Ch 16 RNA Processing

(*T/F*) Insertion of intron sequences is usually involved in the processing of primary mRNA transcripts.

*FALSE* You don't insert intron sequences

Translating from the first start codon to the stop codon? *5'- CGACAUG CCU AAA AUC AUG CCA UGG AGG GGG UAA CCU UUU*, what is the last amino acid in the resulting protein: *Met-Pro-Lys-Ile-Met-Pro-Trp-Arg-Gly-Tyr-Pro-Phe*

*Met-Pro-Lys-Ile-Met-Pro-Trp-Arg-Gly* (no -Tyr-Pro-Phe)

RNA splicing

Removal of introns and joining of exons in a primary transcript.

16.13 What are the two different sequences in the primary mRNA transcript that are critical to its cleavage in preparation for the addition of a poly(A) tail to the 3' end. Are either retained in the mature and modified mRNA?

5'AAU AAA and a GU-rich sequence. The 5' AAU AAA is retained in the mature mRNA.

(Small nuclear RNA) snRNA

A class of short, noncoding RNAs, typically 100 to 200 nucleotides long, found in the nucleus and involved in the splicing of eukaryotic mRNAs.

Exosome

A complex of 3' to 5' exonucleases in eukaryotic cells that processes the 3'ends of rRNAs and tRNAs and is responsible for RNA degradation in higher eukaryotes.

3' poly(A) tail

A length of adenosine residues (typically 80 to 250) added to the 3'end of many mRNAs in eukaryotes (and sometimes in bacteria), which serves as a binding site for proteins that protect the mRNA from exonucleases.

(Small nuclear ribonucleoproteins) snRNP

A protein and snRNA complex, found in the nucleus and a component of the spliceosome.

5' cap

A residue of 7-methylguanosine (7-meG) linked to the 5'-terminal residue of an mRNA through a 5',5'-triphosphate linkage, which protects the mRNA from exoribonucleases.

Spliceosome

A ribonucleoprotein complex that splices mRNAs in eukaryotic cells.

Intron

A sequence of nucleotides in a gene that is transcribed but excised before the gene is translated; also called intervening sequence. Also see exon.

Branch point

An internal A residue just upstream of the 3'splice site of an intron that attacks the phosphate at the 5'splice site, forming the loop of the intron lariat.

16.7 Is it correct to call an RNA molecule that catalyzes a reaction on itself an enzyme?

Enzymes remain unchanged after catalysis. Not the case for self-splicing and self-cleaving RNAs. They *are* catalysts b/c they enhance the rate of bond cleavage and/or joining. But they have only one reaction turnover. Some of these RNAs can be engineered to bind separate substrate molecules and catalyze reactions on multiple molecules, so they are enherently capable of functioning as enzymes; Example of naturally occuring is *RNase P*.

(*T/F) In the reactions that methylate the 5' end of the primary mRNA transcripts, the reaction occurs after the entire transcript is synthesized.

FALSE It occurs after it starts coming out

16.1 What would be the likely cellular effects of a large deletion in the gene encoding the polymerase responsible for adding 3' poly(A) tails to eukaryotic mRNAs?

Inactivation of the polymerase would lead to incomplete pre-mRNA processing, including 3' end formation, splicing, editing and transport. Would be lethal.

16.17 RNA enzymes (ribozymes) have been discovered in cells ranging from bacteria to humans. What kinds of reactions are catalyzed by these naturally occuring ribozymes?

Many naturally occuring ribozymes catalyze reactions involving other RNAs, mainly cleavage or splicing reactions. Ribozymes also catalyze the formation of peptide bonds on ribosomes.

16.6 Strains of bacteria lacking the enzymes required for rRNA modification have been engineered in the lab and seem to grow normally, despite the absence of modified rRNA. What would happen to these bacterial strains if they were forced to compete with wild-type bacteria?

Over many generations, the wild-type bacteria would win out, and the mutant strains would disappear. The normal rRNA modifications add subtle but important thermodynamic stability to the ribosome structure, enabling more robust protein synthesis in the wild type bacteria.

16.4 Self-splicing introns do not require an energy source (ATP or GTP) to catalyze splicing. How does self-splicing proceed with a reasonable yield of products?

Self-splicing catalyzes phosphodiester exchange reactions with no net loss or gain of energy. Bonds are broken and re-formed with different nucleotides, and there is no change in the number of bonds, just in the covalent bonding partners. Thus, no net change in free energy from reactants to products.

(*T/F) In the reactions that methylate the 5' end of the primary mRNA transcripts, the enzymes that catalyze the reactions are associated with the C-terminal domain of RNA polymerase II.

TRUE

(*T/F) In the reactions that methylate the 5' end of the primary mRNA transcripts, the enzymes that catalyze the reactions are guanylyltransferases.

TRUE

(*T/F) In the reactions that methylate the 5' end of the primary mRNA transcripts, the methyl groups are derived from S-adenosylmethionine.

TRUE

(*T/F*) Addition of multiple adenosines to the 3' end is usually involved in the processing of primary mRNA transcripts.

TRUE

(*T/F*) Covalent joining of exons is usually involved in the processing of primary mRNA transcripts.

TRUE

(*T/F*) Methylation of nucleotides at the 5' end is usually involved in the processing of primary mRNA transcripts.

TRUE

16.8 What accounts for the directionality of mRNA transport out of the nucleus?

The binding / hydrolysis of GTP by Ran ensures a cycle in which mRNA is bound in the nucleus and released in the cytoplasm and not in the reverse.

Primary transcript

The immediate RNA product of transcription before any posttranscriptional processing reactions.

16.9 What would happen to the lifetime of a human mRNA if a nonhydrolyzable phosphodiester analog were introduced near its 5' end?

The lifetime would increase b/c mRNAs in higher eukaryotes are degraded by 5'-->3' exonucleolytic digestion.

Exon

The segment of a eukaryotic gene that encodes a portion of the final product of the gene; a segment of RNA that remains after posttranscriptional processing and is transcribed into a protein or incorporated into the structure of an RNA. Also see intron.

Alternative Splicing

The splicing of exons from a single gene in various combinations to produce different mRNAs and thus different polypeptides.

A student is studying the localization of mRNA in the cell. The cells are treated with a monoclonal antibody to a protein contributing to processing (P) body structure. The (*nucleus | cytoplasm | both*) of the cell would most likely show immunofluorescence?

cytoplasm

The genetic code is degenerate because:

one particular amino acid can be encoded by more than one codon.