zentrum für technomathematik mathematik / informatik fachbereich 3 genomics, genetics, genome,...
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Zentrum für Technomathematik Mathematik / InformatikFachbereich 3
Genomics, Genetics, Genome, Gene, Proteins, Proteome,
Proteine Chemistry, Proteomics, …
Attempt of an overview and systematics
Uttendorf 2004
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Zentrum für Technomathematik Mathematik / InformatikFachbereich 3
Overwiev
1. Cells
2. Molecules of live
3. Genes and genome
4. Proteomics
5. On some concepts of signal processing in life science
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Zentrum für Technomathematik Mathematik / InformatikFachbereich 3
1. Cells• procaryotic
/eucariotic
• nucleus (chro-mosomes) / cytoplasma (i.e. mitochon- dria, ribosomes)
• Cell cycle
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Zentrum für Technomathematik Mathematik / InformatikFachbereich 3
2. Molecules of liveSmall molecules• nucleotides (i.e. DNA bases A, C, G and T)• 20 different amino acids as the building blocks for proteins, i.e.
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Zentrum für Technomathematik Mathematik / InformatikFachbereich 3
Proteins
• main building blocks and functional molecules of the cell
• 20% of cell weight (water: 70%)
• four levels of structure
• 3 – 10 nm
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Zentrum für Technomathematik Mathematik / InformatikFachbereich 3
DNA• main information carrier molecule in a cell
• polynucleotide, i.e. consists of several nucleotides A, G, C and T
• simplest case: single stranded; directed chain of 4 different small molecules called nucleotides, i.e. A → G → T → C → C → A → A → G → C → G → A → A → T → G
• Complementary strand: mutually exchange A with T and C with Gand change direction; for our example:T ← C ← A ← G ← G ← T ← T ← C ← G ← C ← T ← T ← A ← C
• Complementary nucleotides bind weakly → longer compl. strands tend to stick together A-G-T-C-C-A-A-G-C-G-A-A-T-G-C| | | | | | | | | | | | | | |T-C-A-G-G-T-T-C-G-C-T-T-A-C-G
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Zentrum für Technomathematik Mathematik / InformatikFachbereich 3
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Zentrum für Technomathematik Mathematik / InformatikFachbereich 3
RNA
• similar to DNA, but single stranded
• functionally different types: mRNA, rRNA, tRNA
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Zentrum für Technomathematik Mathematik / InformatikFachbereich 3
3. Genes and genomesGenome: an organism‘s complete set of DNA
Organism No. ofChrom.
Genome size in base pairs
Bacteria 1 ~400.000 - ~10.000.000
Yeast 12 14.000.000
Worm 6 100.000.000
Fly 4 300.000.000
Weed 5 125.000.000
Human 23 3.000.000.000
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Zentrum für Technomathematik Mathematik / InformatikFachbereich 3
Genes and protein synthesis
• Gene: continuous stretch of DNA, from which a particular type of proteins can be made
• Proteine syntesis
1. Transcription
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Zentrum für Technomathematik Mathematik / InformatikFachbereich 3
2. Splicing
pre-mRNA
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Zentrum für Technomathematik Mathematik / InformatikFachbereich 3
3. Translation
Result: Preprotein
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Zentrum für Technomathematik Mathematik / InformatikFachbereich 3
Protein synthesis (summary)
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Zentrum für Technomathematik Mathematik / InformatikFachbereich 3
Genetics vs. Genomics
Genetics: Study of single genes and their effectsGenomics: study not just of single genes, but of the
functions and interactions
Qualitative shift in medical applications:
concept of one desease ↔ concept of information (Genetics) (Genomics)
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Zentrum für Technomathematik Mathematik / InformatikFachbereich 3
4. ProteomicsOne genome -
different proteomes!
Proteome: Constellation of all proteines in a cell
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Zentrum für Technomathematik Mathematik / InformatikFachbereich 3
Just one special tool: 2D-Gelelektrophorese
I.e. analysis of proteine pattern for brain tissue
More proteine GFAP is produced in case of Alzheimer
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Zentrum für Technomathematik Mathematik / InformatikFachbereich 3
Proteine Chemistry vs. Proteomics
Proteine Chemistry Proteomics
• Individual proteins• Complete sequence analysis• Emphasis on structure and function
• Structural biology
• Complex mixtures• Partial sequence analysis• Emphasis on identification by database matching• Systems biology
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Zentrum für Technomathematik Mathematik / InformatikFachbereich 3
5. On some concepts of signal processing in life
science
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Zentrum für Technomathematik Mathematik / InformatikFachbereich 3
Summary
DNA
mRNA
Proteins
Cell functions
Genome“Genomics”
Proteome“Proteomics”