1. no similarity vs no homology If two (complex) sequences show significant similarity in their primary sequence, they have shared ancestry, and probably similar function. THE REVERSE IS NOT TRUE: PROTEINS WITH THE SAME OR SIMILAR FUNCTION DO NOT ALWAYS SHOW SIGNIFICANT SEQUENCE SIMILARITY for one of two reasons: a) they evolved independently (e.g. different types of nucleotide binding sites); or b) they underwent so many substitution events that there is no readily detectable similarity remaining. Corollary: PROTEINS WITH SHARED ANCESTRY DO NOT ALWAYS SHOW SIGNIFICANT SIMILARITY.

2. Simplify the display  Show only alpha carbons  Turn off show backbone oxygen  Color secondary structure  Turn 3 D display on

3. betaTB and betaE with RMS coloring compared to betaDP  Magic fit -> fit molecules -> RMS coloring  RED: Long wavelength = long distance between structures  BLUE: Short wavelength = short distance between structures  If you need to switch the reference layer, you can do so in the SwissModel menu

4. The 3 point alignment tool  If you want to compare the structure of very dissimilar proteins that use a similar substrate, sometimes it helps to align the substrates.  This can be done through the 3 point alignment tool.

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

6. Replication lagging and leading strand - strand bias

7. Transcription

8.  Prokaryotes  Eukaryotes

9. 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).

10. RNA enzymes:

11. Ribosome

12. Self-splicing introns

13. Group II intron

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

15. 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);

16. 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”

17. Which Type of Coral?

18. 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.

19. The Coral of Life (Darwin)

20. 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.

21. 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

22. 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.