Why is a cap added to mRNA, but not to tRNA or rRNA? Transfer RNA and rRNA exhibit complex structures with double stranded regions. The three-dimensional shapes of these molecules keep the 5' end of the RNA away from the enzymes that process the cap. RNA polymerase II transcribes mRNA, whereas RNA polymerase I transcribes rRNA, and RNA polymerase III transcribes tRNA. The domain that assists other enzymes in adding the cap is found in RNA polymerase II only. Messenger RNA is transcribed and processed in the nucleus, where it can interact with the cap binding proteins that transfer the cap to the 5' end. Transfer RNA and rRNA are transcribed and processed in the cytoplasm and do not encounter capping enzymes. Only mRNA contains introns. Capping occurs simultaneously with intron removal because the same enzymes and proteins involved in both of these processes must bind to RNA at the same time.