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TAMU BIOL 213 - DNA repair and Transcription
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BIOL 213 1st Edition Lecture 15 Outline of Last Lecture I. DNA replication modelsa. Explanation of the three modelsb. Mesleson-Stahl experiment tested these modelsII. DNA replicationa. Origin of replicationb. Replication forki. Leading and lagging strandii. Okazaki fragmentsc. Essential proteinsIII. DNA repaira. DNA polymerase proofreadingOutline of Current Lecture I. DNA mismatch repairII. Chemical damage to DNAa. Leads to mutationsIII. General mechanisms of DNA repaira. Recognition and excisionb. ReplacementThese notes represent a detailed interpretation of the professor’s lecture. GradeBuddy is best used as a supplement to your own notes, not as a substitute.c. Joining IV. Different methods of replacementa. Recombinationi. Homologousii. Non-homologous1. Transposons V. Viruses use non-homologous recombination when inserting their DNA into the host’s DNAa. Retroviruses VI. Transcriptiona. In prokaryotes vs in eukaryotesCurrent LectureI. DNA mismatch repaira. When there’s a DNA base pair mismatch, the repair proteins will recognize it because it doesn’t “feel right”b. They’ll cut out the section of the DNA from the nick to a little bit past the mismatchi. It knows to start at the nick because newly synthesized DNA tends to havenicks in it where the ligase hasn’t joined the two strands together yetc. New DNA will by synthesized by DNA polymerase and joined by ligaseII. Chemical damage to DNAa. DNA base pairs can be completely removed by a chemicali. Depurinationii. This leaves only the sugar-phosphate backboneb. Base pairs can be replaced by other, incorrect base pairsi. Deaminationc. These damages can lead to mutationsi. Depurination: this will lead to a skipped base pair in one of the daughter DNA moleculesii. Deaminated: this will lead to a mismatch in one of the daughter DNA moleculesIII. General mechanisms of DNA repaira. Recognition and excisioni. Damaged DNA is recognized and removedb. Replacementi. DNA polymerase replaces the mutated DNA with new DNA by using the other strand as a templatec. Joiningi. Done by ligaseIV. Different methods of replacementa. Recombinationi. Homologous1. Each cell has two copies of the same chromosome2. If one copy is really badly damaged, the cell can use the good section of the other undamaged chromosome as a template3. The good section of DNA will be cut out of the undamaged chromosome and moved to the damaged chromosome4. The good DNA will attach to the damaged chromosome on each side of the damaged DNA and start base pairing with the damagedchromosome5. The damaged DNA will be cut out of the damaged chromosome6. DNA polymerase will replace the other strand of the bad DNA by using the good DNA as a template7. DNA polymerase will also synthesize new DNA for the undamaged chromosome and fill in the gapii. Non-homologous recombination1. DNA exchange that doesn’t depend on the base pair sequencea. It doesn’t have to be the same like in homologous recombination2. Transposons a. “jumping genes”b. These are pieces of the genome that move from one section of DNA and insert themselves into another piece ofDNA by two methods:c. Cut-and-paste nonreplicative transpositioni. There is one copy of the transposon and it moves from one piece of DNA to anotherd. Replicative transpositioni. One copy is in a piece of DNA and it replicates itselfii. The copy is inserted into another piece of DNA while the original transposon doesn’t movee. If a transposon jumps around too much, it will kill the host,which is bad for the transposon because then what it’s coding for can’t be synthesizedf. Transposons may cause more mutations than normali. This could cause an increase in diversityg. Retrotransposons i. These move DNA by using and RNA intermediateii. Their DNA is used as a template to create a strand of RNA by RNA polymeraseiii. This RNA is then used as a template to create a copy of their DNA by reverse transcriptase1. THIS VIOLATES THE CENTRAL DOGMA OF BIOLOGY because DNA is being synthesized from RNAiv. The DNA is then inserted into the genomeV. Viruses use non-homologous recombination when inserting their DNA into the host’s DNAa. This is the key in bacteriophage reproductioni. Remember that bacteriophages were used in the Hershey-Chase experiment the determine whether the genetic material was DNA or proteinsii. The viruses inject their DNA into the host cell where the viral DNA is inserted into the host DNAiii. This viral DNA codes for viral proteins, which the cell makesiv. When the host cell replicates, it also replicates the viral DNAv. Lysogenic phase1. The host cell keeps replicating and synthesizing viral proteinsvi. Lytic phase1. The viral components inside the host cell come together to create viruses2. The viruses burst out of the host cell, killing itb. Retrovirusesi. These are present only in eukaryotic cellsii. They contain RNA as their genetic material instead of DNAiii. They insert RNA and reverse transcriptase into the host celliv. The reverse transcriptase synthesizes DNA from the RNA templatev. The DNA molecule is completed by the host cell’s DNA polymerasevi. The viral DNA is then inserted into the host’s genomevii. The viral DNA codes for capsid proteins, envelope proteins and reverse transcriptase1. All of which are made by the host cellviii. There are drugs that inhibit viral DNA synthesis1. Acyclovira. Inhibits synthesis of the Herpes virus DNAb. It resembles a G nucleosidec. The drug is nonpolar so it can diffuse through the cell membraned. When it gets in the cell, it’s phosphorylated so that it moreclosely resembles a nucleosidee. The Herpes DNA polymerase isn’t very selective so it will pair the Acyclovir with a C when creating DNAi. Our DNA polymerase is more selective so it won’t use Acyclovir as a Gf. Since the Acyclovir molecule doesn’t have a 3’ -OH, no more nucleosides can be added to it, and synthesis stops2. Azidothymidinea. Inhibits the synthesis of the HIV virus DNAb. The drug is nonpolar so it can diffuse through the cell membranec. When it gets in the cell, it’s phosphorylated so that it moreclosely resembles a nucleosided. The HIV reverse transcriptase isn’t very selective so it will use Azidothymidine instead of thymine when pairing with an Ai. Our DNA polymerase is more selective so it won’t use Azidothymidine as a TVI. Transcriptiona. It amplifies genetic information by making several copies of the same protein that one area of DNA codes fori. The amount of protein


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TAMU BIOL 213 - DNA repair and Transcription

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