Blueprint of Life

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Blueprint of Life

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

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Genome and gene
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Nucleic acid and proteins
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Nucleotide codes
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BASES
Guanine
Adenine
Thymine
Cytosine
Uracil
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The Four Nucleosides of DNA
A nucleoside is a sugar, here deoxyribose, plus a
base
dA deoxyadenosine, etc.
dA dG
dC dT
PYRIMIDINES
PURINES
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Base Pairing
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The monomeric units of nucleic acids are called
nucleotides.
A nucleotide is a phospate, a sugar, and a
purine or a pyramidine base.
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DNA B form (7BNA)
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Amino acid codes
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Sperm whale myoglobin (1MBN)
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StandardGenetic Code
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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. T12alt yeast nuc T13 asc.
mt T14 flat. mt T15 bleph. nuc.
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The central dogma and its evolution
Transcription
Translation
Replication
DNA
RNA
Protein
Reverse-transcription
(RNA World)
RNA
RNA
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Schematic illustration of a eukaryotic cell
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Schematic illustration of a plant cell
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The dual flow of information in lifethe
vertical flow by genetic information
transmission, and the horizontal flow by the
genetic information expression
Development
Organism
Germ Cell Line
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History of structure determination for nucleic
acids and proteins
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DNA Z-type (2ZNA)
DNA A-type (140D)
DNA B-type (7BNA)
Polymorphic DNA tertiary structures
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Yeast alanyl transfer RNA
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Yeast phenylalanine tRNA (1TRA)
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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.
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Human chromosomes idiograms
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Chromosomes
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X-linked recessive disorder. The inheritance
pattern is shown for a recessive gene on the
chromosome X, designated in bold.
Female XX (normal)
Female XX (normal)
Male XY (affected)
Male XY (normal)
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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.
Marker M
Disease gene D
Children
M
M
M
D
D
D
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Reductionistic and synthetic approaches in
biology
Biological System (Organism)
Synthetic Approach (Bioinformatics)
Reductionistic Approach (Experiments)
Building Blocks (Genes/Molecules)
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Basic principles in physics, chemistry and
biology.
Principles Known?
Physics Matter
Chemistry Compound
Biology Organism
Elementary Particles Yes
Genes No
Elements Yes
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The Protein Folding Problem
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Protein Folding Problem(Sequence 3D Structure)

• 1 Protein folding is thermodynamically determined
  (Anfinsens thermodynamic principle)
• Protein Environment
• 2. Protein folding is a reaction imvolving other
  interacting molecules
  (Principle of molecular interactions)
• Protein Chaperonins .

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Central Paradigm