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, that can help them in understanding the future development of this area;
- 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, that can help them in understanding the future development of this area;
- 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
Molecular Biology Unit
Introduction to Molecular Biology
What is it
Where does it come from
Historical experiments
Structure and properties of biological molecules
DNA
RNA
Protein
Carbohydrates
Lipids
Chemical bonds
Molecular interactions
The structure of DNA: discovery, fundamentals, properties
DNA Topology
Concepts
Biological impact
Structure and function of topoisomerases
The genome
Comparison of dimensions, organization and gene density among the main sequenced genes of prokaryotes and eukaryotes.
The chromosome
Primary, secondary and higher order organization of chromatin. The nucleosome: composition and structure. Remodeling of nucleosomes and histone modifications.
DNA replication in procaryotes and eukaryotes
Basic concepts and historical experiments
Replication mutants
Proteins involved in replication
Replication origins
Molecular mechanisms of DNA replication: initiation, elongation, termination
Regulation of replication
The eukaryotic chromosome: structure and functional elements
The cell cycle: basic concepts
Transcription
Basic concepts
Molecular mechanisms of transcription in prokaryotes: initiation, elongation, termination
The bacterial RNA polymerase
Promoters and their structure
Sigma factors
Transcription termination
Molecular mechanisms of transcription in eukaryotes
RNA polymerase I, II, III
Mechanism of RNA polymerase II transcription: initiation, elongation, termination
Structure of eukaryotic promoters
Basal transcriptional apparatus
Transcriptional regulation
Examples from prokaryotes
The regulation of the lambda phage lytic/lysogenic cycle
Examples from eukaryotes
Epigenetics
Transcriptional activators: modular structure and function
Gene silencing
RNA processing
RNA modification
Molecular mechanisms of pre-mRNA maturation
Capping
Splicing
Polyadenylation
RNA degradation
Protein synthesis
Basic concepts
The genetic code
Characteristics of ribosomes
Characteristics of tRNAs
Aminoacyl tRNA synthetases
Mechanism of translation: initiation in prokaryotes and eukaryotes
Mechanism of translation: elongation
Mechanism of translation: termination and ribosome recycling
Quality control
Regulation of protein synthesis
Regulatory RNAs
Small RNAs in bacteria
Small RNA in eukaryotes (siRNA, miRNA, rasiRNA): origin and function
lncRNAs
Postranslational modifications of proteins
Chaperones and folding
Lipid modification
Carbohydrate modification
Phosphorylation, acetylation, methylation
Ubiquination and SUMOylation
Protein degradation
The cellular response to DNA damage
General concepts
Different types of DNA lesions
Lesion reversal
Base Excision Repair
Nucleotide Excision Repair
Mismatch Repair
Double strand breaks repair
Translesion DNA synthesis
Introduction to checkpoint mechanisms
Mobile elements in the genome
Molecular Biology Methods
Analysis of macromolecules: agarose gel electrophoresis, denaturaing polyacrylamide gel electrophoresis, analysis of macromolecules through gradient centrifugation
Model organisms in Molecular Biology
Cell cultures
Extraction of DNA from bacterial cells
Restriction enzymes.
Principles of cloning.
Cloning vectors.
Construction of a recombinant DNA molecule.
Cell transformation
Genomic and cDNA libraries
Polyadenylated mRNA isolation and cDNA preparation.
Southern hybridization
Immunological approaches.
PCR
Gene modification: gene replacement, gene tagging, mutagenesis, genome editin
Measuring gene expression: Northern Blot, reverse transcriptase PCR and quantitative PCR.
Studying protein-protein interactions: two hybrid and biochemical approaches
Studying protein-DNA interactions
Bioinformatics Unit
Historical perspective and the scope of bioinformatics
Experimental and bioinformatics approaches for the sequencing and assembly of genomes.
The concept of a "reference genome", conventions and formats used in the annotation of genomic features and genes.
Structural and functional gene annotation. The gene ontology (GO)
Splicing and alternative splicing of eukaryotic transcripts.
Homology, similarity and alignment
BLAST, local alignment and database searching.
Practical session, BLAST and Genbank
Practical session, Genome Browsers
Practical session, phylogenetics
Whole transcriptome analysis
Analysis of transcription regulatory elements and promoters
Representation of large datasets, heatmaps, boxplots, functional enrichment etc
Introduction to Molecular Biology
What is it
Where does it come from
Historical experiments
Structure and properties of biological molecules
DNA
RNA
Protein
Carbohydrates
Lipids
Chemical bonds
Molecular interactions
The structure of DNA: discovery, fundamentals, properties
DNA Topology
Concepts
Biological impact
Structure and function of topoisomerases
The genome
Comparison of dimensions, organization and gene density among the main sequenced genes of prokaryotes and eukaryotes.
The chromosome
Primary, secondary and higher order organization of chromatin. The nucleosome: composition and structure. Remodeling of nucleosomes and histone modifications.
DNA replication in procaryotes and eukaryotes
Basic concepts and historical experiments
Replication mutants
Proteins involved in replication
Replication origins
Molecular mechanisms of DNA replication: initiation, elongation, termination
Regulation of replication
The eukaryotic chromosome: structure and functional elements
The cell cycle: basic concepts
Transcription
Basic concepts
Molecular mechanisms of transcription in prokaryotes: initiation, elongation, termination
The bacterial RNA polymerase
Promoters and their structure
Sigma factors
Transcription termination
Molecular mechanisms of transcription in eukaryotes
RNA polymerase I, II, III
Mechanism of RNA polymerase II transcription: initiation, elongation, termination
Structure of eukaryotic promoters
Basal transcriptional apparatus
Transcriptional regulation
Examples from prokaryotes
The regulation of the lambda phage lytic/lysogenic cycle
Examples from eukaryotes
Epigenetics
Transcriptional activators: modular structure and function
Gene silencing
RNA processing
RNA modification
Molecular mechanisms of pre-mRNA maturation
Capping
Splicing
Polyadenylation
RNA degradation
Protein synthesis
Basic concepts
The genetic code
Characteristics of ribosomes
Characteristics of tRNAs
Aminoacyl tRNA synthetases
Mechanism of translation: initiation in prokaryotes and eukaryotes
Mechanism of translation: elongation
Mechanism of translation: termination and ribosome recycling
Quality control
Regulation of protein synthesis
Regulatory RNAs
Small RNAs in bacteria
Small RNA in eukaryotes (siRNA, miRNA, rasiRNA): origin and function
lncRNAs
Postranslational modifications of proteins
Chaperones and folding
Lipid modification
Carbohydrate modification
Phosphorylation, acetylation, methylation
Ubiquination and SUMOylation
Protein degradation
The cellular response to DNA damage
General concepts
Different types of DNA lesions
Lesion reversal
Base Excision Repair
Nucleotide Excision Repair
Mismatch Repair
Double strand breaks repair
Translesion DNA synthesis
Introduction to checkpoint mechanisms
Mobile elements in the genome
Molecular Biology Methods
Analysis of macromolecules: agarose gel electrophoresis, denaturaing polyacrylamide gel electrophoresis, analysis of macromolecules through gradient centrifugation
Model organisms in Molecular Biology
Cell cultures
Extraction of DNA from bacterial cells
Restriction enzymes.
Principles of cloning.
Cloning vectors.
Construction of a recombinant DNA molecule.
Cell transformation
Genomic and cDNA libraries
Polyadenylated mRNA isolation and cDNA preparation.
Southern hybridization
Immunological approaches.
PCR
Gene modification: gene replacement, gene tagging, mutagenesis, genome editin
Measuring gene expression: Northern Blot, reverse transcriptase PCR and quantitative PCR.
Studying protein-protein interactions: two hybrid and biochemical approaches
Studying protein-DNA interactions
Bioinformatics Unit
Historical perspective and the scope of bioinformatics
Experimental and bioinformatics approaches for the sequencing and assembly of genomes.
The concept of a "reference genome", conventions and formats used in the annotation of genomic features and genes.
Structural and functional gene annotation. The gene ontology (GO)
Splicing and alternative splicing of eukaryotic transcripts.
Homology, similarity and alignment
BLAST, local alignment and database searching.
Practical session, BLAST and Genbank
Practical session, Genome Browsers
Practical session, phylogenetics
Whole transcriptome analysis
Analysis of transcription regulatory elements and promoters
Representation of large datasets, heatmaps, boxplots, functional enrichment etc
Prerequisites for admission
Participants should possess a sound grasp of basic concepts in genetics and biochemistry
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. The Bioinformatics Unit will also include practical sessions in an informatics lecture theatre.
Teaching Resources
Craig N.L., Cohen-Fix O., Green R., Greider C.W., Storz G., Wolberger C. Molecular Biology principles of genome function. 3rd edition Oxford University Press
Articles and materials provided by the teachers on the dedicated ARIEL site.
Articles and materials provided by the teachers on the dedicated ARIEL site.
Assessment methods and Criteria
Students will have to take exams for each of the two units.
For the Molecular Biology unit, the exam will consist in two partial written exams, each of which is divided into two parts. The first part will consist of 10 multiple choice questions. Only those who pass the first part will be able to take the second part, based on two open questions. The students that will not take or pass the first partial, will have to take the full exam on the complete program after the end of the course. The exam for the Bioinformatics unit consists of 20 multiple choice questions and 4 open questions. Multiple choice and open questions carry the same total weight (50%), the written exam has a duration of 1 h 15 min for each of the two units.
For the Molecular Biology unit, the exam will consist in two partial written exams, each of which is divided into two parts. The first part will consist of 10 multiple choice questions. Only those who pass the first part will be able to take the second part, based on two open questions. The students that will not take or pass the first partial, will have to take the full exam on the complete program after the end of the course. The exam for the Bioinformatics unit consists of 20 multiple choice questions and 4 open questions. Multiple choice and open questions carry the same total weight (50%), the written exam has a duration of 1 h 15 min for each of the two units.
BIO/11 - MOLECULAR BIOLOGY - University credits: 12
Lessons: 96 hours
Professors:
Horner David Stephen, Muzi Falconi Marco
Professor(s)
Reception:
Thursday 14.00 - 17.00
Via Celoria 26, Tower B, 2nd floor
Reception:
to be organized upon request