BIO 3102

MOLECULAR EVOLUTION

Study of evolution of macromolecules - nature of changes (in DNA, protein) & their impact

Evolutionary change involves genetic change

D Genotype

D Phenotype

M.C. Escher Sky & water

 Use of molecular data to help reconstruct evolutionary history - phylogenetic trees modern species

extinct lineages cenancestor - most recent

primordial life form
common ancestor of extant organisms

Brown Fig.16.1

Closely-related organisms have more similar protein sequences than distant organisms

MOLECULAR CLOCKS
www.csmt.ewu.edu/.../ chem163/163LT1.html

Web-of-life

Taking an axe to the Tree of Life...

Ford Doolittle

... far more complex scenario than Darwin could have imagined... Many [microbes] swap genes back and forth, or engage in gene duplication, recombination, gene loss or gene transfers...
www.whoi.edu/cms/images/oceanus/2005/4/v43n2-teske_edwards1en_8591.gif

Dalhousie University News July 11, 2007

1. Which tree is more accurate? 2. Is the frog more closely related to the fish or to the human, based on this tree?
The tree-thinking challenge Science 310:979, 2005

Extant

Fossil

Fossil
Schopf PNAS 91:6735, 1994

Volpe & Rosenbaum Fig.14.3

Mass extinctions, as well as radiations leading to taxonomic diversity App1.Fig.2

Loss and recovery of wings in stick insects

Nature 421: 264, 2003
Male Female

Winged

Partially winged

Wingless

Morphological data

Phylogeny based on molecular data

EVOLUTIONARY INFORMATION FROM DNA SEQUENCES?

GENE - sequence of DNA (or RNA) that is essential for a specific function

1. Protein-coding genes

U.S. Dept of Energy Human Genome Program, http://www.ornl.gov/hgmis

2. RNA-specifying genes 3. Functional DNA elements - regulatory

- structural Do not use term in text (p.9): Untranscribed genes for #3

SILENT GENE - untranscribed, but potentially functional at DNA level PSEUDOGENE - non-functional DNA with high degree of similarity to a functional gene How can pseudogenes arise during evolution?

Orthologous genes - descendants of an ancestral gene that was present in the last common ancestor of two or more species

Paralogous genes - arose by gene duplication within a lineage

TYPICAL EUKARYOTIC PROTEIN-CODING GENE

Where is the promoter? 5 UTR ? 3 UTR ? What regions will be present in the mRNA? Is there an error in this figure? Fig.1.4

TYPICAL BACTERIAL GENE ORGANIZATION

How many promoters in this region? How many proteins encoded? Operon = cluster of co-transcribed genes Evolutionary advantages of operon organization? Fig.1.6

PROTEIN-CODING GENES
5 . ATG GGA TTG CCC GCC . 3 coding strand

DNA

3 . TAC CCT AAC GGG CGG . 5 template strand

mRNA 5 . AUG GGA UUG CCC GCC . 3

- DNA usually shown as single-stranded with coding strand in 5 to 3 orientation so genetic code table can be used directly

Codon families have 1 6 members

5 . AUG GGA UUG CCC CAC . 3 For the 61 sense codons, how many substitution mutations are possible?

Genetic code is not universal Some mitochondria, a few bacteria, a few protists use a non-standard code

Table 1.4

Vertebrate mitochondrial code

UGA = Trp (instead of stop codon) AUA, AUG = Met AGA, AGG = stop codons Possible implications of different codes in nature?

AMINO ACIDS Venn diagram showing properties

Fig. 1.9

Amino acid substitution matrices

Amino acid substitutions: Conservative Ile Radical Cys Table 4.7

BLOSUM62 matrix - based on observed frequencies of amino acids replacing other amino acids during protein evolution, particularly within conserved regions BLOSUM = BLOcks Substitution Matrix

www.doc.ic.ac.uk/