RNA Transcription: the process of copying one of the two strands of DNA into messenger RNA (mRNA). (Kandel, 258) The process of turning on, or activating, a gene. (GNN)
Transcription requires changes in “chromatin” structure that allow “transcription factors” to gain access to and “bind” to the DNA in the “promoter region.” (Brooker, 270) During transcription, "mRNA" forms opposite a portion of one side of the DNA that corresponds to a "gene." (Batiza, 21) Transcription does not permanently alter the structure of DNA. (Brooker, 235) DNA is transcribed in the "nucleus" into messenger RNA, which is then exported to the “cytoplasm” for "translation" into protein. (Watson, 77) Uses the language of "nucleic acids." The protein coding sequence is interrupted by "introns" that (are) included in the first mRNA copy of the gene, but then naturally cut out of that mRNA in a process called “splicing.” The processed mRNA that leaves the nucleus therefore, has no introns. (Batiza, 40) Also referred to as ‘transcription,’ ‘gene transcription,’ and ‘mRNA synthesis.’
Cap: short sequence of modified "nucleotides." Adds “methyl groups’ (to the sequence) The methylated cap is a recognition site for protein synthesis. (Lewis, 184) The cap is placed on the 5’ end of the (mature RNA) strand to be processed. The cap protects the strand and facilitates export of the strand from the nucleus. Also acts as an attachment signal for the small "ribosomal subunit" in the cytoplasm. (Norman Lectures, 7/22/09)
Poly A-Tail: placed on the other end of mRNA, which protects the strand from degradation. (Norman Lectures, 7/22/09) Virtually all mRNAs have a number of adenylate ‘residues’ (AAAAA etc.) at their 3’-end, referred to as the 'poly A-tail.' These A's are not encoded in the genes. Instead, the pre-mRNA is cleaved at a defined site and a 'poly A polymerase' adds 150-200 adenylate residue (nucleotides). (Nobel, Education)
Promoter Region: a specific site in a gene’s DNA. The point on the structural gene where transcription occurs. (Kandel, 257) Sequence that signals the start of the gene. Guides enzymes that carry out DNA replication, transcription, or translation. (Lewis, 183) Binds to RNA polymerase, acts as a start signal for gene transcription. (Norman Lectures, 7/22/09) The promoter region of a eukaryotic gene can be divided into distinct parts. (Micklos, 74) This sequence, along with the “terminator” sequence provides the boundaries for RNA to be synthesized within a defined location. (Brooker, 236) Also referred to as 'control region' and 'promoter.'
TATA Box: so named because of its consensus sequence, which is T-A-T-A-A-A-A. Located approx. 25-30 base pairs upstream of the start point of transcription. (Micklos, 74) Involved in the binding of the complex of "transcription factor" proteins and RNA polymerase required for initiation of transcription. (Lawrence)
TATA-Binding Protein (TBP): protein "subunit" of the transcription factor that binds to the TATA box in the promoters of many genes. (Lawrence) Essential for the initiation of transcription and forms a central part of the ‘pre-initiation complex.’ TBP binds in the narrow groove of DNA at the TATA box and bends the DNA. This forces the “helix” to open slightly, probably allowing better access to RNA polymerase. (Micklos, 74)
Transcriptional Start Site: the site in a promoter (region) where transcription begins. The sequence in the 5’ to 3’ direction is ‘C’ or ‘T,’ then ‘CA,' then five ‘C’s’ or ‘T’s.’ The ‘A’ marks the site of the first ‘A’ in the RNA transcript. (Brooker, G-37)
Splicing: edits out “introns” and joins together the remaining pieces of coding sequence, called “exons,” to form the messenger RNA. (Micklos, 82) The process by which introns (noncoding regions of genes) are excised out of messenger RNA, and the exons are joined together to generate "mature messenger RNA." (GeneReviews) The latter serves as the template for synthesis of a specific protein. (NCI3) "Spliceosomes" consisting of "snRNPs" snip out introns at three distinct "splice sites." (Norman Lectures, 7/22/09) Also referred to as 'RNA clipping,' 'RNA splicing,' and 'splicing mutation.'
snRNPs: small nuclear ribosomal proteins. (Norman Lectures, 7/22/09) Five small uracil-rich RNA's (U1, U2, U4, U5, and U6) are abundant in the nuclei of cells and, along with more than 60 proteins, make up the cellular splicing machinery. They range in size from 107 to 187 nucleotides. (Micklos, 82) Editor's note - pronounced ‘snurps.’
Spliceosome: a structure that cuts introns out and attaches exons to form mature mRNA that exits the nucleus. The introns cut themselves out of the RNA. (Lewis, 185) A complex of several subunits, known as snRNPs, that removes introns from (animal) pre-mRNA. (Booker, G-35) One component of a spliceosome is five small RNA molecules that, working in conjunction with proteins, help to fold pieces of RNA into the right shapes and later splice them into the message. (MeSH)
Splice Site: location in the DNA sequence where RNA removes the noncoding areas to form a continuous gene transcript for "translation" into a protein. (HGPIA)
RNA Transcription Stages: the basic features are identical between prokaryotic and “eukaryotic” organisms. However, in eukaryotes, each step tends to involve a greater complexity of protein components. (Brooker, 238) Editor's note - stages listed below in transcription sequence.
Initiation Stage: DNA transcription stage during which “RNA polymerase” recognizes a “promoter sequence.” (Brooker, 236-237) During this stage RNA polymerase does the following: 1) recognizes promoter region on the DNA strand; 2) RNA polymerase is aided by “transcription factors;” 3) RNA polymerase separates the DNA molecule, forming a ‘transcription bubble;’ and 4) RNA polymerase transcribes DNA. (Norman, 7/21/09)
Elongation Stage: DNA transcription stage during which RNA polymerase synthesizes the RNA transcript. RNA polymerase slides along the DNA. The DNA strands enter the RNA polymerase and are separated. Nucleotides enter the RNA polymerase and the RNA is made in the 5’ to 3’ direction. Both the DNA and the newly made strand of RNA then exit the RNA polymerase. (Brooker, 236-237) In this stage, nucleotides are added to the free strand of DNA (onto the 3’ to 5’ template.) Regulatory sequences influence the rate of transcription. Many RNA polymerases work simultaneously. Process continues until a “terminator sequence” is reached. (Norman, 7/21/09)
Termination Stage: DNA transcription stage during which the newly made RNA transcript dissociates from the DNA. (Brooker, 236-237) During this stage, transcription continues past the termination signal, RNA separates from DNA, and RNA polymerase recycles. (Norman, 7/21/09)