LEC25: mRNA Processing II Flashcards Preview

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Flashcards in LEC25: mRNA Processing II Deck (31):
1

what is the 5' CAP made of? 

what bond is formed by its addition? 

what is the purpose?

5'CAP is a 7-methyl-guanisine 

forms a 5'-5' phosphate diester bond 

makes mRNA look diff from other RNAs, indicates it should be translated

2

what is the structure of an intron?

begins w/ GU 

has an A residue, a branch point, where 2' to 5' phosphodiester bond forms when intron is spliced out 

concentration of pyrimidines toward downstream exon

has 2 loose consensus sequences

ends w/ AG

3

what happens if splicing is incorrect by 1 ntd?

get frameshift mutation downstream

4

what are the consensus sequences required for splicing?

5' splice site consensus, GT 

branch point consensus, A 

3' splice site consensus, AG

5

size of large intro in muscular dystrophy?

250,000 ntds

6

how is it possible that huge introns don't get included in mRNA?

exon definition! 

spliceosome recognizes edges of exons, which are much shorter than introns 

exon definition allows for protein-protein and protein-RNA interactions

7

what is an ESE?

exonic splice enhancer sequence 

RNA box bound by a class of proteins called SR proteins (rich in Ser and Arg) 

the correct 5' GU and 3' AG dinucleotides of splice junctions can be reconigzed specifically by splicing machinery on basis of their proximity to exons in which SR proteins are bound

8

what would happen if there's a silent mutation in an ESE?

SR protein needs certian consensus sequence in ESE to know where to bind 

if change occurs, SR sequence cannot recognize it needs to be 

so get problems 

9

where does the first exon start?

w/ the +1 nucleotide, includes the start codon 

upstream of start codon is the 5' UTR 

10

why must splicing be precise?

in order to not disrupt the coding sequence reading frame, which spreads over multiple exons 

11

what does the final exon contain?

the polyadenylation signal 

12

how is it that just 25,000 genes in the human genome, but we have such great complexity? 

each gene transcript can undergo alternative splicing, gives multiple mRNA products

 

13

what % of transcripts udnergo alternative splicing?

transcripts from >90% of genes undergo alternative splicing

14

what is the transcriptome? why so big?

all the different number of transcripts that can be produced from a particular genome 

per alternative splicing, for humans 

 

15

what are the functions of SR proteins?

1) constituitive: bind EXEs

2) regulated: not always active!

16

is splicing the same for all parts of the body's genes?

no; there is tissue specificity to alternative splicing

17

what is the most common form of alternative splicing?

other forms?

most common: exon skipping 

others: alternative 5' splice site, alternative 3' splice site, intron inclusion

18

what is an ESS?

exonic splice silencers 

RNA boxes in exons that bind SR proteins to suppress splicing of an exon, such that it's not included in final mRNA product

19

what are ISE, ISS?

deep intronic mutations - intronic splice enhancers and intronic splice silencers - that tell gene to splice out or keep an intron 

20

what is the big controller of splicing?

SR proteins!

21

how much of genetic disease is caused by splicing issues?

15%! 

22

what about silent mutation in coding sequence might be involved w/ splicing? 

change in the 3rd ntd position of a codon which doesn't change encoded amino acid now thought to be involved in splicing regulation

23

what are the reactions of splicing?

transesterification reactions:

1) attack of the branch point A to OH group on 5' splice site, makes 2' to 5' phosphodiester bond 

2) attack of the 3' OH of upstream exon on the 3' splice site; joins the upstream and downstream exons in a 3' to 5' phosphodiester bond 

 

24

what is lariat RNA

the form of the intron sequence that is spliced out and degraded by ribonucleases

25

what's the typical poly-a signal?

AAUAAA 

 

26

what is an endonuclease?

ribonuclease that cuts RNA internally 

cuts 20-30 ntds downstream of the Poly-A signal 

results in a free 3'OH

27

how does the poly-A rxn occur?

1) highly conserved poly-A signal (AAUAAA) at end of last exon

2) endonuclease cuts 20-30 ntds downstream of poly-A signal

results in free 3'OH

3) poly-A polymerase adds poly-AAAAA to 3' OH just generated 

28

what protects the poly-A tail when the mRNA is exported to the cytoplasm?

poly-A binding proteins coat the poly-A tail 

protects mRNA from exonucleases

29

what is the EJC?

what is its relation to nonsense mediated decay?

exon junction complex 

deposit of proteins where exons are knit together 

if there's a premature stop codon b/c of nonsense mediated decay, and there's an EJC downstream of the too-early stop  codon, 

when ribosome encounters stop codon, EJC transmits a signal, mutated RNA gets degraded 

30

what happens to mRNAs in cytoplasm? what does it influence?

mRNAs are translated & eventually degraded in cytoplasm 

rate of degradation is a factor that determines the amount of translation from an mRNA

decay of mRNA allows recycling of ntds, enables changes in set of genes being expressed in response to changing conditions

31

what does nonsense-mediated decay pathway do?

rapid, targeted degradation of mRNAs containing a nonsense codon 

ensures that defective mRNAs w/ a premature stop codon are dealt w/ 

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