Fachbereich 3 Mathematik Informatik Zentrum fr Technomathematik Genomics

Fachbereich 3 Mathematik / Informatik Zentrum für Technomathematik Genomics, Genetics, Genome, Gene, Proteins, Proteome, Proteine Chemistry, Proteomics, … Attempt of an overview and systematics Uttendorf 2004

Fachbereich 3 Mathematik / Informatik Zentrum für Technomathematik Overwiev 1. 2. 3. 4. 5. Cells Molecules of live Genes and genome Proteomics On some concepts of signal processing in life science

Zentrum für Technomathematik 1. Cells • procaryotic /eucariotic • nucleus (chromosomes) / cytoplasma (i. e. mitochon- dria, ribosomes) • Cell cycle Fachbereich 3 Mathematik / Informatik

Zentrum für Technomathematik Fachbereich 3 Mathematik / Informatik 2. Molecules of live Small molecules • nucleotides (i. e. DNA bases A, C, G and T) • 20 different amino acids as the building blocks for proteins, i. e.

Zentrum für Technomathematik Proteins • main building blocks and functional molecules of the cell • 20% of cell weight (water: 70%) • four levels of structure • 3 – 10 nm Fachbereich 3 Mathematik / Informatik

Zentrum für Technomathematik Fachbereich 3 Mathematik / Informatik 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 → A → G → C → G → A → T → G • Complementary strand: mutually exchange A with T and C with G and change direction; for our example: T ← C ← A ← G ← T ← C ← G ← C ← 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

Zentrum für Technomathematik Fachbereich 3 Mathematik / Informatik

Zentrum für Technomathematik RNA • similar to DNA, but single stranded • functionally different types: m. RNA, r. RNA, t. RNA Fachbereich 3 Mathematik / Informatik

Zentrum für Technomathematik Fachbereich 3 Mathematik / Informatik 3. Genes and genomes Genome: an organism‘s complete set of DNA Organism No. of Genome size in base Chrom. pairs Bacteria 1 ~400. 000 - ~10. 000 Yeast 12 14. 000 Worm 6 100. 000 Fly 4 300. 000 Weed 5 125. 000 Human 23 3. 000

Zentrum für Technomathematik Fachbereich 3 Mathematik / Informatik Genes and protein synthesis • Gene: continuous stretch of DNA, from which a particular type of proteins can be made • Proteine syntesis 1. Transcription

Zentrum für Technomathematik Fachbereich 3 Mathematik / Informatik 2. Splicing pre-m. RNA

Zentrum für Technomathematik 3. Translation Result: Preprotein Fachbereich 3 Mathematik / Informatik

Zentrum für Technomathematik Protein synthesis (summary) Fachbereich 3 Mathematik / Informatik

Zentrum für Technomathematik Fachbereich 3 Mathematik / Informatik Genetics vs. Genomics Genetics: Study of single genes and their effects Genomics: 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)

Fachbereich 3 Mathematik / Informatik Zentrum für Technomathematik 4. Proteomics One genome - different proteomes! Proteome: Constellation of all proteines in a cell

Zentrum für Technomathematik Fachbereich 3 Mathematik / Informatik Just one special tool: 2 D-Gelelektrophorese I. e. analysis of proteine pattern for brain tissue More proteine GFAP is produced in case of Alzheimer

Zentrum für Technomathematik Fachbereich 3 Mathematik / Informatik Proteine Chemistry vs. Proteomics Proteine Chemistry Proteomics • Individual proteins • Complete sequence analysis • Emphasis on structure and function • Complex mixtures • Partial sequence analysis • Emphasis on identification by database matching • Systems biology • Structural biology