Kelsey+Haugh

__Gene Cloning with Bacterial Plasmids __
Describe: DNA cloning is a method used to isolate a sequence of DNA. Cloning DNA starts with inserting the DNA into a vector. The vector can either be a plasmid or a phage. Analyze: This procedure deals with bacterial plasmids, which normally contains three elements. The elements are a cloning site, a drug-resistance gene, and a replication origin. Gene cloning can be used to find non-resistance drugs for medicine. Apply: This process can make identical copies of certain genes. Synthesize: It reminds me of a copier, because it copies everything, just as a copier copies the paper. Argument: It can be both a good thing and a bad thing. Some people say its good because it could help the medical field in the years to come, but some people say its bad because they feel we should let nature do whatever it wants. I am for it because it could help in the near future.



To see a tutorial depicting this process, click this link: [|Plasmid Cloning]

Sources and Additional Information: [|Cloning Fact Sheet] [|Plasmid Cloning] AP Biology Book

__﻿Nucleic Acid Hybridization __
Describe: A strand of DNA is denatured, normally by heating it. When the DNA is at a certain temperature, the complementary bases of the helix are disrupted and the double stranded helix quickly becomes two separate strands. Then, using the complementary bases, short strands of nucleic acids to find a piece of DNA or RNA. Analyze: Nucleic acid hybridization uses a nucleic acid probe to detect certain genes. This process requires DNA denaturation to do the required job, but heating the DNA so they will split apart. Apply: If one needed to find a certain gene in DNA, they could use nucleic acid hybridization to find the gene. <span style="color: #dc28b5; font-family: Arial,Helvetica,sans-serif;">Synthesize: This process reminds me of a service dog, such as a drug dog, sniffing for particular objects, like drugs, in the midst of everything else. <span style="color: #dc28b5; font-family: Arial,Helvetica,sans-serif;">Argument: I'm completely for this process. This process may help scientist to find specific genes that could help cure a disease, or help find the reason for the disease.



<span style="color: #dc28b5; font-family: Arial,Helvetica,sans-serif;">Video: <span style="color: #dc28b5; font-family: Arial,Helvetica,sans-serif;">[|DNA Test Method]

<span style="color: #dc28b5; font-family: Arial,Helvetica,sans-serif;">Sources and Additional Information: <span style="color: #dc28b5; font-family: Arial,Helvetica,sans-serif;">AP Biology Book <span style="color: #dc28b5; font-family: Arial,Helvetica,sans-serif;">[|Nuclic Acid Hybridization]

__<span style="color: #51d61f; font-family: Arial,Helvetica,sans-serif;">Genomic Library __
<span style="color: #51d61f; font-family: Arial,Helvetica,sans-serif;">Describe: The genomic library is a collection of bacteria that can hold all the DNA of a certain organism. The DNA is broken into chunks and the pieces are inserted into cloning vectros, which are normally plasmids. The amount of DNA stored can vary. <span style="color: #51d61f; font-family: Arial,Helvetica,sans-serif;">Analyze: The genomic library contains all the DNA of a certain organims. It also has the genome of the bacteria. <span style="color: #51d61f; font-family: Arial,Helvetica,sans-serif;">Apply: The genomic library can be used for a multitude of different genetic experiments. Researchers can use it to seek out certain parts of the DNA or use the library to learn more about the genomic structure of the organism. <span style="color: #51d61f; font-family: Arial,Helvetica,sans-serif;">Synthesize: The genomic library is much like a book library because it houses different information in one spot. <span style="color: #51d61f; font-family: Arial,Helvetica,sans-serif;">Argument: There could be two sides to this process. Some people might say it is a positive thing because we can learn more about an organsim's DNA, but somebody else could say we shouldn't insert the DNA into another organism. Personally, I'm against it because people might let the power get to their head and decide to clone humans. I don't think that's right.

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<span style="color: #51d61f; font-family: Arial,Helvetica,sans-serif;">DNA Insertion Tutorial: <span style="color: #51d61f; font-family: Arial,Helvetica,sans-serif;">[|Construction of DNA Library]

<span style="color: #51d61f; font-family: Arial,Helvetica,sans-serif;">Sources and Additional Information: <span style="color: #51d61f; font-family: Arial,Helvetica,sans-serif;">[|DNA Library] <span style="color: #51d61f; font-family: Arial,Helvetica,sans-serif;">[|What is a Genomic Library?] <span style="color: #51d61f; font-family: Arial,Helvetica,sans-serif;">AP Biology Book

__<span style="color: #ff0000; font-family: Arial,Helvetica,sans-serif;">Polymerase Chain Reaction (PCR) __
<span style="color: #ff0000; font-family: Arial,Helvetica,sans-serif;">Describe: This is a process that copies DNA without a cell present, normally in some kind of eppy tube. The DNA that is trying to be replicated is called the target DNA. Several ingredients are used in the PCR, including many enzymes. The process can use any type of DNA, including degraded DNA, but errors may occur. <span style="color: #ff0000; font-family: Arial,Helvetica,sans-serif;">Analyze: PCR uses free nucleotides, DNA primers, and the Taq polymerase. The DNA has to be denatured for the process to be completed properly. <span style="color: #ff0000; font-family: Arial,Helvetica,sans-serif;">Apply: PCR can be used for many things. It can be used to amplify old samples of DNA or create more samples from tissue or blood. <span style="color: #ff0000; font-family: Arial,Helvetica,sans-serif;">Synthesize: This reminds me of someone handwriting the same thing over and over again. Although they know what they should be writing, errors will occur, but they will have extra copies in the long run. <span style="color: #ff0000; font-family: Arial,Helvetica,sans-serif;">Argument: This is a good process because it can help researchers learn about what happened thousands of years ago and help the police force.

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<span style="color: #ff0000; font-family: Arial,Helvetica,sans-serif;">Animation: <span style="color: #ff0000; font-family: Arial,Helvetica,sans-serif;">[|PCR Animation] <span style="color: #ff0000; font-family: Arial,Helvetica,sans-serif;">[|Second PCR Animation]

<span style="color: #ff0000; font-family: Arial,Helvetica,sans-serif;">Sources and Additional Information: <span style="color: #ff0000; font-family: Arial,Helvetica,sans-serif;">AP Biology Book <span style="color: #ff0000; font-family: Arial,Helvetica,sans-serif;">[|PCR Animation] <span style="color: #ff0000; font-family: Arial,Helvetica,sans-serif;">[|PCR]

__<span style="color: #e95a07; font-family: Arial,Helvetica,sans-serif;">Gel Electrophoresis __
<span style="color: #e95a07; font-family: Arial,Helvetica,sans-serif;">Describe: Gel electrophoresis is a procedure used to electrically separate certain molecules, such as DNA or RNA, through a gel-like material. In order to do this, the organic molecule must be charged; either positive or negatively charged. Holes, or wells, are put into the gel that act as reserviors for the substance. Sometimes there is also a control inserted into the wells. Those can be used to compare the molecules. The gel is normally clear so you can easily see the markers. Sometimes the substances are stained so they are seen easier as well. After the electrophoresis has ran, smaller molecules are lower in the gel because they can travel through the gel faster than larger molecules. <span style="color: #e95a07; font-family: Arial,Helvetica,sans-serif;">Analyze: The gel is made of an argose material, which is derived from seaweed. The sample, DNA or RNA, is mixed with a loading solution, such as a purple material. There is an box that is used for an electric current connected to the container the gel is in. The gel is contained in between two glass plates. <span style="color: #e95a07; font-family: Arial,Helvetica,sans-serif;">Apply: Gel electrophoresis can be used to compare DNA. If someone has a sample of DNA, they could collect DNA from someone else, and using the weight marker, compare the two samples of DNA. <span style="color: #e95a07; font-family: Arial,Helvetica,sans-serif;">Synthesize: Gel electrophoresis could improve in a few ways. One way is by making it so the pipets can't push through the gel. A few years ago, I did Western Blots in Laramie, WY for a summer project, and although we were using RNA, it was extremely hard to hold our hand steady enough so we would puncture a hole in the gel. <span style="color: #e95a07; font-family: Arial,Helvetica,sans-serif;">Argument: I'm for gel electrophoresis because it could help catch murderers or criminals. If they have a sample, they could compare the sample from alleged suspects.

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<span style="color: #e95a07; font-family: Arial,Helvetica,sans-serif;">Virtual Lab: <span style="color: #e95a07; font-family: Arial,Helvetica,sans-serif;">[|Gel Electrophoresis Virtual Lab]

<span style="color: #e95a07; font-family: Arial,Helvetica,sans-serif;">Sources and Additional Information: <span style="color: #e95a07; font-family: Arial,Helvetica,sans-serif;">AP Biology Book <span style="color: #e95a07; font-family: Arial,Helvetica,sans-serif;">[|Gel Electrophoresis]

__<span style="color: #de1246; font-family: Arial,Helvetica,sans-serif;">Southern Blotting __
<span style="color: #de1246; font-family: Arial,Helvetica,sans-serif;">Describe: Southern blotting is a procedure used to find a specific sequence of the DNA molecule. It is also used to see if the sequence is absent. The DNA sequence is isolated from the rest of the DNA sample and loaded onto an argose gel. Electrophoresis is than ran on the gel. The results are transfered to a filter, and a nucleic acid probe is added to the filter, where it binds to specific sequences. <span style="color: #de1246; font-family: Arial,Helvetica,sans-serif;">Analyze: DNA samples are used in this procedure. Restriction enzymes are used to cut the DNA at specific places. Argose gels are used in this procedure, just as they are in gel electrophoresis. <span style="color: #de1246; font-family: Arial,Helvetica,sans-serif;">Apply: This procedure can be used to compare seemingly alike or different organisms for a specific mutation. They could run the experiement just for that mutation, and if the nucleic acid probe binds to all the samples, they are complementary. <span style="color: #de1246; font-family: Arial,Helvetica,sans-serif;">Synthesize: This procedure reminds me of a metal detector because metal detectors only are able to find objects that are made of metal, just as this process is used to find specific sequences. <span style="color: #de1246; font-family: Arial,Helvetica,sans-serif;">Argument: This is a good procedure because it can help prove or find evolutions in science, from the beginning of time to now.

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<span style="color: #de1246; font-family: Arial,Helvetica,sans-serif;">Animation: <span style="color: #de1246; font-family: Arial,Helvetica,sans-serif;">[|Southern Blotting Animation]

<span style="color: #de1246; font-family: Arial,Helvetica,sans-serif;">Sources and Additional Information: <span style="color: #de1246; font-family: Arial,Helvetica,sans-serif;">AP Biology Book <span style="color: #de1246; font-family: Arial,Helvetica,sans-serif;">[|Southern Blot] <span style="color: #de1246; font-family: Arial,Helvetica,sans-serif;">[|Ask A Biologist: Southern Blot]

__<span style="color: #9308e7; font-family: Arial,Helvetica,sans-serif;">Microarrays __
<span style="color: #9308e7; font-family: Arial,Helvetica,sans-serif;">Describe: Microarrays are used to detect the expression of many genes at once. This happens by extracting the mRNA. The mRNA is injected back into the DNA and the expressions are visible. <span style="color: #9308e7; font-family: Arial,Helvetica,sans-serif;">Analyze: This process involves many strands of DNA. They are hybridized with flourescent mRNA. Then, on a glass plate, all the gene expression can be visible from different organisms. <span style="color: #9308e7; font-family: Arial,Helvetica,sans-serif;">Apply: Microarrays can help scientist to understand the basic principles of organisms or diseases. <span style="color: #9308e7; font-family: Arial,Helvetica,sans-serif;">Synthesize: This procedure reminds me of anything that has pixels. All the gene expressions are visible in this procedure, just like how all the pixels and colors are together to form a picture or word. <span style="color: #9308e7; font-family: Arial,Helvetica,sans-serif;">Argument: This is a good procedure because you can look at several gene expressions at once and compare them.

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<span style="color: #9308e7; font-family: Arial,Helvetica,sans-serif;">Animation: <span style="color: #9308e7; font-family: Arial,Helvetica,sans-serif;">[|Microarray Lab]

<span style="color: #9308e7; font-family: Arial,Helvetica,sans-serif;">Sources and Additional Information: <span style="color: #9308e7; font-family: Arial,Helvetica,sans-serif;">AP Biology Book <span style="color: #9308e7; font-family: Arial,Helvetica,sans-serif;">[|Microarray Lab] <span style="color: #9308e7; font-family: Arial,Helvetica,sans-serif;">[|Microarray]

__<span style="color: #277aec; font-family: Arial,Helvetica,sans-serif;">Plant Cloning: __
<span style="color: #277aec; font-family: Arial,Helvetica,sans-serif;">Describe: Plant cloning has been around for around fifty years. It happens by taking cells from the root, or carrot, of the plant and incubating the cells. The cells then grow into normal size adult plants that are identical to the parent plant. Many people practice plant cloning when they cut a stem from one plant and plant it somewhere else. <span style="color: #277aec; font-family: Arial,Helvetica,sans-serif;">Analyze: Plant cloning uses cells from the root of the plant that are incubated for a period of time, allowing the plant to grow. The cells that are able to grow are called totipotent. <span style="color: #277aec; font-family: Arial,Helvetica,sans-serif;">Apply: This process is heavily used in agriculture to produce desired characteristics in plants. <span style="color: #277aec; font-family: Arial,Helvetica,sans-serif;">Synthesize: This makes me think of bacteria that are dividing because, just as the offspring of bacteria are identical to the parent, the plant offspring is also identical to the parent plant. <span style="color: #277aec; font-family: Arial,Helvetica,sans-serif;">Argument: Cloning is a very controversial subject, and while I'm not for animal cloning, plant cloning is ok. It makes food readily available that have desired characteristics all over the world.

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<span style="color: #277aec; font-family: Arial,Helvetica,sans-serif;">Sources and Additional Information: <span style="color: #277aec; font-family: Arial,Helvetica,sans-serif;">AP Biology Book <span style="color: #277aec; font-family: Arial,Helvetica,sans-serif;">[|How Cloning Works]

__<span style="color: #dc28b5; font-family: Arial,Helvetica,sans-serif;">Animal Cloning __
<span style="color: #dc28b5; font-family: Arial,Helvetica,sans-serif;">Describe: Unlike plant cells, animal cells normally will not grow in a culture medium. This makes cloning animals much harder than cloning plants. In order to clone animals, the researcher must extract an embryonic cell and place it in an unfertilized egg. The cells are then implanted back into the host mother. <span style="color: #dc28b5; font-family: Arial,Helvetica,sans-serif;">Analyze: This process in conducted using embryonic cells and unfertilized eggs. The nucleus has to be removed from the eggs. After the cells are implanted into the eggs, the eggs are fertilized with electric shocks. They can also be treated with chemical therapy. <span style="color: #dc28b5; font-family: Arial,Helvetica,sans-serif;">Apply: This process is used to clone organisms or stem cells from medical research. <span style="color: #dc28b5; font-family: Arial,Helvetica,sans-serif;">Synthesize: This process reminds me of in vitro fertilization. Although in in vitro fertilization the offspring isn't identical to the parent, the cells still have to be implanted into the mother's eggs. <span style="color: #dc28b5; font-family: Arial,Helvetica,sans-serif;">Argument: I'm against cloning humans, but I feel it is ok to clone some things, such as stem cells, because that could save people.

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<span style="color: #dc28b5; font-family: Arial,Helvetica,sans-serif;">Animation: <span style="color: #dc28b5; font-family: Arial,Helvetica,sans-serif;">[|Animal Cloning Animation]

<span style="color: #dc28b5; font-family: Arial,Helvetica,sans-serif;">Sources and Additional Information: <span style="color: #dc28b5; font-family: Arial,Helvetica,sans-serif;">AP Biology Book <span style="color: #dc28b5; font-family: Arial,Helvetica,sans-serif;">[|Animal Cloning] <span style="color: #dc28b5; font-family: Arial,Helvetica,sans-serif;">[|How Cloning Works]

__ Restriction Fragment Length Polymorphism (RFLPs) __
Describe & Analyze: Restriction fragment length polymorphism is a difference in DNA sequences that exists in the restriction site for a particular enzyme. It makes the site unrecognizable by the enzyme. Its normally inherited can is co-dominant. It is essentially a DNA fingerprinting system. Apply: RFLPs are very useful for law enforcement. It can help determine someone's guilt or innocence. Synthesize: This reminds me of mile markers because they are useful for directions, just as RFLPs are useful genetic markers. Argument: I'm for this because it can help solve murders or other major crimes.



Video: [|RFLP - DNA Fingerprinting]

Sources and Additional Information: AP Biology Book <span style="color: #277aec; font-family: Arial,Helvetica,sans-serif;">[|Restriction Fragment Length Polymorphisms (RFLPs)]

__<span style="color: #ff0000; font-family: Arial,Helvetica,sans-serif;">Gene Therapy __
<span style="color: #ff0000; font-family: Arial,Helvetica,sans-serif;">Describe: Gene therapy is the process of introducing genes into an afflicted individual for therapeutic purposes. It holds great potential for treating disease and disorders. Bone marrow cells are prime candidates for gene therapy because they multiply throughout the individual's life. <span style="color: #ff0000; font-family: Arial,Helvetica,sans-serif;">Analyze: This process includes taking RNA from a donor, putting them in a retrovirus, letting them culture, and then injecting them into the patient, wherever it is needed. They can also use Herpes simplex virus, adenovirus, or adeno-associated viruses in place of the retrovirus.[|Gene Therapy] <span style="color: #ff0000; font-family: Arial,Helvetica,sans-serif;">Apply: Gene therapy is used a lot for cancer patients or patients with curable disorders. Cancer patients, especially ones with leukemia, are good candidates because they can take blood cells. Leukemic patients can get bone marrow cells as well. <span style="color: #ff0000; font-family: Arial,Helvetica,sans-serif;">Synthesize: This process reminds me of a blood transfusion because they both use donors and both could save someone's life. <span style="color: #ff0000; font-family: Arial,Helvetica,sans-serif;">Argument: I'm for this process. It could save someone's life. Also, the donor is also normally willing to donate their cells for a good cause, and if it saves someone's life, it's worth it.

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<span style="color: #ff0000; font-family: Arial,Helvetica,sans-serif;">Animation: <span style="color: #ff0000; font-family: Arial,Helvetica,sans-serif;">[|Gene Therapy]

<span style="color: #ff0000; font-family: Arial,Helvetica,sans-serif;">Sources and Additional Information: <span style="color: #ff0000; font-family: Arial,Helvetica,sans-serif;">AP Biology Book <span style="color: #ff0000; font-family: Arial,Helvetica,sans-serif;">[|Gene Therapy]

__ Transgenic Animals (Genetically Modified Organisms ~ GMOs) __
Describe: Transgenic animals are animlas that carry foreign genes that were directly inserted into their own genome. To do this, researchers use recombinant DNA methodology. The DNA includes a variety of things, like structual genes, and may enable the transgenic genes to help in gene therapy for humans. Analyze: Transgenic animals are made by using recombinant DNA. They also include a structual gene. In order to inject the DNA into the host animal, they must first remove the eggs from the female and then fertilize it in vitro. After the eggs are fertilized, they can be inject the eggs into the host animal. There are two ways to insert the DNA into the animals; the embryonic stem cell method and the pronucleus method. Apply: They use transgenic mice a lot in research. They produce knock-out mice to see what genes are affected by certain sequences. They then take the research and apply it to humans to try and cure diseases. Synthesize: This process reminds me of someone who wears color contacts. Just because they have different colored eyes than normal, they are the same person in the end. Argument: I'm for this process because it helps people. Some people might be against it because they are messing with something that really isn't theirs to mess with, but if it saves lives, it should be allowed to go on until someone is hurt by it.



Video: [|Transgenic Mouse Animation]

Sources and Additional Information: AP Biology Book [|Transgenic Animals]

__ Transgenic Plants (Genetically Modified Organisms ~ GMOs) __
Describe: Transgenic plants also have genes inserted directly into their genome from another plant. Once again, they use recombinant DNA processes to make the plants transgenic. They normally look the same as usual, but they may have slight differences in build or color. It is much easier to create a transgenic plant than a transgenic animal. There is no real distinction between somatic cells and germlike cells, as there is in animals. Analyze: Instead of using eggs to create a transgenic plant, researchers use pollen from a host plant that is put into the host plant. Two methods that are used for creating transgenic plants are by using plasmids as vectors or by shooting microscopic pellets containing the gene directly into the cell. Apply: Researchers are now using plants to create medications for humans. These transgenic plants are called 'pharm' plants because they create the medicines. They use human proteins to help do this. Synthesize: This process reminds me of 'designer babies.' Designer babies are created in the eye of the parent, having the desired characteristics. Argument: Once again, I'm for this process. But, only in some cases. Some tobacco farmers use this process in their tobacco plants and I'm against that use, but as long as it is being used to create medicine, I'm ok with it. Video: [|Transgenic Transformation in Rice Plants]

Sources and Additional Information: AP Biology Book [|Transgenic Plants]

__ Genetic Profiles (DNA Forensic Testing) __
Describe: Genetic profiling is the same thing as DNA fingerprinting. Genetic profiles is the correct term and the one that is more widely used between researchers. Every individuals DNA sequence is unique and scientist can perform electrophoresis to find the specific DNA markers that make up a person's genome. Analyze: In order to do this, scientist must take a little sample of tissue or blood and put the samples in a gel to run electrophoresis through the gel. They can then compare the markers, which is the person's DNA, to other samples. Apply: Law enforcement officials use genetic profiles to compare suspects DNA with victims. Synthesize: This process reminds me of a thesarus because that compares two words that have the same meaning, and genetic profiling can compare DNA samples.

Animation: [|DNA Fingerprinting/Genetic Profiling]

Sources and Additional Information: AP Biology Book [|Genetic Profiling - How a Genetic Profile can Help You]