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Gene Cloning with Bacterial Plasmids
Gene cloning requires plasmids, which are small, circular chromosomes in prokaryotic cells. In gene cloning, a particular gene from another organism can be inserted into a plasmid. This gene of interest can then be replicated along =with the plasmid inside a prokaryotic cell, which is called the host cell.
 * //__Describe it! :__//**

__//**Analyze it! :**//__ The gene cloning process begins with restriction enzymes cutting out the gene of interest from the genome of another organism. Restriction enzymes recognize a specific sequence of nucleotides, and they cut these nucleotides out of the double stranded DNA at restriction sites. The restriction enzymes also cut the plasmid at its restriction site. The sticky ends on both the foreign DNA fragments and the plasmid DNA attach to each other, forming recombinant DNA when DNA ligase forms covalent bonds between them. Then, when the host cell is competent in the Log phase, it takes up the plasmid through transformation. When the host cell replicates, the plasmid and the gene of interest also replicate, forming multiple copies of the gene.

__//**Apply it! :**//__ Cloning genes aids in scientific research. Genetic engineering incorporates desirable genes into organisms in order to make them better. Pest-resistant crops are an example of this. Once cloned genes are transcribed and translated, they produce protein, which can be mass produced and used for various purposes. The protein insulin can be produced in this way and used for diabetes patients.

Consider this analogy: gene cloning is like a trend. Say that it's a current trend to have a charm bracelet, and a new charm has just become popular. The plasmid is like the charm-bracelet, and the new charm is symbolic of the gene of interest. Once people start wearing the new charm, more and more people join in on the trend. Therefore the new charm (gene) will be multiplied.
 * //__Synthesize it!:__//**

One disadvantage of gene cloning is the resistance of bacteria to antibiotics. However, there are far more advantages in genetic engineering than disadvantages. Some of these advantages are present in agriculture, like making crops more nutritious and have longer shelf lives. Other advantages are in medicine, like making proteins and medicines to treat genetic diseases.
 * //__Argue it! :__//**


 * Media:**
 * [| http://faculty.plattsburgh.edu/donald.slish/Transformation.html]**

Animation


 * Sources:** AP Biology Book ; Picture

Nucleic Acid Hybridization
Locating a gene can be tricky, but luckily nucleic acid hybridization makes this seemingly impossible task manageable.This process allows us to detect a gene through the base pairing characteristics of DNA. The DNA a gene can be base-paired to a complementary sequence. Nucleic acid hybridization involves a gene that we are looking for, a complementary nucleic acid sequence to the gene's DNA, and some radioactive chemicals.
 * __Describe it:__**

To begin searching for the gene of interest, a nucleic acid probe must be synthesized or found. A nucleic acid probe is a complementary molecule to the gene of interest that can be composed of DNA or RNA. Next, the gene must become denatured in order for this magic trick to work. By adding either heat or chemicals the double stranded DNA's hydrogen bonds will break apart and become two single stranded DNA. This single stranded DNA is now free to be bound to other strands like a nucleic acid probe. Once the probe and the gene's DNA are bound together, all we need to do is find the dynamic duo. Searching for this pair becomes much simpler when we attach a radioactive isotope to the probe. The radioactive isotope acts like an identifying tag on the probe, enabling us to locate the probe when it has become bound to the gene's DNA.
 * __Analyze it:__**

This process is used to locate genes. Nucleic acid hybridization can be applied to gene cloning. In order for a gene to be cloned, first the gene needs to be found. Hybridization also allows us to isolate and cultivate large amounts of gene. Large quantities of a gene could be useful to make a large product of specific proteins.
 * __Apply it:__**

Today many movies centralize about the fictitious and exciting life of a spy. Off the top of my head when I hear spy movie, I think of Knight and Day starring Tom Cruise and Cameron Diaz. One of the many gadgets of a spy is a tracker. A tiny device that can stick onto the clothing of a person and send out a signal to your device in order for you to track them. A tracker used by a spy similarly makes me think of part of the process of nucleic acid hybridization. In order for us to locate a gene we send a probe with a radioactive tag to attach to the gene in order for us to find it. The probe acts like a tracker, the gene is like the target, and we are the spies searching relentlessly for our target.
 * __Synthesize it:__**

I argue on behalf of my fellow team of scientists in training that nucleic acid hybridization is a process that is being used for good. Yes, there are some cons but the good simply outweigh the bad. There are many beneficial uses of this practice. One is using hybridization as a diagnostic probe. There is a serious case of tomatoes going speckled. This speckling is caused by harmful bacteria towards the tomato, making our tomatoes look simply unappealing. By using hybridization we can locate the cause of our problem and be one step closer to making more tomatoes look delicious. Another use of hybridization is HIV susceptibility testing. Hybridization enables us to study the effect of antiviral agents on the RNA of HIV. Lastly, this process can be used to detect the genetic distance between two species, but this last point can be either a con or pro. Critics of the pro on this last point state that this process is inaccurate when used to study the evolutionary distance between close species. Now when nucleic acid hybridization is put onto the judgement scale, the pro aspects weigh out the cons.
 * __Argue for or against it:__**

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 * __Online Resource:__**

__**Sources**__: [|http://gateway.nlm.nih.gov/MeetingAbstracts/ma?f=102178757.html] [] [] [|Hybridization and Tomatoes.pdf] AP Bio Book

Genomic Library

==== **__Describe it:__** A Genomic Library is a collection of cloned bacteria that store the transformed DNA of an organism. The Genomic Library will always start out with a long strand of DNA that needs to be cut. The more bacterial cells that you have then the larger the collection will be. The bacterial cells can have different types of DNA that the plasmids uptake. Plasmids are circular DNA structures that can come and take up other DNA fragments. ====

__** Analyze it: **__ The library is made when DNA goes through the process that is in the picture to the right. When the DNA separates via restriction enzymes, some of the fragments are then inserted and sealed into the plasmid structures by the enzyme ligase. These new plasmids (which are types of vectors) then are put into the bacterial cells. The more of these cells that we have then the greater the Genomic Library can be. The function of a Genomic Library is to store these cloned bacteria cells with plasmids.


 * __ Apply it: __** Genomic Libraries are used to store the transformed bacteria for later usage. Scientists are able to clone more of the recombinant DNA in petri dishes, which will grow many colonies of this new DNA. Scientists who are conducting experiments can ask other researchers if they have a specific cloned bacterial cell that they can use. This makes it easier than every scientist having to make their own cells every time they needed to do an experiment.

**__ Synthesize it: __** A Genomic Library is essentially just like a real library or book store. Each cloned DNA copy is representing a type of book. There can be many groups of books in one genre, but if that certain book is popular then more people will check it out or buy it. Before long all of the books in that category will be taken. The only way to replenish the stock so that more people can come and get them is to make new "clones" of the books. The many groups of books are many different genes that are able to be cloned. The books that are more popular represent the recombinant DNA that researchers and scientists need for their studies, and the new books that have to be made are the cloned DNA in the Genomic Library.


 * __Argue it:__** The ability to attain a Genomic Library is a great feat in Biotechnology. Having cloned Bacterial Cells that are readily available at all times can be an advantage for both researchers and society itself. If research was being conducted to genetically change certain types of food, then the researchers would be able to go to a Genomic Library to see if there are any extra cloned cells that be used in the study. Having many clones also allows for many tests to ensure they can make the best product. We agree that cloning cells for making plants, fruits, and vegetables resistant to environmental damages is a great idea. However cloning human genomes in order to actually make a human being seems to be a bit out of context. People are not meant to be cloned by scientists, but cloning specific parts of a human like the liver or other organs would be more realistic. Cloning organs would ensure that people with injuries would be able to get a match more easily with readily available cloned cells.


 * __Media: Making a Genomic Library;__**


 * __Source:__** AP Biology Book

**Polymerase Chain Reaction (PCR)**

__//Describe it://__ Polymerase Chain Reaction is another way to copy genetic material. Parts needed for PCR to be completed are: a target sequence (gene(s)) in a segment of double stranded DNA, two primers, a DNA polymerase that is heat-resistant, and free nucleotides in the cytoplasm (all four types). Each primer should be complementary to opposite ends of the target sequence on opposite DNA strands.

//__Analyze it:__// PCR begins with the denaturation of the double stranded DNA. The DNA is heated, and the strands separate into single strands. Then annealing occurs where the DNA is cooled so the primers can attach to the single DNA strands. Finally extension is completed when DNA polymerase adds the free nucleotides from the cytoplasm to the 3' end of the primers. This ends cycle one, with the production of two double stranded DNA segments from one DNA segment. After many cycles are completed, many DNA segments will be identical to the target sequence.

__ Apply it: __ PCR is used for many different procedures including the Human Genome Project. Many labs use the PCR process in order to quickly and efficiently produce many copies of DNA segments. Other uses for PCR is to detect different viruses and bacteria, DNA fingerprinting, and even diagnosis genetic disorders. Compared to other ways that DNA can be copied, using the PCR process is relatively inexpensive, and is able to produce significant amounts of the copied DNA rather than just a few copies at a time.

__Synthesize it:__ The PCR chain reaction reminds me of the seasons. In Summer/Fall you are warm, so you don't need to add any extra clothing, or you might shed some clothing layers. This is like when the DNA stands become heated and pull apart. When Winter comes people put on more clothing layers, like when we cool down the strands so that the primers can be added. Each year there are more and more people who need to my the extra clothing to keep them warm. Each cycle produces double the amount of molecules.

__Argue:__ PCR is a great way to make new copies of the DNA strands not only because it is quick and easy to do in a lab, but because it is also inexpensive. This process is able to make millions of new DNA strands. With every cycle PCR goes through the number then doubles.

__ Sources:PCR Video; What is PCR __

**__Gel Electrophoresis__**

===**__ Define it: __** Gel Electrophoresis includes a gel substance like agarose with wells inserted into it in order for the proteins to move through it. It also includes electricity to get the molecules to move to the other side of the gel. It depends on the fragment size of the DNA or protein to determine how far the fragment will travel through the gel. ===

[[image:15_electrophoresis_set_up_P3020029md.jpg width="474" height="355" align="right"]]
==__**Analyze it:**__ Gel Electrophoresis is a way to separate mixtures of proteins or DNA using an electrical field. When the agarose is poured and made into the gel substance, a “comb” is added to it in order to make the wells. After the gel solidifies you can take the comb out carefully to make sure that you don’t break any of the wells. Then the next step is to insert the DNA into the wells without actually injecting it into the gel. Once these steps are completed then you can turn on the electricity, making sure that you have everything plugged in correctly, and watch how the -DNA is moving throughout the gel towards the positive side of the gel. This is because opposites attract, and DNA is negative because of the negative phosphate groups that make it up. Depending on how long the fragments of DNA are in each well will determine how far they will move. The smaller ones will move the furthest whereas the longer segments will not move very far. ==

==__** Apply it: **__ This method of separating DNA is used in many ways, but the most common ways are Forensics, by getting the fingerprints of a suspect. You can compare the DNA from the crime scene to match whether or not the suspect is guilty. Molecular Biology is another way to help Microbiologists to study DNA and RNA by size. Genetics can use electrophoresis too because it can easily prepare DNA for cloning and genetic engineering. Virology also uses this technique to determine different virus strains. Finally Gel Electrophoresis is used in Biochemistry to easily have DNA and proteins mapped out for them. ==

==__** Synthesize it: **__ Gel Electrophoresis is like running a marathon with all different types of people. The more athletic people will finish the race and challenges faster and easier than those who are out of shape. This is like the different size fragments trying to get to the positive end of the gel. ==

==**__ Argue: __ This process is good to use, because you are able to easily get accurate results when working with DNA. Forensic Analysis heavily relies on Gel Electrophoresis to compare and contrast DNA samples from crime scenes and from several suspects at one time. **== = =

Southern Blotting
//__ Describe it: __// Southern Blotting combines gel electrophoresis with nucleic acid hybridization. The DNA fragments go through gel electrophoresis and then a nucleic acid probe is added to locate a particular gene. //__ Analyze it: __// Many steps make up the process of southern blotting. First, restriction enzymes cut up the DNA from different samples into restriction fragments. Second, the fragments are sorted by size, forming band patterns in gel electrophoresis. Third, the DNA is transferred onto a nitrocellulose membrane by blotting. Blotting uses a heavy weight and sometimes electricity to transfer the single strands of DNA from the gel onto the membrane. Fourth, a radioactive probe is added to the blot in a plastic bag. The probe bonds with the complementary gene, and the fluorescent bands of the gene show up underneath a photographic film that is placed over the blot.

//__ Apply it: __// Southern Blotting is useful in locating a particular gene in the midst of an entire sample of DNA. This process can be used to identify carriers of genetic diseases. A sample of DNA is compared with samples from both homozygous mutant alleles and homozygous normal alleles for a specific gene. If the sample has a pattern that combines the patterns of both types of homozygous alleles, the sample is heterozygous. This means that the sample is a carrier. Sickle cell carriers can be identified this way.

//__ Synthesize: __// Southern blotting is like the suspect identification process in crime investigations. The band patterns of different samples are lined up next to each other like the suspects are lined up. The perpetrator stands out to the victim, so the victim is able to identify which one it is. In comparison, the fluorescent bands of particular genes stand out in southern blotting, allowing the identification of genetic disease carriers.

//__Argue:__// The technique of southern blotting is generally used to society's benefit. Couples who want to have kids can go in for genetic counseling. If one or both of the parents are carriers of a genetic disease, the probability of their baby having the disease can be calculated.

__//Sources://__ __//[|Picture]//__ ; [|AP Biology Book]

__Resources Online:__ []



Microarrays
**__Describe it:__** The human body has thousands of genes and these genes become expressed in different situations. It is amazing that the human race has now come as far as being able to identify specifically what genes are expressed in a specific tissue. We have gotten as far as we have through the help of DNA microarray assays. DNA microarray assays contains a microarray (a slide that contains single-stranded DNA fragments), mRNA molecules from a tissue sample (or any cell sample), and fluorescence. Through this process we are enabled to see which genes are expressed by their twinkling of fluorescents when the tagged molecules from the tissue sample find their way to DNA that represent genes that would have been expressed.

Finding specific genes that become expressed in a specific cell sounds like an impossible task, but thanks to microarrays this task not only becomes manageable but can also be performed on a large scale. This process first involves a tissue sample. From this sample we collect the mRNA produced by the cells. This mRNA is the result of the expression of certain genes in the tissue. We then use reverse transcriptase on the mRNA to make cDNA. This cDNA is single stranded and is labeled with fluorescents for later recognition. Now we involve the DNA microarray. The microarray is a slide that contains single stranded DNA fragments from the organism's genes. mRNA will then hybridize with the DNA fragments that represent the genes. Because the mRNA was labeled with fluorescents when it makes the correct match-up to its single stranded DNA partner we will be able to identify which genes were expressed in the tissue. Lastly the intensity of the fluorescent measures the level of gene expression in the tissue.
 * __Analyze it:__**

DNA microarray assays allow us to identify what genes are specifically expressed in a tissue. They also help reveal to us the general profiles of gene expression over the lifetime of an organism. Another thing is that microarrays allow us to see gene expression patterns on a large scale. Lastly scientist are trying to use microarrays to identify specific genes involved in the development of diseases. This last idea is still going under much research.
 * __Apply it:__**

In order to survive the tough life of an average high //school student, an essential tool is the book bag. Without the book bag we would be left to carry ALL of our supplies from each classroom in our hands while we rush through the crowded hallways to get to our classes. Luckily we avoid the potential disasters by utilizing the efficient book bag. Now a book bag can be utilized in many ways, some people stuff all of their supplies inside and papers are everywhere (who needs folders?!). Or a book bag may contain the pristine condition of organization. In this second situation a common way to keep organization of the book bag in check is the use of binders. Binders can keep all of our papers and in an orderly fashion with colorful tabs to label the types of certain papers into sections. Now this situation is very much like microarrays. A book bag with papers crammed into the bottom isn't very useful for finding homework fast and in unwrinkled condition. Similarly finding a specific gene without the use of microarrays would be very difficult. The tidy binder is like the microarray. The microarray helps us organize and identify which genes have been expressed in a certain tissue. A binder helps us keep our papers organized through labeled tabs to help us identify and find our homework.//
 * __Synthesize:__**

//**__Argue for or Against it:__**// //I am here today to argue for the case of microarrays. Microarrays have many benefits to contribute towards the general welfare of today's people. One might put it that microarrays are still in its infancy stage. We are still finding different methods to utilize this potential brimming process. There are no clear cut consequences that make this process bad. The only downside are some technical issues of precise interpretation of the results from this process. When microarrays are put on a large scale basis it can be difficult to interpret hundreds of lit of spots into a meaningful conclusion. Yet this is not something that should be blamed on the process itself, but on the lack of advanced biostatistical people that can correctly interpret the results. The advances with this process hold more wait than the light-weighted downfall. Microarrays can be used to discover drugs, development of prognostic tests, pharmacology (helps determine the effects of doses of compounds on gene expression in certain tissues), and can help find multiple subcategories of tumors in one diagnosis. Simply put, the good outweighs the bad. This resolves our moral case for today.//

//__**Online Resource:**__// //[| http://www.bio.davidson.edu/courses/genomics/chip/chip.html]//

//__**Sources**__:// //[]// //[]// //[] (4th link, the pdf labeled: the use and analysis of microarray data. I could not save the pdf to link to this page, sorry.)// //AP Bio Book//

** Plant Cloning **
__Describe it:__ //Single plant cells can grow into adult plants if they are cultured with the right nutrients. The clone will be genetically identical to the single cell it was grown from.//

__Analyze it:__ //First, fragments of a plant are put into a nutrient medium. Disrupting the fragments by stirring separates some single plant cells from the fragments. The single cells start to divide into embryos. Plant cells are totipotent, meaning that they can dedifferentiate and then re-specialize into different types of cells. Genes that were once turned "off" because they were not needed in the specialized cell can be turned "on" again. Similarly, genes that were "on" can be turned "off". Once a plant embryo has formed from a single cell, it is cultured on agar until it is big enough to be planted. The resulting adult plant is identical to the plant that was cut up into fragments.//

An important lesson to learn in childhood is how to spend and save money. Some parents give their kids weekly allowance for doing chores to save up. Other kids might take up their first job doing a paper route to earn a few dollars for a shiny new X-box game. A paper route, like many other jobs, can be specialized or general. A person may just deliver the sunday morning paper on summer days in a specific area. Or a person's paper route could take the general approach of delivering the normal newspaper all year round. Similarly during plant cloning a specialized cell can dedifferentiate and have no special function. As a person can change their paper route from a generalized route a specialized route, similarly the paper route could be changed from a specialized route to the generalized route. The dedifferentiating of a specialized cell is an important aspect of plant cloning. This process allows for a specialized cell when isolated and put in a cultured medium to dedifferentiate and then arise from a clone of the parent plant. Now the actual cloning of the plant is similar to the delivery of identical newspapers to all the houses in the neighborhood. One newspaper draft is made and then copied numerous times in a printing press. From a parent plant numerous clones can be made from it.
 * __Synthesize it:__**


 * __Apply it:__** Genetically cloned plant cells are used in many research projects. Scientists are trying to discover how to make plants resistant to several environmental damages that plants may go through like insects eating them. It is a lot easier to clone plant cells rather than animal cells which allows for a faster production. Cloning them also ensures that you will have exact copies of the parent cells of good crops. Plant immunity is improved which allows the cloned plants to fight off any diseases that a plant may get.


 * __Argue:__** Cloning Plant Cells is a good idea because we would be able to modify fruits and vegetables in the future, which may increase the nutrients in them. Also learning how to make the plants resistant to different bacteria and insects that can kill it off would greatly impact how much crop we save each year.

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 * __Resource Online:__**
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AP Biology Book
 * __Source:__**

Animal Cloning
__Describe:__ // Reproductive animal cloning uses a process called nuclear transplantation to make clones that are genetically identical to the animal that donated the nucleus. Though their genes are the same, environmental influences can keep the clones from being exactly identical. The cloning of mammals requires a mammary cell donor, an egg cell donor, and a surrogate mother. Although reproductive cloning of humans is frowned upon, the cloning of human embryos is used to produce stem cells. Embryonic stem (ES) cells and adult stem cells can change into specialized cells to replace damaged tissue. //

__Analyze:__ // To begin animal cloning, cells from a mammary donor organism are dedifferentiated by partial starvation in culture. At the same time, a separate donor supplies an egg cell, but before the egg cell is used, the nucleus is removed. Then nuclear transplantation is performed, where the egg cell is combined with the mammary cell. The cell is then grown //in vitro// until an embryo forms. When the embryo is ready, it is implanted into a surrogate mother, where it develops. Eventually, a clone is born, and is genetically identical to the mammary donor. // // Another type of cloning is embryonic cloning, which is used for the production of stem cells. Embryonic stem (ES) cells are basically undifferentiated, and can be grown in culture with specific growth factors to produce several types of differentiated cells. Alternately, adult stem cells found in certain tissues can only produce types of cells related to the tissue they are found in. //

//__**Synthesize:**__// //Within today’s free markets, monopolies can occur. An example of a very well known monopoly is Wal-mart, the super department store. Now imagine a place without a Wal-mart for a moment. This theoretical place will be a developing city that Wal-mart wants to incorporate itself into. The first steps of adding the new Wally-World will be the actual construction of the store. After the construction and paperwork, all that is needed is the right person to run the store. Luckily Bob, a renown hard worker, decides to transfer to this new town to be the boss of the new Wal-mart. Animal cloning is similar to this bizarre process. Scientists use nuclear transplantation to clone animals. This process involve the transplanting of nuclei. Bob is like the nucleus. He is the boss of Wal-mart, running the store and he has just transferred jobs to be in this new environment. Also before nuclear transplantation can take place scientists starve the cell to dedifferentiate it. This is like Walmart at its beginning stages where before it can open it’s at its bare essentials and still needs a manager. Lastly the actual reproduction of an identical cell is like the reproduction of a basically identical new Wal-mart in a different town.//

//__Apply it:__ Unlike plant cloning, animal cloning is a lot more complex. Researchers have been trying to clone certain genes in cattle, goats, and sheep for their milk and wool. Cloning animals may also help to keep a species alive for thousands of years without becoming extinct. There are many pros and cons to cloning animals because of both money and health issues. Moral standards also come into a big role when talking about cloning something as large and complex as a human.//

//__Argue:__ I would have to vote "yes" for farm animals, but a strong "no" for cloning human beings. There are many great reasons why we should clone animals. For example if a certain cow has a higher protein level in the mild that it produces then scientists can clone that cows DNA to make more cows that have the same trait. This is the same with cloning sheep for a specific type of wool. However there are also many cons to cloning animals considering right now if you would clone a cow farmers wouldn't be able to sell it for its' meat because we don't exactly know if cloned meat would have any other bad effects on humans when they would eat it. Many people do not want to clone any animals at all because it is against their beliefs. Cloning animals may lead to cloning human beings, and this may have many horrible outcomes because the more complex the structure you have for cloning, then the more chance you have for errors. If an error were to happen while making a cloned human how would scientists fix it? You can't just put down a human, or just start over like you are able to when cloning plants. This is the main problem people have with cloning animals.//

Interesting->[| http://www.endanimalcloning.org/factsaboutanimalcloning.shtml] []
 * __Resource Online:__**

AP Biology Book
 * __Source:__**

Restriction Fragment Length Polymorphism (RFLP)
__Describe:__ // A //genetic marker // is a variation in DNA sequence that results in the different alleles of a population. A single nucleotide polymorphism (SNP) is an example of a genetic marker. A SNP is a base pair on DNA that can vary between individuals. SNPs can be found in both genes and noncoding segments of DNA. A SNP found in a restriction sequence is called a restriction fragment length polymorphism (RFLP).//

__Analyze:__ // A RFLP is a change in one base pair of a recognition sequence, causing the restriction enzyme not to recognize the sequence. Consequently, when a restriction enzyme is added to the DNA, the restriction enzyme will no longer cut the DNA at that sequence. The resulting DNA fragment from a sample with a RFLP will be longer than a DNA fragment without the RFLP. //

__Apply:__ // Genetic markers, including SNPs and RFLPs, can be used to identify alleles that cause disease. These genetic markers are usually near the beginning of the allele-coding sequence of DNA. Using gel electrophoresis, the restriction fragments of DNA wi //// th a RFLP can be compared to the restriction fragments of normal DNA. The pattern between the two samples of DNA will be different because the RFLP sample has a longer fragment than the normal DNA fragment. In this way, the disease causing alleles of genetic disorders like Huntington's disease can be found. //

__Synthesize:__ // A RFLP is like a scratch in a CD because it causes a specific recognition sequence to not function properly, like the CD doesn't function properly. The RFLP causes the restriction enzyme to “skip” over the restriction site like a scratch causes the CD to “skip” over the section that is scratched. //

__Argue:__ // Locating genetic markers in individuals is to society's advantage because alleles for genetic diseases, like Huntington's disease, can be found before the actual onset of the disease. Therefore, preparations can be made for when the disease starts to affect the individual. In addition, if people know that they have the disease, they can choose not to reproduce, so the genetic disease is not passed to another generation. //

__Media:__//RFLP Animation//

__Sources://__ Picture1:[] Picture 2: laviejaescuela7.vhost4free.com AP Biology Textbook

Gene Therapy
Describe: Gene therapy involves the insertion of normal genes into an individual with a disorder caused by a defective gene. The process utilizes a retrovirus and the RNA transcribed from a normal gene to transform the cells that express the disorder. Cells that keep reproducing throughout the patient's lifetime are most beneficial to use in gene therapy.

Analyze: First, RNA from the normal gene is inserted into the viral RNA of a retrovirus. Second, the recombinant retrovirus is used as a vector to carry the normal gene into the affected cells by infecting them in culture. Once inside the cell, the retrovirus's RNA goes through reverse transcription to make viral DNA, transcribing the normal gene along with it's own genome. The DNA produced is inserted into the affected cell's DNA. At this point, the transformed host cells are injected back into the patient's affected tissue, where they reproduce. Each new daughter cell contains the normal gene, and if this gene is expressed correctly, the patient's disorder can be cured.

Apply: Gene therapy can be used to treat and potentially cure disorders like severe combined immunodeficiency (SCID). In SCID, a bone marrow gene is defective, and patients cannot produce an enzyme that they need. However, if the normal gene is introduced to the bone marrow cells via gene therapy, the new cells can make the enzyme, curing the patient.

Synthesize: Gene therapy can be compared to physical therapy. Consider this: a person with a back problem hears of exercises that supposedly strengthen the back muscles. In reality, the exercises do the opposite and actually harm the muscles more. If the person starts doing these exercises every day, his or her back will probably hurt even more than it did before. After a while, the person starts to see a physical therapist, who teaches the person helpful exercises instead. The helpful exercises strengthen the person's back, and eventually they are “cured” from their back problem. In this example, the bad exercises are like the defective gene, and the good exercises are like the transformed gene. The physical therapist is like the retrovirus because he or she brings the good exercises to the patient.

Argue: Although gene therapy may be able to cure some disorders, it does have some significant disadvantages. For example, if something goes wrong, gene therapy can cause leukemia, a cancer of the blood. Scientists think that this is caused by the insertion of the new gene near a developmental blood cell gene. In general, there are many things that scientists don't yet understand about gene therapy, like how to insert the desired gene into the DNA so that it's product is produced in the right amounts and in the right conditions.

The idea of gene therapy is also the topic of ethical controversies. Some opposers of gene therapy think that eventually gene therapy may be applied to human germ cells, in an effort to create the perfect genome. If a “perfect” society is produced, there is a risk of extinction of the entire population if the environment changes. Variety needs to be present so that natural selection and evolution can take place. Media: media type="custom" key="8320488"

Animation

Sources: AP Biology Textbook; Picture


 * __ Transgenic Plants __**

===__**Describe it:**__ Transgenic Plants are plants that have been injected by a foreign DNA from another organism. These plants are more proficient and are able to withstand more harm than regular plants can. ===

==__**Analyze it:**__ Transgenic plants are first soaked in a solution of tetracycline. This solution is soaked up by the seed which makes it so that the repressor is blocked, so that the recombinant gene becomes activated. Once the seed is completely soaked then it becomes resistant to certain chemicals and insects. ==

===**__Apply it:__** Many farmers use transgenic plants because it makes their crops more resilient to viruses and other environmental factors. Some farmers also find it to be more cost efficient if they use these types of plants because it also helps to make more of the much needed plant rather than some other plants that are lacking certain proteins or nutrients.===

===**__Synthesize it:__** This reminds me of how when people are sick they need to take medicine in order to get better. Just like the plants need to be transgenic plants in order to produce a better more efficient crop.===

**__Argue:__** I believe that it is a good thing to be able to produce transgenic plants because then people would be able to have more nutrients when eating their fruits and vegetables.
__**Sources: Picture; Extra Food Information; Transgenic Plants**__


 * __ Transgenic Animals __**

__**Describe it:**__ A transgenic animal is an animal that has had a gene inserted into it that has come from a different genome. This foreign gene will integrate itself into the host genome and will produce a different trait that would not have normally been produced __**Analyze** **it**__: In this process an egg is removed from a female animal. This egg will become fertilized and be allowed to grow a little. A cloned gene (transgene) from another mammal will be inserted into these cells. If the cell accepts the foreign DNA and integrates it into its genome the animal will express the gene. These transformed cells will be inserted into a mother animal and if successful the embryo will be produced to form a transgenic animal. This transgenic animal will be able to produce the specific trait when the gene that was inserted is expressed within the animal.

__**Apply it:**__ Transgenic animals serve many purposes. For example better wool can be produced from sheep or leaner meat can be made in pigs. These animals can also serve as medical factories for the traits they can produce. This happens when the specific gene inserted is largely expressed to produce it protein in large amounts. For example a blood clotting factor can be inserted into a cow sow when it produces milk the factor will be secreted into the milk.

__**Synthesize it:**__ This process reminds me of school. School inserts many ideas, facts, and theories into our heads. Some of these ideas you accept others you may reject. These ideas can help shape your future and character. Similarly the theories and ideas are like the genes being inserted into animals. These ideas can be accepted or rejected just like the foreign DNA inserted into a cell. When the animal expresses these genes for the certain protein it is like similar to how we use ideas to shape our selves or character.

__**Argue it:**__ I am for this process as long as it is not abused. The benefits of this process already is very beneficial. Once more research and this process advances, many beneficial products from this process could be used for a great good. For example if we could produce insulin in animals and then successfully insert it into people with diabetes and they could accept it, this process could help a lot of people. But this process could be easily abused. If this technique is done wrong we could be hurting animals for our benefit. Also we are directly changing nature and how things develop naturally, we don’t know if this could drastically effect the future of evolution. This process when used for medical purposes is something that should be advocated for.

__**Sources:**__ AP Bio book []

__**Resources Online:**__ []

__Gene Profile (Forensic Evidence)__
__**Describe it:**__ A gene profile is an individual’s unique set of genetic markers. These markers can be used in the identification of people. Short tandem repeats (STRs) are genetic markers that repeat units of 2-5 base sequences in regions of the genome. Using gene profiling as forensic evidence involves the processes of PCR and electrophoresis.

__**Analyze it: **__ Genetic markers vary in length and base sequences. The chances that a person has the same number of a specific STR marker definitely slims the pickings (meaning it is not common at all) Because of this uniqueness, scientists are able to identify DNA samples quickly and with only small amounts of DNA. In order for gene profiling to be used in forensic evidence, PCR is used to amplify particular STR. The primers used in PCR are labeled with fluorescent tags so when the DNA is put through electrophoresis the number of repeats and length of the region can be determined. This method to determine the number of genetic markers can be done when DNA is in poor condition or is in a very small quantity.

__**Apply it: **__ Gene profiling is used as forensic evidence. More specifically this process can be used to identify a criminal. Another use is solving the question of who is the parent of a child when a person wonders if their spouse is truly the biological parent of their child. This process was used to identify victims in the 9/11 attack. The causalities were so great and in such horrible condition that the only way to identify a person was through their DNA.

__**Synthesize it: **__ Gene profile reminds me of a barcode. In order to identify the item being bought, the item’s barcode is scanned. The barcode on an item consists of varying widths of black bars and varying of numbers of bars. Similarly a gene profile has varying number of STRs and the length of STRs can vary. These aspects of a STR help individualize and identify a person like a barcode identifies an item.

__**Argue for or against it: **__ I argue for the gene profile being used as forensic evidence. Using the gene profile is an accurate way to obtain the identity of a person. These profiles are already accepted as evidence by legal experts in criminal cases. Also the greater the number of markers recognized the more individual the profile becomes. The more known about the profile the less common it becomes. When gene profiling is accurate, efficient, and can be applicable to many various things, I can only see gene profiling being a positive thing.

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 * __Resource online:__**

AP Biology Book [| http://en.wikipedia.org/wiki/DNA_profiling]'
 * __Source:__**