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degree courses
Second cycle
degree courses
Single cycle
degree courses
School of Science
MOLECULAR BIOLOGY
Course unit
STRUCTURAL BIOCHEMISTRY AND BIOPHYSICS
SCP8085069, A.A. 2019/20

Information concerning the students who enrolled in A.Y. 2018/19

Information on the course unit
Degree course Second cycle degree in
MOLECULAR BIOLOGY
SC2445, Degree course structure A.Y. 2018/19, A.Y. 2019/20
N0
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Degree course track Common track
Number of ECTS credits allocated 8.0
Type of assessment Mark
Course unit English denomination STRUCTURAL BIOCHEMISTRY AND BIOPHYSICS
Website of the academic structure http://biologiamolecolare.scienze.unipd.it/2019/laurea_magistrale_molecularbiology
Department of reference Department of Biology
E-Learning website https://elearning.unipd.it/biologia/course/view.php?idnumber=2019-SC2445-000ZZ-2018-SCP8085069-N0
Mandatory attendance
Language of instruction English
Branch PADOVA
Single Course unit The Course unit can be attended under the option Single Course unit attendance
Optional Course unit The Course unit can be chosen as Optional Course unit

Lecturers
Teacher in charge LAURA CENDRON BIO/10
Other lecturers NICOLETTA PLOTEGHER BIO/09

ECTS: details
Type Scientific-Disciplinary Sector Credits allocated
Core courses BIO/09 Physiology 3.0
Core courses BIO/10 Biochemistry 5.0

Course unit organization
Period First semester
Year 2nd Year
Teaching method frontal

Type of hours Credits Teaching
hours
Hours of
Individual study
Shifts
Laboratory 1.0 16 9.0 No turn
Lecture 7.0 56 119.0 No turn

Calendar
Start of activities 30/09/2019
End of activities 18/01/2020
Show course schedule 2019/20 Reg.2018 course timetable

Examination board
Examination board not defined

Syllabus
Prerequisites: General Biochemistry concepts. Basic Mathematics and Physics courses.
Target skills and knowledge: The course provides the students basic knowledge of structural Biochemistry and Biophysics, useful to solve biological problems related to macromolecules activity and structure-to-function relationship. The course gives students experience in how to interpret experimental results from a range of biophysical techniques.

The knowledge acquired in this course can be summarized as follow:
1. basic concepts of light-matter interaction;
2. Introduction to High-energy spectroscopies: scattering, diffraction and absorption
3. basic description of electron and nuclear magnetic spectroscopies
4. concepts of dynamics in biological systems (the time variable meaning in biological systems)
The skills acquired by the students in the course are:
1) scientific terms usage and appropriateness
2) analysis and comprehension of scientific reports and experiments in the fields of Biophysics-Structural biology
3) synthesis capacity and critical assessment on structural studies
Examination methods: Written examination. Both general and specific questions for each of the two parts of the course will be proposed.
Assessment criteria: Criteria for the evaluation of the acquired knowledge can be summarized as follow:
1) Understanding of the proposed concepts and comprehensiveness of the knowledge about course topics;
2) critical analysis of the proposed topics and techniques;
3) ability to synthesize concepts;
4) language usage appropriateness.
Course unit contents: The course will be divided in two parts. The first will be devoted to the introduction of basic principles of Biophysical techniques focused on structural and functional characterization of biological macromolecules, supramolecular assemblies and cells. In the second part, three recently described paradigms in the analysis of sensorial system study will be introduced. Such examples will be proposed mainly focusing on the Byophisical Methods that allowed disclosing important links between structure and function of macromolecules.

First part
- X-ray crystallography
1. Crystals, mathematical lattice, symmetry in crystals, space groups.
2. Crystallization techniques in biochemistry.
3. Production of X-rays;
4. Mathematics (equations useful in the interpretation of diffraction);
5. Diffraction of X-rays (waves, interference);
6. Single crystal X-rays diffraction; Bragg’s law; X-rays diffraction pattern; structure factors; the concept of Resolution
7. X-ray data collection, indexing and processing
8. From diffraction data to the protein model
9. Advanced topics: The phase problem and solution methods, MIR, MAD, MR
10. Structure refinement; The R index; Treatment and analysis of structural data;
- Neutron and Electron diffraction (basic concepts and applications);
- Mid to high resolution microscopy techniques;
- EXAFS/EPR/NMR (basic concepts);
- Examples of structural data usage in the investigation of relevant questions in biochemistry as well as for purposes related to applied research.

Second part:
1. Visual perception and molecular basis of photoperception;
2. Molecules involved in mechano-perception and role of the tactile perception;
3. molecular basis of chemoperception in the gustatory and olfactory systems.
Planned learning activities and teaching methods: The course will be structured into active lectures as well as practicals.
Open critical discussions will be part of the course.
The proposed practicals will be focused on:
1) exercises in laboratory rooms will show how to crystallize a protein;
2) exercises in the computer room will demonstrate:
- how to obtain a protein structure from x-ray diffraction data
- how to interpret an electron density map, visualize, manipulate protein structures.

Open, critical discussion of case studies will be proposed during dedicated lessons.
Additional notes about suggested reading: The following materials will be made available:
1) copy of the slides projected during the course feasible through the Moodle e-learning platform (https://elearning.unipd.it/cmela/);
2) a text in pdf format, regarding the Crystallography lessons;
3) papers, reviews and tutorials (Moodle) concerning specific concepts.
Textbooks (and optional supplementary readings)
  • Campbell, Biophysical Techniques. --: Oxford University Press, 2012. Cerca nel catalogo
  • David Sheehan, Physical Biochemistry: Principles and Applications. --: John Wiley & Sons, 2009. Cerca nel catalogo
  • Gordon G. Hammes,Sharon Hammes-Schiffer, Physical Chemistry for the Biological Sciences. --: John Wiley & Sons, 2015. Cerca nel catalogo
  • Bernhard Rupp, Biomolecular crystallography: principles, practice and applications to structural biology. --: Garland Science, Taylor & Francis Group, 2010. Cerca nel catalogo

Innovative teaching methods: Teaching and learning strategies
  • Laboratory
  • Problem based learning
  • Case study
  • Working in group
  • Problem solving
  • Loading of files and pages (web pages, Moodle, ...)

Innovative teaching methods: Software or applications used
  • Moodle (files, quizzes, workshops, ...)
  • Molecular Graphics

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