Overview of transcription Flashcards
Which enzyme synthesizes RNA
RNA polymerase synthesizes RNA- it catalyzes the DNA-directed coupling of NTPs(nucleoside triphosphates), eg. ATP, UTP, GTP, and CTP in a reaction that releases a pyrophosphate ion (P2O74-): RNAn residues+NTP—– RNAn+1 residues + P2O74-
Explain how RNA polymerase synthesizes RNA
RNA synthesis occurs in the 5’-3’ direction, the incoming nucleotide binds to the free 3’-OH group of the growing RNA chain. RNA polymerase selects the nucleotide that it wants to incorporate based on Watson-Crick base pairs with the DNA strand being transcribed- the template strand(3’-5’). Only one strand is transcribed at a time. This is possible because as RNA polymerase moves along the duplex DNA it is transcribing, it separates a short segment( about 14 bp) of its two strands to form a transcription bubble. This allows this portion of the template strand to form a short DNA-RNA hybrid helix with the newly synthesized RNA. A DNA-RNA hybrid helix consists of antiparallel strands ( RNA=5’-3’ and DNA= 3’-5’).
Do all cells contain RNA polymerase
Yes, all cells contain RNA polymerase. In bacteria, one species of this enzyme synthesizes nearly all of the cell’s RNA. Certain viruses generate RNA polymerases that synthesize only virus-specific RNAs. Eukaryotic cells contain 4 or 5 different types of RNA polymerases that can each synthesize a different class of RNA.
Briefly describe the control sites in transcription
The DNA template strand contains control sites consisting of specific base sequences that specify both the site at which RNA polymerase initiates transcription (the site on the DNA at which the RNAs first 2 nucleotides are joined) and the rate at which RNA polymerase initiates transcription at this site. Specific proteins known in prokaryotes as activators and repressors and in eukaryotes as transcription factors bind to these control sites or to other such proteins that do so and thereby stimulate or inhibit transcriptional initiation by RNA polymerase. For the RNAs that encode proteins(mRNAs), these control sites precede the initiation site (upstream of the initiation site relative to RNA polymerase’s direction of travel).
What controls the rate at which a given protein is synthesized by the cell
The rate at which a cell synthesizes a given protein, or if it is synthesized at all, is governed by the rate of synthesis of the corresponding mRNA is initiated
Explain transcriptional initiation in prokaryotes
Transcriptional initiation in prokaryotes can be simple, eg. the transcriptional initiation of numerous prokaryotic genes requires only that RNA polymerase binds to a control sequence called a promoter, that precedes the transcriptional initiation site. However, not all promoters are created equally- RNA polymerase initiates transcription more often at efficient promoters than those with even slightly different sequences. Thus the rate at which a gene is transcribed depends on the sequence if its associated promoter. A more complex way in which prokaryotes control the rate of transcriptional initiation is shown by E.coli’s lac operon, a cluster of 3 consecutive genes (Z,Y, and A) encoding proteins that the bacteria requires to metabolize lactose. In the absence lactose, a protein named the lac repressor specifically binds to a control site in the lac operon known as an operator. This prevents RNA polymerase from initiating the transcription of lac operon genes, thereby stopping the synthesis of unneeded proteins. However, when lactose is available, the bacterium metabolically modifies a small amount of it to form allolactose. This is an inducer that binds to the lac repressor, thereby causing it to dissociate from the operator DNA so that RNA polymerase can initiate transcription of the lac operon genes.
Explain transcriptional initiation in eukaryotes
In eukaryotes, the control sites regulating transcriptional initiation can be quite extensive and distant from the transcriptional initiation site. Moreover, the eukaryotic transcriptional machinery that binds to these sites and thereby induces RNA polymerase to initiate transcription can be complex.
Explain transcriptional termination
The site on the template strand at which RNA polymerase terminates transcription and releases the completed RNA is governed by the base sequence in this region. However, the control of transcriptional termination is rarely involved in the regulation of gene expression. The cellular machinery involved in transcriptional termination is relatively simple in comparison to the machinery involved in initiation.
Explain post-transcriptional modification of RNA
Most prokaryotic transcripts participate in translation without any further alteration. However, most primary transcripts in eukaryotes require extensive post-transcriptional modifications to become functional. For mRNAs, these modifications include the addition of a 7-methylguanosine-containing “cap” at the 5’-end and a 250-nucleotide polyadenylic acid (poly A) “tail” to its 3’-end. Most eukaryotic transcripts undergo gene splicing, in which one or more RNA segments known as introns are excised from the RNA and the remaining exons are rejoined in their original order to form the mature mRNA. Different mRNAs can be generated from the same gene through the selection of alternate transcriptional initiation sites and/or alternative splice sites leading to the production of different proteins, usually in a tissue-specific manner.
