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BIOPHYSICS

             
Compulsory/Elective Code Semester Lectures Practicals Credits ECTS
Elective 13B033 6th 4 Hrs/Wk  3 Hrs/Wk 5 6,5
Aims:
 
 

The course focuses on the structural study of the molecules that constitute the organisms, the ways in which these molecules form organized supramolecular structures and their structural changes in order to interpret the properties and functions of the organisms.  To achieve this goal, it has mainly employed physical methodologies. Introductory, it explores 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 also focuses on the architecture of proteins through the principles of stereochemistry and conformational analysis, utilizing molecular models and molecular graphics programs. It analyzes the structure and function of biomacro- and micro- molecules and biological structures through the principles of specialized biophysical methodologies and their applications, such as X-ray crystallography, spectroscopies (IR and Raman), electron microscopy and other experimental and theoretical approaches. Finally, it explores the conformational diseases (amyloidosis) through the prism of the mechanisms and the rules of the protein folding.

In addition to the theory, it is learned the research methodology (use of Molecular Models, use of Molecular Graphics Programs, Exploration of Protein Databases and specialized Computational Tools, Crystallization of Proteins, Obtaining and Analyzing IR and Raman Spectra, Prediction of Protein Secondary Structure) so that the student will be in position to apply, combine and analyze the results of the 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 techniques, 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.

Abilities: a) be able to choose a method depending on the query and the type of protein, b) be able to combine biophysical techniques in order to address research questions on protein structure and function, c) be able to interpret results and plan experiments in order to determine the structure of a protein, d) be able to evaluate and organize data regarding protein native folding or misfolding that are associated with diseases, e) managing 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 macro- molecules - 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. Electron microscopy and its techniques.

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. Structural studies of biomacromolecules utilizing Molecular Graphics Programs - 3.  Conformational analysis of biomicro- and macromolecules utilizing semi-empirical classical Energy calculations - 4.  Macromolecular Structure Databases with emphasis to the characterization and classification of Protein structures - 5. Protein Secondary Structure Prediction - 6. Protein crystallization (lysozyme as an example) - 7. X-ray diffraction studies of fibrous biomolecular structures - 8. 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:
 
 

There are no prerequisite courses for the student in order to select and attend the course. However, for the better attendance and understanding of the course, students must have good knowledge of the compulsory courses of the Department related to the scientific field of Biophysics, such as Biochemistry, Genetics, Cell Biology and Molecular Biology.

The course is offered to Erasmus students: Teaching in Greek language - Exams in English language.

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: A. Theory: Written examination with: a) questions that demand extensive answer and b) multiple choice questions (70% of the total grade of the course) - B. Laboratory Exercises: 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, Ass. Prof. Vassiliki A. Iconomidou at Tel: +30-210 727 4871 - Email: veconom[at]biol.uoa[dot]gr