Cells, Molecules and Genes 1

Topic 1. A journey through the cell: from outside to cell compartments.
· Describe the structure of cell membrane and the most important mechanisms of transport across the cell membrane.
· Describe the specialized functions of cell membrane.
· Describe the structure of both rough and smooth endoplasmic reticulum, and know their specific functions.
· Describe the structure of the Golgi apparatus and know its functions.
· Describe the structure of ribosomes and their specific functions.
· Recognize cell membrane, endoplasmic reticulum, Golgi apparatus and ribosomes at the electron microscope level.

Topics 2-3. Vesicle trafficking.Exocytosis and endocytosis. Lysosomes. Peroxisomes. Mitochondria.
· Describe vesicle trafficking and the mechanisms involved in directing vesicles to the different cell compartments.
· Describe the mechanisms of endocytosis.
· Describe the mechanisms of exocytosis.
· Describe the structure of lysosomes and peroxisomes, and their specific functions.
· Recognize lysosomes and peroxisomes at the electron microscope level.
· Describe the structure of mitochondria and their functions.
· Describe mitochondria morphology and localization in relation to cell type and cell function.
· Recognize mitochondria at the electron microscope level.

Topic 4. The cytoskeleton.
· Describe microfilaments with particular attention to their arrangement in apical specializations of epithelial cells, to cell motility and to their role in cell junctions supporting.
· Describe intermediate filaments, with particular attention to their role of stabilizing structures of cell junctions.
· Describe microtubules at the morphological and functional level, with particular attention to their arrangement in apical specializations of epithelial cells.
Clinical drop: epidermolysis bullosa simplex
Clinical drop: primary ciliary dyskinesia

Topic 5. A journey through the cell: from the nucleus to the cell cycle. Introduction to tissues.
· Describe the shape of the nucleus in relation to cell morphology.
· Describe the nucleus and chromatin arrangement.
· Describe the nuclear envelope and the structure of the nuclear pore.
· Describe the nucleolus and its functional role.
· Describe the morphological aspect of the nucleus during mitosis and apoptosis.
· Define the phases of the cell cycle.
· Describe the different cell population according to their pattern of growth.
· Describe the general relationships between cells, tissue, organs and systems.

Topic 6. Special topic: Cell morphology and structure: basic principles in determining cell phenotype.
· Describe epithelial cell phenotype focusing on morphology, cytoskeleton arrangement and motility in carcinoma cells during epithelial-to-mesenchymal transition.

Topics 1-2. The organization of living matter and the structural framework of the cell. Structure and functions of pro- vs. eukaryotic cells. Conservation of developmental programs among different species.
· Define the structural hierarchy of living systems
· Discuss cell organization and the function of distinct compartment
· Explain phylogenetic relationship between species
· Discuss conservation of biological processes
· Discuss principles for organizing whole cells

Topics 3-4. Experimental models in cell biology. Cell models and organisms for the study of biological phenomena.
· Describe different in vitro models used in preclinical studies
· Describe 3D cell cultures and organoids
· Illustrate different model organism in cell biology
· Describe genetically modified organisms as experimental tools
· Animal cloning

Topics 5-6. The stem cell and its relevance for studying pathogenesis of diseases. Definition of stemness. Identification of master regulators of stem cell pluripotency. The induced pluripotent stem cell.
· Describe the biological properties of stem cell
· Define asymmetric division
· Define factors inducing stem cell pluripotency
· Discuss principles of cell therapy

Topics 7-8. Signal transduction. Cell membrane structure. Nature of intercellular communication and receptors. Second messengers.
· Discuss the eukaryotic cell membrane structure
· Explain the function and role of protein kinases in regulating the life of a eukaryotic cell
· Define the nature of intercellular communication
· Define modalities of signal transduction by different types of receptors
· Discus the nature and significance of second messengers

Topic 9. The cell cycle. Cell cycle phases. Regulation of cell cycle by extracellular stimuli. Cell cycle checkpoints. Role and regulation of cyclins.
· Discuss cell cycle phases
· Discuss how extracellular stimuli can regulate cell cycle
· Discuss the significance of cell cycle checkpoints
· Discuss the role of cyclins in regulating cell cycle

Topic 10. Cell death. Differences between necrosis and apoptosis. Milestones in apoptosis research. Roles of apoptosis. Molecular regulation of apoptosis. Caspases. The apoptosome. Extrinsic death pathway.
· Describe developmental, physiological and pathological processes in which apoptosis plays a crucial role
· Define upstream and downstream caspases
· Describe the apoptosome
· Discuss regulator, adaptor and effector molecules in apoptosis
· Discuss apoptosis and neoplastic transformation of the cell

Topic 11. Oncogenes and cancer. Classes of oncogenes. Mechanisms of proto- oncogenes activation. Chromosomal alterations and cancer. Multiple mutations in cancer progression. Tumor suppressor genes
· Discuss molecular mechanisms responsible for altered cell cycle regulation in tumors
· Define classes of oncogenes
· Discuss mechanisms of oncogenesis
· Discuss tumor progression by multiple mutations

Topic 12. Synthesis, folding and protein traffic and degradation. The quality control of proteins within the endoplasmic reticulum (ER) lumen. Folding enzymes and chaperons. The ubiquitin/proteasome system and autophagy
· Illustrate the fate of newly synthesized proteins within the ER lumens
· Discuss the role of folding enzymes and chaperons
· The Unfolded Protein Response (UPR)
· ER associated degradation (ERAD)
· Discuss function the ubiquitin/proteasome system
· Forms of autophagy

Topic 1 Nucleic acids
· Brief introduction to the course and to the relevance of molecular biology in modern medicine.
· The experiments of Griffith, Avery and Harshey demonstrated that DNA is the genetic material.
· The DNA and RNA structures and of their forming nucleotides.
· How to purify DNA/RNA and analyze their concentration and integrity.

Topic 2 Proteins
· Amino acid and protein structure. The importance of protein conformation in health.
· Protein purification and analysis of their concentration and integrity.

Topic 3 Genomes' organization
· Main features of the prokaryotic genome organization and of our organelles.
· The main components of our genome and their discovery through approaches of DNA denaturation and hybridization.
· Several approaches of molecular biology are based on the concept of DNA hybridization and of a "probe".

Topics 4 Main techniques of molecular biology and their medical applications
· Description of the most relevant techniques of molecular biology used in biomedical research and diagnostic. Southern and Northern blot, in situ hybridization, fluorescence hybridization, PCR, real time PCR, microarrays, Sanger sequencing, automated DNA sequencing, pyrosequencing and next generation sequencing.
· Western blots, direct and indirect ELISA, immunofluorescence and immunohistochemistry.

Topic 5 Prokaryotic transcription
Understanding the main concepts of RNA transcription through the prokaryotic mechanism.
· The cycle of RNA transcription in E. coli.
· Isolation and structure of the prokaryotic promoter.
· Transcriptional regulation in prokaryotes and the lactose operon as a paradigm of negative and positive regulation.

Topic 6 Eukaryotic transcription
· Identification of the three RNA polymerases, their general structure and function.
· We will only focus on class II transcription describing the elements composing the class II promoter (core promoter, regulatory elements and enhancer) and how the general factors of class II transcription and RNA polymerase II assemble on a promoter.
· General features of transcriptional factors.

Topic 7 mRNA maturation
· Maturation of transcripts and the splicing process.
· Aberrant splicing in human disorders and splicing therapies.

Topic 8 Chromatin structure
· DNA has to be packed in living organisms; fundamental concepts of DNA topology. DNA topoisomerases and their pharmacological value.
· Discovery of the nucleosomes and the main levels of chromatin condensation.

Topic 9 Epigenetics
· Epigenetics: how does it work and why it is largely used by our cells.
· DNA methylation as one the main epigenetic mechanism: which sequences are methylated in our genome, when do they get methylated and who methylates our DNA. Molecular mechanisms of gene silencing mediated by DNA methylation. Human disorders associated with aberrant DNA methylation and/or reading of its code.
· Chromatin and histone post translational modifications as relevant epigenetic mechanism. The histone code hypothesis and how an aberrant chromatin structure can induce human disorders.
· Non coding RNAs as regulatory mechanisms of gene expression. Relevance of non coding RNAs in medicine.

Topic 10 Protein synthesis
· Structure and decoding of the genetic code.
· Main components of protein synthesis: the ribosomes, the tRNAs, the aminoacyl- tRNA syntehtases.
· Initiation of protein synthesis and the related initiation factors; elongation and termination. Quality controls in protein synthesis.
· Antibiotics might inhibit translation.
· The read through therapy to by pass premature stop codons.

Topic 11 DNA replication and its importance for preserving genome integrity
· Main molecular mechanisms by which DNA is replicated and the genome integrity preserved.
· Few notions on how mutations can be inserted into DNA and on the different mechanisms of DNA repair and their involvement in human disorders.