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Molecular and genetic mechanisms of evolution 529 - Development Study of evolution on molecular level Study of mutations in DNA and RNA and changes in amino acids sequences. Comparison of genomes, comparison of chromosomal segments and structural parts of DNA or proteins between species. Study and comparisons of genome‘s sizes RNA as the first NA molecule The first molecules formed abiotically. Some RNA are able to replicate autonomously. Some have catalytic properties Errors in replication form different sequences, differentiation of RNA molecules, origin of family with closely related RNA molecules. Ribosyms • have auto-replication activity • ribosome, spliceosome have enzymatic properties Coenzyms are non-protein parts of some enzymes. Some are derived from nucleotides. Genetic code is nearly universal with small exceptions. Codons have the same sense in all living organisms, from viruses to humans. The most important exception is in mitochondria of mammals, yeast and other species: 4 different codons (stop codons), further 60 codons in mammalian mitochondria have the same meaning as in the nuclear mRNA. Comparison of genes, genomes The most conserved sequences: genes for rRNA genes for tRNA genes of histons genes for globins genes pro cytochromes (gene repetition) TATA box 70-75% genes of mice have equivalents in humans. 96% to 98% of genome is identical between human and chimpanzee. Comparison of protein sequences Many different types of organisms used the same proteins with small changes in amino acids sequences. Many proteins in human and chimp are similar, 99% percent of their amino acids are identical. Two strongly preserved proteins are cytochrome C and proteins of homeobox, histons, globins. CYTOCHROME C - Cytochrome C occur in all eukaryotes. 20 of 104 amino acids in the molecule of protein occupy the identical positions. Proteins of Homeobox occur in all multicellular species. Sequence of 60 amino acids = homeodomain is highly preserved part of proteins that are encoded by homeobox genes. They are mostly genes for transcription factors. Mechanisms of evolutional changes of genome: 1. Intragenic combinations 2. Duplication 3. Structural chromosomal aberrations 4. Horizontal transfer – parasexual mechanisms 5. Recombination 6. Mutations 1. Intragene combination - exons, introns combination - Insertion of transposons – mobile DNA elements in the genome. They can cause reconstructions, breaks, mutations „jumping genes“ Types: 1. "cut and paste" transposons 2. transposons replicative 3. retrotransposons - similar to retroviruses, mobility based on reverse transcriptase. LTR retrotransposons consist of central coding region for enzymes, bounded by long terminal repeats - LTRs NON-LTR retrotransposons: human LINE, SINE LINE "long interspersed nuclear element about 1kb long, original transposons, encode enzymes, proliferate and migrate SINE "short interspersed nuclear element" less than 400 bp long – inactive, no code for protein 44-45% od human genome derived from the trans. elements Heterochromatin, repetitive DNA is a cemetery of inactive transposons. 2. Gene duplication Caused by unequal crossing-over Duplication of chromosome parts leads to: • degradation of gene, origin of pseudogene • new function • same or similar function - become a member of gene family Consequences of duplication Strachan and Read: Human genetics ,2. edition Types of sequential duplicates: Partial gene duplication internal duplication Exons duplication and exon shuffling Complete gene duplication - gene families Partial or complete duplication of chromosomes - very rare Polyploidy - duplication of entire genome - general mechanism in plants, animals (beetles, fish, amphibian) Gene families occur is Eukaryotic genomes. They have similar nucleotide sequence and encode very similar proteins - isoforms with the same or overlapping functions. They could occur in one chromosome or scattered over the genome. Pseudogenes - a secondary non-active product of evolution. Superfamily - immunoglobulin gene family, HLA (MHC) genes, TCR genes on chromosomes 2, 14, 22, 6, 7 - genes for LDL receptor - alpha, beta-globin family on chromosomes 16, 11 evolution of globin family Globin family on 11 a 16 chromosome Density of coding genes Density of coding genes relates to the number of duplicated genes. Eukaryotic genomes have a lower density of coding genes as these genomes contain a considerable amount of repetitive DNA. Yeast ........... 30% of duplicated genes Cenorhabditis ..... 10% of medium repetetive DNA Mammalian DNA genomes .. 45% of medium repetetive DNA sequences - most derived from transposons 3. Structural chromosomal aberration Translocation, inversion, duplication, fusion Synteny - co-localization of genetic loci within individuals or species, based on preservation, conservation of segments and blocks of genes. There wasn‘t recombination in time, also because of incomplete gene linkage. Comparison of chromosomes: human chromosome 17, bovine chromosome 19, pig chromosome 12. Large chromosome segments - chromosome 2 Combination of chromosome segments - chromosome 3, 21 Karyotype of human (left) and karyotype of chimpanzee (right) Differences: fusion between chromosomes 15 and 17 with origin of chromosome 2, also inversions and duplications. http://www.riverapes.com/Me/Work/HumanHybridisationTheory.htm High resolution chromosome banding Human chromosome banding patterns compared to the great apes (From Strachan & Dean 1998 p 344) Notes H, C, G, O for Human, Chimpanzee, Gorilla and Orang-utan respectively. Chromosomes 2, 5 & 6 shown only. Gonosomes Sexual chromosomes developed from a pair of homologous autosomes by mutation, deletions, translocation and unequal crossing over. Lower vertebrates (fish, amphibians, reptiles) - is no morphological differentiation from gonosomes Higher vertebrates – shape of chromosome Y is different only a small part are homologous = pseudoautosomal area 4. Horizontal transfers of NA between species provide recombination of genomes predominantly of prokaryotic organisms; bacteria could developed in time, adapt to new environment and become resistant to changes and to new conditions. endosymbiosis somatic hybridization – fusion of cells parasexual processes: transformation – free income of DNA conjugation - direct transfer of DNA transduction - transfer of DNA by virus transfer of plasmids Bacterial transformation = free intake of DNA into bacterial cells. Only competent bacteria with relevant enzymes are capable of transformation (not Escherichia coli) Proof that DNA carries genetic information: Griffith (1928) 1. Experiment with S. pneumoniae Avery, McLeod, McCarthy (1944) - the same effect with an isolated DNA Exchange, recombination of homologous parts after transfer Bacterial conjugation = direct transfer of DNA The F+ plasmid of donor cell is transferred to the acceptor F- by conjugation bridge F pilli on the surface of F+ bacteria (encoded by F plasmid) Hfr strain „High frequency of recombination“ is strain with the F plasmid integrated into genomic DNA (episom) Conjugation F+ into F- bacteria Conjugation Hfr into F- bacteria Transduction = when bacteriophages spontaneously transmit bacterial genes It comes to pass for all bacteria. Specialized = incorrect cut out of the genome of bacteriophage from the bacterial genome during the transition from lysogenic to lytic cycle General = into small number of phage particles are packaged molecules of bacterial DNA instead of phage‘s DNA molecules Application in history - mapping of DNA: How often the genes are transmitted together in the general transduction, more about that are localized closer. General transduction 5. Recombination – sexual reproduction evolutionary significance of diploidy - masking of recessive alleles evolutionary significance of sexual reproduction – origin of new combinations and genetic variants due to combination of parental genomes in offspring and alternation of haploid and diploid phase of their cells Variability is done by • a combination of genomes in zygotes • a combination of chromosomes in the gametes • crossing-over in meiosis 6. Mutation - origin of alleles Mutations are sources of new genetic variations. More variants of one locus is called polymorphism. Polymorphism of standard alleles – caused by neutral mutations pathologic alleles – caused by negative mutations Mutations positive - advantageous negative - disadvantageous, losing neutral Selection, genetic drift, migration, non-random mating Genetika, D P. Snustad M.J. Simmons, 5. edition, 2009 Human genetics, Ricki Lewis, 5. vydání, 2003 Thank you for your attention