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Restriction Enzyme

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Enzyme that cuts DNA at a specific sequence of nucleotides

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Gel Electrophoresis

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Separates DNA fragments by size using an electric current

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Restriction Map

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diagram that shows the lengths of fragments between restriction sites in the strand of DNA

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Polymerase Chain Reaction (PCR)

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A method of producing thousands of copies of DNA segment using the enzyme DNA polymerase

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Primer

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A molecule (a short strand of RNA or DNA) whose presence is required for formation of another molecule (a longer chain of DNA)

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DNA Fingerprint

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Analysis of sections of DNA that have little or no known function, but vary widely from one individual to another, in order to identify individuals

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Clone

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a group of genetically identical cells or organisms derived from a single cell or individual by some kind of asexual reproduction

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Genetic Engineering

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A technology that includes the process of manipulating or altering the genetic material of a cell resulting in desirable functions or outcomes that would not occur naturally.

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Recombinant DNA

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A section of DNA, often in the form of a plasmid, which is formed by joining DNA sections from two different sources.

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Plasmid

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A small, circular section of extra DNA that confers one or more traits to a bacterium and can be reproduced separately from the main bacterial genetic code.

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Transgenic

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genetically modified organism whose source of new genetic material is a different species

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Gene Knockout

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genetic manipulation in which one or more of an organism's genes are prevented from being expressed

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Genomics

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Study and comparison of genomes within a single species or among different species.

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Gene Sequencing

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process of determining the order of DNA nucleotides in genes and genomes

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Human Genome Project

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An international collaborative effort to map and sequence the DNA of the entire human genome.

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Bioinformatics

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Application of mathematics and computer science to store, retrieve, and analyze biological data

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DNA Microarray

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A glass slide carrying thousands of different kinds of single-stranded DNA fragments arranged in an array (grid). A DNA microarray is used to detect and measure the expression of thousands genes at one time. Tiny amounts of a large number of single-stranded DNA fragments representing different genes are fixed to the glass slide. These fragments, ideally representing all the genes of an organism, are tested for hybridization with various samples of cDNA molecules.

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Proteomics

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Study of the structure and function of proteins in the human body

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Genetic Screening

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analyzing a group of people to determine genetic susceptibility to a particular disease

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Gene Therapy

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The insertion of working copies of a gene into the cells of a person with a genetic disorder in an attempt to correct the disorder

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9.1 Manipulating DNA

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Biotechnology relies on cutting DNA at specific places. Bacterial enzymes called restriction enzymes are used to cut DNA. Each restriction enzyme cuts DNA at a specific DNA sequence. After DNA is cut with a restriction enzyme, the fragments of DNA can be separated using gel electrophoresis. A restriction map of the DNA is made based on the lengths of the fragments. -Scientists use several techniques to manipulate DNA -Restriction enzymes cut DNA -Restriction maps show the lengths of DNA fragments

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List a few of the ways that scientists can use to manipulate DNA.

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Artificial Nucleotides. Artificial copies. Chemical Mutagens. Computers. Enzymes. Bacteria.

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What determines how DNA will be cut by a restriction enzyme?

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The sequence of DNA that the enzyme recognizes.

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How does gel electrophoresis separate fragments from each other?

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DNA molecules, which have an overall negative charge, are drawn through a semisolid gel by an electric current toward the positive electrode within an electrophoresis chamber. The fragments are seperated by size.

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Suppose you cut DNA. You know that you should find four DNA fragments on a gel, but only three appear, and one fragment is very large. Explain what happened.

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In order to get 4 bands you need four pieces of DNA. In order to get 4 pieces of DNA it needs to be cut 3 times. If this stand only gets cut twice than the restriction enzyme that you used only recognized 2 parts of the DNA and cut it. There for the enzyme you used could be the wrong enzyme or if it was the correct enzyme, during the reaction the enzyme broke down before it could cut the third time due to the environment. Even more unlikely is that you let the gel run to long and the smallest band ran off into the buffer.

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What is the relationship between restriction sites and a restriction map?

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The map will show where the restriction sites are located on the DNA, and what the distance is between the sites.

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Would a mutation in a gene always be detectable by using restriction maps? Why or why not?

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Usually, mutation cannot be detected by restriction mapping until mutation occurs in restriction sites. The mutation may be detectable after it is get mapped and taken away and then it is put under PCR. the mutation be detected.

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9.2 Copying DNA

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The polymerase chain reaction rapidly copies segments of DNA. The polymerase chain reaction (PCR) is based on the process of DNA replication. By combining the DNA to be copied, DNA nucleotides, primers, and specific polymerase enzymes, a desired segment of DNA can be copied in the laboratory. -PCR uses polymerases to copy DNA segments -PCR is a three step process

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Briefly describe the function of polymerase chain reaction (PCR).

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The polymerase chain reaction (PCR) uses enzymes to mass replicate a portion of a DNA strand for easier analysis, such as searching for genes of interest.

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Summarize the cycle involved in the PCR process.

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1. Separation of two strands of DNA by temperatures of around 90 degrees Celsius (194 degrees Fahrenheit) 2. Binding of DNA primer to the separated strands. Occurs at 50 degrees Celsius (131 degrees Fahrenheit) 3. Elongation of the strands using the DNA primer with heat-stable DNA polymerases. Occurs at 72 degrees Celsius (152 degrees Fahrenheit)

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Describe how heating double stranded DNA separates the strands. Why does heating also inactivate DNA polymerases from many organisms?

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The hydrogen bonds between A & T and G & C are broken. G-C bonds require more heat to separate because they have 3 hydrogen bonds whereas A-T have only 2. Heating will denature the enzyme by destroying the precise 3-D structure.

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Explain two reasons why primers are important in PCR.

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PCR needs two primers, each complementary to a different strand, because the primers define the region that will be amplified. In the first cycle, the double stranded DNA is heated, so that the hydrogen bonds holding the 2 strands together break, and the 2 strands fall apart. When the temperature goes down, complementary sequences will start to bind to each other. Because there are many more primers than template DNA, the chance that a primer will bind to its complementary sequence is much higher than that the 2 original full length template strands will find each other. One primer is designed to bind on one strand, the other primer will bind the other strand. The enzyme DNA polymerase will extend these primers, and use the template as a template.

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9.3 DNA Fingerprinting

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DNA fingerprints identify people at the molecular level. DNA has many repeating base sequences. The number of repeats differ from person to person. DNA fingerprinting uses restriction enzymes and gel electrophoresis to detect these differences. By using DNA fingerprinting on several regions of DNA, one particular person can be identified. -A DNA fingerprint is a type of restriction map -DNA fingerprinting is used for identification

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On what, in a person's DNA, is a DNA fingerprint based?

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It is based on non-coding DNA. This DNA has a high enough mutation rate that it is specific to individuals.

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How are DNA fingerprints and restriction maps similar? Explain.

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A restriction map is a map of known restriction sites within a sequence of DNA. These might be like a fingerprint because fingerprints are judged by certain points as well and the shapes at those points determine who the print belongs to.

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Briefly describe how restriction enzymes, gel electrophoresis, and PCR are used in DNA fingerprinting.

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Restriction enzymes are used to cut DNA sequences at specific areas. They have a nucleotide code on them. So when this restriction enzyme finds that code in your DNA it cuts it there. First your DNA is amplified using PCR, then cut into your restriction enzymes, then filtered to show your unique banding pattern with gel electrophoresis.

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9.4 Genetic Engineering

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DNA sequences of organism can be changed. Clones, or identical genetic copies, of many organisms can be made. Organisms can also be implanted with genes that give then new traits. Often, genes are inserted into plasmids to make recombinant DNA. Genetically engineered plasmids are inserted into bacteria, producing a transgenic organism. Transgenic bacteria, plants, and animals are used in several different ways. -Entire organisms can be cloned -New genes can be added to an organism's DNA -Genetic engineering produces organisms with new traits

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Why is the offspring of asexual reproduction a clone?

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With asexual reproduction there is only one parent. All genetic material comes from this sole parent.

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What are plasmids, and how are they used in genetic engineering?

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Plasmids are DNA molecules, usually circular, that are independent of the chromosomal DNA. In bacteria these can replicate independently as well. In genetic engineering, plasmids are called vectors, and are used to isolate and multiply a specific gene. Since they are independent of chromosomal DNA, they can be transferred into other organisms.

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Describe two applications of transgenic organisms.

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Genetic engineering in plants such as traits for resistance to frost, diseases, and some insects. Also, genetic engineering in animals can help scientists learn about diseases and cell growth.

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How is the cloning of genes different from the cloning of animals?

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Cloning genes means you isolate/cut/remove a particular gene from the DNA sequence using rectriction enzymes. This gene usually will be inserted into other organism to produce a transgenic organism. Cloning animals means you clone animals. Asexual reproduction means to reproduce organisms without fusion between male gamete and female gamete.

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How are restriction enzymes used to make both recombinant DNA and transgenic organisms?

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Restriction enzyme use is basically the same for both the production of recombinant DNA and for transgenic organisms since an organism can synthesize the DNA that has been inserted into it once it has been placed within the organism. In the case of unicellular organisms the restriction enzyme is first introduced to break apart the DNA and then the plasmid is introduced to create the desired effect. Then the organism can express those genes through further processing of the newly introduced DNA and through mitosis (which is how unicellular organisms reproduce) it can give that gene to its offspring.

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9.5 Genomics and Bioinformatics

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Entire genomes are sequenced, studied, and compared. Through DNA sequencing, the genomes of several organisms, including humans, have been found and studied. Genomic data are organized and analyzed through bioinformatics. DNA microarrays are used to study interactions among genes in a genome. In addition, genomics has led to the study and comparison or proteins through proteomics. -Genomics involves the study of genes, gene functions, and entire functions -Technology allows the study and comparison of both genes and proteins

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Describe the goals of the Human Genome Project.

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The goal of the Human Genome Project was to identify the location and function of every human gene.

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Why is bioinformatics important in genetic research?

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Bioinformatics is important to genetic research because genetic data has a context. The context is biology. Life forms have certain rules of behavior. The same applies to tissues and cells, genes and proteins. They interact in certain ways and regulate each other in certain ways. The large-scale, complex data that is generated in genomics wouldn't make sense without the contextual knowledge of how life forms work.

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Describe the difference between gene sequencing and DNA fingerprinting.

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Gene sequencing looks at the sequence of nucleotides in a sample whereas DNA fingerprinting does not. It looks at the pattern of fragments produced when the sample is digested.

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How is the study of specific genes different from the study of a genome?

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A genome is a full set of chromosomes or genes rather than the study of one single gene.

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9.6 Genetic Screening and Gene Therapy

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Genetics provides a basis for new medical treatments. Genetic screening is used to test people for genes that are linked to genetic disorders. One method to correct these faulty genes or to replace missing genes is gene therapy. Gene therapy is experimental, but has the potential to cure many diseases.

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How does genetic screening use both old and new methods of studying human genetics?

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Genetic Screening applies the principle of synthetic lethality to a gene of interest in mammalian cells. Most "new methods" are recycled from the oldest ones, but the original old methods are no longer used as often. -Genetic screening can detect genetic disorders -Gene therapy is the replacement of faulty genes

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Briefly describe the goals and methods of gene therapy.

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Gene therapy is an experimental technique that uses genes to treat or prevent disease. Researchers are testing several approaches to gene therapy, including: Replacing a mutated gene that causes disease with a healthy copy of the gene, inactivating a mutated gene that is functioning improperly, and introducing a new gene into the body to help fight a disease.

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How is gene therapy similar to, and different from, making a transgenic organism?

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Transgenesis is much like gene therapy in that both transform cells for a specific purpose. However, whereas gene therapy targets only certain cells in order to cure a defect in them, transgenesis seeks to produce an entirely modified organism by incorporating the transgene into all the cells of the mature organism and changing the genome.

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How are restriction enzymes and recombinant DNA important for gene therapy?

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Recombinant DNA is the technology that allows us to insert genes from one organism into another to make it produce a protein product, copy the gene multiple times, or give it a new trait. The discovery of recombinant DNA was considered the "birth" of modern biotechnology.

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How is the cloning of genes different from the cloning of animals?

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The cloning of genes only requires that you clone the gene itself. Cloning an animal means cloning all of its genes and cells.

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