Consiglia TEDESCO | STRUCTURAL ANALYSIS OF BIOMOLECULES

cod. 0522100019

STRUCTURAL ANALYSIS OF BIOMOLECULES

	0522100019
	DEPARTMENT OF CHEMISTRY AND BIOLOGY "ADOLFO ZAMBELLI"
	EQF7
	BIOLOGY
	2018/2019

PERCORSO COMUNE

	OBBLIGATORIO
	YEAR OF COURSE 1
	YEAR OF DIDACTIC SYSTEM 2016
	SECONDO SEMESTRE

TEACHING UNITS

	SSD	CFU	HOURS	ACTIVITY	TYPE OF ACTIVITY
1	TECNICHE DI ANALISI STRUTTURALE PER BIOMOLECOLE (MODULO A)
	CHIM/02	4	32	LESSONS	SUPPLEMENTARY COMPULSORY SUBJECTS
	CHIM/02	2	24	LAB	SUPPLEMENTARY COMPULSORY SUBJECTS
2	TECNICHE DI ANALISI STUTTURALE PER BIOMOLECOLE (MODULO B)
	CHIM/06	4	32	LESSONS	SUPPLEMENTARY COMPULSORY SUBJECTS
	CHIM/06	2	24	LAB	SUPPLEMENTARY COMPULSORY SUBJECTS

PROFESSORS

	CONSIGLIA TEDESCO1 T Curriculum
	MARGHERITA DE ROSA2 Curriculum

	Objectives
	KNOWLEDGE AND UNDERSTANDING: THE COURSE PROVIDES AN INTRODUCTION TO THE BASICS OF SPECTROSCOPIC TECHNIQUES (NMR, IR, UV, MASSA), HIGHLIGHTING WHAT INFORMATIONS CAN BE OBTAINED FROM SIMPLE SPECTROSCOPIC EXPERIMENTS AND THEIR IMPORTANCE AS TOOLS FOR THE ANALYSIS OF MACROMOLECULAR STRUCTURES AND FUNCTIONS. THE COURSE AIMS TO INTRODUCE STUDENTS TO THE PROBLEMS OF THE STUDY OF PROTEIN STRUCTURES AND COMPLEXES BETWEEN PROTEINS AND OTHER BIOLOGICAL MACROMOLECULES, BOTH AT THE ATOMIC LEVEL AND AT THE MOLECULAR LEVEL, IN ORDER TO UNDERSTAND HOW THIS KNOWLEDGE CAN BE USED FOR THE STUDY OF COMPLEX BIOLOGICAL SYSTEMS. THE REPORT OUTLINES THE MAIN COMPUTATIONAL AND EXPERIMENTAL TECHNIQUES APPROPRIATE TO ACQUIRE SUCH SKILLS. THE STUDENT WILL THUS UNDERSTAND THE COMPLEXITY AND THE INTERDISCIPLINARY NATURE OF THIS TYPE OF RESEARCH, AND THE POTENTIAL KNOWLEDGE RESULTING FROM THESE STUDIES. APPLYING KNOWLEDGE AND UNDERSTANDING: AT THE END OF THE COURSE, THE STUDENT WILL BE ABLE TO IDENTIFY THE STRUCTURE OF ORGANIC MOLECULES BY COMPARATIVE ANALYSIS OF DIFFERENT SPECTROSCOPIC TECHNIQUES, TO ANALYZE THE THREE-DIMENSIONAL STRUCTURE OF PROTEINS, AND TO UNDERSTAND THE FUNDAMENTALS AND STRATEGIES THAT HAVE LED TO THE OBTAINING OF THE EXPERIMENTAL RESULT. HE WILL ALSO BE ABLE TO KNOW THE LIMITATIONS OF EACH TECHNIQUE PRESENTED AND TO ASSESS WHAT KNOWLEDGE ARE OBTAINABLE FROM EACH APPROACH. HE WILL ALSO BE ABLE TO UNDERSTAND HOW TO DERIVE OTHER INFORMATION FROM THIS KNOWLEDGE, IN ORDER TO UNDERSTAND THE WORKINGS OF LIVING BEINGS AT THE MACROSCOPIC LEVEL. MAKING JUDGMENTS: WITH THE EXPERTISE GAINED IN THIS COURSE, THE STUDENT WILL BE ABLE TO CRITICALLY ANALYZE THE DIFFERENT APPROACHES, TO IDENTIFY POSSIBLE STRENGTHS AND WEAKNESSES OF THE RESULTS OBTAINED FROM THESE APPROACHES, CONSIDERING THEN INDEPENDENTLY THEIR VALIDITY. HE WILL ALSO BE ABLE TO RESEARCH AND EVALUATE INDEPENDENTLY THE INFORMATION CONTAINED IN SPECIALIZED DATABASES ACCESSIBLE VIA THE WEB, TO EXTRACT THE CORRECT AND RELEVANT INFORMATION. COMMUNICATION SKILLS: THE COURSE WILL ENABLE STUDENTS TO ACQUIRE SPECIFIC TECHNICAL LANGUAGE SUITABLE FOR ACCURATELY DESCRIBE THE DIFFERENT TECHNIQUES AND DIFFERENT APPROACHES STUDIED, ALSO WITH THE READING OF ARTICLES PUBLISHED IN INTERNATIONAL SCIENTIFIC JOURNALS OR THROUGH THE DIRECT ANALYSIS OF DATA RESULTING FROM SCIENTIFIC DATABASES. LEARNING SKILLS: THE KNOWLEDGE GAINED FROM THIS COURSE WILL ALLOW STUDENTS TO LEARN THE INFORMATION THAT CAN BE OBTAINED FROM THE MOLECULAR POINT OF VIEW ON PROTEINS AND MACROMOLECULAR COMPLEXES OF THE CELLS, DEALING WITH ADVANCED TECHNIQUES FOR OBTAINING SUCH INFORMATION. FURTHERMORE, THE STUDENTS WILL ACQUIRE AN OVERVIEW OF SPECTROSCOPIC TOOLS AVAILABLE FOR THE ANALYSIS OF MACROMOLECULAR STRUCTURES AND FUNCTION.

KNOWLEDGE AND UNDERSTANDING:
THE COURSE PROVIDES AN INTRODUCTION TO THE BASICS OF SPECTROSCOPIC TECHNIQUES (NMR, IR, UV, MASSA), HIGHLIGHTING WHAT INFORMATIONS CAN BE OBTAINED FROM SIMPLE SPECTROSCOPIC EXPERIMENTS AND THEIR IMPORTANCE AS TOOLS FOR THE ANALYSIS OF MACROMOLECULAR STRUCTURES AND FUNCTIONS.
THE COURSE AIMS TO INTRODUCE STUDENTS TO THE PROBLEMS OF THE STUDY OF PROTEIN STRUCTURES AND COMPLEXES BETWEEN PROTEINS AND OTHER BIOLOGICAL MACROMOLECULES, BOTH AT THE ATOMIC LEVEL AND AT THE MOLECULAR LEVEL, IN ORDER TO UNDERSTAND HOW THIS KNOWLEDGE CAN BE USED FOR THE STUDY OF COMPLEX BIOLOGICAL SYSTEMS. THE REPORT OUTLINES THE MAIN COMPUTATIONAL AND EXPERIMENTAL TECHNIQUES APPROPRIATE TO ACQUIRE SUCH SKILLS. THE STUDENT WILL THUS UNDERSTAND THE COMPLEXITY AND THE INTERDISCIPLINARY NATURE OF THIS TYPE OF RESEARCH, AND THE POTENTIAL KNOWLEDGE RESULTING FROM THESE STUDIES.

APPLYING KNOWLEDGE AND UNDERSTANDING:
AT THE END OF THE COURSE, THE STUDENT WILL BE ABLE TO IDENTIFY THE STRUCTURE OF ORGANIC MOLECULES BY COMPARATIVE ANALYSIS OF DIFFERENT SPECTROSCOPIC TECHNIQUES, TO ANALYZE THE THREE-DIMENSIONAL STRUCTURE OF PROTEINS, AND TO UNDERSTAND THE FUNDAMENTALS AND STRATEGIES THAT HAVE LED TO THE OBTAINING OF THE EXPERIMENTAL RESULT. HE WILL ALSO BE ABLE TO KNOW THE LIMITATIONS OF EACH TECHNIQUE PRESENTED AND TO ASSESS WHAT KNOWLEDGE ARE OBTAINABLE FROM EACH APPROACH. HE WILL ALSO BE ABLE TO UNDERSTAND HOW TO DERIVE OTHER INFORMATION FROM THIS KNOWLEDGE, IN ORDER TO UNDERSTAND THE WORKINGS OF LIVING BEINGS AT THE MACROSCOPIC LEVEL.

MAKING JUDGMENTS:
WITH THE EXPERTISE GAINED IN THIS COURSE, THE STUDENT WILL BE ABLE TO CRITICALLY ANALYZE THE DIFFERENT APPROACHES, TO IDENTIFY POSSIBLE STRENGTHS AND WEAKNESSES OF THE RESULTS OBTAINED FROM THESE APPROACHES, CONSIDERING THEN INDEPENDENTLY THEIR VALIDITY. HE WILL ALSO BE ABLE TO RESEARCH AND EVALUATE INDEPENDENTLY THE INFORMATION CONTAINED IN SPECIALIZED DATABASES ACCESSIBLE VIA THE WEB, TO EXTRACT THE CORRECT AND RELEVANT INFORMATION.

COMMUNICATION SKILLS:
THE COURSE WILL ENABLE STUDENTS TO ACQUIRE SPECIFIC TECHNICAL LANGUAGE SUITABLE FOR ACCURATELY DESCRIBE THE DIFFERENT TECHNIQUES AND DIFFERENT APPROACHES STUDIED, ALSO WITH THE READING OF ARTICLES PUBLISHED IN INTERNATIONAL SCIENTIFIC JOURNALS OR THROUGH THE DIRECT ANALYSIS OF DATA RESULTING FROM SCIENTIFIC DATABASES.

LEARNING SKILLS:
THE KNOWLEDGE GAINED FROM THIS COURSE WILL ALLOW STUDENTS TO LEARN THE INFORMATION THAT CAN BE OBTAINED FROM THE MOLECULAR POINT OF VIEW ON PROTEINS AND MACROMOLECULAR COMPLEXES OF THE CELLS, DEALING WITH ADVANCED TECHNIQUES FOR OBTAINING SUCH INFORMATION. FURTHERMORE, THE STUDENTS WILL ACQUIRE AN OVERVIEW OF SPECTROSCOPIC TOOLS AVAILABLE FOR THE ANALYSIS OF MACROMOLECULAR STRUCTURES AND FUNCTION.

	Prerequisites
	A BASIC KNOWLEDGE OF ORGANIC CHEMISTRY BIOCHEMISTRY, IN PARTICULAR, KNOWLEDGE OF THE STRUCTURAL ELEMENTS OF THE PROTEINS.

	Contents
	THE COURSE CONSITS OF TWO MODULES: MODULE A AND MODULE B, EACH CONSISTING OF 56 HOURS. PLEASE NOTE THAT THE FIRST MODULE CORRESPONDS TO THE TEACHING COURSE OF CRYSTALLOGRAPHY FOR CHEMISTRY STUDENTS. THE TOPICS ADDRESSED IN MODULE A ARE: HISTORY OF CRYSTALLOGRAPHY. CRYSTALLINE SOLIDS. UNIT CELL AND ASYMMETRIC UNIT. SYMMETRY ELEMENTS. CRYSTALLIZATION OF NUCLEIC ACIDS AND PROTEINS. EXPERIMENTAL TECNIQUES FOR THE CRYSTALLIZATION OF BIOLOGICAL MACROMOLECULES.VAPOUR DIFFUSION CRYSTALLIZATION (HANGING DROP, SITTING DROP), DIFFUSION CRYSTALLIZATION, BATCH CRYSTALLIZATION.“HIGH THROUGH-PUT” CRYSTALLIZATION. CRIOCRYSTALLOGRAPHY. CRYOPROTECTORS. DATA COLLECTION. RADIATION AND MATTER. X-RAY DIFFRACTION. X-RAY SOURCES: X-RAY TUBES AND SYNCHRTRON LIGHT. X-RAY DETECTORS: CCD AND IMAGE PLATE.ROTATING CRYSTAL METHOD. HOW TO SOLVE THE STRUCTURE: THE PHASE PROBLEM. STRUCTURE FACTOR AND ELECTRON DENSITY. HEAVY ATOM METHOD, SIR, MIR, MOLECULAR REPLACEMENT, SAD, MAD. ELECTRON DENSITY MAPS. CRYSTALLOGRAPHIC DISAGREEMENT INDICES. CRYSTALLOGRAPHIC DATABASES. PROTEIN DATA BANK. CARTESIAN COORDINATES AND CRYSTALLOGRAPHIC COORDINATES. PDB FILES. PROGRAMS FOR THE VISUALIZATION OF CRYSTAL STRUCTURES. ELECTRON MICROSCOPY AND ELECTRON DIFFRACTION. CIRCULAR DICHROISM. THE TOPICS ADDRESSED IN MODULE B ARE: GENERAL PRINCIPLES OF SPECTROSCOPY. NUCLEAR MAGNETIC RESONANCE., 1H-NMR AND 13C-NMR AND MULTIPULSE MULTIDIMENSIONAL NMR TECHNIQUES. MASS SPECTROMETRY: INTRODUCTION, IONISATION PROCESSES, FRAGMENTATION PROCESSES, APPLICATIONS. ULTRAVIOLET AND VISIBLE SPECTROSCOPY: MOLECULAR ORBITAL AND ELECTRONIC TRANSITIONS, CHROMOPHORES,APPLICATIONS. INFRARED SPECTROSCOPY.

Contents

THE COURSE CONSITS OF TWO MODULES: MODULE A AND MODULE B, EACH CONSISTING OF 56 HOURS.
PLEASE NOTE THAT THE FIRST MODULE CORRESPONDS TO THE TEACHING COURSE OF CRYSTALLOGRAPHY FOR CHEMISTRY STUDENTS.

THE TOPICS ADDRESSED IN MODULE A ARE:
HISTORY OF CRYSTALLOGRAPHY. CRYSTALLINE SOLIDS. UNIT CELL AND ASYMMETRIC UNIT. SYMMETRY ELEMENTS.
CRYSTALLIZATION OF NUCLEIC ACIDS AND PROTEINS.
EXPERIMENTAL TECNIQUES FOR THE CRYSTALLIZATION OF BIOLOGICAL MACROMOLECULES.VAPOUR DIFFUSION CRYSTALLIZATION (HANGING DROP, SITTING DROP), DIFFUSION CRYSTALLIZATION, BATCH CRYSTALLIZATION.“HIGH THROUGH-PUT” CRYSTALLIZATION. CRIOCRYSTALLOGRAPHY. CRYOPROTECTORS.
DATA COLLECTION. RADIATION AND MATTER. X-RAY DIFFRACTION. X-RAY SOURCES: X-RAY TUBES AND SYNCHRTRON LIGHT. X-RAY DETECTORS: CCD AND IMAGE PLATE.ROTATING CRYSTAL METHOD.
HOW TO SOLVE THE STRUCTURE: THE PHASE PROBLEM. STRUCTURE FACTOR AND ELECTRON DENSITY. HEAVY ATOM METHOD, SIR, MIR, MOLECULAR REPLACEMENT, SAD, MAD. ELECTRON DENSITY MAPS. CRYSTALLOGRAPHIC DISAGREEMENT INDICES.
CRYSTALLOGRAPHIC DATABASES. PROTEIN DATA BANK. CARTESIAN COORDINATES AND CRYSTALLOGRAPHIC COORDINATES. PDB FILES. PROGRAMS FOR THE VISUALIZATION OF CRYSTAL STRUCTURES.
ELECTRON MICROSCOPY AND ELECTRON DIFFRACTION.
CIRCULAR DICHROISM.

THE TOPICS ADDRESSED IN MODULE B ARE:
GENERAL PRINCIPLES OF SPECTROSCOPY. NUCLEAR MAGNETIC RESONANCE., 1H-NMR AND 13C-NMR AND MULTIPULSE MULTIDIMENSIONAL NMR TECHNIQUES. MASS SPECTROMETRY: INTRODUCTION, IONISATION PROCESSES, FRAGMENTATION PROCESSES, APPLICATIONS. ULTRAVIOLET AND VISIBLE SPECTROSCOPY: MOLECULAR ORBITAL AND ELECTRONIC TRANSITIONS, CHROMOPHORES,APPLICATIONS. INFRARED SPECTROSCOPY.

	Teaching Methods
	THE COURSE IS SUPPLEMENTED BY TWO MODULES: MODULE A AND MODULE B. IN DETAIL FOR EACH MODULE 32 HOURS (4 CFUS) ARE DEVOTED TO LECTURES AND 24 HOURS (2 CFUS) FOR CLASSROOM EXERCISES OR PRACTICAL SESSIONS. DURING THE LECTURES SLIDE PRESENTATIONS ARE USED TOGETHER WITH MULTIMEDIA MATERIAL VIA THE WEB. MOREOVER, AT THE END OF THE COURSE. FOR THE MODULE A DURING THE PRACTICAL SESSIONS THE STUDENTS PERSONALLY CARRY OUT EXPERIMENTS RELATED TO THE STRUCTURAL CHARACTERIZATION OF A PROTEIN, AS CRISTALLIZATION AND STRUCTURAL DETERMINATION AND VALIDATION. FOR THE MODULE B ARE PROVIDED: (A) INTERACTIVE CLASSROOM EXERCISES (12 HOURS) AS A GUIDE TO SOLVING SPECTRAL PROBLEMS RELATED TO STRUCTURE DETERMINATION OF ORGANIC MOLECULE ANALYSING EXAMPLE SPECTRA ; B) LABORATORY SESSION (12 HOURS) WHERE THE STUDENTS CARRY OUT SPECTROSCOPY EXPERIMENTS WITH SUPERVISION.

Teaching Methods

THE COURSE IS SUPPLEMENTED BY TWO MODULES: MODULE A AND MODULE B.
IN DETAIL FOR EACH MODULE 32 HOURS (4 CFUS) ARE DEVOTED TO LECTURES AND 24 HOURS (2 CFUS) FOR CLASSROOM EXERCISES OR PRACTICAL SESSIONS.
DURING THE LECTURES SLIDE PRESENTATIONS ARE USED TOGETHER WITH MULTIMEDIA MATERIAL VIA THE WEB. MOREOVER, AT THE END OF THE COURSE.

FOR THE MODULE A DURING THE PRACTICAL SESSIONS THE STUDENTS PERSONALLY CARRY OUT EXPERIMENTS RELATED TO THE STRUCTURAL CHARACTERIZATION OF A PROTEIN, AS CRISTALLIZATION AND STRUCTURAL DETERMINATION AND VALIDATION.
FOR THE MODULE B ARE PROVIDED: (A) INTERACTIVE CLASSROOM EXERCISES (12 HOURS) AS A GUIDE TO SOLVING SPECTRAL PROBLEMS RELATED TO STRUCTURE DETERMINATION OF ORGANIC MOLECULE ANALYSING EXAMPLE SPECTRA ; B) LABORATORY SESSION (12 HOURS) WHERE THE STUDENTS CARRY OUT SPECTROSCOPY EXPERIMENTS WITH SUPERVISION.

	Verification of learning
	THE EXAM CONSISTS OF: A) THE DETAILED DESCRIPTION, VIA A SLIDE SHOW, OF A THREE-DIMENSIONAL STRUCTURE CHOSEN BY THE STUDENT. STARTING FROM WHAT EMERGED DURING THE DISCUSSION, OTHER ISSUES ARE ADDRESSED RELATED TO THE COURSE TOPICS.B) RESOLUTION OF THE STRUCTURE OF BIOMOLECULES BY SPECTROSCOPIC NMR, IR, UV AND MASSA. THE FINAL ASSESSMENT TAKES INTO ACCOUNT THE DEGREE OF UNDERSTANDING OF THE STUDENT, THE EXACTNESS OF THE TERMS USE, CRITICAL THINKING AND ABILITY TO CREATE AND UNDERSTAND CONNECTIONS TO OTHER ISSUES ADDRESSED DURING THE DISCUSSION. THE EXAM AIMS TO ASCERTAIN THE KNOWLEDGE AND THE UNDERSTANDING OF THE COURSE CONTENTS, THE ABILITY TO APPLY THE ACQUIRED SKILLS AND TO DEVELOP INDEPENDENT SOLUTIONS.

Verification of learning

THE EXAM CONSISTS OF: A) THE DETAILED DESCRIPTION, VIA A SLIDE SHOW, OF A THREE-DIMENSIONAL STRUCTURE CHOSEN BY THE STUDENT. STARTING FROM WHAT EMERGED DURING THE DISCUSSION, OTHER ISSUES ARE ADDRESSED RELATED TO THE COURSE TOPICS.B) RESOLUTION OF THE STRUCTURE OF BIOMOLECULES BY SPECTROSCOPIC NMR, IR, UV AND MASSA. THE FINAL ASSESSMENT TAKES INTO ACCOUNT THE DEGREE OF UNDERSTANDING OF THE STUDENT, THE EXACTNESS OF THE TERMS USE, CRITICAL THINKING AND ABILITY TO CREATE AND UNDERSTAND CONNECTIONS TO OTHER ISSUES ADDRESSED DURING THE DISCUSSION.
THE EXAM AIMS TO ASCERTAIN THE KNOWLEDGE AND THE UNDERSTANDING OF THE COURSE CONTENTS, THE ABILITY TO APPLY THE ACQUIRED SKILLS AND TO DEVELOP INDEPENDENT SOLUTIONS.

	Texts
	A. IMMIRZI, C. TEDESCO LA DIFFRAZIONE DEI CRISTALLI, LIBRERIAUNIVERSITARIA.IT EDIZIONI, 2017. A. DUCRUIX, R. GIEGE' CRYSTALLYZATION OF NUCLEIC ACIDS AND PROTEINS A PRACTICAL APPROACH, OXFORD UNIVERSITY PRESS METODI SPETTROSCOPICI IN CHIMICA ORGANICA M. HESSE - H. MEIER - B. ZEEH , ED. EDISES ESERCIZI DI IDENTIFICAZIONE E CARATTERIZZAZIONE STRUTTURALE DI COMPOSTI ORGANICI-ROSSI, NAVA, ABBIATI, CELENTANO, PANDINI, ED. EDISES SPECTROSCOPY FOR THE BIOLOGICAL SCIENCES GORDON G. HAMMES, ED. JOHN WILEY & SONS

Texts

A. IMMIRZI, C. TEDESCO LA DIFFRAZIONE DEI CRISTALLI, LIBRERIAUNIVERSITARIA.IT EDIZIONI, 2017.
A. DUCRUIX, R. GIEGE' CRYSTALLYZATION OF NUCLEIC ACIDS AND PROTEINS A PRACTICAL APPROACH, OXFORD UNIVERSITY PRESS
METODI SPETTROSCOPICI IN CHIMICA ORGANICA M. HESSE - H. MEIER - B. ZEEH , ED. EDISES
ESERCIZI DI IDENTIFICAZIONE E CARATTERIZZAZIONE STRUTTURALE DI COMPOSTI ORGANICI-ROSSI, NAVA, ABBIATI, CELENTANO, PANDINI, ED. EDISES
SPECTROSCOPY FOR THE BIOLOGICAL SCIENCES GORDON G. HAMMES, ED. JOHN WILEY & SONS

	More Information
	THE COURSE NOTES ARE MADE AVAILABLE ON THE WEBSITE.

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Consiglia TEDESCO | STRUCTURAL ANALYSIS OF BIOMOLECULES