Concepts Summary

RNA molecules can function as biological catalysts and may have been the first carriers of genetic information.

RNA is a polymer, consisting of nucleotides joined together by phosphodiester bonds. Each RNA nucleotide consists of a ribose sugar, a phosphate, and a base. RNA contains the base uracil; it is usually single stranded, which allows it to form secondary structures.

Ribosomal RNA is a component of the ribosome, messenger RNA carries coding instructions for proteins, and transfer RNA helps incorporate the amino acids into a polypeptide chain. Other RNA molecules found in eukaryotic cells include pre-mRNAs, the precursor of mRNA; snRNAs, which function in the processing of pre-mRNAs; snoRNAs, which process rRNA; and scRNAs, which exist in the cytoplasm.

The template for RNA synthesis is single-stranded DNA. In transcription, RNA synthesis is complementary and antiparallel to the DNA template strand. A transcription unit consists of a promoter, an RNA-coding region, and a terminator.

The substrates for RNA synthesis are ribonucleoside triphosphates. In transcription, two phosphates are cleaved from a ribonucleoside triphosphate and the remaining phosphate takes part in a phosphodiester bond with the 3'-OH group at the growing end of the RNA molecule. RNA polymerase in bacterial cells consists of a core enzyme, which catalyzes the addition of nucleotides to an RNA molecule, and other subunits, which join the core enzyme to provide additional functions. The sigma factor controls the binding of the core enzyme to the promoter; rho and NusA assist in the termination of transcription. Eukaryotic cells contain three RNA polymerases: RNA polymerase I, which transcribes rRNA; RNA polymerase II, which transcribes pre-mRNA and some snRNAs; and RNA polymerase III, which transcribes tRNAs, small rRNA, and some snRNAs.

The process of transcription consists of three stages: initiation, elongation, and termination. Promoters are recognized by the transcription apparatus and are required for transcription. They contain short consensus sequences imbedded within longer stretches of DNA.

Transcription begins at the start site, which is determined by the consensus sequences. A short stretch of DNA is unwound near the start site, RNA is synthesized from a single strand of DNA as a template, and the DNA is rewound at the lagging end of the transcription bubble.

Terminators consist of sequences within the RNA coding region; RNA synthesis ceases after the terminator has been transcribed. Bacterial cells have two types of terminators: rho-independent terminators, which RNA polymerase can recognize by itself, and rho-dependent terminators, which RNA polymerase can recognize only with the help of the rho protein.

In eukaryotic cells, DNA is complexed to histone proteins, which interfere with the binding of transcription factors and RNA polymerase. Chromatin may be modified by acetylation, chromatin-remodeling proteins, and other factors, allowing transcription factors and RNA polymerase to bind to the DNA. Two classes of sequences affect transcription in eukaryotic cells: promoters, which are adjacent to genes, and enhancers, which may be distant to the genes that they affect.

A promoter for RNA polymerase II consists of a core promoter, which is required for minimal levels of transcription, and a regulatory promoter, which affects the rate of transcription.

General transcription factors bind to the core promoter and are part of the basal transcription apparatus. Transcriptional activator proteins bind to sequences in regulatory promoters and enhancers and interact with the basal transcription apparatus at the core promoter.

The three types of RNA polymerase in eukaryotic cells recognize different types of promoters, all of which have consensus sequences that serve as binding sites for transcription factors.

The three RNA polymerases found in eukaryotic cells use different mechanisms of termination.

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