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  1. IB Genetics Topic 4: Genetic Engineering

  2. Topics in Genetic Engineering • Polymerase Chain Reaction (PCR) • Gel electrophoresis • DNA profiling • The genome project • Gene transfer • Genetic modification in plants and animals • Cloning

  3. We will be brief! • The Blog has videos and games for you to cement your understanding of each topic! • Virtual labs are located on Utah genetics

  4. Key techniques in DNA identification Polymerase Chain reaction (PCR) • Takes a tiny quantity of DNA and copies all the nucleic acids to make millions of copies of the DNA • Only a portion of DNA is amplified, not the whole genome… Gel electrophoresis • This technique separates fragments of DNA in an attempt to identify its origin • Used for DNA ‘fingerprinting’ (profiling) • Used for many diagnostic procedures

  5. What do we do with this DNA? • All sorts of forensic and genetic tests…

  6. The DNA sequences amplified by PCR and matched by gel electrophoresis are used for: • Forensic identification - crime (CSI….) • Paternity suits • Diagnosing diseases and genetic disorders – genotype analysis • Detection of bacteria and viruses in the environment • The Genome project: determination of the entire human genetic code • Evolutionary research

  7. 4.4.1: The Polymerase Chain Reaction • Kary Mullis, 1984, Nobel Prize 1993 • ‘Reviewers and Biographers often latch on to his enjoyment of drugs, womanising and surfing to paint him as some sort of cool rock star rebel…but…’

  8. What does PCR do? • It mimics the process of DNA replication • It quickly amplifies a tiny sample of DNA into millions of identical copies • This produces enough DNA to allow further analysis and study.

  9. How does PCR work? First, you need to extract DNA from cells. Next, PCR requires: • Custom-made DNA primers • (TAQ) DNA polymerase • Nucleotides for complementary base pairing • HEATING and COOLING: Thermocycler machine PCR can produce 100 billion copies of the DNA sample in a few hours

  10. Let’s do it! • PCR the movie • PCR the cartoon • PCR the game

  11. Gel electrophoresis • Used to separate fragments of DNA and match against ‘known’ or ‘test’ samples • Forensic identification - crime (CSI….) • Paternity suits • Diagnosing diseases and genetic disorders – genotype analysis • Detection of bacteria and viruses in the environment

  12. 4.4.2: Gel electrophoresis • Commonly the DNA sample is first amplified by PCR • The DNA sample is chopped into fragments using restriction enzymes • Gel electrophoresis separates fragments of DNAaccording to their size • DNA samples are placed in a gel, fluorescent marker added (tag attached to a triplet), and an electric charge is applied to push fragments along • The shortest fragments travel furthest through the gel, while the longest (heaviest) remain closer to their origin • This lets us ‘match’ the sample against another DNA sample or standard

  13. Gel electrophoresis step by step • animation 1 • Animation 2 • and the real thing....in 90 seconds...

  14. Let’s do it! • Virtual Lab 1 • Virtual lab

  15. DNA profiling and forensic analysis • An introduction

  16. 4.4.3: DNA profiling HOW? APPLICATIONS Numerous techniques for DNA profiling: Criminal forensics Paternity suits Ecology – identifying relationships in migrating birds, whales etc Evolutionary genetics • DNA sample (blood, semen, cheek swab) • Sample is amplified by PCR, then matched against known samples using gel electrophoresis • We look for standard tandem repeating DNA: highly repetitive sequences from non-coding region of DNA • STR’s are unique to individuals

  17. Famous examples of DNA profiling • The innocence project • The famous blue dress • Identifying the Mona Lisa • Identifying the Romanovs

  18. DNA profiling: paternity and forensics • The fluorescent banding pattern shows up for each DNA fragment and can be compared with test/ known sample • Usually 13 ‘STR’ sites are used to establish paternity or identity • PATERNITY: bands will be shared with relatives • CRIME SCENE: ‘perfect match’

  19. Past paper questions How can fragments of DNA be separated? A. Using polymerase chain reaction (PCR) B. Using gel electrophoresis C. Using gene transfer D. Using gene cloning (Total 1 mark) What could be achieved by DNA profiling using gel electrophoresis? A. The chromosome number of an organism could be counted. B. It could be shown that human tissue found at the site of a crime did not come from a person suspected of having committed the crime. C. A karyotype could be produced. D. Extinct species of living organisms could be brought back to life. (Total 1 mark)

  20. Past paper questions A new allele that provides herbicide resistance is identified in soybean plants. The allele is dominant.Which of the following would be carried out in a herbicide-resistant plant to find out if it is homozygous or heterozygous for the gene? A. Gel electrophoresis B. Karyotyping C. Test cross D. DNA profiling (Total 1 mark) A small amount of a suspect’s DNA is obtained from a crime scene. What techniques would be used to carry out DNA profiling? A. Gel electrophoresis and paternity testing B. Paternity testing and the polymerase chain reaction (PCR) C. Polymerase chain reaction (PCR) and gel electrophoresis D. Test crossing and pedigree analysis (Total 1 mark)

  21. Past paper questions What type of enzyme could be used to cut a DNA molecule as indicated by the dotted line on the diagram below? A. DNA ligase B. DNA polymerase C. Helicase D. Restriction enzyme (Total 1 mark) Which process is used in polymerase chain reaction (PCR)? A. Transcription B. Translation C. Replication D. Mutation (Total 1 mark)

  22. 4.4.6: The Human Genome project We’re all the same! We’re all different! Welcome to the human genome

  23. Started in 1990, first draft published in 2003, ongoing refinement… Amazing international effort • The BBC tell us about the genome 10 years on • Hank tells us some surprises about the human genome project • ..so what has the human genome project achieved, so far?

  24. The brave new world of genomics GENOMICS – analysis of the structure and function of genomes…

  25. Key outcomes of the Human Genome project • We identified the number (30,000) and loci of all the genes of our genome 1. The Bio-informatic and genomic industries: Genetic databases and the bio-informatics industry 2. Human health: Medical diagnostics, treatments, pharmacogenomics, gene therapy • We identified many new proteins and their functions 3. Evolutionary genetics and evolutionary history We compared human DNA with that of other species 4. Transgenics:move production of beneficial proteins from one species to another, design novel proteins

  26. Bio-informatics: The HGP and human health (1) • 2 out of 3 of us will die of a genetically related disease • Many (some say all) diseases have a genetic cause • Genetic report cards can identify ‘potential risk’ of future illnesses

  27. Bio-informatics: Do you want to know your genome? Do you want to know your genome? Are you sure?

  28. The human genome and health: medical advances (1): Gene therapy • Find defective genes and ‘fix them’ • Insert a healthy normal gene or gene product (lipid, protein)to achieve normal function • Most effective for single gene disorders: cystic fibrosis, Sickle Cell disease,

  29. The human genome and health: medical advances (1): Pharmacogenomics Uses information about your genetic make-up to determine the drug, and drug doses, that will work best for you Currently used for treatment of: • HIV • Breast cancer • Colon cancer • Mental illness more info here...

  30. 3. Using the HGP to understand human evolution By sequencing and databasing genes, we can see similarities and differences between species • The closer the genome match, the closer their evolutionary history • Human Chromosome 2 came from fusion of two great ape chromosomes • Karl Miller on human evolution • The time-tree of evolution

  31. Tracing human migrations using mitochondrial DNA (SNP’s)

  32. Ethics and the human genome How companies are patenting your genetic code

  33. Ethical Issues surrounding the human (and other) genomes • Shared nature and ownership of genetic information • Limitations of genetic testing • Gender selection? • Gene patenting? • Genetic discrimination? • Forensic databases • Limits of cloning and genetically modified organisms (plants and animals)

  34. 4.4.8: GENETIC ENGINEERING, (MODIFICATION, TRANSGENICS)BIOTECHNOLOGY

  35. The basic premise for genetic engineering… The genetic code is universal • All living things share the same code • Each codon codes for the same animo acid, regardless of the species • Genes can be transferred from species to species, to produce the same product We can cut, copy and paste DNA between species

  36. Transgenic organism An organism which contains genetically altered material Synonyms: Genetically engineered; genetically modified

  37. Gene transfer 101: the basics of cutting, copying, pasting and cloning genes • An introduction • Step-by-step

  38. How does genetic engineering work? • Cut out desired DNA using restriction endonuclease • Prepare plasmid using the same restriction enzyme • Insert DNA into plasmid using DNA ligase • Insert plasmid (vector) into host cell

  39. Applications of Genetic Engineering • Gene Therapy – treatment of SCIDs, cystic fibrosis, ?Huntingdon’s Disease?... • ‘Pharming’: Transgenic organisms used to produce human insulin, Human factor IX, growth hormone • Vaccines – hepatitis B vaccine • Diagnostic tests and targeted drugs • Xenotransplantation – production of genetically modified organs in pigs

  40. Genetic Engineering: Making Human insulin • E. Coli make human insulin