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6 Evoluce 2015 Katalýza (& kód). uspořádanost (organization)

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Prezentace na téma: "6 Evoluce 2015 Katalýza (& kód). uspořádanost (organization)"— Transkript prezentace:

1 6 Evoluce 2015 Katalýza (& kód)

2 uspořádanost (organization)

3

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5 Vmax = k cat.[E t ]

6 Rychlost reakce je tedy funkcí koncentrací substrátu reakce [S] a efektivní koncentrace enzymu [E t ]: v = k cat.[E t ].[S] / (K M + [S]) Jestliže [S] << K M (běžný případ, K M se pohybuje v rozmezí [S]), pak v = [E t ].[S].k cat /K M Obě konstanty - K M a k cat - souvisí s nutností udržet kompromis mezi rigiditou molekuly proteinu a její flexibilitou.

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9 (S. Kauffman: Čtvrtý zákon) pokusy s náhodnými peptidy

10 Replikace: opisovat nebo obtisknout Kód: jednat podle návodu

11 Gabriel Tobie Nature 519, 162–163, (12 March 2015)Gabriel Tobie

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13 The replication of nucleic acids is central to the origin of life. On the early Earth, suitable non-equilibrium boundary conditions would have been required to surmount the effects of thermodynamic equilibrium such as the dilution and degradation of oligonucleotides. One particularly intractable experimental finding is that short genetic polymers replicate faster and outcompete longer ones, which leads to ever shorter sequences and the loss of genetic information. Here we show that a heat flux across an open pore in submerged rock concentrates replicating oligonucleotides from a constant feeding flow and selects for longer strands. Our experiments utilize the interplay of molecular thermophoresis and laminar convection, the latter driving strand separation and exponential replication. Strands of 75 nucleotides survive whereas strands half as long die out, which inverts the above dilemma of the survival of the shortest. The combined feeding, thermal cycling and positive length selection opens the door for a stable molecular evolution in the long-term microhabitat of heated porous rock.

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17 replikovat se a ovlivňovat svět

18 Svět RNA: život bez kódu

19 A:T G:U afinita ne kód

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23 Problémy: * s vysokými nároky na vazebná místa RNA polymerázy A, C, U nebo T se přikládá k A, C, U, nebo T na konci řetězce 16 různých kombinací i dnešní protein dělá hodně chyb * se stabilitou RNA v prostředí

24 Avšak: možnost vazby na povrchy možnost vázat jiné sloučeniny

25 Hypercyklus Manfred Eigen, Peter Schuster

26 Here is what I ride

27 katalytická uzávěra (catalytic closure)

28 hypercycklus M. Eigen

29 Szostak lab (tibosa, threhalosa, glycerol)

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31 Cairns-Smith, A. G.: Genetic takeover and the mineral origins of life. Cambridge: Cambridge University Press Cairns-Smith, A. G.: Seven Clues to the Origin of Life Cambridge: Cambridge University Press 1985.

32 Cairns-Smith

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36 Kaolinit Al 2 (Si 2 O 5 )(OH) 4 Saukonit (Si 6,94 Al 1,06 ) IV (Al 0,44 Fe 0,34 Mg 0,36 Zn 4,80 ) VI O 20 (OH) 4.n aq M + 0,67

37 Cairns-Smith

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40 &&&&&&&&&&&&&&&&&&&&& &&&&&&&&&&&&&&&&&&&&& ~~~~~~~~~~~~~~~~~~~~~ &&&&&&&&&&&&&&&&&&&&& &&&&&&&&&&&&&&&&&&&&&

41 &&&&&&&&&&&&&&&&&&&&& ~~~~~~~~~~~~~~~~~~~~~ &&&&&&&&&&&&&&&&&&&&& &&&&&&&&&&&&&&&&&&&&&

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43 Cairns-Smith

44 Model granátové jablko – dutinky v hornině

45 K počátkům: Jaké chemikálie Jaké struktury Jaké dráhy Jaké katalyzátory ?

46 Membrány dnes

47 Nature 454, 37, 2008 Samoskládání (fosfo)lipidových membrán

48 2 Rapid evolutionary innovation during an Archaean genetic expansion. David, Lawrence; Alm, Eric Nature. 469(7328):93-96, January 6, DOI: /nature09649 Figure 1 |: Rates of macroevolutionary events over time. Average rates of gene birth (red), duplication (blue), HGT (green), and loss (yellow) per lineage (events per 10 Myr per lineage) are shown. Events that increase gene count are plotted to the right, and gene loss events are shown to the left. Genes already present at the Last Universal Common Ancestor are not included in the analysis of birth rates because the time over which those genes formed is not known. The Archaean Expansion (AE) was also detected when 30 alternative chronograms were considered (Supplementary Fig. 9). The inset shows metabolites or classes of metabolites ordered according to the number of gene families that use them that were born during the Archaean Expansion compared with the number born before the expansion, plotted on a log2 scale. Metabolites whose enrichments are statistically significant at a false discovery rate of less than 10% or less than 5% (Fisher's Exact Test) are identified with one or two asterisks, respectively. Bars are coloured by functional annotation or compound type (functional annotations were assigned manually). Metabolites were obtained from the KEGG database release 51.0 (ref. 27) and associated with clusters of orthologous groups of proteins (COGs) using the MicrobesOnline September 2008 database 28. Metabolites associated with fewer than 20 COGs or sharing more than two-thirds of gene families with other included metabolites are omitted. Abbreviations are defined in Supplementary Table 3.


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