i want 25 mutiple choice questions with their model answer below each question about all of the following: 
Very sensitive
Moderately sensitive
Transcription of Eukaryotes
a. Initiation
• Transcription initiation needs promoter and upstream regulatory regions.
• The cis-acting elements are the specific sequences on the DNA template that regulate the transcription of one or more genes.
b. Elongation
• The elongation is similar to that of prokaryotes.
• The transcription and translation do not take place simultaneously since they are separated by nuclear membrane.
Posttranscriptional modifications of RNA
Most newly transcribed RNA molecules (primary transcripts) undergo various alterations to yield the mature product. RNA processing is the collective term used to describe the molecular events allowing the primary transcripts to become the mature RNA. Primary Transcript: the initial molecule of RNA produced hnRNA （heterogenous nuclear RNA ). In prokaryotes, DNA→RNA→protein in cytoplasm concurrently In eukaryotes nuclear RNA >> Cp RNAA) CUTTING AND TRIMMING TO GENERATE ENDS:
rRNA, tRNA and mRNA.
B) COVALENT MODIFICATION:
• Add a cap and a polyA tail to mRNA.
• Add a methyl group to 2’-OH of ribose in mRNA and rRNA.
• Extensive changes of bases in tRNA.
C) SPLICING:
pre-rRNA, pre-mRNA, pre-tRNA by different mechanisms. Processing of mRNA:
prokaryotes
• In prokaryotic organisms the primary transcripts of mRNA are
subject to little processing before translation, this is because
the site of transcription is not compartmentalized into nucleus
as in eukaryotes.
• It can start to be translated before it has finished being
transcribed.
• Prokaryotic mRNA is degraded rapidly from the 5’ end.Processing of mRNA in eukaryotes
In eukaryotes, mRNA is synthesized by RNA Pol II as longer
precursors called heterogeneous nuclear RNA (hnRNA).
Among hnRNA, those processed to give mature mRNAs are
called pre-mRNAs
Pre-mRNA molecules are processed to mature mRNAs by 5’-
capping, 3’-cleavage and polyadenylation, splicing and
methylation.
Processing occurs primarily within the nucleus.5’ and 3’ ends of eukaryotic mRNA
5’-UTR
3’-UTR
Add a GMP
Methylate it and
1st few nucleotides
Cut the pre-mRNA
and add A’sEukaryotic mRNA processing: overview5’ Capping
• Very soon after RNA Pol II starts making a transcript, and before the RNA chain is more then 20 -30 nt long, the 5’end is chemically modified.
• A cap formed of 7-methylguanosine is covalently attached to the 5´ end of pre-mRNA.
• Linked 5´  5´ triphosphates linkage. • Occurs shortly after initiation.Function of 5´cap
Protection of the 5’ end of mRNA from attack by 5’ exonuclease.
Increased translational efficiency (Eukaryotic translation
initiation factor 4 (eIF4) recognizes and binds to the cap
as part of initiation).
Transport to cytoplasm.
Stimulate splicing of first exon.Polyadenylation of mRNA at the 3’ end
In most pre-mRNAs, the mature 3’-end of the molecule is generated by cleavage
followed by the addition of a run, or tail, of A residues which is called the poly(A) tail.
Pre-mRNA is cleaved ~20 nucleotides downstream of polyadenylation signal
(AAUAAA).
~250 AMPs are then added to the 3´ end by poly (A) polymerase enzyme.
Almost all mRNAs have poly(A) tail.Consensus sequence for 3’ process
AAUAAA: CstF (cleavage stimulation factor F)
GU-rich sequence: CPSF (cleavage and polyadenylation specificity
factor)Function of poly(A) tail
Increased mRNA stability.
Increased translational efficiency.
Splicing of last intron.mRNA splicing
Splicing (removal of introns and ligation of exons):-
oThe large mRNA precursor (hnRNA) contains 2 types of

sequences.
◦ Exons:- These are the coding sequences.
◦ Introns:- These are non-coding sequences.
oIntrons must be removed by a process called splicing.
oit takes place in the nucleus before the mature mRNA can be
exported to the cytoplasm.Spliceosome
 Spliceosome:- Is a special structure, involved in
converting the primary transcript into mature mRNA. It
consists of :
1- The primary mRNA transcript.
2- 5 small muclear RNAs (U1, U2, U4 , U5 and U6).
3- More than 60 polypeptides.
Collectively, they form a nucleoprotein complex sometimes
called “snurp”. There are conserved sequences at each of the 2 exon-intron junctions and at the branch site, which is located 20-40 nucleotides upstream from the 3’ splice site e.g the yeast consensus sequences.ALTERNATIVE mRNA
PROCESSING
Alternative splicing
RNA editingAlternative splicing
The generation of different mature mRNAs from
a particular type of gene transcript can occur by
varying the use of 5’- and 3’- splice sites in
different ways:
(i) By retaining certain introns.
(ii) By retaining or removing certain exons. Sex in Drosophila is largely
determined by alternative splicing
Note
Mutations in splice sites can lead to abnormal proteins. For example, mutations that interfere with proper splicing of B-globin mRNA are responsible for some cases of B-thalassemia.
Faulty splicing can cause disease. At least one form of β-thalassemia, a disease in which the ẞ-globin gene of hemo- globin is severely under-expressed, appears to result from a nucleotide change at an exon-intron junction, precluding removal of the intron and therefore leading to diminished or absent synthesis of the B-chain protein. This is a consequence of the fact that the normal translation reading frame of the mRNA is disrupted by a defect in the fundamental process of RNA splicing, underscoring the accuracy that the process of RNA-RNA splicing must maintain.
RNA editing
An unusual form of RNA processing in which the sequence of the primary transcript is altered is called RNA editing. Changing
RNA transcription). sequence (afterApolipoprotein-B mRNA in mammalian intestine and liver.
(Base modification: A or C deamination)
Liver
IntestinePre-mRNA methylation
The final modification or processing event that many pre-mRNAs undergo is specific methylation of certain bases. The methylations seem to be largely conserved in the mature mRNA. Secondary methylation of the mRNA molecules, on the 2’-hydroxy and the N6 of adenylyl residues, occur after the mRNA molecule has appeared in the cytoplasm. The rRNA genes are transcribed in nucleolus by RNA Pol I.
The eukaryotic 5S rRNA is transcribed by RNA Pol III .the transcript
undergoes little or no processingThe precursor contains:
one copy of the 18S coding region.
one copy each of the 5.8S and 28S coding regions, which together are the
equivalent of the 23S rRNA in prokaryote
The large precursor RNA undergoes a number of cleavages to yield mature RNA and
ribosome.Reverse TranscriptionCentral DogmaNormal transcription involves synthesis of RNA from DNA.
Reverse transcription is the transcription of single stranded RNA
into double stranded DNA
With the help of the enzyme Reverse Transcriptase.Retrovirus Replication Cycl