Course syllabus

Course-PM

Lecturer and Examiner

Marcus Wilhelmsson; office 5020

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

 

Lecturer

Fredrik Westerlund; office 2056 (physics building overpass)

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

 

Tutorial leader

Hanna Larsson; office 5064; email: hlar@chalmers.se

 

Project leaders

Pauline Pfeiffer; office 5064; email: paupfe@chalmers.se

Alma Karlsson; office 5076; email: almak@chalmers.se

Sriram Kesarimangalam; office 5022; email: sriramk@chalmers.se

Elin Persson; office 4020; email: perelin@chalmers.se

Kylee Widner; office 5051; email: widner@chalmers.se

Vinoth Sundar Rajan; office 5051; email: edal@chalmers.se

 

Course representatives

Vera Andersson (vera.h.j@hotmail.com)

Emil Hörnquist (emil.hornquist@hotmail.com)

Sonia Ramm (emil.hornquist@hotmail.com)

 

INFORMATION ABOUT THE COURSE

 

Course literature and material

1. Course book: Joseph R. Lakowicz: "Principles of Fluorescence Spectroscopy” (2006, 3^rd edition), chapters and pages included at the end of this document.
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 entrance qualifications

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) 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 its implications on 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

 

Changes made since the last occasion

Some of the lecture materials is updated to include recent findings in the field.

 

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.

 

Schedule (note: TimeEdit merely shows that there is a teaching element and where the location is - for Schedule details see Lectures/Tutorials below and/or in the course PM)

TimeEdit Chalmers - KFK022, Biofysikalisk kemi

 

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 6 10-12

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

 

Nov 11, 8-10

L3 (MW): Fundamentals of absorption of light continued. Excited States. Fundamentals of fluorescence and instrumentation for fluorescence and absorption. (Lakowicz chap. 1-2)

 

Nov 13, 10-12

L4 (MW): Fluorophores (emphasis on biomimicking fluorophores and fluorescent proteins) (Lakowicz chap. 3 + 16 + 20 + lecture notes)

 

Nov 18, 10-12

L5 (MW): Solvent effects and Quenching of fluorescence. (Lakowicz chap. 6-9)

 

Nov 20, 10-12

L6 (MW/FW): Guest lectures by Dr Philip Nevin, Senior Scientist at Discovery Sciences, AstraZeneca, Mölndal, and Professor Stefanie Kath-Schorr, University of Cologne, Germany.

 

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 9, 8-10

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

 

Dec 9, 10-12

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

Dec 11, 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)

Examination

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

 

   2. 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.

 

Literature (– what pages are included in the course?)

Pages from the Lakowicz-book that are included in the course (other pages may contain examples that could also help your learning process) are given below. Also, the lecture notes (especially the handed-out ones can contain extra information) and background information from basic chemistry courses covered during lectures 1 and 2 is part of the course (for advice on what books to refer to for repetition of those subjects ask the examiner):

 

Chapter 1 Introduction/Overview of Fluorescence: pages 1-24

Chapter 2 Instrumentation: pages 27-60

Chapter 3 Fluorophores: pages 63-89 + comprehensive lecture notes

Chapter 4 Fluorescence lifetimes: pages 97-114 (stop at 4.5) 117-121, 141-144 (i.e. 4.11) (exclude parts in chapter about the phase and modulation method)

Chapter 6 Solvent effects: pages 205-226 (stop at 6.9) 231-232 (Summary)

Chapter 7 Dynamics of solvent effects: pages 237-240 (stop at 7.2)

Chapter 8 Quenching: pages 277-287

Chapter 9 Dynamics of quenching: pages 331-336 (stop at 9.3)

Chapter 10 Anisotropy: pages 353-370 (stop at 10.6)

Chapter 13 Energy transfer/FRET: pages 443-453 (stop at 13.4), 459-462 (13.6-7), 467-468 (13.11)

Chapter 16 Protein fluorescence: pages 529-538, 560-562 (16.10)

Chapter 18 Multiphoton: pages 607-610

Chapter 19 Sensing: pages 623-627 (stop at 19.3)

Chapter 20 Novel fluorophores: pages 675-691 (stop at 20.3.6)

Chapter 21 DNA technology: pages 705-730 (stop at 21.8)

Chapter 22 FLIM: pages 741-743 (stop at 22.1), 748-750 (stop at 22.6)

Chapter 23 Single-molecule detection: pages 757-768 (stop at 23.5)

Chapter 24 Fluorescence correlation spectroscopy: pages 797-805 (stop at 24.3)

 

Recommended questions and exercises (from Lakowicz’ book and handed out thermodynamics-, kinetics- and quantum mechanics and absorption-booklet; underlined exercises are for the Tutorials)

 

Tutorial 1 (Nov 11, 10-12): Thermodynamics and kinetics booklet

Question 1,2,3,4,5,6,7,8,9,10,11

Tutorial 2 (Nov 18, 8-10): Quantum mechanics and absorption booklet

Question 12,13,14,15,16,17

Tutorial 3 (Nov 25, 8-10): Chapter 1:

P1.1, 1.2, 1.3, 1.4, 1.5, 1.6, 1.7 – Q2 from “Typical exam questions” 

Tutorial 3 (Nov 25, 8-10): Chapter 2:

P2.1, 2.2

Chapter 3:

P3.2 (after reading chapter 8)

Tutorial 4 (Nov 27, 10-12): Chapter 4:

P4.1 (only time-domain), 4.2, 4.4, 4.6, 4.7, 4.8 – Q3 from Exam 2023

Tutorial 4 (Nov 27, 10-12): Chapter 6:

P6.1, 6.2

Tutorial 5 (Dec 2, 10-12): Chapter 8:

P8.1, 8.3, 8.4, 8.6, 8.8, 8.9 – Q3 from “Typical exam questions”

Tutorial 5 (Dec 2, 10-12): Chapter 10:

P10.1, 10.2, 10.5, 10.6, 10.7

Tutorial 6 (Dec 4, 10-12): Chapter 13:

P13.1, 13.2, 13.3, 13.6, 13.7, 13.9 – Q4 from Exam 2020

Chapter 16:

P16.1, 16.2B-C, E(only for steady-state)

Chapter 19:

P19.3

Chapter 23:

P23.1