Ateneo - UPO

Reccomanded:
-Jeremy M Berg John L Tymoczko Lubert Stryer. Biochimica. Zanichelli 2012
- David L Nelson Michael M Cox. Principi di biochimica di Lehninger. Zanichelli 2018
- Donald Voet Judith G Voet Charlotte W Pratt. Fondamenti di biochimica. Zanichelli 2017

In addition:
- Bruce Alberts , Alexander Johnson , Julian Lewis , David Morgan , Martin Raff , Keith Roberts , Peter Walter. Biologia molecolare della cellula. Zanichelli 2016
- Metodologie biochimiche Espressione, purificazione e caratterizzazione delle proteine, Seconda edizione, Zanichelli. A cura di Maria Carmela Bonaccorsi Di Patti, Roberto Contestabile, Martino Luigi Di Salvo
- Metodologie biochimiche e biomolecolari, Strumenti e tecniche per il laboratorio del nuovo millennio, Zanichelli Mauro Maccarrone
- PRINCIPI DI METODOLOGIA BIOCHIMICA di C. De Marco, C. Cini – Ed. Piccin

To teach the student the basis for a molecular approach to physiology and pathology, through the definition of the structure-function relationship of biological macromolecules, with particular attention to proteins.
The student must be able to describe the structure of biological matter, knowing how to recognize the role of the structure on the function of macromolecules. They will also have to master the main mechanisms of action of enzymes and achieve adequate knowledge of signal transduction mechanisms
On this basis, the student will be able to acquire the knowledge of metabolism and the ability to describe its main processes.
A further objective is the ability to relate these processes to the different functional states of the body together with the hormonal regulation mechanisms of the main biochemical processes.
Advanced objective is the integration of these notions at the molecular level with what was previously learned at the cellular, histological and anatomical level.
Theoretical lessons provide the student with an overview of modern biochemical techniques and their applications and the tools for a critical reading of the literature.
The exercises aim at acquiring the practical skills required for the use of basic biochemical techniques and for a successful thesis internship.

In order to understand the contents of the course and to be able to express what has been learned in an appropriate language, it is required to pass the exams of:
- general chemistry, with particular attention to the properties of the elements and chemical compounds
- organic chemistry with particular attention to the properties of the functional groups and to the structure of the main biological compounds.
- "safety in chemical and biological laboratories" course.
It is suggested to overcome:
- physics with particular attention to thermodynamics.
- Basic knowledge of cell biology.

The course includes lectures with slide projection + interactive multimedia material such as quiz (generally on DIR) + some scientific articles.
To prepare for the exam, students must use the textbooks and recommended readings to supplement the material provided by the teacher (pdf copy of the slides projected in class and any handouts that explore the topics covered during the course).
The laboratory module (compulsory attendance) includes:
- computer simulations of the main bioinformatics techniques and exercises
- exercises in chemical-biological didactic laboratories.

A pdf copy of the projected slides, the in-depth material and all the information regarding the course and examination methods will be made available on the DIR (https://www.dir.uniupo.it/).
At the end of the exercises the student will present a laboratory notebook which together with the performance in the laboratory will form the basis for the subsequent evaluation.

The exam consists of a structural biochemistry text consisting of 50 questions divided into: multiple choice quiz, true / false, structure recognition
molecular, numerical problems (sufficient 27/50 questions). This exam allows to evaluate the knowledge (theoretical questions), the skills and the ability to apply the knowledge learned (exercises), the critical sense, the ability to understand the text.
After the attendance of the laboratory module, the oral exam of functional biochemistry takes place (on the blackboard or with a sheet for formulas and diagrams) to evaluate in addition to the knowledge possessed, the properties of language, also formal and the ability to contextualize. At the same time, the laboratory notebook and the techniques described in class are discussed.

1.Biological macromolecules. Chemical bonds and interactions between molecules in the chemistry of life: carbohydrates, lipids and membranes, nucleic acids RNA and DNA, amino acids and proteins.
The amino acid sequence; secondary structures; tertiary structure; supersecondary structures, structural motifs and functional domains; quaternary structure: fibrous proteins and globular proteins.
2.Enzymes and enzymatic kinetics. The laws of thermodynamics in biological reactions.
Enzymes, coenzymes, prosthetic groups: general mechanisms of action and catalysis. Enzymatic kinetics and fundamental kinetic parameters.
Competitive, mixed and incompetitive inhibition.
General mechanisms of regulation of enzymes: covalent and non-covalent
3. Structure-localization-function relationship of biological macromolecules. Organization of cellular and subcellular membranes, the fluid mosaic model, the "lipid rafts".
Modifications of proteins and signals for localization.
Proteins that bind O2: heme group, myoglobin and hemoglobin.
Thalassemia, hemoglobinopathies and meteglobinemias.
Proteins with recognition and defense functions: immunoglobulins.
Contractile structural unit: the muscle fiber, biochemical mechanism of contraction.
Proteins of the cytoskeleton, actin, tubulin and molecular motors.
The intermediate filaments
4. Transport of molecules across membranes: biochemistry of vesicular trafficking, transporters and channels.
Ion pumps, co-transport and antiport systems.
5.Glycolysis, gluconeogenesis and the pentose phosphate pathway:
6.The metabolism of glycogen in animals. Maintenance of blood sugar.
7. The citric acid cycle. Oxidative phosphorylation.
8. Digestion, transport and catabolism of fatty acids. The ketone bodies.
9.Biosynthesis of lipids: fatty acids, triacylglycerols, membrane phospholipids, cholesterol.
10.Degradation of amino acids and urea production.
11. Organization of nitrogen and biosynthesis of amino acids, nucleotides and related molecules.
12. Photosynthesis and C3 and C4 carbon organization.
13. Principles of metabolic and hormonal regulation applied to metabolic pathways. Integration of metabolism in mammals.
14.The measure in the biological field.
15.Spectrophotometry.
16. Radioisotopes in the laboratory.
17 Chromatography.
18.Electrophoresis.
19.Characterization of proteins.
20 Antibodies in biotechnology.
21.Enzymes in diagnostics and research.

To be able to:
- identify biological macromolecules,
- grasp the interconnections between macromolecular structures, function and regulation
- acquire autonomy of judgment in the evaluation of biochemical problems relating to the structure and functioning of biomolecules inside the cell and in the extracellular environment.
- understand and use correctly the language and formulation typical of biochemistry
- integrate / contextualize the phenomena at the molecular level with the other levels of organization of the living (cellular / histological / anatomical)

Know:
- the mechanisms of enzyme activity and knowing how to solve simple problems related to enzymatic kinetics.
- the bases of signal transduction and of the mechanisms of transport and cellular mobility.

To describe:
- the main metabolic pathways.
- the main biochemical techniques at a sufficient level for reading scientific articles.

The exercises allow you to move fruitfully in the laboratory also in view of the degree internship. For this purpose, the practice in compiling the laboratory notebook is important.

Introduction
Chemical bonds and interactions between molecules in the chemistry of life

Structural Biochemistry
Structure, classification and function of biological macromolecules.
Simple and complex glycides; lipids and structure of biological membranes.
Nucleic acids and general mechanisms of information transmission.
Amino acids and proteins: structures and folding.
Co and post-translational modifications of proteins and signals for localization.
Enzymes and enzymatic kinetics.
Extracellular transport proteins, proteins that bind oxygen, iron and copper. Contractile structural unit: organization
morphological and molecular.
Cytoskeleton proteins
Extracellular matrix proteins.
Transport of molecules: biochemistry of vesicular traffic, transport of molecules across membranes.
Transmission of regulatory signals from outside to inside the cell: fundamental mechanisms of signal transduction. The main signaling routes in the
multicellular organisms
Laboratory
The measure in the biological field.
Sample preparation.
Spectrophotometry.
Radioisotopes in the biomedical laboratory.
Chromatography.
Electrophoresis.
Characterization of proteins.
Antibodies in biotechnology.
Enzymes in diagnostics and research.
Binding and association assays.

Functional Biochemistry
1. Carbohydrate digestion with aerobic and anaerobic glycolysis.
2. Pyruvate dehydrogenase and cycle of tricarboxylic acids.
3. Oxidative phosphorylation and ROS.
4. Pentose phosphates + gluconeogenesis.
5. Glycogen metabolism.
6. Regulation of glucose and glycemic catabolism.
7. Glycogen and blood sugar regulation.
8. Lipids: digestion, transposed and lipoproteins, fatty acid catabolism.
9. Catabolism of odd C fatty acids, peroxisome ketone bodies and unsaturated fatty acids.
10. Biosynthesis of fatty acids and phospholipids with hints of sphingolipids.
11. Cholesterol: synthesis and catabolism to bile acids.
12. Steroid hormones, production and physiological roles.
13. Photosynthesis and Calvin cycle.
14. Nitrogen organization and amino acid biosynthesis, essential amino acids.
15. Protein digestion, transport in the blood (alanine, glutamine), degradation of amino acids for example (tyrosine), urea cycle.
16. Amino acid derivatives: bioactive amines, NO, heme.
17. Nucleotide and deoxynucleotide anabolism with regulation.
18. Nucleotide catabolism and uric acid.
19. Nutrition / fasting cycle metabolism integration.
20. Appetite and body mass control.