RNA Structure and Synthesis (II) PDF

RNA Structure and Synthesis (II) Transcription of Eukaryotic genes Learning Outcomes:
Elaborate the function of RNA polymerase I, II and III
Elaborate various post-transcriptional modifications of RNA.
Compare between prokaryotic and eukaryotic transcriptions. Nuclear RNA polym...

RNA Structure and Synthesis (II) Transcription of Eukaryotic genes Learning Outcomes:
Elaborate the function of RNA polymerase I, II and III
Elaborate various post-transcriptional modifications of RNA.
Compare between prokaryotic and eukaryotic transcriptions. Nuclear RNA polymerases of eukaryotic cells
There are three distinct classes of RNA polymerase.
Each class of RNA polymerase recognizes particular types of genes 1. RNA polymerase I This enzyme synthesizes the precursor of the large ribosomal RNAs (28S, 18s and 5.8S) in the nucleolus. 2. RNA polymerase II
Synthesis the precursors of mRNA
Also synthesis certain small nuclear RNAs (snRNA), used by some viruses to produce viral RNA. A. promoters or class II genes 
In addition, many promoters contain a GC box (GGGCGG)
These DNA sequences are on the same molecule of DNA as the genes being transcribed, they are called cis-acting genetic elements
They serve as binding sites for proteins called general transcription factors. Direction of transcription Role of enhancers in eukaryotic gene regulation
Enhancers are special cis-acting DNA sequences that increase the rate of initiation of transcription by RNA polymerase II.
Enhancers must be on the same chromosome as the gene whose transcription they stimulate.  Can be located “upstream” (5’) or “downstream” (3’) of the transcription start site  Can be close to or thousands of base pairs away from the promoter  Can occur on either strand of DNA. Some possible locations of enhancer sequences Enhancer stimulation of RNA polymerase II.
Enhancers contain DNA sequences called ‘response elements” that bind specific transcription factors called activator. http://bcs.whfreeman.com/thelifewi re/content/chp14/1402002.html Inhibitors of RNA polymerase II
RNA polymerase II is inhibited by α-amanitin – potent toxin produced by the poisonous mushroom Amanita phalloides
α-amanitin forms a tight complex with the polymerase, thereby inhibiting mRNA synthesis and ultimately protein synthesis Mitochondrial RNA polymerase
Mitochondria contain a single RNA polymerase that resembles bacterial RNA polymerase more closely than it does the eukaryotic enzyme  Posttranscriptional modification of RNA A. Ribosomal RNA rRNAs of both prokaryotic and eukaryotic cells are synthesized from long precursor molecules called preribosomal RNAs. Prokaryotic and eukaryotic rRNAs The 23S, 16S and 5S rRNAs of prokaryotes are produced from a single RNA precursor molecule, as are the 28S, 18S and 5.8S rRNAs of eukaryotes Eukaryotic 5S rRNA is synthesized by RNA polymerase III and modified separately B. Transfer RNA (tRNA) C. Eukaryotic messenger RNA (mRNA)
Synthesized by RNA polymerase II C. Eukaryotic messenger RNA (mRNA)
The collection of all the precursor molecules for mRNA is known heterogeneous nuclear RNA (hnRNA).
The primary transcripts are extensively modified in the nucleus after transcription.
These modification include: 1. 5’ capping 2. Addition of a poly-A tail 3. Removal of introns 4. Alternative splicing of mRNA molecules  5’-Capping
The cap is a 7-methyl-guanosine attached ‘backward’ to the 5’-terminal end of the mRNA, forming unusual 5’5’ triphosphate linkage.
The addition of the guanosine triphosphate part of the cap is catalyzed by the nuclear enzyme guanylyltransferase.
Methylation of this terminal guanine occurs in the cytosol, and is catalyzed by guanine-7-methyltranferase.
S-adenosylmethionine is the source of the methyl group. Why adding 7-methylguanosine ‘cap’?
Permits the initiation of translation
Help stabilize the mRNA Eukaryotic mRNAs lacking the cap are not efficiently translated. Addition of a poly-A tail
Chain of 40 to 200 adenine nucleotides attached to the 3’-end.
This poly-A tail is not transcribed from the DNA.
It is added after transcription by nuclear enzyme, polyadenine polymerase. 
Polyadenylation signal sequence (AAUAAA) : found near the 3’-end of the RNA molecule Signals that a poly-A tail is to be added to the mRNA.
These tails help stabilize the mRNAs Facilitate exit from the nucleus
After mRNA enters the cytosol, the poly-A tail is gradually shortened. Removal of introns
Maturation of eukaryotic mRNA usually involves the removal of RNA sequences, which do not code for protein (introns, or intervening sequences) from the primary transcript.
The remaining coding sequences, the exons, are spliced together to form the mature mRNA.
The molecular machine that accomplishes these tasks is known as spliceosome. 4. Alternative splicing of mRNA molecules
The pre-mRNA molecules from some genes can be spliced in 2 or more alternative ways in different tissues.
This produces multiple variations of mRNA, and therefore, of its protein product.
This appears to be a mechanism for producing a diverse set of proteins from limited set of genes. Summary