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Chapter 12 DNA Technology and Genomics PowerPoint Lectures for Campbell Biology: Concepts & Connections, Seventh Edition Reece, Taylor, Simon, and Dickey © 2012 Pearson Education, Inc. Lecture by Edward J. Zalisko Introduction DNA technology – has rapidly revolutionized the field of forensics, – permits the use of gene cloning to produce medical and industrial products, – allows for the development of genetically modified organisms for agriculture, – permits the investigation of historical questions about human family and evolutionary relationships, and – is invaluable in many areas of biological research. © 2012 Pearson Education, Inc. Figure 12.0_1 Chapter 12: Big Ideas Gene Cloning Genetically Modified Organisms DNA Profiling Genomics GENE CLONING © 2012 Pearson Education, Inc. 12.1 Genes can be cloned in recombinant plasmids Biotechnology is the manipulation of organisms or their components to make useful products. For thousands of years, humans have – used microbes to make wine and cheese and – selectively bred stock, dogs, and other animals. DNA technology is the set of modern techniques used to study and manipulate genetic material. © 2012 Pearson Education, Inc. Figure 12.1A 12.1 Genes can be cloned in recombinant plasmids Genetic engineering involves manipulating genes for practical purposes. – Gene cloning leads to the production of multiple, identical copies of a gene-carrying piece of DNA. – Recombinant DNA is formed by joining nucleotide sequences from two different sources. – One source contains the gene that will be cloned. – Another source is a gene carrier, called a vector. – Plasmids (small, circular DNA molecules independent of the bacterial chromosome) are often used as vectors. © 2012 Pearson Education, Inc. 12.1 Genes can be cloned in recombinant plasmids Steps in cloning a gene 1. Plasmid DNA is isolated. 2. DNA containing the gene of interest is isolated. 3. Plasmid DNA is treated with a restriction enzyme that cuts in one place, opening the circle. 4. DNA with the target gene is treated with the same enzyme and many fragments are produced. 5. Plasmid and target DNA are mixed and associate with each other. © 2012 Pearson Education, Inc. 12.1 Genes can be cloned in recombinant plasmids 6. Recombinant DNA molecules are produced when DNA ligase joins plasmid and target segments together. 7. The recombinant plasmid containing the target gene is taken up by a bacterial cell. 8. The bacterial cell reproduces to form a clone, a group of genetically identical cells descended from a single ancestral cell. Animation: Cloning a Gene © 2012 Pearson Education, Inc. Figure 12.1B E. coli bacterium Plasmid Bacterial chromosome 1 A cell with DNA containing the gene of interest 2 A plasmid is isolated. The cell’s DNA is isolated. Gene of interest 3 DNA The plasmid is cut with an enzyme. Examples of gene use 4 The cell’s DNA is cut with the same enzyme. Gene of interest 5 6 The targeted fragment and plasmid DNA are combined. DNA ligase is added, which joins the two DNA molecules. Examples of protein use Recombinant DNA plasmid Gene of interest 7 The recombinant plasmid is taken up by a bacterium through transformation. Recombinant bacterium 8 Clone of cells Genes may be inserted into other organisms. The bacterium reproduces. 9 Harvested proteins may be used directly. Figure 12.1B_s1 E. coli bacterium Bacterial chromosome A cell with DNA containing the gene of interest Plasmid 1 2 A plasmid is isolated. Gene of interest The cell’s DNA is isolated. DNA Figure 12.1B_s2 E. coli bacterium Bacterial chromosome A cell with DNA containing the gene of interest Plasmid 1 2 A plasmid is isolated. The cell’s DNA is isolated. Gene of interest 3 DNA The plasmid is cut with an enzyme. 4 The cell’s DNA is cut with the same enzyme. Gene of interest Figure 12.1B_s3 E. coli bacterium Bacterial chromosome A cell with DNA containing the gene of interest Plasmid 1 2 A plasmid is isolated. The cell’s DNA is isolated. Gene of interest 3 DNA The plasmid is cut with an enzyme. 4 The cell’s DNA is cut with the same enzyme. Gene of interest 5 The targeted fragment and plasmid DNA are combined. Figure 12.1B_s4 E. coli bacterium Bacterial chromosome A cell with DNA containing the gene of interest Plasmid 1 2 A plasmid is isolated. The cell’s DNA is isolated. Gene of interest 3 DNA The plasmid is cut with an enzyme. 4 The cell’s DNA is cut with the same enzyme. Gene of interest 5 6 Recombinant DNA plasmid The targeted fragment and plasmid DNA are combined. DNA ligase is added, which joins the two DNA molecules. Gene of interest Figure 12.1B_s5 Recombinant DNA plasmid Gene of interest 7 Recombinant bacterium The recombinant plasmid is taken up by a bacterium through transformation. Figure 12.1B_s6 Recombinant DNA plasmid Gene of interest 7 The recombinant plasmid is taken up by a bacterium through transformation. 8 The bacterium reproduces. Recombinant bacterium Clone of cells Figure 12.1B_s7 Genes may be inserted into other organisms. Recombinant DNA plasmid Gene of interest 7 The recombinant plasmid is taken up by a bacterium through transformation. Recombinant bacterium 8 Clone of cells The bacterium reproduces. 9 Harvested proteins may be used directly. 12.2 Enzymes are used to “cut and paste” DNA Restriction enzymes cut DNA at specific sequences. – Each enzyme binds to DNA at a different restriction site. – Many restriction enzymes make staggered cuts that produce restriction fragments with single-stranded ends called “sticky ends.” – Fragments with complementary sticky ends can associate with each other, forming recombinant DNA. DNA ligase joins DNA fragments together. Animation: Restriction Enzymes © 2012 Pearson Education, Inc. Figure 12.2_s1 1 DNA Restriction enzyme recognition sequence A restriction enzyme cuts the DNA into fragments. 2 Sticky end Restriction enzyme Sticky end Figure 12.2_s2 1 DNA Restriction enzyme recognition sequence A restriction enzyme cuts the DNA into fragments. 2 Sticky end A DNA fragment from another source is added. Restriction enzyme Sticky end 3 Gene of interest Figure 12.2_s3 1 DNA Restriction enzyme recognition sequence A restriction enzyme cuts the DNA into fragments. 2 Sticky end A DNA fragment from another source is added. Two (or more) fragments stick together by base pairing. 4 Restriction enzyme Sticky end 3 Gene of interest Figure 12.2_s4 1 DNA Restriction enzyme recognition sequence A restriction enzyme cuts the DNA into fragments. 2 Sticky end A DNA fragment from another source is added. Restriction enzyme Sticky end Gene of interest 3 Two (or more) fragments stick together by base pairing. 4 DNA ligase pastes the strands together. 5 DNA ligase Recombinant DNA molecule 12.3 Cloned genes can be stored in genomic libraries A genomic library is a collection of all of the cloned DNA fragments from a target genome. Genomic libraries can be constructed with different types of vectors: – plasmid library: genomic DNA is carried by plasmids, – bacteriophage (phage) library: genomic DNA is incorporated into bacteriophage DNA, – bacterial artificial chromosome (BAC) library: specialized plasmids that can carry large DNA sequences. © 2012 Pearson Education, Inc. Figure 12.3 A genome is cut up with a restriction enzyme or Recombinant plasmid Recombinant phage DNA Bacterial clone Phage clone Plasmid library Phage library 12.4 Reverse transcriptase can help make genes for cloning Complementary DNA (cDNA) can be used to clone eukaryotic genes. – In this process, mRNA from a specific cell type is the template. – Reverse transcriptase produces a DNA strand from mRNA. – DNA polymerase produces the second DNA strand. © 2012 Pearson Education, Inc. 12.4 Reverse transcriptase can help make genes for cloning Advantages of cloning with cDNA include the ability to – study genes responsible for specialized characteristics of a particular cell type and – obtain gene sequences – that are smaller in size, – easier to handle, and – do not have introns. © 2012 Pearson Education, Inc. Figure 12.4 CELL NUCLEUS Exon Intron DNA of a eukaryotic gene Exon Intron Exon 1 Transcription RNA transcript 2 RNA splicing (removes introns and joins exons) mRNA 3 Isolation of mRNA from TEST TUBE Reverse transcriptase cDNA strand being synthesized the cell and the addition of reverse transcriptase; synthesis of a DNA strand 4 Breakdown of RNA Direction of synthesis 5 Synthesis of second DNA strand cDNA of gene (no introns) Figure 12.4_1 CELL NUCLEUS Exon Intron DNA of a eukaryotic gene Exon Intron Exon 1 Transcription RNA transcript 2 RNA splicing (removes introns and joins exons) mRNA Figure 12.4_2 3 Isolation of mRNA from TEST TUBE Reverse transcriptase cDNA strand being synthesized the cell and the addition of reverse transcriptase; synthesis of a DNA strand 4 Breakdown of RNA Direction of synthesis 5 Synthesis of second DNA strand cDNA of gene (no introns) GENETICALLY MODIFIED ORGANISMS © 2012 Pearson Education, Inc. 12.6 Recombinant cells and organisms can mass-produce gene products Recombinant cells and organisms constructed by DNA technologies are used to manufacture many useful products, chiefly proteins. Bacteria are often the best organisms for manufacturing a protein product because bacteria – have plasmids and phages available for use as genecloning vectors, – can be grown rapidly and cheaply, – can be engineered to produce large amounts of a particular protein, and – often secrete the proteins directly into their growth medium. © 2012 Pearson Education, Inc. 12.6 Recombinant cells and organisms can mass-produce gene products Yeast cells – are eukaryotes, – have long been used to make bread and beer, – can take up foreign DNA and integrate it into their genomes, – have plasmids that can be used as gene vectors, and – are often better than bacteria at synthesizing and secreting eukaryotic proteins. © 2012 Pearson Education, Inc. 12.6 Recombinant cells and organisms can mass-produce gene products Mammalian cells must be used to produce proteins with chains of sugars. Examples include – human erythropoietin (EPO), which stimulates the production of red blood cells, – factor VIII to treat hemophilia, and – tissue plasminogen activator (TPA) used to treat heart attacks and strokes. © 2012 Pearson Education, Inc. Table 12.6 12.6 Recombinant cells and organisms can mass-produce gene products Pharmaceutical researchers are currently exploring the mass production of gene products by – whole animals or – plants. Recombinant animals – are difficult and costly to produce and – must be cloned to produce more animals with the same traits. © 2012 Pearson Education, Inc. Figure 12.6A 12.7 CONNECTION: DNA technology has changed the pharmaceutical industry and medicine Products of DNA technology are already in use. – Therapeutic hormones produced by DNA technology include – insulin to treat diabetes and – human growth hormone to treat dwarfism. – DNA technology is used to – test for inherited diseases, – detect infectious agents such as HIV, and – produce vaccines, harmless variants (mutants) or derivatives of a pathogen that stimulate the immune system. © 2012 Pearson Education, Inc. Figure 12.7A 12.8 CONNECTION: Genetically modified organisms are transforming agriculture Genetically modified (GM) organisms contain one or more genes introduced by artificial means. Transgenic organisms contain at least one gene from another species. © 2012 Pearson Education, Inc. 12.8 CONNECTION: Genetically modified organisms are transforming agriculture The most common vector used to introduce new genes into plant cells is – a plasmid from the soil bacterium Agrobacterium tumefaciens and – called the Ti plasmid. © 2012 Pearson Education, Inc. Figure 12.8A_s1 Agrobacterium tumefaciens DNA containing the gene for a desired trait Ti plasmid Restriction site 1 The gene is inserted into the plasmid. Recombinant Ti plasmid Figure 12.8A_s2 Agrobacterium tumefaciens DNA containing the gene for a desired trait Ti plasmid Restriction site 1 The gene is inserted into the plasmid. Plant cell 2 Recombinant Ti plasmid The recombinant plasmid is introduced into a plant cell. DNA carrying the new gene Figure 12.8A_s3 Agrobacterium tumefaciens DNA containing the gene for a desired trait Ti plasmid Restriction site 1 The gene is inserted into the plasmid. Plant cell 2 Recombinant Ti plasmid The recombinant plasmid is introduced into a plant cell. DNA carrying the new gene 3 The plant cell grows into a plant. A plant with the new trait 12.8 CONNECTION: Genetically modified organisms are transforming agriculture GM plants are being produced that – are more resistant to herbicides and pests and – provide nutrients that help address malnutrition. GM animals are being produced with improved nutritional or other qualities. © 2012 Pearson Education, Inc. Figure 12.8B 12.9 Genetically modified organisms raise concerns about human and environmental health Scientists use safety measures to guard against production and release of new pathogens. Concerns related to GM organisms include the potential – introduction of allergens into the food supply and – spread of genes to closely related organisms. Regulatory agencies are trying to address the – safety of GM products, – labeling of GM produced foods, and – safe use of biotechnology. © 2012 Pearson Education, Inc. 12.10 CONNECTION: Gene therapy may someday help treat a variety of diseases Gene therapy aims to treat a disease by supplying a functional allele. One possible procedure is the following: 1. Clone the functional allele and insert it in a retroviral vector. 2. Use the virus to deliver the gene to an affected cell type from the patient, such as a bone marrow cell. 3. Viral DNA and the functional allele will insert into the patient’s chromosome. 4. Return the cells to the patient for growth and division. © 2012 Pearson Education, Inc. 12.10 CONNECTION: Gene therapy may someday help treat a variety of diseases Gene therapy is an – alteration of an afflicted individual’s genes and – attempt to treat disease. Gene therapy may be best used to treat disorders traceable to a single defective gene. © 2012 Pearson Education, Inc. Figure 12.10 Cloned gene (normal allele) 1 An RNA version of a normal human gene is inserted into a retrovirus. RNA genome of virus Retrovirus 2 Bone marrow cells are infected with the virus. 3 Viral DNA carrying the human gene inserts into the cell’s chromosome. Bone marrow cell from the patient 4 The engineered cells are injected into the patient. Bone marrow Figure 12.10_1 Cloned gene (normal allele) 1 An RNA version of a normal human gene is inserted into a retrovirus. RNA genome of virus Retrovirus Figure 12.10_2 2 Bone marrow cells are infected with the virus. 3 Viral DNA carrying the human gene inserts into the cell’s chromosome. Bone marrow cell from the patient 4 The engineered cells are injected into the patient. Bone marrow 12.10 CONNECTION: Gene therapy may someday help treat a variety of diseases The first successful human gene therapy trial in 2000 – tried to treat ten children with SCID (severe combined immune deficiency), – helped nine of these patients, but – caused leukemia in three of the patients, and – resulted in one death. © 2012 Pearson Education, Inc. 12.10 CONNECTION: Gene therapy may someday help treat a variety of diseases The use of gene therapy raises many questions. – How can we build in gene control mechanisms that make appropriate amounts of the product at the right time and place? – How can gene insertion be performed without harming other cell functions? – Will gene therapy lead to efforts to control the genetic makeup of human populations? – Should we try to eliminate genetic defects in our children and descendants when genetic variety is a necessary ingredient for the survival of a species? © 2012 Pearson Education, Inc. DNA PROFILING © 2012 Pearson Education, Inc. 12.11 The analysis of genetic markers can produce a DNA profile DNA profiling is the analysis of DNA fragments to determine whether they come from the same individual. DNA profiling – compares genetic markers from noncoding regions that show variation between individuals and – involves amplifying (copying) of markers for analysis. © 2012 Pearson Education, Inc. Figure 12.11 Crime scene Suspect 1 1 DNA is isolated. 2 The DNA of selected markers is amplified. 3 The amplified DNA is compared. Suspect 2 12.12 The PCR method is used to amplify DNA sequences Polymerase chain reaction (PCR) is a method of amplifying a specific segment of a DNA molecule. PCR relies upon a pair of primers that are – short, – chemically synthesized, single-stranded DNA molecules, and – complementary to sequences at each end of the target sequence. PCR – is a three-step cycle that – doubles the amount of DNA in each turn of the cycle. © 2012 Pearson Education, Inc. Figure 12.12 Cycle 1 yields two molecules Genomic DNA 3 5 Cycle 2 yields four molecules 5 3 5 3 separates DNA strands. 5 5 3 Target sequence 5 2 Primers bond 1 Heat 3 3 polymerase adds nucleotides. with ends of target sequences. 3 5 Primer 3 3 DNA 3 5 5 5 5 5 3 New DNA Cycle 3 yields eight molecules Figure 12.12_1 Cycle 1 yields two molecules Genomic DNA 3 5 1 Heat 3 5 5 3 separates DNA strands. 3 5 5 2 Primers bond with ends of target sequences. Target sequence 3 5 3 3 DNA polymerase adds nucleotides. 3 5 5 3 5 3 Primer 5 5 5 New DNA 3 Figure 12.12_2 Cycle 2 yields four molecules Cycle 3 yields eight molecules 12.12 The PCR method is used to amplify DNA sequences The advantages of PCR include – the ability to amplify DNA from a small sample, – obtaining results rapidly, and – a reaction that is highly sensitive, copying only the target sequence. © 2012 Pearson Education, Inc. 12.13 Gel electrophoresis sorts DNA molecules by size Gel electrophoresis can be used to separate DNA molecules based on size as follows: 1. A DNA sample is placed at one end of a porous gel. 2. Current is applied and DNA molecules move from the negative electrode toward the positive electrode. 3. Shorter DNA fragments move through the gel matrix more quickly and travel farther through the gel. 4. DNA fragments appear as bands, visualized through staining or detecting radioactivity or fluorescence. 5. Each band is a collection of DNA molecules of the same length. Video: Biotechnology Lab © 2012 Pearson Education, Inc. Figure 12.13 A mixture of DNA fragments of different sizes Longer (slower) molecules Power source Gel Completed gel Shorter (faster) molecules Figure 12.13_1 A mixture of DNA fragments of different sizes Longer (slower) molecules Power source Shorter (faster) molecules Gel Completed gel Figure 12.13_2 12.14 STR analysis is commonly used for DNA profiling Repetitive DNA consists of nucleotide sequences that are present in multiple copies in the genome. Short tandem repeats (STRs) are short nucleotide sequences that are repeated in tandem, – composed of different numbers of repeating units in individuals and – used in DNA profiling. STR analysis – compares the lengths of STR sequences at specific sites in the genome and – typically analyzes 13 different STR sites. © 2012 Pearson Education, Inc. Figure 12.14A STR site 1 STR site 2 Crime scene DNA The number of short tandem repeats match Suspect’s DNA The number of short tandem repeats do not match Figure 12.14B Crime scene DNA Suspect’s DNA Longer STR fragments Shorter STR fragments 12.15 CONNECTION: DNA profiling has provided evidence in many forensic investigations DNA profiling is used to – determine guilt or innocence in a crime, – settle questions of paternity, – identify victims of accidents, and – probe the origin of nonhuman materials. © 2012 Pearson Education, Inc. 12.16 RFLPs can be used to detect differences in DNA sequences A single nucleotide polymorphism (SNP) is a variation at a single base pair within a genome. Restriction fragment length polymorphism (RFLP) is a change in the length of restriction fragments due to a SNP that alters a restriction site. RFLP analysis involves – producing DNA fragments by restriction enzymes and – sorting these fragments by gel electrophoresis. © 2012 Pearson Education, Inc. Figure 12.16 Restriction enzymes added DNA sample 1 DNA sample 2 w Cut z x Cut Cut y Longer fragments y Sample 1 Sample 2 z x Shorter fragments w y y Figure 12.16_1 Restriction enzymes added DNA sample 1 DNA sample 2 w Cut z x Cut y Cut y Figure 12.16_2 Longer fragments Sample 1 Sample 2 z x Shorter fragments w y y GENOMICS © 2012 Pearson Education, Inc. 12.17 Genomics is the scientific study of whole genomes Genomics is the study of an organism’s complete set of genes and their interactions. – Initial studies focused on prokaryotic genomes. – Many eukaryotic genomes have since been investigated. © 2012 Pearson Education, Inc. Table 12.17 12.17 Genomics is the scientific study of whole genomes Genomics allows another way to examine evolutionary relationships. – Genomic studies showed a 96% similarity in DNA sequences between chimpanzees and humans. – Functions of human disease-causing genes have been determined by comparing human genes to similar genes in yeast. © 2012 Pearson Education, Inc. 12.18 CONNECTION: The Human Genome Project revealed that most of the human genome does not consist of genes The goals of the Human Genome Project (HGP) included – determining the nucleotide sequence of all DNA in the human genome and – identifying the location and sequence of every human gene. © 2012 Pearson Education, Inc. 12.18 CONNECTION: The Human Genome Project revealed that most of the human genome does not consist of genes Results of the Human Genome Project indicate that – humans have about 20,000 genes in 3.2 billion nucleotide pairs, – only 1.5% of the DNA codes for proteins, tRNAs, or rRNAs, and – the remaining 98.5% of the DNA is noncoding DNA including – telomeres, stretches of noncoding DNA at the ends of chromosomes, and – transposable elements, DNA segments that can move or be copied from one location to another within or between chromosomes. © 2012 Pearson Education, Inc. Figure 12.18 Exons (regions of genes coding for protein or giving rise to rRNA or tRNA) (1.5%) Repetitive DNA that includes transposable elements and related sequences (44%) Introns and regulatory sequences (24%) Unique noncoding DNA (15%) Repetitive DNA unrelated to transposable elements (15%) 12.20 Proteomics is the scientific study of the full set of proteins encoded by a genome Proteomics – is the study of the full protein sets encoded by genomes and – investigates protein functions and interactions. The human proteome includes about 100,000 proteins. Genomics and proteomics are helping biologists study life from an increasingly holistic approach. © 2012 Pearson Education, Inc. You should now be able to 1. Explain how plasmids are used in gene cloning. 2. Explain how restriction enzymes are used to “cut and paste” DNA into plasmids. 3. Explain how plasmids, phages, and BACs are used to construct genomic libraries. 4. Explain how a cDNA library is constructed and how it is different from genomic libraries constructed using plasmids or phages. 5. Explain how a nucleic acid probe can be used to identify a specific gene. © 2012 Pearson Education, Inc. You should now be able to 6. Explain how different organisms are used to massproduce proteins of human interest. 7. Explain how DNA technology has helped to produce insulin, growth hormone, and vaccines. 8. Explain how genetically modified (GM) organisms are transforming agriculture. 9. Describe the risks posed by the creation and culturing of GM organisms and the safeguards that have been developed to minimize these risks. © 2012 Pearson Education, Inc. You should now be able to 10. Describe the benefits and risks of gene therapy in humans. Discuss the ethical issues that these techniques present. 11. Describe the basic steps of DNA profiling. 12. Explain how PCR is used to amplify DNA sequences. 13. Explain how gel electrophoresis is used to sort DNA and proteins. 14. Explain how short tandem repeats are used in DNA profiling. © 2012 Pearson Education, Inc. You should now be able to 15. Describe the diverse applications of DNA profiling. 16. Explain how restriction fragment analysis is used to detect differences in DNA sequences. 17. Explain why it is important to sequence the genomes of humans and other organisms. 18. Describe the structure and possible functions of the noncoding sections of the human genome. 19. Explain how the human genome was mapped. © 2012 Pearson Education, Inc. You should now be able to 21. Compare the fields of genomics and proteomics. 22. Describe the significance of genomics to the study of evolutionary relationships and our understanding of the special characteristics of humans. © 2012 Pearson Education, Inc. Figure 12.UN01 Bacterial clone Cut Bacterium DNA fragments Cut Plasmids Recombinant DNA plasmids Recombinant bacteria Genomic library Figure 12.UN02 A mixture of DNA fragments A “band” is a collection of DNA fragments of one particular length Longer fragments move slower Shorter fragments move faster DNA is attracted to pole due to PO4 groups Power source Figure 12.UN03 DNA amplified via (a) Bacterial plasmids DNA sample treated with treated with (b) DNA fragments sorted by size via (c) Recombinant plasmids are inserted into bacteria Add (d) Particular DNA sequence highlighted are copied via (e) Figure 12.UN03_1 DNA amplified via (a) Bacterial plasmids DNA sample treated with (b) treated with Figure 12.UN03_2 DNA fragments sorted by size via (c) Recombinant plasmids are inserted into bacteria Add (d) Particular DNA sequence highlighted are copied via (e)