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BIOPHYSICS

             
Compulsory/Elective Code Semester Lectures Practicals Credits ECTS
Elective 13A606 6th 4 Hrs/Wk 3 Hrs/Wk 5 6.0 
Aims:
 
 

The course focuses on structural studies of molecules that act as the building blocks of living organisms, the ways these molecules form organized supramolecular structures, and their structural changes in order to elucidate the properties and functions of the organisms. In order to achieve this goal, physical methodologies are mainly employed. Initially, it introduces the relationship between Biophysics and other disciplines and sub-disciplines. It analyzes the weak interactions and their role in life, as well as the structure of water.  It focuses on protein architecture by means of stereochemistry and conformational analysis, utilizing molecular models and softwares of molecular graphics. It analyzes the structure and function of biomolecules, small molecules and biological structures based on the principles of specialized biophysical methods and their applications, such as X-ray Crystallography, Spectroscopy (Infrared, Laser-Raman) and other theoretical approaches. Finally, it examines conformational diseases (amyloidosis) through the prism of the mechanisms and the rules of protein folding.

In parallel with the theoretical topics, the research methodology is taught (use of molecular models, use of molecular graphics programs, use of protein databases and specialized computational tools, protein crystallization, collection and analysis of infrared and Raman spectra, secondary structure prediction), in order students should be able to apply, combine and analyze the results of these techniques.

 
Objectives:
 
 

At the end of the course (lectures and practicals) students are expected to be conversant with: a) the forces  that determine the native and functional structure of biomolecules, b) the ways that biomolecules form organized supramolecular structures and their structural modifications, c) the structure and functionality of the most well studied biomolecules, d) the ways that biomolecules interact with each other, e) the biophysical methods that are used  to reveal the structural and dynamic characteristics of biomolecules – Knowledge: a) significance of the covalent bond, b) the role of weak interactions in protein folding, c) correlation of protein structure with function, d) characteristics of the protein structure, e) theoretical and experimental methodologies that reveal the biomolecular structure, f) conformational diseases – Skills: a) be conversant with the use of molecular models for conformational analysis, b) be conversant with the use of molecular graphics programs for representations and studies of biomacromolecular structures, c) be conversant with protein crystallization, d) be conversant with the analysis of X-ray diffraction patterns from protein crystals for the determination of protein structure, e) be conversant with the collection of Raman and infrared spectra to find the secondary structure of proteins, f) be conversant with the analysis and interpretation of infrared and Raman spectra, g) be conversant with the search and the data retrieval in macromolecular databases, h) be conversant with specialized computational tools utilized for the study of the structure and function of proteins – Capacities: a) to choose a method depending on the query and the type of protein, b) to combine biophysical techniques in order to address research questions on protein structure and function, c) to interpret results and plan experiments in order to determine the structure of a protein, d) to evaluate and organize data regarding native or improper protein folding that are associated with diseases, e) capacity for group or individual work

 
Lectures:
 
 

Introduction (10 Hours): Goals and branches of Biophysics, Weak interactions and their role in life phenomena, Structure of H2O and its role in the folding and interactions of biomolecules, Principles of Stereochemistry, Conformation-Molecular models- Symmetry, Conformational analysis of biomicro- and macromolecules, Molecular modelling,  Folding of biomacromolecules,  Liquid crystals.

Molecular Biophysics (36 Hours):

Protein Architecture

Globular, water-soluble proteins: Amino acid sequence, Secondary structure, Super-secondary structure, Domains, Tertiary structure, Protein-protein interactions.

Membrane proteins: Hydrophobicity and protein-lipid interactions, Membrane protein structure. Energy and signal transduction – molecular machines (bacteriorhodopsin, rhodopsin etc.), GPCRs, G-proteins and effectors

Fibrous (Structural) proteins: Keratins, Silks, Collagens, etc

Biopolymers/Biomaterials, Amyloids-amyloidoses

Polysaccharides (Chitin, Cellulose) and bipartite fibrous composite protein-polysaccharide systems (e.g cuticle)

Theoretical methods for structure prediction of biomicro- and macromolecules - Applications.

Analysis of structure and function of biomolecules and biomolecular complex structures – Principles of methodologies and applications: X-ray diffraction, neutron diffraction, electron diffraction, laser diffraction,    X-ray crystallography - Applications - Vibrational spectroscopies (IR and Raman) - Applications - O.R.D and C.D spectroscopy - Applications - E.S.R and N.M.R spectroscopy - Applications.

Cellular Biophysics (6 Hours):

Molecular Recognition (Structure and function of drugs, neurotransmitters, etc.).

Biophysics of Sensory systems with emphasis on the Photoreceptor.

 
Practicals:
 
 

1. Use of molecular models – Conformational analysis utilizing molecular models – Polypeptide chains. 2. Conformational analysis of biomicro- and macromolecules utilizing semi-empirical classical energy calculations. 3. Macromolecular Structure and Sequence Databases and analysis tools in the web. 4. Databases for structural classification of proteins (CATH, SCOP, PFAM). 5. Structural studies of biomacromolecules utilizing molecular graphics programs. 6. Protein secondary structure prediction. 7. Protein crystallization (lysozyme as an example). 8. X-ray diffraction studies of fibrous biomolecular structures. 9. FT-Raman and FT-IR spectroscopy: Collection, analysis and interpretation of spectra from biomolecules and biomolecular structures.

 
Instructors:
 
  Lectures: Vassiliki A. IconomidouAssistant Professor of Biophysics – Molecular Biophysics (Coordinator) - Dr. Nikolaos Papandreou, Laboratory Teaching Staff
 
  Practicals: Vassiliki A. Iconomidou, Assistant Professor of Biophysics – Molecular Biophysics (Coordinator) - Dr. Nikolaos Papandreou, Laboratory Teaching Staff - Dr. Zoi Litou, Laboratory Teaching Staff
 
Notes:
 
 

The evaluation process is conducted in Greek (there is the possibility of examining in English for Erasmus students) during the Semester final exams and includes: Theory: Written examination with a) questions that demand extensive answer and b) multiple choice questions (70% of the total grade of the course), Practicals: Oral examination during the conduction of the practicals and evaluation of the written exercises that have been deposited after the end of each practical through the e-class platform. (30% of the total grade of the course). The total score is the sum of the above individual evaluations.

 
Contact:
 
  If you require more information, please contact the Course Coordinator, Assist. Prof. Vassiliki A. Iconomidou at: Tel: (+30) 210 727 4871; e-mail: veconom[at]biol.uoa[dot]gr