Physical Chemistry of Life Sciences

Course goals

Upon successful completion of this course, students will be able to:

1. Justify with evidence the arrangement of the periodic table and can apply periodic properties to chemical reactivity.
2. Can describe covalent bonds and their properties in organic molecules in terms of valence bond and molecular orbital theory.
3. Can interpret spectroscopic information in terms of molecular structure and properties.
4. Can explain what thermodynamic quantities such as enthalpy, entropy and free energy entail.
5. Can predict the direction of spontaneous change and equilibrium conditions for chemical and physical processes.
6. Can describe why and how the rate of a chemical reaction depends on reaction conditions and reaction mechanism.
7. Can analyse and report on the precision of quantitative data obtained in an experiment.

Content

In this course students are introduced to the fundamental principles that determine the properties and behaviour of atoms and molecules. An introduction to the foundations of spectroscopy and thermodynamics make-up the core of this course.

Introduction:
Atoms and molecules are the building blocks of all matter that surrounds us. Investigating atoms and molecules is challenging: due to their extremely small size they cannot be “looked at” in the classical sense by means of light (photons) that our eyes can detect.  Nevertheless, the interaction of matter with photons gives rise to a wide range of spectroscopic methods which are among a chemist's finest tools. Some spectroscopic techniques such as infrared spectroscopy are now routinely performed in any chemistry lab. Others, such as Nuclear Magnetic Resonance (NMR), are not only a powerful investigation method of molecular structure but have extended far beyond chemistry to biology and medicine. Whilst spectroscopy enables us to identify the properties of atoms and molecules, thermodynamics helps us determine their behaviour. Thermodynamics enables us to decide whether molecular processes, ranging from chemical reactions to the flow of molecules from one cellular compartment to another, can occur spontaneously or require input of energy.

Set up of this course:
In the first part of this course students learn how molecular shape, rigidity, charge distribution, and stability can be understood using valence bond and molecular orbital theory. Students are introduced to, and familiarized with, the basic principles and applications of infrared (IR), ultraviolet-visible light (UV-vis), fluorescence, NMR spectroscopy, and the use of mass-spectrometry (MS), which allows for the accurate determination of the masses of molecules and their fragments. In a 3-day laboratory practical students learn how to apply spectroscopic techniques and are trained in data handling and statistics.

In the second part of this course the behavior of molecules and molecular processes is viewed from a very different perspective, namely that of thermodynamics. Students study the following concepts: internal energy, enthalpy, entropy, and free energy and learn to perform calculations to answer questions such as the following one: ‘What difference in ion concentration on either side of a membrane can be achieved by a sodium-pump that consumes 1 ATP molecule per sodium ion transported if there is a potential difference of 1 Volt over the membrane?’. Although thermodynamics predicts which chemical processes can happen spontaneously, it cannot predict how fast they will proceed. The latter topic is dealt with in an introductory lecture on chemical kinetics.

Relation to other courses:
This course expands on the introduction in chemical equilibrium and free energy provided in Cell Biology (MBLS-101). Statistical concepts introduced in Mathematics and Programming (MBLS-102) are applied during the practical sessions. The course is closely interlinked with the course Organic Chemistry of Drug Molecules (MBLS-103) that runs in parallel. Whereas in Physical Chemistry for the Life Sciences the concepts of atomic structure and bonding are mainly dealt with in the context of spectroscopy, the focus in MBLS-103 is on structure and reactivity. The practical part of MBLS-103 includes applications of NMR and IR and the determination of reaction order. In the foundation course (MBLS-202, second year, level 2) “Biophysical Methods and Structural Biology” the theory of NMR, MS, and fluorescence will be expanded upon and applied to the study of biological macromolecules.

Teaching format course (estimation): 
Lectures 20%
Tutorials 20%
Presentation 10%
Practicals 30%
Self study 20%

The course content is studied through a series of lectures, each followed by a tutorial in which students engage with the content through practical exercises. At the end of part 1, students work in pairs to perform spectroscopy experiments in a 4-day laboratory assignment. To teach students how to record their results during an experiment, students are required to keep a lab notebook. The data obtained in these experiments is analyzed using the computing and programming skills that students acquired in ‘Mathematics and Programming’. Students present their analyses in a formal laboratory report.

Grading (check course manual for details):

1. Written exam 1: Spectroscopy (40%)
2. Written exam 2: Thermodynamics (40%)
3. Labjournal of the practicals & hand-in exercise/report (20%)

For each of the two exams a 5.5 is the minimal grade to pass. For the practical part, a 5.5 as average for the practical assignments is the minimal grade to pass. Requirement for attendance for exam component.