OVERVIEW

Molecular Biology is a 64-hour intensive course divided into 32 two-hour lectures, which takes place in the second semester of the second year of the Biotechnology Studies Course. The timetable is three lessons per week. The teaching programme covers general aspects of molecular biology, from the structure of genomes and the mechanisms that control their integrity to the regulation of gene expression in prokaryotes and eukaryotes.

AIMS AND CONTENT

LEARNING OUTCOMES

The course is organized in 32 units of 2 hours. The course aims to equip the student with a basic knowledge of the complexity of prokaryotic and eukaryotic genomes, of their structural and functional organization and of the aspects related to their evolution. The course covers the aspects related to the stability of the genomes, including the accuracy of the replication machinery and the mechanisms of DNA repair. Particular emphasis is dedicated to regulation of gene expression both in prokaryotes and eukaryotes. Information about the techniques to produce transgenic animals are provided. The course is highly interactive and the students are encouraged to formulate hypothesis and possible strategies to test them.

AIMS AND LEARNING OUTCOMES

The aim of the course is to provide students with knowledge on the structure, organization and complexity of prokaryotic and eukaryotic genomes, DNA replication and repair mechanisms and their accuracy, Regulation of gene expression in prokaryotes and eukaryotes, with particular emphasis on metazoa. The lessons are organized in such a way as to stimulate active participation of students who are encouraged to think critically about the topics addressed and solve problems and with conceptual experiments in ways.

At the end of the course, the student is expected to be able to:

- describe with correct terminology the processes of gene information transmission, the general structure of prokaryotic and eukaryotic genomes, the mechanisms underlying the regulation of gene expression

- to frame the role that evolutionary processes have played in defining the accuracy of the different levels of transmission of gene information

- to appreciate the degree of reliability of theses and statements relating to the molecular biology of the cell on the basis of the type of experimental evidence on which they are based

- apply the knowledge acquired to design simple experimental designs to demonstrate simple hypotheses relating to molecular biology problems.

PREREQUISITES

In addition to the preparatory rules, it would be useful to have clear basic concepts of the computer science course (information, boolean logic) and mathematics (properties of logarithms, generalities on continuous functions) in order to follow the course more easily.

TEACHING METHODS

Lectures, summary questionnaires conducted with computer tools, seminar lesson.

Any Student with documented Specific Learning Disorders (SLD), or with any special needs, should contact the Lecturer(s) and to the dedicated SLD Representative in the Department before class begins, in order to liaise and arrange the specific teaching methods so that the learning aims and outcomes may be met.

SYLLABUS/CONTENT

Lesson 1: Biomolecules, biological process control and catalysis. Aminoacyl-tRNA synthetases and the maintenance of genetic code.

Lesson 2: RNA catalysis: Group I introns; hammerhead ribozymes. The world at RNA.

Lesson 3: DNA basics, pairing, major and minor sulcus, DNA-protein interactions. The genetic code, reading charts, frequency of codons.

Lesson 4: Structure of bacterial genomes and eukaryotic genomes. Considerations on the organization of the prokaryotic genome.

Lesson 5: Gene families and duplications of genomic regions. The unequal crossing over. Evolution of globine clusters.

Lesson 6: Modularity of proteins. The organization in introns and exons and its likely evolutionary significance. Transposons as the engine of genomic rearrangements.

Lesson 7: Kinetics of reassociation and curves C0t. Repeated sequences. The satellite DNA. The dynamics of simple repeated sequences. Mini and micro satellites.

Lesson 8: Transposable elements. IS elements and typical bacterial transposons. The life cycle of retroviruses. Non-retroviral retrotransposons. Transposable elements in mammalian genomes. LINES and SINES

Lesson 9: DNA replication general considerations on mutation frequency. Considerations on replication accuracy and the need for RNA primers.

Lesson 10: Considerations on replication accuracy and the need for RNA primers. Molecular anatomy of the replicative fork. Polymerase III holoenzyme. Elysaces, Ssbp, ligases.

Lesson 11: DNA topology, bond number. Class I and II topoisomerases.

Lesson 12: Eukaryotic DNA polymerases. The importance of methylation. Origins of replication in eukaryotes. Speed of replication. Telomerase.

Lesson 13: Repair of mismatches on the neosynthesized filament.

Lesson 14: DNA damage and repair strategies for common damage. NER, BER, SOS systems.

Lesson 15: General recombination, crossing-over and gene conversion.

Lesson 16: Knock-out and knock-in transgenic animals. Targeting constructs, methods for the selection of homologous recombinant. Site specific CRE/LoxP recombination. Conditional knock-outs.

Lesson 17: Example of using transgenic animals and the Cre/Lox recombination: The progeny of the radial glia (Organized on the model of scientific seminar with material in English).

Lesson 18: The emerging properties of complex systems. Local iterative rule systems and cellular automata.

Lesson 19: Control of gene expression. Transcriptional controls: the bacteria paradigm. RNA polymerases and the structure of E-coli’s RNA polymerase.

Lesson 20: Transcription control strategies of operations. Sigma subunits. Termination of transcription. Control strategies based on Rho-dependent termination.

Lesson 21: Bacterial transcriptional repressors, DNA binding domains. Tryptophan operon attenuator. Riboswitches. Eukaryotic polymerases. Structural and functional differences.

Lesson 22: Eukaryotic RNA polymerases. Distribution of transcription work. Transcriptional factories and nucleolus. The role of Pol-III.

Lesson 23: The regulation of transcription by Pol-II. Basal promoters of RNA polymerase II. "general" factors and specific tissue. Cooperative and combinatorial activation/inhibition strategies.

Lesson 24: Transcription factors, their most common structural domains. The determination of the anteroposterior axis of Drosophila. Gap genes. Promoters of primary and secondary pair-rule genes.

Lesson 25: Logical circuits of transcriptional regulation. Wide-ranging controls, Histone modifications. Chromatin remodeling. DNA methylation and imprinting.

Lesson 26: Post-transcriptional Processes. Capping and polyadenylation. The editing of messengers. Splicing. Role of SnuRPs and RNA catalysis. Splicing and alternative splicing order.

Lesson 27: Splicing control and sex determination in Drosophila. Nuclear transport and NMD control. Location of messengers.

Lesson 28: The stability of messengers. Nanos and Bicoid in controlling the stability of messengers. RNA interference and MicroRNAs and the concept of "programmable" nucleases. The use of artificial microRNAs in the laboratory.

Lesson 29: Nucleases programmable for DNA: the discovery of CRISPR-CAS systems. Genomic editing and other examples of the use of CRISPR-CAS systems in laboratory practice.

Lesson 30: Translation: mechanics, energies in play, accuracy control.

Lesson 31: Control of folding: the chaperones hsp70 and hsp60.

Lesson 32: Examination of a literature article.

RECOMMENDED READING/BIBLIOGRAPHY

Alberts et al. (2016) - Biologia molecolare della cellula. Ed. 6.

Watson et al. (2015) - Biologia molecolare del gene. Ed. 7.

TEACHERS AND EXAM BOARD

Exam Board

IRENE APPOLLONI (President)

PAOLO MALATESTA (President)

DAVIDE CERESA

LESSONS

LESSONS START

II semester, in March.

Class schedule

The timetable for this course is available here: Portale EasyAcademy

EXAMS

EXAM DESCRIPTION

Oral examination.

ASSESSMENT METHODS

The assessment of the achievement of the objectives of the course is evaluated, during the course itself, with 3 tests on the road consisting of questionnaires with multiple choice questions whose result is not reflected in the grade of the exam, but that allows to evaluate the effectiveness of the teaching in the course of work, allowing any adjustments.

The final exam consists of an oral test, which lasts on average one hour per candidate and is divided into three parts: the first part consists of asking the candidate to draw the structure formula for one of the nucleotides or correctly matched base pairs. Any error at this stage precludes the continuation of the test. The second part is about a subject chosen by the candidate to which detailed questions are asked in the recruitment that the topic chosen is the one best known. Finally, the third part consists of three or four questions on any point in the programme aimed at clarifying the level of coverage of the programme.

Exam schedule