Justin+Grosdidier

=// DNA Cloning/Recombinant DNA/Genetic Engineering //=

Gene Cloning with Bacterial Plasmids
__Description:__ Bacterial plasmids are circular DNA molecules that replicate separately from the bacterial chromosome. During the cloning process, researchers isolate the plasmid and then insert foreign DNA, DNA from another sourse, into the plasmid. This creates a recombinant DNA molecule. __Analysis:__ During cloning, biologists isolate the plasmids and insert foreign DNA making it recombinant DNA. This recombinant DNA is then inserted back into the bacterium where they divide and produce a population of genetically identical cells. This action replicates the plasmid and passes it on the further generations. This is called Gene Cloning. __Application:__ This has 2 basic purposes: making copies of a specific gene and producing protein products __Synthesis:__ This would be very useful if you could use it to mass produce all the favorable genes to make your body as strong or healthy as possible and to get rid of genetically transfered diseases __Importance:__ This is important because you can implant the specific genes you want and have them reproduce to prevent unwanted problems or genetic issues.

Link: [] Sources: AP Biology Book, []

Nucleic Acid Hybridization
__ Description: __ Uses complementary molecules, short single-stranded nucleic acids, that can be either RNA or DNA to detect the genes's DNA by its ability to base-pair with the complementary sequence. The complementary molecule is called a nucleic acid probe. __ Analysis: __ Uses a nucleic acid probe to detect the gene's DNA by its ability to base-pair with the probe. If you know part of the nucleotide sequence of the gene, you can create a complementary probe for it. In the process, the 2 DNA strands are denatured by heating them to the point of the helix separating (a to b). The strands are then renatured (b to a). This creates a hybrid strand of DNA or RNA __ Application: __ You can use hybridization to find a specific gene in population and track it. __ Synthesis: __ This action makes me think of a metal detector. It is attracted to only specific nucleotides like how a metal detector searches for metal objects and notifies you when it finds one __ Importance: __ This is helpful because it can be used to track the trail of a gene to possibly locate problem areas that gene could lead to



__﻿ Link: __ __ [] __ __ Sources: __ AP biology book, []

Genomic Library
__ Description: __ The genomic library is the complete set of plasmid-containing cell clones, each carrying copies of a particular segment from the initial genome. Thousands of recombinant plasmids are produced during the cloning process, and a clone of cells, and a clone of cells carrying each type of plasmid becomes a white colony. Each plasmid clone in the library contains specific infromation __ Application: __ Today scientists can store genes in these libraries and go back during later research or even present these libraries to other scientists. __ Synthesis: __ Genomic Libraries work much like real libraries that we all use with each plasmid clone being a book. Similar plasmids are grouped together just like the sections of a library. __ Importance: __ This is very useful in the research fields to be able to conviently find a specific plasmid needed to study or test on. It is nice to have these readily available.

__ Link ____ : __ __ [] __ __ Sourses: __ AP Biology Book

Polymerase Chain Reaction (PCR)
__ Description: __ This technique is quicker and more selective than DNA cloning. It is best used when the DNA source is scanty or impure. With automation, PCR can make billions of copies of a targeted DNA segment in only a couple hours. __ Analysis: __ In this technique, any specific target segment within one or many DNA molecules can be quickly amplified. PCR involves a three-step cycle. First ther mixture is heated to denature the DNA strands and then cooled to allow bonding of short, single-stranded DNA primers complementary to sequences on opposite strands at each end of the target sequence, and finally a heat-stable DNA polymerase extends the primers in the 5' to 3' direction. __ Application: __ This process can be used to quickly make a large amount of DNA molecule copies in a test tube. __ Synthesis: __ This is like using the table of contents to skip to a desired part of a book, bypassing all the unneeded information and steps. __ Importance: __ This can greatly speed up the process when you don't have the time to create an entire genomic library

__ Link: __ __ [] __ __ Sources: __ AP Biology Book

= Studying Expression and Function of Gene =

Gel Electrophoresis
__ Description: __ Gel Electrophoresis uses a polymer gel such as a polysaccharide. __ Analysis: __ The gel works as a sieve to separate nucleic acids or proteins by size, electrical charge, and other properties. Nucleic acid molecules are negatively charged on their phosphate groups so they travel toward the positive pole of the electric field. As they move, the polymers slow down the longer molecules more than the shorter ones and separate them by length into bands consisting of DNA molecules of the same length __ Application: __ One application is restrictino fragment analysis which provides useful information about DNA sequences. It also sort of groups the DNA molecules into bands with molecules of the same length. __ Synthesis: __ This reminds me of a strainer where it has more effect on larger things than small ones. The small molecules can move through the fibers easier while the larger ones meet more resistance. __ Importance: __ This allows you to get quick and easy information about DNA sequences as well as protein and nucleic acids. It works to group the DNA molecules.

__ Link: __ [] __ Sources: __ AP Biology Book

Southern Blotting
__ Description: __ Southern Blotting was developed by the British scientist Edwin Southern. This combines gel electrophoresis and nucleic acid hybridization. The principle is pretty similar to nucleic acid hybridization for screening clones, and the probe is usually a radioactive single-stranded DNA molecule complementary to the desired gene. __ Analysis: __ This procedure allows scientists to dectec only the bands that include parts of the B-globin gene. This involves 5 steps: preparation of restriction fragments, gel electrophoresis, DNA transfer also called blotting, hybridization with radioactive probes, and probe detection. __ Application: __ This results in band patterns that are clearly different. This method can be used to identify heterozygous carriers of the sickle-cell allele, as well as people with the disease. __ Synthesis: __ This could be used to identify a variety of different diseases and disorders such as cancer by isolating the desired DNA molecules. __ Importance: __ One disadvantage I could see in this method would be that it would take a long time because it uses both gel electrophoresis and hybridization __ Link: __ __ [] __ __ Sources: __ AP Biology Book, []

Microarrays
__ Description: __ These make genome-wide expression studies possible. These consist of timy amounts of many single-stranded DNA fragments that represent different genes which are fixed to a glass slide in a tightly spaced grid. __ Analysis: __ In a perfect setting, these fragments represent all the genes of a certain organism. The fragments are tested for hybridization with cDNA molecules prepared from mRNAs in certain cells and labeled by fluorescent dyes. __ Application: __ This process is used to measure the expression of many genes across a genome. They can use this gene information to research gene development in many different organisms __ Synthesis: __ This could be used to look at the differences between the expression of certain genes in a healthy person, and the genes in a person with some disorder. You could possibly use these differences to alter the expression of the genes to prevent certain disorders or diseases. __ Importance: __ This allows you to look at many if not all the genes in a genome instead of just a select few at a time. __ Link: __ [] __ Sources: __ AP Biology Book, []

= Cloning Organisms =

Plant Cloning
__Description and Analysis:__ Plant cloning is used to create plant specimans that are genetically identical to the parent. Differentiated cells are taken from the root and incubated in culture medium to grow normal adult plants. This showed that differentiation is not necessarily irreversible and that some plants can dedifferentiate and give rise to the specialized cell types of the organism. These cells are sait to be totipotent. __Application:__ Plant cloning is used all the time in agriculture. For many plants, cloning is the only logical way of reproduction for sale use. This is also used to produce a plant with valuable characteristics. __Synthesis:__ Plant cloning reminds me of copying homework. It is a fast and easy way to get stuff done and the end product is the an exact replica of the other persons work. HAHA __Importance:__ Plant cloning is important because it allows you to create an exact replica of the parent. This means that if you have a plant that you are getting good growth and production from you can create many of the same exact thing to maximize your yeild. This is very helpful to farmers. __Link:__ [] __Sources:__ AP Biology Book

Animal Cloning
__ Description and Analysis: __ Differentiated cells in animals usually won't divide or develop in culture. Because of this, scientists must use a different process when it comes to animal cloning called Nuclear Transplantation. In nuclear transplantation, the nucleus is taken out of an unfertilized or fertilized egg and replaced with the nucleus of a differentiated cell. This was successful but the age of the donor had an effect on the the development. __ Application: __ This could be used to clone endangered species. It could also be used by farmers who want to raise livestock with specific traits that make them superior. __ Synthesis: __ It would be much better if we could design a version of this cloning that would decrease the rate of defects and develpoment problems. __ Importance: __ I'm not a big fan of animal cloning. Yes the possiblilties of this technology could be endless, but you know that once this is worked out and most of the kinks are resolved they are going to start talks on human cloning which I think is ethically wrong and should never happen. __ Link: __ [] This is an article about the pros and cons of animal cloning. __ Sources: __ AP Biology Book

=﻿ Practical Application of DNA =

Restriction Fragment Length Polymorphism (RFLPs)
__Description and Analysis:__ RFLPs the result of SNPs or Single nucleotide polymorphisms. SNPs alter the sequence recognized by a restriction enzyme just like how there is a single-nucleotide difference between the allele for sickle-cell glovin and the normal allele. These create change in the lengths of the restriction fragments during digestion with the enzyme. This sequence change can happen in either coding or noncoding regions. __Application:__ RFLPs and SNPs can help us diagnose certain genetic disorders by the presence of an abnormal allele __Synthesis:__ This reminds me of entering a password wrong. If you have just one letter in the wrong spot it will change the entire word and not work right. __Importance:__ If there were no RFLPs and no sequence changes like these that would get rid of many genetic disorders that harm millions of people around the world.

__Link:__ [] __Sources:__ AP Biology Book

Gene Therapy
__ Description and Analysis: __ Gene Therapy holds enormous potential for treating single defective gene disorders. This is the practice of introducing genes into an afflicted individual for therapeutic purposes. According to theory, a normal allele of the harmful gene could be inserted into the somatic cells of the affected tissue. For this to be permanent, the cells that receive the normal allele must be ones that multiply throughtout the patient's life. __ Application: __ These new techniques could be used to reverse any number of single defective gene disorders __ Synthesis: __ It would be better if they could be used to reverse all genetic disorders not just ones of with only one defective gene __ Importance: __ With more research and advances this could be used as a very effective treatment for many genetic disorders

__ Link: __ [] __ Sources: __ AP Biology Book, []

Transgenic Animals (Genetically Modified Organisms-GMOs)
__ Description and Analysis: __ Sometimes scientists can use whole animals to produce large quantities of protein product. Scientists can introduce a gene from an animal of one genotype into the genome of another, ofter of a different species. This individual is now a transgenic animal. This is done by removing eggs froma female and fertilizing them in vitro. They then inject the desired clone DNa into the nuclei of the fertilized eggs. The engineered embryos are then implanted in a surrogate mother to hopefully develop into a transgenic animal containing a gene froma third "parent" possibly of a different species. __ Application: __ These can be used to produce large quantities of protein products. __ Synthesis: __ This would be better if you could put multiple desired genes from the third "parent" animal into the new engineered speciman. __ Importance: __ This is important because the new transgenic animals can now act as a kind of pharmaceutical "factory" producing large quantities of a desired protein.

__ Sources: __ AP Biology Book, []

Transgenic Plants (Genetically Modified Organisms-GMOs)
__ Description and Analysis: __ A transgenic plant is a plant that contains genes that are artificially inserted of aquiring them naturally. The inserted gene may come from a relative of that plant or even from a completely different species. __ Application: __ Transgenic plants are used all the time in farming. Scientists are also beginning to develop "pharm" plants with new medical advantages. __ Synthesis: __ Similar to animals, it would be better if you could insert multiple genes into the new engineered plant. __ Importance: __ This is very important because of all of the uses in the agriculture industry. Pretty much all crops now days are genetically modified. __ Sources: __ AP Biology Book, []

Genetic Profiles (DNA forensic testing)
__ Description and Analysis: __ The genetic profile is like an individual's "DNA fingerprint". It is made up of every individual's unique set of genetic markers. These markers are used in DNA testing mainly for identification purposes. __ Application: __ Genetic profiles are used everyday in the forensic science field. They can be used for identification in crime cases and are extremely accurate because every person has their own unique DNA sequence __ Synthesis ____ : __ Genetic profiles use pretty much the same principle as a regular old fingerprint. They are used for identification and every person has their own unique set. __ Importance: __ This is very important to forensic scientists. It makes their job of crime solving so much easier and more accurate which is good because you want to make sure you have the right person.

__ Link: __ [] __ Sources: __ AP Biology Book, []