Ateneo - UPO

1. The basis of the biological and molecular organization of life 2. The cellular mechanisms of transmission and control of genetic and epigenetic information 3. The flow of information 4. The cellular mechanisms of transmission and control of wild-type and mutated traits 5. Cellular structures: biogenesis, morphology, and functions 6. The cell and the environment, cell signaling, and signal transduction 7. The control of cell proliferation and survival

The Biology course aims to provide students with a solid and integrated foundation in the fundamentals of biology, an essential foundation for understanding the physiological and pathological processes addressed in subsequent courses in the biomedical area.

Knowledge of mathematics, physics, chemistry, and biology is required, consistent with the preparation promoted by educational institutions that organize educational and teaching activities consistent with the National Guidelines for high schools and the Guidelines for technical institutes and vocational institutes.

Teaching methods include lectures, active learning in the classroom, and distance learning. Lectures and classroom activities: - Lectures supported by PowerPoint presentations with graphic illustrations, mind maps, light and electron microscopy photographs, and animated videos of cellular processes.
- Classroom activities with active student participation (representation of cellular processes, instant polls, and exercise solutions). Online activities and materials (Moodle):
- Teaching materials presented in class.
- Video summaries of the topics covered in class.
- Quizzes, forums, and workshops for learning and self-assessment.
- Optional materials for further study.

Support Activities (Tutoring/Students with Disabilities)
• Students can ask questions and find study support through the Moodle teaching forum.
• Students with learning disabilities (e.g., colorblind, visually impaired, hearing impaired, dyslexic, or physically disabled students) are encouraged to contact the instructor so that they can adjust their teaching materials, in-person and online activities, and assessment methods.

The program is consistent with the provisions of MUR (Syllabus_BIOLOGIA) and can be found at the link: https://www.mur.gov.it/it/news/venerdi-19062026/semestre-aperto-aa-2026-2027Teaching Unit 1. Foundations of the Biological and Molecular Organization of Life (0.5 CFU): The tree of life. Living organisms and the Cell Theory. Fundamental properties of living matter. Viruses. General characteristics. Structure of viruses: nucleic acid, capsid, and lipid envelope. Major classes of animal viruses. Lytic and lysogenic cycles of bacteriophages. Replication cycle of animal viruses. Replication cycle of retroviruses. Mechanisms of viral entry into and release from animal cells. The prokaryotic cell. Plasma membrane, cell wall, outer membrane, capsule, fimbriae, pili, and flagella. Gram-positive and Gram-negative bacteria (Gram staining). Eubacteria and Archaea. Horizontal gene transfer in bacteria: transformation, conjugation, and transduction, including their mechanisms and biological significance. The eukaryotic cell. The endomembrane system. Evolution of the nucleus and the endosymbiotic origin of mitochondria. From unicellular organisms to complex multicellular organisms. Structure and function of biological macromolecules. Carbohydrates and sugars. Lipids. Amino acids, peptide bonds, proteins, protein structure, protein domains, and active sites. Enzymes: basic concepts and major enzyme classes (e.g., kinases/phosphatases, ubiquitin ligases/deubiquitinases, acetyltransferases/deacetylases). Major post-translational protein modifications (e.g., phosphorylation, acetylation, glycosylation, and lipidation). Nucleotides and nucleic acids. The Watson and Crick model of DNA and the DNA double helix. RNA structure and functions. Coding and non-coding RNAs. Basic principles of metabolism. Concepts of anabolism and catabolism. Condensation and hydrolysis reactions.Teaching Unit 2. Cellular Mechanisms Governing the Transmission and Regulation of Genetic and Epigenetic Information (0.5 ECTS): The eukaryotic genome. Linear chromosomes in eukaryotic cells. Basic organization of a eukaryotic chromosome. Centromeric and telomeric DNA. Chromatin. Nucleosomes. DNA packaging and histone proteins. Histone H1 and the 30-nm chromatin fiber. Euchromatin and heterochromatin. DNA methylation. Chromatin remodeling. Histone post-translational modifications and epigenetic regulation, with particular emphasis on histone acetylation. Condensin complexes and higher-order chromatin organization. The human genome. Organization and characteristics of genomic sequences. Single-copy sequences. Gene families (e.g., globins and ribosomal RNA genes). Repetitive DNA sequences, tandem repeats (minisatellites and microsatellites), interspersed repetitive elements (LINEs, SINEs, and endogenous retroviruses), and mobile genetic elements.Teaching Unit 3. The Flow of Genetic Information (1.0 CFU): DNA replication in prokaryotes and eukaryotes. The semiconservative model of DNA replication. Replication origins, assembly of the initiation complex, and the replication fork. DNA unwinding: DNA helicases and topoisomerases. Primase and primer synthesis. DNA polymerases and proofreading activity. Leading and lagging strand synthesis. Okazaki fragments. RNA primer removal and DNA ligase. Telomeres and telomerase. Telomeres and replicative senescence. Genes. Definition of a gene. Organization of prokaryotic and eukaryotic genes. Polycistronic and monocistronic genes. Promoters and cis-regulatory elements. Transcription in prokaryotes and its regulation through the lac operon model. Regulation of gene expression in eukaryotes. Transcriptional, post-transcriptional, translational, and post-translational regulation. Transcription in eukaryotes. The three RNA polymerases (RNA polymerases I, II, and III). General transcription factors. The TATA box. Proximal and distal promoters (enhancers and silencers). Sequence-specific transcription factors, exemplified by steroid hormone receptors. Initiation, elongation, and termination of transcription. RNA processing. Messenger RNA maturation: 5′ capping, polyadenylation, splicing and alternative splicing, the spliceosome, and small nuclear RNAs (snRNAs). Ribozymes. RNA editing. Regulation of mRNA stability through deadenylation, decapping, microRNAs (miRNAs), and RNA interference (RNAi). Processing of ribosomal RNA (rRNA) and transfer RNA (tRNA). Protein synthesis. Mechanism of translation. Components of the translational machinery: rRNA, tRNA, and mRNA. Aminoacyl-tRNA synthesis. Ribosome structure and function. The genetic code, codons, and anticodons. Redundancy, degeneracy, non-ambiguity, and universality of the genetic code. Regulatory roles of untranslated regions (UTRs). Initiation, elongation, and termination factors involved in translation.Protein maturation. The importance of correct protein folding. Molecular chaperones. Protein misfolding and its biological consequences. Regulation of protein activity. Protein degradation. Ubiquitin-dependent proteasomal degradation. Ubiquitin-like proteins (UBLs).Teaching Unit 4. Cellular Mechanisms Governing the Transmission and Regulation of Wild-Type and Mutant Traits (0.75 CFU): Genome variation. Nucleotide substitutions, insertions, and deletions. Gene mutations and chromosomal mutations. Expansion of repetitive DNA sequences. General principles of DNA damage repair mechanisms affecting single-stranded and double-stranded DNA. Alleles and inheritance. Homozygosity, heterozygosity, and compound heterozygosity. Dominant and recessive inheritance. Genotype and phenotype. Mendel's laws. Monogenic traits, segregation, and independent assortment. Incomplete dominance and codominance. Multiple alleles (e.g., the ABO blood group system). Pleiotropy. Epistasis and non-Mendelian inheritance patterns. Complete and incomplete genetic linkage. Physical and genetic maps. Environmentally modulated gene expression. Concepts of penetrance and expressivity. Polygenic traits and quantitative inheritance. Genomic imprinting. Human chromosomes and the karyotype. Diploidy and homologous chromosomes. Chromosome banding techniques. Euploidy and alterations of the human karyotype, including numerical abnormalities (aneuploidy and polyploidy) and structural abnormalities (translocations, inversions, deletions, and insertions). Trisomy 21 as an example of chromosomal aneuploidy. Pedigree analysis. Autosomal inheritance (dominant and recessive), X-linked inheritance (dominant and recessive), Y-linked inheritance, and mitochondrial inheritance.Teaching Unit 5. Cellular Structures: Biogenesis, Morphology and Function (1.75 CFU): Biological membranes. Structure and composition of biological membranes. The fluid mosaic model. Biological significance of the glycocalyx. Membrane asymmetry. Transport across the plasma membrane. Osmosis, diffusion, and passive transport. Channel proteins and membrane transporters. Active transport. ATP-driven pumps and ATP-binding cassette (ABC) transporters. Biological basis of the membrane potential and the action potential. Protein sorting. Intracellular compartments and their topological relationships. Protein targeting signals and intracellular protein trafficking. The nucleus. Nuclear envelope. Nucleolus and other nuclear condensates. Nuclear pore complexes (NPCs). Nucleoporins. Nucleocytoplasmic transport. Nuclear localization signals (NLSs) and nuclear export signals (NESs). Functions of importins, exportins, Ran, RanGEF, and RanGAP. Regulation of nuclear import, including steroid hormone receptors, NF-κB, and SREBP1 as representative examples. Nuclear export of RNA molecules. Mitochondria. Structure and functions. The mitochondrial genome and the flow of genetic information within mitochondria. Principles of cellular bioenergetics: glycolysis, cellular respiration (tricarboxylic acid cycle, electron transport chain, oxidative phosphorylation, and ATP synthesis), and overall energy balance. The mitochondrial network and its dynamics: mitochondrial fusion and fission together with their major regulatory proteins. Protein import into mitochondria through the TOM, TIM, SAM, and OXA translocase complexes for targeting proteins to the mitochondrial matrix, outer membrane, inner membrane, and intermembrane space.Peroxisomes. Structure and biosynthetic, catabolic, and detoxifying functions. Protein targeting to peroxisomes. Peroxisomal targeting signals and receptor-mediated import. Peroxins and peroxisome biogenesis. Peroxisome-related disorders, with Zellweger syndrome as a representative example. The secretory pathway. Smooth and rough endoplasmic reticulum, cis-Golgi network, Golgi apparatus, and trans-Golgi network. Protein targeting to the endoplasmic reticulum: signal peptide, signal recognition particle (SRP), SRP receptor, translocon, and signal peptidase. Protein maturation within the endoplasmic reticulum. Protein glycosylation and its role in protein folding through calnexin and calreticulin. Endoplasmic reticulum quality control, with calnexin and immunoglobulins as representative examples. Molecular chaperones during protein synthesis and intracellular trafficking. The unfolded protein response (UPR) and activation of the endoplasmic reticulum-associated degradation (ERAD) pathway. Cystic fibrosis as an example. Constitutive and regulated secretion. Vesicular trafficking. Vesicle formation. Coat proteins and their biological functions. Vesicle tethering, docking, and membrane fusion. Roles of NSF, SNAPs, SNARE proteins, and Rab GTPases. Biological functions of phosphoinositides. Endocytosis. Fluid-phase and receptor-mediated endocytosis. Endocytosis of transferrin, low-density lipoproteins (LDL), and epidermal growth factor (EGF): mechanisms and distinguishing features. Early sorting endosomes, recycling endosomes, late endosomes, multivesicular bodies, and lysosomes. Lysosomal targeting via the mannose-6-phosphate pathway. Lysosomal dysfunction and lysosomal storage disorders. Endocytosis in polarized cells. Transcytosis, exemplified by immunoglobulin transport. Phagocytosis and its biological functions. Autophagy. Macroautophagy, microautophagy, and chaperone-mediated autophagy. Mitophagy as a representative example. Biological consequences of impaired autophagy. The cytoskeleton. Microtubules: structure and functions; nucleation, elongation, and depolymerization; the role of GTP in microtubule dynamics; the centrosome and the γ-tubulin ring complex (γ-TuRC); motor and non-motor microtubule-associated proteins (MAPs); dyneins and kinesins; examples of diseases associated with cytoplasmic dynein dysfunction; cilia and flagella. Actin microfilaments: structure and functions; actin polymerization and the role of ATP and the Arp2/3 complex; actin-binding proteins; myosins; cytoskeletal linker proteins, including dystrophin; sarcomere organization; regulation of the actin cytoskeleton by the Rho family of small GTPases (Rho, Rac, and Cdc42); cell migration, with neutrophil polarization and chemotaxis as representative examples. Intermediate filaments: assembly, structure, and biological functions; keratins and the nuclear lamina; interactions among cytoskeletal systems; connections between the nucleoskeleton and the cytoskeleton.Teaching Unit 6. The Cell and Its Environment: Cell Signalling and Signal Transduction (0.75 CFU): The extracellular matrix (ECM). Structure and biological functions. Extracellular matrix remodeling and degradation. Cell anchorage through integrins. General principles of mechanotransduction and its relationship with the cytoskeleton. Fibronectin as a representative example. Cell-cell communication. Cell recognition and tissue organization. Cadherins and cell adhesion molecules (CAMs). Cell junctions: tight junctions, adherens junctions, desmosomes, hemidesmosomes, and gap junctions. Cell signalling. Contact-dependent, autocrine, paracrine, endocrine, and synaptic signalling. Principles of signal transduction: signalling components and regulatory cascades. Cell-surface receptors and intracellular receptors. Nitric oxide and lipid-soluble hormones as signalling molecules. Ligand-gated ion channels. G protein-coupled receptors (GPCRs). Monomeric and heterotrimeric G proteins in signal transduction. Regulatory proteins: guanine nucleotide exchange factors (GEFs) and GTPase-activating proteins (GAPs). Second messengers and signal amplification. Receptor desensitization, with phototransduction as a representative example. Enzyme-linked receptors, including receptor tyrosine kinases (RTKs) and the Ras–MAP kinase signalling pathway. Oncogenes and signal transduction. Insulin receptor signalling, epidermal growth factor receptor (EGFR) signalling, and phosphoinositide signalling pathways.Teaching Unit 7. Regulation of Cell Proliferation and Survival (0.75 CFU): The cell cycle. Cell cycle phases and checkpoints. Cyclins, cyclin-dependent kinases (CDKs), and their regulation. Commitment to cell-cycle progression and entry into S phase. Role of growth factors. Cyclin D–CDK4/6 complexes. Phosphorylation of the retinoblastoma protein (Rb) and activation of E2F transcription factors. Cyclin-CDK inhibitors. DNA damage responses and activation of p53 leading to DNA repair or apoptosis. Proto-oncogenes, oncogenes, and tumour suppressor genes. Oncogenic viruses.Mitosis. Molecular events underlying mitotic entry. Chromosome condensation. Assembly of the mitotic spindle: astral, kinetochore, and interpolar microtubules. Mitotic motor proteins. Nuclear lamina disassembly and organelle dynamics during mitosis. The NDC80 complex. Chromosome congression and spindle dynamics. Completion of mitosis: the anaphase-promoting complex/cyclosome (APC/C), degradation of cyclins and securin, sister chromatid separation, cytokinesis, and asymmetric cell division. Meiosis. Molecular mechanisms of meiotic division in germ cells and their genetic consequences. Homologous recombination and crossing-over. Comparison between mitosis and meiosis. Mechanisms leading to aneuploidy. Meiosis during human spermatogenesis and oogenesis. The concept of stem cells. Cell death. Necrosis and apoptosis. Intrinsic and extrinsic apoptotic pathways. Initiator and executioner caspases. Mitochondrial outer membrane permeabilization (MOMP), cytochrome c release, and apoptosome assembly. Pro-apoptotic and anti-apoptotic proteins of the BCL-2 family. Death receptors and their downstream signalling pathways.

Knowledge and Understanding Upon completion of the course, students will be able to: • Describe the structure and function of major biological macromolecules and understand the molecular basis of living matter. • Understand cellular organization and compartmentalization, intracellular trafficking, and interactions between cells and the external environment. • Illustrate the molecular and cellular mechanisms that regulate the expression and transmission of genetic and epigenetic information, identifying their implications for hereditary diseases. Illustrate the fundamentals of cellular communication and signal transduction, with particular attention to the control of cell proliferation and death, as well as the processes regulating mitosis and meiosis in germ cells. Ability to apply knowledge and understanding At the end of the course, the student will be able to: • Apply the acquired knowledge to understand normal and pathological cellular processes relevant to the medical field. • Interpret experimental data relating to the structure and function of the cell and its various components, gene regulation, and intracellular and intercellular signaling mechanisms. • Use this knowledge and the acquired methodological approaches for future biomedical studies. Making judgments At the end of the course, the student will be able to: 1. critically evaluate information; 2. form informed opinions; 3. make independent decisions. Communication skills: At the end of the course, the student will be able to: 1. express their information and knowledge clearly and effectively. Learning skills At the end of the course, the student will be able to: to: 1. learn independently and continuously 1. 2. update one's skills and knowledge