Ch 7

The following segment of DNA is from a transcribed region of a chromosome. You know that RNA polymerase moves from left to right along this piece of DNA, that the promoter for this gene is to the left of the DNA shown, and that this entire region of DNA is made into RNA. 5′-GGCATGGCAATATTGTAGTA-3′ 3′-CCGTACCGTTATAACATCAT-5′ Given this information, a student claims that the RNA produced from this DNA is: 3′-GGCATGGCAATATTGTAGTA-5′ Give two reasons why this answer is incorrect

1) The RNA molecule should have uracil instead of thymine bases. 2) The polarity of the molecule is incorrectly labeled. The correct RNA molecule produced, using the bottom strand of the DNA duplex as a template, would be: 5′-GGCAUGGCAAUAUUGUAGUA-3′

Below is the sequence from the 3′ end of an mRNA. 5′-CCGUUACCAGGCCUCAUUAUUGGUAACGGAAAAAAAAAAAAAA-3′ If you were told that this sequence contains the stop codon for the protein encoded by this mRNA, what is the anticodon on the tRNA in the P site of the ribosome when release factor binds to the A site? [see genetic code, last page]

5′-CCA-3′ The stop codon (UAA) is underlined in the mRNA sequence below; this is the only stop codon on this piece of mRNA. The codon (UGG) preceding the stop codon will be binding to a tRNA in the P site of the ribosome when release factor binds to the A site. The anticodon of the tRNA will bind to the codon UGG and will be CCA. 5′-CCGUUACCAGGCCUCAUUAUUGG*UAA*CGGAAAAAAAAAAAAAA-3′

Which of the following molecules of RNA would you predict to be the most likely to fold into a specific structure as a result of intramolecular base-pairing? A) 5′-CCCUAAAAAAAAAAAAAAAAUUUUUUUUUUUUUUUUAGGG-3′ B) 5′-UGUGUGUGUGUGUGUGUGUGUGUGUGUGUGUGUGUGUGUG-3′ C) 5′-AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA-3′ D) 5′-GGAAAAGGAGAUGGGCAAGGGGAAAAGGAGAUGGGCAAGG-3′

A) 5′-CCCUAAAAAAAAAAAAAAAAUUUUUUUUUUUUUUUUAGGG-3′ In order to base pair, intrastrand complementarity is required (C-G pairs and U-A pairs). More complementarity will lead to a greater likelihood for the formation of a specific structure.

What might decrease the transcription of only one specific gene in a bacterial cell

Amutation that introduced extensive sequence changes into the DNA that precedes the gene's transcription start site. Changes in the DNA in the region that precedes the gene's transcription site would probably destroy the function of the promoter, making RNA polymerase unable to bind to it. Decreasing the amount of sigma factor or RNA polymerase would affect the transcription of most of the genes in the cell, not just one specific gene. Introducing a stop codon before the coding sequence would have no effect on transcription of the gene, because the transcription machinery does not recognize translational stops.

You have a piece of DNA that includes the following sequence: 5′-ATAGGCATTCGATCCGGATAGCAT-3′ 3′-TATCCGTAAGCTAGGCCTATCGTA-5′ Which of the following RNA molecules could be transcribed from this piece of DNA? A) 5′-UAUCCGUAAGCUAGGCCUAUGCUA-3′ B) 5′-AUAGGCAUUCGAUCCGGAUAGCAU-3′ C) 5′-UACGAUAGGCCUAGCUUACGGAUA-3′ D) none of these answers are correct.

B) 5′-AUAGGCAUUCGAUCCGGAUAGCAU-3′ RNA molecules are synthesized from a 5′-to-3′ fashion and must have the correct polarity.

Which of the following statements about prokaryotic mRNA molecules is false? A) A single prokaryotic mRNA molecule can be translated into several proteins. B) Ribosomes must bind to the 5′ cap before initiating translation. C) mRNAs are not polyadenylated. D) Ribosomes can start translating an mRNA molecule before transcription is complete

B) Ribosomes must bind to the 5′ cap before initiating translation. Bacterial mRNAs do not have 5′ caps. Instead, ribosome-binding sites upstream of

Which of the following statements is true? A) Ribosomes are large RNA structures composed solely of rRNA. B) Ribosomes are synthesized entirely in the cytoplasm. C) rRNA contains the catalytic activity that joins amino acids together. D) A ribosome binds one tRNA at a time.

C) rRNA contains the catalytic activity that joins amino acids together. Ribosomes contain proteins as well as rRNA. rRNA is synthesized in the nucleus, and ribosomes are partly assembled in the nucleus. A ribosome must be able to bind two tRNAs at any one time.

Which of the following statements is false? A) RNA polymerase can start making a new RNA molecule without a primer; DNA polymerase cannot. B) RNA polymerase does not proofread its work; DNA polymerase does. C) RNA polymerase catalyzes the linkage of ribonucleotides while DNA polymerase catalyzes the linkage of deoxyribonucleotides. D) RNA polymerase adds bases in a 3′-to-5′ direction; DNA polymerase adds bases in a 5′-to-3′ direction.

D) RNA polymerase adds bases in a 3′-to-5′ direction; DNA polymerase adds bases in a 5′-to-3′ direction. Both RNA and DNA polymerases add bases in a 5′-to-3′ direction

Which of the following statements is false? A) A new RNA molecule can begin to be synthesized from a gene before the previous RNA molecule's synthesis is completed. B) If two genes are to be expressed in a cell, these two genes can be transcribed with different efficiencies. C) RNA polymerase is responsible for both unwinding the DNA helix and catalyzing the formation of the phosphodiester bonds between nucleotides. D) Unlike DNA, RNA uses a uracil base and a deoxyribose sugar.

D) Unlike DNA, RNA uses a uracil base and a deoxyribose sugar.

snRNAs... A) are translated into snRNPs. B) are important for producing mature mRNA transcripts in bacteria. C) are removed by the spliceosome during RNA splicing. D) can bind to specific sequences at intron-exon boundaries through complementary base-pairing.

D) can bind to specific sequences at intron-exon boundaries through complementary base-pairing snRNAs are part of the snRNPs, which include proteins and RNA molecules. The proteins within the snRNPs are encoded by their own genes and not translated from snRNPs. Bacteria do not have introns.

T/F: Since introns do not contain protein-coding information, they do not have to be removed precisely from the primary transcript during RNA splicing. In other words, leaving in an extra nucleotide or two should not make a difference to the protein produced

False Although it is true that the sequences within the introns are mostly dispensable, the introns must still be removed precisely because an error of one or two nucleotides would shift the reading frame of the resulting mRNA molecule and change the protein it encodes.

A poison added to an in vitro translation mixture containing mRNA molecules with the sequence 5′- AUGAAAAAAAAAAAAUAA-3′ has the following effect: the only product made is a Met-Lys dipeptide that remains attached to the ribosome. What is the most likely way in which the poison acts to inhibit protein synthesis?

It inhibits movement of the small subunit relative to the large subunit [see Fig. 7-37 in current textbook] Inhibition of peptidyl transferase activity would prevent all peptide bond formation. Inhibiting release factor would have no effect on translation until the stop codon was reached. Mimicking release factor would be likely to result in a mixture of polypeptides of various lengths; a poison mimicking a release factor could conceivably cause only Met-Lys to be made, but this dipeptide would not remain bound to the ribosome.

What do you predict would happen if you created a tRNA with an anticodon of 5′-CAA-3′ that is charged with methionine, and added this modified tRNA to a cell-free translation system that has all the normal components required for translating RNAs? [see genetic code, last page]

Methionine would be incorporated into proteins at some positions where leucine should be. The 5′-CAA-3′ anticodon binds to the 5′-UUG-3′ codon, which normally codes for leucine.

The following RNA sequence includes the beginning of a sequence coding for a protein. What would be the result of a mutation that changed the *C* to an A? [see genetic code, last page] 5′-AGGCUAUGAAUCGACACUG*C*GAGCCC . . .

The change creates a stop codon (TGA, or UGA in the mRNA) very near the beginning of the protein-coding sequence and in the correct reading frame (the beginning of the coding sequence is indicated by the ATG). Thus, translation would terminate after only four amino acids had been joined together, and the complete protein would not be made.

The piece of RNA below includes the region that codes for the binding site for the initiator tRNA needed in translation. 5′-GUUUCCCGUAUACAUGCGUGCCGGGGGC-3′ Which amino acid will be on the tRNA that is the first to bind to the A site of the ribosome? [see genetic code, last page]

arginine The initiator methionine is underlined on the RNA molecule below. 5′-GUUUCCCGUAUAC*AUG*CGUGCCGGGGGC-3′ The first tRNA to bind at the A site is the second codon of the protein, because the initiator tRNA is already bound to the P site when translation begins. The codon that follows the binding site for the initiator tRNA is CGU, which codes for arginine.

Total nucleic acids are extracted from a culture of yeast cells and are then mixed with resin beads to which the polynucleotide 5′-TTTTTTTTTTTTTTTTTTTTTTTTT-3′ has been covalently attached. After a short incubation, the beads are then extracted from the mixture. When you analyze the cellular nucleic acids that have stuck to the beads, what is most abundant?

mRNA mRNA is the only type of RNA that is polyadenylated, and its poly-A tail would be able to base-pair with the strands of poly T on the beads and thus stick to them. DNA would not be found in the sample, because the poly-A tail is not encoded in the DNA and long runs of T are rare in DNA.

The sigma subunit of bacterial RNA polymerase

recognizes promoter sites in the DNA.

A mutation in the tRNA for the amino acid lysine results in the anticodon sequence 5′-UAU-3′ (instead of 5′-UUU-3′). Which of the following aberrations in protein synthesis might this tRNA cause? [see genetic code, last page]

substitution of lysine for isoleucine The mutant tRNALys will be able to pair with the codon 5′-AUA-3′, which codes for isoleucine.

For a cell's genetic material to be used, the information is first copied from the DNA into the nucleotide sequence of RNA in a process called __________. Various kinds of RNA are produced, each with different functions. __________ molecules code for proteins, __________ molecules act as adaptors for protein synthesis, __________ molecules are integral components of the ribosome, and __________ molecules are important in the splicing of RNA transcripts.

transcription mRNA tRNA rRNA snRNA