1. DNA TECHNOLOGY AND GENOMICS CHAPTER 20 P. 384-410

2. BIOTECHNOLOGY Manipulation of organisms (or components) to make useful products Recombinant DNA: inserting genes into different organisms Fermentation: using yeast & bacteria to make cheese, wine, bread, etc Selective breeding: of livestock, pets, etc Cloning: of genes, proteins, organisms RFLP analysis: compares DNA sequences of different people &/or species Microassay: compares how genes are expressed in different tissues/under different conditions

3. DNA CLONING: AN OVERVIEW DNA is very large molecule; only small portion are genes Gene Cloning: separates gene-size pieces of DNA & makes copies 1) bacterial plasmid isolated 2) foreign gene inserted 3) recombinant plasmid replicates 4) copies of gene/protein used for practical purposes

4. GENE CLONING

5. RESTRICTION ENZYMES Cut DNA at specific sites (“restriction sites”) Creates several restriction fragments with “sticky ends” (single-stranded ends) Bonds other restriction fragments cut with same enzyme Bond is sealed w/ DNA ligase

6. DNA VECTORS Cloning vector: original plasmid (bacterial DNA) into which foreign (human) DNA is inserted Used to copy desired DNA

7. GENE CLONING PROCEDURE 1) Isolate bacterial vector & DNA fragment containing gene 2) Cut both w/ same restriction enzyme Creates several fragments of DNA, incl. one w/ gene of interest Vector & DNA will have complementary sticky ends (due to S-P backbone) 3) Insert DNA into vector Sticky ends bond together w/ DNA ligase

8. GENE CLONING PROCEDURE (CON’T) 4) Cloning of cells (genes) Use transformation to introduce cloning vector into a bacterial cell Use antibiotics to ensure only recombinant plasmids cloned 5) Identify clones w/ gene of interest Nucleic Acid Hybridization: base-pairing gene w/ another nucleic acid Nucleic Acid Probe: complement of gene of interest; labeled w/ radioactive isotope to easily identify

9. CLONING & EXPRESSING EUKARYOTIC GENES While efficient, bacterial cloning of eukaryotic genes can be problematic: -Gene expression simpler in bacteria -Human DNA has non-coding regions (bacteria do not have spliceosomes) -Bacteria can not modify proteins after translation Can use yeast instead -Eukaryotic, single-celled, rapid reproduction -YAC: contains origin, centromere, telomeres; can undergo mitosis

10. POLYMERASE CHAIN REACTION (PCR) Quickly amplifies (copies) DNA w/out cells (in vitro) 1) Heat separates DNA strands 2) Primers bond to each single strand 3) Heat-stable DNA polymerase build compliments 4) repeat cycle Used to increase amount of DNA in ancient organisms, crime scene samples, fetal genetic testing, etc

11. RESTRICTION FRAGMENT ANALYSIS Uses gel electrophoresis to separate DNA fragments by size Yields bands of DNA in specific pattern 1) Digest DNA w/ restriction enzyme 2) Load DNA samples into gel & run (towards + pole) 3) Each fragment produces different band patterns Different alleles (sickle-cell); Compare individuals

12. SOUTHERN BLOTTING Reveals DNA sequences & restriction fragments Transfers electrophoresis bands to paper to be probed Isolates gene of interest Used to compare coding sections of DNA from several organisms Can detect heterozygous carriers of genetic diseases RFLP’s: Different non-coding segments of DNA Used to compare different organisms (unique to individuals) May serve as genetic markers for linkage (location on chromosome) Detected by Southern Blotting

14. HUMAN GENOME PROJECT To determine complete nucleotide sequence of all human chromosomes (April, 2003) 3 Stages: 1) Genetic Mapping Map 1,000’s genetic markers spaced evenly in each chromosome 2) Physical mapping Cuts DNA into known restriction fragments & arranges them in order Fragments prepared w/ cloning vectors (i.e.: YAC, BAC) 3) DNA Sequencing Determine nucleotide sequence in each fragment at a time Uses labeling, synthesis, & electrophoresis “Sanger Method” synthesizes DNA complement to one being sequenced (see Fig. 20.12)

16. GENOMICS (STUDY OF GENES) 1)Identify protein-coding genes in a DNA sequence Most DNA is non-coding (98.5% in humans!) Size of genome ≠ greater complexity (see Table 20.1) Human gene expression highly regulated 2) Determine function of genes Disable gene & observe consequence In vitro mutagenesis: mutate gene & observe phenotype 3) Study “Grouped” genes DNA Microarray Assay: shows which genes are expressed, when, and what factors may influence expression 4) Compare genomes of different species High degree of similarity within non-coding sequences BLAST: database of genomes NCBI BLAST Site

17. PRACTICAL APPLICATIONS OF DNA TECHNOLOGY 1)Medical Diagnose disease; Human gene therapy 2)Pharmaceutical Hormone production (insulin, human growth hormone) 3)Forensic DNA Fingerprinting 4)Environmental Bacteria & microbes clean up waste 5)Agricultural Transgenic animals & GMOs