Lecture 10 - Splicing

Front 1

RNA Pol I & Pol III share several subunits with Pol __

Back 1

II

Front 2

RNA Pol I only transcribes one gene, the ________________.
But many copies of this gene are present. It is the most highly
expressed gene in the cell.

Back 2

RNA Pol I only transcribes one gene, the rRNA precursor.
But many copies of this gene are present. It is the most highly
expressed gene in the cell.

Front 3

Human RNA polymerase I promoter consist of..
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Back 3

UCE (UPSTREAM CONTROL ELEMENT) AND CORE PROMOTER. THESE TWO ELEMENTS ARE VERY CLOSE TOGETHER

Front 4

In addition to Pol I, initiation requires two other factors, called _____ and _____. ____ comprises TBP and three TAFs specific for Pol I transcription. This complex binds to the _______________.

Back 4

UBF,SL1,SL,core element

Front 5

SL1 binds DNA only in the presence of ____. This factor binds to ____, bringing in SL1 and stimulating transcription from the core promoter by recruiting Pol I.

Back 5

UBF, UCE,

Front 6

Most RNA pol III promoters are _________________ from the start site

Back 6

DOWNSTREAM

Front 7

Pol III transcribes _______ and the 5_____________.

Back 7

tRNA, 5s rRNA genes

Front 8

The RNA pol III promoters contain...
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Back 8

box a
box b
box c and
TFIIIA TFIIIB and TFIIIC.

Front 9

TFIIIA is also needed for transcription of _________ genes.
It binds to _________.

Back 9

5s rRNA genes.
Box C.

Front 10

Sequences at intron-exon boundaries:

Three conserved sequences in an intron required for removal of the intron

Back 10

GU at 5' end
AG at 3' end
branch site A in the middle

Front 11

What initiates the intron splicing?

Back 11

2'OH on branch site attack the 5' phosphate at the beginning of the intron and creates a lariat.

Front 12

What happens next?

Back 12

3' oh on DNA attack the other end of the intro, thus realing it. the products are intron lariats and spliced exons.

Front 13

in trans splicing, you get a __ shaped intermediate that gets removed.

Back 13

Y

Front 14

Splicing is carried out by over ____ proteins and __ RNAs in the ______________ complex

Back 14

150, 5, spliceosome

Front 15

spliceosome consist of

Back 15

snRNPS

Front 16

what are the 5 snRNPS ?

Back 16

U1, U2, U4, U5, and U6

Front 17

Early (E) complex - ___ binds 5’-splice site
__________________ binds branch point
_______________ binds pyrimidine tract
and 3’ branch site.

Back 17

u1, BBP (branch binding protein), U2AF (U2 auxillary factor)

Front 18

A complex– ______ binds branch point and displaces BBP causing the branch point A to bulge out.
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Back 18

U2

Front 19

B complex – ___, ___, ___ (tri-SNRNP particle) bind bringing the 5’ and 3’ ends and branch point_____________.
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Back 19

U4, U5, and U6, together

Front 20

___ displaces U1 at the 5’-branch point. U1 and U4 exit allowing the _________ to form.

This complex has a ______ interaction responsible for cleavage of the 5’-splice site.

___ helps bring the 5’ & 3’ splice sites together where they can be linked after 3’-splice site cleavage.

Back 20

U6, C complex, U2:U6, U5

Front 21

U6:U2 makes the ___________ for catalysis of splicing reaction.
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Back 21

active site

Front 22

Group II self- splicing mechanism....

Back 22

two transesterification reactions initiated by branch site A attacking 5' end of splice site.

two transesterification reactions initiated by free G binding pocket and then attacking 5' end of splice site.

Front 23

Group I self- splicing mechanism...

Back 23

two transesterification reactions initiated by free G binding pocket and then attacking 5' end of splice site.

5’ splice site binds 3’ splice
site leaving linear intron
with G as the first nucleotide

Front 24

two errors that can occur during splicing.

Back 24

exon skipping and pseudo splice-site selection

Front 25

pseudo splice-site selection: A false (similar sequence)
__-splice site used. result is shorter ______ sequence.

Back 25

3', exon

Front 26

___________________ proteins recruit splicing components
to the splice sites to ensure they are recognized.

Back 26

SR (serine arginine-rich)

Front 27

SR proteins bind ______________________ sites in exons.

Back 27

exonic splicing enhancer (ESE)

Front 28

SR proteins recruit ___ to 5’ splice site and _____ to 3’ splice site.

Back 28

U1, U2AF

Front 29

Loading of splicing factors onto ___ _____________ ____ also
ensures the splice sites are encountered in the right order.

Back 29

RNA polymerase tail (c terminal domain tail)

Front 30

____ and ______ replace U1 and U2.
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Back 30

u11, u12

Front 31

Many of these introns have:
__ instead of GU at the 5’-splice site
and ___ instead of AG at the 3’-splice site
so different sequences are recognized.

Back 31

AU, AC

Front 32

U12 BINDS THE ___________________ SITE.

Back 32

BRANCHING

Front 33

U11 BINDS THE...

Back 33

AU on 5' end

Front 34

Alternative splicing in troponin T: exons in the spliced mRNA on alpha troponin T.
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Back 34

1,2,3,5

Front 35

Alternative splicing in troponin T: exons in the spliced mRNA on beta troponin T.

Back 35

1,2,4,5

Front 36

75 % of human genes are _____________ spliced.
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Back 36

alternatively

Front 37

5 ways to splice pre-mRNA.

Back 37

normal (all exon present)
exon skipped
exon extended
intron retained
alternative exons (where you get multiple exons put together, but never all at the same time. example 1+2, 2+3, but never 1+2+3)

Front 38

Alternative ________ and alternative ______ sites may also be
involved in alternative exon usage.

Back 38

promoters, poly-A

Front 39

Monkey virus SV40 T antigen alternative splicing:

If the transcript is not spliced, a ____ codon is encountered & the
_______ antigen is made. If it is spliced the ________ antigen is made

Back 39

small, small t (t-ag), large T (T-ag)

Front 40

2 more mechanisms that yield mutually exclusive splicing
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Back 40

review slide 23

Front 41

Splicing ________ &
__________ binding sites
are present at intron-exon
junctions. Positively or negatively regulates splicing depending on bound protein at site.

Back 41

enhancer, repressor

Front 42

the hnRNP I protein is a splicing _________.


bindin of the ____________ protein blocks access to the splice site.

Back 42

repressor, repressor, splice sites

Front 43

Exons often encode... (three words)

Example-a homodimeric DNA
binding protein

Back 43

independent protein domains

Front 44

So exons shuffled by recombination
to a different protein often lead to _______ _______ with _____ __________.

Back 44

stable hybrids, new functions

Front 45

______ ________________ led to the creation of the LDL receptor gene.


It contains exons from these two genes...

Back 45

exon shuffling, c9 complement, egf precursor

Front 46

In RNA editing of apolipoprotein B gene, C is ________________ to ___.

This happens in the _______________ because of _____________ _________________ ___________________ that catalyzes the reaction

Back 46

deaminated, U, cytidine deaminase enzyme

Front 47

When there is no editing of the gene (happens in liver), the message CAA is translated as _____________ where as editing in liver causes it to be translated into a ________ codon UAA

Back 47

glutaine, stop codon

Front 48

Another enzyme that performs RNA editing:

Back 48

ADENOSINE DEAMINASE ACTING ON RNA (ADAR)

Front 49

ADENOSINE DEAMINASE causes adenine to turn into ___________.

This can basepair with ____.

What is edited in the brain using this mechanism?

Back 49

inositol, C


an ion channel

Front 50

U's are added into mRNA by

Back 50

gRNA (guide-RNA)

Front 51

Each gRNA is divided into three regions. The first, at the 5' end, is called the___________and directs the gRNA to the region of the mRNA it will edit. also called region of ______________.

the second, called the ___________ region, determines exactly where the Us will be inserted within the edited sequence;


and the third, at the 3' end, is a ____________ stretch.

Back 51

anchor, homology

editing

poly-U

Front 52

What cuts at mismatch?

Back 52

endonuclease

Front 53

gRNA mediated U insertion is common in (2 words)

Back 53

trypanosome mitochondria