no similarity vs no homology If two complex

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.

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

beta. TB and beta. E with RMS coloring compared to beta. DP 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 Swiss. Model menu

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.

The central dogma Why might this be wrong or incomplete

Replication lagging and leading strand - strand bias

Transcription

Transcription Prokaryotes Eukaryotes

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

RNA enzymes:

Ribosome

Self-splicing introns

Group II intron

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

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

Tree, Web, or Coral of Life? “The tree of life should perhaps be called the coral of life, base of branches dead” Page B 26 from Charles Darwin’s (1809 -1882) notebook (1837) Charles Darwin Photo by J. Cameron, 1869

Which Type of Coral?

Darwin’s coral was a red algae (Bossea orbignyana) 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. From Florian Maderspacher: “The captivating coral--the origins of early evolutionary imagery. ” Curr Biol 16: R 476 -8 2006

The Coral of Life (Darwin)

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.

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

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