AP Biology Name: Chapter 20 Guided Reading Assignment

AP Biology Name: Chapter 20 Guided Reading Assignment 1. Define the following a. Recombinant DNA A DNA molecule made in vitro with segments from different sources. b. Genetic engineering It is the direct manipulation of genes for practical purposes. c. Biotechnology The manipulation of organisms or their components to produce useful products. d. Gene cloning The production of multiple copies of a gene. 2. What are the two broad areas of use and two examples after a host cell grown in culture to form a clone of cells containing the “cloned gene of interest.” DNA cloning is useful for making many copies of a particular gene and to produce a protein product. A resistance gene present in one crop species might be cloned and transferred into plants of another species. A protein with medical usages, such as a growth hormone, can be harvested into large quantities from cultures of bacteria carrying the cloned gene for the protein. 3. What is the other name for restriction enzymes and what do these enzymes do for bacteria in “Nature”? The other name for restriction enzymes is restriction nucleases. Restriction enzymes protect the bacterial cell by cutting up foreign DNA from other organisms or phages. 4. Define the following terms a. Restriction site A specific sequence on a DNA strand that is recognized and cut by a restriction enzyme. b. Restriction fragments A DNA segment that results from the cutting of DNA b a restriction enzyme. c. Sticky end A sticky end is a single-stranded end of a double-stranded restriction fragment. 5. Explain in your own words two ways that we know the cell clones carry the recombinant plasmids? The plasmids have a "reporter gene" inside it, generally resistance to specific antibiotic. the plasmid is transformed into bacteria that don't have resistance to that specific antibiotic drug, and then the cultured on a Petri-dish that contain the antibiotic drug. Only bacteria that had receive the plasmid will have resistance and grow, all the other will die. 6. What is the purpose of nucleic acid hybridization? Why is the word hybrid used? Nucleic acid hybridization is used to detect the DNA of a specific gene, by being able to base-pair it with a complementary sequence on another nucleic acid molecule. This is only doe using nucleic acid hybridization. Each probe molecule will hydrogen bond specifically to a complementary sequence in the desired gene. 7. What is a complementary, short, single stranded nucleic acid that can be either DNA or RNA called? It is called a nuclear probe. 8. Why do scientists use a radioactive isotope tag for the probes? It is easier to track a probe when is tagged with a radioactive isotope. 9. How is DNA denaturation different than protein denaturation? 10. Define genomic library. A set of clones containing all the DNA segments from a genome, each with a plasmid, phage, or other cloning vector. 11. How are bacteriophages used for making genomic libraries and what are some of the advantages of this? Fragments of foreign DNA can be spiced into trimmed –down versions of a phage genome, as into a plasmid, by using a restriction enzyme and DNA ligase. The standard plasmid can carry a DA insert no longer than 12,000 base pars, a phage can carry an insert of about 25,000 pairs. The normal infection process also allows production of many of many new phage particles, each carrying the foreign DNA. 12. What are the steps in making complementary DNA – cDNA? First reverse transcriptase has to be added to a test tube containing mRNA isolated from the cell. Then the reverse transcriptase makes the first DNA strand using the RNA as a template and a stretch of dT”s as a DNA primer. Third the mRNA is degraded by another enzyme. This is followed by DNA polymerase synthesizing the second strand, using a primer in the reaction mixture. Finally, the result is cDNA which carries the complete coding sequence of the gen but not of introns. 13. Compare and contrast the advantages of cDNA libraries and genomic libraries. If there is a gene that has to be studied and you do not know what cell type expresses it a genomic library is the one that would certainly contain the gene. Anything that requires the genomic sequence of a gene, which includes introns, has to use the genomic library because in cDNA introns are not found. A cDNA library is useful in studying the set of genes responsible for the specialized functions of a particular cell type, such as brain or liver cells. Researches can also trace changes in pattern of gene expression during development using a cDNA library. 14. What is an expression vector and what problem does it solve? To overcome differences in promoter and other DNA control sequences, scientists usually employ an expression vector. An expression vector is a cloning vector that contains a highly active bacterial promoter just upstream of a restriction site where the eukaryotic gene can be inserted in the correct reading frame. 15. Why do molecular biologists use yeast as opposed to bacteria for expressing genes of interest? Biologists use yeast because yeast is eukaryotic and therefore they can clone and express eukaryotic genes. Yeast is as easy to grow as bacteria is and they have plasmids which is rare among eukaryotes. 16. Define yeast artificial chromosomes. A cloning vector that combines the essentials of a eukaryotic chromosome – an origin for DNA replication, a centromere, and two telomeres- with foreign DNA. 17. What is electroporation? Electroporation is a technique used to introduce recombinant DNA into cells by applying a brief electrical pulse to a solution that contains the cells. The pulse creates temporary holes in the cells’ plasma membranes, through which DNA can enter. 18. Why is PCR – polymerase chain reaction important in many aspects of biotechnology? With automation, PCR can make billions of copies of a target segment of DNA in a few hours, significantly faster than the days it would take to obtain the same number of copies by screening a DNA library for a clone with the desired gene and letting it replicate within host cells. It is used to make enough of a specific DNA garment to insert it directly into a vector entirely skipping the steps of making and screening a library. 19. Define and explain the significance of RFLP’s – restriction length polymorphisms. Variations in the length of restriction fragments resulting from action by a specific endonuclease. 20. What was the purpose of the Human Genome Project? After years of multi-billion-dollar research, the Human Genome Project and Celera Genomics (a non-government biotechnology company) jointly announced drafts of the human genome sequence in 2000. By mid-2001, scientists associated with these ventures had presented the true nature and complexity of the digital code inherent in DNA. We now understand that there are approximately 35,000 genes in each human DNA molecule, comprised of approximately 3 billion chemical bases arranged in precise sequence. Even the DNA molecule for the single-celled bacterium, E. coli, contains enough information to fill all the books in any of the world's largest libraries. We now appreciate that the DNA structure is one of the greatest scientific discoveries of all time, only first discovered at its base level in 1953 by James Watson and Francis Crick. 21. Why is genetic mapping considered a “relative mapping” as opposed to physical mapping? The chromosome is so small that the actually physical mapping cannot be determined. Genetic mapping gives us a relative place where the chromosomes could be placed. 22. What is the goal of DNA sequencing? By knowing the sequence of a gene allows researchers to compare it directly with genes in other species, where the function of the gene product maybe known. If two genes from different organisms are similar in sequence it is reasonable to assume that these two genes are similar in function. 23. Define genomics. Genomics is the branch of genetics that studies organisms in terms of their genomes (their full DNA sequences). 24. Is there a direct correlation between size of the genome and the complexity of the organism? Yes, there is a direct correlation between size of the genome and complexity of the organisms. The bigger the genome of an organism, the more complex it is. 25. What is in vitro mutagenesis and what does it help the scientist understand? In vitro mutagenesis is a specific mutation that is introduced to a cloned gene and then that mutated gene is returned to a cell in such a way that it disables the normal cellular copies of the same gene. In vitro mutagenesis helps scientists determine the function of certain genes. 26. What is proteomics? Proteomics is the branch of genetics that studies the full set of proteins encoded by a genome. 27. Define single nucleotide polymorphisms. single-nucleotide polymorphism (SNP, pronounced snip) is a DNA sequence variation occurring when a single nucleotide — A, T, C, or G — in the genome (or other shared sequence) differs between members of a species or paired chromosomes in an individual. 28. What are some of the examples of the medical applications of biotechnology? • New tests to confirm a diagnosis of a disease or disability. This means being able to accurately tell if the person has a particular condition or not. • New tests to predict a disease or disability. This means being able to tell if the person has a condition that will lead to the development of certain symptoms. The most well known form of predictive testing is newborn screening, and this is applied to all new babies for a limited range of conditions for which there is some treatment option. • New tests for susceptibility to a disease or disability. This means being able to tell if a person has the genetic makeup that means a particular condition is possible or even likely to devel- op, but in most cases, without any certainty that it will develop, or if it does, how mild or severe it will be. • New test for carrier status for inherited conditions. This means being able to tell if the parents or other relatives are carriers of the genetic characteristics that might lead to their children inheriting a particular disease or disability. • New technology and tests for pre-implantation genetic diagnosis. This means using tests in conjunction with in-vitro fertilization techniques, to determine if a fertilized embryo is affected by a particular disease or disability, prior to the implantation of an embryo into the woman so she will become pregnant. 29. What are the basic steps in human gene therapy with a retroviral vector? The RNA version of the normal allele has to be inserted into the retrovirus. The retrovirus has to infect bone marrow cells that have been removed from the patient and cultured. Viral DNA carrying the normal allele inserts into chromosome. The engineered cells have to be injected into the patient. 30. Have there been problems with this procedure? Yes, there have been problems with this procedure. In 2002, in France ten young children with SCID were treated by the same procedure. Nine of these patients showed really good improvement after two years However, three of the patients developed leukemia later on, and one of them died. 31. What is a DNA fingerprint? A DNA fingerprint is biometric identification obtained by examining a person's unique sequence of DNA base pairs; often used for evidence in criminal law cases 32. What is a transgenic animal? Transgenic animals are animals that have had genes from other species inserted into their genetic code. 33. How are plasmids used in agriculture and genetic engineering in plants? Plasmids carry foreign DNA that is of an interest to plants. The plasmid is inserted in the plants. Useful traits are inserted in the plant, such as pest resistance and resistance of destructive insects. In some cases the nutritional value of plants is increased through these plasmids. 34. What are genetically modified foods and do you think that you have eaten any? These are food plants that have been genetically altered by the addition of foreign genes to enhance a desired trait. I do believe I have eaten genetically modified foods. Longer Molecules Shorter Molecules 1. Each sample, a mixture of DNA molecules, is placed in a separate well near one end of a thin slab of gel. The gel is set into small plastic support and immersed in an aqueous solution. In a tray with electrodes at each end. 2. When the current is turned on, the negatively charged DNA molecules move toward the positive electrode, with shorter molecules moving faster than longer ones. Bands are shown here in blue, but on an actual gel, the bands would not be visible at this time. Denaturation : Heat briefly to separate DNA strands. Annealing: Cool to allow primers to form hydrogen bonds with ends of target sequence. Extension : DNA polymerase adds nucleotides to the 3’ end of each primer. Page 7 of 7 This study source was downloaded by from CourseH on :28:33 GMT -06:00