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 and recombination of genetic material. The description of mechanisms required to express 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 some approaches, techniques and models that are currently adopted to study the molecular biology of the cell.

Molecular Biology: Principles of Genome Function.
Nancy Craig et al. Oxford University Press, 2021.
Selected Reviews and A/V material. In the absence of copyright issues, the presentations used during the lectures will be made available to the students at the end of each "macro-section", as "read-only" files; they are intended for triggering student's further independent study on the taught subjects.

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 cell biology and general biochemistry is required.
Upper-intermediate level of mastery of the English language (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.

Written test. The first part consists of 18 questions, each containing 3 statements that must be judged "true" or "false"; 3 correct answers to the 3 statements in a question=1 pt; each correct answer to the single statement=0.25 pt. The choice of the option "false" should be briefly explained (max. 18 pt). In the second part, students are asked to write the legend of the 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 (max. 10 points). All the three parts of the test should be answered, obtaining at least the following scores: 1st part 6/18; 2nd part: 3/6; open question: 6/10. Up to 3 further points will be assigned on the basis of the proficient participation of the students to working in team.

The timeline of "molecular biology". Nucleic acids structure. DNA topology and topoisomerases. Genes and genomes. Overview of transposable elements and mechanisms of transposition. The mitochondrial DNA. DNA replication: a molecular view. The replication machinery: analogies and differences between prokaryotes and eukaryotes. The mechanistic aspects of DNA replication. Integration and control of replication during the cell cycle progression. Mutations and agents that can induce mutagenic stress. DNA repair mechanisms: an overview. Examples of direct DNA damage repair. Multi-step DNA repair pathways: Base Excision Repair (BER) and Nucleotide Excision Repair (Global Gene, GG-NER and Transcription-coupled, TC-NER). 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. ATR/ATRIP and ATM. An overview of RNA synthesis in prokaryotes and in 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. mRNAs processing: molecular mechanisms of capping, splicing and polyadenylation. Group I and II auto-splicing introns. Trans-splicing. Alternative Splicing. 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. Modulation of gene expression based on mRNA distribution. Post-translational modifications, with particular emphasis on molecular mechanisms of ubiquitination and sumoylation.
Focus on some 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 students will have acquired knowledge and understanding of the topics covered and developed the ability to apply such knowledge autonomously, in addressing 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 responsible for the transmission of genetic information and for 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 students 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 gene expression, and c) the development of new methods of molecular analysis. During the course the students have been 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 apply the same method to studying other disciplines (e.g. Pharmacology, Drug Design and Discovery, Structural Biology) 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.