Anna MARABOTTI | ADVANCED BIOCHEMISTRY

cod. 0522100020

ADVANCED BIOCHEMISTRY

	0522100020
	DEPARTMENT OF CHEMISTRY AND BIOLOGY "ADOLFO ZAMBELLI"
	EQF7
	BIOLOGY
	2020/2021

PERCORSO SHARED STUDY PATHWAY

	OBBLIGATORIO
	YEAR OF COURSE 2
	YEAR OF DIDACTIC SYSTEM 2016
	PRIMO SEMESTRE

TEACHING UNITS

SSD	CFU	HOURS	ACTIVITY	TYPE OF ACTIVITY
BIO/10	4	32	LESSONS	COMPULSORY SUBJECTS, CHARACTERISTIC OF THE CLASS
BIO/10	2	24	LAB	COMPULSORY SUBJECTS, CHARACTERISTIC OF THE CLASS

	Objectives
	KNOWLEDGE AND UNDERSTANDING: THE TEACHING, FOCUSED ON THE BIOMOLECULAR CONTEXT, AIMS TO INTRODUCE THE STUDENT TO THE PROBLEMS OF THE STUDY OF PROTEINS 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 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 ANALYZE THE INFORMATION ON 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 WHICH KNOWLEDGE IS 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.

KNOWLEDGE AND UNDERSTANDING:
THE TEACHING, FOCUSED ON THE BIOMOLECULAR CONTEXT, AIMS TO INTRODUCE THE STUDENT TO THE PROBLEMS OF THE STUDY OF PROTEINS 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 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 ANALYZE THE INFORMATION ON 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 WHICH KNOWLEDGE IS 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.

	Prerequisites
	THE STUDENT MUST HAVE ACQUIRED THE BASIC KNOWLEDGE IN THE BIOCHEMISTRY SUPPLIED BY THE STUDY PROGRAM OF THE BACHELOR DEGREE IN BIOCHEMICAL SCIENCES, WITH PARTICULAR REFERENCE TO THE KNOWLEDGE OF THE STRUCTURAL FEATURES OF THE PROTEINS. IN PARTICULAR IT IS REQUIRED THE KNOWLEDGE OF: MAIN CHEMICAL BONDS OF THE BIOLOGICAL MACROMOLECULES, CHEMICO-PHYSICAL FEATURES OF DIFFERENT AMINO ACIDS, KNOWLEDGE OF THE 1- AND 3-LETTER CODES FOR THEIR REPRESENTATION, DIFFERENT STRUCTURE LEVELS OF THE BIOLOGIC MACROMOLECULES AND THEIR FUNCTIONAL SIGNIFICANCE .

Prerequisites

THE STUDENT MUST HAVE ACQUIRED THE BASIC KNOWLEDGE IN THE BIOCHEMISTRY SUPPLIED BY THE STUDY PROGRAM OF THE BACHELOR DEGREE IN BIOCHEMICAL SCIENCES, WITH PARTICULAR REFERENCE TO THE KNOWLEDGE OF THE STRUCTURAL FEATURES OF THE PROTEINS. IN PARTICULAR IT IS REQUIRED THE KNOWLEDGE OF: MAIN CHEMICAL BONDS OF THE BIOLOGICAL MACROMOLECULES, CHEMICO-PHYSICAL FEATURES OF DIFFERENT AMINO ACIDS, KNOWLEDGE OF THE 1- AND 3-LETTER CODES FOR THEIR REPRESENTATION, DIFFERENT STRUCTURE LEVELS OF THE BIOLOGIC MACROMOLECULES AND THEIR FUNCTIONAL SIGNIFICANCE .

	Contents
	THE COURSE INCLUDES HOURS OF DIDACTICS IN THE FORM OF FRONTAL LESSONS AND HOURS OF GUIDED AND AUTONOMOUS EXERCISES IN THE LABORATORY OF BIOINFORMATICS, DURING WHICH THE STUDENTS DIRECTLY CHECK WHAT THE TEACHER INTRODUCES DURING THE LESSON (WITH A LEARNING-BY-DOING APPROACH). THE TOPICS PRESENTED IN THE CLASSROOM LESSONS AND EXERCISES ARE: - THE PROTEINS: DEEP ANALYSIS OF THEIR DIFFERENT STRUCTURAL FEATURES (ABOUT 6 H OF FRONT DIDACTICS + 2 H GUIDED EXERCISES IN THE BIOINFORMATORY LABORATORY) - METHODS FOR THE VALIDATION OF THE PROTEIN STRUCTURES, OBTAINED BY BOTH "WET" AND "IN SILICO" APPROACHES (ABOUT 4 H OF FRONT DIDACTICS + 2 H OF GUIDED EXERCISES IN THE BIOINFORMATORY LABORATORY) - METHODS FOR THE STUDY OF PROTEINS BY "IN SILICO" APPROACHES: APPLICATIONS OF COUPLE AND MULTIPLE ALIGNMENT ALGORITHMS, PREDICTION OF THE STRUCTURAL AND FUNCTIONAL PROPERTIES OF PROTEINS THROUGH PROFILES, MODELING OF THE STRUCTURE OF PROTEINS WITH TEMPLATE-BASED AND TEMPLATE-FREE COMPUTATIONAL APPROACHES (ABOUT 12 H OF FRONT DIDACTICS + 6 H OF GUIDED EXERCISES IN THE BIOINFORMATORY LABORATORY) - MOLECULAR MECHANICS WITH PARTICULAR REFERENCE TO FORCE FIELD CONCEPT, MINIMIZATION, MOLECULAR DYNAMICS, SIMULATED ANNEALING (ABOUT 6 H OF FRONT DIDACTICS) - THE STRUCTURAL BASES OF THE PROTEIN FUNCTIONS: FLEXIBILITY, CHAMELEON PROTEINS AND MOONLIGHTING PROTEINS, INTRINSICALLY DISORDERED PROTEINS (ABOUT 2 H OF FRONTAL TEACHING) - DOCKING PROTEIN/LIGAND (ABOUT 2 H OF FRONT DIDACTICS + 2 H GUIDED EXERCISES IN THE BIOINFORMATIC LABORATORY) THE TOPICS TREATED IN THE COMPUTATIONAL LABORATORY ACTIVITIES (12 H) CONCERN THE PRACTICAL APPLICATION OF ALL TECHNIQUES LEARNT FOR THE SOLUTION OF A PRECISE BIOLOGICAL PROBLEM, TO BE ADDRESSED THROUGH GROUP WORK (SEE FINAL TEST SECTION).

Contents

THE COURSE INCLUDES HOURS OF DIDACTICS IN THE FORM OF FRONTAL LESSONS AND HOURS OF GUIDED AND AUTONOMOUS EXERCISES IN THE LABORATORY OF BIOINFORMATICS, DURING WHICH THE STUDENTS DIRECTLY CHECK WHAT THE TEACHER INTRODUCES DURING THE LESSON (WITH A LEARNING-BY-DOING APPROACH).

THE TOPICS PRESENTED IN THE CLASSROOM LESSONS AND EXERCISES ARE:
- THE PROTEINS: DEEP ANALYSIS OF THEIR DIFFERENT STRUCTURAL FEATURES (ABOUT 6 H OF FRONT DIDACTICS + 2 H GUIDED EXERCISES IN THE BIOINFORMATORY LABORATORY)
- METHODS FOR THE VALIDATION OF THE PROTEIN STRUCTURES, OBTAINED BY BOTH "WET" AND "IN SILICO" APPROACHES (ABOUT 4 H OF FRONT DIDACTICS + 2 H OF GUIDED EXERCISES IN THE BIOINFORMATORY LABORATORY)
- METHODS FOR THE STUDY OF PROTEINS BY "IN SILICO" APPROACHES: APPLICATIONS OF COUPLE AND MULTIPLE ALIGNMENT ALGORITHMS, PREDICTION OF THE STRUCTURAL AND FUNCTIONAL PROPERTIES OF PROTEINS THROUGH PROFILES, MODELING OF THE STRUCTURE OF PROTEINS WITH TEMPLATE-BASED AND TEMPLATE-FREE COMPUTATIONAL APPROACHES (ABOUT 12 H OF FRONT DIDACTICS + 6 H OF GUIDED EXERCISES IN THE BIOINFORMATORY LABORATORY)
- MOLECULAR MECHANICS WITH PARTICULAR REFERENCE TO FORCE FIELD CONCEPT, MINIMIZATION, MOLECULAR DYNAMICS, SIMULATED ANNEALING (ABOUT 6 H OF FRONT DIDACTICS)
- THE STRUCTURAL BASES OF THE PROTEIN FUNCTIONS: FLEXIBILITY, CHAMELEON PROTEINS AND MOONLIGHTING PROTEINS, INTRINSICALLY DISORDERED PROTEINS (ABOUT 2 H OF FRONTAL TEACHING)
- DOCKING PROTEIN/LIGAND (ABOUT 2 H OF FRONT DIDACTICS + 2 H GUIDED EXERCISES IN THE BIOINFORMATIC LABORATORY)

THE TOPICS TREATED IN THE COMPUTATIONAL LABORATORY ACTIVITIES (12 H) CONCERN THE PRACTICAL APPLICATION OF ALL TECHNIQUES LEARNT FOR THE SOLUTION OF A PRECISE BIOLOGICAL PROBLEM, TO BE ADDRESSED THROUGH GROUP WORK (SEE FINAL TEST SECTION).

	Teaching Methods
	THE TEACHING PROVIDES 56 HOURS OF TEACHING PARTITIONED INTO FRONT LESSONS, EXERCISES AND PRACTICAL LABORATORY (6 CFUS). IN PARTICULAR, THERE ARE 32 HOURS OF CLASSROOM LESSONS (4 CFUS), 12 HOURS OF LABORATORY GUIDED EXERCISES (1 CFU) AND 12 HOURS OF AUTONOMOUS LABORATORY EXERCISES (1 CFU). CLASSROOM LESSONS WILL BE HELD WITH THE HELP OF PROJECTIONS AND ACCESS TO FREELY AVAILABLE ONLINE MEDIA. GUIDED EXERCISES WILL TAKE PLACE IN A BIOINFORMATICS LABORATORY AND WILL INCLUDE ACTIVITIES LED BY THE TEACHER ON THE SUBJECTS DESCRIBED IN THE THEORETICAL LESSONS. STUDENTS WILL WORK IN PAIRS ON TERMINALS. LABORATORY ACTIVITIES WILL TAKE PLACE IN GROUPS OF UP TO 4 STUDENTS: THE TEACHER WILL GIVE A TOPIC AND GIVE DIRECTIONS ON THE COMPUTATIONAL MEANS TO DO IT, AFTER WHICH THE STUDENTS WILL DO THE WORK AUTONOMOUSLY. LABORATORY EXERCISES WILL LAST 3 HOURS EACH.

Teaching Methods

THE TEACHING PROVIDES 56 HOURS OF TEACHING PARTITIONED INTO FRONT LESSONS, EXERCISES AND PRACTICAL LABORATORY (6 CFUS). IN PARTICULAR, THERE ARE 32 HOURS OF CLASSROOM LESSONS (4 CFUS), 12 HOURS OF LABORATORY GUIDED EXERCISES (1 CFU) AND 12 HOURS OF AUTONOMOUS LABORATORY EXERCISES (1 CFU).
CLASSROOM LESSONS WILL BE HELD WITH THE HELP OF PROJECTIONS AND ACCESS TO FREELY AVAILABLE ONLINE MEDIA.
GUIDED EXERCISES WILL TAKE PLACE IN A BIOINFORMATICS LABORATORY AND WILL INCLUDE ACTIVITIES LED BY THE TEACHER ON THE SUBJECTS DESCRIBED IN THE THEORETICAL LESSONS. STUDENTS WILL WORK IN PAIRS ON TERMINALS.
LABORATORY ACTIVITIES WILL TAKE PLACE IN GROUPS OF UP TO 4 STUDENTS: THE TEACHER WILL GIVE A TOPIC AND GIVE DIRECTIONS ON THE COMPUTATIONAL MEANS TO DO IT, AFTER WHICH THE STUDENTS WILL DO THE WORK AUTONOMOUSLY. LABORATORY EXERCISES WILL LAST 3 HOURS EACH.

	Verification of learning
	THE ACHIEVEMENT OF THE TEACHING OBJECTIVES IS CERTIFIED BY AN EXAMINATION. THE EXAMINATION IS DIVIDED IN TWO PARTS: A FIRST PART IS THE PRODUCTION OF A RELATIONSHIP IN ENGLISH LANGUAGE ON THE ACTIVITIES CARRIED OUT BY EACH GROUP OF STUDENTS WHO WORKED DURING THE HOURS OF COMPUTATIONAL LABORATORY ON A TOPIC INDICATED BY THE TEACHER. THE REPORT MUST INCLUDE THE BIOLOGICAL PROBLEM, THE VARIOUS METHODS USED TO SOLVE IT, THE RESULTS OBTAINED. THE TEST IS PASSED WITH THE MINIMUM OF 18/30. THE VOTE IS ATTRIBUTED TO EVERY STUDENT BELONGING TO THE GROUP THAT HAS MADE THE RELATIONSHIP. THE SECOND PART OF THE EXAM INCLUDES AN ORAL TEST CONSISTING IN A FINALIZED DISCUSSION (POSSIBLY SUPPORTED BY MEANS OF A POWERPOINT PRESENTATION) TO FIND THE LEVEL OF KNOWLEDGE AND UNDERSTANDING ABOUT THE STUDENT ON THE THEORETICAL AND METHODOLOGICAL CONTENT INDICATED IN THE PROGRAM. THE ORAL TEST ALSO ALLOWS TO VERIFY THE ABILITY TO COMMUNICATE THE STUDENT WITH THE LANGUAGE PROPERTY AND THE AUTONOMOUS ORGANIZATION OF THE EXHIBITION ON THE SAME ARGUMENTS WITH THEORETICAL CONTENT. IN THE DISCUSSION, BY EACH INDIVIDUAL STUDENT, THE PROBLEMS POSED BY THE BIOLOGICAL PROBLEM COMPARED DURING GROUP WORK, THE ADOPTED METHODOLOGICAL SETTING AND THE ANALYSIS OF THE OBTAINED RESULTS ARE DISPLAYED. THE DISCUSSION CAN BE MADE BY SLIDES AND CAN INCLUDE THE REQUEST OF THEORETICAL INSIGHTS AND CLARIFICATION OF DETAILS BY THE MEMBERS OF THE COMMISSION EXAMINATION. THE EXAM IN ITS ENTIRETY ENABLES TO UNDERSTAND THE ABILITY OF KNOWLEDGE AND UNDERSTANDING, AND THE ABILITY TO APPLY THE COMPETENCES ACQUIRED, AND THE ABILITY OF EXHIBITION, AND THE ABILITY TO LEARN AND TO PROCESS SOLUTIONS IN THE JUDGMENT AUTONOMY. THE FINAL VOTE OF EVERY STUDENT TAKES ACCOUNT OF THE KNOWLEDGE EXPOSED BY THE SINGLE STUDENT DURINGF THE ORAL TEST FOR A 70% CONTRIBUTION AND OF THE PRACTICAL ELABORATE FOR A 30% CONTRIBUTION.

Verification of learning

THE ACHIEVEMENT OF THE TEACHING OBJECTIVES IS CERTIFIED BY AN EXAMINATION.
THE EXAMINATION IS DIVIDED IN TWO PARTS: A FIRST PART IS THE PRODUCTION OF A RELATIONSHIP IN ENGLISH LANGUAGE ON THE ACTIVITIES CARRIED OUT BY EACH GROUP OF STUDENTS WHO WORKED DURING THE HOURS OF COMPUTATIONAL LABORATORY ON A TOPIC INDICATED BY THE TEACHER. THE REPORT MUST INCLUDE THE BIOLOGICAL PROBLEM, THE VARIOUS METHODS USED TO SOLVE IT, THE RESULTS OBTAINED. THE TEST IS PASSED WITH THE MINIMUM OF 18/30. THE VOTE IS ATTRIBUTED TO EVERY STUDENT BELONGING TO THE GROUP THAT HAS MADE THE RELATIONSHIP.
THE SECOND PART OF THE EXAM INCLUDES AN ORAL TEST CONSISTING IN A FINALIZED DISCUSSION (POSSIBLY SUPPORTED BY MEANS OF A POWERPOINT PRESENTATION) TO FIND THE LEVEL OF KNOWLEDGE AND UNDERSTANDING ABOUT THE STUDENT ON THE THEORETICAL AND METHODOLOGICAL CONTENT INDICATED IN THE PROGRAM. THE ORAL TEST ALSO ALLOWS TO VERIFY THE ABILITY TO COMMUNICATE THE STUDENT WITH THE LANGUAGE PROPERTY AND THE AUTONOMOUS ORGANIZATION OF THE EXHIBITION ON THE SAME ARGUMENTS WITH THEORETICAL CONTENT.
IN THE DISCUSSION, BY EACH INDIVIDUAL STUDENT, THE PROBLEMS POSED BY THE BIOLOGICAL PROBLEM COMPARED DURING GROUP WORK, THE ADOPTED METHODOLOGICAL SETTING AND THE ANALYSIS OF THE OBTAINED RESULTS ARE DISPLAYED. THE DISCUSSION CAN BE MADE BY SLIDES AND CAN INCLUDE THE REQUEST OF THEORETICAL INSIGHTS AND CLARIFICATION OF DETAILS BY THE MEMBERS OF THE COMMISSION EXAMINATION.
THE EXAM IN ITS ENTIRETY ENABLES TO UNDERSTAND THE ABILITY OF KNOWLEDGE AND UNDERSTANDING, AND THE ABILITY TO APPLY THE COMPETENCES ACQUIRED, AND THE ABILITY OF EXHIBITION, AND THE ABILITY TO LEARN AND TO PROCESS SOLUTIONS IN THE JUDGMENT AUTONOMY.
THE FINAL VOTE OF EVERY STUDENT TAKES ACCOUNT OF THE KNOWLEDGE EXPOSED BY THE SINGLE STUDENT DURINGF THE ORAL TEST FOR A 70% CONTRIBUTION AND OF THE PRACTICAL ELABORATE FOR A 30% CONTRIBUTION.

	Texts
	TEXT AND IMAGE MATERIALS DISTRIBUTED AFTER CLASSROOM LESSONS (LESSON SLIDES, SCIENTIFIC ARTICLES, ONLINE VIDEOS)

	More Information
	THE REGULAR ATTENDANCE TO FRONTAL LESSONS IS STRONGLY RECOMMENDED. THE ATTENDANCE TO GUIDED PRACTICALS AND INDIVIDUAL LABORATORY ACTIVITIES IS MANDATORY FOR AT LEAST 60% OF THE ACTIVITIES. IF THE STUDENT DOES NOT REACH THIS MINIMUM FREQUENCY LIMIT, IT WILL BE HELD TO DEMONSTRATE, DURING THE ORAL TEST, THE ACHIEVEMENT OF THE NECESSARY PRACTICAL KNOWLEDGE, THROUGH A COMPUTATIONAL TEST. FOR FURTHER INFORMATION PLEASE CONTACT THE TEACHER DURING THE RECEIVING TIME OR BY EMAIL AT AMARABOTTI@UNISA.IT

More Information

THE REGULAR ATTENDANCE TO FRONTAL LESSONS IS STRONGLY RECOMMENDED. THE ATTENDANCE TO GUIDED PRACTICALS AND INDIVIDUAL LABORATORY ACTIVITIES IS MANDATORY FOR AT LEAST 60% OF THE ACTIVITIES. IF THE STUDENT DOES NOT REACH THIS MINIMUM FREQUENCY LIMIT, IT WILL BE HELD TO DEMONSTRATE, DURING THE ORAL TEST, THE ACHIEVEMENT OF THE NECESSARY PRACTICAL KNOWLEDGE, THROUGH A COMPUTATIONAL TEST.

FOR FURTHER INFORMATION PLEASE CONTACT THE TEACHER DURING THE RECEIVING TIME OR BY EMAIL AT AMARABOTTI@UNISA.IT

BETA VERSION Data source ESSE3 [Ultima Sincronizzazione: 2022-05-23]

Anna MARABOTTI | ADVANCED BIOCHEMISTRY

ADVANCED BIOCHEMISTRY

PERCORSO SHARED STUDY PATHWAY

TEACHING UNITS

PROFESSORS

SHEET

-

Anna MARABOTTI | ADVANCED BIOCHEMISTRY