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COMPUTATIONAL BIOCHEMISTRY

Anna MARABOTTI COMPUTATIONAL BIOCHEMISTRY

0522100044
DEPARTMENT OF CHEMISTRY AND BIOLOGY "ADOLFO ZAMBELLI"
EQF7
BIOLOGY
2024/2025

OBBLIGATORIO
YEAR OF COURSE 2
YEAR OF DIDACTIC SYSTEM 2022
AUTUMN SEMESTER
CFUHOURSACTIVITY
432LESSONS
224LAB
ANNA MARABOTTI T Curriculum
Objectives
GENERAL AIM:
THE PURPOSE OF TEACHING IS FOR STUDENTS TO ACQUIRE THE SKILLS NECESSARY TO UNDERSTAND THE BASIC CONCEPTS OF STUDYING THE THREE-DIMENSIONAL STRUCTURES OF BIOMOLECULES (IN PARTICULAR, PROTEINS) THROUGH BIOINFORMATICS APPROACHES, AND TO APPLY THESE CONCEPTS INDEPENDENTLY THROUGH EXAMPLES OF RESEARCH PROJECTS TO BE PERFORMED DURING COMPUTATIONAL LABORATORY ACTIVITIES.

KNOWLEDGE AND UNDERSTANDING SKILLS:
STUDENTS:
- WILL UNDERSTAND THE DIFFERENT STRUCTURAL LEVELS OF BIOLOGICAL MACROMOLECULES AND THEIR IMPORTANCE IN RELATION TO THE FUNCTION PERFORMED BY THESE MACROMOLECULES IN CELLS AND ORGANISMS;
- WILL UNDERSTAND THE SCIENTIFIC INFORMATION CONVEYED BY THE DIFFERENT GRAPHICAL REPRESENTATIONS OF PROTEIN STRUCTURES;
- WILL UNDERSTAND THE METHODS FOR EVALUATING THE GOODNESS-OF-FIT OF STRUCTURES OBTAINED BY EXPERIMENTAL METHODS;
- WILL KNOW THE THEORETICAL PRINCIPLES OF BIOINFORMATIC METHODS FOR THE ANALYSIS OF STRUCTURES OBTAINED BY EXPERIMENTAL METHODS;
- WILL KNOW THE THEORETICAL PRINCIPLES OF VARIOUS PREDICTIVE ALGORITHMS FOR THE STRUCTURAL CHARACTERISTICS OF PROTEINS FROM THEIR SEQUENCES;
- WILL KNOW THE THEORETICAL PRINCIPLES OF VARIOUS ALGORITHMS FOR THE PREDICTION OF TERTIARY AND QUATERNARY STRUCTURES OF PROTEINS;
- WILL KNOW THE THEORETICAL PRINCIPLES OF VARIOUS ALGORITHMS FOR PREDICTING PROTEIN-SMALL LIGAND INTERACTIONS FROM KNOWN STRUCTURES
- WILL KNOW THE THEORETICAL PRINCIPLES OF VARIOUS ALGORITHMS FOR SIMULATING CONFORMATIONAL VARIABILITY OF PROTEINS;
- WILL KNOW THE FUNCTIONAL SIGNIFICANCE OF PROTEINS WHOSE THREE-DIMENSIONAL STRUCTURE IS UNDEFINED, AND OF BIOINFORMATICS METHODOLOGIES DEVELOPED FOR THE STUDY OF SUCH PROTEINS

ABILITY TO APPLY KNOWLEDGE AND UNDERSTANDING:
STUDENTS WILL BE ABLE TO:
- CONSULT AVAILABLE ONLINE DATABASES CONTAINING STRUCTURAL AND FUNCTIONAL INFORMATION ABOUT PROTEINS;
- REPRESENT PROTEIN STRUCTURES IN A WAY THAT IS FUNCTIONAL IN DESCRIBING THEIR VARIOUS STRUCTURAL PROPERTIES;
- USE DIFFERENT METHODS AND COMPARE RESULTS TO EVALUATE THE GOODNESS-OF-FIT OF EXPERIMENTALLY AND COMPUTATIONALLY DETERMINED PROTEIN STRUCTURES;
- DERIVE AND USE INFORMATION OBTAINED FROM SERVERS AVAILABLE ONLINE TO PREDICT STRUCTURAL FEATURES OF PROTEINS;
- INTEGRATE KNOWLEDGE DERIVED FROM PREDICTIONS OF DIFFERENT STRUCTURAL FEATURES TO CORRECTLY PREDICT THE THREE-DIMENSIONAL STRUCTURE OF A PROTEIN USING SERVERS AVAILABLE ONLINE;
- USE PROTEIN STRUCTURE INFORMATION TO PREDICT AFFINITY TO POTENTIAL LIGANDS;
- SET UP A PROPER PROCEDURE FOR SIMULATING CONFORMATIONAL VARIABILITY OF PROTEINS;
- IDENTIFY PROTEINS OR PORTIONS THEREOF THAT ARE NOT STRUCTURED IN A DEFINED MANNER, AND TO CORRELATE THESE PROPERTIES WITH FUNCTIONAL SIGNIFICANCE

AUTONOMY OF JUDGMENT:
STUDENTS WILL BE ABLE TO INDEPENDENTLY ASSESS:
- THE LEVEL OF RELIABILITY OF INFORMATION CONTAINED WITHIN PUBLIC DATABASES CONSULTED;
- THE LEVEL OF RELIABILITY EXPECTED FOR ALGORITHMS AND METHODS OF STRUCTURAL FEATURE PREDICTIONS;
- THE LEVEL OF RELIABILITY OF THREE-DIMENSIONAL STRUCTURE PREDICTIONS OBTAINABLE FROM SUCH ALGORITHMS AND METHODS;
- THE INFORMATION CONTENT OF SUCH RESULTS, IN RELATION TO THE FUNCTION PERFORMED BY MACROMOLECULES IN DIFFERENT CELLS AND ORGANISMS; AND

COMMUNICATION SKILLS:
STUDENTS WILL BE ABLE TO:
- PRODUCE WRITTEN REPORTS IN ENGLISH, USING APPROPRIATE SCIENTIFIC TERMINOLOGY, CONCERNING THE LABORATORY ACTIVITIES CARRIED OUT, IN WHICH THEY SHOULD DESCRIBE IN SUFFICIENT DETAIL THE PROCEDURES ADOPTED AND CRITICALLY ANALYZE THE RESULTS OBTAINED, ORGANIZING THEM IN A STRUCTURE SIMILAR TO THAT OF A SCIENTIFIC ARTICLE;
- PRODUCE CONCISE PRESENTATIONS OF SUCH RESULTS, ORGANIZING THEM IN A STRUCTURE SIMILAR TO THAT OF A PAPER AT A SCIENTIFIC CONFERENCE;
- SUPPORT A DISCUSSION FROM THESE PRESENTATIONS, ENUNCIATING THEORETICAL PRINCIPLES AND ANSWERING RELEVANT QUESTIONS.

LEARNING SKILLS:
STUDENTS WILL BE ABLE TO:
- USE TRADITIONAL BIBLIOGRAPHIC TOOLS AND COMPUTER RESOURCES FOR WORD PROCESSING, PRESENTATION PRODUCTION, DATA ANALYSIS AND ARCHIVING;
- CARRY OUT RESEARCH ACTIVITIES, UNDERSTAND AND INTERPRET COMPLEX TEXTS, DRAWN FROM THE SCIENTIFIC LITERATURE, IN ENGLISH;
- PROCEED TO THE CONTINUOUS UPDATING OF THEIR KNOWLEDGE, USING TECHNICAL AND SCIENTIFIC LITERATURE
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 32 HOURS OF DIDACTICS IN THE FORM OF FRONTAL LESSONS AND 24 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 4 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 2 H OF FRONT DIDACTICS + 2 H OF GUIDED EXERCISES IN THE BIOINFORMATICS 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 BIOINFORMATICS LABORATORY)
- MOLECULAR MECHANICS WITH PARTICULAR REFERENCE TO FORCE FIELD CONCEPT, MINIMIZATION, MOLECULAR DYNAMICS, SIMULATED ANNEALING (ABOUT 6 H OF FRONT DIDACTICS + 4 H OF GUIDED EXERCISES IN THE BIOINFORMATICS LABORATORY)
- 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 INDEPENDENT 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 (6 ECTS) OF TEACHING PARTITIONED INTO FRONT LESSONS (32 HOURS), GUIDED ACTIVITIES (12 HOURS) AND INDEPENDENT ACTIVITIES (12 HOURS) IN THE COMPUTATIONAL LABORATORY.
FRONT LESSONS WILL BE HELD WITH THE HELP OF PROJECTIONS AND ACCESS TO FREELY AVAILABLE ONLINE MEDIA.
GUIDED ACTIVITIES IN THE COMPUTATIONAL LABORATORY WILL SHOW PRACTICAL APPLICATIONS OF THE SUBJECTS DESCRIBED IN THE THEORETICAL LESSONS.
INDEPENDENT ACTIVITIES IN THE COMPUTATIONAL LABORATORY 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.
Verification of learning
HE ACHIEVEMENT OF THE OBJECTIVES OF THE TEACHING IS CERTIFIED BY PASSING AN EXAMINATION GRADED IN THIRTIETHS.
THE EXAMINATION IS DIVIDED INTO TWO PARTS: A FIRST PART INVOLVES THE PRODUCTION OF A REPORT IN ENGLISH ON THE ACTIVITIES CARRIED OUT BY EACH GROUP OF STUDENTS WHO WORKED DURING THE COMPUTATIONAL LABORATORY HOURS ON A TOPIC INDICATED BY THE LECTURER. THE REPORT MUST INCLUDE THE BIOLOGICAL PROBLEM ADDRESSED, THE VARIOUS METHODS USED TO SOLVE IT, AND THE RESULTS OBTAINED. THE TEST IS CONSIDERED PASSED WITH A MINIMUM GRADE OF 18/30. THE GRADE IS GIVEN TO EACH STUDENT BELONGING TO THE GROUP THAT WROTE THE PAPER.
THE SECOND PART OF THE EXAM INCLUDES AN ORAL TEST CONSISTING OF A DISCUSSION (POSSIBLY WITH THE SUPPORT OF A POWER POINT PRESENTED BY THE STUDENT) AIMED AT ASCERTAINING THE LEVEL OF KNOWLEDGE AND ABILITY TO UNDERSTAND REACHED BY THE STUDENT ON THE THEORETICAL AND METHODOLOGICAL CONTENTS INDICATED IN THE PROGRAM. THE ORAL TEST ALSO ALLOWS TO VERIFY THE STUDENT'S ABILITY TO COMMUNICATE WITH PROPERTIES OF LANGUAGE AND AUTONOMOUS ORGANIZATION OF EXPOSITION ON THE SAME TOPICS WITH THEORETICAL CONTENT.
IN THE DISCUSSION ARE ILLUSTRATED, BY EACH INDIVIDUAL STUDENT, THE PROBLEMS POSED BY THE BIOLOGICAL PROBLEM ADDRESSED DURING THE GROUP WORK, THE METHODOLOGICAL APPROACH ADOPTED, THE ANALYSIS OF THE RESULTS OBTAINED. THE DISCUSSION MAY MAKE USE OF SLIDES AND INCLUDE REQUESTS FOR THEORETICAL INSIGHTS AND DETAILED CLARIFICATIONS BY MEMBERS OF THE EXAMINATION COMMITTEE.
THE TEST AS A WHOLE MAKES IT POSSIBLE TO ASCERTAIN BOTH THE ABILITY TO KNOW AND UNDERSTAND, THE ABILITY TO APPLY THE SKILLS ACQUIRED, THE ABILITY TO EXPOUND, THE ABILITY TO LEARN AND DEVELOP SOLUTIONS IN AUTONOMOUS JUDGMENT, AND THE ABILITY TO COLLABORATE WITH OTHERS TO ACHIEVE THE FINAL OBJECTIVE.
EACH STUDENT'S FINAL GRADE TAKES INTO ACCOUNT THE KNOWLEDGE EXHIBITED BY THE INDIVIDUAL STUDENT IN THE ORAL EXAMINATION FOR A 70% CONTRIBUTION AND THE PRACTICAL PAPER FOR A 30% CONTRIBUTION.
MINIMUM GRADE (18/30) IS GRANTED WHEN THE STUDENT DEMONSTRATES LIMITED KNOWLEDGE AND ABILITY TO ESTABLISH CONNECTIONS BETWEEN THE ARGUMENTS COVERED.
MAXIMUM SCORE (30/30) IS GRANTED WHEN THE STUDENT SHOWS COMPLETE AND APPROPRIATE KNOWLEDGE AND IS ABLE TO ESTABLISH CONNECTIONS BETWEEN THE TOPICS COVERED.
HONORS WILL BE AWARDED TO STUDENTS WHO HAVE ANSWERED ALL QUESTIONS CORRECTLY, DEMONSTRATING EXCELLENT LANGUAGE SKILLS AND CRITICAL ABILITY IN EXPOSITION, IN ADDITION TO THE KNOWLEDGE REQUIRED TO ACHIEVE THE HIGHEST MARK.
Texts
REFERENCE TEXT:
PASCARELLA, PAIARDINI: "BIOINFORMATICA" (ZANICHELLI) (ITALIAN ONLY)
THE LECTURER WILL INDICATE FROM TIME TO TIME WHICH CHAPTERS AND PARAGRAPHS IT IS USEFUL TO CONSULT FOR CONTENT LEARNING

OTHER TEXTS FOR FURTHER STUDY:
PETSKO, RINGE: "STRUCTURE AND FUNCTION OF PROTEINS" (ZANICHELLI)
WILLIAMSON: "HOW PROTEINS WORK," ZANICHELLI
TRAMONTANO: "THE 10 MOST WANTED SOLUTIONS IN PROTEIN BIOINFORMATICS" (TAYLOR&FRANCIS) (ENGLISH ONLY)
ZVELEBIL M, BAUM J: "UNDERSTANDING BIOINFORMATICS" (GARLAND SCIENCE) (ENGLISH ONLY)
THE LECTURER WILL INDICATE FROM TIME TO TIME WHICH CHAPTERS AND PARAGRAPHS IT IS USEFUL TO CONSULT FOR FURTHER STUDY OF PARTICULAR TOPICS.

OTHER MATERIALS:
AT THE END OF EACH LECTURE, THE LECTURER PROVIDES A BULLETED LIST OF ADDITIONAL MATERIALS CONSULTED, ACCESSIBLE ONLINE, PROVIDING LINKS DIRECTLY IN THE SLIDES THAT ARE PROVIDED TO STUDENTS.
More Information
THE REGULAR ATTENDANCE TO FRONTAL LESSONS IS STRONGLY RECOMMENDED. ATTENDANCE AT GUIDED ACTIVITIES AND INDIVIDUAL LABORATORY ACTIVITIES IS MANDATORY TO THE EXTENT OF 60% OF THE TOTAL NUMBER OF LECTURES. IF THE STUDENT DOES NOT REACH THIS MINIMUM ATTENDANCE LIMIT, HE/SHE WILL BE REQUIRED TO DEMONSTRATE, DURING THE ORAL EXAMINATION, THE ACHIEVEMENT OF THE NECESSARY PRACTICAL KNOWLEDGE THROUGH A THEORETICAL/PRACTICAL TEST.

FURTHER INFORMATION CAN BE OBTAINED BY CONTACTING THE LECTURER DURING OFFICE HOURS OR BY E-MAIL AMARABOTTI@UNISA.IT OR VIA TEAMS PLATFORM.
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