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the specific sequence of bases along the DNA strands

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If E. coli DNA polymerase was used instead of thermus aquaticus DNA polymerase in a pcr polymerase chain reaction procedure then will reaction be carried out in waterbath?

No, the reaction will not be carried out in a water bath. E. coli DNA polymerase requires higher temperatures to function optimally for PCR, typically around 72°C. Therefore, a thermal cycler with the ability to cycle through different temperatures is needed to perform PCR with E. coli DNA polymerase.


Why is a thermostable polymerase used in PCR?

The thermostable polymerase (or Taq polymerase) is a thermostable DNA polymerase (named after the thermophilic bacterium Thermus aquaticus from which it was originally isolated by Thomas D. Brock in 1965), is often abbreviated to "Taq Pol" (or simply "Taq"), and is frequently used in polymerase chain reaction (PCR). Taq polymerase is as an enzyme able to withstand the protein-denaturing conditions (high temperature) required during PCR; Therefore it replaced the DNA polymerase from E. coli originally used in PCR. Taq's optimum temperature for activity is 75-80°C, with a half-life of greater than 2 hours at 92.5°C, 40 minutes at 95°C and 9 minutes at 97.5°C, and can replicate a 1000 base pair strand of DNA in less than 10 seconds at 72°C.


What is the attachment site for RNA polymerase?

according to information from http://www.rothamsted.ac.uk/notebook/courses/guide/trans.htm " if the RNA polymerase attaches to a special sequence called a promoter, an additional small protein, the factor sigma, will also attach to the polymerase and lock it on the DNA. The factor 'sigma' will only attach itself to the complex DNA / RNA polymerase when the RNA polymerase is attached to a promoter. Another hypothesis is that the factor sigma attaches to RNApol anyway and the enzyme is then able to slide along the DNA until it finds a promoter. It prevents detaching and speeds up promoter location, and decreases the affinity of RNApol for general regions of DNA. " Therefore, the answer seems to be, RNA attaches to DNA through a small protein called the factor sigma once the RNA polymerase attaches itself to a chain sequence called a "promoter". according to information from http://www.rothamsted.ac.uk/notebook/courses/guide/trans.htm " if the RNA polymerase attaches to a special sequence called a promoter, an additional small protein, the factor sigma, will also attach to the polymerase and lock it on the DNA. The factor 'sigma' will only attach itself to the complex DNA / RNA polymerase when the RNA polymerase is attached to a promoter. Another hypothesis is that the factor sigma attaches to RNApol anyway and the enzyme is then able to slide along the DNA until it finds a promoter. It prevents detaching and speeds up promoter location, and decreases the affinity of RNApol for general regions of DNA. " Therefore, the answer seems to be, RNA attaches to DNA through a small protein called the factor sigma once the RNA polymerase attaches itself to a chain sequence called a "promoter". role of sigmaActually RNA Polymerase can bind to DNA anywhere in the entire genome but sigma factor attaches to polymerase only when it is at promotor. sigma factor dissociates when polymerase crosses promotor. sigma factor stablises the pre initiatiation complex. Actually there are many promoter and many genes but which gene to be transcribed is decided by sigma factor.


Describe the significance of Okazaki fragments?

Okazaki fragments are created during DNA replication because DNA Polymerase can only add nucleotides in a 5' to 3' direction. This means that one strand (the leading strand) can be continuously created, but the other strand (the lagging strand) runs in the opposite direction. This means that loops must be created and shorter parts of DNA replicated one at a time. This creates fragments on the lagging strand. The RNA primers on this strand are later replaced with DNA by DNA Polymerase I, and joined together with DNA ligase.


Why do enzymes work in opposite detections in replication?

In DNA replication, enzymes (DNA polymerases) work in the 3 prime to 5 prime end, creating the new strand in the 5 prime to 3 prime direction. This is due to their structure- they add bases to preexisting 3 prime anchors. Of the five carbons on the deoxyribose, the 3 prime is joined to a hydroxyl and the 5 prime is joined to a phosphate group.

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DNA polymerase is an enzyme that finctions best when itis placed in the right ionic environment. All buffers and all other constituents required for the PCR reaction are added first. The buffers ensure the maintainace of the correct ionic environment for the polymerase to function optimally. Therefore, the DNA polymerase is added last AFTER addition of template and primer


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If E. coli DNA polymerase was used instead of thermus aquaticus DNA polymerase in a pcr polymerase chain reaction procedure then will reaction be carried out in waterbath?

No, the reaction will not be carried out in a water bath. E. coli DNA polymerase requires higher temperatures to function optimally for PCR, typically around 72°C. Therefore, a thermal cycler with the ability to cycle through different temperatures is needed to perform PCR with E. coli DNA polymerase.


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