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Flashcards in RNA Synthesis Deck (26)
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differences between RNA struct and DNA

-the sugar is a rebose, not a deoxyribose
-thymine is replaced with uracil


folding of RNA chains

single stranded pieces of RNA and DNA can fold and bind to itself giving it well defined secondary structure


can RNA forma double helix>

no, due to the presence of the 2'hydroxyl


coding strand

the single strand of DNA which codes for the RNA that will eventually be made into a functional protein. However, this is not the strand that is transcribed, it is the minues strand, which allows the RNA to have the same sequence the coding strand but instead of T there is U


one capability of RNA pol vs DNA pol

RNA pol is capable of initiating transcription, synthesis of a strand, on its own using a nucleoside triphosphate as its first building block


RNA Pol 1

-located in the nucleolus
-responsible for the synthesis of rRNA


RNA pol 2

-located in the nucleus but outside of the nucleolus
-carries out the transcription of genes encoding for cellular proteins


RNA pol 3

-located in the nucleus, outside f the nucleolus
-transcribes the DNA that codes for small RNA pieces such as tRNA and 5s rRNA


rRNA trnascription unit

-contains information for the three rRNA chains and a large amount of additional sequences
-arranged in multiple, tandemly arrayed copies in the genome seperated by a DNA segment called a spacer


factor B, factor S, and RNA Pol 1
-terminator sites

-Factors B enhances binding of RNA Pol 1 to the DNA within the regulatory region, Factor S is what stimulates the binding of factor B to RNA Pol 1.
-Binding of these 3 proteins allows transcription to begin
-termination of transcription is signaled by the presence of a string of T residues


TF3A,B, and C
what they do
mechanism break down

-transcription factors that aid RNA Pol 3 in the transcription of RNA sequences for small RNA particles (tRNA, snRNA, and 5S rRNA)
-TF3A and C bind the activation region of the DNA sequence which enables the binding of TF3B
-TF3B is recognized by RNA Pol 3 and transcription begins
-termination ocurs at a string of T residues
-processing varies depending on the product


TATA box

the sole highly conserved sequence utilized during RNA pol 2 transcription


basal trancription factors

-required for the initiation of transcription in all genes
-TF2D: TATA binding protein, binds to the TATA box, is the only transcription factor that binds to DNA
-TF2B: binds RNA pol 2 and helps direct it to the promoter and interacts with TF2D
-without these TFs, RNA pol can not locate the promoter



-live within the vicinity of the promoter and increase trancsription and in many cases are required
- can operate from a great distance and stimulation is independent of the enhancers orientation
-it is thought that loops in the DNA juxtapose the enhancer next to its target
-has binding sites for modulating proteins called activators


mRNA cap

-7 methylguanylate is added to the 5' end of the nascent RNA
-the cap is then methylated along with the 2' residue of the first nucleotide. GTP and adenosylmethionine are used to methylate
-cap is thought to block nascent RNA from degradation and play a role in translation


Poly A addition during RNA processing
cleavage and polyadenilation specificity factor
poly a polymerase

-most nascent pre-mRNA is cleaved at a nearby poly A site
-CPSF cleaves the nascent pre-mRNA 15 nt downstream of an AAUAAA sequence
-once CPSF does its job, poly A polymerase adds 250 A residues to the 3' terminus. this enzymes requires ATP and does not require a template
-This poly A tail is exclusive to RNA chains that become functional mRNA



-premRNA contains segments which do not code for a protein which are located in between the coding regions, these noncoding region termed introns need to be spliced out
-intron can be 30-210,000nt in length
-could be to keep coding sequences intact during crossing over


-composition (2)

-the highly organized structure in witch splicing takes place on
-assembled from pre-mRNA and snRNP's (small nuclear ribonucleoproteins)


composition of introns

-GU at 5' side and AG at 3' side
-pyrimidine rich region just upstream of the 3' splice site


steps in splicing

1. cleaving of the 5' exon/intron junction
2. circularization of the intron to form a lariat with a branch point between the 5'G residue linked to an A residue near the 3' end of the intron
3.the 3/ junction is cleaved and neighboring exons are ligated together


U1,2, and 5 and their job on the spliceosome

-these are all different snRNPs
-U1 binds to the 5' exon intron junction
-U2 binds to the branch point
-U5 binds just upstream of the 3' junction


alpha and beta thallasemia and splicing of pre-mRNA

-they are both defined by incorrect synthesis of one or more hemoglobin chains
-about 25% of the mutations for thalassemias are in sequences required for correct splicing


Alternative splicing

-process that often produces two or more forms of a protein, these forms are needed at different stages and cell types in life


example of alternative splicing

-IgM either exists on the cell surface or floating around in the blood
-the soluble protein lacks two exons due to alternative splicing which encode hydrophobis amino acids


actinomycin D

-general inhibitor of DNA dependent RNA synthesis
-intercalates itself between GC base pairs, distorting the DNA.
-RNA pol 2 and 3 are inhibited by alpha-amanitin which is derived from mushrooms
-bacterial RNa pol is sensitive to rifampicin by it inhibiting the initiation step of RNa synthesis


cDNA cloning

-purpose is to use mRNA to create a DNA clone
1. isolate mRNA by running running your sample through a collumn of oliog dT's which will complimentary base pair with the poly A tails on mRNA
2. now mix in oligonucleotide primers of about 20deoxythymidines which will act as primers for the reverse trancriptse which creates a complimentary DNA molecule