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.
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.
