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RNA

RNA. Coding strand = sense. Template strand = antisense. Three types of RNA mRNA: messenger RNA tRNA: transfer RNA-- amino acid transfer rRNA: ribosomal RNA-- components of ribosomes, the protein assemble apparatus. Transfer RNA Forms a Cloverleaf. Covalent bond. pseudouridine.

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RNA

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  1. RNA Coding strand = sense Template strand = antisense Three types of RNA mRNA: messenger RNA tRNA: transfer RNA-- amino acid transfer rRNA: ribosomal RNA-- components of ribosomes, the protein assemble apparatus.

  2. Transfer RNA Forms a Cloverleaf Covalent bond pseudouridine dihydrouridine Loop Stem CLOVERLEAF Class I tRNAs: small extra arm, 3-5 bp, ~75%, Class II tRNAs: large extra arm, 13-21 bp, ~25%,

  3. The acceptor stem and anticodon are at ends of tertiary structure of tRNAs The TC 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

  4. The Meaning of a tRNA Is Determined by Its Anticodon Aminoacyl-tRNA synthetase Cysteinyl-tRNACys Reduced Alanyl-tRNACys

  5. Messenger RNA Is Translated by Ribosomes Ribonucleoprotein particle: rRNAs: Proteins Bacteria: 23S, 16S, 5S 62 Mammalian: 28S, 18S, 5.8S, and 5S 82 S: Svedburgs: sedimentation rate. Bigger particle: higher S. Most Important use of S: Characterize ribosomes and source organism • Bacteria ribosome: • ~70S (50S + 30S) • Higher eukaryotic cytoplasm ribosome: ~80S (60S + 40S) The assembly of the ribosomal two subunits needs Mg2+

  6. Polyribosomes bacteria: 10 ribosomes per mRNA; eukaryotes: ~8 30S subunit associates with mRNA; 50S S subunit carries the newly synthesized protein; tRNA spans both subunits.

  7. The Cycle of Ribosomes

  8. The Life Cycle of Messenger RNA • In 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.

  9. 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!

  10. 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) 5’ - 5’ Cleavage Cleavage Splicing? Transport Translation

  11. The starting nt of an mRNA: 5’ ppp(A/G) pNpNpNp... GTP 5’ -5’ Gppp ApNpNpNp… + pp + p The 5’ End of Eukaryotic mRNA Is Capped 1 methyl group, Cap0 (guanine-7-methyl-transferase) Cap1 (2 methyl groups) 7 (2’-O-methyl-transferase) 5’ 5’ + Cap2 (3 metyl groups) Gppp pppApNpNpNp... Guanylyl transferase Maturation

  12. 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 mRNA 2. Removal (both polyA or PABP) will inhibit translation The histone mRNAs do not have PolyA!

  13. Prokaryote mRNA Degradation Involves multiple Enzymes Endonucleases and exonucleases Endonucleases 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

  14. Eukaryote mRNA Degradation Pathways Yeast Deadenylation (exonuclease?) Decapping 5’ – 3’ degradation by XRN1 (an exonuclease)

  15. The Destabilization Elements on the Eukaryotic mRNAs ARE(AU-Rich Element, 50 bps, at 3’ trailer)initiates degradation in unstable mRNAs Block of IRE (Iron Response Element) sequences prevents degradation. Deadenylation The general model for the stabilization of mRNA: Stability is conferred by inhibiting the function of destabilizing sequences.

  16. Nonsense mutations trigger a surveillance system 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. Nonsense mutations may cause mRNA to be degraded.

  17. Eukaryotic RNAs are transported

  18. 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. mRNA can be specifically localized Ash1 mRNA forms a ribonucleoprotein containing a myosin motor that moves it along an actin filament.

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