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FCH 532 Lecture 18. Exam on Friday, Mar. 19 Extra Credit due on Friday Chapter 31: RNA processing. Messenger RNA splicing. A pulse-chase experiment. Pulse-chase labeling studies indicated two important characteristics of eukaryotic RNA:

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fch 532 lecture 18
FCH 532 Lecture 18

Exam on Friday, Mar. 19

Extra Credit due on Friday

Chapter 31: RNA processing

messenger rna splicing
Messenger RNA splicing

A pulse-chase experiment

  • Pulse-chase labeling studies indicated two important characteristics of eukaryotic RNA:
  • 1. Most of the rapidly-synthesized RNA in the nucleus never reached the cytoplasm.
  • 2. The rapidly-synthesized nuclear RNA was much larger on average than cytoplasmic RNA.

+ 32P phosphate for

30 seconds (“pulse”)


+31P for 10 minutes (“chase”)



heteroduplex analysis the first evidence of splicing
Heteroduplex analysis-the first evidence of splicing

Viral DNA

  • The annealing of viral DNA also occurred


Virus-infected cells

Isolate mRNA

Anneal, shadow with heavy metals,

analyze in EM

heteroduplex analysis continued
Heteroduplex analysis-continued


  • The appearance of D-loops (displacement loops) in the DNA-RNA hybrid indicated the presence of regions of DNA that were transcribed, but later discarded from the RNA product.

Intron sequences not present in

mature mRNA


eukaryotic genes alternating expressed and unexpressed sequences
Eukaryotic genes: alternating expressed and unexpressed sequences
  • Most eukaryotic genes are intersperesed with unexpressed regions.
  • Primary sequences vary greatly in length (~2000 - 20,000 nt); much larger than expected based on the proteins encoded-heterogeneous nuclear RNA (hnRNA).
  • premRNAs are processed by the excision of internal sequences (introns) which can be 4-10 times longer in aggregate length than the expressed seqeuences (exons).
dna rna heteroduplexes
DNA-RNA heteroduplexes
  • Annealing RNA from virus-infected cells with viral DNA revealed the existence of seven introns-transcribed regions of the DNA removed from the mature mRNA. How would you prove the loops were DNA and not RNA?

Interpretation of the EM image:

Figure 31-47 The sequence of steps in the production of mature eukaryotic mRNA as shown for the chicken ovalbumin gene.

Page 1258

rna sequence at the exon intron junctions
RNA sequence at the exon-intron junctions
  • Introns contain invariant 5’-GU and AG-3’sequences at their borders
  • Internal intron sequences are highly variable even between closely related homologous genes.
exons spliced in two stage reaction
Exons spliced in two-stage reaction
  • 1. The 2’-OH group of a specific intron A residue nucleophilically attacks the 5’-phosphate at the 5’ intron boundry to create a 2’-5’-phosphodiester bond (lariat structure).
  • 2. The free 3’-OH group forms a 3’,5’-phosphodiester bond with the 5’ terminal residue of the 3’ exon, thereby splicing the two exons together and releasing the intron as a larioat with a free 3’-OH.
overall process of splicing pre mrna
Overall process of splicing pre-mRNA
  • Two trans-ester-ification reactions occur: first, between the G at the 5’ end of the intron and an A 2’OH near the 3’ end of the intron; second, between the released 3’ end of the first exon and and the 5’ end of the second exon.
ribozyme activity
Ribozyme activity
  • Group I introns found in nuclei, mitochondria, and chloroplasts. RNA acts as an enzyme in this group (ribozyme).
  • Studies performed by Thomas Cech with Tetrahymena thermophila.
figure 31 50 the sequence of reactions in the self splicing of tetrahymena group i intron
Figure 31-50 The sequence of reactions in the self-splicing of Tetrahymena group I intron.

1. The 3’-OH group of the guanosine forms a phosphodiester bond with the intron’s 5’ end, liberating the 5’ exon.

2. The terminal 3’-OH group of 5’ exon forms a phosphodiester bond with the 5’ terminal phosphate of the 3’ exon-this splices together the two exons and releases the intron.

3. The 3’-terminal OH group of the intron forms a phosphodiester bond with the phosphate of the nucleotide 15 residues form the intron’s 5’ end, yielding the 5’-terminal fragment with a cyclized intron.

Page 1260

ribozyme activity14
Ribozyme activity
  • Group II introns occur in mitochondria of fungi and plants are also self-splicing.
  • Nuclear pre-mRNA splicing is mediated by spliceosomes.
  • Mediated by small nuclear ribonucleoproteins (snRNPs).
  • U1-snRNA-U-rich snRNA; partially complementary to the consensus sequence of the 5’ splice site.
  • U2-snRNP, U4-U6-snRNP, U5-snRNP.
summary of the three steps in pre mrna processing
Summary of the three steps in pre-mRNA processing
  • The final mRNA may represent less than 5% of the transcribed DNA sequence
Alternative splicing and/or poly A sites increase the effective coding capacity of eukaryotic genomes
why introns
Why introns?
  • 1. Evolutionary arguments-represent sites of recombination between primordial mini-genes-the exons
  • 2. Function in mRNA export from the nucleus?
  • 3. Allow a variety of protein products from a single gene by alternative splicing.
  • 4. Selfish DNA (no function)
  • RNA processing occurs by a variety of mechanisms to convert a primary transcript into a final function RNA product
  • Eukaryotic pre-mRNAs are capped, polyadenylated, and spliced to yield one or more mature mRNAs before transport to the cytoplasm. These processes are coupled in the nucleus so that only properly processed mRNAs are exported to the cytoplasm
  • The role of introns is still controversial but the favored hypothesis is that they arose early in evolution and allowed recombination between mini-genes. They have been almost eliminated in bacteria and many lower eukaryotes perhaps because these organisms require a small genome for rapid replication.
  • Translation-the synthesis of polypeptides from mRNA.
  • Genetic code-degenerate codons.
  • 3 nucleotides per codon. Reading frames can be disrupted by changes in the triplet codon.
chemical mutagenesis
Chemical mutagenesis
  • One way of changing the genetic code occurs through chemical mutagenesis-addition of substances that chemically induce mutations.
  • 2 major classes of mutations:
  • Pointmutations-one base pair replaces another.
    • Transitions-one purine or pyrimidine is replaced by another.
    • Transversions-purine is replaced by a pyrimidine or vice versa.
  • Insertion/deletion mutants-one or more nucleotide pairs are inserted into or deleted from DNA.
figure 32 1 bromouracil
Figure 32-1 Bromouracil.
  • 5-bromouracil a base analog that resembles T but because of the electronegative Br, tautomerizes to to pair with G instead of A.
  • If 5 BU is incorporated into DNA in place of T, can induce A-T to G-C transitions.
  • Can also incorporate in place of C to generate G-C to A-T transitions.

Page 1286


Figure 32-2 Base pairing by the adenine analog 2-aminopurine. It normally base pairs with thymine (a) but occasionally also does so with cytosine (b).

Page 1286


Figure 32-3 Oxidative deamination by nitrous acid.(a) Cytosine ® uracil, which pairs with A.(b) Adenine ® hypoxanthine, which pairs with C.

Page 1287

Figure 32-4 Reaction with hydroxylamine converts cytosine to a derivative that base pairs with adenine.

Page 1287

Figure 32-5 The three potential reading frames of an mRNA. Each reading frame would yield a different polypeptide.

Page 1289

genetic code
Genetic code
  • mRNAs are read in the 5’  3’ direction.
  • UAG, UAA, and UGA are Stop codons.
  • Stop codons are sometimes called nonsense codons and the individual codons are called amber (UAG), ochre (UAA) and opal (UGA) codons.
  • AUG and GUG are the most typical start codons - there can be others!
genetic code29
Genetic code
  • Genetic code is degenerate-3 amino acids (Arg, Leu, Ser) are specified by 6 codons.
  • Most others are specified by 2,3, or 4 codons.
  • Synonyms - different codons that specify the same amino acid.
  • Met and Trp have their own codons (AUG and UGG).
  • Most synonyms differ only in the third nucleotide position of the codon.
  • Most point mutations at a third position in a codon are silent mutations.
  • Degeneracy accounts for as much as 33% of the 25-75% G+C content among DNAs from different organisms.
  • High conc. of Arg, Ala, Gly, and Pro = high G+C content.
  • High conc. of Asn, Ile, Lys, Met, Phe, and Tyr = low G+C content.

Figure 32-7The adaptor hypothesis. It postulates that the genetic code is read by molecules that recognize a particular codon and carry the corresponding amino acid.

Page 1292

transfer rna trna
transfer RNA (tRNA)
  • tRNAs have a clover leaf structure.
  • tRNAs have many modified bases (up to 25%).
  • 5’ phosphate group.
  • 7-bp stem including a 5’ terminal nucleotid that may contain non-Watson-Crick base pairs (G-U) -acceptor or amino acid stem.
  • The amino acid is attached to the 3’-terminal OH group to form aminoacyl-tRNA.
  • Amino acids are attached by amino-acyl-tRNA synthetases (aaRSs).










+ PPi




transfer rna trna35
transfer RNA (tRNA)
  • Aminoacyl-AMP + tRNA aminoacyl-tRNA + AMP
  • 2 classes of aminoacyl-tRNA synthetases
  • Class I and Class II aaRSs have the same 10 members in all organisms.
  • Class I enzymes have two homologous polypeptide segments not found in other proteins
  • HIGH and KMSKS
  • Class II enzymes have 3 other sequences in common with Class I enzymes.
transfer rna trna37
transfer RNA (tRNA)
  • tRNA anticodons can recognize multiple codons.
  • Example, yeast tRNAPhe has the anticodon GmAA
  • Non-Watson-Crick base pairing can occur at the 3rd codon-anticodon position (site of degeneracy).
  • Wobble hypothesis
  • assumes that the first two codon-anticodon pairings have normal Watson-Crick pairing structures.
  • The third position has some “wobble” that allows for limited conformational adjustments in pairing geometry.







figure 32 25a wobble pairing a u g and i a wobble pairs both have been observed in x ray structures
Figure 32-25a Wobble pairing. (a) U · G and I · A wobble pairs. Both have been observed in X-ray structures.

Page 1307

wobble hypothesis
Wobble hypothesis
  • At least 32 tRNAs are required to translate all 61 triplet codons. 1 is used for the initiation codon.
  • Most cells have > 32 codons.
  • Mammals have > 150 tRNAs.
nonsense suppression
Nonsense suppression
  • Nonsense mutations (insertion of stop codon UAG, UAA, UGA) are usually lethal when inserted into an essential protein and prematurely terminating translation.
  • Can be rescued by a second mutation in another part of the genome (intergenic suppression).
  • Nonsense suppressor tRNA add an amino acid instead of stopping the sequence.
  • Amber (UAG), ochre (UAA) and opal (UGA) suppressors have been found.
  • Suppressors are mutants of minor tRNAs (not all of the tRNAs in that cell are suppressor tRNAs).
other suppressors
Other suppressors
  • Missense suppressors - act similarly to nonsense suppressors. They substitute one amino acid for another.
  • Frameshift suppressors- have 8 nucleotides in their anticodon loops instead of 7 so the read a 4-base codon.