CHAPTER 21 LECTURE SLIDES
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1 CHAPTER 21 LECTURE SLIDES Prepared by Brenda Leady University of Toledo To run the animations you must be in Slideshow View. Use the buttons on the animation to play, pause, and turn audio/text on or off. Please note: once you have used any of the animation functions (such as Play or Pause), you must first click in the white background before you advance the next slide. Copyright The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
2 The unifying theme of biology is evolution The genome of every living species is the product of over 3.5 billion years of evolution All species evolved from an interrelated group of ancestors 2
3 Prokaryotic genomes Of interest because Bacteria cause diseases Can apply knowledge to more complex organisms Origin of first eukaryotic cell probably involved the union between an archaeal and bacterial cell 3
4 Venter, Smith, and Colleagues Sequenced the First Complete Genome in 1995 Haemophilus influenzae causes a variety of human diseases Relatively small genome 1.8 Mb One strategy for mapping large genomes is extensive mapping Alternative is shotgun DNA sequencing Randomly sequence fragments Does not require extensive mapping but you may waste time sequencing the same DNA region
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6 Eukaryotic genomes Nuclear genome usually found in sets of linear chromosome Extranuclear DNA found in mitochondria and chloroplasts Entire nuclear genome sequenced for several species 6
7 4 motivators to sequence genome 1. Great benefit from identifying and characterizing genes in model organisms 2. More information to identify and treat human diseases 3. Improved strains of agricultural species 4. Way to establish evolutionary relationships 7
8 Genome size is not the same as the number of genes In general, increases in the amount of DNA are correlated with increasing cell size, cell complexity and body complexity However, major variations are observed between organisms with similar form and function 8
9 Eukaryotic genomes have repetitive sequences Many copies of short DNA sequences Moderately repetitive sequences Few hundred to several thousand times rrna genes, multiple origins of replication, or role in gene transcription and translation Highly repetitive sequences Tens of thousands or millions of times Most have no known function Coding regions are only 2% of our genome 9
10 Percentage in the human genome Copyright The McGraw-Hill Companies, Inc. Permission required for reproduction or display % % 15% 0 2% Regions of Introns and Unique genes that other parts noncoding encode of genes DNA proteins such as (exons) or enhancers give rise to rrna or trna Classes of DNA sequences Repetitive DNA 10
11 Repetitive Sequences Within a species, sequences of repeat units are conserved. However, the number of repeat units is variable among individuals DNA fingerpriniting exploits differences in DNA polymorphisms 11
12 12
13 Transposable elements Transposition short segment of DNA moves from original site to a new site Transposable elements (TEs) DNA segments that move Jumping genes Found in all species examined First discovered by Barbara McClintock 1983, awarded Nobel Prize 13
14 DNA transposons Both ends have inverted repeats (IRs), DNA sequences that are identical (or very similar) but run in opposite directions TEs may contain a central region that encodes transposase, an enzyme that facilitates transposition 14
15 Cut-and-paste mechanism Transposase recognizes IR and then removes sequence from original site Complex moves to new location where transposase inserts it into the chromosome 15
16 RNA intermediates Common only in eukaryotes Retroelement contains reverse transcriptase and transposase Reverse transcriptase uses RNA as a template to make a complementary copy of DNA Retroelements may accumulate rapidly in a genome Alu elements are 10% of human genome 16
17 Role of transposable elements Selfish DNA hypothesis TEs exist solely because they have characteristics that allow them to insert themselves into the host cell DNA Resemble parasites, can do harm Others argue TEs may benefit a species Promote genetic variation 17
18 Gene duplication Provide raw material for the addition of more genes into a species genome Create homologous genes Two or more genes that are derived from the same ancestral gene Over the course of many generations, each version of the gene accumulates different mutations Genes with similar but not identical DNA sequences 18
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20 Mechanism Gene duplication caused by misaligned crossovers 2 homologous chromosomes have paired during meiosis but the homologs are misaligned If a crossover occurs, one chromosome gets a gene duplication, one a gene deletion and 2 are normal 20
21 Copyright The McGraw-Hill Companies, Inc. Permission required for reproduction or display. A B C D A A B C B C D D A B C D Following meiosis 21
22 Copyright The McGraw-Hill Companies, Inc. Permission required for reproduction or display. A B C D A A B C B C D D Misaligned crossover between homologous chromosomes A B C D Following meiosis A B C D A B C C D A B D Gene duplication A B C D Deletion (b) Mechanism of gene duplication 22
23 Paralogs Two or more homologous genes within a single species Gene family Two or more paralogous genes that carry out related functions 23
24 Globin genes Encode polypeptides that are subunits of proteins that function in oxygen binding 14 paralogs derived from a single ancestral globin gene Duplications and rearrangements occurred Mutations have created specialized globins Hemoglobin, myoglobin, embryonic and fetal forms Based on differences in oxygen transport needs 24
25 Millions of years ago (mya) Copyright The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Chromosome 22 Mb Chromosome 16 Chromosome 11 α2 α1 α 2 α 1 e g G g A C β β α-globins β-globins 400 Myoglobin Hemoglobins ,000 Pseudogenes Ancestral globin Genes that have been produced by gene duplication but have accumulated mutations that make them nonfunctional Not transcribed into RNA Nonfunctional pseudogenes 25
26 Human Genome Project Officially began October 1, 1990 Largely finished by end of 2003 Goals Identify all human genes Sequence entire human genome Develop technology Analyze genomes of model organisms Develop legal, ethical and social programs addressing the results 26
27 Proteomes Relative abundance of proteins Abundance in genome Number of genes that encode a particular type of category of protein Abundance in cell Amount of a given protein or protein category actually made by a living cell Liver/muscle cell example Same genes so % in genome identical Cellular abundance very different 27
28 Copyright The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Liver cell Skeletal muscle cell Abundance in genome Abundance in genome Genes for metabolic 25% enzymes Genes for structural 5% proteins Genes for motor < 2% proteins Abundance in cell Genes for metabolic 25% enzymes Genes for structural 5% proteins Genes for motor < 2% proteins Abundance in cell Metabolic enzymes > 50% Structural proteins < 10% Motor proteins < 5% Metabolic enzymes < 10% Structural proteins 20 30% Motor proteins 25 40% 28
29 Proteomes are larger than genomes Due to Alternative splicing A single pre-mrna can be spliced into more than one version Often cell specific or related to environmental conditions Post-translational covalent modification Permanent or reversible Involved in assembly and construction of protein Phosphorylation, methylation, acetylation 29
30 pre-mrna Exon 1 Exon 2 Exon 3 Exon 4 Exon 5 Exon 6 Alternative splicing Translation Copyright The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Permanent modifications Proteolytic processing Exon 1 Exon 4 Exon 6 Exon 2 Exon 5 or SH SH Disulfide bond formation S S Exon 1 Exon 4 Exon 6 Exon 3 Exon 5 or Exon 1 Exon 4 Exon 2 Exon 6 Attachment of prosthetic groups, sugars, or lipids Sugar Heme group (a) Alternative splicing Phospholipid Reversible modifications Phosphorylation Acetylation PO 4 2 O C CH 3 Phosphate group Acetyl group Methylation CH 3 Methyl group (b) Post-translational covalent modification 30
31 Bioinformatics Use of computers, mathematical tools, and statistical techniques to record, store, and analyze biological information More than just DNA sequences Highly interdisciplinary, incorporating principles from mathematics, statistics, information science, chemistry, and physics 31
32 Issues of size and speed in analyzing huge volumes of data Computational molecular biology Uses computers to characterize the molecular components of living things 32
33 First step is to collect and store data Then write programs to analyze sequences in particular ways Translate DNA sequence into amino acid sequence results for all 3 reading frames May also not know which strand is coding strand so results for both strands 33
34 34
35 Databases Collect large numbers of files and store them in one place for rapid search and retrieval Additional descriptive information included Research community has collected genetic information from thousands of research labs and created several large databases 35
36 Identify homologous sequences Can use computer to identify genes that are evolutionarily related Closely related organisms tend to have genes with similar DNA sequences Ortholog homologous genes in different species Helps us understand evolutionary relationships 36
37 Time Copyright The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Mouse GGGCAGGTTGGTATCCAGGTTACAAGG C AGCTC AC AAGTAGAAG C T G GGTGCTTGGAGAC GGGCAGGTTGGTATCCAGGTTACAAGG T AGCTC CT AAGTAGAAG T T T GGTGCTTGGAGAC Rat (a) A comparison of one DNA strand of the mouse and rat -globin genes X X X X X Mus musculus Random mutations Rattus norvegicus -globin gene in common ancestor to mice and rats (b) The formation of homologous -globin genes during evolution of mice and rats 37
38 A matrix can be used to compare 2 sequences DNA sequences are long so use more complex dynamic programming methods 38
39 BLAST Homologous genes usually carry out similar or identical functions First indication of function for a new sequence is through homology to known sequences Basic Local Alignment Search Tool (BLAST) Uses particular genetic sequence to find homologous sequences in a large database 39
40 Sample BLAST Order follows evolutionary relatedness of various species to humans Main power of the BLAST program is its use with newly identified sequences, in which a researcher does not know the function of a gene or an encoded protein 40
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