1	Homology and Evolution
2	Attribution Much of this material was taken directly from, or modified from: Fundamentals of Molecular Evolution, 2^nd Ed Grauer,D and Wen_Hsiung, L Sinauer Associates, Inc Sunderland, MA, 2000 ISBN 0-87893-266-6
3	Homology Definition Similarity in a sequence (peptide or nucleic acid) or Similarity in the structure of a protein reflecting a common evolutionary origin.
4	Homology How do sequences go from identical to homologue? BY MUTATION !
5	Mutation Deletion (single nucleotide) Insertion (single nucleotide) Substitution (single nucleotide) Missense→Different codon Synonymous (silent mutation in a gene)→ Same aa Non-synonymous (replacement in a gene) →Different aa Nonsense→stop codon Transposition (recombination) >2bp Inversion >2bp
6	The Genetic Code A mutation will likely persist if the protein coded for is functional Generally that means that the protein folds properly Recall the redundancy in the 3^rd digit of the genetic code triplet-no mutation Recall also the hydrophobicity/hydrophilicity properties of amino acids. Hydrophobic -> Hydrophobic-------maybe ok Hydrophilic -> Hydrophobic ------------potential problem
7	Gene Duplication Gene elongation makes more complex genes Copies can be variant or invariant Copies can mutate separately and diverge (immunoglobulin)
8	Overlapping Genes Most likely dysfunctional, but a mechanism to begin divergence Reading frame shift Mutation into start or stop codon in intron
9	Transposable Elements These “mobile DNA” or “Jumping Gene” elements leave accumulations of sequence throughout the molecule, mostly in introns. Effects Carry genes Can alter expression of adjacent genes Promote Genomic Rearrangement Reduce rate of conversion between members of a gene family Increase mutation rates Change immobile to mobile DNA Assimilate into chimeric genes
10	Transposable Elements Insertion Sequences (700-2000) Only genes for the insertion itself Transposons (2.5-7Kbp) Necessary + exogenous genes
11	Transposable Elements-cont Retroelements Reverse Transcriptase→cDNA Retrovirus Coding flanked by long terminal repeats (LTRs) Retroposon (lack envelope gene, not viruses) May or may not have LTRs Retrotransposon May or may not have LTRs
12	Transpositions Over (evolutionary) time, there is significant buildup of this transposed DNA Mobile DNA insertion produces short repeats at flanking ends of the host sequence. The short repeats are necessary for the process by which transposons enter the host DNA.
13	Low Complexity Regions In Prokaryotes transposons are more common than retrotransposons In Eukaryotes Retrovirus (rare in mammals) lead to significant repeats Long terminal repeats (LTRs) 250-600bp flanking repeats Non viral retrotransposons are more common in mammals No LTRs Long interspersed elements (LINES) - 7000bp 10,000 copies Short interspersed elements (SINES) - 300bp 100,000-million copies
14	Human Genome LINES L1 element: 600,000 copies (15% of genome) A/T rich at one end Contains ORF with an endonuclease and a reverse transcriptase (self-specific)
15	SINES SINES No 2 copies identical 80% intraspecies conservation 50% interspecies conservation 100bp No ORFs Origin 7SLRNA (primate Alu) tRNA (all else) Restriction enzyme AluI ferrets them out: called Alu ‘s 300 bp, 10⁶sites, 10% of genome A/T rich at one end
16	Forensics Non-Coding DNA Sequence Polymorphisms SNPs Length Polymorphism Variable Number of Short Tandem Repeats loci (Engine-nBoxcars-Caboose analogy) Repeats are short 3-4bp (STRs) Can be 15-20 alleles in such a locus Example HLADg1 242 bp with 6 alleles and 21 possible genotypes
17	Mitochondrial DNA Circular 16.5 Kbp Specific region of variability 100 bp Sperm are packed with the Nuclear DNA at the head and mitochondria behind. On entering the egg, typically the sperm nuclear DNA enters and mitochondrial do not, leaving the inheritance of mitochondrial genes exclusively maternal
18	Forensic Approaches All in junk DNA either nuclear or mitochondrial Focus is primarily on Strs, not so much on SNPs Identify loci of STRs and develop probes for endpoints of those loci Approach the DNA analysis with either restriction enzymes or with probes Use a lot of different loci (typically 6 or 7) to get discriminatory power