Dit document omvat de info van de slides plus mijn lesnotities van les 1 van concepts, gegeven door Xaveer Van Ostade. De lessen van Kurt Boonen (Les 2,3,4 en 8) heb ik ook, maar de notities staan op de slides. Moest je hierin ook geïnteresseerd zijn, mag je me altijd contacteren via messenger :))
Lecture 1: 29/9
General info
- Given by two professors
- There is a syllabus
o Consists of all the slides
- Proteomics can be used for a lot of things
- Advanced protein technology and proteome analysis
o Theory of 34 hrs
- Concepts of protein technology and applica?on
o Theory 25 hrs
o Prac?cal of 25 hrs
- Ar?cle
o Read it and understand it
o What are the authors doing? Why did the authors use that machine? What is told in this
sentence?
o 1 big of 2 ques?ons
o 10 points of the 40 points
- Examina?on: wriKen
o Around 5 ques?ons
§ 2 ques?ons (Prof. Boonen), may include an exercise (15 points)
§ 2 ques?ons (Prof. Van Ostade), may include an exercise (15 points)
§ 1 ques?on: ar?cle
o Not successful in part prof. Boonen or Van Ostade (< 8/20) -> no credits
- Textbooks
o Basics of electrophoresis, chromatography and mass spectrometry techniques:
Principles and Techniques of Biochemistry and Molecular Biology
o Basics of proteins
§ D. Voet en J. Voet Biochemistry 4th Edi?on
§ D. Voet, J. PraK en J. Voet Principles of Biochemistry, 5th Edi?on
Defini-on proteomics
- Determina?on of the complete set of proteins that is present in a system, under specific
circumstances
o System
§ Protein complex (even two proteins that are interac?ng)
§ Subcellular compar?ment, like a ribosome
§ Cell
§ Tissue
§ Organism
• Yeast, Drosophila
o Circumstances
§ Treatment (for 30 minutes, but also for 4 days)
§ Time a_er treatment
§ Condi?on of the cell (age, normal, infected, tumor…)
, Why proteomics
Compared to genomics, proteomics is “the real thing”
- Proteins are the workhorses of the cell
o Motorcycle contains many parts
§ The list is the genome -> but these words mean nothing -> need to be translated
to these different words -> these words need to work together = proteins -> then
you can drive your motorcycle
- Genome sequencing
o Es?ma?on: humans ± 20-40.000 genes, yeast 6000, Drosophila 13000, Caenorhabdi?s
18.000, plant 26.000
o S?ll difficult to predict genes: verifica?on of gene product by proteomic analysis is s?ll
necessary
ð proteogenomics
mRNA vs. Protein profiling
- A lot of cells have a high amount of mRNA but not a lot of proteins or visa versa
- The amount of mRNA not always correlate with the amount of proteins => microarrays/RNA
seq are insufficient to measure protein expression
o Le_: many mRNA that are expressed at a high level, yet no proteins are produced
o Right: some proteins that are expressed at a high level, but a low amount of mRNA is
present for these proteins
More (6-8) proteins/gene
- PosKransla?onal modifica?ons
o A RNA is translated into a protein but this protein can differ by heaving aKach different
posKransla?onal tags
§ Phosphoryla?on, glycosyla?on…
§ Many ways to modify the protein
o To make to dis?nc?on we need to develop proteomic technics that make the difference
between the two and also to iden?fy the post transla?onal modifica?ons
- Alterna?ve splicing -> isoforms
o One gene can splice
§ Normal splicing: a_er transla?onal -> protein
§ Alterna?ve splicing: some parts of the protein could be missing or you have
addi?onal parts
Protein interacCon networks
- Proteins needs to interact with each other -> important to know how cell works, live, how
cells react on medicines …
- Higher order of complexity without dras?c increase of number of components. About 78% of
yeast proteins is involved in complex.
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