Biotechnology

1. Biotechnology

2. Biotechnology • Genetic engineering techniques can manipulate the heritable information of DNA and, in special cases, RNA.

3. To foster student understanding of this concept, instructors can choose an illustrative example such as: • We will do virtual labs on all of these!!! • Electrophoresis • Plasmid-based transformation • Restriction enzyme analysis of DNA • Polymerase Chain Reaction (PCR)

4. Learning Objectives: • LO 3.1 The student is able to construct scientific explanations that use the structures and mechanisms of DNA and RNA to support the claim that DNA and, in some cases, that RNA are the primary sources of heritable information. [See SP 6.5] Protein synthesis…DNA to RNA, RNA viruses • LO 3.2 The student is able to justify the selection of data from historical investigations that support the claim that DNA is the source of heritable information. [See SP 4.1] • Griffith, Avery, Hershey and Chase, Chargaff, etc…

5. LO 3.3 The student is able to describe representations and models that illustrate how genetic information is copied for transmission between generations. [See SP 1.2] • DNA replication! • LO 3.4 The student is able to describe representations and models illustrating how genetic information is translated into polypeptides. [See SP 1.2] • Transcription/ Translation/polypeptide

6. LO 3.5 The student can justify the claim that humans can manipulate heritable information by identifying at least two commonly used technologies. [See SP 6.4] PCR, gel electrophoresis, plasmid transformation etc. • LO 3.6 The student can predict how a change in a specific DNA or RNA sequence can result in changes in gene expression. [See SP 6.4] • Types of mutations: sickle cell as one example

7. f. Illustrative examples of products of genetic engineering include: • Genetically modified foods • Transgenic animals • Cloned animals • Pharmaceuticals, such as human insulin or factor X

8. viruses • Essential knowledge 3.C.3: Viral replication results in genetic variation, and viral infection can introduce genetic variation into the hosts. • a. Viral replication differs from other reproductive strategies and generates genetic variation via various mechanisms. [See also 1.B.3]

9. b. The reproductive cycles of viruses facilitate transfer of genetic information. • Evidence of student learning is a demonstrated understanding of each of the following: • 1. Viruses transmit DNA or RNA when they infect a host cell. [See also 1.B.3] know the process of viral infection! • To foster student understanding of this concept, instructors can choose an • illustrative example such as: • Transduction in bacteria • Transposons present in incoming DNA

10. 2. Some viruses are able to integrate into the host DNA and establish a latent (lysogenic) infection. These latent viral genomes can result in new properties for the host such as increased pathogenicity in bacteria. • Examples like the E.coli and diptheria examples, where the plasmid contains genes for producing toxins!

11. Learning Objectives: • LO 3.29 The student is able to construct an explanation of how viruses introduce • genetic variation in host organisms. [See SP 6.2] Adding new genes to the genome! • LO 3.30 The student is able to use representations and appropriate models to • describe how viral replication introduces genetic variation in the viral population. • [See SP 1.4] New capsids, viral envelopes, what types of cells the virus is capable of infecting can change. No corrective enzymes means mutations stay with the virus!

12. Evidence of student learning is a demonstrated understanding of each of the following: • 1. Viruses have highly efficient replicative capabilities that allow for rapid evolution and acquisition of new phenotypes. • 2. Viruses replicate via a component assembly model allowing one virus to produce many progeny simultaneously via the lytic cycle. • 3. Virus replication allows for mutations to occur through usual host pathways. • 4. RNA viruses lack replication error-checking mechanisms, and thus have higher rates of mutation. • 5. Related viruses can combine/recombine information if they infect the same host cell. • 6. HIV is a well-studied system where the rapid evolution of a virus within the host contributes to the pathogenicity of viral infection.

13. DNA Technology • 1. Genetic engineering • 2. Restriction enzyme • 3. Recombinant DNA • 4. Plasmid • 5. Cloning • 6. Transgenic organism

14. Genetic engineering • 1. What is genetic engineering? • A WAY TO MANIPULATE DNA BY INSERTING EXTRA DNA OR DNA FROM ANOTHER ORGANISM

15. Genetic Engineering Genetic engineers manipulate DNA for practical purposes. Restriction enzymes cleave DNA into fragments that have short sticky ends. Sticky ends allow DNA fragments from different organisms to join together to form recombinant DNA. 2. What is the name for all of the DNA present in the nucleus of a cell? GENOME

16. Restriction enzyme • proteins made by bacteria that can cut DNA at specific places

17. 4. What is the benefit of the “sticky ends” left by restriction enzymes? THEY ALLOW OTHER FRAGMENTS OF DNA WITH THE SAME STICKY ENDS TO JOIN TOGETHER • 5. When fragments of DNA from one source are combined with those from another source what is this new DNA called? • RECOMBINANT DNA

18. Recombinant DNA • DNA made from combining DNA from 2 or more different sources.

19. Plasmid • A small circular, double stranded DNA molecule found in bacterial cells used as a vector to get recombinant DNA into a host cell.

20. 7. In order to get the recombinant DNA into the host cell a vector is needed, a PLASMID is a small circular piece of DNA that can be cut with restriction enzymes and then the gene can be inserted and joined with DNA ligase. • 8. The plasmid gets into the bacterial cell by TRANSFORMATION when the cell is heated or shocked electrically.

21. Cloning • When the bacterial cell copies its own DNA it also copies the plasmid and any recombinant DNA inserted in the plasmid. This is called cloning the DNA. • Multiple copies of the DNA can be made this way. • 6. Bacteria are often the host cell for doing what to the new DNA? COPY IT/clone it! • 9. Bacteria will copy the plasmid along with their own DNA and this is how CLONING occurs.

22. PCR • PCR (polymerase chain reaction) is a method to analyze a short sequence of DNA (or RNA) even in samples containing only minute quantities of DNA or RNA. PCR is used to reproduce (amplify) selected sections of DNA or RNA.

23. PCR Animation • http://learn.genetics.utah.edu/content/labs/pcr/ • Complete the virtual lab and make the DNA replicate! • Write down the major steps of the process!

24. PCR • http://users.ugent.be/~avierstr/principles/pcrani.html • Denaturation: At 94 C (201.2 F), the double-stranded DNA melts and opens into two pieces of single-stranded DNA. • Annealing: At medium temperatures, around 54 C (129.2 F), the primers pair up (anneal) with the single-stranded "template" (The template is the sequence of DNA to be copied.) On the small length of double-stranded DNA (the joined primer and template), the polymerase attaches and starts copying the template. • Extension: At 72 C (161.6 F), the polymerase works best, and DNA building blocks complementary to the template are coupled to the primer, making a double stranded DNA molecule

25. 10. When a scientist mixes an unknown sample of DNA with DNA polymerase and tagged A,C,G and T what are they trying to do? DETERMINE THE SEQUENCE OF THE DNA • 11. PCR stands for what? POLYMERACE CHAIN REACTION • 12. What does PCR do? MAKE MILLIONS OF COPIES OF A SPECIFIC REGION OF A DNA FRAGMENT

26. 6. Transgenic organism • Organisms that have had genes from other species inserted into their genome • . • There are ethical and health concerns regarding this practice… • GMO: An organism whose genetic characteristics have been altered by the insertion of a modified gene or a gene from another organism using the techniques of genetic engineering.

27. 13. What is a transgenic organism? ORGANISMS THAT HAVE A GENE FROM A DIFFERENT ORGANISM INSERTED INTO THEIR DNA. • 14. Are there transgenic animals? YES_ Give an example _GOATS WITH PROTEINS TO STOP BLOOD CLOTTING. FISH TO GROW FASTER. • 15. What are some of the transgenic uses for plants? 1. Cotton_RESISTANT TO BOWEEVILS. • 2. rice: WITH INCREASED NUTRIENTS • 16. What are some of the uses for transgenic bacteria? TO MAKE INSULIN, GROWTH HORMONES AND MEDICAL SUBSTANCES.

28. Virtual lab on biotechnology • http://www.montereyinstitute.org/courses/AP%20Biology%20I/course%20files/multimedia/chapter9virtuallab02/lessonp.html

29. 2. What is the name for all of the DNA present in the nucleus of a cell? ____________________________ • 3. What are proteins made by bacteria that can cut DNA at specific places called? ____________________ • 4. What is the benefit of the “sticky ends” left by restriction enzymes? _____________________________ • 5. When fragments of DNA from one source are combined with those from another source what is this new DNA called? ________________________________________

31. 6. Bacteria are often the host cell for doing what to the new DNA? _____________________________ • 7. In order to get the recombinant DNA into the host cell a vector is needed, a ___________________is a small circular piece of DNA that can be cut with restriction enzymes and then the gene can be inserted and joined with DNA ligase. • 8. The plasmid gets into the bacterial cell by _____________________________when the cell is heated or shocked electrically. • 9. Bacteria will copy the plasmid along with their own DNA and this is how ___________________occurs. • 10. When a scientist mixes an unknown sample of DNA with DNA polymerase and tagged A,C,G and T what are they trying to do?

32. 11. PCR stands for what? _______________________________________________________________ • 12. What does PCR do? _________________________________________________________________ • 13. What is a transgenic organism? ________________________________________________________ • 14. Are there transgenic animals? _______ Give an example ____________________________________ • 15. What are some of the transgenic uses for plants? 1. Cotton____________________________________ • 2. rice ________________________________________ • 16. What are some of the uses for transgenic bacteria?

36. SECTION 2 ANSWERS • 1. What is genetic engineering? A WAY TO MANIPULATE DNA BY INSERTING EXTRA DNA OR DNA FROM ANOTHER ORGANISM • 2. What is the name for all of the DNA present in the nucleus of a cell? GENOME • 3. What are proteins made by bacteria that can cut DNA at specific places called? RESTRICTION ENZYMES • 4. What is the benefit of the “sticky ends” left by restriction enzymes? THEY ALLOWOTHER FRAGMENTS OF DNA WITH THE SAME STICKY ENDS TO JOIN TOGETHER • 5. When fragments of DNA from one source are combined with those from another source what is this new DNA called? RECOMBINANT DNA • 6. Bacteria are often the host cell for doing what to the new DNA? COPY IT

37. 7. In order to get the recombinant DNA into the host cell a vector is needed, a PLASMID is a small circular piece of DNA that can be cut with restriction enzymes and then the gene can be inserted and joined with DNA ligase. • 8. The plasmid gets into the bacterial cell by TRANSFORMATION when the cell is heated or shocked electrically. • 9. Bacteria will copy the plasmid along with their own DNA and this is how CLONING occurs. • 10. When a scientist mixes an unknown sample of DNA with DNA polymerase and tagged A,C,G and T what are they trying to do? DETERMINE THE SEQUENCE OF THE DNA • 11. PCR stands for what? POLYMERACE CHAIN REACTION • 12. What does PCR do? MAKE MILLIONS OF COPIES OF A SPECIFIC REGION OF A DNA FRAGMENT • 13. What is a transgenic organism? ORGANISMS THAT HAVE A GENE FROM A DIFFERENT ORGANISM INSERTED INTO THEIR DNA. • 14. Are there transgenic animals? YES_ Give an example _GOATS WITH PROTEINS TO STOP BLOOD CLOTTING. FISH TO GROW FASTER. • 15. What are some of the transgenic uses for plants? 1. Cotton_RESISTANT TO BOWEEVILS. • 2. rice: WITH INCREASED NUTRIENTS • 16. What are some of the uses for transgenic bacteria? TO MAKE INSULIN, GROWTH HORMONES AND MEDICAL SUBSTANCES.

38. The human Genome • 1. DNA fingerprinting • 2. Gene therapy • 3. Pharmacogenomics • 4. Genomics

39. The Human Genome Project was an effort to determine the nucleotide sequence of and map the location of every gene on each human chromosome by the year 2003. • It was determined that only 2% of the DNA coded for proteins!! The remaining 98% was called noncoding sequences and was found to be the DNA unique to individuals.

40. DNA fingerprinting • The use of gel electrophoresis to identify sections of DNA that are unique to an individual. • Nova DNA virtual lab • http://www.teachersdomain.org/asset/tdc02_int_creatednafp2/

41. Gel electro virtual lab • http://learn.genetics.utah.edu/content/labs/gel/

42. Electrophoresis uses an electric field within a gel to separate DNA fragments by their size. • .

43. Gene therapy • A way of fixing mutated genes by inserting normal genes to replace the mutated ones. • Human Genome project link • http://www.ornl.gov/sci/techresources/Human_Genome/project/about.shtml • Researchers also are experimenting with introducing a 47th (artificial human) chromosome into target cells. This chromosome would exist autonomously alongside the standard 46 --not affecting their workings or causing any mutations. It would be a large vector capable of carrying substantial amounts of genetic code, and scientists anticipate that, because of its construction and autonomy, the body's immune systems would not attack it. A problem with this potential method is the difficulty in delivering such a large molecule to the nucleus of a target cell.

44. What factors have kept gene therapy from becoming an effective treatment for genetic disease? • Short-lived nature of gene therapy - Before gene therapy can become a permanent cure for any condition, the therapeutic DNA introduced into target cells must remain functional and the cells containing the therapeutic DNA must be long-lived and stable. Problems with integrating therapeutic DNA into the genome and the rapidly dividing nature of many cells prevent gene therapy from achieving any long-term benefits. Patients will have to undergo multiple rounds of gene therapy. • Immune response - Anytime a foreign object is introduced into human tissues, the immune system is designed to attack the invader. The risk of stimulating the immune system in a way that reduces gene therapy effectiveness is always a potential risk. Furthermore, the immune system's enhanced response to invaders it has seen before makes it difficult for gene therapy to be repeated in patients. • Problems with viral vectors - Viruses, while the carrier of choice in most gene therapy studies, present a variety of potential problems to the patient --toxicity, immune and inflammatory responses, and gene control and targeting issues. In addition, there is always the fear that the viral vector, once inside the patient, may recover its ability to cause disease. • Multigene disorders - Conditions or disorders that arise from mutations in a single gene are the best candidates for gene therapy. Unfortunately, some the most commonly occurring disorders, such as heart disease, high blood pressure, Alzheimer's disease, arthritis, and diabetes, are caused by the combined effects of variations in many genes. Multigene or multifactorial disorders such as these would be especially difficult to treat effectively using gene therapy. For more information on different types of genetic disease, see Genetic Disease Information. • http://www.ornl.gov/sci/techresources/Human_Genome/medicine/genetherapy.shtml

45. Ethical questions about gene therapy • What is normal and what is a disability or disorder, and who decides? • Are disabilities diseases? Do they need to be cured or prevented? • Does searching for a cure demean the lives of individuals presently affected by disabilities? • Is somatic gene therapy (which is done in the adult cells of persons known to have the disease) more or less ethical than germline gene therapy (which is done in egg and sperm cells and prevents the trait from being passed on to further generations)? In cases of somatic gene therapy, the procedure may have to be repeated in future generations. • Preliminary attempts at gene therapy are exorbitantly expensive. Who will have access to these therapies? Who will pay for their use?

46. . The Food and Drug Administration (FDA) has not yet approved any human gene therapy product for sale. Current gene therapy is experimental and has not proven very successful in clinical trials. Little progress has been made since the first gene therapy clinical trial began in 1990. According to the human genome project web site! • . http://www.ornl.gov/sci/techresources/Human_Genome/medicine/genetherapy.shtml#status

47. Pharmacogenomics • Pharmacogenomics is the study of how an individual's genetic inheritance affects the body's response to drugs. • The term comes from the words pharmacology and genomics and is thus the intersection of pharmaceuticals and genetics.

48. What are the anticipated benefits of pharmacogenomics? • More Powerful MedicinesPharmaceutical companies will be able to create drugs based on the proteins, enzymes, and RNA molecules associated with genes and diseases. This will facilitate drug discovery and allow drug makers to produce a therapy more targeted to specific diseases. This accuracy not only will maximize therapeutic effects but also decrease damage to nearby healthy cells. • Better, Safer Drugs the First TimeInstead of the standard trial-and-error method of matching patients with the right drugs, doctors will be able to analyze a patient's genetic profile and prescribe the best available drug therapy from the beginning. Not only will this take the guesswork out of finding the right drug, it will speed recovery time and increase safety as the likelihood of adverse reactions is eliminated. Pharmacogenomics has the potential to dramatically reduce the the estimated 100,000 deaths and 2 million hospitalizations that occur each year in the United States as the result of adverse drug response (1). • More Accurate Methods of Determining Appropriate Drug DosagesCurrent methods of basing dosages on weight and age will be replaced with dosages based on a person's genetics --how well the body processes the medicine and the time it takes to metabolize it. This will maximize the therapy's value and decrease the likelihood of overdose.

49. Advanced Screening for DiseaseKnowing one's genetic code will allow a person to make adequate lifestyle and environmental changes at an early age so as to avoid or lessen the severity of a genetic disease. Likewise, advance knowledge of a particular disease susceptibility will allow careful monitoring, and treatments can be introduced at the most appropriate stage to maximize their therapy. • Better VaccinesVaccines made of genetic material, either DNA or RNA, promise all the benefits of existing vaccines without all the risks. They will activate the immune system but will be unable to cause infections. They will be inexpensive, stable, easy to store, and capable of being engineered to carry several strains of a pathogen at once • Source: http://www.ornl.gov/sci/techresources/Human_Genome/medicine/pharma.shtml

50. 4. Genomics • The study of the organism’s genome. Understanding all of the genes and how they work.