Molecular Biology and Bioinformatics
A.Y. 2024/2025
Learning objectives
Aim of this course is to provide students with a solid background in Molecular biology and Bioinformatics, with the description of basic processes such as DNA replication, transcription and translation both in prokaryotes and eukaryotes, and 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 basic molecular biology techniques and with the use of software for sequence analysis and for the query of sequence databases, fundamental tools in era of genome sequencing and post-genomic analyses.
Expected learning outcomes
At the end of the course, students will acquire:
- basic knowledge of molecular biology;
- principles of basic molecular biology techniques
In addition, the student will acquire the basic knowledge of bioinformatics necessary to:
- understand the biological data associated to the huge amount of sequence data stored in the biological database;
- query the sequence databases with the appropriate tools;
- use and correctly understand the results of sequence similarity search tools based on local or global similarity searches.
- basic knowledge of molecular biology;
- principles of basic molecular biology techniques
In addition, the student will acquire the basic knowledge of bioinformatics necessary to:
- understand the biological data associated to the huge amount of sequence data stored in the biological database;
- query the sequence databases with the appropriate tools;
- use and correctly understand the results of sequence similarity search tools based on local or global similarity searches.
Lesson period: Second semester
Assessment methods: Esame
Assessment result: voto verbalizzato in trentesimi
Single course
This course can be attended as a single course.
Course syllabus and organization
Single session
Responsible
Lesson period
Second semester
Course syllabus
Introduction to Molecular Biology
Structure and properties of biological molecules
DNA
RNA
Protein
Carbohydrates
Lipids
Molecular Biology Methodologies Part 1
Restriction enzymes.
Hybridization of Southern.
Principles of cloning.
Cloning vectors.
Construction of a recombinant DNA molecule.
Construction of genomic libraries.
Evolution of Genomes
Comparison of dimensions, organization and gene density among the main sequenced genes of prokaryotes and eukaryotes.
Primary, secondary and higher order organization of chromatin. The nucleosome: composition and structure. Remodeling of nucleosomes and histone modifications.
Basic concepts of the cell cycle
DNA replication
Replication origins
Proteins involved in replication
Regulation of replication
Gene expression
Mechanisms of transcription in prokaryotes: beginning, lengthening and term.
bacterial RNA polymerase. Promoters and their structure. The sigma factors. Regulation at the transcriptional level in prokaryotes. The termination of rho-dependent and independent transcription.
The mechanisms of transcription in eukaryotes: RNA polymerase I, II and III. The transcriptional mechanism operated by RNA polymerase II. The structure of a eukaryotic promoter. The basal transcriptional apparatus and the elements of the "core" promoter. Eukaryotic transcriptional activators: modular structure and function. Study techniques of transcriptional activators.
Pre-mRNA maturation: capping, splicing and polyadenylation. Splicing mechanism of nuclear pre-mRNAs.
Molecular biology methodologies part 2
polyadenylated mRNA isolation and cDNA preparation.
Construction of cDNA libraries.
Northern Blot.
Reverse Transcritase PCR.
Protein synthesis
Characteristics of ribosomes. Characteristics of tRNAs: secondary and tertiary structure of tRNAs. Activation of amino acids. Aminoacyl tRNA synthetases. The phenomenon of staggering.
How to start protein synthesis in prokaryotes and eukaryotes.
The stages of protein synthesis in prokaryotes and eukaryotes.
Levels of regulation of gene expression.
Introduction to post-translational modifications of proteins.
Mechanisms of DNA repair.
Mobile elements in the genome
Model systems in Molecular Biology
Bioinformatics:
Introduction to bioinformatics.
Genomic sequencing, and "Next Generation Sequencing" (NGS).
Annotation of genes and genomes.
The gene structure and the annotation of genes and transcripts: introns, exons, promoters, alternative splicing.
Genomic browsers
Primary and specialized biological databases.
Sequence similarity and local and global alignments.
Substitution matrix for protein sequence alignments (PAM, BLOSUM).
Search by similarity in sequence databases (BLAST).
Outline of comparative genomics: homology, orthology and paralogy.
Notes on the application of NGS techniques to the chromatin studies
Structure and properties of biological molecules
DNA
RNA
Protein
Carbohydrates
Lipids
Molecular Biology Methodologies Part 1
Restriction enzymes.
Hybridization of Southern.
Principles of cloning.
Cloning vectors.
Construction of a recombinant DNA molecule.
Construction of genomic libraries.
Evolution of Genomes
Comparison of dimensions, organization and gene density among the main sequenced genes of prokaryotes and eukaryotes.
Primary, secondary and higher order organization of chromatin. The nucleosome: composition and structure. Remodeling of nucleosomes and histone modifications.
Basic concepts of the cell cycle
DNA replication
Replication origins
Proteins involved in replication
Regulation of replication
Gene expression
Mechanisms of transcription in prokaryotes: beginning, lengthening and term.
bacterial RNA polymerase. Promoters and their structure. The sigma factors. Regulation at the transcriptional level in prokaryotes. The termination of rho-dependent and independent transcription.
The mechanisms of transcription in eukaryotes: RNA polymerase I, II and III. The transcriptional mechanism operated by RNA polymerase II. The structure of a eukaryotic promoter. The basal transcriptional apparatus and the elements of the "core" promoter. Eukaryotic transcriptional activators: modular structure and function. Study techniques of transcriptional activators.
Pre-mRNA maturation: capping, splicing and polyadenylation. Splicing mechanism of nuclear pre-mRNAs.
Molecular biology methodologies part 2
polyadenylated mRNA isolation and cDNA preparation.
Construction of cDNA libraries.
Northern Blot.
Reverse Transcritase PCR.
Protein synthesis
Characteristics of ribosomes. Characteristics of tRNAs: secondary and tertiary structure of tRNAs. Activation of amino acids. Aminoacyl tRNA synthetases. The phenomenon of staggering.
How to start protein synthesis in prokaryotes and eukaryotes.
The stages of protein synthesis in prokaryotes and eukaryotes.
Levels of regulation of gene expression.
Introduction to post-translational modifications of proteins.
Mechanisms of DNA repair.
Mobile elements in the genome
Model systems in Molecular Biology
Bioinformatics:
Introduction to bioinformatics.
Genomic sequencing, and "Next Generation Sequencing" (NGS).
Annotation of genes and genomes.
The gene structure and the annotation of genes and transcripts: introns, exons, promoters, alternative splicing.
Genomic browsers
Primary and specialized biological databases.
Sequence similarity and local and global alignments.
Substitution matrix for protein sequence alignments (PAM, BLOSUM).
Search by similarity in sequence databases (BLAST).
Outline of comparative genomics: homology, orthology and paralogy.
Notes on the application of NGS techniques to the chromatin studies
Prerequisites for admission
Suggested: Genetics and Biological Chemistry
Teaching methods
Frontal teaching with a high level of teacher interaction supported by projected teaching material which is available to students from a dedicated website. Extensive discussions to allow development of critical faculties and encourage constructive individual involvement in the teaching/learning process. Discussion and self-assessment are planned during the course using the Wooclap platform.
Teaching Resources
Craig N.L., Cohen-Fix O., Green R., Greider C.W., Storz G., Wolberger C.
Biologia Molecolare-Principi di funzionamento del genoma. Pearson
Citterich M., Ferrè F., Pavesi G., Romualdi C., Pesole G. Fondamenti di bioinformatica. Zanichelli
Biologia Molecolare-Principi di funzionamento del genoma. Pearson
Citterich M., Ferrè F., Pavesi G., Romualdi C., Pesole G. Fondamenti di bioinformatica. Zanichelli
Assessment methods and Criteria
The examination consists of two written tests structured with multiple choice questions and open-ended questions (Molecular Biology and Bioinformatics). Students regularly attending classes can take two in itinere tests (in the middle and at the end of the course for Molecular Biology) in the same way and a final test for Bioinformatics.
BIO/11 - MOLECULAR BIOLOGY - University credits: 12
Lessons: 96 hours
Professors:
Lazzaro Federico, Zambelli Federico
Professor(s)
Reception:
Friday 15.00-16.00 by appointment
Beacon Lab, 2nd floor, B Tower, Dept. of Biosciences / MS Teams