Blueprint of Life Based on Chapter 1 of Post-genome Informatics by Minoru Kanehisa, Oxford University Press, 2000

Genome and gene

Nucleic acid and proteins

Nucleotide codes

Adenine Guanine ThymineCytosineUracil BASES

The Four Nucleosides of DNA dA dG dC dT A nucleoside is a sugar, here deoxyribose, plus a base dA = deoxyadenosine, etc. PYRIMIDINESPURINES

Base Pairing

A nucleotide is a phospate, a sugar, and a purine or a pyramidine base. The monomeric units of nucleic acids are called nucleotides.

DNA: B form (7BNA)

Amino acid codes

Sperm whale myoglobin (1MBN)

Standard Genetic Code

Variation of genetic codes T1: standard T2: vert mt T3: yeast mt T4: other mt T5: invert. mt T6: cil. etc nuc. T9: ech. mt T10: eup. nuc. T12:alt yeast nuc T13: asc. mt T14: flat. mt T15: bleph. nuc.

The central dogma and its evolution Replication Transcription DNA Reverse- transcription RNA Translation Protein (RNA World) RNA

Schematic illustration of a eukaryotic cell

Schematic illustration of a plant cell

The dual flow of information in life: the vertical flow by genetic information transmission, and the horizontal flow by the genetic information expression Development Organism Germ Cell Line

History of structure determination for nucleic acids and proteins

DNA A-type (140D)DNA B-type (7BNA) DNA Z-type (2ZNA) Polymorphic DNA tertiary structures

Yeast alanyl transfer RNA

Yeast phenylalanine tRNA (1TRA)

The information content of various species in terms of the number of nucleotides in the genome. The complete genome sequences were determined in the years as designated. The increase of the GenBank nucleotide sequence database is also shown together with the release dates.

Human chromosomes: idiograms

Chromosomes

X-linked recessive disorder. The inheritance pattern is shown for a recessive gene on the chromosome X, designated in bold. Male XY (normal) FemaleX (normal) Female XX (normal) Female XX (normal) Male XY (normal) Male XY (affected)

Linkage analysis. The relative distance between the disease gene (D) and a marker (M) can be estimated from the frequency that both D and M are transmitted together to offspring. Father Mother Children Marker M Disease gene D M D MM DD

Reductionistic and synthetic approaches in biology Biological System (Organism) Building Blocks (Genes/Molecules) Synthetic Approach (Bioinformatics) Reductionistic Approach (Experiments)

Basic principles in physics, chemistry and biology. Principles Known? Physics Matter Chemistry Compound Biology Organism Elementary Particles Yes Elements Yes Genes No

The Protein Folding Problem

Protein Folding Problem (Sequence 3D Structure) 1 Protein folding is thermodynamically determined (Anfinsen’s thermodynamic principle ) Protein + Environment 2. Protein folding is a reaction imvolving other interacting molecules (Principle of molecular interactions) Protein + Chaperonins +….

Central Paradigm