RNA processing
Define a codon
A set of three nucleotides in a mRNA that specifies a protein
How is the guanine nucleotide attached to the 5' end of mRNA? what does it replace?
A unique 5'-5' bond It replaces one of the three 5' phosphate groups
In the addition of the 5' cap, what is added?
An extra guanine nucleotide methyl groups are added to the base in that guanine to the 2' -OH group of the sugar of one or more nucleotides at the 5' end ^ ask long
How does transcription and translation occur simultaneously in bacteria?
The 3' end of mRNA is undergoing transcription while the ribosomes attach to the free 5' end containing the Shine-Delgarno sequence and begin translation
Where do ribosomes bind on a eukaryotic mRNA?
The 5' end It does not contain the Shine-Delgarno sequence
After the pre-mRNA is cut at the 5' splice sit, what does it attach to?
The 5' end of the intron attaches to the branch point
T or F: the 5' cleavage and lariat from at different times
false: the occur in a single step
Cleavage at the ____3' cleavage site produces a short mRNA compared to the mRNA produces at the ____ 3' cleavage site of alternative splicing
first second
What is the protein coding region in mRNA?
location of codons that specify amino acid sequence of the protein begins with a start codon and ends with a stop codon
RNA that carries genetic information from DNA to ribosome
mRNA
RNA that does *not* contain introns
mRNA
RNA that helps to assemble amino acids in their correct order
mRNA
RNA that is the primary transcript in bacteria
mRNA
RNA that is the template for protein synthesis
mRNA
RNA that undergoes translation
mRNA
The spliceosomal mechanism of nuclear pre-mRNAs requires what molecule?
small nuclear RNAs
In spliceosome mediated splicing, what attaches to the 5' splice site
snRNP U1
In spliceosome mediated splicing, what attaches to the branch point?
snRNP U2
U1, U2, U4, U5, U6 are types of
snRNPs
The 5' ______ of the guanine nucleotides becomes attached to the ____ group of the adenine nucleotide at the branch point
phosphate 2'-OH
Processing the 3' end of the pre-mRNA requires _______ __________ located both upstream and downstream of the site where cleavage occurs
polyadenylation signal (sequences)
Where is the first methyl group added in the addition of the 5' cap? where is the second methyl group added?
position 7 of the base of the terminal guanine nucleotide the 2' position of the sugar in the second and third nucleotides
"immature" RNA that is the primary transcript of transcription in eukaryotes
pre-mRNA
RNA that contains introns
pre-mRNA
The first step of splicing:
pre-mRNA is cut at the 5' splice site
Alternative splicing is controlled by ____ and _____ that bind to sites within introns and exons and determine which splice and cleavage sites are used
proteins ribonucleoprotein
The poly A tail facilitates attachment of the ________ to the mRNA and plays a role in the _________ of mRNA to the cytoplasm
ribosome export
Alternative splicing enables exons to be spliced together in different combinations to yield mRNAs that encode different proteins. Multiple 3′ cleavage sites allow pre-mRNA to be cleaved and polyadenylated at different sites.
section summary
Eukaryotic pre-mRNAs are processed at their 5′ and 3′ ends. A cap, consisting of a modified guanine nucleotide and several methyl groups, is added to the 5′ end. The 5′ cap facilitates the binding of a ribosome, increases the stability of the mRNA, and may affect the removal of introns. Processing at the 3′ end includes cleavage downstream of an AAUAAA consensus sequence and the addition of a poly(A) tail. The poly(A) tail confers stability on the mRNA, plays a role in its export to the cytoplasm, and facilitates attachment of the ribosome.
section summary
Splicing of nuclear pre-mRNA introns is a two-step process: (1) the 5′ end of the intron is cleaved from the upstream exon and attached to the branch point to form a lariat, and (2) the 3′ end of the intron is cleaved from the downstream exon and the ends of the two exons are spliced together. In the process, the intervening intron is removed. These reactions take place within the spliceosome.
section summary
_______ possess the ability to remove themselves from an RNA molecule without the aid of enzymes or proteins.
self splicing introns
Splicing mechanism of group I introns
self-splicing
splicing mechanism of group II introns
self-splicing
There are multiple ____ cleavage sites that can produce a different protein from the same mRNA
3'
The 5' end of the intron is close to the ___ end of exon 1, and the 3' end of the intron is near the ___ of the exon 2
3' 5'
The __ end of exon 1 becomes attached to the __ end of exon 2 during splicing
3' 5'
The sequence of nucleotides at the 3' end of the mRNA that is not translated into amino acids
3' UTR
Three consensus sequences that determine where splicing will occur
3' and 5' splice site, and the branch point
Where is the poly A consensus sequence located in reference to the cleavage site?
11-30 nucleotides upstream
splicing by the minor spliceosome consists of introns with different consensus sequences at the ______ splice site and ____
5' branch point
Region of bacterial mRNA that Shine-Delgarno is located
5' UTR
3 regions of a mRNA molecule
5' UTR Protein coding region 3' UTR
Splicing requires the presence of three sequences in the intron called:
5' splice site consensus sequence 3' splice site consensus sequence branch point
How far is the Shine-Delgarno sequence from the start codon?
7 nucleotides
Group I introns fold into a common secondary structure with ______ during self splicing
9 hairpins
What does the Shine-Delgarno sequence pair to during translation?
A complementary sequence on the ribosome
What is the function of the 3' UTR?
Affects the stability of mRNA and regulates translation of mRNA into a protein coding sequence.
The tail on the 3' end is made up of which nucleotides? How many?
Adenine 50-250
Why does bacterial mRNA have little opportunity to be modified before translation?
Because transcription and translation occur simultaneously
Immediately following splicing, a group of proteins called the ________ is deposited about 20 nucleotides upstream of each exon-exon junction
Exon junction complex
The _____ promotes the export of the mRNA from the nucleus to the cytoplasm
Exon-junction complex
T or F: pre-mRNA is nucleotides only
False: pre-mRNA is nucleotides and phosphates
most introns in pre-mRNAs begin with the nucleotides __ and end with __
GU AG so GU is near the 5' end and AG is near the 3' end
Three types of introns
Group I Group II Nuclear pre-mRNA introns
What extra nucleotide is added to the 5' end of mRNA?
Guanine
Are the adenine nucleotides encoded in the DNA?
No, they are added via polyadenylation after transcription
how it is possible for a translated protein to have an amino acid sequence that differs from that of the encoded gene.
RNA editing
What is the function of the Shine-Delgarno sequence?
Ribosome binding site during translation
The UAAGGAGGU sequence of bacterial mRNA is called
Shine-Delgarno
What evidence from Berget et al. demonstrated that not all genes are continuous?
The DNA was much longer than mRNA because regions of DNA looped out from the hybridized molecules. These regions of DNA contained nucleotide sequences that were absent from the coding nucleotides in the mRNA. Confirmed that coding sequences in genes may be interrupted by noncoding sequences.
What does the ribosome bind to on the 5' end of the mRNA?
The cap binding proteins that are bound to the 5' cap
How does the 5' cap function in the initiation of translation?
The cap-binding proteins recognize the cap and attach to it the ribosome binds to these proteins and moves downstream along the mRNA until the start codon is reached and translation begins
In spliceosome mediated splicing, what causes a conformational change in the spliceosome?
The complex of U4, U5, and U6 joining the spliceosome
When the complex of U4, U5, and U6 causes a conformational change in the spliceosome, what occurs?
The intron loops over and the 5' splice site is brought close to the branch point
What does the poly A consensus sequence determine?
The point where cleavage will take place
Why are three phosphate groups at the 5' end of all RNA molecules?
They are not cleaved from the first nucleotide triphosphate in the transcription reaction
How are transcription and translation related in eukaryotes?
They are separated in both time and space
How are transcription and translation related in bacteria?
They take place simultaneously
Where does transcription and translation occur in eukaryotes?
Transcription: nucleus Translation: ribosomes
What features allows eukaryotic RNA to be modified before it is translated?
Translation and transcription occur at separate times
Particles ___ and ___ dissociate from the spliceosome once the 5' splice site is brought close to the branch point
U1 and U4
Base pairing occurs between ___ and ___ and between the ____ and 5' splice site during splicing
U6 and U2 U6
A sequence rich in _______ is usually downstream of the cleavage site
Uracil
Define a gene
a DNA sequence that encodes an RNA molecule the entire DNA sequence required to transcribe and encode an RNA molecule
The second step of splicing includes:
a cut is made at the 3' splice site and simultaneously, the 3' end of exon 1 becomes covalently attached (spliced) to the 5' end of exon 2
What forms when the 5' end attaches to the branch point during splicing?
a lariat
List the 3 types of RNA processing that mRNA undergoes
addition of 5' cap addition of poly(a) tail modification of eukaryotic pre-mRNA (RNA splicing)
The branch point consists of what nucleotide? Where is the branch point located relative to the 3' splice site?
adenine 18-40 nucleotides upstream of the 3' splice site
when does the addition of the 5' cap occur?
after the initiation of transcription
a single pre-mRNA can be processed in different ways to produce alternative types of mRNA, resulting in the production of different proteins from the same DNA sequence. this is an example of
alternative processing pathways
Term for the same pre-mRNA can be spliced in more than one way to yield different mRNAS that are translated into different amino acid sequences
alternative splicing
in RNA editing, the ____ of an mRNA molecule is altered after transcription, so that the translated protein has an amino acid sequence that differs from that encoded by the gene.
coding sequence
One way that eukaryotic cells regulate expression of genes is by controlling the ______ of mRNA
degradation
The ______ nucleotide in the consensus sequence at the 5' splice site bonds with the ____ nucleotide at the branchpoint through a _______ reaction
guanine adenine transesterification
what molecules play a crucial role in RNA editing
guide RNAs (gRNAs)
Where does splicing occur?
in the nucleus, before it moves to the cytoplasm
The 5' cap increases/decreases stability of the mRNA and influences the removal of ____
increases introns
How does guide RNA confer RNA editing?
it adds nucleotides to the mRNA that were not encoded by the DNA
o Key catalytic steps: § snRNP U1 attaches to the 5' splice site § U2 attaches to the branch point § Complex with U4, U5, and U6 form a single snRNP and join the spliceosome. § Addition of complex to spliceosome causes a conformational change in the spliceosome · Intron loops over and the 5' splice site is brought close to the branch point. § Particles U1 and U4 dissociate from the spliceosome, and base pairing occurs between U6 and U2 and between the U6 and 5' splice site. § The 5' splice site, 3' splice site, and branch point are now close in proximity, held together by the spliceosome.
key catalytic steps in spliceosome mediated splicing
When the two exons become covalently attached, the intron is released as a
lariat
group II introns are self spliced via a mechanism like spliceosome mediated splicing because they generate a ____
lariat
This enzyme breaks the bind at the branch point to produce a linear intron that is degraded by nuclear enzymes
lariat debranching enzyme
___ RNA consists of exons spliced together and is exported to the cytoplasm after splicing
mature
Mature RNA that has been completely processed is called
messenger RNA (mRNA)
__________ are present in the pre-mRNA for cleavage and polyadenylation
multiple 3' cleavage sites
Does the 5' and 3' UTR contain codons?
no
Experimental design of Berget et al. that demonstrated that not all genes are continuous (5 steps)
o Researchers observed four coding sequences in a gene from a eukaryote-infecting virus that were interrupted by nucleotides that did not specify amino acids. o Viral DNA was hybridized with the mRNA transcribed from it. § The DNA was much longer than mRNA because regions of DNA looped out from the hybridized molecules. § These regions of DNA contained nucleotide sequences that were absent from the coding nucleotides in the mRNA. o Concluded that eukaryotic genes consist of stretches of coding and noncoding nucleotides. (In eukaryotes, not all genes are colinear with the proteins they encode).
splicing mechanism of nuclear pre-mRNA introns
spliceosomal
Splicing of pre-mRNA takes place in the ______, which consists of snRNAs and proteins
spliceosome
removal of introns from pre-mRNA is called
splicing
The poly a tail and 5' cap are important in controlling degradation of the mRNA because they confer ______ on the mRNA by protecting them from 5' and 3' exonucleases. Thus they increase the _____ during which mRNA remains intact and available for translation before it is degraded by enzymes
stability time
Where are the adenine tail added?
the 3' end
3 regions where are changes made to alter mRNA after transcription in eukaryotes?
the 5' and 3' end, and the protein coding region.
Are adenine nucleotides added with or without a template to the 3' end to create the poly A tail
without a template
Two _____ reactions join the two exons together and release the intron as a lariate The __ snRNP catalyzes both reactions
transesterification U6
