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 SIMILARITYfor 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

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

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

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).

RNA enzymes:

Ribosome

Self-splicing introns

Group II intron

The RNA world concept

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

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);

Tree, Web, or Coral of Life?

Charles DarwinPhoto 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”

“The tree of life should perhaps be called the coral of life, base of branches dead”

Which Type of Coral?

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.

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

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.