Inquiry into Life Biotechnology and Genomics Lecture Outline PDF

Because learning changes everything. ® INQUIRY INTO LIFE...

Because learning changes everything. ® INQUIRY INTO LIFE Seventeenth Edition Sylvia S. Mader Michael Windelspecht Chapter 26 Biotechnology and Genomics Lecture Outline © McGraw Hill LLC. All rights reserved. No reproduction or distribution without the prior written consent of McGraw Hill LLC.  26.1 DNA Technology 1 Biotechnology—the use of natural biological systems to create a product or achieve some other end. DNA knowledge enabled gene manipulation. Scientists can modify genomes through genetic engineering to improve an organism’s characteristics, make biotechnology products, or treat cancer and genetic disorders. © McGraw Hill LLC 2  26.1 DNA Technology 2 Cloned genes are used to alter the genome of viruses or cells. Bacterial, plant, or animal cells. A genetically modified organism (GMO) has modified genome; usually with DNA technology. Example: a transgenic organism has had a gene from another species inserted into its genome. © McGraw Hill LLC 3  Cloning 1 Cloning. Production of identical copies of an organism, cell, or DNA through asexual means. Examples: bacteria from the same colony, identical twins. Gene cloning. Production of many identical copies of a single gene. © McGraw Hill LLC 4  Cloning 2 Uses of gene cloning. Produce large quantities of the gene’s protein product; for example, insulin. Use the genes to create a GMO. Perform gene therapy to treat human disease. © McGraw Hill LLC 5  Recombinant DNA Technology 1 Recombinant DNA (rDNA). Contains DNA from two or more different sources. To make rDNA, need a vector—piece of DNA that foreign DNA can be added to. Plasmids are accessory rings of DNA in bacteria, commonly used as vectors. They are not part of the bacterial chromosome. © McGraw Hill LLC 6  Cloning a Human Gene Figure 26.1 Access the text alternative for slide images. © McGraw Hill LLC 7  Recombinant DNA Technology 2 Two enzymes needed to introduce foreign DNA into vector DNA. Restriction enzyme—to cleave vector DNA. Hundreds occur naturally in bacteria. Act as a primitive immune system in bacteria to restrict the growth of invading viruses by cutting up viral DNA. Used in cloning as molecular scissors that cut DNA at precise sequences; cut double-stranded DNA at a specific site. DNA ligase—will seal the foreign DNA into the opening in the vector DNA created by the restriction enzyme. © McGraw Hill LLC 8  Recombinant DNA Technology 3 After the cutting, a gap is created in which pieces of foreign DNA can be placed if there is complementary pairing. Foreign DNA and vector DNA are cleaved with same restriction enzyme. Single-stranded, complementary ends of the two DNA molecules are called “sticky ends” because they can bind to each other by complementary base pairing. Sticky ends facilitate the insertion of foreign DNA into vector DNA. DNA ligase, an enzyme that functions in DNA replication, is then used to seal the foreign piece of DNA into the vector. © McGraw Hill LLC 9  Restriction Enzymes Figure 26.2 Access the text alternative for slide images. © McGraw Hill LLC 10  DNA Sequencing DNA sequencing is a procedure that determines the order of nucleotides in a segment of DNA. Helps identify specific alleles and sequences. Can facilitate development of disease treatments. Can reveal evolutionary history and relationships. Foundation of forensic biology. Dyes attached to nucleotides can show order of nucleotides in automated sequencers. Many copies of the DNA segment or gene to be sequenced have to be made using the polymerase chain reaction. © McGraw Hill LLC 11  The Polymerase Chain Reaction 1 The polymerase chain reaction (PCR) can create billions of copies of a segment of DNA in a test tube in hours. Amplifies only specifically targeted DNA sequence. Targeted sequence is usually a few hundred bases in length. Uses DNA polymerase and DNA nucleotides. Three basic steps that occur repeatedly, usually for about 35 to 40 cycles. © McGraw Hill LLC 12  The Polymerase Chain Reaction 2 Three basic steps in PCR occur repeatedly. Denaturation—DNA heated at 95 degrees Celsius to become single-stranded. Annealing—usually between 50 and 60 degrees Celsius to allow the binding of a primer on the end of each DNA strand. Extension—occurs at 72 degrees Celsius where a unique DNA polymerase adds complementary bases to each of the single DNA strands, creating a double- stranded DNA. © McGraw Hill LLC 13  Polymerase Chain Reaction (PCR) Figure 26.4 Access the text alternative for slide images. © McGraw Hill LLC 14  The Polymerase Chain Reaction 3 PCR is a chain reaction because the targeted DNA is repeatedly replicated. The amount of DNA doubles with each cycle. Automation is possible because of the use of a temperature-insensitive DNA polymerase extracted from Thermus aquaticus, a bacteria that lives in hot springs. The enzyme tolerates the high temperature used to separate the DNA strands (95 degrees Celsius). © McGraw Hill LLC 15  DNA Analysis 1 DNA analysis has improved over time. Previous method involved entire genome being treated with restriction enzymes. Fragments separated by gel electrophoresis. Smaller fragments move faster than larger ones. The result was distinctive pattern of bands, called DNA fingerprint. © McGraw Hill LLC 16  Figure 26.5 DNA Fingerprinting Access the text alternative for slide images. © McGraw Hill LLC 17  DNA Analysis 2 Short tandem repeat (STR) profiling is used now. STRs are the same short sequence of DNA bases that recur several times. GATAGATAGATA. Fragments in samples amplified by PCR are different lengths because each person has his or her own number of repeats at the particular location of the STR on the chromosome. The more STR loci employed, the more confident scientists can be of distinctive results for each person. © McGraw Hill LLC 18  DNA Analysis 3 STR profiling. PCR is used to amplify fluorescently labeled target sequences of DNA. Creates fluorescently labeled PCR products. Products are run through automated DNA sequencer. Laser detects and records lengths of DNA fragments. The greater the number of STRs at a locus, the longer the DNA fragment will be. Can be used to identify samples at a crime scene, detect genetic disorders, identify relatives or victims. © McGraw Hill LLC 19  Genome Editing 1 A relatively new advance in DNA technology. Targets specific sequences in DNA for removal or replacement. There are several methods. CRISPR (clustered regularly interspaced short palindromic repeats) is the most widely used. © McGraw Hill LLC 20  Genome Editing 2 CRISPR. First discovered in prokaryotes, acting as immune defense against invading viruses. The CRISPR system involves an endonuclease enzyme called Cas9. Identifies specific nucleotides sequences in genomic DNA of invading virus, breaks both DNA strands, inactivating the virus. Uses a guide RNA molecule that complementary base-pairs to the genomic DNA sequence. © McGraw Hill LLC 21  Genome Editing 3 Cas9. Scientists can study a gene’s role in the cell after Cas9 break inactivates the gene. Cas9 can insert new nucleotides at specific DNA locations. CRISPR can target specific sequence of nucleotides for editing in almost any organism. © McGraw Hill LLC 22  CRISPR and Genome Editing Figure 26.6 Access the text alternative for slide images. © McGraw Hill LLC 23  Genome Editing 4 CRISPR applications include: Treatments for diseases, such as sickle-cell disease and cancer. New rapid tests for viruses such as SARS-CoV- 2. Scientists are continuously working to make the system more efficient and develop new applications. © McGraw Hill LLC 24  Uses of CRISPR in Humans Figure 26.7 Access the text alternative for slide images. © McGraw Hill LLC 25  26.2 Biotechnology Products Organisms that have had a foreign gene inserted into their genome are called transgenic organisms. Transgenic bacteria, plants, and animals are often called genetically modified organisms (GMOs). The products they produce are called biotechnology products. © McGraw Hill LLC 26  Genetically Modified Bacteria 1 Transgenic bacteria are produced by recombinant DNA technology. Grown in large vats called bioreactors. Bacteria express the cloned gene. Gene product collected from the media. Biotechnology products produced by transgenic bacteria include insulin, human growth hormone, tPA (tissue plasminogen activator), and hepatitis B vaccine. © McGraw Hill LLC 27  Genetically Modified Bacteria 2 Other uses of transgenic bacteria. Bacteria that live on plants have been altered from frost-plus to frost-minus bacteria. As a result, new crops such as frost-resistant strawberries are being developed. Bacteria that colonize the roots of corn plants have been engineered to have genes whose products are toxic to the insects that may damage the roots. © McGraw Hill LLC 28  Genetically Modified Bacteria 3 Transgenic bacteria. Figure 26.8 Can be selected for their ability to degrade a particular substance. Ability can be enhanced by bioengineering. Eat oil, remove sulfur from coal. © McGraw Hill LLC Accent Alaska.com/Alamy Stock Photo 29  Genetically Modified Plants 1 Foreign genes can be introduced into: Immature plant embryos. Protoplasts—plant cells with cell wall removed. Exposed to an electric current while in a liquid containing foreign DNA. Self-sealing pores are formed that allow the desired DNA to enter. Go on to develop into mature plants that express the foreign gene. © McGraw Hill LLC 30  Genetically Modified Plants 2 The pomato is one result of this technology. Produces potatoes below ground and tomatoes above ground. Pest resistance in cotton, corn, and potato strains can be created. Soybeans are resistant to herbicide. Plants can also be engineered to produce human proteins. © McGraw Hill LLC 31  Example of a Genetically Modified Plant Figure 26.9 © McGraw Hill LLC Okanagan Specialty Fruits Inc. 32  Genetically Modified Animals 1 Technology has been developed to insert genes into the eggs of animals. It is possible to microinject foreign genes into eggs by hand or by vortex mixing. Vortex mixing. Eggs are placed in an agitator with DNA and silicon-carbide needles. The needles make tiny holes in the eggs, allowing the DNA to enter. When the eggs are fertilized, transgenic offspring are produced. The gene for bovine growth hormone (BGH) has been inserted to produce larger fish, cows, pigs, rabbits, and sheep. © McGraw Hill LLC 33  Genetically Modified Animals 2 Example: the AquAdvantage salmon. 99.9% Atlantic salmon, plus gene products from two other fish. The growth hormone gene from the Chinook salmon; for faster growth. A gene promoter from the Ocean Pout; keeps growth hormone gene “on.” Gene products grown on bacterial plasmids, isolated, then mixed with fertilized Atlantic salmon eggs. Reaches adult size three times faster than wild salmon and with less food. © McGraw Hill LLC 34  Transgenic Salmon Figure 26.10 Access the text alternative for slide images. © McGraw Hill LLC (b): AquaBounty Technologies, Inc. 35  Producing Transgenic Animals Gene pharming. Transgenic farm animals can be used to produce pharmaceuticals. Genes that code for therapeutic and diagnostic proteins are incorporated into an animal’s DNA. Proteins can be harvested from animals’ milk. Plans exist to produce drugs for the treatment of cystic fibrosis, cancer, blood diseases. © McGraw Hill LLC 36  Production of Transgenic Animals 1 Figure 26.11a Access the text alternative for slide images. © McGraw Hill LLC 37  Cloning Transgenic Animals 1 Scottish scientists produced cloned sheep Dolly in 1997. Since then, calves, goats, pigs, rabbits, and cats have been cloned. The process is difficult; low success rate. 1 or 2 viable embryos per 100 attempts. © McGraw Hill LLC 38  Cloning Transgenic Animals 2 Cloning process: Donor eggs are microinjected with nuclei from one transgenic animal, then coaxed to begin development in vitro. Development continues in host females until clones are born. The female clones have the same product in their milk as the original transgenic animal. © McGraw Hill LLC 39  Production of Transgenic Animals 2 Figure 26.11b Access the text alternative for slide images. © McGraw Hill LLC 40  26.3 Gene Therapy Gene therapy is the insertion of genetic material into human cells for the treatment of genetic disorders and other illnesses, such as cardiovascular disease and cancer. Various methods of gene transfer have been used. Viruses, genetically modified to be safe, can be used to introduce a normal gene into the body. Liposomes, microscopic globules of lipids, can also be used to introduce normal genes. Sometimes the gene is injected directly into a specific region of the body. © McGraw Hill LLC 41  Gene Therapy Figure 26.12 Access the text alternative for slide images. © McGraw Hill LLC 42  Ex Vivo Gene Therapy 1 Ex vivo method for treating SCID (severe combined immunodeficiency). Used for children who lack the enzyme ADA (adenosine deaminase), involved in the maturation of T and B cells. They are prone to constant infections; may die without treatment. Gene therapy treatment steps: Remove bone marrow stem cells from body. Infect cells with a virus that carries the normal gene that codes for the enzyme, ADA. Return cells to patient with the hope they will divide, expressing the normal gene for ADA. © McGraw Hill LLC 43  Ex Vivo Gene Therapy in Humans Figure 26.13 Access the text alternative for slide images. © McGraw Hill LLC 44  Ex Vivo Gene Therapy 2 Treatment of familial hypercholesterolemia. Liver cells lack a receptor protein for removing cholesterol from the blood. High blood cholesterol levels make a patient subject to heart attacks at a young age. A liver portion is surgically excised and then infected with a virus containing a normal gene for the receptor. The liver portion is returned to patient. © McGraw Hill LLC 45  In Vivo Gene Therapy 1 In vivo gene therapy. Cystic fibrosis patients lack a gene coding for chloride transporter membrane protein. A thick mucus forms in the lungs, leading to infections of the respiratory tract. Treatment. The gene needed to cure cystic fibrosis is sprayed into the nose or delivered to the lower respiratory tract by an adenovirus vector or by using liposomes. Limited success so far. © McGraw Hill LLC 46  In Vivo Gene Therapy 2 Increasingly relied upon as a part of cancer treatment. Used to make healthy cells more tolerant of chemotherapy. Make tumor cells more sensitive to chemotherapy. Find way to introduce the tumor suppressor gene p53 into cancer cells. © McGraw Hill LLC 47  RNA Interference 1 RNA interference, or RNAi. RNA pieces are used to “silence” expression of specific alleles. Sequences are complementary to mRNA transcribed by a certain gene. They bind with the target RNA in the cell, producing double-stranded RNA molecules, which are then broken down by enzymes. © McGraw Hill LLC 48  RNA Interference 2 RNA interference, or RNAi. First discovered in worms. Believed to have evolved in eukaryotic organisms as a protection against viruses. Research into developing RNAi treatments for human diseases is currently underway. Including cancer and hepatitis. © McGraw Hill LLC 49  26.4 Genomics, Proteomics, and Bioinformatics Genetics in the 21st century largely concerns genomics. Study of the complete genetic sequences of humans and other organisms. First step is knowing the sequence of bases in genomes. Of the 3.2 billion bases in the human genome, 98% is noncoding and contains many repetitive sequences. Second step is mapping the location of genes on the chromosomes. Approximately 20,000 genes code for proteins in humans. © McGraw Hill LLC 50  Sequencing the Genome 1 Human Genome Project (HGP). The HGP was a 13-year effort that involved both university and private laboratories. We now know the sequence of the roughly 3 billion pairs of DNA bases in our genome. New DNA sequencing technology helped speed the process. New genomes are being sequenced all the time and at a much faster rate now. Recently, the African clawed frog was sequenced in less than 1 year. © McGraw Hill LLC 51  Sequencing the Genome 2 Discovery of single nucleotide polymorphisms (SNPs). Difference of only one nucleotide between individuals. Many have no effect. Others contribute to protein-coding difference. May change susceptibility to disease or response to medical treatments. Raise the possibility of “designer drugs” tailored to individual’s genotype. © McGraw Hill LLC 52  Sequencing the Genome 3 The HGP, along with identification of RNAs in cells, led to the determination that humans have approximately 20,000 genes. Structural genomics—knowing the sequence of the bases and how many genes we have. Functional genomics—what does it code for? Most genes are expected to code for proteins. Noncoding or “junk DNA” may have important functions. © McGraw Hill LLC 53  Genome Architecture 1 Genome architecture. Nearly 98% of the human genome is DNA that does not directly code for amino acid sequences. Some is transcribed into rRNA or tRNA. Both are involved in protein assembly. The rest of the genome consists of a variety of sequences. Some are repeated, others are not. © McGraw Hill LLC 54  Genome Architecture 2 Genome architecture. Transposable elements (or transposons). 44% of human genome. Discovered by Barbara McClintock in 1950. Thought to be driving force in evolution. Repetitive DNA elements. Same sequence of two or more nucleotides repeated. May not be useless—centromeres and telomeres have this structure. Sequences with unknown function. © McGraw Hill LLC 55  Redefining the Gene 1 What is a gene? Historically, a gene was thought of as a particular location (locus) of a chromosome. Eukaryotic genes appear to be randomly distributed along chromosomes. Eukaryotic genes are fragmented into exons with intervening introns. 95% or more of most human genes are introns. Introns may be regulators of gene expression. Exons can be put together in various ways. © McGraw Hill LLC 56  Redefining the Gene 2 What is a gene? Modern definition focuses on result of transcription. A gene is a genomic sequence (either DNA or RNA) directly encoding functional products, either RNA or protein. Gene product may not necessarily be a protein. Gene may not be found at a particular locus on a chromosome. Genetic material need not be only DNA—some prokaryotes have RNA genes. © McGraw Hill LLC 57  Functional and Comparative Genomics 1 Comparative genomics. Compare genomes of organisms. Identify similarities between the sequence of human bases and those of other organisms. Provide way to study genome changes through time. Track evolution of HIV. Understand the evolutionary relationships among organisms. Human and chimpanzee are 98% alike. Human and mouse are 85% alike. © McGraw Hill LLC 58  Comparison of Sequenced Genomes TABLE 26.1 Comparison of Sequenced Genomes Estimated Approximate Number Chromosome Organism Size of Genes Number 3.0 billion Homo sapiens (human) bases ~20,000 46 2.5 billion Mus musculus (mouse) bases ~20,000 40 180 million Drosophila melanogaster (fruit fly) bases ~14,000 8 120 million Arabidopsis thaliana (flowering plant) bases ~26,000 10 100 million Caenorhabditis elegans (roundworm) bases ~19,000 12 12.1 million Saccharomyces cerevisiae (yeast) bases ~6,300 32 (human): Image Source/JupiterImages/Getty Images; (mouse): Judith Thomandl/ImageBroker/Superstock; (fruit fly): Hermann Eisenbeiss/Science Source; (plant): Peggy Greb/USDA; (roundworm): Sinclair Stammers/Science Source; (yeast): Science Photo Library/Alamy Stock Photo © McGraw Hill LLC 59  Functional and Comparative Genomics 2 Functional genomics. Understand the function of the various genes discovered within each genomic sequence and how these genes interact. Help deduce the function of human genes by comparison to other genomes. Uses DNA microarrays to tell which genes are turned on in a specific cell or tissue at a certain time or under certain conditions. A person’s genetic profile: DNA microarrays identify various mutations to determine if certain genetic diseases are likely. © McGraw Hill LLC 60  Proteomics Proteomics is the study of the structure, function, and interactions of cellular proteins. Proteins differ depending on each cell type. Each cell produces hundreds of different proteins that can vary between or within cells depending on conditions. Computer modeling of the three-dimensional shape of these proteins is important. Protein shape and function is essential to the discovery of better drugs. © McGraw Hill LLC 61  Bioinformatics 1 Bioinformatics. Computer technologies, specially developed software, and statistical techniques can be used to study biological information, particularly databases that contain much genomic and proteomic information. Bioinformatics can find significant patterns in the raw data of DNA sequences. Computers can help make correlations between genomic differences among large numbers of people and certain diseases. © McGraw Hill LLC 62  Bioinformatics 2 BLAST—stands for basic local alignment search tool. BLAST is used to identify homologous genes among the genomic sequences of model organisms. Homologous genes code for the same proteins, though the base sequence may be slightly different. Finding these differences can help identify the putative function of genes as new organisms’ genomes are sequenced. © McGraw Hill LLC 63 Because learning changes everything.® www.mheducation.com © McGraw Hill LLC. All rights reserved. No reproduction or distribution without the prior written consent of McGraw Hill LLC.