Color--ChapterNine-GeneGenome.pdf

Chapter 9 How Genes and Genomes Evolve Genome •the content of genetic material unique for each species •species members have same set of genes; individuals have slightly different versions (alleles) How do we study the organization of the genome? •To hybridize the two single strands must have...

Chapter 9 How Genes and Genomes Evolve Genome •the content of genetic material unique for each species •species members have same set of genes; individuals have slightly different versions (alleles) How do we study the organization of the genome? •To hybridize the two single strands must have complementary nt sequences Figure 10-10 DNA can undergo reversible strand separation See Figure 10-10 FISH (fluorescence in situ hybridization) Renaturation makes hybridization of two or more DNA molecules possible FISH of satellite DNA α-satellite DNA See Fig. 10-23 Chromosomal localization of a nonrepeated DNA sequence •gene encodes nuclear lamin protein •present on the two homologues of chromosome 10 •Why are there four dots? See Fig. 10-23 DNA sequence variation •any two humans have ~99.9% similar nucleotide sequence •only ~1 out of every 1000 nts is different •these differences are mainly single nt changes (e.g., an A for a G) due to mutation; Single nucleotide polymorphisms (SNPs) •of the total 3 million SNPs, only 60,000 are found in protein-coding sequences that lead to different aa; these aa differences may change the function of the protein; thus we all have different phenotypes (look different) Genes and Genomes can be altered by several mechanisms Genes and Genomes can be altered by several mechanisms •May help or hurt organism; most often neutral (e.g., within intron or same aa) •Synonymous mutation (aka silent)-- both forms lead to same polypeptide •Nonsynonymous mutation- a different polypeptide is produced Mutations in germ-line and somatic cells are different Figure 9-3 Mutations in germ-line and somatic cells are different Figure 9-4 Mutation rates can be measured in the laboratory •~ 3 mistakes per 1010 nucleotides copied •Based on size of genome and number of bacteria in overnight growth, statistically every single nonlethal base pair substitution is present in culture •(humans 1 mistake per 1010 nucleotides) Figure 9-5 Humans 20-200 divisions --fertilized egg to female gamete (20-30 genome replications) --fertilized egg to sperm (200 genome replications) -- ~ 0.1–1 mutations per replication -- 10–100 mutations between individual and gametes they make Genes and Genomes can be altered by several mechanisms Mutations can change the regulation of a gene •Some mutations don’t lead to an aa change, but to the level of expression of a gene •10,000 years ago mutation that allowed lactase to be expressed in adults (not just in infants- 3 years) •Individuals that can digest milk sugar (lactose) from domesticated cows may have an advantage during starvation Figure 9-6 Genes and Genomes can be altered by several mechanisms •Can occur during repair of doublestrand DNA breaks or meiosis Genetic recombination (crossing-over) Gene duplication/deletion by unequal crossing over during meiosis Fig. 9-8 Evolution of globin genes See Fig. 9-9 Fig. 9-10 Chromosomal localization of a duplicated gene Genes and Genomes can be altered by several mechanisms Homologous recombination between exons Correspondence between exons and protein domains •part of a protein sequence that can function, evolve and exist independently of the rest of the protein chain •usually 25-500 AA in length •multi-domain proteins probably evolved by the fusion of genes that once encoded separate proteins Exon shuffling can generate proteins with new combinations of domains •It has been proposed that of all of the proteins encoded in the human genome (~21,000) arose from duplication/shuffling of a few thousand distinct domains of 30-50 aa Figure 9-12 An exon can be duplicated by recombination Genes and Genomes can be altered by several mechanisms The evolution of genomes has been accelerated by movement of mobile genetic elements (jumping genes) • ~ 45% human genome • 100-1000’s base pairs long • copied and inserted into a new site in the genome by the process of transposition • may be 0.5-1 million copies • sequences appear to serve no useful function • > 99% can no longer move (due to mutation) • Can generate mutations (1 in 500 human diseasescausing mutations) I. DNA only • enzyme catalyzing transpostion is transposase (most common genes in euks are transposases!) • the transposon DNA encodes the transposase • Common in bacterial Fig. 9-24 Transposons can create new exon arrangements— exons move to another gene Figure 9-26 II. RNA-mediated retrotransposon pathway— unique to eukaryotes •L-1 (LINE-1) elements--(15% of genome; ~6000 bp long) •Alu sequence--(10% of genome; ~300 bp long) See Fig. 9-27 •LINE 1 RNA needed for mouse embryo development •The RNA acts as a “molecular glue” to assemble molecules needed to leave 2-cell stage •Blocking jumping ability did not affect embryonic development •Embryos may be able to make LINE1 RNA, but prevent them from jumping in the genome The Atlantic Genes are sparsely distributed in the human genome: a comparision DNA segments of 50,000 nt pairs contains: 26 yeast genes 11 fly genes 4 human genes Figure 9-34 Most of the human genome is made of noncoding and repetitive sequences Includes rRNA, tRNA genes •Average gene 27,000 nucleotides, but only ~ 1,300 nucleotides in exons •Only ~ 1.5% of DNA in protein-coding regions •3.5% conserved with other mammals and do note encode for protein Figure 9-33