Course syllabus for Biophysical chemistry

Course syllabus adopted 2024-02-07 by Head of Programme (or corresponding).

Overview

  • Swedish nameBiofysikalisk kemi
  • CodeKFK022
  • Credits7.5 Credits
  • OwnerMPBIO
  • Education cycleSecond-cycle
  • Main field of studyBioengineering, Chemical Engineering
  • DepartmentCHEMISTRY AND CHEMICAL ENGINEERING
  • GradingTH - Pass with distinction (5), Pass with credit (4), Pass (3), Fail

Course round 1

  • Teaching language English
  • Application code 08128
  • Maximum participants50 (at least 10% of the seats are reserved for exchange students)
  • Block schedule
  • Open for exchange studentsYes

Credit distribution

0119 Examination 6 c
Grading: TH		 6 c
  • 15 Jan 2025 am J
  • Contact examiner
  • Contact examiner
0219 Laboratory 1.5 c
Grading: UG		 1.5 c

In programmes

Examiner

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Eligibility

General entry requirements for Master's level (second cycle)
Applicants enrolled in a programme at Chalmers where the course is included in the study programme are exempted from fulfilling the requirements above.

Specific entry requirements

English 6 (or by other approved means with the equivalent proficiency level)
Applicants enrolled in a programme at Chalmers where the course is included in the study programme are exempted from fulfilling the requirements above.

Course specific prerequisites

General knowledge in chemistry, including physical chemistry.

Aim

By "Biophysical Chemistry" we mean the application of the concepts and tools of physical chemistry, i.e. in the form of models (thermodynamics, quantum mechanics) and analytical techniques (fluorescence spectroscopy, hydrodynamics, microscopy), to problems of biological significance. Biological systems are complex and their function is based on various macromolecules (DNA, RNA, proteins, polysaccharides) and defined aggregates (lipid membranes), and on a wide variety of receptor-ligand interactions. A typical approach to understanding is therefore to thoroughly characterize minimal model systems using biophysical methods and then add increasing levels of complexity to more closely resemble the cellular or biological system that you would like to increase the understanding of. Since it is methods rather than problems that typify the field of biophysical chemistry, we mainly introduce these by illustrating how they can be applied to problems concerning DNA and RNA. However, the principles are general and examples showing how the techniques are equally applicable to proteins are also dealt with. The course is an extension and specialization of general physical chemistry with focus on biophysical and biological applications. It also focusses on fluorescence-based methods and fluorescence theory as a vital basis for further specialization within the expanding field of fluorescence-based microscopy. This knowledge is suitable for those who want to later work in, for example, pharmaceutical industry or with biochemical, biophysical, biotechnical or biomedical research. Together with other courses in spectroscopy and analytical chemistry, surface and colloidal chemistry, organic synthesis, and molecular biology or microbiology, the course will provide a general platform for problem-solving in the bio-science area, but is also useful in nano-science, polymer, energy and soft-matter science contexts.

Learning outcomes (after completion of the course the student should be able to)

The students get trained in understanding and being able to discuss principles, theories and methods (focus on fluorescence-based) within biophysical chemistry applied especially on nucleic acids (DNA and RNA) but also other biomolecules. The student should after the course be able to:
  • understand and apply (bio)physical chemistry (for example, thermodynamics, chemical equilibria, and kinetics relevant in bio-applications) and biophysical methods  
  • understand and describe the phenomenon of fluorescence, molecular states, fluorescence-based methods, fluorophores and their relevant applications in chemistry, biology, and pharmaceutical industry
  • understand and describe fluorescence-based microscopy as well as a few single-molecule techniques relevant in bio- and pharma-applications
  • practically apply several of the biophysical chemistry methods presented in the course
  • apply knowledge in design of experiments and perform literature studies
  • write a scientific report as well as orally presenting scientific results

Content

The course contains lectures within the following focus areas: a) receptor-ligand interactions (drug-target; intermolecular forces), b) DNA, RNA and nucleic acid based drugs, c) molecular states and absorption/ excitation processes, d) excited states and fluorescence, e) fluorescence-based techniques, f) fluorescent molecules (including GFPs), g) fluorescence-based structure and dynamics studies, h) microscopy, i) single-molecule biophysics studies of DNA/RNA. In more detail the course deals with:

  • modern biophysical chemistry and biophysical methods and their applicability within chemistry, biology, physics as well as research within pharmaceutical industry
  • characteristics of DNA and RNA that are relevant to understand their biological function
  • theoretically explaining and understanding the phenomenon of fluorescence
  • theoretically explaining and understanding electronic states of molecules and its implications on absorption processes, fluorescence and in spectroscopy (including polarized)
  • theoretically explaining, understanding and utilizing fluorescence-based methods (including polarized and time-resolved methods)
  • theoretically explaining and in biological and pharmaceutical contexts applying kinetics, kinetic analysis, thermodynamics, molecular recognition as well as intermolecular forces (receptor-ligand interactions)
  • training the students how to use their theoretical skills in spectroscopy and fluorescence for further efficient specialization within and use as well as development of fluorescence-based microscopy methods
  • theoretically explaining and understanding design and development of biologically relevant fluorescent molecules including the GFPs (Green Fluorescent Protein and its analogues displaying other colors)
  • training the students how to perform analysis of biomolecular structure and dynamics in solution using methods in biophysical chemistry
  • training the students how to understand and in part perform single-molecule biophysics experiments (for example, using nanochannels in DNA-nanotechnology)
  • training the students to reach a theoretical level in biophysical chemistry facilitating their involvement in the development of new analytical tools, biotechnological methods and therapeutical strategies for nucleic acid-based drugs

Organisation

Lectures, Tutorials and Laboratory Project

Literature

"Principles of Fluorescence Spectroscopy" (Joseph Lakowicz) complemented by material that will be confirmed at the start of the course

Examination including compulsory elements

Written final examination (6 ECTS) and approved project course (1.5 ECTS).

The course examiner may assess individual students in other ways than what is stated above if there are special reasons for doing so, for example if a student has a decision from Chalmers on educational support due to disability.