Molecular biology (2018/2019)

Course code
4S00800
Credits
12
Coordinator
Daniele Guardavaccaro
Academic sector
BIO/11 - MOLECULAR BIOLOGY
Language of instruction
Italian
Teaching is organised as follows:
Activity Credits Period Academic staff Timetable
teoria 9 II semestre Daniele Guardavaccaro

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laboratorio [laboratorio 1° turno] 3 II semestre Daniele Guardavaccaro

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laboratorio [laboratorio 2° turno] 3 II semestre Massimiliano Perduca

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Learning outcomes

The main goal of this course is to provide the students with the basic knowledge of the composition, structure and interactions of cellular molecules, such as nucleic acids and proteins, that carry out essential biological processes in eukaryotic and prokaryotic cells.

Syllabus

THEORY
DNA AND CHROMSOMES
The structure and function of DNA
Chromosomal DNA and its packaging in the chromatin fiber
Chromatin structure and function
The global structure of chromosomes
DNA REPLICATION, REPAIR AND RECOMBINATION
DNA replication mechanisms
The initiation and completion of DNA replication in chromosomes
DNA repair
Homologous recombination
Transposition and conservative site-specific recombination
HOW CELLS READ THE GENOME: FROM DNA TO PROTEIN
From DNA to RNA
From RNA to protein
Protein degradation and the ubiquitin-proteasome system
CONTROL OF GENE EXPRESSION
Control of transcription by sequence specific DNA-binding proteins
Transcription regulators
Molecular genetic mechanisms that create and maintain specialized cell types
Mechanisms reinforcing cell memory in plants and animals
Post-transcriptional controls
Regulation of gene expression by non-coding RNAs
ANALYZING CELLS AND MOLECULES
Isolating cells and growing them in culture
Analyzing and manipulating DNA
Studying gene expression and function
MEMBRANE STRUCTURE
The lipid bilayer
Membrane proteins
TRANSPORT OF SMALL MOLECULES ACROSS MEMBRANES
Principles of membrane transport
Transporters and active membrane transport
INTRACELLULAR COMPARTMENTS AND PROTEINS SORTING
The compartmentalization of cells
The transport of molecules between the nucleus and cytosol
The endoplasmic reticulum
Molecular mechanisms of protein translocation across the ER membrane
INTRACELLULAR MEMBRANE TRAFFIC
Molecular mechanisms of membrane transport
Transport from the ER through the Golgi apparatus
Transport from the trans-Golgi network to lysosomes
Transport into the cell from the plasma membrane: endocytosis
Transport from the trans-Golgi network to lysosomes
Transport from the trans-Golgi network to the cell exterior: exocytosis
CELL SIGNALING
Principles of cell signaling
Signaling through G-protein-coupled receptors
Signaling through enzyme-coupled receptors
Alternative signalling routes in gene regulation
THE CYTOSKELETON
Function of the cytoskeleton
Actin and actin-binding proteins
Myosin and actin
Microtubules
Intermediate filaments and septins
Cell polarization and migration
THE CELL CYCLE
Overview of the cell cycle
The cell cycle control system
S-phase
Mitosis
Cytokinesis
Meiosis
Control of cell division and cell growth
CELL JUNCTIONS AND THE EXTRACELLULAR MATRIX
Cell-cell junctions
The extracellular matrix of animals
Cell-matrix junctions
CANCER
Cancer as a microevolutionary process
Cancer-critical genes: oncogenes and tumor suppressors
Cancer therapy

One credit of the course (corresponding to 8 hours) will be kept for the students to discuss a topic chosen from the research literature in molecular biology.

PRACTICAL:
Subcloning and protein expression:
PCR
Electrophoresis and DNA gel extraction
Plasmid DNA purification
Digestion with restriction enzymes and ligation
Transformation and colony PCR
Heterologous expression of a recombinant protein in E. coli and analysis by SDS-PAGE and Western Blotting.

Assessment methods and criteria

Oral examination. The final exam consists of three questions concerning any of the topics treated during the course. It is passed if all answers are positive.

Reference books
Activity Author Title Publisher Year ISBN Note
teoria Jocelyn E. Krebs, Elliott S. Goldstein, Stephen T. Kilpatrick Lewin's Genes XII (Edizione 12) Jones & Bartlett Pub 2017 1284104494
teoria Bruce Alberts, Alexander Johnson, Julian Lewis, David Morgan, Martin Raff Molecular Biology of the Cell (Edizione 6) Garland Science 2014 0815344643
teoria Nancy Craig, Rachel Green, Carol Greider, Gisela Storz, Cynthia Wolberger, Orna Cohen-Fix Molecular Biology: Principles of Genome Function (Edizione 2) OUP Oxford 2014 0199658579
teoria Arnold Berk, Chris A. Kaiser, Harvey Lodish, Angelika Amon, Hidde Ploegh, Anthony Bretscher, Monty Krieger, Kelsey C. Martin Molecular Cell Biology (Edizione 8) WH Freeman 2016 1464187444
teoria Erik Pierre Molecular Cloning (Edizione 1) Ml Books International 2015 1632394685
teoria Michael R. Green e Joseph Sambrook Molecular Cloning: A Laboratory Manual, Fourth Edition (Edizione 4) CSHL Press 2012 978-1-936113-42-2
teoria Geoffrey M. Cooper, Robert E. Hausman The cell: a molecular approach (Edizione 6) Sinauer Associates, Inc 2013 978-1-60535-155-1
Teaching aids
Title Format (Language, Size, Publication date)
01 PCR di amplificazione del frammento da Miniprep  pdfpdf (it, 130 KB, 14/02/19)
02 Preparazione gel di agarosio 0.8% per la purificazione dell’amplificato  pdfpdf (it, 18 KB, 14/02/19)
03 Purificazione dell’inserto da gel utilizzando il GenElute™ Gel Extraction Kit  pdfpdf (it, 21 KB, 14/02/19)
04 Clonaggio del cDNA di una proteina umana in vettore pET22-b  pdfpdf (it, 143 KB, 14/02/19)
05 Ligazione dell’inserto nel vettore pET22-b  pdfpdf (it, 183 KB, 14/02/19)
06 Preparazione delle piastre di agar per XL1-Blue  pdfpdf (it, 12 KB, 14/02/19)
07a Preparazione delle cellule competenti XL1Blue  pdfpdf (it, 29 KB, 14/02/19)
07b Scheda preparazione delle cellule competenti XL1Blue  pdfpdf (it, 31 KB, 14/02/19)
08 Trasformazione delle cellule di di E. coli XL1Blue  pdfpdf (it, 28 KB, 14/02/19)
09 Colony PCR e piastre replica  pdfpdf (it, 129 KB, 14/02/19)
10a Miniprep Sigma  pdfpdf (it, 148 KB, 14/02/19)
10b Tagli enzimatici di controllo  pdfpdf (it, 143 KB, 14/02/19)
11 Trasformazione ceppo BL21  pdfpdf (it, 31 KB, 14/02/19)
12 Induzione ceppo BL21  pdfpdf (it, 174 KB, 14/02/19)
13 SDS PAGE  pdfpdf (it, 151 KB, 14/02/19)
14 Western Blot  pdfpdf (it, 228 KB, 14/02/19)
I-1 Ballas et al  pdfpdf (it, 1206 KB, 18/04/19)
I-2 Busino et al  pdfpdf (it, 11191 KB, 18/04/19)
I-3 Carrano et al  pdfpdf (it, 1079 KB, 18/04/19)
I-4 Cepeda et al  pdfpdf (it, 6333 KB, 18/04/19)
I-5 Duan et al  pdfpdf (it, 3841 KB, 18/04/19)
I-6 Duan2 et al  pdfpdf (it, 10278 KB, 18/04/19)
I-7 Jin et al  pdfpdf (it, 7501 KB, 18/04/19)
I-8 Koo et al  pdfpdf (it, 12248 KB, 18/04/19)
II-1 Lee et al  pdfpdf (it, 17023 KB, 18/04/19)
II-2 Mamely et al  pdfpdf (it, 645 KB, 18/04/19)
II-3 Mohamed et al  pdfpdf (it, 8060 KB, 18/04/19)
II-4 Nakano et al  pdfpdf (it, 9787 KB, 18/04/19)
II-5 Raducu et al  pdfpdf (it, 6537 KB, 18/04/19)
II-6 Strohmaier et al AND Koepp et al  pdfpdf (it, 4440 KB, 18/04/19)
II-7 Tomás-Loba et al  pdfpdf (it, 11117 KB, 18/04/19)
II-8 Zhang et al  pdfpdf (it, 3446 KB, 18/04/19)
Laboratorio Didattico Biologia Molecolare II Turno  pdfpdf (it, 111 KB, 06/03/19)
Laboratorio Didattico Biologia Molecolare I Turno  pdfpdf (it, 111 KB, 06/03/19)
Sequenza genica e primers  pdfpdf (it, 191 KB, 14/02/19)

STUDENT MODULE EVALUATION - 2017/2018