CHAPTER 7. FROM DNA TO PROTEIN: HOW CELLS READ THE GENOME

Export of RNA from the nucleus requires the RNA to have which characteristic(s)? a. 5′ cap b. poly-A tail c. 5′ cap and poly-A tail d. introns

5′ cap and poly-A tail FEEDBACK: To be exported, RNAs must have the features of a processed mRNA. This includes being properly spliced (no introns), having a 5′ cap and a poly-A tail.

Which of the following is a difference between the mechanisms of DNA polymerase and RNA polymerase? a. The direction of polymerization for DNA polymerase is 5′ to 3′, but RNA polymerase is 3′ to 5′. b. DNA polymerase uses DNA as a template for making DNA copies; RNA polymerase uses RNA as a template for making RNAs. c. DNA polymerase uses the energy from the hydrolysis of the nucleotide triphosphates to drive the reaction; RNA polymerase uses reduced electron carriers. d. DNA polymerase needs a base-paired 3′ −OH for a polymerization reaction to occur; RNA polymerase can polymerize two nucleotides without a base-paired 3′ −OH.

DNA polymerase needs a base-paired 3′ −OH for a polymerization reaction to occur; RNA polymerase can polymerize two nucleotides without a base-paired 3′ −OH. FEEDBACK: DNA polymerase needs a primer to provide a base-paired 3′ −OH to catalyze the polymerization reaction. RNA polymerase does not need a base-paired 3′ −OH, it can join two nucleotides together without a primer.

Protein concentration can be regulated by all of the steps listed EXCEPT a. nuclear export. b. RNA processing. c. mRNA stability. d. DNA replication

DNA replication. FEEDBACK: Protein levels can be tuned by changing the amount of processed mRNA available to ribosomes. Protein levels are not typically regulated by making more copies of the DNA instructions.

Shown below is a gene with the direction of transcription noted. How does the RNA polymerase know which strand to use as a template for the RNA, and which strand would it choose in this case? a. It would use the top strand as a template because the polymerase always moves from left to right. b. It would use the top strand as a template because the promoter marks beginning of the gene. c. It would use the bottom strand because the promoter sets the direction and the polymerase moves from 3′ to 5′ along the template strand. d. It would use the bottom strand because the bottom strand is always the template strand.

It would use the bottom strand because the promoter sets the direction and the polymerase moves from 3′ to 5′ along the template strand. FEEDBACK: RNA polymerase binds to promoter sequences in a specific orientation. The RNA polymerase will then move away from the promoter using the promoter-dictated directionality and uses the 3′ to 5′ strand as a template to make a new RNA in the 5′ to 3′ direction.

Using the genetic code below, determine the amino acids that a polynucleotide of UC would code for. a. Leu, Ser b. His, Thr c. Phe, Leu d. Ser, His

Leu, Ser FEEDBACK: A poly-UC molecule would be UCUCUCUCUCUC, and thus would have nonoverlapping triplets of UCU and CUC. Based on the genetic code, these triplets code for Ser (UCU) and Leu (CUC).

What is the benefit of protein synthesis in polyribosomes? a. More protein can be produced from a single RNA. b. Protein translation is more accurate. c. Ribosomes can stay in the nucleus. d. Uncharged tRNAs can be used.

More protein can be produced from a single RNA. FEEDBACK: Having more than one ribosome bound to a single mRNA allows many polypeptide chains to be synthesized simultaneously. This allows much more protein to be produced from one mRNA molecule than if each ribosome had to wait for the previous one to finish.

Which nucleic acid often base pairs with itself to fold into complex three-dimensional shapes in the cell? a. RNA b. DNA c. both RNA and DNA d. neither RNA nor DNA

RNA RNA is often single stranded and complementary regions will base pair with each other to form secondary and tertiary structures.

Which of the following properties could help RNA be both an information storage unit and a self-replicating molecule? a. RNA can act as a template for making copies of itself. b. RNA is a short-lived molecule. c. RNA cannot catalyze reactions. d. RNA must be made from DNA.

RNA can act as a template for making copies of itself. FEEDBACK: RNA carries information and, through base-pairing rules, can act as a template for self-replication. This, in addition to its ability to catalyze reactions, suggests it may have been a primitive autocatalytic system on early Earth.

The splicing of introns out of an mRNA molecule is catalyzed by a. RNA molecules that base pair with the splice sites to promote intron removal. b. proteins that contain metal ions to pull electrons from the phosphate bonds. c. RNA molecules that act as a template for new RNA synthesis using exons only. d. proteins that act as nucleases to chew away and remove the introns.

RNA molecules that base pair with the splice sites to promote intron removal. FEEDBACK: Splicing is actually an RNA-catalyzed reaction. The RNA molecules in the snRNPs base pair with regions of the RNA that are to be spliced. This base pairing helps promote the rearrangement of bonds to remove the intron.

Why does RNA polymerase make more mistakes than DNA polymerase? a. RNA polymerase does not use a template molecule. b. RNA polymerase does not have proofreading activity. c. RNA polymerase uses completely different base-pairing rules. d. RNA polymerase has a faulty mismatch repair system.

RNA polymerase does not have proofreading activity. FEEDBACK: RNA polymerase lacks the ability to proofread its work, so if an incorrectly base-paired nucleotide is added, it cannot excise the nucleotide and add the correct one.

Which characteristic of a replicating RNA polymerase allows multiple transcripts to be made simultaneously from the same region of DNA? a. The RNA transcript dissociates from the DNA template immediately once complete. b. RNA polymerase is very small. c. RNA remains bound to the gene and helps template more transcripts. d. RNA polymerases can jump over slower RNA polymerases to make more transcript.

The RNA transcript dissociates from the DNA template immediately once complete. FEEDBACK: RNA transcripts dissociate immediately from the DNA template once they are made. This allows many RNA polymerases to form a "caravan" on the gene, producing many transcripts.

Why is RNA thought to predate DNA in evolution? a. The sugar in RNA is easier to make with the organic molecules that were present on primitive Earth. b. RNA forms many different types of functional molecules, like snRNA, rRNA and tRNA. c. RNA is less stable than DNA. d. rRNA genes are more conserved through evolution.

The sugar in RNA is easier to make with the organic molecules that were present on primitive Earth. FEEDBACK: Although the other selections are true, none of them provide evidence for RNA predating DNA in evolution except that the sugar in RNA, ribose, is more easily produced from formaldehyde, which was abundant in the early environment of Earth.

How do tRNAs become attached to the correct amino acid? a. aminoacyl-tRNA synthetases b. RNA polymerases c. rRNA ribozymes d. translation initiation factors

aminoacyl-tRNA synthetases FEEDBACK: Enzymes called aminoacyl-tRNA synthetases recognize tRNAs with a specific anticodon as well as the amino acid for that tRNA and catalyze a reaction to join them together. This is called "charging" a tRNA.

At which step of gene expression can cells amplify the number of copies of a protein made from a single gene? a. transcription b. translation c. neither transcription nor translation d. both transcription and translation

both transcription and translation FEEDBACK: Proteins can be made in large quantities by transcribing many mRNAs from the gene, and then each mRNA can be translated into many copies of the protein. In contrast, if just a few mRNAs are made, only a few copies of the protein are made.

What performs the function of bacterial sigma factor in eukaryotes? a. general transcription factors b. initiation proteins c. nucleosomes d. promoters

general transcription factors FEEDBACK: Sigma factor is an accessory protein to RNA polymerase in bacteria that helps the polymerase bind to the promoter region. In eukaryotes, this function is performed by a set of proteins called the general transcription factors.

The catalytic sites for peptide bond formation during translation is found in which part of the ribosome? a. large subunit RNAs b. large subunit proteins c. small subunit RNAs d. small subunit proteins

large subunit RNAs FEEDBACK: The catalysis of the peptide bonds in the growing polypeptide chain during translation is performed by the rRNA of the large subunit. The ribosome is a ribozyme; proteins play a largely structural role.

The reading frame to use for translating an mRNA into functional protein is determined by the a. location of an AUG. b. promoter sequence. c. 5′ cap. d. replication origin.

location of an AUG. FEEDBACK: The translation of an mRNA in eukaryotes begins when the initiator tRNA encounters the first AUG in an mRNA. The complex containing the initiator tRNA starts scanning the mRNA from the 5′ end to find the AUG.

Which type of RNA is converted into protein for performing its cellular function? a. tRNA b. rRNA c. mRNA d. miRNA

mRNA FEEDBACK: There are many different types of RNA that perform functions as RNA in the cell and are never translated into protein. These include tRNA, rRNA, and miRNA. The only RNAs that code for proteins are mRNAs.

What is the name of the complex that degrades proteins that have reached the end of their lifespan, are damaged, or are misfolded? a. proteasome b. nuclease c. ribosome d. nuclear pore complex

proteasome FEEDBACK: Large molecular machines called proteasomes act as garbage disposals for degrading proteins that are old or damaged.

What recognizes the stop codons in an mRNA? a. release factor b. a specialized tRNA linked to methionine c. nothing d. the 3′ poly-A tail

release factor FEEDBACK: When the ribosome encounters a stop codon, instead of a tRNA binding, a protein called release factor binds and catalyzes the addition of a water molecule to the carboxyl end of the polypeptide and releases it.

Shown below is a tRNA for tryptophan. Which of the locations on the tRNA accommodates looser base-pairing rules? a. site 1 b. site 2 c. site 3 d. All of the sites maintain strict base-pairing rules.

site 3 FEEDBACK: The third base in a codon can base pair loosely with the corresponding base in an anticodon in a tRNA. This allows specific tRNAs to recognize more than one codon (called wobble base pairing) for a redundant genetic code.

DNA is a better molecule for long-term storage of genetic information than RNA because a. the deoxyribose sugar stabilizes DNA chains. b. the uracil in DNA is less easily mutated. c. DNA is able to make complex folded secondary structures. d. DNA is able to autocatalyze its own repair.

the deoxyribose sugar stabilizes DNA chains. FEEDBACK: The deoxyribose sugar allows the nucleotide chains to be more stable and grow to longer lengths, making DNA a superior molecule for genetic information storage. In addition, the presence of thymine (rather than uracil) facilitates the detection and repair of damage.

The information in an mRNA molecule is converted into protein sequence using a. three consecutive bases, with one nucleotide overlapping between triplets. b. three consecutive bases, with no overlap between triplets. c. four consecutive bases, with two nucleotides overlapping between quadruplets. d. four consecutive bases, with no overlap between quadruplets.

three consecutive bases, with no overlap between triplets. FEEDBACK: The genetic code consists of three consecutive bases and is read in a nonoverlapping fashion. That is, the nucleotides for one triplet are not the part of the next triplet.

The process of gene expression always involves which process(es) described in the central dogma? a. transcription b. translation c. replication d. transcription and translation

transcription FEEDBACK: Some genes that are expressed are functional RNA genes. These RNAs don't undergo translation to protein because they do their job in the cell as an RNA.

The structure of a proteasome is shown below. What group is recognized by region A to indicate that the protein is marked to be eliminated? a. ubiquitin b. phosphate c. methyl d. amino

ubiquitin FEEDBACK: Proteins marked for elimination have a chain of ubiquitin groups added to them. This is recognized by region A and the protein is then threaded into the central cylinder (B) to be degraded by the protease active sites (D).