Assignment mRNA into the mature mRNA that only

 

Assignment no.2

Bio302

MC170404186

QNO.1
What is a pre-initiation complex? How a pre-initiation complex is formed?

Answer:
Pre-initiation complex:

              The complete set of general
transcription factors and polymerase, bound together at the promoter and
suspended for initiation, is called the pre-initiation complex.

Formation
of pre-initiation complex:

The general
transcription factors help polymerase bind to the promoter and melt the DNA.

They also help the
polymerase escape from the promoter and embark on the elongation phase. any
polymerase II promoters contain a TATA
element (which are 30 base pairs upstream of the transcription start site. The
formation of pre-initiation complex is start from this site. The TATA element
is recognized by th general transcription factor called TFIID.

TFII denotes the
transcription factor for polymerase II.Like many other general transcription
factors, TFIID is in fact, a multi subunit compound. The component of TFIID
that binds to the TATA DNA sequence is called TBP (TATA binding protein).The other subunits in this complex are
called TAFs, for TBP associated factors. Some TAFs recognize other core
promoter elements such as the initiator, DPE and DCE, although the strongest
binding is between TBP and TATA. Thus TFIID is a critical factor in promoter
recognition and establishment of pre-initiation complex.

Upon binding DNA TBP
extensively distorts the TATA sequence. The resulting TBP DNA complex provides
a platform to recruit other general transcription factors and polymerase itself
to the promoter In vitro these proteins assemble at the promoter in the
following order. First TFIIA, TFIIB
then TFIIF together with polymerase
and then TFIIE and TFIIH.

The formation of
pre-initiation complex is followed by the promoter melting.(separation of
DNA  strands).

 

Q
NO2:What is RNA splicing? Describe the major events that occur in splicing
pathway?

Answer:
RNA splicing:

In this process removal of intron takes
place and RNA splicing convert the pre- mRNA into the mature mRNA that only
contain exons.

RNA splicing must occur with great accuracy
to avoid the loss or addition of even a single nucleotide at the site at which
the exons are joined.

 

Major
events that occur in splicing pathway

In a splicing pathway, a number of the
steps may differ slightly in their order or might even reverse.

Initially the 5’splice site is recognized by
the U1 snRNP. U2AF is made up of 2 subunits the larger subunit is (65) which
binds to the Py tract and the smaller is (35) binds to the 3’splice site. The
former subunit interacts with BBP (SF1) and helps that protein bind to the
branch site. This arrangement of protein and RNA is called early (E) complex.U2
snRNP then binds to the branch site, aided by U2AF and displacing BBP(SF1).
This arrangement is called the A complex.The base pairing between theU2 snRNP
and the branch site A residue is extruded from the resulting stretch of
double-helical RNA as a single nucleotide bulge. This A residue is thus unpaired
and available to react with the 5′ splice site. The
next step is a rearrangement of the complex to bring together all three splice
site. This is achieved as follows, the U4 andU6snRNPs, along with the U5snRNP
join the complex. Together these three snRNPs are called the tri- sn RNP particle.
With in this particle the U4 and U6 snRNP are held together by complementary
base pairing between their RNA components and the U5 snRNP is more loosely
associated through protein-protein interactions. With the entry of the tri-
snRNP the A complex is converted into the B complex.In the next step, U1 leaves the complex U6
replaces it at the 5’splice site. This requires that the base pairing between
the U1 snRNP and the pre- mRNA be broken it is allowing the U6 RNA to anneal
with the same region. Those steps complete the assembly pathway. The
next rearrangement triggers catalysis and occurs as follows.U4 is released from
the complex, allowing U6  to interact
with U2 through the RNA;RNA base pairing. This arrangement is called the C
complex which produces the active site.That is the rearrangement brings
together within the spliceosomethose component that together form the active site.
The same arrangement also ensures that the substrate RNA is properly positioned
to be acted upon. The formation of the active site juxtaposes the 5’splice site
of the pre- mRNA and the branch site facilitating the first transesterification
reaction. The second reaction between the 5’and 3’splice sitesis aided by theU5
snRNP which help to bring the two exons together.The final step involves release of mRNA and
snRNPs. The snRNPs are initially still bound to the lariat but they get
recycled after rapid degradation of that piece of RNA.