Chapter 7

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.

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 transcription. Various kinds of RNA are produced, each with different functions. mRNA molecules code for proteins, tRNA molecules act as adaptors for protein synthesis, rRNA molecules are integral components of the ribosome, and snRNA molecules are important in the splicing of RNA transcripts.

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.

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.

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.

Intronic sequences are removed from RNA molecules by the spliceosome, which works in the nucleus.

Which of the following molecules is thought to have arisen first during evolution? a. protein b. DNA c. RNA d. All came to be at the same time.

RNA Because RNA is known to catalyze reactions within the cell, because the components of RNA are thought to be more readily formed in the conditions on primitive Earth, and because RNA can contain genetic information, it is the most likely of the three molecules to have arisen first in evolution.

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.

RNA polymerase (along with its sigma subunit) can initiate transcription on its own. Eukaryotic cells, but not bacteria, require general transcription factors. There is only a single type of RNA polymerase in bacterial cells. The general transcription factor TFIIH phosphorylates the C-terminal tail of RNA polymerase in eukaryotic cells but not in bacteria.

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.

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.

Ribozymes are known to catalyze which of the following reactions in cells? a. DNA synthesis b. transcription c. RNA splicing d. protein hydrolysis

RNA splicing

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.

Ribosomes must bind to the 5′ cap before initiating translation. Bacterial mRNAs do not have 5′ caps. Instead, ribosome-binding sites upstream of the start codon tell the ribosome where to begin searching for the start of translation.

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.

The Abd RNA from the mutant strain will be longer than normal.

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.

The catalytic site for peptide bond formation is formed primarily from an rRNA.

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.

The genetic code is redundant. Most amino acids can be specified by more than one codon. Each codon specifies only one amino acid. Tryptophan and methionine are encoded by only one codon. Some codons specify translational stop signals.

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.

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

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 RNA a. contains uracil and uses ribose as the sugar. b. bases cannot form hydrogen bonds with each other. c. nucleotides use a different chemical linkage between nucleotides compared to DNA. d. is single-stranded.

is single-stranded. Although RNA contains uracil and uses ribose as the sugar, this is not the main reason why different RNA molecules can form different three-dimensional structures (although ribose does increase potential hydrogen-bonding potentials compared to deoxyribose).

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.

it is single-stranded and can fold up into a variety of structures.

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.

molecule that could catalyze its own replication. Although providing a template is an important step in self-replication, it would not by itself be sufficient. Being a double-stranded DNA helix and being a molecule that could direct protein synthesis are likely stages in the evolution of the cell that must have succeeded the formation of the first self-replicating molecules.

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.

scanning along the mRNA from the 5′ end.

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

the deletion of a sequence that encodes sites at which ubiquitin can be attached to the protein

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 transcribed at different rates, producing different amounts of RNA within the same cell. d. If gene A is transcribed in a cell, gene B must be transcribed.

. Gene A and gene B can be transcribed at different rates, producing different amounts of RNA within the same cell.

Name three covalent modifications that are made to most eukaryotic RNA molecules before the RNA molecule becomes a mature mRNA.

1. A poly-A tail is added. 2. A 5′ cap is added. 3. Introns can be spliced out.

List three ways in which the process of eukaryotic transcription differs from the process of bacterial transcription.

1. Bacterial cells contain a single RNA polymerase, whereas eukaryotic cells have three. 2. Bacterial RNA polymerase can initiate transcription without the help of additional proteins, whereas eukaryotic RNA polymerases need general transcription factors. 3. In eukaryotic cells, transcription regulators can influence transcriptional initiation thousands of nucleotides away from the promoter, whereas bacterial regulatory sequences are very close to the promoter. 4. Eukaryotic transcription is affected by chromatin structure and nucleosomes, whereas bacteria lack nucleosomes.

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′ ANS: A

5′-CCA-3′

In eukaryotic cells, general transcription factors are required for the activity of all promoters transcribed by RNA polymerase II. The assembly of the general transcription factors begins with the binding of the factor __________ to DNA, causing a marked local distortion in the DNA. This factor binds at the DNA sequence called the __________ box, which is typically located approximately 30 nucleotides upstream from the transcription start site. Once RNA polymerase II has been brought to the promoter DNA, it must be released to begin making transcripts. This release process is facilitated by the addition of phosphate groups to the tail of RNA polymerase by the factor __________. It must be remembered that the general transcription factors and RNA polymerase are not sufficient to initiate transcription in the cell and are affected by proteins bound thousands of nucleotides away from the promoter.

: In eukaryotic cells, general transcription factors are required for the activity of all promoters transcribed by RNA polymerase II. The assembly of the general transcription factors begins with the binding of the factor TFIID to DNA, causing a marked local distortion in the DNA. This factor binds at the DNA sequence called the TATA box, which is typically located approximately 30 nucleotides upstream from the transcription start site. Once RNA polymerase II has been brought to the promoter DNA, it must be released to begin making transcripts. This release process is facilitated by the addition of phosphate groups to the tail of RNA polymerase by the factor TFIIH. It must be remembered that the general transcription factors and RNA polymerase are not sufficient to initiate transcription in the cell and are affected by proteins bound thousands of nucleotides away from the promoter.

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

RNA

Once an mRNA is produced, its message can be decoded on ribosomes. The ribosome is composed of two subunits: the __________ subunit, which catalyzes the formation of the peptide bonds that link the amino acids together into a polypeptide chain, and the __________ subunit, which matches the tRNAs to the codons of the mRNA. During the chain elongation process of translating an mRNA into protein, the growing polypeptide chain attached to a tRNA is bound to the __________ site of the ribosome. An incoming aminoacyl-tRNA carrying the next amino acid in the chain will bind to the __________ site by forming base pairs with the exposed codon in the mRNA. The __________ enzyme catalyzes the formation of a new peptide bond between the growing polypeptide chain and the newly arriving amino acid. The end of a protein-coding message is signaled by the presence of a stop codon, which binds the __________ called release factor. Eventually, most proteins will be degraded by a large complex of proteolytic enzymes called the __________.

: Once an mRNA is produced, its message can be decoded on ribosomes. The ribosome is composed of two subunits: the large subunit, which catalyzes the formation of the peptide bonds that link the amino acids together into a polypeptide chain, and the small subunit, which matches the tRNAs to the codons of the mRNA. During the chain elongation process of translating an mRNA into protein, the growing polypeptide chain attached to a tRNA is bound to the P site of the ribosome. An incoming aminoacyl-tRNA carrying the next amino acid in the chain will bind to the A site by forming base pairs with the exposed codon in the mRNA. The peptidyl transferase enzyme catalyzes the formation of a new peptide bond between the growing polypeptide chain and the newly arriving amino acid. The end of a protein-coding message is signaled by the presence of a stop codon, which binds the protein called release factor. Eventually, most proteins will be degraded by a large complex of proteolytic enzymes called the proteasome.

Which of the following statements is FALSE? a. Information determining the lifetimes of mRNA molecules is encoded in the nucleotide sequences of the mRNA molecule. b. An mRNA molecule in bacteria will typically have a shorter lifetime compared to an mRNA molecule in a eukaryotic cell. c. Eukaryotic mRNA molecules do not have lifetimes longer than 30 minutes. d. mRNA molecules are degraded into nucleotides by ribonucleases in the cytosol.

Eukaryotic mRNA molecules do not have lifetimes longer than 30 minutes. There is a wide range of lifetimes for eukaryotic mRNAs. Abundant proteins tend to be translated from mRNAs with long lifetimes, which can be more than 10 hours!

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.

Misfolded proteins are delivered to the proteasome, where they are sequestered from the cytoplasm and can attempt to refold. Once proteins are sent to the proteasome, proteases degrade them. Chaperone proteins provide a place for misfolded proteins to attempt to refold.

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.

Nuclear pore complexes can regulate the speed at which newly synthesized proteins are exported from the nucleus into the cytoplasm.

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

Primase can initiate RNA synthesis without the need for a base-paired primer. Both primase and RNA polymerase can initiate RNA synthesis without a base-paired primer, so it does not describe why primase cannot be used for gene transcription.

The instructions specified by the DNA will ultimately specify the sequence of proteins. This process involves DNA, made up of __________ different nucleotides, which gets __________ into RNA, which is then __________ into proteins, made up of __________ different amino acids. In eukaryotic cells, DNA gets made into RNA in the __________, while proteins are produced from RNA in the __________. The segment of DNA called a __________ is the portion that is copied into RNA; this process is catalyzed by RNA __________.

The instructions specified by the DNA will ultimately specify the sequence of proteins. This process involves DNA, made up of 4 different nucleotides, which gets transcribed into RNA, which is then translated into proteins, made up of 20 different amino acids. In eukaryotic cells, DNA gets made into RNA in the nucleus, while proteins are produced from RNA in the cytoplasm. The segment of DNA called a gene is the portion that is copied into RNA; this process is catalyzed by RNA polymerase.

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. A guanine nucleotide with a methyl group is added to the 5′ end of the mRNA. d. RNA polymerase dissociates.

The ribosome binds to the mRNA. Ribosomes are in the cytosol and will bind to the mRNA once it has been exported from the nucleus.

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.

The transcription of a eukaryotic gene can be influenced by proteins that bind far from the promoter.

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

a mutation that introduced extensive sequence changes into the DNA that precedes the gene's transcription start site

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. Without complementarity, base pairing cannot occur.

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.

can bind to specific sequences at intron-exon boundaries through complementary base-pairing.

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. The bottom strand is the template strand; RNA polymerase moves along this strand from 3′ to 5′. The bottom strand can hybridize with the RNA molecule and thus is the template strand. The polymerase moves along the DNA in a 3′-to-5′ direction, because the RNA nucleotides are joined in a 5′-to-3′ polarity.

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.

nucleotide polymerization occurs only in the 5′-to-3′ direction. Both RNA and DNA molecules are made in a 5′-to-3′ direction. An RNA transcript is made by a single polymerase molecule that proceeds from the start site to the termination site without falling off. The enzyme used to make primers during DNA synthesis is indeed an RNA polymerase, but it is a special enzyme, primase, and not the enzyme that is used for transcription.

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.

rRNA contains the catalytic activity that joins amino acids together.

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.

recognizes promoter sites in the DNA.

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.

three different types of peptides, each made up of a single amino acid.