genomics, genetics, genome, gene, proteins, proteome, proteine chemistry, proteomics, …

Zentrum für Technomathematik Mathematik / InformatikFachbereich 3

Genomics, Genetics, Genome, Gene, Proteins, Proteome,

Proteine Chemistry, Proteomics, …

Attempt of an overview and systematics

Uttendorf 2004

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

Zentrum für Technomathematik Mathematik / InformatikFachbereich 3

1. Cells• procaryotic

/eucariotic

• nucleus (chro-mosomes) / cytoplasma (i.e. mitochon- dria, ribosomes)

• Cell cycle

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.

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

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

Zentrum für Technomathematik Mathematik / InformatikFachbereich 3

Zentrum für Technomathematik Mathematik / InformatikFachbereich 3

RNA

• similar to DNA, but single stranded

• functionally different types: mRNA, rRNA, tRNA

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

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

Zentrum für Technomathematik Mathematik / InformatikFachbereich 3

2. Splicing

pre-mRNA

Zentrum für Technomathematik Mathematik / InformatikFachbereich 3

3. Translation

Result: Preprotein

Zentrum für Technomathematik Mathematik / InformatikFachbereich 3

Protein synthesis (summary)

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)

Zentrum für Technomathematik Mathematik / InformatikFachbereich 3

4. ProteomicsOne genome -

different proteomes!

Proteome: Constellation of all proteines in a cell

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

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

Zentrum für Technomathematik Mathematik / InformatikFachbereich 3

5. On some concepts of signal processing in life

science

Zentrum für Technomathematik Mathematik / InformatikFachbereich 3

Summary

DNA

mRNA

Proteins

Cell functions

Genome“Genomics”

Proteome“Proteomics”