Molecular Biology and Bioinformatics
A.Y. 2018/2019
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.
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
Undefined
Lesson period: Second semester
Assessment methods: Esame
Assessment result: voto verbalizzato in trentesimi
Single course
This course cannot be attended as a single course. Please check our list of single courses to find the ones available for enrolment.
Course syllabus and organization
Single session
Responsible
Course syllabus
Structure and physical properties of DNA: B DNA and other alternative structures. DNA bending and DNA topology. Physico-chemical methods to isolate and study DNA molecules. Structure and physical properties of RNA: composition, structure and physico-chemical properties. The functions of the RNAs.
Comparison in size, organization and gene density among the genomes in prokaryotes and eukaryotes.
Methodologies part 1: restriction enzymes, basic principles of recombinant DNA technology, genomic library
The chromosome structure. The nucleosome: composition and structure. Higher levels of organization of chromatin. Chromatin remodelling and histone modifications.
Replication and stability of DNA: DNA replication in prokaryotes, the general structure and functions of the DNA polymerases. Enzymology of the DNA replication in prokaryotes and eukaryotes. The replication of the chromosome ends. Telomers and telomerases. Techniques of DNA sequencing and PCR.
Origins of replication. The control of S phase.
Mechanisms of DNA repair in prokaryotes and eukaryotes.
Gene expression: transcription: general mechanism. The RNA polymerases and their properties. Prokaryotic and eukaryotic promoters. The initiation of transcription in prokaryotes and eukaryotes. Methods to study protein-DNA and protein-protein interactions.
Maturation of the pre-mRNA: capping, polyadenylation and splicing. Splicing of the introns of group I, II and III. Theories on the origin of the introns. The RNA world.
Methodologies part 2: purification of poly(A)+ RNA and preparation of cDNA, cDNA libraries. Northern hybridization and Reverse-transcriptase PCR
Mechanisms of protein synthesis. Transport of mRNA to the cytoplasm. The ribosomes. Structure of the tRNA and charging by the aminoacyl-tRNA synthetases. Molecular mechanisms of protein synthesis. Initiation and elongation reactions in prokaryotic and eukaryotic cells. Role of the G proteins in protein synthesis. Mechanism of action of antibiotics that inhibit protein synthesis.
Regulation of translation, general and specific: examples in prokaryotes and eukaryotes. Mechanisms of regulation of the bacterial ribosomal proteins and of eukaryotic proteins (ferritin). The eIF2 phosphorylation and the attenuation of protein synthesis in eukaryotes.
The various levels of regulation of gene expression: a summary. Control of protein activity/localization. Mechanisms of protein sorting and transport to the final destination. Post-translational modifications of proteins.
Bioinformatics:
Introduction: definition and aims of Bioinformatics. Genome projects and next-generation sequencing. 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.
Textbooks
J.D.Watson, T.Baker, S.P. bell, A.Gann, M.Levine, R.Losick "Molecular Biology of the gene" 7th edition. Pearson education Inc. 2014
- Pascarella S.; Paiardini A. Bioinformatica. Zanichelli Ed.
- Valle G, Helmer-Citterich M, Attimonelli M. e Pesole G. Introduzione alla Bioinformatica. Zanichelli ed. (Bologna, 2003). (at the Unimi Library)
Prerequisites and examination procedures
No pre-requisite
Exam: for Molecular biology: first part written and then oral or whole exam oral.
For bioinformatics: written test with open questions.
Teaching Methods
Traditional lessons aided by powerpoint slides, videos on molecular biology techniques and tutorials on Genome Browser and Blast for Bioinformatics.
Attendance is strongly recommended
Recommended Prerequisites
The exams of Genetics and Biochemistry should be passed before attending this course
Program information
The course is held in parallel to the English course "Molecular Biology and Bioinformatics"
WEB Page
Visit the web site of the course "Biologia molecolare e Bioinformatica" (Popolo-Gissi) at the portal ARIEL of the University of Milan http://ariel.unimi.it/User/Default.aspx
Comparison in size, organization and gene density among the genomes in prokaryotes and eukaryotes.
Methodologies part 1: restriction enzymes, basic principles of recombinant DNA technology, genomic library
The chromosome structure. The nucleosome: composition and structure. Higher levels of organization of chromatin. Chromatin remodelling and histone modifications.
Replication and stability of DNA: DNA replication in prokaryotes, the general structure and functions of the DNA polymerases. Enzymology of the DNA replication in prokaryotes and eukaryotes. The replication of the chromosome ends. Telomers and telomerases. Techniques of DNA sequencing and PCR.
Origins of replication. The control of S phase.
Mechanisms of DNA repair in prokaryotes and eukaryotes.
Gene expression: transcription: general mechanism. The RNA polymerases and their properties. Prokaryotic and eukaryotic promoters. The initiation of transcription in prokaryotes and eukaryotes. Methods to study protein-DNA and protein-protein interactions.
Maturation of the pre-mRNA: capping, polyadenylation and splicing. Splicing of the introns of group I, II and III. Theories on the origin of the introns. The RNA world.
Methodologies part 2: purification of poly(A)+ RNA and preparation of cDNA, cDNA libraries. Northern hybridization and Reverse-transcriptase PCR
Mechanisms of protein synthesis. Transport of mRNA to the cytoplasm. The ribosomes. Structure of the tRNA and charging by the aminoacyl-tRNA synthetases. Molecular mechanisms of protein synthesis. Initiation and elongation reactions in prokaryotic and eukaryotic cells. Role of the G proteins in protein synthesis. Mechanism of action of antibiotics that inhibit protein synthesis.
Regulation of translation, general and specific: examples in prokaryotes and eukaryotes. Mechanisms of regulation of the bacterial ribosomal proteins and of eukaryotic proteins (ferritin). The eIF2 phosphorylation and the attenuation of protein synthesis in eukaryotes.
The various levels of regulation of gene expression: a summary. Control of protein activity/localization. Mechanisms of protein sorting and transport to the final destination. Post-translational modifications of proteins.
Bioinformatics:
Introduction: definition and aims of Bioinformatics. Genome projects and next-generation sequencing. 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.
Textbooks
J.D.Watson, T.Baker, S.P. bell, A.Gann, M.Levine, R.Losick "Molecular Biology of the gene" 7th edition. Pearson education Inc. 2014
- Pascarella S.; Paiardini A. Bioinformatica. Zanichelli Ed.
- Valle G, Helmer-Citterich M, Attimonelli M. e Pesole G. Introduzione alla Bioinformatica. Zanichelli ed. (Bologna, 2003). (at the Unimi Library)
Prerequisites and examination procedures
No pre-requisite
Exam: for Molecular biology: first part written and then oral or whole exam oral.
For bioinformatics: written test with open questions.
Teaching Methods
Traditional lessons aided by powerpoint slides, videos on molecular biology techniques and tutorials on Genome Browser and Blast for Bioinformatics.
Attendance is strongly recommended
Recommended Prerequisites
The exams of Genetics and Biochemistry should be passed before attending this course
Program information
The course is held in parallel to the English course "Molecular Biology and Bioinformatics"
WEB Page
Visit the web site of the course "Biologia molecolare e Bioinformatica" (Popolo-Gissi) at the portal ARIEL of the University of Milan http://ariel.unimi.it/User/Default.aspx
BIO/11 - MOLECULAR BIOLOGY - University credits: 12
Lessons: 96 hours
Professors:
Guerrini Luisa Francesca Isotta, Zambelli Federico
Professor(s)
Reception:
Friday 15.00-16.00 by appointment
Beacon Lab, 2nd floor, B Tower, Dept. of Biosciences / MS Teams