Ch 14 RNA Molecules & RNA Processing Flashcards
RNA coding regions
exons
RNA noncoding regions (intervening sequences)
introns
are introns more common in eukaryotes or bacteria?
introns are more common in eukaryotes
sequence of 3 nucleotides that encode an amino acid of a protein
codon
bacterial mRNA structure
5’ untranslated region (5’ UTR) (w/ Shine-Dalgarno sequence)
protein-coding region
3’ untranslated region (3’ UTR)
sequence of nucleotides at 5’ end of mRNA that do not encode any amino acids
5’ untranslated region (5’ UTR)
consensus sequence in bacterial mRNA only within 5’ UTR
serves as ribosomal binding site
Shine-Dalgarno sequence
codons that specify protein amino acid sequence from start to stop codon
protein-coding region
sequence of nucleotides at 3’end of mRNA that do not encode any amino acid
affects mRNA stability and regulates mRNA’s protein-coding sequence translation
3’ untranslated region (3’ UTR)
three steps of pre-mRNA processing in eukaryotes
- addition of 5’ cap
- addition of 3’ poly(A) tail
- removal of introns
why is there no pre-mRNA processing in prokaryotes?
transcription and translation occur simultaneously, and there is no pre-mRNA
describe the addition of 5’ cap process
- one of the three phosphates at the 5’end of mRNA is removed
- guanine nucleotide added
- methyl groups added
function of the addition of 5’ cap
- facilitates binding of 5’ ribosome to 5’ end of mRNA
- increases mRNA stability
- influences intron removal
describe the addition of poly(A) tail process
- pre-mRNA cleaved downstream of consensus sequence AAUAAA in 3’UTR
- adenine nucleotides (polyadenylation) added to 3’ end of pre-mRNA
50-250 adenine nucleotides added to 3’ end of pre-mRNA
poly(A) tail
what is the polyadenylation signal
consensus sequence AAUAAA located upstream of cleavage site
sequence rich in uracil located downstream of cleavage site
function of addition of poly(A) tail
- increases stability of mRNA
- facilitates ribosome attachment to 5’ cap
- helps exports mRNA to cytoplasm
removal of introns
RNA splicing
where does splicing occur?
in the spliceosome in the nucleus
what does the spliceosome consist of
five snRNAs (U1, U2, U4, U5, U6) combining with proteins to form 5 snRNPs, along with hundreds of other proteins
what are the three sequences in an intron that are present for splicing to occur
5’ splice site
3’ splice site
branch point
5’ end of intron
5’ splice site
3’ end of intron
3’ splice site
adenine nucleotide 5’ and 3’ splice sites
branch point
what would happen if the adenine nucleotide (branch point) of an intron was deleted?
splicing would not occur
describe pre-mRNA splicing
- pre-mRNA cut at 5’ splice site
- 5’ end of intron attaches to branch point to form lariat - pre-mRNA cut at 3’ splice site
- lariat branching enzyme breaks bond at branch point and lariat is released
- intron is degraded by nuclear enzymes
- exons spliced together
one pre-mRNA processed in different ways to produce different types of mRNA
alternative RNA processing
what’s the purpose of alternative splicing?
pre-mRNA spliced in more than one way to yield different mRNAs –> diff amino acids –> diff proteins
what’s the purpose of multiple 3’ cleavage sites?
3’ cleavage could occur at different locations and therefore produce different proteins
two parts of addition of poly(a) tail
cleavage
polyadenylation
coding sequence of mRNA molecule altered AFTER transcription
RNA editing
RNAs that contain partly complementary sequences to unedited RNA
guide RNAs (gRNAs)
describe RNA editing
- unedited mRNA pairs with guide RNA
- Guide RNA serves as template for addition, deletion, or alteration of bases
- mature mRNA released
carries specific amino acid to ribosome to be incorporated into growing polypeptide chain
tRNA
how do modified bases arise?
t-RNA-modifying enzymes chemically change a nucleotide base after transcription
describe structure of tRNA
- cloverleaf structure due to complementary base pairing
- acceptor arm
- TΨC arm
- anticodon arm
- DHU arm
what is the acceptor arm
stem formed from 5’ and 3’ ends base pairing, and contains CCA, which is where amino acid attaches
what is the TΨC arm
contains thymine, pseudourine, and cytosine
what is the anticodon arm
comprises three bases (anticodon) and interacts with codon in mRNA
describe tRNA processing
tRNA may undergo cleavage, splicing, base addition, and base modification
complex where genetic instructions of mRNA are translated into amino acid sequence of polypeptides
ribosomes
structure of ribosomes
protein + rRNA
large ribosomal subunit and small ribosomal subunit
describe prokaryotic rRNA processing
each rRNA gene transcribed into 30S rRNA precursor, which is methylated, cleaved, and trimmed
describe eukaryotic rRNA processing
snoRNAs associate with proteins to form snoRNPs, which help to cleave, modify, and assemble into mature rRNA
defense mechanism to limit invasion of foreign genes by controlling expression of their own genes
RNAi (RNA interference)
what triggers RNAi?
double-stranded RNA molecules
chops up double stranded RNA to produce miRNAs or siRNAs
dicer
how do dsRNA arise?
- inverted repeats in RNA base pair with self to form dsRNA
- two complementary RNA pair to form dsRNA
- infection from viruses form dsRNA
describe miRNAs (origin, cleavage of, complementarity, action, target)
- cleaved from RNA transcribed from distinct gene
- form from cleavage of single-strand RNA that forms short hairpins
- limited complementarity with target mRNAs
- inhibit translation
- target genes different than those from which they were transcribed
describe siRNAs (origin, cleavage of, complementarity, action, target)
- cleaved from mRNA, transposons, RNA viruses
- form from cleavage of RNA duplex of 2 diff RNA or ssRNA that form long hairpins
- exact complementarity with target RNA or DNA
- degrade mRNA
- target genes from which they were transcribed
miRNAs and siRNAs combine with proteins to form
RNA-induced silencing complex (RISC)
describe how miRNAs are used for RNAi
- transcription of an inverted repeated produces primary miRNA, which is cleaved to produce RNA with hairpin
- dicer chops up terminal loop of hairpin
- miRNA + proteins = RISC
- RISC pairs with mRNA to inhibit translation
describe how siRNAs are used for RNAi
- double stranded RNA cleaved by dicer to produce siRNAs
- siRNAs + proteins = RISC
- RISC pairs with and cleaves mRNA, leading to degradation
series of palindromic sequences separated by spacers
CRISPR array
what do CRISPR RNAs do?
combine with Cas proteins to provide defense against invasion of foreign DNA
describe the CRISPR-Cas system
aquisition
expression
interference
foreign DNA enters cell, identified, processed, and inserted into CRISPR array as a new spacer and serves as a memory
aquisition
CRISPR array transcribed into long precursor RNA; cleaved by Cas proteins; processed into crRNAs (each with a foreign DNA spacer sequence)
expression
crRNA + Cas protein
effector complex
foreign DNA enters cell again; effector complex binds and cleaves foreign DNA
interference
