The learning objectives of the course are intended to introduce students to basic Molecular Biology, i.e. the study of genes and their activities at molecular level. The topics covered include DNA replication, repair, transcription, protein synthesis, as well as genetic recombination. Special attention will be paid to the multiple mechanisms regulating gene expression in both bacteria and eukaryotes, with an in depth look to some rapidly evolving fields, like epigenetic regulation and the role of different types of non-coding RNAs. Finally, lectures will emphasize the theoretical basis of the most common techniques used by molecular biologists for the analysis of gene expression.

1. Nucleic acids: DNA and RNA
1.1 From the discovery of DNA as genetic material to the "Human Genome Project".
1.2 Chemistry of nucleic acids.
1.3 Primary, secondary and tertiary structures of DNA and their properties.
1.4 DNA topology.
1.5 RNA: structure and function (ribozymes).
2. DNA replication
2.1 General features and enzymology of DNA replication.
2.2 Replication of bacterial genome.
2.3 Replication of mitochondrial DNA.
2.4 Replication of viral genomes.
2.5 Replication of eukaryotic genome and cell cycle.
3. DNA damage and repair
3.1 Types and consequences of DNA damage.
3.2 Endogenous and exogenous (environmental) damages.
3.3 DNA repair: directly undoing DNA damage; excision repair (BER; NER); recombination repair; mismatch repair (MMR); double-strand break (DSB) repair.
4. DNA restructuring (molecular mechanisms)
4.1 Homologous recombination.
4.2 Site-specific recombination.
4.3 Transposition.
5. RNA synthesis from DNA templates: transcription
5.1 General features and key players of transcription: RNA polymerases; promoters.
5.2 The mechanism of transcription in bacteria: initiation, elongation, termination.
5.3 Transcription in eukaryotes: RNA polymerases and their promoters; transcription factors.
5.4 Messenger RNA processing: splicing; capping; polyadenylation; editing.
5.5 Ribosomal RNA and transfer RNA processing.
5.6 RNA degradation.
6. From RNA to proteins: translation
6.1 Genetic code.
6.2 Structure and function of the major participants in translation: mRNA; tRNA; ribosomes.
6.3 The mechanism of translation in bacteria: initiation, elongation and termination.
6.4 Translation in eukaryotes.
6.5 Protein folding, post-translational modification and trafficking.
7. Regulation of gene expression in prokaryotes
7.1  The operon model: Lac operon; Trp operon. Negative and positive control of transcription; transcriptional attenuation.
7.2 Gene regulation of phage lambda lytic and lysogenic cycles.
7.3 Translational control.
7.4 Riboswitches.
7.5 The CRISPR cas system.
8. Regulation of gene expression in higher eukaryotes
8.1 Different layers of gene expression regulation.
8.2 Regulation at genomic level: selective alterations of DNA; chromatin remodelling; post-translational modifications of histones (histone code).
8.3 Transcriptional regulation: enhancers; silencers; gene-specific transcription factors.
8.4 Post-transcriptional regulation: processing, export, translation and stability of mRNA.
8.5 Regulation by non-coding RNAs (ncRNAs): microRNAs; siRNAs; PIWI-interacting RNAs (piRNAs); long non-coding RNAs (lncRNAs).
9. Techniques for gene expression analysis 
9.1 In situ hybridization.
9.2 Northern blotting.
9.3 Ribonuclease protection assay (RPA).
9.4 Reverse transcription (RT)-PCR.
9.5 Microarrays.

None.

D1 - Knowledge and ability of comprehension.  After completing the course, students will need to show: to have acquired a good knowledge of the key principles and basic mechanisms of molecular biology; a deep understanding and ability to discuss on topics related to gene expression, DNA replication and repair, genome and chromatin structure, regulatory RNAs; to have learned the multilayer regulatory mechanisms underlying gene expression in prokaryotes and eukaryotes; to have become familiar with the mainstream molecular biology techniques employed to analyze gene expression and with their application.

D2 - Ability to apply knowledge and comprehension. Students must be able to implement/use this knowledge in the biotechnology field, and to understand more complex topics in other related courses.

D3 - Autonomy of judgement. Students will be able to critically evaluate the theoretical background acquired during lectures, and the main molecular biology techniques which led to current knowledge.

D4 - Communication skills. Students must acquire adequate scientific language skills by taking a participatory and critical attitude to the topics of the lectures.

D5 - Learning skills. Students will demonstrate the ability to independently increase the basic knowledge of newly emerging fields of molecular biology.

The teaching material prepared by the lecturer in addition to recommended textbooks (such as for instance slides, lecture notes, exercises, bibliography) and communications from the lecturer specific to the course can be found inside the Moodle platform › blended.uniurb.it

A laboratory experience (focused on a gene expression analysis technique) will be scheduled during the course.

Teaching

Lectures.

Attendance

It is strongly suggested that students attend the lab hours.

Course books

·  F. Amaldi, P. Benedetti, G. Pesole, P. Plevani. BIOLOGIA MOLECOLARE, Terza edizione, Casa Editrice Ambrosiana, 2018.

·  J. Zlatanova, K. E. van Holde. BIOLOGIA MOLECOLARE, Struttura e dinamica di genomi e proteomi, Zanichelli, 2018.

Supplementary books:

·  J.D. Watson, T.A. Baker, S.P. Bell, A. Gann, M. Levine, R. Losick. BIOLOGIA MOLECOLARE DEL GENE, Zanichelli, 2015.

·  N. L. Craig, O. Cohen-Fix, R. Green, C. W. Greider, G. Storz, C. Wolberger. BIOLOGIA MOLECOLARE, Principi di funzionamento del genoma, Pearson, 2013.

·  D. Clark, N. Pazdernik. MOLECULAR BIOLOGY, 2nd Ed. Elsevier Science & Technology, 2012.

·  R. F. Weaver. BIOLOGIA MOLECOLARE, McGraw-Hill, 2009.

Scientific articles (reviews) will be indicated during the course.
  

Assessment

Oral examination. The oral final test will comprise at least three questions on different topics of the syllabus illustrated during the lessons, and will be aimed at determining the acquired knowledge, the degree of understanding and the ability to connect different problems. The ability to illustrate the concepts using an appropriate scientific language will be also evaluated.

Disability and Specific Learning Disorders (SLD)

Students who have registered their disability certification or SLD certification with the Inclusion and Right to Study Office can request to use conceptual maps (for keywords) during exams.

To this end, it is necessary to send the maps, two weeks before the exam date, to the course instructor, who will verify their compliance with the university guidelines and may request modifications.

Teaching

Lectures.

Attendance

It is strongly suggested that students attend the lab hours.

Course books

·  F. Amaldi, P. Benedetti, G. Pesole, P. Plevani. BIOLOGIA MOLECOLARE, Terza edizione, Casa Editrice Ambrosiana, 2018.

·  J. Zlatanova, K. E. van Holde. BIOLOGIA MOLECOLARE, Struttura e dinamica di genomi e proteomi, Zanichelli, 2018.

Supplementary books:

·  J.D. Watson, T.A. Baker, S.P. Bell, A. Gann, M. Levine, R. Losick. BIOLOGIA MOLECOLARE DEL GENE, Zanichelli, 2015.

·  N. L. Craig, O. Cohen-Fix, R. Green, C. W. Greider, G. Storz, C. Wolberger. BIOLOGIA MOLECOLARE, Principi di funzionamento del genoma, Pearson, 2013.

·  D. Clark, N. Pazdernik. MOLECULAR BIOLOGY, 2nd Ed. Elsevier Science & Technology, 2012.

·  R. F. Weaver. BIOLOGIA MOLECOLARE, McGraw-Hill, 2009.

Scientific articles (reviews) will be indicated during the course.
  

Assessment

Oral examination. The oral final test will comprise at least three questions on different topics of the syllabus illustrated during the lessons, and will be aimed at determining the acquired knowledge, the degree of understanding and the ability to connect different problems. The ability to illustrate the concepts using an appropriate scientific language will be also evaluated.

Disability and Specific Learning Disorders (SLD)

Students who have registered their disability certification or SLD certification with the Inclusion and Right to Study Office can request to use conceptual maps (for keywords) during exams.

To this end, it is necessary to send the maps, two weeks before the exam date, to the course instructor, who will verify their compliance with the university guidelines and may request modifications.

The student can request to sit the final exam in English with an alternative bibliography.