Ateneo - UPO

The first part of the course introduces the students to the fundamental discoveries in Molecular Biology, the main areas of application, the structure of nucleic acids and genomes organisation. The following lectures will cover the molecular details of genomes replication and maintenance, putting a particular emphasis on the repair of genetic material. The description of mechanisms underlying the expression of the genetic information will follow: transcription and transcription regulation, the processing of different classes of RNA, protein synthesis and control, post-translational modifications of proteins, protein sorting, and basic concepts of cell signalling, focusing on eukaryotic systems. The final part of the course will describe advanced approaches and techniques that are currently adopted to study the molecular biology of the cell.

Nancy Craig et al. Oxford University Press, 2021. Molecular Biology: Principles of Genome Function Further readings and audio/video material will be suggested by the Lecturer. The presentations used during the lessons will be made available to the students at the end of each course macro-section and must be considered a guide for studying the corresponding topics in the recommended textbook and as a starting point for further individual study.

The "Molecular Biology" course aims to provide the student with an up-to-date view of a topic that, perhaps more than others, represents as an area of integration of knowledge in the biology field, with deep medical and biotechnological implications. By the end of the course the student will have achieved an integrated and detailed knowledge of the molecular mechanisms that are responsible for the proper flow and expression of the genetic information in biological systems, under physiological and pathological conditions.

An adequate knowledge of basic concepts in cell biology and general biochemistry is required.
Upper-intermediate mastery of English (B2-level).

Standard lessons.
Further non-mandatory studying activities will be planned, to be carried out in team and evaluated on a "peer-to-peer" basis.

Students with physical disabilities, Learning Disabilities or Special Education Needs can request specific services and tools via the Staff Sviluppo e Coordinamento Carriere e Servizi alle Studentesse e agli Studenti, consulting the University webpage: https://www.uniupo.it/en/services/services-students-physical-or-learning-disabilities

Students with disabilities, learning disabilities or special education needs, once they have contacted the University Staff, can refer to the tutor in charge of the course to define the examination modalities, concerning academic aspects.

Written test. The first part consists of 18 questions, each containing 3 statements that must be judged "true" or "false"; the choice of the option "false" should be briefly explained (3 correct answers to the 3 statements in a question=1 pt; each correct answer to the single statement=0.25 pt; max. 18 points). In the second part, students are asked to write the legend of a printed figure that illustrates a given biological phenomenon/molecular mechanism (max. 6 points). The third part is an open question aimed at verifying the student's ability to describe a given biological phenomenon/molecular mechanism in a clear and concise manner, using the correct terminology (max. 10 points). The test should be answered in its entirety, obtaining at least the following scores: 1st part=8/18; 2nd part=3/6; open question= 5/10. Up to 3 further points will be assigned on the basis of the proficient and active participation of the students to class discussions and teamwork.

The timeline of "molecular biology". Nucleic acids structure. DNA topology and topoisomerases. Genes and genomes. Overview of transposable elements and selected examples of transposition mechanisms. The mitochondrial DNA. DNA replication: a molecular view. The replication machinery: analogies and differences between E. coli and eukaryotes. Integration and control of replication during the cell cycle progression. Mutations and agents that can induce mutagenic stress: an overview. DNA repair mechanisms; examples of direct DNA damage repair (e.g. photolyase, MGMT) and multi-step DNA repair pathways: Base Excision Repair (BER); Nucleotide Excision Repair; Mismatch-repair (MMR). Double strand break (DSB) repair by homologous recombination (HR) and non-homologous end joining (NHEJ). The cross-talk between DNA replication and repair.
An overview of RNA synthesis in eubacteria (E. coli) and eukaryotes. RNA polymerases. Protein-coding genes: transcription initiation and regulation of the phenomenon in eukaryotes. Basal transcription factors, activators, repressors, co-activators and co-repressors. Enhancers, silencers and insulators. Chromatin remodelling. The maturation of rRNA, tRNA, miRNA. The maturation of mRNAs: molecular mechanisms of capping, splicing and polyadenylation. Alternative Splicing. Group I and II auto-splicing introns. Trans-splicing. Examples of RNA editing. Protein synthesis: basic concepts and molecular mechanisms of translation. Protein synthesis control. Non-stop mediated decay and nonsense mediated decay phenomena. Riboswitch, miRNA, and lncRNA. Post-translational modifications, with particular emphasis on molecular mechanisms of ubiquitination and sumoylation.
Focus on current techniques that are used in the study of the molecular biology of the cell: microarray technologies in gene expression analysis; next generation sequencing methods; technologies for genome manipulation and editing.

Upon the successful completion of the course, the student will have acquired knowledge and understanding of the topics covered and developed the ability to apply such knowledge autonomously, in approaching the study of new topics, focused on the molecular aspects of cell biology. In detail, the students will know and understand: a) the composition, distribution and structural organisation of nucleic acids and genomes; b) the molecular mechanisms underlying the flow of genetic information, allowing gene expression in the correct time and way; c) the main levels of integration of these phenomena; and d) the main consequences of a malfunctioning of these phenomena and/or their de-regulation. The student will be able to apply the acquired knowledge to other areas such as a) the description of the molecular basis of diseases, b) the development of new small-molecule or biotechnological drugs targeting functions acting in genome maintenance and/or gene expression, and c) the development of new methods of molecular analysis. During the course the students will be also trained to integrate and re-evaluate the notions previously acquired in other courses (e.g. Biochemistry, Applied Biochemistry, General Biology) in the context and from the standpoint of molecular biology; therefore, they will be able to adopt the same method to the study of other disciplines (e.g. Pharmacology, Drug Design and Discovery) that they will encounter in the following of their studies. Finally, the students will be able to communicate Molecular Biology notions and concepts using the appropriate terminology.