Ateneo - UPO

- Introduction to molecular biology
- Epigenetics and molecular biology: chromatin structure and regulation
- Regulation of gene expression: transcription
- mRNA processing and post-transcriptional regulation
- microRNAs and Short-interferingRNAs
- DNA repair
- DNA replication
- Cell cycle regulation
- Cell response to stress
- Apoptosis
- Genetic manipulations in mice

- Alberts et al. “Molecular biology of the Cell” VI E
- Watson et al. "Molecular biology of the gene" VII E
- Allison et al. "Fondamenti di biologia molecolare." (ed. Zanichelli)
- Lewin “Genes X”

Provide basic knowledge of molecular biology with a focus for eukaryotic organisms and with particular reference to bio-medical applications, their research. perspectives and the understanding of the major cellular biomolecular processes.

General knowledge on cellular biology.

PowerPoint presentations of classes and articles provided by the lecturer.

No additional information.

Multiple-choice written exam.

Outline
- Introduction to molecular biology. DNA structure, role of DNA as genetic material.
- Genomics, complexity and gene regulation.
- Comparative genomics. Homologous, paralogous and orthologous genes.
- Gene Families (e.g. globin, tubulin); evolution and gene duplication.

Molecular basis of epigenetics: chromatin structure and regulation.
- Structure of nucleosomes and chromatin organization.
- Histones and their modifications (acetylation, methylation).
- Mechanisms of histone remodeling and chromatin modifications and their role in the regulation of gene expression. Bromodomains and chromodomains. Role and examples of histone modifier enzymes: histone acetyl transferase (HAT), histone deacetylase, hystone demethylases. Histone remodeling complexes.
- Insulators
- DNA metilation: biological significance, DNA metil-transferase, the role of DNA methylation in regulating gene expression.

Gene expression regulation: transcription.
- differences between transcription in prokaryotes and eukaryotes Transcription and gene expression regulation in eukaryotes: RNA polymerase II, promoter structure, basal transcription factors, Pol II and formation of the initiation complex. The role of the transcription initiation complex.
- Recognition of transcription start sites: TATA box the transcription initiation complexes.
- Transcription regulatory sequences and transcription factors (modular and dimeric organization of transcription factors).
- Interactions between transcription factors and chromatin and remodeling complexes.
- Mechanisms for transcription repression
- Regulatory transcription activator strategies. Examples (NF-kB)
- The main four structural classes of transcription factors: helix-loop-helix, helix-turn-helix (Myc / MAx / Mad), leucine zipper (Jun-Fos, AP1), zinc fingers (steroid hormone receptors).

For each class: structural elements and interaction mechanisms with DNA; functional regulation; functions and regulated genes.

RNA processing and post-transcriptional control
- Meaning of capping and poly-adenylation of transcripts. Capping mechanisms polyadenylation and termination of mRNA.
- The meaning of splicing.
- Spliceosome and molecular mechanisms of splicing. Alternative splicing.
- Splicing site recognition elements: ESE / ISE and ESS / ISS sequences. The role of SR proteins (containing RRS domains) and hRNPs proteins in splicing regulation.
- Examples of pathologies caused by mutations affecting splicing.
- mRNA editing mechanisms.
- Regulation of mRNA transport and localization.
- RNA stability (the IRE sequences for the control of stability and translation for mRNAs involved in the Transferrin and Ferritin Receptor).
- MicroRNA: genomic structure, transcription and processing, the Dicer complex.
- RISC complex, microRNA-mediated mechanisms for regulating gene expression (mRNA stability and translation regulation). Combinatorial nature of the interactions between microRNA and target genes. Examples.
- Impact of microRNA discovery in understanding gene functions. Involvement in tumors. Clinical perspectives.
- Short-interfering RNAs; basic research usage and clinical implications. DNA Repair Systems
- DNA damage repair by base excision, repair of DNA replication errors, repair of DNA breaks on both filaments. DNA Replication
- replication mechanism in eukaryotes. Telomeres and telomeres replication.

Cell Cycle Regulation
- General principles of cell cycle control.
- Role of cyclin / Cdk complexes in cell cycle progression.
- Molecular mechanisms of Cdk regulation: interaction with cyclins, activating phosphorylation and inhibiion, interaction with inhibitory proteins (p21, p16, p27 etc.). Mechanisms of regulation of cyclines: transcription, ubiquitination / degradation.
- The role of the various cyclin / cdk complexes in the progression of the different phases of the cycle and the concept of "Checkpoint".
- Regulation of cyclin / cdk complexes in G1 and S phase: activation of Jun / Fos and Myc and of Myc target genes; regulation of E2F1 by Cyclin D / Cdk4, Rb and cyclin E / Cdk2;

Regulation of the cell cycle by tumor suppressors: the p21 family, p16, p27. The regulatory protein p53. Cellular response to stress
- The response to DNA damage: transducers and effector complexes: Atm, ChK1 / 2, Cdc25 and p53 in the signal transduction cascade activated by DNA damage.
- p53: structure, regulation (from Mdm2, Arf and phosphorylation via Atm / Chk) and function in response DNA damage, cellular senescence, and hypoxia response. Role and mechanisms through p53 promotes cell cycle arrest and apoptosis. Meaning of p53 mutations in tumors.
- Cell transformation, general concepts for oncogenesis. Oncogenes and Proto-Oncogenes, fefinition and function. Mechanisms of activation of oncogenes (gain of function). Some examples of oncogenes (tyrosine kinases receptors, cytoplasmic kinase tyrosine, src, bcr-abl, RAS). Cancer suppressors (loss of function); loss of heterozygosity. Definition of caretaker and gatekeeper. Rb; cell cycle inhibitors; p53.
- The role of apoptosis in cellular homeostasis.
- Extrinsic way for apoptosis activation: pro-apoptotic receptors, death domain (DD) and death effector domain (DED) and the transduction of the apoptotic signal up to the activation of caspases regulators (caspase 8).
- Caspase activation mechanism (caspase 3) and the role of their substrates in determining apoptosis (shape change, fragmentation of DNA, phosphoididylserine) and recognition of cells with phagocytic activity.

Intrinsic way for apoptosis activation: central role of regulation of permeability of external mitochondrial membrane in determining the release of cytochrome C, Smac / Diablo and other proteins which regulate apoptosis. Activation of caspases 9 by cytochrome c. Role for the IAP proteins (caspase inhibitors) in apoptosis regulation.
- Different regulatory mechanisms for the 3 major caspase families (caspases 8, 9 and 3).
- External mitochondrial membrane pore formation: pro-apoptotic proteins Bcl2, proteins Bcl2 and anti-apoptotic one. Functional Meaningof Domains BH1, BH2e BH3.
- Necrosis: distinctive features from apoptosis Genetic Manipulations in the Mouse
- Standard transgenesis, gene targeting, Cre-Lox systems (constituent vs inducible systems). Examples of mice transgenic or knock-out genes for the study of pathologies (Alzheimer's disease, p53 - / -).

The student must know the molecular and cellular mechanisms that regulate replication, cell growth and gene expression programs in eukaryotic organisms with some parallels in prokaryotic organisms. Must be able to independently read and understand research articles in the field of molecular biology, with references to biomedical applications, in particular relating to cancer. Finally, the student must be able to pass a written molecular biology exam with multiple choice questions.