Chapter 10: RNA Modifications

5’ end capping

When a 7-methylguanosine (7-mG) is added to the 5’ end

3’ end polyadenylation

When a string of adenine is added to the 3’ end of RNA called a polyA tail

RNA splicing

Where RNA introns are spliced out and the exons are spliced together to make mature mRNA

RNA Processing

When Exonucleases cut larger RNA into smaller RNA. Typically happens with rRNA

RNA editing

When the nucleotide sequence of mRNA is changed before translation

Base Modification

When bases are modified by the addition of chemical groups such as methyl groups

RNA 5’ Triphosphate

Kinase used to remove one of the 3 phosphates from the first nucleotide. First nucleotide still has 3 phosphates.

Guanylyl Transferase

Cleaves GTP to GMP and attaches it to the 2 phosphate groups on 5’ end of RNA. Does weird 5’ to 5’ linkage.

Methyl Transferase

Attaches a methyl group to the added guanine

1) Binding siter for proteins that transport mRNA

2) Recognition site for translation factor proteins that help ribosome bind to mRNA

3) Protects from exonuclease digestion

3 Functions of 5’ Capping

CPSF

Cleavage Polyadenylation Specificity Factor is an endonuclease that recognizes the polyadenylation signal sequence of AAUUAAA. Cleaves pre-mRNA and releases RNAPII and mRNA

CstF

Cleavage Stimulatory Factor protein binds to a GU rich sequence. Activates CPSF

PAP

Poly (A) - Polymerase attaches 250 adenines to newly generated 3’ end of pre-mRNA. Does not require a template and only forms phosphodiester bonds between adenines

1) Protect 3’ end from exonuclease degradation

2) Promote transport of mRNA to cytoplasm from nucleus

3) Help ribosome bind to mRNA and initiate translation

3 functions of 3’ end polyadenylation

Group I

Remove introns in rRNAF

Group II

Remove introns in tRNA and mRNA

Self Splicing

Removing Group I introns is ____________ where pre-RNA catalyzes the removal of its own intron

Ribozymes

RNA enzymes

1) Free Guanosine Nucleoside (meaning no phosphates) binds to a pocket in the intron and serves as an enzyme cofactor

2) Break forms at junction between 3’ end of 1st exon and 5’ end of intron

3) Released 3’ end of first exon cleaves phosphodiester bond between the 3’ end of intron and 5’ end of second exon.

4) Phosphodiester bond is formed that links 1st and 2nd exons. Intron is released and degraded.

Steps in splicing of Group I introns by self splicing

1) 2’ OH group of adenine nucleotide within intron cleaves a phosphodiester bond between 3’ end of 1st exon and 5’ end of intron. adenine is an enzyme cofactor

2) Released 3’ end of 1st exon cleaves phosphodiester bond between 3’ end of intron and 5’ end of second exon.

3) Bond is formed between 2 exons and intron is degraded

Steps of removing group II introns

5’ Splice site

GU sequence at 5’ end of intron

Branch Site

An Adenine nucleotide near the middle of the intron

3’ splice site

AG sequence at 3’ end of intron

U1

snRNP that binds to 5’ splice site in intron and cuts it.

U2

snRNP that binds to branch site adenine

U5

snRNP that binds to 3’ end of intron and cuts it.

Lariat

Structure that is formed when 5’ splice site is cut and covalently linked to 2’ OH of branch site adenine

Mature mRNA

mRNA that has been modified and had it’s introns spliced out.

R Loop

This is a loop that is formed when doing a test for introns in mRNA. It forms because the mRNA binds to the template strand and so when the coding strand tries to bond it forms this loop

intron loops

These loops are formed when mature mRNA binds to template strand, the introns have been spliced out so the introns in template strand form a loop.

Genomic DNA

DNA found in the genome

cDNA

Complementary DNA is DNA that is formed by reverse transcription from mature mRNA

Alternative Splicing

WHen you splice pre-mRNA in different ways to produce multiple different mature mRNA’s. Allows for slightly different proteins to be produced

Isoforms

Proteins that are slightly different due to alternative splicing

Allows you to carry fewer genes that code for a vast array of proteins

Advantage of Alternative Splicing

Constitutive Exons

Exons that are in all versions of the proteins that are isoforms

Alternative Exons

Exons that are only found in certain proteins that are isoforms.

Splicing Factor Proteins

Proteins that allow the spliceosome to determine which intron splice sites to cut during RNA splicing.

Splice Repressors

Prevent spliceosome from recognizing 3’ splice sit in an intron and cause exon skipping

Splice enhancer sequences

Allow the splice activator protein to bind and make sure an exon will not be skipped.