From self-organization to evolution of RNA molecules The origin of - - PowerPoint PPT Presentation

From self-organization to evolution of RNA molecules

The origin of biological information Peter Schuster Institut für Theoretische Chemie und Molekulare Strukturbiologie der Universität Wien Self-formation. Theory and application Vilnius, 26.– 28.11.2003

Web-Page for further information: http://www.tbi.univie.ac.at/~pks

1. Autocatalytic chemical reactions in the flow reactor 2. Replication, mutation, selection and Shannon information 3. Evolution in silico and optimization of RNA structures 4. Random walks and ‚ensemble learning‘ 5. Sequence-structure maps, neutral networks, and intersections

1. Autocatalytic chemical reactions in the flow reactor 2. Replication, mutation, selection and Shannon information 3. Evolution in silico and optimization of RNA structures 4. Random walks and ‚ensemble learning‘ 5. Sequence-structure maps, neutral networks, and intersections

Isolated system dS U = const., V = const.,

• dS 0
• dS 0
• dS 0
• Closed system

dG dU pdV TdS T = const., p = const., =

• Open system

dS dS d S d S d S

i e i

dS = + = +

• dSenv

p T T

d S

i

deS dSenv

Entropy changes in different thermodynamic systems

Stock Solution [a] = a0 Reaction Mixture [a],[b]

A A A A A A A A A A A A A A A A A A A B B B B B B B B B B B B

Flow rate r =

1

• R
• * A

A B A Ø B A B Ø

Reactions in the continuously stirred tank reactor (CSTR)

2.0 4.0 6.0 8.0 10.0 Flow rate r [t ]

• 1

1.0 0.8 0.6 1.2 C

• n

c e n t r a t i

• n

a [ a ]

A B

k = 1

• k = 1
• Reversible first order reaction in the flow reactor

0.25 0.50 1.00 0.75 1.25 Flow rate r [t ]

• 1

1.0 0.8 0.6 1.2 Concentration a [a ]

A A + B B 2 B

• = 0

k = 1/(1+ )

• k

= 1/(1+ )

• k

= /(1+ )

• k

= /(1+ )

• Autocatalytic second order reaction and uncatalyzed reaction in the flow reactor

0.25 0.50 1.00 0.75 1.25 Flow rate r [t ]

• 1

1.0 0.8 0.6 1.2 C

• n

c e n t r a t i

• n

a [ a ]

A A + B B 2 B

• = 0
• = 0.001

k = 1/(1+ )

• k

= 1/(1+ )

• k

= /(1+ )

• k

= /(1+ )

• Autocatalytic second order reaction and uncatalyzed reaction in the flow reactor

0.25 0.50 1.00 0.75 1.25 Flow rate r [t ]

• 1

1.0 0.8 0.6 1.2 C

• n

c e n t r a t i

• n

a [ a ]

A A + B B 2 B

• = 0
• = 0.001
• = 0.1

=

k = 1/(1+ )

• k

= 1/(1+ )

• k

= /(1+ )

• k

= /(1+ )

• Autocatalytic second order reaction and uncatalyzed reaction in the flow reactor

0.10 0.08 0.06 0.04 0.02 0.12 0.14 0.16 0.18 Flow rate r [t ]

• 1

1.0 0.8 0.6 1.2 Concentration a [a ]

A B A +2 B 3B

• = 0

k = 1/(1+ )

• k

= 1/(1+ )

• k

= /(1+ )

• k

= /(1+ )

• Autocatalytic third order reaction and uncatalyzed reaction in the flow reactor

0.10 0.08 0.06 0.04 0.02 0.12 0.14 0.16 0.18 Flow rate r [t ]

• 1

1.0 0.8 0.6 1.2 Concentration a [a ]

A B A +2 B 3B

• = 0
• = 0.001

k = 1/(1+ )

• k

= 1/(1+ )

• k

= /(1+ )

• k

= /(1+ )

• Autocatalytic third order reaction and uncatalyzed reaction in the flow reactor

0.10 0.08 0.06 0.04 0.02 0.12 0.14 0.16 0.18 Flow rate r [t ]

• 1

1.0 0.8 0.6 1.2 Concentration a [a ]

A B A +2 B 3B

• = 0
• = 0.001
• = 0.0025

k = 1/(1+ )

• k

= 1/(1+ )

• k

= /(1+ )

• k

= /(1+ )

• Autocatalytic third order reaction and uncatalyzed reaction in the flow reactor

0.10 0.08 0.06 0.04 0.02 0.12 0.14 0.16 0.18 Flow rate r [t ]

• 1

1.0 0.8 0.6 1.2 Concentration a [a ]

A B A +2 B 3B

• = 0
• = 0.001
• = 0.0025
• = 0.007

=

k = 1/(1+ )

• k

= 1/(1+ )

• k

= /(1+ )

• k

= /(1+ )

• Autocatalytic third order reaction and uncatalyzed reaction in the flow reactor

Autocatalytic third order reactions A + 2 X 3 X

• Direct,

, or hidden in the reaction mechanism (Belousow-Zhabotinskii reaction). Multiple steady states Oscillations in homogeneous solution Deterministic chaos Turing patterns Spatiotemporal patterns (spirals) Deterministic chaos in space and time

Pattern formation in autocatalytic third order reactions

G.Nicolis, I.Prigogine. Self-Organization in Nonequilibrium Systems. From Dissipative Structures to Order through

• Fluctuations. John Wiley, New York 1977

Autocatalytic second order reactions A + I 2 I

• Direct,

, or hidden in the reaction mechanism Chemical self-enhancement Selection of laser modes

Selection of molecular or

• rganismic species competing

for common sources

Combustion and chemistry

• f flames

Autocatalytic second order reaction as basis for selection processes. The autocatalytic step is formally equivalent to replication or reproduction.

Stock Solution [A] = a0 Reaction Mixture: A; I , k=1,2,...

k

A + I 2 I

1 1

A + I 2 I

2 2

A + I 2 I

3 3

A + I 2 I

4 4

A + I 2 I

5 5 k1 k2 k3 k4 k5 d1 d2 d3 d4 d5

Autocatalytic competition in the flow reactor

P.Schuster & K.Sigmund, Dynamics of evolutionary optimization, Ber.Bunsenges.Phys.Chem. 89: 668-682 (1985)

Flow rate r =

R-1

Concentration of stock solution a0 A + I1 A + I + I

1 2

A A + I 2 I

2 2

A + I 2 I

3 3

A + I 2 I

4 4

A + I 2 I

5 5

A + I 2 I

1 1

k > k > k > k > k

1 2 3 4 5

Selection in the flow reactor: Reversible replication reactions

Flow rate r =

R-1

Concentration of stock solution a0 A + I1 A A + I 2 I

2 2

A + I 2 I

3 3

A + I 2 I

4 4

A + I 2 I

5 5

A + I 2 I

1 1

k > k > k > k > k

1 2 3 4 5

Selection in the flow reactor: Irreversible replication reactions

RNA

RNA as scaffold for supramolecular complexes

ribosome ? ? ? ? ?

RNA as adapter molecule

GAC ... CUG ...

leu genetic code

RNA as transmitter of genetic information

DNA

messenger-RNA protein transcription translation RNA as

• f genetic information

working copy

RNA as carrier of genetic information RNA RNA viruses and retroviruses as information carrier in evolution and evolutionary biotechnology in vitro

RNA as catalyst ribozyme

The RNA DNA protein world as a precursor of the current + biology

RNA as regulator of gene expression

gene silencing by small interfering RNAs

RNA is modified by epigenetic control RNA RNA editing Alternative splicing of messenger RNA is the catalytic subunit in

supramolecular complexes

Functions of RNA molecules