The aim of the course is to provide students with:

D1 - Knowledge and learning abilities, and in particular:
- an understanding of the structure and function of biomolecules, with particular emphasis on proteins.
- an understanding of basic aspects of signal tansduction and membrane transport
- knowledge on basic metabolism and its regulation by intra- and extracellular factors

D1 - The capacity to apply thier knowledge and understanding, and in particular:
- knowledge of biochemical methods and of the instruments used to isolate and characterize biomoleculees (cell lysis, electrophoresis, chromatographic methods, spectroscopic and spectrometric techniques), and to know when to use them, also in other contexts.
-an understanding the functional mechanisms of enzime activity and regulation as well as aspects of enzyme kinetics, and to apply them to obtain data such as maximum velocities, binding constants and inhibition contstants.

D3 - Autonomy of judgement: the capacity to use the aquired notions to evaluate and understand new and more cmplex aspects of biochemistry, also integrating them with notions aquired in other courses.

D4 - Comunication skills: the capacity to ask and answer questions on essential aspects of biochemistry, succinctly and effectively, during the course, and if required in the thesis internship, or during subsequent PhD studies or in the workplace.

D5 - Learning skills: the capacity to apply the acquired understanding to aquire new knowledge, from appropriate appropriate tools such as text books and bibliographic sources, if required during the thesis internship, subsequent doctoral studies or in the workplace.

This course requires a background in general, organic and physical chemistry, and basic biology

The previous courses in general organic and physical chemistry as well as physics are very useful for this course.

Definition of biochemistry: basic concepts and molecular interactions. Presentation of biologically relevant molecules and macromolecules and their context (amino acids, sugars, coenzymes, etc.).

Structure, organization, and characterization of proteins. Introduction to the concept of the relationship between structure and function. Methods for analyzing and purifying proteins from biological samples. Biological roles of proteins: immunoglobulins (with detailed methodologies) and enzymes. Characterization of enzymes, examples of reactivity, kinetics, inhibition, and regulation (allosteric and non-allosteric).

Biological membranes. Structure and function, membrane proteins, transport systems, and signaling with examples. Mechanisms and examples of signal transduction.

Introduction to metabolism. Glycolysis, Krebs cycle, gluconeogenesis, and glycogen metabolism (reactions, stoichiometry, regulation and integration). Cellular respiration, oxidative phosphorylation, and ATP synthesis. Fatty acid metabolism: synthesis and degradation.

Lehninger principles of Biochemistry, Nelson e Cox, 7th Ed. Freeman NY

or

Biochemistry Berg, Tymoczko, e Stayer, 7th ed. Freeman

INTRODUCTION TO THE COURSE – Definition biochemistry/chemical biology, hints on abiogenesis, brief review of cellular architecture and systems and their dimensions. structure-function relationships.

BIOLOGICALLY RELEVANT MOLECULES; amino acids, nucleic acids, sugars, lipids; ATP and other NTP, NAD/NADH, FAD/FADH, and coenzyme A as stoichiometric enzymes.

REVERSIBLE AND IRREVERSIBLE INTERACTIONS, covalent bonds of biological relevance, H-bonds, electrostatic bonds, VdW interactions, hydrophobic interactions and solvent mediated interactions.

STRUCTURE AND CHARACTERIZATION OF PROTEINS

- Structural hierarchies; peptide chain conformation; primary structure; secondary structure (the alpha-helix, beta-sheet, random coil, turns); tertiary and quaternary structures; intermediate levels of structuring and supramolecular structures.

- Folding of proteins: folding models, role of chaperonines and isomerases

- Computer exercises in moleuclar visualization of proteins

PREPARATION, PURIFICATION & ANALYSIS OF PROTEINS & PEPTIDES
Extraction, purification & characterization techniques; gel electrophoresis, chromatographic methods (supports, methods & techniques), peptide quantification and analysis; mass spectrometry; circular dichroism; X-ray crystallography and NMR.

BIOLOGICAL ROLES OF PROTEINS
- Proteins of the immune system: immunoglobulines – biogenesis, structure and function; MHC I e II receptors, structure/function and their role in the immune response; polyclonal and monoclonal antibodies as tools, examples of immunochemical techniques (Western blot, ELISA).

- Enzymes and enzymatic reactions: General architecture and characteristics of enzymes and their classification; catalytic strategies (clycosdase, RNAse, proteases (serine, cisteine, aspartic & metallo); regulatory strategies (allosteric control and mechanisms, inhibition, reversible and irreversible covalent modification, genetic control), enzyme chains and cascades and role in digwestion and coagulation; hemoglobin and the cooperative binding of oxygen as an example of an allosteric process; Michaelis-Menten kinetics and determination of Km and Vmax; vitamins, catalytic coenzymes and thier roles; enzyme inhibition and effect on kinetics, enzyme inhibitors as drugs, (inhibitors of HIV protease).

BIOLOGICAL MEMBRANES AND MEMBRANE PROTEINS
- Phospholipids, glycolipids, membrane proteins & glycoprotein and structural characteristics of biological membranes;
- Active and passive transmembrane transport systems (membrane ion pumps, translocators & ion channels) membrane receptors and signal transduction (hormones, first and second messengers, G-protein associated receptors, tyrosine kinase receptors).

METABOLISM
Introduction to catabolism & anabolism; glycolisis; Krebs cycle; gluconeogenesis; synthesis & degradation of glycogen (reactions, regulation and stoichiometry), cellular respiration (mitochondrial electrons transport chain, chemiosmotic coupling, oxidative phosphorylation, ATP synthyesis, P/O number and ATP production from glucose degradation).

Breif overview of fatty acid metabolism (synthesis and degradation).

- Lectures with powerpoint presentation

- Experimental technique modules

- Lectures and relaevant animations available on moodle.

The exam consists of a single written test with both multiple choice and open questions. According to the desire of most of the student, and in agreement with the teacher, the exam can be divided in two lerning progress checks. The objective of the exam is to verify the understanding of the topics covered and the level of achievement of the training objectives. There are no negative marks for incorrect questions and partial marks are expected for partially correct questions. It is asked to design the correct structure of small biomolecules (amino acids, nucleotides peptides and metabolic intermediates) and to be able to identify the structures provided with more complex biomolecules (including phospholipids, signal molecules, coenzymes and prosthetic groups). Other questions may concern the structure and / or function of proteins, mechanisms of enzymatic catalysis, structure and / or transport of membranes, signal transduction or description, different aspects and regulation of the main metabolic pathways considered in the course. Short application exercises in enzyme kinetics are also possible.

The course will not cover topics related to the Goals of the 2030 Agenda for Sustainable Development.