1. Describe basic structure, chemistry, and function of the main classes of biomolecules;
2. Explain the relevance of non-covalent interactions and water for biomolecular structure, self-assembly, and interaction;
3. Explain the kinetics and thermodynamics of in vitro and in vivo protein folding mechanisms;
4. Describe regulatory mechanisms of protein-ligand interactions, including cooperativity and allostery;
5. Justify general principles and specific examples of enzyme catalysis and inhibition with proof through kinetic calculations;
6. Quantitate and explain specificity in protein-protein interactions;
7. Describe molecular events and common chemical principles of metabolic processes
8. Describe molecular events and understand the relevance of kinetic and thermodynamic factors in replication, transcription, and translation
9. Propose and execute an experimental plan based on established assays in order to answer a research question.

In this course students acquire knowledge and understanding of how protein structure, modification and interaction allow proteins to control biological processes, including signal transduction, DNA replication, translation and metabolism.

Introduction:
Understanding life at the molecular level is incomplete without an understanding of how “the molecules of life” are capable of shaping cells and performing complex processes. What is it that enables lipids to control membrane fluidity and proteins to function as sensors or motors and perform basic logical calculations like “if (condition) then (action 1) else (action 2)”? How all this is achieved by the molecules of life is the focus of this course.

Set up of this course:
Throughout this course students study the physical and chemical properties of the molecules of life, with an emphasis on proteins. This course has 2 lectures, an online group assignment, and 1 laboratory session or computer practical every week. In lectures, fundamental molecular concepts such as self-assembly are addressed.
Students learn that self-assembly of proteins is governed by the principles determining protein structure and the mode of action of chaperones, which assist proteins during folding. The homology of protein sequence, structure and function is investigated. In computer practicals students explore how the chemical and 3-dimensional structure of proteins correlate with function. In an online group assignment, students explore how allostery and cooperativity endow proteins with considerable “intelligence” and discover the social life of proteins. In paired laboratory assignments students find answers to questions about how protein folding, stability and activity is affected by environmental conditions including temperature. The laboratory work in this course includes the purification of recombinant Green Fluorescent Protein (GFP) from bacterial culture, SDS-PAGE, fluorescence spectroscopy, UV/Vis, and performing enzyme kinetic assays, which convey basic concepts in protein chemistry. Finally, the knowledge acquired in this course is integrated into the concept of how all this (protein structure, modification and interaction) allows proteins to control a diverse array of biological processes.


Relation to other courses:
The course both deepens and extends knowledge and understanding of the molecules of life taught in the course Cell Biology and applies the thermodynamic and kinetic principles covered in Physical Chemistry for the Life Sciences. The book The Molecules of Lifeassumes students have a basic knowledge of cell biology; the Cell Biology course provides this basis. Knowledge about protein structure and function provides a basis for the group project in the course Biophysical Methods and Structural Biology.

Teaching format course (estimation):
Lectures 20%
Tutorials 10%
Practicals 15%
Writing 10%
Self study 45%

Grading (check course manual for details):
test/exam 1 (40%)
test/exam 2 (40%)
Practicals (20%)