Ch 6 Notes AB
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RNA pol 1
5.8, 18, and 28S rRNA
RNA pol III
tRNA, 5S rRNA
Which general TF binds first?
it contains a TBP subunit taht specifically recognizes the TATA sequence on the promoter
it causes bending of the DNA
tail of polypeptide with lots of serines that get phosphorylated; unique to RNA pol II
What is another important general TF?
uses ATP to act as a helicase; also a kinase involved in phosphorylation of serine residues in CTD
After CTD region is phosphorylated, what occrs?
conformational change that allows the rudder to peel off and TFs to dissociate
How does the mediator work?
it randomly bumps into and binds other components of the complex. It will then bind the promoter sequence to allow transcription to start
How can ribosomes distinguish between mRNA ffrom others?
A single transcript can do what?
What flanks the coding sequence?
make several mRNA sequences
What are the steps for capping?
- 1) remove a phosphate: 3 P--> 2 P
- 2) get GTP and use the energy associated with removal of two phosphates and attach the one phosphate to the end of a nascent message
- 3) add a methyl group to the G residue--> ending up with a 7-methylguanosine
What is alternative splicing and what does it do?
coming up with alternate ways of splicing; picking and choosing which exons are used gives proteins different functions
Where are beginning and ends of introns and exons?
People identified small consensus sequences common to particular function at exon-intron boundaries
Nucleotide sequence IDed as binding sites for RNA and proteins
How is the adenine nucleotide found?
- In two ways:
- - initially, A is recognized by the brotein BBP (branch point) in formation of the lariat
- - protein has a site that specifically recognizes nucleotide
What is the process of splicing with the snRNAs/
1) The Adenine is identified b BBP, which recognizes it.
2) The BBP is replaced by other proteins that have RNA= snRNP; now A is recognized by RNA
3) U1 then binds to splice site after A is identified. More snRNPs are brought in and lasso begins to form
4) Activated A brought to splice site; backbone is broken--> lasso forms, causing a conformational change, which brings the two exon ends together
What makes the snRNAs able to perform their function?
They base pair with RNA to position them appropriately
the proteins hydrolyze ATP and undergo conformational changes that will move things around
How is ATP used in splicing?
to allow proteins to rearrange things; they also form a catalytic site
What errors in splicing can occur?
exon skipping: missing an exon
crytic splicing: caused by nucleotide changes
What helps to avoid problems in splicing?
size of the exons and introns; average exon is around 150 bases long
What is a disease caused by improper splicing?
problems with splicing of beta-hemoglobin
What is a hypothesis regarding hnRNP?
- it is done during transcription
- --> proteins immediately grab onto mRNA= SR protiens (Concentrated in serine and arginine residues); they bind to exons
introns produced; large complexes with introns and protiens bunched together; allows snRNPs to better interact
have roles in alternative and constitutive splicing resulting in differential gene expression and also play a part in mRNA export, genome stabilization, non-sense mediated decay, and translation
What are some ways in which beta thalassemia can be formed?
exon skipping caused by nucleotide changes that destroy a normal splice site
new exon incorporation by nucleotide chainges
What do poly-A binding proteins do?
bind to the poly-A tail that was made by PAP
Explain the eIF factors?
4E binds to the 5' cap
4G binds to 3' poly A tail
must be present in cytoplasm for translation
cap binding complex: binds to the 5' cap of pre-mRNA
What signifies that the RNA is rRNA?
a pseudouridine and 2'-O-methylated nucleotide
What does a snoRNA do in the nucleolus?
it works in conjunction with snoRNP; they determine the sites of modification by base pairing to complementary sequences on the precursor rRNA; bound to proteins, and the complexes are called snoRNPs, which contain both the guide sequences and the enzymes taht modify the rRNA
What is the pre-mRNA splicing mechanism?
The exchange of U1 snRNP for U6 snRNP occurs before the first transesterification; this exchange requires the 5' splice site to be read by two different snRNPs, thereby increasing the accuracy of 5' splice site to be read by two different snRNPs, thereby increasing the accuracy of the 5' splice site selection
The branch point site is recognized by BBP and then U2; this check and recheck strategy provides icnreased accuracy of site selection.
U2 binds, forcing the appropriate adenine to be unpaired adn activated for the attack on the 5' splice site.
This, in combo with recognition by BBP is the way the spliceosome chooses the right adenine.
After the first transesterification, a series of rearrangements brings the two exons together for the second transesterification.
The snRNAs both position the reactants and provide the catalytic sites for the two reactions.
The U5 is present in the spliceosome before the rearrangement
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