1. Cenancestor (aka MRCA or LUCA) as placed by ancient duplicated genes (ATPases, Signal recognition particles, EF) The “Root” strictly bifurcating no reticulation only extant lineages based on a single molecular phylogeny branch length is not proportional to time The Tree of Life according to SSU ribosomal RNA (+) PHYLOGENY: from Greek phylon, race or class, and -geneia, born. “the origin and evolution of a set of organisms, usually of a species” (Wikipedia);

2. Tree, Web, or Coral of Life? Charles Darwin Photo by J. Cameron, 1869 Page B26 from Charles Darwin’s (1809-1882) notebook (1837) “The tree of life should perhaps be called the coral of life, base of branches dead”

3. Which Type of Coral?

4. Darwin’s coral was a red algae (Bossea orbignyana) From Florian Maderspacher: “The captivating coral--the origins of early evolutionary imagery.” Curr Biol 16: R476-8 2006 The captivating coral. According to the ideas of Horst Bredekamp, parts of the diagram in Darwin's origin of species (centre) more or less directly reflect the branching properties of a specimen Darwin collected himself.

5. The Coral of Life (Darwin)

6. Gene Transfer and Phylogenetic Reconstruction: Friends or Foes? Popular view  Gene transfer is a disruptive force in phylogenetic reconstruction. New view  Events of ancient gene transfer are valuable tools for reconstructing organismal phylogeny.

7. 1. Any ancient gene transfer to the ancestor of a major lineage implicitly marks the recipient and descendents as a natural group. 2. The donor must exist at the same time or earlier than the recipient. Ancient HGTs

8. Gene “ping-pong” between different lineages can be used to build correlations between different parts of the tree/net of life. Presence of a transferred gene is a shared derived character that can be useful in systematics.

9. The central dogma Why might this be wrong or incomplete

10. Replication lagging and leading strand - strand bias

11. Transcription

12.  Prokaryotes  Eukaryotes

13. RNA processing  Intron types  RNA can be the catalyst Simple illustration of a pre-mRNA, with introns (top). After the introns have been removed via splicing, the mature mRNA sequence is ready for translation (bottom).

14. RNA enzymes:

15. Ribosome

16. Self-splicing introns

17. Group II intron

18. The RNA world concept  What arguments support an “RNA world” preceding a two biopolymer world?

19. Protein structure:

20. Angles in the protein backbone

21. spdbf - viewer aka Deep View Free and powerful program Steep learning curve Interacts with modeling server available at http://ca.expasy.org/ http://spdbv.vital-it.ch/http://ca.expasy.org/ http://spdbv.vital-it.ch/ Gale Rhodes’ Tutorial is at http://www.usm.maine.edu/~rhodes/SP VTut/index.html http://www.usm.maine.edu/~rhodes/SP VTut/index.html

23. Simplify the display  Show only alpha carbons  Color secondary structure  Turn 3 D display on

24. 1HEW  Backbone as ribbon  Sidechains only in binding pocket  Substrate in yellow  Non-polar residues of binding pocket in turquoise

25. mind map 1

26. mind map 2