Biochemistry: RNA Synthesis and Transcription Flashcards Preview

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Flashcards in Biochemistry: RNA Synthesis and Transcription Deck (25):

What chemical reaction is is catalyzed by RNA polymerase?

5' to 3' formation of RNA. It catalyzes phosphdiester bonds between ribonucleotides.


Why is the RNA polymerase reaction unidirectional?

Because there is a reactive hydroxyl group at the 3' carbon. The 5' carbon is stable with a phosphodiester bond.


Describe 3 common steps between bacterial and eurkaryotic RNA polymerases in the transcription cycle.

Initiation, Elongation, Termination


What are the 3 steps of Initiation?

RNA pol binds to promoter sequence on DNA, pol melts DNA near transcription start site forming transcription bubble, pol catalyzes phosphdiester link of 2 rNTPs


What happens during elongation?

Polymerase advances 3' to 5' down template strand melting DNA and linking rNTPs


What happens during termination?

At transcription stop site, Pol releases completed RNA and disasscoiates from DNA.


Name 4 cellular RNA polymerases and their main functions.

E.Coli - transcribes all RNA in E.ColiRNA I   [human] - makes rRNARNA II  [human] - makes mRNARNA III [human] - makes tRNA


What is a promoter?What are common sequence elements in promoters?

A sequence of DNA upstream of the transcription start site where RNA pol binds.TATA - in lots but not all eukaryotic genes, approx 30 base pairs from start


How does alpha amanitin block transcription?

Alpha amanitin is a non-competitive inhibitor of RNA pol II. It binds the bridge helix and prevents the polymerase from sliding down the DNA chain.


How does rifampicin work?

Rifampicin, a broad spectrum antibiotic, binds the beta subunit of bacterial RNA pol which blocks the RNA exit channel.


What are the five components of RNA pol II pre-initiation complex?

 TFIIB - places RNA Pol @ correct start site TFIID - recognizes TATA boxTFIIE - attracts/regulates TFIIHTFIIF - stabilizes RNA pol action, attracts E+HTFIIH - unwinds DNA @ start point, releases RNA pol from promoter


What clinical syndromes might one get with a mutation(s) in their TFIIH subunits?

Xeroderma pigmentosum, cockaynes syndrome, TrichothiodystrophyBecause TFIIH functions in transcription and DNA repair


What are the three ways that pre mRNA gets processed? 

1. Capping - 5' triphosphate gets replaced by 7-methylguanosine2. Splicing - excision of introns by spliceosome3. Cleavage by endonuclease and polyadenylation at the 3' end* This all happens while RNA is being made


What are the differences between pre-mRNA and mature mRNA?

Pre-mRNA is longer, has a triphosphate group at the 5' end, and lacks a poly A tail.


What are the functions of the 5' methyl cap?

It makes the 5' end resistant to exonucleases. It also helps with splicing/processing through a cap binding complex. The cap is recognized for transport to ribosome. Cap removal is signal for degradation.


What are the three reactions necessary to add a 5' cap to pre-mRNA?

1. Remove the 3rd/last phosphate 2. Add guanosine triphosphate 3. Methylate the 7 position of the guanine cap


What is the conserved sequence at the 5' and 3' ends at most introns?

5': GU3': AG


What is the consensus sequence at the poly-A site?



How does alternative splicing permit production of multiple proteins?

Exons can be retained or removed, truncated at the 5' or 3' end, mutually exclusive. Plus, introns can be retained.


What are two examples of genetic orders caused by splicing defects?

Marfan's syndrom - mutations that disrupt splicing of fibrillin gene. Which produces protein for walls of heart = weak -> aneurysmsCD44 - cell surface glycoprotein is a predictor of tumor metastasis. 


What is U1 snRNA? U2 snRNA?

U1 snRNA binds to the GU splice site of intronsU2 binds to the branch point between 5' and 3' splice sites.


What two reactions make the mature 3' end of mRNAs?

Cleavage and polyadenylation


What is the relationship between 3' end processing of the pre-mRNA and termination of transcription at the end of a gene?

3' end formation by cleave/polyadenylation is coupled to termination of transcription by RNA pol II.


What are the two major functions of mRNA's poly-A tail?

Translation + Stability


Give an example of how alternative poly-A sites can be used to make more than one protein from a single gene.

A common gene may have multiple AAUAAA sequences.Depending on which poly-A site is used, two different forms of IgM are made: heavy chains and light chains.