Section 3: Gene Technologies in Detail

1. Section 3: Gene Technologies in Detail Preview • Bellringer • Key Ideas • Basic Tools for Genetic Manipulation • Major Gene Technology Processes • Exploring Genomes • Summary

2. Bellringer Genetic Engineering in Agriculture Write the name of a fruit or vegetable that you don’t like to eat and explain why you don’t like it. Then write about ways in which the fruit or vegetable could possibly be changed by genetic engineering so that you would like it.

3. Key Ideas • What are the basic tools of genetic manipulation? • How are these tools used in the major processes of modern gene technologies? • How do scientists study entire genomes?

4. Basic Tools for Genetic Manipulation • The basic tools of DNA manipulation rely on the chemical nature of genetic material and are adapted from natural processes discovered in cells. • These tools include restriction enzymes, polymorphisms, gel electrophoresis, denaturation, and hybridization.

5. Basic Tools for Genetic Manipulation, continued Restriction Enzymes • A restriction enzyme cuts double-stranded DNA into fragments by recognizing specific nucleotide sequences and cutting the DNA at those sequences. • These enzymes can be used to cut up a DNA sample in specific ways and to create sticky ends for splicing DNA.

6. Visual Concept: Action of Restriction Enzymes

7. Basic Tools for Genetic Manipulation, continued Polymorphisms • Differences between the DNA sequences of individuals are called DNA polymorphisms. • Differences of just one nucleotide are called single nucleotide polymorphisms (SNPs). • Differences in restriction sites results in restriction fragment length polymorphisms (RFLPs).

8. Basic Tools for Genetic Manipulation, continued Gel Electrophoresis • Electrophoresis is a process in which electrically charged particles move through a liquid or semisolid • Often, DNA fragments are forced though a gel. • Shorter fragments will move faster through the gel. • The result is a lane of fragments sorted by size. • There are many types of electrophoresis.

9. Visual Concept: Gel Electrophoresis

10. Basic Tools for Genetic Manipulation, continued Denaturation • Some conditions, can cause DNA to denature, or untwist and split into single strands. • Scientists can easily denature and renature DNA for further manipulations. Hybridization • Under the right conditions, complementary segments of DNA or RNA will bind together, or hybridize. • Genetic tools that take advantage of this natural process includs: • Primers • Probes • cDNA

11. Major Gene Technology Processes • The major methods for working with genes use some combination of the basic tools and mechanisms of cellular machinery. • These methods include PCR, blotting, DNA sequencing, and gene recombination.

12. Major Gene Technology Processes, continued Polymerase Chain Reaction (PCR) • The polymerase chain reaction (PCR) process is widely used to clone DNA sequences for further study or manipulation. • PCR imitates the normal process of DNA replication in cells. • The process is called a chain reaction because it is repeated over and over.

13. Visual Concept: Polymerase Chain Reaction

14. Major Gene Technology Processes, continued Blotting Processes and Applications • Several gene technologies use a combination of restriction enzymes, gel electrophoresis, and hybridization with probes. • The goal is to find or compare genetic sequences. • These processes include: • Southern Blot • Fingerprints and Bar Codes • Northern Blot • Microarrays

15. Southern Blot Click to animate the image.

16. Visual Concept: Making a DNA Fingerprint

17. Major Gene Technology Processes, continued DNA Sequencing • DNA sequencing is the process of determining the exact order of every nucleotide in a gene. • The major modern method is chain termination sequencing. • The steps are: • Start Copying a Template • Randomly Terminate the Copies • Sort the Copies by Size

18. Chain Termination Sequencing Click to animate the image.

19. Major Gene Technology Processes, continued Gene Recombination and Cloning • The first attempts at gene recombination and cloning were done by inserting a gene into an organism that replicates easily. • The steps were: • Cut DNA Samples • Splice Pieces Together • Place into Host • Replicate Gene • Screen for Gene • Other methods may use similar steps.

20. Visual Concept: Using Plasmids to Produce Insulin

21. Exploring Genomes • One can view a map of an entire nation or “zoom in” to view a particular state, city, neighborhood, or street. • In a similar way, one can explore and map a genome at many levels, including species, individual, chromosome, gene, or nucleotide.

22. Exploring Genomes, continued Managing Genomic Data • The application of information technologies in biology is bioinformatics. • Genomic bioinformatics starts with the mapping and assembly of the many parts of each genome. • The major stages of this work include the following: • Mapping and Assembly • Organized Storage • Annotation • Analysis

23. Exploring Genomes, continued Mapping Methods • Genome mapping is the process of determining the relative position of all of the genes on chromosomes in an organism’s genome. • To help track genes, any detectable physical, behavioral, or chemical trait can be used as a marker. • To determine the relative locations, genome mapping may use several methods: • Linkage Mapping methods identify the relative order of genes along a chromosome. • Physical Mapping methods determine the exact number of base pairs between specific genes. • Human chromosome mapping has mostly used historical family records.

24. Basic Genome Mapping

25. Exploring Genomes, continued Genome Sequence Assembly • The process of deducing and recording the exact order of every base and gene in a genome is called sequence assembly. • A collection of clones that represent all of the genes in a given genome is called a genetic library. • Two kinds of genetic libraries are made: • genomic library • expressed sequence tag (EST) library • The data can be searched for any specific gene or sequence. • Robotic devices are now used to sequence genomes rapidly.

26. Summary • The basic tools of DNA manipulation rely on the chemical nature of genetic material and are adapted from natural processes discovered in cells. These tools include restriction enzymes, polymorphisms, gel electrophoresis, denaturation, and hybridization. • The major methods for working with genes use some combination of the basic tools of cellular machinery. These methods include PCR, blotting, DNA sequencing, and gene recombination. • One can explore and map a genome at many levels, including species, individual, chromosome, gene, or nucleotide. Genomic bioinformatics starts with the mapping and assembly of the many parts of each genome.