Molecular biology (2016/2017)
The teaching is organized as follows:
The aim of this course is to provide a detailed description at the molecular level of the main issues regarding the mechanisms involved transmission, variation and expression of the information contained in the genome of prokaryotes and eukaryotes. The main themes of the course will be a detailed description of the processes of gene transcription and translation and those related to DNA replication and mutagenesis.
At the end of the course, the student will have understood in detail the processes and mechanisms that regulate the flow of genetic information in the cell and use this knowledge in various aspects of Bioinformatics.
Program of Molecular Biology module:
The genetic information and informational molecules
General introduction and history. The structure of DNA and RNA. From genes to proteins, messenger RNA, transfer RNA and ribosomal RNA. The genetic code.
DNA and gene structure
The definition of gene. Coding and regulatory regions. Genes interrupted; introns.
Organization and evolution of genomes
DNA content and number of genes. Repetitive DNA. Gene families and gene duplication. Mutation, rearrangements of DNA and evolution of genomes.
The genomes of organelles.
Mobile genetic elements
Transposons,retrotransposons and retrovirus.
Chromatin and chromosomes
The nucleosomes; histones and their modifications. Higher levels of organization of chromatin. Eterochromatin and euchromatin. Eukaryotic chromosomes,telomers and centromeres.
The DNA polymerase. Proofreading activities of DNA polymerase.
The mechanism of replication in bacteria and eukaryotes.
Mutations and DNA repair
Spontaneous mutations and mutations caused by physical and chemical mutagens. Pre and post replication rapair systems. Recombination in immune system cells.
RNAs and transcription
The different types of RNA: synthesis and maturation. Bacterial RNA polymerase. The sigma factors. The eukaryotic RNA polymerase. Eukaryotic mRNA : capping, polyadenilation, transport in the cytoplasm. The process of transcription in bacteria and eukaryotes.
Regulation of gene expression
Bacterial promoters. Operons. Eukaryotic promoters. The regulation elements: enhancers, silencers, insulators, LCR. Gene expression and chromatin modifications. Epigenetic effects.
Introns and RNA Splicing
Spliceosomal introns. The spliceosome and mechanism of splicing. Alternative splicing and trans-Splicing. Other types of introns: group I and II introns. RNA editing. Ribozymes and riboswitch.
The ribosomes. Structure and function of tRNA. Synthesis of aminoacil-tRNA. Beginning of translation in bacteria and eukaryotes. Synthesis of polypeptides and termination of translation. Regulation of the translation. Location of proteins.
The teaching material used in class lessons is available on the e-learning platform of the course.
Program of Lab. II module:
Bioinformatic tools for the analysis of molecular evolution and phylogenesis: Molecular clock, substitution models, methods for the construction of phylogenetic trees.
Protein structural preditions: Comparative modeling, Fold recognition and ab initio methods.
Microarrays: databases and programs for the analysis of expression data.
Introduction to the energetic treatment of proteins: MD simulations, ligand-protein and protein-protein docking.
Reference Text: Testi di riferimento: Bioinformatica di di Stefano Pascarella, Alessandro Paiardini - Zanichelli
The teaching includes: front lectures and hands-on excersices on the PC. The students are also involved in a project to be developed in groups.
See examination details for each of the modules
|Stefano Pascarella e Alessandro Paiardini