1.Please describe the feature and biological roles of the CT

1.Please describe the feature and biological roles of the CTD tail of RNA Polymerase Ⅱ.
2.What are the chemistry and mechanism of the spliceosome-mediated splicing,group Ⅱintron splicing and group Ⅰintron splicing?
3.What is alternative splicing?What is the biological importance of alternative splicing?How alternative splicing is regulated (Note the involvement of the cis-acting elements and trans-acting factors)?

第一题：THE FEATURE：The largest subunit in RNA polymerase II has a carboxy-terminal domain (CTD)（羧基末端域）,which consists of multiple repeats of a consensus sequence of 7 amino acids.The CTD can be highly phosphorylated on serine or threonine residues.
BIOLOGICAL ROLES：(1) During promoter escape,phosphorylation of the CTD by the kinase activity of TFIIH may help the polymerase leave behind the promoter and GTFs and enter elongation phase.(2) During transcription elongation and processing,many elongation factors and RNA professing proteins are loaded to polymerase,nascent mRNA and/or processing machinery through the CTD tails.Therefore,through the CTD tail,synthesis and processing of the new mRNAs are highly coupled and coordinated to ensure the production of high quality mRNA for translation.
(Note:区分真核和原核.题目中指明为RNAP ⅱ,说明为真核生物.另外原核生 物pol的CTD称为α-CTD.)
第二题CHEMISTRY：splicing occurs as two sequential ester-transfer reactions（两个连续的转酯反应）.Firstly,the 2’OH of the branch point A attacks the phosphoryl group of a conserved 5’ G at he 5’ splice site,resulting in the free of 5’ exon from the intron.Then,the 3’ OH of the
free 3’ end of 5’ exon attacks a phosphoryl group at the 3’ splice site,resulting in the ligation of the 5’ and 3’ exons and release of a lariat form (套索结构)of intron.
MECHANISM：步骤一,formation of the E (early) complex by recognition of the 5’ splice site,3’ splice site and A branch point by U1 snRNP,U2AF and BBP respectively.
步骤2,U2 snRNP bind to the branch site to replace BBP forms A complex.The base-pairing between U2 snRNA with the branch site make the conserved A residue in the branch site extruded from the paired region,and thus this A is ready to carry the nucleophile attack.The tri-snRNP U4/U6/U5 joins and A complex is arranged to B complex in which the three splice sites are brought together.In this complex U4/U6 snRNPs are held together tightly by extensive base-pairing between U4 and U6 snRNAs.
步骤三,U1 leaves the complex,and U6 occupies the 5’ splice site by base-pairing.U4 leaves the complex,allowing the RNA components of U2 and U6 to base pair to produce the active site.The branch site A attacks the 5’ splice site,forming the 3-way junction and C complex.The 5’ splice site then attacks the 3’ splice site,freeing the intron lariat and forming the mRNA product.
二类内含子剪接:the chemistry is the same as that of the
spliceosome-mediated mRNA splicing,but the splicing is catalyzed by the intron RNA itself,which is also named as self-splicing.
一类内含子剪接：Chemistry:the 3’ OH of an exogenous G nucleotide or nucleoside attacks the 5’ splice site to undergo the first ester-transfer reaction.Then the 3’OH of the 5’ exon attacks 5’ phosphate of at the 3’ splice site,resulted in the release of a linear intron and ligated exons.The splicing is catalyzed by the intron RNA itself as the group II intron does.
第三题：Alternative splicing（选择性剪接） :many protein-encoded genes in higher eukaryotes contain multiple introns and can be spliced in alternative ways to generate two or more different mRNAs.
Biological functions （生物学作用）:Alternative splicing allows individual genes to produce multiple protein isoforms,thereby playing a central part in expanding protein diversity from a limited number of genes and regulating gene expression in higher eukaryotes .Alternative splicing also has a largely hidden function in quantitative gene control,by targeting RNAs for nonsense-mediated decay.
Regulatory mechanisms（调节机制） :alternative splicing is regulated by trans-acting factors （顺式作用因子）(activators or repressors) that recognize an arrangement of positive and/or negative cis-acting sequence elements（反式作用元件） called exonic (or intronic) splicing enhancers or silencers.An interplay between cis-acting sequences and trans-acting factors
modulates the splicing of regulated exons.Activators include members of the SR protein family and can activate splicing by binding to exon splicing enhancers (ESEs) using RNA-recognition domain and recruiting the splicing machinery using RS domain.Repressors are frequently members of the heterogeneous nuclear
ribonucleoprotein (hnRNP) family,which bind to exonic/intronic splicing silencers,blocking specific splice site