properties of foods and beverages. These topics will be discussed in the context of key agri-food supply chains, including wine, dairy, bakery, fermented meat, and fermented vegetables.
Specific Skills

a) Knowledge and Understanding
Knowledge of the main microbiological aspects related to raw materials used in the agri-food sector, including the criteria for the selection and application of microbial starters, as well as the main biotechnological approaches for producing high-quality foods and beverages.

b) Applying Knowledge and Understanding
Ability to independently identify and apply appropriate biotechnological methods for food processing, hygiene, and safety within various agri-food production contexts.

c) Making Judgments
Ability to evaluate and propose biotechnological strategies aimed at achieving desired quality standards—organoleptic, technological, hygienic, and nutritional—in fermented food products.

d) Communication Skills
Ability to effectively communicate the role and significance of microorganisms, as well as the objectives of biotechnological processes, in the control and transformation of raw materials into food products that meet specific quality requirements.

e) Learning Skills
Ability to independently update and deepen knowledge of food biotechnological processes through the study of scientific literature in the microbiological field, with particular attention to applications in oenology, dairy production, leavened baked goods, fermented meats, and vegetables.

Educational objectives

Specific skills

a) knowledge and understanding:
Knowledge of the structure and functions of the major biomolecules; the digestion, absorption and transport processes; the main metabolic pathways and their regulation and interrelations; the roles of hormones in digestion; the role of macro-and micro-nutrients, nutraceuticals, food supplements, and dietary products.

b) applying knowledge and understanding:
Ability to identify the nutritional potential of the different foods, nutraceuticals, food supplements and to describe the main nutrition deficiencies; Ability to correlate metabolic pathways and hormones functionality to the processes of digestion, absorption and transport of nutrients in blood circulation.

c) making judgments:
Ability to describe and to analyze the metabolic processes involving foods included in diet; identification, through metabolic evidence, of the potential nutritional deficiencies in subjects under unbalanced diet.

d) communication skills:
Ability to describe the biochemical pathways relevant to nutrient metabolism and the main biochemical techniques for the investigation of the nutrient metabolism.

e) learning skills:
Critical reading of scientific articles in nutritional biochemistry.

Educational objectives

After completing the course, learners will be able to:
Run Python programs
Store data in programs
Use built-in functions
Detect syntax errors occurring in programs
Read tabular data
Visualise and statistically analyse tabular data
Plot biological data
Create functions
Repeat actions with loops
Make choices
Determine where errors occurred
Manage errors and exceptions
Make programs readable
Use software that other people have written
Recognize various data formats to represent DNA/RNA sequence data
Independently write Python scripts to
Read in sequence data using Python or BioPython modules
Parse data files
Run external programs
Read input from the command line
Describe a wide range of machine learning techniques
Recognize what machine learning method is most applicable to given data analysis problems
Transform biological data for ML application. In particular, transform sequence data into a machine-readable format for input into a machine learning pipeline
Preprocess Biological Sequence Data for Natural Language Processing
Build a Random Forest model (RF) to classify a set of sequences

Educational objectives

EDUCATIONAL GOALS
The course contributes to the achievement of the training objectives set out in the Manifesto of Studies of the Master Degree in Industrial Chemistry (ARES curriculum: Environment, Resources, Energy, Safety).
In particular, the course aims to provide an overview on the application of chemical, physical, and biotechnological processes in the field of environmental protection, with particular reference to the main processes involved in waste and wastewater treatment, including their valorization, as both secondary resources and for energy purposes.
In this context, the course also intends to provide the key elements of the analysis and description of the aforementioned processes, also based on chemical engineering methods (kinetic analysis, mass and energy balances, thermodynamic relationships), providing specific examples for the cases studied.

Students who have passed the examination will have known and understood (descriptor 1 - acquired knowledge):
- Fundamentals of the main chemical, physical, and biological processes for the treatment of waste and wastewater and for energy and materials recovery
- Methods of quantitative representation of processes and preliminary sizing of the related equipment
- Use of specific techniques for measurement, monitoring, and control of relevance in the studied processes

Students who have passed the examination will be able (descriptor 2 - acquired skills):
- To apply methodologies for the analysis of processes of industrial relevance in the field of treatment and valorization of waste and wastewater and for the production of energy from renewable resources (up to the preliminary design of the main process units)
- To frame the contents learned in the more general context of environmental protection, also with reference to the regulatory framework
- To frame the contents learned in the more general context of development of chemical industry, with particular reference to environmental sustainability.

Along with lectures, the execution of numerical exercises and participation to laboratory activities, with self-employment of written reports on the studied topics, will allow to increase the critical and judgmental skills (descriptor 3) and the ability to communicate what has been learned (descriptor 4)