Ateneo - UPO

Functional Biochemistry
0. Introduction
1. Carbohydrate digestion; aerobic and anaerobic glycolysis.
2. Pyruvate dehydrogenase and the tricarboxylic acid (TCA) cycle.
3. Oxidative phosphorylation and ROS.
4. Pentose phosphate pathway and gluconeogenesis.
5. Glycogen metabolism.
6. Regulation of glucose catabolism and blood glucose levels.
7. Regulation of glycogen metabolism and blood glucose levels.
8. Lipids: digestion, transport and lipoproteins, fatty acid catabolism.
9. Fatty acid catabolism: odd-chain fatty acids, ketone bodies, peroxisomes, and unsaturated fatty acids.
10. Fatty acid and phospholipid biosynthesis; overview of sphingolipids.
11. Cholesterol: synthesis and catabolism to bile acids.
12. Steroid hormones: production and physiological roles.
13. Photosynthesis and the Calvin cycle.
14. Nitrogen assimilation and amino acid biosynthesis; essential amino acids.
15. Protein digestion, blood transport (alanine, glutamine), amino acid degradation (examples including tyrosine), and the urea cycle.
16. Amino acid derivatives: bioactive amines, NO, heme.
17. Nucleotide and deoxynucleotide anabolism and their regulation.
18. Nucleotide catabolism and uric acid.
19. Metabolic integration: fed/fasting cycles.
20. Control of appetite and body mass.

Recombinant Technology Laboratory
Theoretical principles and practical aspects of key recombinant DNA techniques.

David L Nelson Michael M Cox, I principi di biochimica di Lehninger. Eight Italian edition by Edon Melloni 2022
Jeremy M Berg John L Tymoczko Gregory J. Gatto Lubert Stryer, Biochimica. Eight Italian edition 2020
AAVV Biochimica. Edi ERMES La Biochimica di Thomas M. Devlin di D' Andrea - Altieri - Baldanzi - Borriello - Devlin - AAVV 2023
Jeremy Dale, et al. "Dai Geni ai Genomi" - EDISES (third edition)
James D.Watson et al. "DNA Ricombinante" - Zanichelli (second edition)
Terry A. Brown "Biotecnologie Molecolari" - Zanichelli (second edition).

The theoretical lectures provide students with an overview of key metabolic pathways as well as modern biochemical techniques and their applications, with a particular focus on protein study. At the same time, the theoretical module aims to equip students with the tools for a critical reading of scientific literature. The fundamental objective is to acquire knowledge of metabolism sufficient to describe the processes of digestion, absorption, transport, storage, catabolism, interconversion, excretion, and biosynthesis regarding carbohydrates, amino acids and proteins, lipids, nucleotides, and the heme group. Achieving this requires mastering formal terminology (chemical formulas) and using it appropriately to present the knowledge acquired. A further objective is the ability to relate these processes to the organism's various functional states and to the hormonal regulation mechanisms governing key biochemical processes. An advanced objective is to integrate these concepts—understood at the molecular level—with knowledge previously acquired at the cellular, histological, and anatomical levels, thereby establishing a solid foundation for understanding physiology and pathology.
The laboratory component aims to provide the theoretical and practical foundations of the methods and technologies used to study and analyze gene expression. Particular emphasis will be placed on recombinant DNA techniques used to clone, express, and analyze gene products of biomedical and applied interest. To support this, the module requires mandatory attendance at a practical laboratory course.

To grasp the course content and articulate the material learned using appropriate terminology, students are required to have passed the General Chemistry exam, with a specific focus on the properties of elements and chemical compounds.

Students must also be familiar with organic chemistry—specifically the properties of functional groups and the structure of key biological compounds—as well as cell biology and basic genetics, particularly the molecular and cellular mechanisms governing replication, cell growth, and gene expression programs in both prokaryotic and eukaryotic organisms.

It is recommended to have passed Physics, with a particular focus on thermodynamics.

This module comprises lectures with slide presentations, interactive multimedia material (generally on DIR), selected scientific articles, and self-assessment tests. It also includes a mandatory laboratory component.

Students with disabilities, Specific Learning Disorders (SLD), or Special Educational Needs (SEN) may request specific services and tools tailored to their needs
by contacting the Student Career Development and Coordination and Student Services Staff and consulting the dedicated page on the University website:
https://uniupo.it/it/servizi/servizi-studenti-disabili-e-dsa
Once they have established contact with the University staff, students with disabilities, SLD, or SEN may contact the course instructor to discuss the specific arrangements for exams and other teaching-related aspects.

A written test (multiple-choice questions) covering the laboratory component will be administered; participation is restricted to students who have attended the laboratory sessions.
Students who pass this test may then take an oral exam in functional biochemistry (conducted at the board or using paper for formulas and diagrams) to assess their knowledge, command of terminology (including formal language), and ability to place concepts in context.
Final score will be the weighted mean of the two.

Functional Biochemistry
Review of bioenergetics and types of biochemical reactions:
1) Bioenergetics and thermodynamics
2) Chemical logic and common biochemical reactions
3) Phosphoryl group transfers and ATP
4) Biological redox reactions
Glycolysis, gluconeogenesis, and the pentose phosphate pathway:
1) Glycolysis, pathways feeding into glycolysis, and the fate of pyruvate under anaerobic conditions: fermentation.
2) Gluconeogenesis.
3) Glucose oxidation via the pentose phosphate pathway.
3) Coordinate regulation of glycolysis and gluconeogenesis.
Glycogen metabolism in animals; coordinate regulation of glycogen synthesis and breakdown. Maintenance of blood glucose levels.
The citric acid cycle:
1) Production of acetyl-CoA (activated acetate).
2) Reactions of the citric acid cycle.
3) Regulation of the citric acid cycle.
4) The glyoxylate cycle in plants.
Oxidative phosphorylation:
1) Electron flow in mitochondria.
2) ATP synthesis.
3) Regulation of oxidative phosphorylation.
4) Role of mitochondria in thermogenesis, steroid synthesis, and apoptosis.
Fatty acid catabolism: Digestion, mobilization, and transport of fatty acids. Fatty acid oxidation; oxidation of unsaturated and odd-chain fatty acids. Ketone bodies.
Lipid biosynthesis: Fatty acid biosynthesis. Triacylglycerol biosynthesis. Membrane phospholipid biosynthesis. Cholesterol, steroids, and isoprenoids: biosynthesis, regulation, and transport. Amino acid oxidation and urea production: Metabolic fate of amino groups. Nitrogen excretion and the urea cycle. Amino acid degradation pathways.
Nitrogen assimilation and the biosynthesis of amino acids, nucleotides, and related molecules. Special focus on heme metabolism and iron transport.
Photosynthesis and light energy capture: Light absorption and photophosphorylation; the central photochemical event: light-induced electron flow. ATP synthesis coupled to photophosphorylation. C3 and C4 plants. Carbohydrate biosynthesis in plants and bacteria.
Principles of metabolic regulation:
1) Regulation of metabolic pathways. Metabolic control analysis.
2) Hormonal regulation and metabolic integration in mammals.
3) Hormonal mechanisms controlling appetite and body mass.

Recombinant Technologies Laboratory
Concept of cloning. Knowledge of key gene manipulation strategies. Key characteristics of cloning vectors. Recombinant protein expression. Knowledge of key strategies for constructing and maintaining genetically modified organisms. Knowledge of technologies applied to genetic diagnostics. Cloning and genomic library analysis strategies. PCR: principles and applications. Site-directed mutagenesis. Gene transformation methods. Transgene expression in model animals. Introduction to proteomics. Genetic strategies for the phenotypic improvement of organisms of socioeconomic interest. Animal and plant pharming. DNA cloning and analysis in forensics and archaeology.

Be able to:
- describe the main metabolic pathways.
- understand and correctly use the language and terminology typical of biochemistry.
- possess a basic understanding of hormonal and metabolic regulatory systems.
- integrate/contextualize molecular-level phenomena with other levels of biological organization (cellular, histological, anatomical).
- understand key biochemical techniques well enough to read scientific articles.
Acquire:
- the theoretical and practical foundations of methods and technologies used to study and analyze gene expression.
- the main techniques used to clone, express, and analyze gene products of biomedical and applied interest.
- familiarity with the instrumentation and working procedures of a research or analysis laboratory.