5 ECTS credits
125 h study time
Offer 1 with catalog number 4012689ENR for all students in the 2nd semester at a (E) Master - advanced level.
The content of the course will comprise two parts:
Part 1:
Protein maturation and trafficking are essential processes that ultimately determine life at cellular level. Good functioning of these processes is a prerequisite for cells and organisms to survive, to adapt to ever-changing conditions in a flexible way and to defend themselves against attacks from the outer world.
In order to be able to understand life, it is a prerequisite to investigate the properties of the cellular environment into which enzymes and other proteins operate. Therefore, this course deals first with the cytoskeleton and the properties of the different elements belonging to this intricate structural network are discussed.
In the next chapter, emphasis is put on the association of proteins to form heterologous protein-protein aggregates. Such interactions are essential not only for the regulation of metabolic pathways (which relies on the formation of metabolons and channeling of metabolites) but for virtually every process taking place in a living cell/organism (e.g. in transcription and translation, signal transduction, in the immune system, during apoptosis, etc..).
The next chapter deals with protein trafficking. It is indeed essential for a cell that newly synthesized proteins are directed towards their correct final destination. Transport of proteins following the general export route via the endoplasmic reticulum and the Golgi apparatus is discussed. In close connection to this issue we look into the different types of protein glycosylation. These co-/post-translational modifications take place when newly synthesized proteins are transported through the ER and the Golgi complex. Next we discuss the import of newly synthesized proteins into eukaryotic subcellular organelles such as mitochondria, chloroplasts, peroxisomes, the nucleus and lysosomes.
Another chapter deals with folding of proteins in the cell. An overview is given of PDIs and PPIases, and of different chaperones and chaperonins that are essential molecules for the in vivo folding of proteins towards their correct three-dimensional structure. Recent structural information on these molecules and on their action is given.
Finally a last chapter describes the degradation of proteins inside the cell, which is a strictly regulated process. We discuss on the structure and the action of the proteasome, which is an essential machinery involved in eukaryotic protein degradation. Attention is paid to the role of ubiquitin in this and in other cellular processes.
All topics dealt with in this course have been amply investigated during recent years, and an overwhelming number of papers and reviews have been published lately.
Part 2:
An important cellular process is the communication of the cells with the ‘outside world’ by which they can adapt to changing circumstances. With this respect plasma membrane receptors are key players. They are proteins that have a double function; recognition of neurotransmitters or hormones (denoted as chemical mediators) as well as translation of their binding into a cellular effect. This part comprises the following chapters:
1. Chemical mediators and their receptors : definitions
2. Classification of receptors (on basis of structure/function)
In these two chapters of this part these endogenous chemical mediators are divided according to their mode of transmission (hormones, neurotransmittors) and according to their hydrophobicity (hydrophobic hormones which pass the cell membrane/ hydrophilic/large signalling molecules whose receptors are at the outside of the plasma membrane). These latter receptors are divided in the ways they trigger the cell response (activation of G proteins, endogenous phosphorylation, opening of ion channels).
3. Ligand-gated ion channels
This chapter deals with ligand mediated ion channels. With two typical examples the action mechanism of these receptor is explained. It concerns nicotinic acetylcholine receptor that operate the opening of sodium channels involved in the contraction of skeletal muscles and the glutamate and GABA mediated ion channels that are involved in rapid signal transduction in neurons.
4. G-protein coupled receptors
This chapter deals with G-protein coupled receptors. They represent a large family of plasma membrane receptors that are involved in a very broad range of (patho)-physiological processes. It is therefore not surprising that about 50 % of all commercial drugs act via modulation of these receptors. In this chapter their general mechanism of signal transduction is explained as well as their classification on basis of their structure/amino acid sequence.
5. Growth factor receptors
The next category of receptors are the growth factor or tyrosin kinase receptors. The binding of their ligands i.e. growth factors activates their intrinsic property of endogenous phosphorylation. As their name indicates, the binding of these ligands are involved in the regulation of cell growth and division.
6. Steroïd receptors
The last category of receptors are located intracellularly. They mainly recognize steroid hormones, which are apolar mediators that are able to cross the plasma membrane barrier.
7. Methodology : Radioligand receptor binding
8. Methodology : Functional experiments
9. Methodology : Functional receptor assays : inhibition experiments
The next chapters deal with widely used technical approaches to investigate the interaction between signalling molecules (and their synthetic analogues: agonists and antagonists) and their receptors. First, the technique of 'radioligand binding' is thoroughly reviewed (saturation binding, competition binding, competitivity, 2-site analysis, autoradiography..) and the obtained parameters (Bmax, IC50, KD, Ki) are compared to those (EC50, pA2) obtained by functional tests (dose-response curves, Schild plot analysis). With respect to the functional tests, attention will be paid to concepts 'intrinsic activity', 'receptor reserve' and ‘partial agonism'. Special attention is paid to
- distinction between agonists and antagonists
- different kinds of antagonists, inverse agonists, allosteric modulators, functional antagonists and biased agonists.
10. Pharmacological classification of receptors
The concepts of the previous chapters will be illustrated in the pharmacological classification of adrenergic receptors
11. Glucose homeostasis by insulin
While G-protein coupled receptors classically recognize hormones and neurotransmitters, it now appears that intermediates of the carbohydrate and lipid metabolism can also bind to such receptors. This chapter deals with receptors that bind free fatty acids. As this receptors are involved in the homeostatic regulation of glucose they can be considered as potential therapeutic targets for the development of anti-diabetic drugs. This therapeutic approach will be compared with the action mechanism of current treatments.
Practical
In the practical aims to better understand and illustrate essential concepts of the pharmacology part of the course. Attention will be devoted to two techniques involved in the study of signal transduction. It will comprise radioligand binding in a cell line that expresses recombinant G-protein coupled receptors. In the same cell line we will measure agonist mediated activation of these receptors. In this respect the release of intracellular calcium will be measured.
Participation to the practicals is mandatory.
To provide the student insight in the domain of Molecular Pharmacology. The acquired knowledge during this course is useful in a research-oriented career. It provides the bio-engineers the basic knowledge to perform pre-clinical research and to function within multi-disciplinary teams in the pharmaceutical industry.
This course aims to analyze various processes taking place within the living cell.
Students will:
-be able to describe the structural organization of the intracellular components of the cytoskeleton and its associating proteins.
-know and understand the properties of the intracellular environment.
-know and understand the advantages of heterologous protein-protein interactions and of metabolite channeling.
-be able to explain the problem of protein trafficking in the cell in all its aspects.
-know and understand the process of protein folding in the cell.
-be able to describe the process of protein degradation in the cell.
-know and understand the different functions of the protein ubiquitin and of ubiquitin-like molecules.
-be able to make an analysis of different technologies that are used in these domains of research.
The final grade is composed based on the following categories:
Oral Exam determines 67% of the final mark.
PRAC Lab Work determines 33% of the final mark.
Within the Oral Exam category, the following assignments need to be completed:
Within the PRAC Lab Work category, the following assignments need to be completed:
Exam:
The oral exam will consist of two parts:
Part 1: Concerning the part on regulation of cellular processes for which maximally one hour is foreseen.:
1A: Presentation of a general topic which can be prepared on basis of two review papers that are provided in advance
1B: Subsequently a general question related to the course slides related to regulation of cellular processes will be posed. This question will be provided ¼ hour before the start of the oral exam (1/2 hour).
Part2: Concerning the part on receptors: for which maximally ½ hour is foreseen
This part involves the discussion of a previously provided scientific article. The exam comprises a short (about 5 min) presentation by the student of this article which deals with the aim, methodology, results and conclusion(s). Subsequently the lecturer asks questions to assess the insight of the student in the related concepts. This part of the exam is open book, the student can use notes, texts, slides during the exam. For this part about 1/2 hour is foreseen.
Evaluation:
The evaluation will be done on the oral exam as well as the writing of the paper of the first part of the exam. The quotation, which is summative, has the following distribution
1/2 op Part 1 of the oral exam
1/4 op Part 2 of the oral exam
Attendance of the practical is obligatory! After the practicum the students need to submit a written report in which the following items are included: introduction, aim, used techniques, analysis and discussion of the results and conclusion(s). This report together with the contribution during the practical will be quoted in a summative way and comprises ¼ of the points.
This offer is part of the following study plans:
Master of Bioengineering Sciences: Cell and Gene Biotechnology: Molecular Biotechnology (only offered in Dutch)
Master of Biology: Molecular and Cellular Life sciences (only offered in Dutch)
Master of Biology: Molecular and Cellular Life sciences