Chapter 7

7-13 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

7-26 Transcription in bacteria differs from transcription in a eukaryotic cell because __________________________. (a) RNA polymerase (along with its sigma subunit) can initiate transcription on its own. (b) RNA polymerase (along with its sigma subunit) requires the general transcription factors to assemble at the promoter before polymerase can begin transcription. (c) the sigma subunit must associate with the appropriate type of RNA polymerase to produce mRNAs. (d) RNA polymerase must be phosphorylated at its C-terminal tail for transcription to proceed.

A

7-27 Which of the following does not occur before a eukaryotic mRNA is exported from the nucleus? (a) The ribosome binds to the mRNA. (b) The mRNA is polyadenylated at its 3′ end. (c) 7-methylguanosine is added in a 5′-to-5′ linkage to the mRNA. (d) RNA polymerase dissociates.

A

7-33 Genes in eukaryotic cells often have intronic sequences coded for within the DNA. These sequences are ultimately not translated into proteins. Why? (a) Intronic sequences are removed from RNA molecules by the spliceosome, which works in the nucleus. (b) Introns are not transcribed by RNA polymerase. (c) Introns are removed by catalytic RNAs in the cytoplasm. (d) The ribosome will skip over intron sequences when translating RNA into protein.

A

7-40 Which amino acid would you expect a tRNA with the anticodon 5′-CUU-3′ to carry? (a) lysine (b) glutamic acid (d) leucine (d) phenylalanine

A

7-43 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? (a) 5′-CCA-3′ (b) 5′-CCG-3′ (c) 5′-UGG-3′ (d) 5′-UUA-3′

A

7-6 Figure Q7-6 shows a ribose sugar. RNA bases are added to the part of the ribose sugar pointed to by arrow _____. (a) 3. (b) 4. (c) 5. (d) 6.

A

7-67 When using a repeating trinucleotide sequence (such as 5′-AAC-3′) in a cell-free translation system, you will obtain: (a) three different types of peptides, each made up of a single amino acid (b) peptides made up of three different amino acids in random order (c) peptides made up of three different amino acids, each alternating with each other in a repetitive fashion (d) polyasparagine, as the codon for asparagine is AAC

A

7-18 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 the above

B

7-24 There are several reasons why the primase used to make the RNA primer for DNA replication is not suitable for gene transcription. Which of the statements below is not one of those reasons? (a) Primase initiates RNA synthesis on a single-stranded DNA template. (b) Primase can initiate RNA synthesis without the need for a base-paired primer. (c) Primase synthesizes only RNAs of about 5-20 nucleotides in length. (d) The RNA synthesized by primase remains base-paired to the DNA template.

B

7-25 You have a bacterial strain with a mutation that removes the transcription termination signal from the Abd operon. Which of the following statements describes the most likely effect of this mutation on Abd transcription? (a) The Abd RNA will not be produced in the mutant strain. (b) The Abd RNA from the mutant strain will be longer than normal. (c) Sigma factor will not dissociate from RNA polymerase when the Abd operon is being transcribed in the mutant strain. (d) RNA polymerase will move in a backward fashion at the Abd operon in the mutant strain.

B

7-30 Which of the following statements about RNA splicing is false? (a) Conventional introns are not found in bacterial genes. (b) For a gene to function properly, every exon must be removed from the primary transcript in the same fashion on every mRNA molecule produced from the same gene. (c) Small RNA molecules in the nucleus perform the splicing reactions necessary for the removal of introns. (d) Splicing occurs after the 5′ cap has been added to the end of the primary transcript.

B

7-37 Which of the following statements about the genetic code is correct? (a) All codons specify more than one amino acid. (b) The genetic code is redundant. (c) All amino acids are specified by more than one codon. (d) All codons specify an amino acid.

B

7-38 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? (a) methionine (b) arginine (c) cysteine (d) valine

B

7-46 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? (a) read-through of stop codons (b) substitution of lysine for isoleucine (c) substitution of lysine for tyrosine (d) substitution of lysine for phenylalanine

B

7-48 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? (a) methionine would be incorporated into proteins at some positions where glutamine should be (b) methionine would be incorporated into proteins at some positions where leucine should be (c) methionine would be incorporated into proteins at some positions where valine should be (d) translation would no longer be able to initiate

B

7-53 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? (a) It inhibits peptidyl transferase activity. (b) It inhibits movement of the small subunit relative to the large subunit. (c) It inhibits release factor. (d) It mimics release factor.

B

7-54 In eukaryotes, but not in prokaryotes, ribosomes find the start site of translation by ____________________________. (a) binding directly to a ribosome-binding site preceding the initiation codon. (b) scanning along the mRNA from the 5′ end. (c) recognizing an AUG codon as the start of translation. (d) binding an initiator tRNA.

B

7-55 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

7-57 You have discovered a protein that inhibits translation. When you add this inhibitor to a mixture capable of translating human mRNA and centrifuge the mixture to separate polyribosomes and single ribosomes, you obtain the results shown in Figure Q7-57. Which of the following interpretations is consistent with these observations? (a) The protein binds to the small ribosomal subunit and increases the rate of initiation of translation. (b) The protein binds to sequences in the 5′ region of the mRNA and inhibits the rate of initiation of translation. (c) The protein binds to the large ribosomal subunit and slows down elongation of the polypeptide chain. (d) The protein binds to sequences in the 3′ region of the mRNA and prevents termination of translation.

B

7-65 You are studying a disease that is caused by a virus, but when you purify the virus particles and analyze them you find they contain no trace of DNA. Which of the following molecules are likely to contain the genetic information of the virus? (a) high-energy phosphate groups (b) RNA (c) lipids (d) carbohydrates

B

7-14 Which one of the following is the main reason that a typical eukaryotic gene is able to respond to a far greater variety of regulatory signals than a typical prokaryotic gene or operon? (a) Eukaryotes have three types of RNA polymerase. (b) Eukaryotic RNA polymerases require general transcription factors. (c) The transcription of a eukaryotic gene can be influenced by proteins that bind far from the promoter. (d) Prokaryotic genes are packaged into nucleosomes.

C

7-22 The sigma subunit of bacterial RNA polymerase ___________________. (a) contains the catalytic activity of the polymerase. (b) remains part of the polymerase throughout transcription. (c) recognizes promoter sites in the DNA. (d) recognizes transcription termination sites in the DNA.

C

7-3 Consider two genes that are next to each other on a chromosome, as arranged in Figure Q7-3. Which of the following statements is true? (a) The two genes must be transcribed into RNA using the same strand of DNA. (b) If gene A is transcribed in a cell, gene B cannot be transcribed. (c) Gene A and gene B can be t. (d) If gene A is transcribed in a cell, gene B must be transcribed.

C

7-4 RNA in cells differs from DNA in that ___________________. (a) it contains the base uracil, which pairs with cytosine. (b) it is single-stranded and cannot form base pairs. (c) it is single-stranded and can fold up into a variety of structures. (d) the sugar ribose contains fewer oxygen atoms than does deoxyribose.

C

7-41 Which of the following pairs of codons might you expect to be read by the same tRNA as a result of wobble? (a) CUU and UUU (b) GAU and GAA (c) CAC and CAU (d) AAU and AGU

C

7-45 A strain of yeast translates mRNA into protein inaccurately. Individual molecules of a particular protein isolated from this yeast have variations in the first 11 amino acids compared with the sequence of the same protein isolated from normal yeast cells, as listed in Figure Q7-45. What is the most likely cause of this variation in protein sequence? (a) a mutation in the DNA coding for the protein (b) a mutation in the anticodon of the isoleucine-tRNA (tRNAIle) (c) a mutation in the isoleucyl-tRNA synthetase that decreases its ability to distinguish between different amino acids (d) a mutation in the isoleucyl-tRNA synthetase that decreases its ability to distinguish between different tRNA molecules

C

7-50 The ribosome is important for catalyzing the formation of peptide bonds. Which of the following statements is true? (a) The number of rRNA molecules that make up a ribosome greatly exceeds the number of protein molecules found in the ribosome. (b) The large subunit of the ribosome is important for binding to the mRNA. (c) The catalytic site for peptide bond formation is formed primarily from an rRNA. (d) Once the large and small subunits of the ribosome assemble, they will not separate from each other until degraded by the proteasome.

C

7-51 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

7-34 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

7-5 Transcription is similar to DNA replication in that ___________________. (a) an RNA transcript is synthesized discontinuously and the pieces are then joined together. (b) it uses the same enzyme as that used to synthesize RNA primers during DNA replication. (c) the newly synthesized RNA remains paired to the template DNA. (d) nucleotide polymerization occurs only in the 5′-to-3′ direction.

D

7-60 Which of the following methods is not used by cells to regulate the amount of a protein in the cell? (a) Genes can be transcribed into mRNA with different efficiencies. (b) Many ribosomes can bind to a single mRNA molecule. (c) Proteins can be tagged with ubiquitin, marking them for degradation. (d) Nuclear pore complexes can regulate the speed at which newly synthesized proteins are exported from the nucleus into the cytoplasm.

D

7-63 According to current thinking, the minimum requirement for life to have originated on Earth was the formation of a _______________. (a) molecule that could provide a template for the production of a complementary molecule. (b) double-stranded DNA helix. (c) molecule that could direct protein synthesis. (d) molecule that could catalyze its own replication.

D

7-68 You have discovered an alien life-form that surprisingly uses DNA as its genetic material, makes RNA from DNA, and reads the information from RNA to make protein using ribosomes and tRNAs, which read triplet codons. Because it is your job to decipher the genetic code for this alien, you synthesize some artificial RNA molecules and examine the protein products produced from these RNA molecules in a cell-free translation system using purified alien tRNAs and ribosomes. You obtain the results shown in Table Q7-68. From this information, which of the following peptides can be produced from poly UAUC? (a) Ile-Phe-Val-Tyr (b) Tyr-Ser-Phe-Ala (c) Ile-Lys-His-Tyr (d) Cys-Pro-Lys-Ala

D

7-69 An extraterrestrial organism (ET) is discovered whose basic cell biology seems pretty much the same as that of terrestrial organisms except that it uses a different genetic code to translate RNA into protein. You set out to break the code by translation experiments using RNAs of known sequence and cell-free extracts of ET cells to supply the necessary protein-synthesizing machinery. In experiments using the RNAs below, the following results were obtained when the 20 possible amino acids were added either singly or in different combinations of two or three: RNA 1: 5′-GCGCGCGCGCGCGCGCGCGCGCGCGCGC-3′ RNA 2: 5′-GCCGCCGCCGCCGCCGCCGCCGCCGCCGCC-3′ Using RNA 1, a polypeptide was produced only if alanine and valine were added to the reaction mixture. Using RNA 2, a polypeptide was produced only if leucine and serine and cysteine were added to the reaction mixture. Assuming that protein synthesis can start anywhere on the template, that the ET genetic code is nonoverlapping and linear, and that each codon is the same length (like the terrestrial triplet code), how many nucleotides does an ET codon contain? (a) 2 (b) 3 (c) 4 (d) 5 (e) 6

D

7-58 The concentration of a particular protein, X, in a normal human cell rises gradually from a low point, immediately after cell division, to a high point, just before cell division, and then drops sharply. The level of its mRNA in the cell remains fairly constant throughout this time. Protein X is required for cell growth and survival, but the drop in its level just before cell division is essential for division to proceed. You have isolated a line of human cells that grow in size in culture but cannot divide, and on analyzing these mutants, you find that levels of X mRNA in the mutant cells are normal. Which of the following mutations in the gene for X could explain these results? (a) the introduction of a stop codon that truncates protein X at the fourth amino acid (b) a change of the first ATG codon to CCA (c) the deletion of a sequence that encodes sites at which ubiquitin can be attached to the protein (d) a change at a splice site that prevents splicing of the RNA

C

7-61 Which of the following statements about the proteasome is false? (a) Ubiquitin is a small protein that is covalently attached to proteins to mark them for delivery to the proteasome. (b) Proteases reside in the central cylinder of a proteasome. (c) Misfolded proteins are delivered to the proteasome, where they are sequestered from the cytoplasm and can attempt to refold. (d) The protein stoppers that surround the central cylinder of the proteasome use the energy from ATP hydrolysis to move proteins into the proteasome inner chamber.

C

7-62 Which of the following molecules is thought to have arisen first during evolution? (a) protein (b) DNA (c) RNA

C

7-64 Ribozymes catalyze which of the following reactions? (a) DNA synthesis (b) transcription (c) RNA splicing (d) protein hydrolysis

C

7-7 Figure Q7-6 shows a ribose sugar. The part of the ribose sugar that is different from the deoxyribose sugar used in DNA is pointed to by arrow ____. (a) 1. (b) 4. (c) 5. (d) 6.

C

7-8 Figure Q7-6 shows a ribose sugar. The part of the ribose sugar where a new ribonucleotide will attach in an RNA molecule is pointed to by arrow ____. (a) 1. (b) 3. (c) 4. (d) 5.

C

7-11 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

7-12 Unlike DNA, which typically forms a helical structure, different molecules of RNA can fold into a variety of three-dimensional shapes. This is largely because ___________________. (a) RNA contains uracil and uses ribose as the sugar. (b) RNA bases cannot form hydrogen bonds with each other. (c) RNA nucleotides use a different chemical linkage between nucleotides compared to DNA. (d) RNA is single-stranded.

D

7-20 You have a segment of DNA that contains the following sequence: 5′-GGACTAGACAATAGGGACCTAGAGATTCCGAAA-3′ 3′-CCTGATCTGTTATCCCTGGATCTCTAAGGCTTT-5′ You know that the RNA transcribed from this segment contains the following sequence: 5′-GGACUAGACAAUAGGGACCUAGAGAUUCCGAAA-3′ Which of the following choices best describes how transcription occurs? (a) the top strand is the template strand; RNA polymerase moves along this strand from 5′ to 3′ (b) the top strand is the template strand; RNA polymerase moves along this strand from 3′ to 5′ (c) the bottom strand is the template strand; RNA polymerase moves along this strand from 5′ to 3′ (d) the bottom strand is the template strand; RNA polymerase moves along this strand from 3′ to 5′

D

7-23 Which of the following might decrease the transcription of only one specific gene in a bacterial cell? (a) a decrease in the amount of sigma factor (b) a decrease in the amount of RNA polymerase (c) a mutation that introduced a stop codon into the DNA that precedes the gene's coding sequence (d) a mutation that introduced extensive sequence changes into the DNA that precedes the gene's transcription start site

D

7-28 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, which of the following is most abundant? (a) DNA (b) tRNA (c) rRNA (d) mRNA

D