Bioinformatics

Main goal of the course is to give to the students a general view of the molecular mechanisms which are at the base of the biological processes. For each argument a methodological section will introduce the students to the main technical approaches used at the state of the art. Practical training (2 CFU) will make the students to breath the atmosphere of a molecular biology laboratory. Particular attention will be given to the high throughput methods utilized in “Omic” approaches to the comprehension of biological processes. General aims: The course is focused on the deep connection between DNA and protein structure and their functions. The student will learn the molecular mechanisms which are at the base of the processes of Replication, Recombination, Transcription, DNA repair, RNA processing and splicing, protein Sythesis and their regulatory circuits. Specific aims: 1. Knowledge and understanding: The student should learn the basic molecular mechanisms of the cellular omeostasis and gene regulation and the most used techniques of Molecular Biology. 2. Ability to apply Knowledge and understanding: The student should be able to apply this knowledge in the discussion of recent arguments of general interest in Molecular Biology research. 3. Critical Judgement abilities: The student should demonstrate critical judgement abilities in solving problems related to theoretical and practical Molecular Biology projects and should communicate his conclusions to the colleagues and to the teacher in an effective way. 4. the student should demonstrate to be able to apply the learned concepts to his future work in molecular biology. Molecular Biology and applied Molecular Biology Laboratory part I The polimorphic DNA – Chemical components of DNA: bases, sugars and phosphodiesteric backbone (0.1 cfu). DNA B basic structure (0.2). Alternative DNA conformations, unusual structures (crucifiorms, triple helix) (0.2) – Conformational variability of structural parameters, curvature and bendability (0.2). DNA topology, winding and unwinding; linking number; DNA topoisomerases (0.2). The Genetic Code - the code decrypting; the structure and function of the code (0.2). DNA replication: machinery and mechanisms in prokaryotes and eukaryotes (0.2). Replicons organization; topological and end-replication problems (0.1). DNA mutability and repair; damage checkpoints (0.4). DNA transcription: transcription in bacteria and bacteriophages; transcriptional machinery and RNA polymerase positioning signals (0.2). Methodological approach to the study of transcription: in vitro transcription systems (0.2). Transcription regulation in prokaryotic systems: activation and repressions; operon structures and function (0.2). Transcription in eukaryotic systems (0.1); transcriptional machinery and RNA polymerase positioning signals (0.2). Methodological approaches to the study of transcription: eukaryotic in vitro transcription systems. Coordinate regulation of the three eukaryotic RNA polymerases (0.2). Transcription factors and transcription regulation in eukaryotes (0.2). The RNA molecule (chemical and structural features) (0.2); Chromatin basic structure in eukaryotes and prokaryotes (0.2). The structure of nucleosomes and further organization levels (0.2). Histone modifications and their regulatory effects; the histone code. (0.3). DNA methylation and its regulatory role (0.2). Histone variants and their regulatory role. Chromatin structure and chromatin remodelling at promoters (0.2). Chromosomes structure: centromers, telomers and origin of replication (0.1). Molecular Biology techiniques (Nucleic Acid sequencing, Techniques for gene expression and DNA protein interaction analysis and the use of reporter genes) 0.5 CFU Pratic Training (Nucleic Acids purification; PCR; Real time PCR; use of reporter genes) 1 CFU

Basic knowledge in Cell Biology and Chemistry

Watson JD, Baker TA, Bell SP, Gann A, Levine M. - Molecular Biology Of The Gene, 7Th Edn or Alberts B, Morgan DO - Molecular Biology of the Cell

4 hours/week

Written test with open and multiple choice questions and oral exam