Biochem 8- -RNA structure, folds and function

what % of genome is active and what does it produce?

5% is active and makes mRNA which codes for proteins and regulatory RNAs that control gene expression

what does snRNA and snRNPs do in mRNA?

• snRNA with snRNPs form the spliceosome

• snRNA U1/U2- with recognise the boundaries 5’ and 3’ ends of introns, between the intron/exons and remove the introns,

• snRNP- U4/U5/U6- brings ends of introns together and they’re looped out

where is ribosomal rRNA made? how’s it made and processed? WHAT is rRNA?

• made in the nucleolus of the nucleus as a precursor called 45S rNA

• cut into smaller fragments: 18S(small), 5.8S(large), 28S(large)

• rRNA is modified by small nucleolar RNA- snoRNA

rRNA is made to make the ribosome and make the small and large ribosomal subunits and holding proteins in the right positions. guides translocation of tRNA, aligns mRNA and tRNA

whyis rRNA modified and how is it modified

1. C/D small nucleolar RNA- insert methylation

2. H/ACA small nucleolar RNA- loops and ribosomal RNA is fed here to make pseudouridine which breaks the bond and movement of the uridine base

done to function properly in the ribosome

key functions of rRNA

1. recognises tRNA and anti-codon checking. 16S small ensures correct tRNA pairs with the mRNA on the A site for accurate translation

2. peptidyl transferase activity- 28S forms the PTC- peptide bonds are formed during translation, rRNA catalyses this reactions for elongation- links tRNA in A site to the peptide in the P site

what is the structure and function of tRNA in translation?

L shaped molecule with

1. anticodon loop which recognises mRNA codons

2. acceptor site- attaches the correct Amino acids- RNA is needed for this

describe what RNase P- what it is, function, mechanism

a ribozyme where RNA acts as the catalytic component- needed for mature tRNA

• RNA carries out the cleavage to make mature tRNA

• RNase P removes extra 5’ sequence from tRNA and leaves a terminal 5’

• does this by taking 3 magnesium ions in a pyramid shape- helps with hydrolysis of phosphodiester bond

• reusable!

what are endogenous siRNA- what do they do?

• made from hairpin RNA inside the cell

• chopped into 21 nucleotides accommodated by RISC complex- REPRESSED TRANSPOSONS by binding and degrading them- to protect the genome

how are microRNAs made and how do they regulate gene expression?

• start as long pri-miRNA in the nucleus

• Drosha- trims it into pre-miRNA hairpins

• Dicer in the cytoplasm- 22 nucleotide mature miRNA

• miRNA loaded onto miRISC

• binds to sequences on mRNA- to degrade it or block translation, up to 60% of human mRNA is bound by miRNA- if no miRNA-heart problems, cancer

what is piRNA- what do they do? where are they?

found in the gremlin cells like sperm

• long stranded transcripts and cut into 23-29nucleotide piRNAs

• bind to Piwi proteins to form piRISC complex

• silence transposons more strongly than miRNA- destroy the RNA and recruit methylation machinery- stop mutations during sperm/egg formation

what do small RNAs do- examples

• siRNA- RISC complex chops hairpin RNA into 21nt- binds to transposon RNA

• miRNA- regulates coding genes- drosha trims to pre-miRNA, dicer makes it mature by chopping to 22nt, loaded to miRISC- binds to mRNA to degrade it and stop translation- 60% human mRNA bound to miRNA

• piRNA- chopped into 23-29nt- piRISC complex(kiwi)- destroys transposon RNA and recruits methylation to stop mutations during egg/sperm

what is Xist? how does it work?

long non coding RNA- works in cis and regulates the chromosome its made from

• in females XX- one must be shut down and be a Barr body

• Xist is made from X inactivation centre in the chromosome that will be silences

• List coats the chromosome and replaces normal histones- PRC1/2 places repressive methylation at places like H3K27 . compaction by macroH2A

what is HOTAIR and how does it regulate genes?

HOTAIR long non coding RNA

• made from HOX-C cluster

• works in TRANS- regulates genes far away- HOTAIR is important for development and controls HOX genes which control patterns

• binds and recruits PRC2/PRC1- adds repressive histone marks like methylated H3K27 and turns off the gene(heterochromatin) and LSD1- removes active marks like methylated H3K4

HOTAIR guides PRC1 and LSD1 to distant HOX regions specific genes

compare and contrast Xist vs HOTAIR

where it acts: xist in cis(same chromosome), HOTAIR(trans)

purpose: Xist turns off one X chromosome, HOTAIR guides silencing of HOX genes

recruits: Xist macroH2A and PRC1/2, HOTAIR: PPRC2, LSD-1

effect: Xist: silences entire chromosome, HOTAIR silences gene for body patterning