RNA

Three types of RNA

mRNA: messenger RNA

tRNA: transfer RNA-- amino acid transfer

rRNA: ribosomal RNA-- components of ribosomes, the protein assemble apparatus.

Template strand = antisense

Coding strand = sense

Transfer RNA Forms a Cloverleaf

dihydrouridine pseudouridine

Class I tRNAs: small extra arm, 3-5 bp, ~75%,Class II tRNAs: large extra arm, 13-21 bp, ~25%,

Covalent bond

CLOVERLEAF

LoopStem

The TC arm and the acceptor arm form continuous helix and so are the D arm and the anticodon arm.

The tertiary structure of tRNA is like the letter L

The acceptor stem and anticodon are at ends of tertiary structure of tRNAs

Aminoacyl-tRNA synthetase

Alanyl-tRNACys

Cysteinyl-tRNACys

Reduced

The Meaning of a tRNA Is Determined by Its Anticodon

Messenger RNA Is Translated by Ribosomes

•Bacteria ribosome: ~70S (50S + 30S)

•Higher eukaryotic cytoplasm ribosome: ~80S (60S + 40S)

S: Svedburgs: sedimentation rate.Bigger particle: higher S.Most Important use of S:Characterize ribosomes and source organism

The assembly of the ribosomal two subunits needs Mg2+

Ribonucleoprotein particle:rRNAs:

ProteinsBacteria:

23S, 16S, 5S 62Mammalian:

28S, 18S, 5.8S, and 5S 82

Polyribosomesbacteria: 10 ribosomes per mRNA;eukaryotes: ~8

30S subunit associates with mRNA;

50S S subunit carries the newly synthesized protein;

tRNA spans both subunits.

The Cycle of Ribosomes

The Life Cycle of Messenger RNAIn bacteria: transcription and translation occur in the single cellular compartment and are closely related. •mRNA life span: short, several minutes.•Transcription speed: ~40 nt/sec;•Translation speed: ~15 aa/sec;•Degradation speed: half of the speed of transcription & translation.

In eukaryotic cells: •transcription and maturation occur at nucleus; translation happens in the cytoplasm. •mRNA life span: longer, several hours.

Ribosomes bind to mRNA as soon as its 5’ was transcribed.

For each cistron in the polycistronic mRNA, a new ribosome is used sequentially.

Wait!

Eukaryotic mRNA is modified during or after transcription“Cap (a nucleotide (usually G) in

reverse 3’->5’ orientation) & Shoe (polyA)”,

Transcription, modification, processing, nucleocytoplasmic transport, and translation (animal cells)

Cleavage

Splicing?

Transport

Translation

Cleavage

5’ - 5’

The 5’ End of Eukaryotic mRNA Is Capped

The starting nt of an mRNA:5’ ppp(A/G) pNpNpNp...

pppApNpNpNp...Gppp5’ 5’+

ApNpNpNp… + pp + pGppp5’ -5’

Guanylyl transferaseMaturation

1 methyl group, Cap0 (guanine-7-methyl-transferase)

7

(2’-O-methyl-transferase)GTP

Cap1 (2 methyl groups)

Cap2(3 metyl groups)

The 3’ Terminus Is Polyadenylated

Poly(A) polymerase

Poly(A) binding protein (PABP)(One PABP monomer of ~70 kDa, binding polyA every 10-20 nts)

Functions of PolyA and PABP:1. Stablizing mRNA2. Removal (both polyA or PABP) will inhibit translation

The histone mRNAs do not have PolyA!

Prokaryote mRNA Degradation Involves multiple Enzymes

Endonucleases and exonucleasesEndonucleases degrading direction: 5’ -> 3’;Exonucleases degrading direction: 3’ -> 5’;

Bacterial polyA may play a role in mRNA degradation by proving a binding site for nucleases

Eukaryote mRNA Degradation Pathways

Deadenylation (exonuclease?)

Decapping

5’ – 3’ degradation by XRN1 (an exonuclease)

Yeast

The general model for the stabilization of mRNA:Stability is conferred by inhibiting the function of destabilizing sequences.

ARE (AU-Rich Element, 50 bps, at 3’ trailer) initiates degradation in unstable mRNAs

Block of IRE (Iron Response Element) sequences prevents degradation.

The Destabilization Elements on the Eukaryotic mRNAs

Deadenylation

Nonsense mutations trigger a surveillance system

Nonsense mutations may cause mRNA to be degraded.

A surveillance system could have two types of components. Protein(s) must bind in the nucleus to mark the result of a splicing event. Other proteins could bind to the mark either in the nucleus or cytoplasm. They are triggered to act to degrade the mRNA when ribosomes terminate prematurely.

Eukaryotic RNAs are transported

mRNA can be specifically localized

Ash1 mRNA forms a ribonucleoprotein containing a myosin motor that moves it along an actin filament.

Ash1 mRNA is exported from the nucleus into the cytoplasm where it is assembled into a complex with the She proteins. The complex transports it along actin filaments to the bud.