Binding Of RNA Polymerase To A DNA Promoter Biology Essay

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DNA (deoxyribonucleic acid) is a macromolecule located in the nucleus of all cells. Its function is to instruct a cells activity, with coding the production of proteins, which are carried out by genes. For this to happen the DNA must first be copied into RNA (ribonucleic acid). DNA has four nucleotide bases, adenine(A), guanine(G), cytosine(C), and thymine(T), and they pair up as (A-T) and (C-G), giving DNA its double helical shape. However with RNA, uracil (U) is used in place of thymine, and pairs with adenine, forming (A-U). The synthesis of proteins starts with the process, transcription. Transcription is the first stage of transcribing DNA into RNA, using the enzyme RNA polymerase to produce the mRNA (messenger RNA). There are four stages to transcription, first being binding, then ignition, elongation, and the last being termination.

The binding of RNA polymerase to a DNA promoter is the first step in transcription. In prokaryotes, RNA polymerase specifically knows where to bind to the promoter. This is where a specific sequence of a few dozen base pairs decides where the synthesis of DNA begins and what strand DNA strand should be used as the template. This sequence happens in the direction of 5'- 3' of the coding strand. When the DNA polymerase and promoter have bound together by the sigma subunit, there are two separate exposed strands of DNA, through the unwinding of the DNA. In this next stage, initiation, one of the exposed strands of DNA will be used to synthesis the RNA, using the incoming substrates, ribonucleoside triphosphate molecules (NTPs). The promoter sequence then decides which DNA strand is to be transcribed, by working out which way the RNA polymerase should face when transcribing. When the first two arriving NTPs are hydrogen bonded to the matching bases of the DNA strand, the RNA polymerase is quickly catalysed to form a phosphodiester bond between the first NTP 3'-hydroxyl group and the 5'-phosphateof the second NTP, present with release of the pyrophosphate (PPi) (Becker et al., 2006). When RNA polymerase moves along the promoter, further nucleotides are added, linking the 5'-phosphate of the new nucleotides to the 3'-hydroxyl group of the increasing RNA chain. About nine nucleotides down the chain, the sigma factor separates from the RNA polymerase, causing initiation to finish. In elongation, the RNA molecule travels along the DNA template strand in the direction of 3'-5', causing the helix to unwind, adding a matching nucleotide to the increasing RNA chain. Elongation happens in the 5'-3' direction, with the RNA chain base pairing with the DNA template strand, forming a RNA-DNA hybrid, as the RNA polymerase moves along the template, the DNA in front is unwound to allow the RNA-DNA hybrid to form and the DNA behind is rewound into a double helix again(Becker et al., 2006). Elongation is then stopped when termination signal is copied, causing the final stage of transcription, termination. Prokaryotes have two termination signals and it all depends whether they need the help of the rho factor protein or not. The rho factor is not needed when the RNA molecule has a sequence that is plentiful in GC with a few U residues close to the 3' end of the RNA. The three hydrogen bonds holding the GC bonds together and the two hydrogen bonds holding the AU base pairs together, cause the RNA to suddenly fold into a hairpin loop[, causing the RNA molecule to detach from the DNA and the U residues to break away from the DNA template, freeing the newly formed RNA molecule (Becker et al., 2006). The RNA molecules that are not GC rich need the help of the rho factor to terminate transcription. Now the newly formed RNA molecule is ready for instant use as a mRNA to be translated.

Transcription in eukaryotes is the same as for prokaryotes, but it is more of a complex process. Unlike prokaryotes, eukaryotes use three different RNA polymerases to transcribe DNA, and the binding of RNA polymerase needs the aid of transcription factor proteins. After termination, eukaryotes have to go through a modification before he mRNA can be translated. Also transcription in eukaryotes happens in the nucleus, where it the moves to the cytoplasm to be translated, whereas prokaryotes transcribe and translate both in the cytoplasm. In eukaryotes the initiation of transcription and the binding of RNA polymerase are done by a group of transcription factors. The transcription initiation is when the RNA polymerase II binds to the promoter when transcription factors have joined to it. Now the DNA strand starts unwinding (Campbell et al., 2008). In elongation the two exposed DNA strands are base paired with the RNA nucleotides in the direction of 3'-5', the RNA is then detached from the DNA template, with the DNA reforming back into its double helix again. In eukaryotes the polyadenylation (AAUAAA) makes the RNA polymerase II to transcribe a sequence on the DNA, causing the pre-mRNA to be freed from the RNA polymerase. Now the pre-mRNA needs to be modified before it can be translated. The 5' end of the pre-mRNA gets a 5' cap, which is a modified (G) nucleotide added to the first 20-40 nucleotides, and the 3' end receives about 50-250 (A) nucleotides forming a poly A tail (Campbell et al., 2008). These modifications help the mRNA transport out the nucleus, protection from damage, and helps ribosomes to attach to it when it reaches the cytoplasm. Most eukaryotic genes are non-coded that will not be translated, so the RNA transcript is split into parts of non-coding (introns) and coding segments (exons) (Campbell et al., 2008). The process of splicing is when the introns are cut out of the transcript and the exons are joined together, making a continuous mRNA molecule. Now the mRNA is complete and can now be transported into the cytoplasm, where it can be translated.