Biotechnologies

Activity type

Discipline biotecnologiche comuni

SSD

BIO/11

Year

2nd year

Semester

2nd semester

CFU

6

Hours distribution

32 classroom hours, 72 laboratory hours

Lecturers

CARLO PRESUTTI
FRANCESCA CUTRUZZOLA'

Activity type

Discipline biotecnologiche comuni

SSD

BIO/11

Year

2nd year

Semester

1st semester

CFU

6

Hours distribution

40 classroom hours, 36 laboratory hours

Lecturers

RODOLFO NEGRI
CARLO PRESUTTI

General Aims: The course aims to introduce the student to the understanding of the link between the structure of nucleic acids and proteins and their main biological functions, namely: DNA replication, transcription, recombination and repair, RNA processing and protein synthesis and quality controls and their regulatory circuits.
Specific goals:
1. Knowledge and comprehension: The student will have to know the basic molecular mechanisms of cellular homeostasis and gene regulation and the most utilized techniques in molecular biology.
2. Ability to apply knowledge and comprehension: the student will have to be able to apply this knowledge in the discussion of arguments of general interest in the recent scientific literature.
3. Ability of formulate critical judgement: The student will have to show ability to solve scientific and technical problems and to communicate to teacher and colleagues his conclusions.
4. The student will have to show abilities in applying the learned notions and methods in solving specific problems in experimental strategies.

The course is divided into four modules that introduce students to the molecular biology of DNA, RNA, and proteins, and to the main methods for characterizing nucleic acids and analyzing gene expression.

The course aims to educate students on the intimate relationship between the structure of DNA, RNA, and proteins and their functions, exploring the molecular mechanisms underlying the processes of replication and transcription, DNA recombination and repair, RNA processing, and protein synthesis, as well as their regulatory circuits.

Specific objectives:
1. Knowledge and understanding: Students will be familiar with the basic molecular mechanisms of cellular homeostasis and gene regulation, and the most commonly used techniques in molecular biology.
2. Ability to apply knowledge and understanding: Students will be able to apply this knowledge by discussing topics of recent and general interest in molecular biology research.
3. Critical thinking and judgment: Students must demonstrate critical thinking and judgment in solving problems related to molecular biology investigations and communicating their findings to the instructor and colleagues. This will also be the case during the planned technical and practical exercises.
4. Students must demonstrate the ability to further apply the analytical tools learned, for example, by developing a technical approach to a specific molecular biology problem.

Basic knowledge of Cell Biology and Inorganic and Organic Chemistry

Molecular Biology of DNA
The polimorphic DNA – Chemical components of DNA: bases, sugars and phosphodiesteric backbone – introduction to their bre-biotic synthesis (0.1 cfu). DNA B basic structure – historical framework, analytical methodologies and hyconographic representation (0.2). Alternative A and Z conformations, unusual structures (crucifiorms, triple helix) (0.1) – Conformational variability of structural parameters, curvature and bendability (0.1). DNA topology, winding and unwinding; linking number; DNA topoisomerases (0.2). The Genetic Code.: the code decrypting; the structure and function of the code (0.2). DNA replication: machinery and mechanisms in prokaryotes and eukaryotes (0.1). Replicons organization; topological and end-replication problems (0.1). DNA mutability and repair (0.2). DNA transcription: transcription in bacteria and bacteriophages; transcriptional machinery and RNA polymerase positioning signals (0.1). Metodological approach to the study of transcription: in vitro transcription systems (0.1). Transcription regulation in prokaryotic systems: activation and repressions; operon structures and function (0.1). Transcription in eukaryotic systems (0.2). ; transcriptional machinery and RNA polymerase positioning signals (0.1). Metodological approach to the study of transcription: eukaryotic in vitro transcription systems (0.1). Coordinate regulation of the three eukaryotic RNA polymerases (0.1). Transcription factors and transcription regulation in eukaryotes (0.2). Genome structure. Instruments to approach genomic sudies (0.1). Necessity of information compaction in the genomes. Chromatin basic structure in eukaryotes and prokaryotes (0.1). The structure of nucleosomes and further organization levels (0.1). Histone modifications and their regulatory effects; the histone code. (0.2). Chromatin structure and chromatin remodelling at promoters (0.1). Chromosomes structure: centromero, telomers and origin of replication (0.1).

Molecular Biology of RNA

1- The RNA molecule: chemical and functional characteristics
2- The different types of cellular RNA: characteristics and function of tRNA, rRNA, pre- and mRNA, snRNA, and snoRNA
3- "mRNA Factory":
a) Transcription initiation: sequences and protein factors involved
b) mRNA elongation and function of the Pol II CTD tail
c) Capping and its correlation with the transcription process
d) Splicing:
1) Splicing and small nuclear RNAs
2) RNA/RNA interactions and structural rearrangements in the formation of the active spliceosome
3) Protein/protein interactions in the spliceosome and involvement of SR proteins
4) Regulation of alternative splicing (sex determination in Drosophila - dsx, tra, tra-2, and sxl; ribosomal proteins)
e) Biochemical aspects of polyadenylation and its regulation
4- Transport mRNA Nucleus-Cytoplasm
5- RNA Translation and Stability (Deadenylation, Decapping, 5'-3' Interaction of the mRNA, AUUUA Sequences) - IRE Sequences and Translation/Stability of Ferritin and Transferrin Receptor mRNAs)
6- RNA World:
a) Self-Splicing (Group I and II Introns) and Evolutionary Correlations between Nuclear Splicing and Self-Splicing
b) Catalytic RNAs: Group I and II Introns, RNase P
c) Ribozymes and Their Applications
d) Considerations on the Origin of Life and the Importance of RNA (Molecular Fossils)
rRNA Processing and the Role of SnoRNPs
RNAi (Interference) and Its Applications
Introduction to Laboratory Methodologies:
1- Model Organisms and Cellular Systems for Studying the Regulation of Gene Expression
2- Identification of Interaction Partners: 2/3-Hybrid Systems Protein tagging (GST, His, Prot A, TAP)
3- Protein-nucleic acid interaction analysis: EMSA (electrophoretic mobility shift assay), RNA and DNA footprinting, UV crosslinking, TRAP assay
4- In vivo transcript analysis: Northern blot, RNase protection, S1 mapping, RT-PCR
I

James D. Watson, Tania A. Baker, Stephen P. Bell, Alexander Gann, Michael Levine, Richard Losick
Molecular Biology of the gene
or
Gene VIII - Lewin et al.

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Front lessons with videoprojection and lab training

3 hours/week

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