RNA Polymerases

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RNA Polymerases

RNA polymerases are enzyme complexes that synthesize RNA molecules using DNA as a template , in the process known as transcription. The RNAs created by transcription are either used as is (as ribosomal RNAs, transfer RNAs, or other types), or serve to guide the synthesis of a protein (as messenger RNAs). The word "polymerase" derives from "-ase," a suffix indicating an enzyme, and "polymer," meaning a large molecule composed of many similar parts, in this case the RNA nucleotides A, U, C, and G (abbreviations for adenine, uracil, cytosine, and guanine).

Types of Polymerases

Prokaryotic organisms (Eubacteria and Archaea) have only one type of RNA polymerase. Eukaryotic organisms (animals, plants, fungi, and protists) have three types, called pol I, II, and III, and each transcribes a different set of genes. Pol I synthesizes RNA for the large subunit of the ribosome (the protein-making machinery of the cell), and one piece of RNA for the small subunit. Pol II creates messenger RNAs, which provide a template for protein synthesis. Pol II also creates numerous small nuclear RNAs (snRNAs), which modify RNAs after they are formed. Pol III synthesizes transfer RNAs (tRNAs), the RNA for the small subunit of the ribosome, and other snRNAs.

The three eukaryotic polymerases can be distinguished in the laboratory by the degree to which they are inhibited by the alpha-amanitin poison from the mushroom Amanita phalloides. Pol I is completely resistant to its effects, pol III is moderately sensitive, and pol II is highly sensitive. (The reason this poison is so deadly is precisely because it inhibits RNA polymerase.)

Each eukaryotic RNA polymerase is composed of a dozen or more subunits. Some of these are small and unique to each type, but the two largest subunits are similar among all three polymerases, and similar as well to the two largest prokaryotic subunits. This is clear evidence that all of them evolved from the same original polymerase. These shared subunits are thought to form the functional core of the polymerases, while the smaller subunits may provide the gene specificity of each type.

Transcription

Transcription begins when RNA polymerase binds to the DNA double helix. This occurs at a site just "upstream" of the gene to be transcribed, called the promoter site. In eukaryotes, RNA polymerase is directed to the promoter site by transcription factors , proteins that bind to the DNA and provide a docking site for attachment of the polymerase enzyme. Once RNA polymerase binds to the DNA at the promoter, transcription can begin.

During transcription, the polymerase unwinds a portion of the double-stranded DNA, exposing the DNA template strand that will be copied into RNA. Individual RNA nucleotides enter the enzyme complex, and are paired with the DNA. C pairs with G, T (on DNA) pairs with A, and A (on DNA) pairs with U. Nine DNA-RNA nucleotide pairs exist within the polymerase molecule at any one time. After each new RNA nucleotide is paired, it is linked to the preceding RNA nucleotide, forming a growing strand of polymerized RNA called the primary transcript. This stage of transcription is called elongation.

Recent X-ray analysis of RNA polymerase has revealed important structural details that help explain the precise mechanism of transcription. Double-helical DNA enters a long cleft in the surface of the enzyme, and is held in place by a large flexible portion of the enzyme termed the "clamp." Within the cleft, the DNA is separated and RNA is paired to it. A magnesium ion, sitting at the critical point where RNA nucleotides are added to the primary transcript, is thought to help catalyze this reaction. An internal barrier forces a bend in the growing DNA-RNA duplex, exposing the RNA end for addition of the incoming nucleotide. A short protein extension, termed the "rudder," helps to separate the RNA from the DNA, and the two exit the polymerase along separate paths.

The average maximum rate of elongation in bacteria is 5 to 10 nucleotides per second. However, during transcription, the polymerase enzyme may pause for seconds to minutes. These pauses are thought to be part of a regulatory mechanism. Transcription continues until RNA polymerase reaches a special DNA sequence called the termination sequence, at which point it detaches from the DNA.

see also Nucleotide; RNA; RNA Processing; Transcription; Transcription Factors.

Richard Robinson