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Course Details

Course Department: Department of Physics
Course Code: PHY 415
Course Title: Biophysics
Number of ECTS: 6
Level of Course: 1st Cycle (Bachelor's Degree) 
Year of Study (if applicable): 4 
Semester/Trimester when the Course Unit is Delivered: Spring Semester 
Name of Lecturer(s): Georgios Archontis 
Lectures/Week: 2 (2 hours per lecture) 
Laboratories/week: -- 
Tutorials/Week: 1 (1 hours per lecture) 
Course Purpose and Objectives: Introduction to Molecular Biophysics.  
Learning Outcomes:
The students should:

  • Classify the biomolecules into categories.
  • Distinguish between the various intramolecular or intermolecular interactions in biomolecules and biomolecular complexes in solution or a membrane environment. 
  • Describe the effect of water on electrostatic and nonpolar interactions.
  • Know the naturally occurring aminoacids and classify them into categories based on their physical and chemical properties. 
  • Understand the chemical composition, main degrees of freedom and geometrical properties of the protein main chain.
  • Know the properties of the protein secondary structures, the basic taxonomy of the protein tertiary-structure motifs, and charasteristic examples of tertiary structures. 
  • Recognize that protein folding is usually a two-state transition between a native structure and a multitude of denatured structures.
  • Explain the importance of protein heteropolymeric character for the stabilization of a unique native protein structure.
  • Apply basic polymer models to study protein folding.
  • Solve statistical mechanical models of the helix – coil transition.
  • Describe characteristic examples of protein action.
  • Understand the structural properties of hemoglobin and its regulation.
  • Solve main allostery models (MWC, KNF).
  • Know main examples of empirical energy functions used in biomolecular modeling.
  • Describe the application of normal mode analysis in the study of protein properties.
  • Know the basic principles (algorithms – methodology) of Molecular Dynamics simulations, and their use in the study of protein properties and function.
  • Understand various implicit solvent models (the Poisson-Boltzmann and the Generalized Born approximation).
  • Express the free-energy change due to a perturbation as an expectation value.
  • Apply implicit-solvent models and free-energy methods in the computation of binding free energies.
 
Prerequisites:
It is expected though that the students will have attended classes in General Physics (1st – 2nd year), Classical Mechanics and Electrodynamics (2nd year), Thermodynamics and Statistical Physics (3rd year).
 
Co-requisites: Not Applicable 
Course Content:
Description of the various biomolecular classes.
Intra- and intermolecular interactions. The role of water.
The 20 naturally occurring amino acids and their physicochemical properties. Protein primary, secondary and tertiary structure. 
Protein thermodynamics and folding. Importance of heteropolymeric character for the stabilization of a unique native structure. Application of the Random Energy Model in protein stability. The helix-coil transition.
Examples of protein action.
Hemoglobin and models of allostery. 
Basic elements of biomolecular modeling. Typical energy functions used in biomolecular modeling. 
Normal mode calculations and their application in the study of protein properties. 
Biomolecular dynamics simulations. 
Implicit solvent models. Continuum electrostatic approximations (Poisson-Boltzmann and Generalized Born). 
MD-based Free-energy calculations (method of thermodynamics integration and thermodynamic perturbation). Application of implicit-solvent and MD-based free-energy methods in the study of biomolecular association). 
 
Teaching Methodology:
There are four lecture hours / week. A typical lecture starts by a short discussion and review of previously covered material. Students are engaged in the discussions via suitable questions.

The lectures utilize Powerpoint presentations and short videos of relevant animations/simulations. In the recitation hour we discuss problems and appilcations, go over the solutions of assignments and answer student questions.

The students are given ~4-6 home assignments that they have to complete in a course of 7-10 days each. Student collaboration is permitted, but the preparation of individual reports is very strongly encouraged.
 
Bibliography:
  • Philip Nelson. Biological Physics. Freeman. 
  • Meyer Jackson. Molecular and Cellular Biophysics. Cambridge University Press. 
  • John Kuriyan. The Molecules of Life. Garland Science.
  • Ivet Bahar, Robert Jernigan, Ken Dill. Protein actions: Principles and Modeling.
  • Rob Philips, Jane Kondev, Julie Theriot and Niger Orme. Physical Biology of the Cell. Garland Science. 
  • Alasdair Steven, Wolfgang Baumeister, Louise Johnson, Richard Perham. Molecular Biology of Assemblies and Machines.
 
Assessment:
Home assigmenets (20%), one mid-semester exam (40%) and one final exam (40%).
 
Language of Instruction: Greek
Delivery Mode: Face-To-Face 
Work Placement(s): Not Applicable