MOLECULAR BIOLOGY
Course unit partition: Cognomi N-Z

Academic year 2011/12
2° year of course - Second semester
Professor
Academic discipline
Biologia molecolare (BIO/11)
Field
Ambito aggregato per crediti di sede
Type of training activity
Base
72 hours
of face-to-face activities
9 credits
hub: -
course unit
in - - -

Course unit partition: MOLECULAR BIOLOGY

Learning objectives

The main objective of the course is the understanding of the fundamental biochemical aspects of nucleic acids. Particular attention will be given to the understanding the DNA structure elements on the basis of which the peculiar characteristics of stability, informational content and legibility of the genetic material will be explained. The molecular mechanisms at the basis of the DNA replication, repair, transcription and translation processes will be analysed in depth. A large part of the course will be dedicated to the understanding of the fundamental regulatory strategies operating in bacteria and bacteriophages and their possible implication for the control of gene expression in more complex organisms.

For better understanding of the course it is essential for the student to know the basic principles of chemistry, biochemistry and genetics.

Teaching method. The course consists of classroom lectures held with a frequency of three two-hour lectures per week. Assessment is based on a written and oral exam. The written test consists of ten questions to assess the level of learning and critical analysis of the topics dealt with.

Prerequisites

- - -

Course unit content

STRUCTURE OF NUCLEIC ACIDS

DNA REPLICATION

DNA REPAIR

TRANSCRIPTION

RNA SPLICING

TRANSLATION

GENE REGULATION IN PROKARYOTES

MOLECULAR BIOLOGY TECHNIQUES

Full programme

STRUCTURE OF NUCLEIC ACIDS
Properties of genetic material: The transforming principle, Avery's discovery, Chargaff rule; chemico-physical properties of nucleotides; chemical modifications, protonation and keto-enolic tautomerism of nitrogenous bases; the primary structure of DNA; the thermodynamics of the phosphodiester bond; weak bonds and strong bonds; the double helix and base pairing according to the Watson and Crick model; semi-conservative DNA replication; alternative secondary DNA structures (DNA A, DNA Z, DNA H); repeated direct, inverted and specular sequences; and intrinsic curvature of DNA; structural DNA recognition elements (read-out); specific DNA-protein interactions; stability of the double helix: fusion and renaturation of DNA; primary and secondary structure and distinguishing characteristics of RNA; alkaline hydrolysis of RNA and mechanism of action of RNase A; topology elements: supercoiling, bond number and conformational variations of DNA; topoisomerase I and II; condensation of nucleic acids: histones, nucleosome, fibres and higher-order chromatin structures.


DNA REPLICATION
General outline of replication: DNA thermodynamics and synthesis mechanism; structure of the active DNA polymerase site; processivity and sliding clamp; DNA polymerase proof-reading activities; semi-discontinuous DNA synthesis: leading strand, lagging strand, Okazaki fragments and removal of primers; mechanism of action of DNA ligase; origins of replication; DNA polymerase III, replisome structure and assembly; DNA primase, DNA helicase, DNA topoisomerase and other proteins involved in replication; bidirectional replication of the E. coli genome; replication of eukaryotic genomes; the problem of DNA ends.

DNA REPAIR
Point mutations; hydrolytic damage and chemical modifications of nitrogenous bases; Ames test; mismatch repair; repair by photoreactivation; repair by excision of bases; repair by nucleotide excision; repair by homologous recombination; translesion DNA synthesis; induction of SOS response.

TRANSCRIPTION
General structure of genes and prokaryotic operons; bacterial promotors: regions -10 and -35, UP elements, extended element -10; bacterial RNA polymerase structure; the sigma factor; general outline of the transcription process: initiation, elongation, termination. Transcription in eukaryotes: promotors, the pre-initiation complex, the mediator, RNA polymerase II; capping and polyadenylation of RNA; RNA polymerases I and III.

RNA SPLICING
Introns, exons and post-transcriptional processing of the primary transcripts; splicing chemistry; the spliceosome; splicing of group I and II introns; alternative splicing; RNA editing; transport of mRNA out of the nucleus.

TRANSLATION
The genetic code; messenger RNA (mRNA) structure; transfer RNA (tRNA) structure; attachment of amino acids to tRNA; aminoacyl-tRNA synthetases; the ribosome; peptide bond formation; molecular mechanism and functional phases of translation: initiation, elongation, termination; translation fidelity and energetics; the problem of broken RNAs.

GENE REGULATION IN PROKARYOTES
General principles of transcriptional regulation; positive and negative regulation of transcription; remote action; lactose operon: LacI, Cap; alternative sigma factors; NtrC, MerR and AraC; tryptophan operon (TrpR) and attenuation; transcriptional regulation and the lysis-lysogeny decision of lambda phage; structure a function of cI and cro repressors; cooperativity in the repressor bond; positive and negative transcriptional control, antitermination, RNA-mediated regulation, riboswitch. Lambda integration and excision by site-specific recombination.

MOLECULAR BIOLOGY TECHNIQUES
Polymerase (PCR) chain reaction; DNA sequencing by the Sanger method.

Bibliography

BIOLOGIA MOLECOLARE DEL GENE Sesta edizione - autore James Watson, casa ed. Zanichelli

BIOLOGIA MOLECOLARE - autori: Amaldi, Benedetti, Pesole, Plevani. Casa ed. Ambrosiana, dist. Zanichelli

I PRINCIPI DI BIOCHIMICA DI LEHNINGER Quinta edizione - autore David Nelson e Michael Cox, casa ed. Zanichelli

REGOLAZIONE GENICA - autore Mark Ptashne, casa ed. Zanichelli

Teaching methods

Lecture

Assessment methods and criteria

Written and oral examination

Other information

- - -