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Deoxyribonucleic Acid Synthesis - Mechanisms of DNA Repair

BY: Zandro Cabaral | Category: Bioinformatics | Submitted: 2011-01-29 20:07:56
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Article Summary: "The DNA polymerase III also proofreads the newly synthesized strands removing any incorrect nucleotide and inserting the correct one. This enzyme is supposed to correct the 1/10,000 mutations occurring during DNA replication.."


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The DNA polymerase III also proofreads the newly synthesized strands removing any incorrect nucleotide and inserting the correct one. This enzyme is supposed to correct the 1/10,000 mutations occurring during DNA replication. The 3'-5' exonuclease activity or proofreading allows checking of the new chain as it grows 5'-3' direction. The new strand being synthesized complementary to the old 3' to 5' strand is called the leading strand and can be synthesized without interruption. It is copied continuously. The new strand complementary to the old 5' to 3' strand is called lagging strand and is synthesized as fragments called Okazaki fragments, which are later joined together by ligases. The lagging strand is copied "discontinuously".

Prokaryotes have one site of initiation of replication called the "origin of replication," or replicon. In DNA repair or excision, DNA polymerase 1 recognizes the gap or the nick, removes the Ribonucleic Acid primer, and fills the gap. DNA polymerase III is responsible for synthesizing the new Deoxyribonucleic Acid. Eukaryotes have many sites at which replication of DNA may be initiated.
Deoxyribonucleic Acid synthesis always occurs in the unidirectional 5' to 3' direction. DNA synthesis always requires a primer-RNA polymerase or primase is required. However, Ribonucleic Acid synthesis does not require a primer.

There are many factors that can cause destruction and mutation to a Deoxyribonucleic acid. Some of these are the radiation and deamination which is the loss of amino group. When the DNA is exposed to these factors, certain mechanisms of DNA repair occurs. These mechanisms are:

• U.V. endonuclease removes pyrimidine-pyrimidine dimers that occur, usually between two thymines (T-T), in the same strand due to exposure to ultraviolet light. Then polymerase I or α fills in the gap with the appropriate nucleotides. Dimers can lead to mutations. Therefore, finding the mistake and repairing it is important.

• Xeroderma Pigmentosum is a disease occurring in people who cannot repair damage caused by U.V. light, often due to a defect or deficiency in U.V. endonuclease. This leads to skin cancer-malignant melanoma.

• Alkylating Agents remove -NH3 groups from A, G, or C, forming mutant bases.

• Nitrous Acid is an alkylating agent produced in cells by metabolism of nitrites and nitrates which are often used as food reservatives.

• Cytosine can spontaneously lose its -NH3 group forming uracil.

• Mutant Base Endonucleases are group of enzymes each of which recognize and remove a specific mutant base containing nucleotides.

• Mutant Base Glycosylases are enzymes which recognize and remove specific mutant nitrogen bases from their deoxyribose.

The next process is the Transcription of DNA to RNA. Here are some generalizations for RNA. RNA is single-stranded except in some viruses like Rotavirus and Reovirus. It contains ribose instead of deoxyribose, and uracil instead of thymine. Base pairing may occur within the single strand. Base pairing can occur between RNA and DNA. There are 3 types of RNA involved in protein synthesis. These are the messenger RNA, transfer RNA, and ribosomal RNA. The Prokaryotic DNA transcription to RNA occurs in the cytoplasm. It starts with a process called Invitation. It is when a short area of single stranded DNA is exposed by the binding of RNA polymerase at a site known as the promoter region. A holoenzyme, a delta factor complex, recognizes this specific DNA binding site. The promoter is the region of DNA that binds the RNA polymerase to initiate transcription. Usually the first base is a purine and is usually Adenine.

The next step is Elongation. As RNA polymerase moves along, it maintains an area of single stranded DNA on either side of it. RNA poluymerase reads the DNA strand in the 3' to 5' direction and uses triphosphate ribonucleotides to synthesize an RNA strand in the 5' to 3' direction as in DNA replication which always grows in the 5' to 3' direction. There is no proofreading in RNA polymerase since there is no RNA 3' to 5' exonuclease activity. This result in more errors when transcribing DNA to RNA compared to the relatively error-free DNA to DNA replication.
The last step is the Termination. In prokaryotes, termination of RNA synthesis is coded for by palindrome DNA sequences. RNA transcribed from these sequences can base pair within the sequence forming a hairpin loop causing termination. A DNA sequence which is representative of many promoters from different bacteria is called a Consensus Sequence.

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