chapter 8 part 3 Flashcards
what part of the mRNA transcript becomes the mature mRNA
exons
are introns in bacterial genes?
rarely - not really
are there introns in archaeal gene?
occasionally
2 methods for removing introns
- spliceosome complex
- self-splicing
how are group I and II introns removed
self-splicing
how are pre-mRNA introns removed
spliceosome complex
how are rRNA and tRNA introns removed
enzymatic activity
why does intron splicing have to be precise?
to remove nucleotides accurately, errors would lead to inccorect protein sequences
who is responsible for the discovery of “split genes”
Roberts and Sharp - 1993 Nobel prize
R-looping
DNA gene is isolated, denatured, and hybridized to mature mRNA from the same gene
- regions of DNA where introns are present have no complementary region within the mRNA and loop out visibly
intron splicing signals
- 5’ splice site
- 3’ splice site
- branch site
5’ splice site
has consensus sequence with an invariant GU dinucleotide
3’ splice site
11 nucleotide consensus w/ pyrimidine-rich region and nearly invariant AG
branch site
20-40 nucleotides upstream of 3’ end of intron
- pyrimidine-rich
- contains invariant adenine called branch point adenine near 3’ end of consensus
splicing action of spliceosome
- 5’ splice site cleaved first
- variant intron structure formed when 5’ intron binds to branch point adenine
- 3’ splice site cleaved
- exons ligated together
are introns always removed by the spliceosome in order?
no
composition of spliceosome
small nuclear ribonucleoprotein particles (snRNPs U1-U6)
is the composition of spliceosome steady?
no, always changing through steps of splicing
how are spliceosome components recruited to splice sites
SR proteins that bind to exotic splicing enhancers to ensure accurate splicing
what is the function of the carboxyl terminal domain (CTD) of RNA polymerase II?
assembly platform and regulator pre-mRNA processing machinery
gene expression machines
proteins that carry out capping, intron splicing, and polyadenylation associate with CTD of pol II
CTD and RNase
degrades residual transcript resulting from 3’ cleavage and trigger termination of transcription
how many proteins are produced for one gene
can be many due to alternative mRNA processing
3 transcription-associated mechanisms that explain more proteins than genes
- pre-mRNA spliced in alternative patterns
- alternative promoters can initiate transcription at different start points
- alternative sites for polyadenylation
how many human genes are thought to undergo alternative splicing
70%
human calcitonin/calcitonin gene-related peptide and alternative splicing
- gene has 6 exons, 2 alternative polya sites
- thyroid cells: exon 4 polya site to produce calcitonin
- neuronal cells: splice exon 4, use exon 6 polya site to produce CGRP
Drosophila Dscam gene
- 24 exons: 4, 6, 9, and 17 have alternative sequences
- more than 38,000 dif polypeptides can be produced
alternative promoters
occur when 1+ sequence upstream of a gene can initiate transcription
alternative polyadenylation
requires 1+ polyadenylation signal in a gene
group I introns and self-splicing
takes place via 2 transesterification reactions that excise intron and ligate exon ends
what are group I and group II introns?
large, self-splicing ribozymes that catalyze own excision
- group I: bacteria, simple eukaryotic, plants
- group II: archaea, bacteria, mitochondrial and chloroplast
group II introns and self-splicing
form very complex secondary structures and their self-splicing takes place in a lariat-like manner
how are bacteria and eukaryotic rRNAs transcribed?
in large precursor molecules that are cleaved into smaller molecules by the removal of spacer sequences between the rRNA genes
what do rRNAs do after processing
fold into complex secondary structures and join ribosomal proteins to form ribosomal subunits
what do all tRNAs have in common?
similar structure, but dif nucleotide sequences
overview of bacterial tRNA production
some produced simultaneously with rRNAs, others transcribed as large pre-tRNA transcript and cleaved into ind. molecules
overview of eukartyouic tRNA production
each tRNA gene individually transcribed
how many organisms do tRNAs usually produce?
30-40, fewer than 61 due third-base wobble
what do bacterial tRNAs required before assuming their function role?
processing
processing of bacterial tRNAS
- CLEAVAGE from large precursor molecule to small
- TRIM nucleotides from 3’ and 5’ ends
- CHEMICALLY MODIFY certain nucleotides
- fold into 3D STRUCTURE
- postranscriptional ADDITION of bases (CCA at 3’ end)
3D structure of tRNA
4 double-stranded stems, 3 of which capped by single-stranded loops
do eukaryotic tRNAs undergo processing?
yes, may also include small introns that are removed
RNA editing
responsible for post-transcriptional modifications to nucleotide sequence and protein produced of some mRNAs
guide RNA
takes part in a kind of RNA editing, and adds uracils to mRNA
base substitution
replacing one base with another
frequent base substitution
replacing cytosine with uracil
example of base substitution
production of 2 different apolipoprotein B proteins from single gene in human liver and intestinal cells
- intestinal: produces premature stop codon, produces smaller protein than liver
cis-splicing
connecting exons from single mRNA
trans-splicing
connecting exons from multiple different mRNAs
intragenic splicing
exons from single mRNA, often repeated exons
intergenic splicing
exons from more than 1 type of mRNA
