Biochemistry (2015/2016)

Course code
4S00103
Credits
12
Coordinator
Paola Dominici
Other available courses
Teaching is organised as follows:
Unit Credits Academic sector Period Academic staff
ELEMENTI DI BIOCHIMICA 6 BIO/10-BIOCHEMISTRY I semestre Paola Dominici
LABORATORIO DI BIOINFORMATICA I 6 BIO/10-BIOCHEMISTRY II semestre Daniele Dell'Orco

Learning outcomes

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MM: ELEMENTI DI BIOCHIMICA
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MM: LABORATORIO DI BIOINFORMATICA I
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The course will provide the theoretical and practical basis to understand and employ algorithms and programs currently used in Bioinformatics. Major biological databases will be introduced with a special focus on genomic, proteomic and biochemical information. The students will also be introduced to the most modern fields of structural bioinformatics and systems biology.

Syllabus

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MM: LABORATORIO DI BIOINFORMATICA I
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Theoretical Module - Overview of the main structural features of proteins and nucleic acids in relation to the concept of evolution. Introduction to biomolecular databases: online resources and their use - Biological databases: organization and integration of information concerning: a) protein and nucleic acid sequences; b) biomolecular structures; c) bibliographic and scientific literature. Retrieve of specific information: use of limitations and Boolean operators. - Sequence comparison and alignments: static and dynamic algorithms; substitution matrices (PAM,BLOSUM) - - Search-algorithms: FASTA and BLAST; Smith-Waterman; Needleman-Wunsch; statistic significance for an alignment (z-score, expectation values and probability) - Multiple sequence alignments: ClustalW, search on specific databases, other algorithms, PSI-BLAST - Short introduction on philogenetic trees - Introduction to Structural Bioinformatics: visualization and analysis of protein and nucleic acid 3D structures - Methods to predict protein secondary structure elements starting from the sequence - Introduction to Systems Biology: Spatial and temporal scales, static and dynamic models, mathematical frameworks, introduction on signal transduction networks Laboratory Module - Introduction to Linux - NCBI databases: Entrez interface, Gene, UniGene, Protein, Uniprot and EBI - Single and multiple sequence alignments, score matrices, optimal methods; online resources and spreadsheets - BLAST,PSI-BLAST and BLAT: online tools and their use - Tools for multiple alignments, the Homologene databank, computation and visualization of multiple alignments - Tools for phylogenesis : Mobyle (Institut Pasteur and Phylogeny.fr) - Introduction to PyMol and molecular visualization. Use of PSI-PRED and JPRED for predicting secondary structures from sequences - Systems biology: numerical simulation of simple biochemical reactions. Building simple kinetic models by using SBOTOOLBOX2 for Matlab; application to G-potein signalling cycles.

Assessment methods and criteria

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MM: LABORATORIO DI BIOINFORMATICA I
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Written exam for both modules. The two marks will be averaged. Students can chose to prepare a presentation in groups of 3-4 students on a selected database, which will also contribute to the final mark. An oral examination can be chose in addition, in order to improve the final mark.

Reference books
Author Title Publisher Year ISBN Note
BERG-TYMOCZKO- STRYER BIOCHIMICA (Edizione 7) ZANICHELLI 2012