Bailey+Eich

=** Part 1﻿ ** = ==** DNA Cloning/Recombinant DNA/Genetic Engineering﻿ ** ==

===**Gene Cloning ** ===

Describe : Biologists take a certain favorable DNA code and construct it to work with a plasmid. After the favorable code is turned, they can replicate it as many times as they like.
=== Analyze: The DNA from an organism is transferred to this self-replicating bacterial plasmid.This plasmid is a circular, double-stranded DNA molecule that is replicated separately from the bacterial chromosome. This vector can then carry the fragment to the host and start cloning. Learn more about the steps of cloning [|here]. ===

** Nucleic Acid Hybridization **
Describe: Nucleic acid hybridization is combining two complementary strands in a non-covalent bond. This can happen for DNA-DNA DNA-RNA or RNA-RNA.

Analyze: The hybrids are heated to break the hydrogen bonds between nucleic bases after the strands are separate. The process is repeated to be a longer strand that can be made into a polymerase chain reaction.

Apply: The process can help find a certain gene in a strand.

Synthesize: The nucleic acid hybridization is like an investigator finding and solving mysteries. The Hybridization goes in and finds a specific gene that is wanted. Then, it goes through a process just like a detective or investigator goes through certain steps to slove the mystery.

Argue: This could be used to find and remove DNA that causes deadly diseases. Again, this can improve and/or save lives. Learn more about diseases tested with nucleic acid hybridization [|here].

Genomic Library
== Describe: This is also called a clone bank or gene bank. The different sizes of DNA in a certain organism are selected and then digested to be put into a vector or a plasmid (talked about earlier). The vectors then go to their hosts and inject the DNA. ==

Analyze : Bacteriophages are often used in genomic libraries. The DNA is consumed by an enzyme called the endonuclease restriction enzyme. Then phages or vectors carry the large DNA.
Apply : The library is made for the storage of the phage clones. Learn more about the genomic library and phages [|here].

Synthesize: The genomic library reminds me of a library, but also a storage unit. The clones are intended to be used, just not now. The storage unit stores the genes until the vectors inject them into the host.

Argue: I really can't argue against this, it looks like scientists are researching and finding ways to look at cancer tissue and help other organisms.

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Polymerase Chain Reaction (PCR)
Describe: The PCR is a fast way to replicate many specific DNA. The PCR is a technique used in a test tube and makes billions of copies in a few hours.

Analyze: The reaction starts as a chain reaction. The procedure has three-step cycles that first heat the DNA to denature the strands, then cool to let the hydrogen bond connect short strands. Lastly, the DNA polymerase used can withstand the heat of the first cycle is used to extend primers. Each cycle yields double the last. This adds up fast! Learn more in detail about the steps of PCR [|here].

Apply: The Polymerase Chain Reaction is used to replicate genes fast with a result of trillions of copies.

Synthesize: The PCR reminds me of a family of rabbits. The parent bunnies find a home and then go crazy! The babies look like copies of the parents, and end up growing and doing the same thing.

Argue: PCR was discovered and used to study a 40,000 year old wolly mammoth. It also can answer questions like: Are all alleles the same or do they differ from people to people, and Where is the gene located on the genome? media type="youtube" key="HMC7c2T8fVk?fs=1" height="385" width="480"

Gel Electrophoresis
Describe: ﻿Gel electrophoresis is used to separate DNA, RNA, nucleic acids or proteins based on physical properties. As the molecules separate polymer fibers effect the longer sections more than the smaller sections, this separates them by size. THen they can be compared and analyzed.

Analyze : DNA is separated to look at different properties such as size, electric charge, and other properties. The gel used is a crosslinked polymer that forms a solid yet its porosity is based on the specific molecule. The gels are composed of agarose, polyacrylamide, or starch.

Apply: Gel electrophoresis is often used after PCR to further analyze the characteristics.

Synthesize : Gel electrophoresis first reminded me of panning for gold. The miner goes out in search for a specific metal, which is gold, and goes to the river to dig up dirt and run water through the pan until he sees the glimmer of the gold.

Argue: Gel electrophoresis is used in forensics to retrieve the DNA from a criminal. They can analyze and compare the DNA from the scene to the suspect! Also, in genetics it prepares DNA for cloning. Learn more of the uses of gel electrophoresis [|here]. media type="youtube" key="_uoPkavtXgs?fs=1" height="385" width="480" Sources [|Gel Electrophoresis uses] [|Gel Electrophoresis wikipedia] AP Biology 7th Edition

Southern Blotting
Describe: ﻿Southern Blotting is a combination of nucleic acid hybridization and gel electrophoresis. Southern Blotting is used to compare alleles of a certain gene. It shows a particular sequence in the gene and the size of the restriction fragments.

Analyze : Southern Blotting separates the DNA is digested with an enzyme and then go onto a agarose gel to be separated. The DNA is filtered by a film and radio active nucleic acid probe binds to certain DNA segments. Scientist then observe and compare the genes to each other. Learn more [|here].

Apply: Southern Blotting is used to compare nucleotide sequences within DNA.

Synthesize : The process of southern blotting reminds me of the process of buying a car. A person has an idea of the car they want, and usually have their selection down to two or three certain cars. Out of these two or three cars they find out everything they can and then start to compare and pick which car suits them the best. Southern blotting is narrowed down to a segment and then compares between different alleles.

Argue : Comparing different alleles help scientist learn more about each one. They compare normal to mutated and this helps to learn more about the mutation that can be fatal to humans. With new knowledge, the scientist can work to find a cure. media type="youtube" key="6FjjjATsr50?fs=1" height="385" width="480" Sources AP Biology Book 7th Edition

Microarray
Describe: Microarray is used to test many different genes and compare the tiny amounts under different environmental conditions or developmental stages.

Analyze: Tiny amounts of single-stranded DNA of different condtions are fixed to a slide in an array or grid. The fragments are tested for hybridization with samples of cDNA molecules prepared from mRNAs in cells that are dyed to show differences. Learn more about the arrays and process [|here].

Apply: Microarrays display gene interactions and show gene function to help understand diseases.

Synthesize: ﻿Microarray reminds me of shopping for a prom dress! A girl tries on a dress and looks into the mirror. She imagines herself getting pictures taken, eating and dancing. She imagines different conditions, and through a million dresses she finally finds the dress that makes her feel perfect! In microarrays genes are compared and dyed to show differences and comparisons.

Argue: Microarray is doing a lot to compare patterns of gene expressions in breast cancer tumors and non-cancerous tissue. This results in more effective treatments. Sources AP Biology Book 7th Edition

= =

Cloning Organisms
= Plant Cloning = Describe : Cloning plants is not a new discovery, plants have been cloning for thousands of years as well as people taking parts of plants and growing the same plant from that piece. Recently though, scientists can take desirable traits from different plants and create the "perfect plant". Analyze: Scientists take a vector to introduce a gene onto the cells with a plasmid called the Ti plasmid. The plasmid integrates DNA into the plant DNA and produces a transgenic plant. This introduction into the cells is done by electroporation. These favorable traits include making plants resistant to harmful bugs and improving nutritional values in plants. Apply : Cloning plants can be used to create stronger, healthier and more helpful plants. Synthesize: Scientist cloning always reminds me of the making of Frankenstein's monster. The scientists find all different desirable traits and put them all into one single plant like when Frankenstein took different body parts and stuck them all together to make one man (or monster). Learn more about the desirable traits in Frankenstein's monster [|here]. Argue: I agree with cloning stronger, healthier plants. There is a transgenic rice plant that contains a load of vitamin A. This plant is being fed to tons of young kids in Southeast Asia that suffer from a vitamin A deficiency. Sources: AP Biology Book 7th Edition [|How cloning works!]

Cloning Animals
Describe : A cloned animal is made by injecting foreign DNA into the nuclei of an embryo. The cells integrate the DNA into their genomes and express the desirable gene. Analyze: Cloning animals is introducing a gene from one animal into the genome of another animal. Two types of animal cloning are DNA cloning, reproductive cloning. In DNA cloning the interested DNA is transferred from one organism to the next by plasmids. Reproductive cloning takes DNA from an adult cell to and egg and then is treated with chemicals or electric currents. The egg is cultured until it can be injected into a female animal. Apply: Cloning animals can create stronger, healthier organisms that can help humans. Argue: There are pros and cons of cloning animals and of course humans. I can't really say yes or no. I can agree cloning stems cells to help save lives is good, but taking control of human and animal lives to trace and manipulate all their life can get risky and very controversial. Learn more about the pros and cons [|here]. media type="youtube" key="Jy15BWVxTC0?fs=1" height="385" width="480" Sources: [|Cloning Animals] [|How cloning works] AP Biology Book 7th Edition

= Part 4  = = =

Practical Applications of DNA Technology
= Restriction Fragment Length Polymorphism (RFLPs) = Describe: DNA nucleotide sequences of homologous chromosomes have different lengths of restriction fragments produced by restriction enzymes. These differences in the DNA sequences can help to find disorders and diseases. Analyze: The differences in DNA sequences can be caused by mutations in the sites where the enzymes link. These enzymes can change the lengths, numbers and production of DNA fragments. The differences are called polymorphisms and are used in DNA typing. In the process of RFLP electrophoresis and southern blotting is used. Apply: RFLPs can be used in disease status and genetic mapping. Synthesize: RFLP is like a GPS. In using the enzymes like a GPS, it can tell you what you want to know and guide you to your destination. Argue: I can't argue against RFLP. It is used to solve crimes and help to discover diseases and paternity. Learn a little more about how RFLP can help at a crime scene [|here]. Sources: [|RFLP uses] [|RFLP defintion] [|RFLP understandable definition]

Gene Therapy Transgenic Animals (GMOs)
Describe: Proteins in genes are very important to the body. If a protein cannot function properly, disorders occur. Gene Therapy corrects genes that do not function properly. This is done much like cloning in a normal gene replaces a gene that doesn't contribute positively to the organism. Analyze: Scientists can take many different approaches to fixing a genetic disorder. They can insert a normal gene into a nonspecific location to replace the faulty gene. Learn more about this process [|here].They can swap genes through recombination or use selective reverse mutation which repairs the dis-functional gene. Apply : Gene Therapy is used to cure diseases and disabilities. Synthesize: Gene Therapy reminds me of exchanging a christmas or birthday gift! You receive a gift from your parents just like you receive the gene. You don't like the gift so you go to the store with the receipt and ask to exchange for something that would benefit you better. Argue: I think that after more research this could be very useful in curing diseases and disabilities. Right now they cannot sell gene therapy because of the short-lived cures and human immune systems job to attack this foreign invader. Sources: [|Gene Therapy]

Gene Therapy Transgenic Plants (GMOs)
Describe : Gene Therapy in plants is much like that in animals and humans. Just like in human cells, the integrating vector is equipped with a promoter to complete the expression. Analyze: In plants, the plasmid is used to transfer the specific genes and integrate the plasmid sequence into the plants chromosome. Apply: This is used to produce greater amounts of healthier, stronger plants. Synthesize: Again, this is like exchanging a gift at the store. Argue: And again, this seems like a great idea but scientists are still trying work out the problems and gene therapy is definetly still in experiments. Learn more about the development in Gene Therapy [|here]. Sources: [|Gene Therapy in Plants]

Genetic Profiles (DNA forensic testing)
Describe: DNA profiling is a procedure to identify an individuals DNA profiles. These profiles are different for every single peerson and and can help forensic testing and criminal investigation. Genetic profiles are also used to prove or disprove paternity. Analyze: In this forensic and investigation process the method uses a sample of blood, saliva or semen. Any fluid or tissue from one person. Next a restriction enzyme is used while southern blotting and polymorphism or the polymerase chain reaction are used soon after the enzyme digestion. Investigators can then use the allele lengths or in the PCR the colored spots correspondence. Apply: This is used in criminal investigations and paternity tests, as well as forensic testing. Synthesize: Genetic profiles remind me of fingerprinting. Instead of fingerprinting they can take evidence of the fluids or tissues at the crime scene to know exactly who committed the crime. Argue: I have no arguments against the DNA profiling. Solving investigations is awesome! Learn more about forensic science and DNA profiling [|here]. Sources: [|DNA profiling wikipedia]