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Chapter 21 GENOMES AND THEIR EVOLUTION • Genomics is the study of whole sets of genes and their interactions • http://www.youtube.com/watch?v=mmgIClg0Y1k • Bioinformatics is the application of computational methods to the storage and analysis of biological data • http://www.youtube.com/watch?v=xODTm4a6nsM &feature=related Figure 21.2-4 Chromosome bands Cytogenetic map Genes located by FISH 1 Linkage mapping Genetic markers 2 Physical mapping Overlapping fragments 3 DNA sequencing Whole-Genome Shotgun Approach to Genome Sequencing • The whole-genome shotgun approach was developed by J. Craig Venter in 1992 • http://www.wiley.com/legacy/wileychi/reecegenes/ chapter9_ani.html • This approach skips genetic and physical mapping and sequences random DNA fragments directly • Powerful computer programs are used to order fragments into a continuous sequence Figure 21.3-3 1 Cut the DNA into overlapping fragments short enough for sequencing. 2 Clone the fragments in plasmid or phage vectors. 3 Sequence each fragment. 4 Order the sequences into one overall sequence with computer software. Identifying Protein-Coding Genes and Understanding Their Functions • Using available DNA sequences, geneticists can study genes directly in an approach called reverse genetics • The identification of protein coding genes within DNA sequences in a database is called gene annotation • Gene annotation is largely an automated process • Comparison of sequences of previously unknown genes with those of known genes in other species may help provide clues about their function Understanding Gene and Gene Expression at the Systems Level • Proteomics is the systematic study of all proteins encoded by a genome • Proteins, not genes, carry out most of the activities of the cell Figure 21.5 Glutamate biosynthesis Translation and ribosomal functions Mitochondrial functions Vesicle fusion RNA processing Peroxisomal functions Transcription and chromatinrelated functions Metabolism and amino acid biosynthesis Nuclearcytoplasmic transport Secretion and vesicle transport Nuclear migration and protein degradation Mitosis DNA replication and repair Cell polarity and morphogenesis Protein folding, glycosylation, and cell wall biosynthesis Serinerelated biosynthesis Amino acid permease pathway Table 21.1 • About 25% of the human genome codes for introns and gene-related regulatory sequences (5%) • Intergenic DNA is noncoding DNA found between genes – Pseudogenes are former genes that have accumulated mutations and are nonfunctional – Repetitive DNA is present in multiple copies in the genome • About three-fourths of repetitive DNA is made up of transposable elements and sequences related to them Figure 21.7 Exons (1.5%) Regulatory sequences (20%) Repetitive DNA that includes transposable elements and related sequences (44%) L1 sequences (17%) Alu elements (10%) Introns (5%) Unique noncoding DNA (15%) Repetitive DNA unrelated to transposable elements (14%) Simple sequence DNA (3%) Large-segment duplications (56%) Transposable Elements and Related Sequences • The first evidence for mobile DNA segments came from geneticist Barbara McClintock’s breeding experiments with Indian corn • McClintock identified changes in the color of corn kernels that made sense only by postulating that some genetic elements move from other genome locations into the genes for kernel color • These transposable elements move from one site to another in a cell’s DNA; they are present in both prokaryotes and eukaryotes • http://www.youtube.com/watch?v=_Ol492CLk dY Figure 21.9 Transposon DNA of genome Transposon is copied Mobile transposon New copy of transposon Insertion Figure 21.10 Retrotransposon New copy of retrotransposon Formation of a single-stranded RNA intermediate RNA Insertion Reverse transcriptase Genes and Multigene Families • Many eukaryotic genes are present in one copy per haploid set of chromosomes • The rest of the genome occurs in multigene families, collections of identical or very similar genes • Some multigene families consist of identical DNA sequences, usually clustered tandemly, such as those that code for rRNA products • The classic examples of multigene families of nonidentical genes are two related families of genes that encode globins • α-globins and β-globins are polypeptides of hemoglobin and are coded by genes on different human chromosomes and are expressed at different times in development Figure 21.11 DNA RNA transcripts Nontranscribed Transcription unit spacer -Globin -Globin Heme DNA 18S 5.8S 28S rRNA 28S 5.8S 18S (a) Part of the ribosomal RNA gene family -Globin gene family Chromosome 16 Embryo 2 1 2 1 -Globin gene family Chromosome 11 G A Fetus and adult Embryo Fetus Adult (b) The human -globin and -globin gene families Duplication, rearrangement, and mutation of DNA contribute to genome evolution • The basis of change at the genomic level is mutation, which underlies much of genome evolution • The earliest forms of life likely had a minimal number of genes, including only those necessary for survival and reproduction • The size of genomes has increased over evolutionary time, with the extra genetic material providing raw material for gene diversification Figure 21.14 Ancestral globin gene Evolutionary time Duplication of ancestral gene Mutation in both copies Transposition to different chromosomes Further duplications and mutations 2 1 2 1 -Globin gene family on chromosome 16 G A -Globin gene family on chromosome 11 Figure 21.15 EGF EGF EGF EGF Epidermal growth factor gene with multiple EGF exons F F F Exon shuffling Exon duplication F Fibronectin gene with multiple “finger” exons F EGF K K K Plasminogen gene with a “kringle” exon Portions of ancestral genes Exon shuffling TPA gene as it exists today Figure 21.UN01 Bacteria Genome size Number of genes Gene density Introns Other noncoding DNA Archaea Most are 16 Mb 1,5007,500 Higher than in eukaryotes None in protein-coding genes Present in some genes Very little Eukarya Most are 104,000 Mb, but a few are much larger 5,00040,000 Lower than in prokaryotes (Within eukaryotes, lower density is correlated with larger genomes.) Unicellular eukaryotes: present, but prevalent only in some species Multicellular eukaryotes: present in most genes Can be large amounts; generally more repetitive noncoding DNA in multicellular eukaryotes