Course syllabus

Course-PM

KFK022 Biophysical chemistry lp2 HT19 (7.5 hp)

Course is offered by the department of Chemistry and Chemical Engineering

 

Contact details

 

Lecturer and Examiner

Marcus Wilhelmsson; office 5020

Telephone 031-7723051; email: marcus.wilhelmsson@chalmers.se

 

Lecturer

Fredrik Westerlund; office 2056

Telephone 031-7723049; email: fredrik.westerlund@chalmers.se

 

Tutorial leader

Axel Olesund; office 5076; email: axel.olesund@chalmers.se

 

Project leaders

Axel Olesund; office 5076; email: axel.olesund@chalmers.se

Anna Mårtensson; office 5076; email: marann@chalmers.se

Sriram Kesarimangalam; office 2052A; email: sriramk@chalmers.se

Nima Sasanian; office 4012; email: sasanian@chalmers.se

 

External guest lecturers

Professor Mark Williams, Northeastern University, US. https://cos.northeastern.edu/people/mark-williams/

Professor Penny Beuning, Northeastern University, US. https://web.northeastern.edu/dna/?page_id=23

 

Course student representatives 

Kajsa Ahlgren

Fritjof Havemeister

Nuttida Issdisai

Luis Mario Leal Garza

Oscar Nordin

 

Course purpose

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.

 

Schedule

TimeEdit

 

Course literature

1. Course book: Joseph R. Lakowicz: "Principles of Fluorescence Spectroscopy” (2006, 3^rd edition). The parts that are included are listed in the complete word document course PM. The book is available electronically via Chalmers Library or can be bought online.
2. Lecture notes
3. Parts of exams from previous version of the course (KFK021)

General physical chemistry literature like "Physical Chemistry" by Atkins or "Physical Chemistry - Quanta, Matter and Change" by Atkins, de Paula and Friedman serves as background knowledge. Further reading regarding biological fluorescent molecules: “Fluorescent analogues of Biomolecular Building Blocks: Design and Applications” by Wiley; 2016.

Course design

Contents

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. 

Course planning and mandatory elements

The course contains 12 lectures, 6 tutorials, an exam and a laboratory project (including oral presentation of results), of which the exam and the laboratory projects are mandatory elements. The lectures will cover various subjects of the course contents (see detailed lecture list below) and will facilitate the students’ learning process and reading of the course literature and materials. The tutorials will give the students training in various aspects of the course contents. The tutorial leader will show examples and the students will also work with the exercises by themselves with coaching by the tutorial leader. The laboratory project will include a small literature search, lab work, data analysis, report writing, an oral presentation of the results and actively asking questions at the occasion of oral presentations (being an “opponent”). During the oral presentation fellow students and teachers will listen, ask questions and give feedback on the project and the presentation.

 

Lectures

Nov 4, 10-12

 L1 (MW + FW):           Introduction and Overview of the Course using ongoing research at our divisions; Biomacromolecules with focus on Nucleic Acids; Drug-Target interactions – Ligand Equilibria; Thermodynamics; Drug-Target Kinetics; Examples from research. (lecture notes + recommended reading)

Nov 11, 8-10

 L2 (MW):                      Basic quantum mechanics and fundamentals of absorption of light. Transition dipole moments. (lecture notes + recommended reading)

Nov 8, 10-12

 L3 (MW/FW):            Guest lectures by Profs. Mark Williams and Penny Beuning

Nov 18, 8-10

 L4 (MW):                      Fundamentals of absorption of light continued. Excited States. Fundamentals of fluorescence and instrumentation for fluorescence and absorption. (Lakowicz chap. 1-2)

Nov 18, 10-12

 L5 (MW):                      Fluorophores (emphasis on biomimicking fluorophores and fluorescent proteins) (Lakowicz

chap. 3 + 16 + 20 + lecture notes)

Nov 25, 8-10

 L6 (MW):                      Solvent effects and Quenching of fluorescence. (Lakowicz chap. 6-9)

Nov 25, 10-12

L7 (MW):                      Time-resolved fluorescence measurements; Fluorescence anisotropy including fundamentals of polarized absorption spectroscopy. (Lakowicz chap. 4 + 10 + lecture notes)

Dec 2, 8-10

 L8 (MW):                      Förster Resonance Energy Transfer (FRET) – emphasis on nucleic acid systems. (Lakowicz chap. 13 + lecture notes)

Dec 2, 10-12

 L9 (FW):                       Multiphoton excitation; Microscopy – epifluorescence, confocal. (Lakowicz chap 18, 19, 21-24 + lecture notes)

Dec 9, 8-10

 L10 (FW):                     Microscopy continued – Super resolution techniques; FLIM; TIRF etc. (Lakowicz chap 21-24 + lecture notes)

Dec 9, 10-12

 L11 (FW):                     Single-molecule detection; FCS; Single-molecule biophysics – optical tweezers. (Lakowicz chap 23 + lecture notes)

Dec 16, 8-12

 L12/13:                          Presentation of laboratory projects

Dec 18, 10-12

 L14 (FW):                     Single-molecule biophysics continued: Nucleic acid in nanoconfinements. Polymer reptation models, nucleic acid reptation in nanochannels and electrophoresis. (Lakowicz chap 23 + lecture notes)

 

Tutorials

Nov 6, 10-12, Tutorial 1

Nov 13, 10-12, Tutorial 2

Nov 20, 10-12, Tutorial 3

Nov 27, 10-12, Tutorial 4

Dec 4, 10-12, Tutorial 5

Dec 11, 10-12, Tutorial 6

 

Changes made since the last occasion

This is a new course replacing the old Biophysical Chemistry KFK021.

Learning objectives and syllabus

Learning objectives:

The students get trained in understanding and being able to discuss principles, theories and methods (focus on fluorescence) within biophysical chemistry applied especially on nucleic acids (DNA and RNA) but also other biomolecules. The student should after the course be able to:

• describe important modern biophysical chemistry and biophysical methods and their applicability within chemistry, biology, physics as well as research within pharmaceutical industry
• describe characteristics of DNA and RNA that are relevant to understand their biological function
• theoretically explain and understand the phenomenon of fluorescence
• theoretically explain and understand electronic states of molecules and their implications for absorption processes, fluorescence and in spectroscopy (including polarized)
• theoretically explain, understand and utilize fluorescence-based methods (including polarized and time-resolved methods)
• theoretically explain and in biological and pharmaceutical contexts apply kinetics, kinetic analysis, thermodynamics, molecular recognition as well as intermolecular forces (receptor-ligand interactions)
• 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 explain and understand design and development of biologically relevant fluorescent molecules including the GFPs (Green Fluorescent Protein and its analogues displaying other colors)
• perform analysis of biomolecular structure and dynamics in solution using methods in biophysical chemistry
• understand and in part perform single-molecule biophysics experiments (for example, using nanochannels in DNA-nanotechnology)
• 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
• 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

Link to the syllabus on Studieportalen.

Study plan

Examination form

Examination is done through the laboratory projects and a written exam. To pass the course you have to:

 

1. get the grade pass on the laboratory projects. This includes, apart from active participation in the lab work, a written report for each lab group and an oral presentation of the results. (1.5 ECTS)

 

and

1. get a minimum of grade 3 on the written exam. (6 ECTS)

 

Details for the written exam

To pass the exam which gives you 6 ECTS you need grade 3 or above. The grading of the written exam is as follows: <12.5 – fail; 12.5-16 grade 3; 16.5-19.5 – grade 4 and ≥20 – grade 5. For 10.5-12 points an extra oral exam could be arranged by the examiner provided that the student asks for it. The outcome of this oral exam is that the grade could be changed from fail to pass (i.e. grade 3) if the student shows significant improvements during the oral exam compared to the written one.

 

Allowed material at the written exam:

1. Any kind of calculator.
2. Papers containing formulas and equations will be handed out with the written exam.
3. English dictionary in book form.
4. Physics Handbook. Beta.

 For all answers to exam questions without a correct unit a deduction of points will be made.

Time and location of written exam will be given in Studieportalen (look up course KFK022). Remember that you have to bring your exam code (tentakod) to the exam. Time and location for solutions to exam questions and for reviewing your graded exam will be given on the first page of the written exam.