Molecular biology and bioinformatics

A.Y. 2016/2017
Overall hours
Learning objectives
The aim of this course is to provide the students of a solid background in Molecular biology and Bioinformatics that can help them in understanding the future development of this area. Beside the description of basic processes such as DNA replication, transcription and translation both in prokaryotes and eukaryotes, the final part of the Molecular Biology program will be devoted to some examples of regulation of these processes and of the function of proteins that are the final executers of the genetic program of a cell.
In addition the students will acquaint with the principles of some basic molecular biology techniques and with the use of software for sequence analysis and for the query of sequence databases. Indeed, these are fundamental tools in era of genome sequencing and post-genomic analyses. Therefore the course consists of a part of molecular biology (9CFU) and a second part of bioinformatics (3 CFU). The aim of the Bioinformatics part is to provide the students of the main knowledge that will be useful to: (i) understand the biological data associated to the huge amount of sequence data stored in the biological database; (ii) query the sequence databases with the appropriate tools; and (iii) use and correctly understand the results of sequence similarity search tools based on local or global similarity searches.
Expected learning outcomes
Course syllabus and organization

Single session

Lesson period
Second semester
Course syllabus
Molecular Biology:
The peer reviewing system for publishing papers; models systems in molecular biology
DNA structure; mutations, phenotypes and diseases
DNA bending
DNA topology/DNA topoisomerases
DNA sequencing and analysis
Open reading frames (theory & practice);
The chromosome cycle and cell division
Antibodies and their applications in molecular biology
Techniques (cloning, vectors, cDNA preparation)
Genomic and expression libraries; reverse genetics
PCR and applications
DNA replication
Origins of replication
The control of DNA replication
Techniques to visualize protein-DNA interactions
DNA damage response
DNA repair
Genome instability and cancer
Regulation of gene expression
Techniques to study protein/protein interactions
RNA splicing and regulation of splicing
Translational control
Gene editing techniques
Career in science

Introduction: definition and aims of Bioinformatics. Bioinformatics and genome projects. Gene and genome annotations. A bioinformatic view of the structure of protein-coding genes: exons, introns, promoters, and alternative splicing. The structure of mature eukaryotic mRNAs. Primary and specialized biological databases. Genome browsers. Definition of sequence similarity, homology, orthology, and paralogy. Global and local alignments. Scoring matrices for nucleotide and amino acid sequence alignments (PAM and BLOSUM). BLAST sequence similarity search: algorithm and usage. Multiple sequence alignments.

Reference Material
Molecular Biology of the Gene, by: J.Watson, T.Baker, S.Bell, A.Gann, M.Levine, R.Losick, Ed: Benjamin Cummings.
Valle G, Helmer-Citterich M, Attimonelli M. e Pesole G. Introduzione alla Bioinformatica. Zanichelli ed. (Bologna, 2003).
Slides and on-line tutorials on the usage of the main bioinformatic tools and resources.

Prerequisites and examination procedures
Written tests

Recommended Prerequisites
Genetics, Biochemistry

Teaching Methods
Bioinformatics: lessons with PowerPoint slides that will be shared with students; practicals in the lab where students will use a computer.

Language of instruction
BIO/11 - MOLECULAR BIOLOGY - University credits: 12
Lessons: 96 hours