Biologia Molecolare 3

1. Knowledge and Understanding

By the end of the course, students will have acquired a comprehensive understanding of the structure and organization of nucleic acids, the flow of genetic information, and the major mechanisms regulating gene expression. In particular, students will understand the structure and organization of genomic DNA and the different classes of cellular RNA, as well as the molecular mechanisms underlying DNA replication, transcription, and translation in prokaryotic and eukaryotic systems. Students will also gain knowledge of the major mechanisms controlling transcription, chromatin modifications and their impact on gene expression, DNA repair and recombination processes, and the biology of mobile genetic elements. In addition, they will become familiar with the theoretical and experimental principles underlying the main methodologies used for the analysis of nucleic acids, proteins, and gene expression.

2. Applying Knowledge and Understanding

Students will be able to apply the knowledge acquired during the course to the interpretation of data from both classical and modern molecular biology experiments. They will understand the principles, potential, and major applications of fundamental molecular biology techniques, including PCR, electrophoresis, molecular cloning, and DNA sequencing. Students will also be able to relate alterations affecting genes, RNA molecules, or proteins to their molecular, cellular, and phenotypic consequences.

3. Making Judgements

Students will be able to critically evaluate experimental data and results in molecular biology and develop scientifically sound interpretations based on the knowledge acquired during the course. They will also be able to critically approach introductory scientific literature in the field and draw independent conclusions from experimental results and information retrieved from biological databases.

4. Communication Skills

Students will be able to clearly and accurately communicate the molecular concepts and mechanisms covered in the course, both orally and in writing, using appropriate scientific terminology. They will also be able to describe and discuss complex biological processes, adapting the level of communication to different contexts and audiences, including both specialists and non-specialists.

5. Learning Skills

Students will develop the skills required to independently expand and update their knowledge of molecular biology through the consultation of scientific literature and the use of relevant biological databases. They will also acquire the conceptual and methodological foundations needed to undertake advanced studies in molecular biology, genetics, biotechnology, and related disciplines, and to pursue further academic or professional training.

The course consists of lectures supported by in-class exercises.

Should the course be delivered in a blended or online format, the necessary adjustments to the teaching methods described above may be introduced in order to ensure completion of the planned course content.

Students are required to have successfully completed the Biochemistry examination included in the degree programme. Successful completion of the Genetics examination is also recommended.

Course attendance is mandatory to the extent required by the Degree Programme Regulations, subject to the exceptions provided for therein. To be eligible to take the mid-term assessments, students are required to attend at least 80% of the scheduled teaching activities.

• DNA structure: historical experiments; structure and conformation of the DNA double helix; chemical structure of nitrogenous bases and nucleotides; tautomeric forms of the bases; DNA denaturation and hybridization; conformations of the DNA double helix; unusual DNA structures.
• DNA topology: DNA supercoiling; topological parameters; topoisomerases and their molecular mechanisms.
• RNA structure: chemical and structural features; formation of secondary structures; classes of RNA and their biological roles; ribozymes.
• Organization of DNA within the cell: prokaryotic and eukaryotic genomes: general organization and physical properties; genetic content and repetitive DNA; reassociation kinetics; histones and nucleosomes; nucleosome assembly; structural elements of chromosomes and chromatin; molecular aspects of chromosome duplication and segregation.
• DNA replication in prokaryotes and eukaryotes: structure and function of bacterial and eukaryotic DNA polymerases and their catalytic mechanisms; structure and function of the different enzymes involved in DNA replication; initiation of DNA replication; structure and organization of replication origins and replicators; termination of DNA replication; regulation of DNA replication.
• DNA mutability: major types of DNA mutations; DNA repair systems.
• Recombination: general principles of homologous recombination and its molecular machinery; adaptations of homologous recombination in prokaryotes and eukaryotes and their biological significance; specialized uses of recombination: site-specific recombination; major enzymes involved in genetic recombination.
• Transposition and retrotransposition: DNA transposons and molecular mechanisms of transposition; retrotransposons and retroviruses and their molecular mechanisms of mobility; regulation of transposition.
• Transcription in prokaryotes and eukaryotes: general principles and molecular mechanisms; structure and function of RNA polymerases; general organization of bacterial and eukaryotic promoters; initiation and termination of transcription; eukaryotic transcription factors.
• RNA processing: modifications of the ends of eukaryotic mRNAs; modifications of tRNAs and rRNAs; splicing and its molecular machinery, general principles and mechanism; alternative splicing; RNA editing; major molecular mechanisms regulating RNA processing.
• Protein synthesis in prokaryotes and eukaryotes: genetic code and suppressor mutations; classes of RNA involved in translation; structure and function of the ribosome; tRNA charging; stages of translation; regulation of gene expression at the translational level; regulation of mRNA and protein stability.
• Regulation of gene expression in bacteriophages and prokaryotes: regulation of transcription initiation in prokaryotes; activators and repressors; the operon model and attenuation; regulation of gene expression in bacteriophage lambda.
• Regulation of gene expression in eukaryotes: mechanisms of transcriptional regulation in eukaryotes; transcription factors and DNA-binding domains; signal transduction; regulation of chromatin structure; gene silencing; regulatory RNAs.
• Molecular biology techniques: electrophoresis of biological macromolecules; hybridization; principles of gene cloning and recombinant DNA technology; PCR and sequencing.

There are two alternative assessment pathways:

• Preliminary written test and oral examination. Admission to the oral examination requires successful completion of a preliminary written test consisting of 15 questions: 6 multiple-choice questions, 8 open-ended questions, and 1 question involving either a structural formula or an exercise. Each question is awarded a score ranging from 0 (zero) to +2 points. The overall score is calculated as the sum of the scores obtained for each question. A minimum score of 13.5 points is required to proceed to the oral examination. Students who achieve a score of 18 points or higher may choose either to accept the grade obtained in the written test without taking the oral examination, or to continue the examination by taking the oral test.
  
• Mid-term assessments. Two mid-term tests are scheduled during the course, each consisting of 60 multiple-choice questions with only one correct answer. Each correct answer is awarded +2 points, while incorrect or unanswered questions receive 0 (zero) points. A minimum score of 72 points is required to pass each test. A score between 60 and 70 points is considered a “conditional pass”, and the insufficient result must be compensated for in the subsequent test. This assessment pathway also includes a final test and the option of taking an additional oral examination. To pass the examination through this assessment pathway, students must successfully complete all three tests and achieve an overall final score of at least 72 points.
  

Assessment may also be conducted remotely should circumstances require it.

• What are the main structural features of A-DNA, B-DNA, and Z-DNA?
• Describe the main molecular mechanisms of DNA replication in prokaryotes and eukaryotes.
• Describe the sites of DNA replication initiation in prokaryotes and eukaryotes and their regulation.
• Describe the main features of DNA polymerases in prokaryotes and eukaryotes.
• Describe the structure and function of telomerase.
• Describe the main classes of cellular RNA, their characteristics, and their relative abundance.
• Describe the processing and maturation of the different types of RNA transcripts in prokaryotes and eukaryotes.