Biophysical Chemistry

Master Chemie, Master Life Science, Master Nanoscience
Winter Semester 2023/2024

Instructors:
Prof. Dr. Malte Drescher Phone: +49 7531 88 5262 malte.drescher@uni-konstanz.de
Dr. Annalisa Pierro
Florian Johannsen


Teaching Assistants:
Eva Schaefer
Berk Yildirim


Course info in ILIAS

Information about the course, including course materials, problem sets, and announcements can be
found in ILIAS.

Course overview

The course will focus on the application of concepts and techniques from Physical Chemistry to
practical problems in Life Science. Spectroscopic techniques providing information on structure and dynamics of biological systems as well as thermodynamic and quantum mechanistic concepts to describe biological macromolecules will be discussed. For each subtopic, the relevant theory, corresponding experimental spectroscopic and computational approaches will be covered, and applications in current research fields will be presented.


Learning Objectives

The aim of the course is to provide the student with a toolbox of Physical Chemistry to address
problems in Life Science. After completion of the course the student will be familiar with principles
and is able to discuss, evaluate, and apply the concepts and techniques covered. The student can
select the appropriate tool for a problem at hand. Optional extension of the course with a research
internship (see below) gives the student the opportunity to apply and extend course topics in the
scientific practice.


Lectures

Lectures will take place on Mondays (L0829, 13:30-15:00, starting Oct. 30, 2023).

Tutorials

Tutorials will take place on Thursdays (L0829, 13:30-15:00) starting Nov. 2.

The problem sets will be released on Thursdays, beginning on Oct 26 via Ilias.  

All students prepare their own solution set and hand it in on the following Thursday before 1pm via Ilias.

The solutions will be evaluated by the teaching assistants with either a pass or a fail. In order to participate in the oral exam, a student must have passed 9 out of the 12 problem sets. The solutions to the problem sets will be discussed in tutorials.

Exam

The grade will be based on a 30-min oral exam (individual appointments).

Study Material

The course is largely covered in the text book “Molecules of Life” by Kuriyan,
Konforti, and Wemmer. Miscellaneous study material will be posted in ILIAS.

Credits

The credit for the course is 6 ECTS. The course can be extended with an additional 6 ECTS by doing a
research internship (5 weeks full-time) in one of the biophysical chemistry groups: Drescher,
Hauser, Kovermann, Mathies, Peter, Zumbusch.

Course Schedule – Winter Semester 2023-2024
 

Oct 23, Lecture 1:  Practicalities, Intro Biophysical Chemistry (Drescher)

Oct 30, Lecture 2: Diffusion and transport of molecules: theory: random walk, Fick`s laws of diffusion (Drescher)

Nov 6, Lecture 3: Computational approaches: pseudo-random numbers, numerical integration of the diffusion equation (Johannsen)

Nov 13, Lecture 4: Diffusion and transport of molecules: experiment: single molecule microscopy, fluorescence correlation spectroscopy  (Drescher)

Nov 20: ---

Nov 27, Lecture 5: Protein Folding: theory: interactions, Entropy, Boltzmann distribution (Drescher)

Dec 4: --

Dec 11,  Lecture 6: IR-Spectroscopy, FT techniques (Drescher)

Dec 18, Lecture 7: Computational approaches: FT (Johannsen)

Jan 8, Lecture 8: Protein structure: experiment: cryo-EM, SAXS (Pierro)

Jan 15, Lecture 9: Protein Computational approaches: Molecular Dynamics Simulation, structure determination by NMR (Drescher)

Jan 22, Lecture 10: Protein structure determination by EPR (Pierro)

Jan 29, Lecture 11: Protein structure: experiment: X-ray structure determination, theory: free energy landscape, conformational ensembles (Drescher)

Feb 5, Lecture 12: Molecular interactions and molecular recognition: experiment (Pierro)

Feb 12, Lecture 13: Molecules at work: experiment: intracellular spectroscopy (Pierro)

Physikalische Chemie Ia (Einführung in die Quantenmechanik)

Diese Veranstaltung findet im SS 2023 statt. In dieser Anleitung finden Sie Details zum Ablauf.

Vorlesung:

Dienstags, 08:15h - 09:45h, L602
Freitags, 10:00h - 11:30h, G300

Übung:

Freitags, 11:45h - 13:15h, M627 bzw. L601

Bitte melden Sie sich bei ILIAS UND ZEUS an.

Die aufgezeichneten Vorlesungen finden Sie hier.

Physical chemistry Ia (Introduction to quantum mechanics)

This course will take place in summer semester 2023. This overview provides details on how to register as well as course dates and content.

Lecture:

Tuesdays, 08:15 - 09:45, room L602
Fridays, 10:00 - 11:30, room G300

Practice tutorial:
Fridays, 11:45 - 13:15, room M627 and room L601 (2 groups)

Please register via ILIAS AND ZEuS.

You can find the lecture recordings online.

Biophysical Chemistry WS22/23

Master Chemie, Master Life Science, Master Nanoscience
Winter Semester 2022/2023

Instructors:
Prof. Dr. Malte Drescher Phone: +49 7531 88 5262 malte.drescher@uni-konstanz.de
Prof. Dr. Karin Hauser Phone: +49 7531 88 5356 karin.hauser@uni-konstanz.de
Dr. Annalisa Pierro Phone:+49 7531 88 4844 annalisa.pierro@uni-konstanz.de

Teaching Assistants:
Eva Schaefer, eva.schaefer@uni-konstanz.de
Johannes Mause, johannes.mause@uni-konstanz.de
Shane Maguire, shane.maguire@uni-konstanz.de

Course info in ILIAS

Information about the course, including course materials, problem sets, and announcements can be
found in ILIAS.

Course overview

The course will focus on the application of concepts and techniques from Physical Chemistry to
practical problems in Life Science. The first part of the course (M. Drescher) will cover spectroscopic techniques that can provide information on structure and dynamics of biological systems. The second part of the course (K. Hauser) will focus on thermodynamic concepts and kinetics to describe biological macromolecules. Applications in current research fields will be presented.

Learning Objectives

The aim of the course is to provide the student with a toolbox of Physical Chemistry to address
problems in Life Science. After completion of the course the student will be familiar with principles
and is able to discuss, evaluate, and apply the concepts and techniques covered. The student can
select the appropriate tool for a problem at hand. Optional extension of the course with a research
internship (see below) gives the student the opportunity to apply and extend course topics in the
scientific practice.
 

Lectures

Lectures will take place on Mondays (L0829, 13:30-15:00, starting Oct. 24, 2022).

Tutorials

Tutorials will take place on Thursdays (L0829, 13:30-15:00) starting Nov. 3.

The problem sets will be released on Thursdays, beginning on Oct. 27 via Ilias.  

All students prepare their own solution set and hand it in on the following Thursday before 1pm via Ilias.

The solutions will be evaluated by the teaching assistants with either a pass or a fail. In order to participate in the oral exam, a student must have passed 9 out of the 12 problem sets. The solutions to the problem sets will be discussed in tutorials which take place on Thursdays (L0829, 13:30-15:00, starting Nov. 3, 2022).

Exam

The grade will be based on a 30-min oral exam (individual appointments).

Study Material

The biophysical part of the course is largely covered in the text book “Molecules of Life” by Kuriyan,
Konforti, and Wemmer. Miscellaneous study material will be posted in ILIAS.

Credits

The credit for the course is 6 ECTS. The course can be extended with an additional 6 ECTS by doing a
research internship (5 weeks full-time) in one of the biophysical chemistry groups: Drescher,
Hauser, Kovermann, Mathies, Peter, Zumbusch.


Course Schedule – Winter Semester 2022-2023

Part 1: Malte Drescher / Eva Schaefer / Johannes Mause

Lecture:  Practicalities, Intro Structural Biology
Mon. Oct. 24

Lecture Eigenvalues and Eigenvectors,
Structure of Atoms and Molecules,
Interaction with Light
Mon. Oct. 31
Tutorial  Thu. Nov. 3

Lecture Fluorescence and Phosphorescence,
Fluorescence Microscopy, Diffusion, Fluorescence Correlation
Spectroscopy
Mon. Nov. 7
Tutorial  Thu. Nov. 10

Lecture Magnetic Resonance Spectroscopy,
Fourier Transformations, Spin,
Solution NMR, Magic-angle spinning NMR
Mon. Nov. 14
Tutorial  Thu. Nov. 17

Lecture EPR spectroscopy (Annalisa Pierro)
Mon. Nov. 21
Tutorial Thu. Nov. 24

Lecture X-ray Diffraction, Cryo–Electron Microscopy
Mon. Nov. 28
Tutorial Thu. Dec. 1

Lecture Computer Chemistry, SQLM
Mon. Dec. 5
Tutorial  Thu. Dec. 8

Part 2: Karin Hauser / Shane Maguire

Lecture Molecular Interactions
Mon. Dec. 12
Tutorial Thu. Dec. 15

Energy and Entropy
Mon. Dec. 19
Tutorial Thu. Dec. 22

Lecture Bioenergetics and Driving Forces
Mon. Jan. 09
Tutorial Thu. Jan. 12

Membrane Transport
Mon. Jan. 16
Tutorial Thu. Jan. 19

Kinetics and Rates of Molecular Processes
Mon. Jan. 23
Tutorial Thu. Jan. 26

Pathways and Transition States in
Protein Folding
Mon. Jan. 30
Tutorial Thu. Feb. 2

Mon. Feb. 6 no lecture
Thu. Feb. 9 lab tour

Physikalische Chemie Ia (Einführung in die Quantenmechanik)

Diese Veranstaltung findet im SS 2022 statt. In dieser Anleitung finden Sie Details zum Ablauf.

Vorlesung:

Dienstags, 08:15h - 09:45h, R512
Freitags, 10:00h - 11:30h, R513

Übung:

Freitags, 11.45h - 13.15h, M627 bzw. L601

Bitte melden Sie sich bei ILIAS UND ZEUS an.

Die aufgezeichneten Vorlesungen finden Sie hier.