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