iGenetics: A Molecular Approach, 3e (Russell/Bose)Chapter 5 Gene Expression: Transcription

MATCHING

Please select the best match for each term.

A) Encodes the amino acid sequence of a polypeptideB) With ribosomal proteins, makes up the ribosomesC) Forms the initiation complex with RNA polymerase in eukaryotesD) Forms complexes that are used in eukaryotic RNA processingE) Brings amino acids to ribosomes during translation

1) mRNASkill: Factual recall

2) tRNASkill: Factual recall

3) rRNASkill: Factual recall

4) snRNASkill: Factual recall

5) GTFSkill: Factual recall

Answers: 1) A 2) E 3) B 4) D 5) C

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MULTIPLE CHOICE

6) In eukaryotes, the initiation complex binds DNA at theA) Pribnow box.B) GC box.C) CAAT box.D) TATA box.E) GTF region.Answer: DSkill: Factual recall

7) The process by which genetic information is transferred from DNA to RNA is calledA) replication.B) transcription.C) translation.D) transversion.E) transformation.Answer: BSkill: Factual recall

8) Which of the following proteins is found only in the RNA polymerase holoenzyme?A) AlphaB) BetaC) EpsilonD) SigmaE) RhoAnswer: DSkill: Factual recall

9) During the initiation step of transcription, which molecule binds the promoter region of a DNA molecule?A) DNA polymeraseB) Reverse transcriptaseC) RNA polymeraseD) DNA primaseE) TopoisomeraseAnswer: CSkill: Factual recall

10) During transcription, the synthesis of the mRNA strand proceeds in which direction?A) 5' to 3' onlyB) 3' to 5' onlyC) Both 5' to 3' and 3' to 5'D) Either 5' to 3' or 3' to 5'E) First 5' to 3', and then 3' to 5'Answer: ASkill: Factual recall

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11) Which type of RNA is found only in eukaryotes?A) mRNAB) tRNAC) rRNAD) snRNAE) All of theseAnswer: DSkill: Factual recall

12) Which of the following catalyzes the synthesis of ribosomal RNA in eukaryotes?A) RNA polymerase IB) RNA polymerase IIC) RNA polymerase IIID) Both RNA polymerase I and IIE) Both RNA polymerase I and IIIAnswer: ESkill: Factual recall

13) Prokaryotic transcription begins when RNA polymerase binds to which site of the gene region?A) -35B) -10C) +1D) +10E) +35Answer: CSkill: Factual recall

14) Sequences that contain information about the stability of a transcript are found in theA) 5' UTR.B) coding sequence.C) 3' UTR.D) leading strand.E) lagging strand.Answer: CSkill: Factual recall

15) Which of the following is not found in a eukaryotic promoter?A) -10 boxB) TATA boxC) GC boxD) CAAT boxE) None of theseAnswer: ASkill: Factual recall

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16) In eukaryotes, where does transcription take place?A) In the cytoplasmB) Anywhere in the cellC) In the nucleusD) In both the cytoplasm and nucleusE) In the mitochondriaAnswer: CSkill: Factual recall

17) In eukaryotes, precursor mRNA molecules are processed in theA) ribosomes.B) nucleus.C) mitochondria.D) cytoplasm.E) nucleolus.Answer: BSkill: Factual recall

18) The single strand of mRNA that is produced during transcription has the same polarity as the ________ strand of DNA.A) templateB) nontemplateC) leadingD) laggingE) nonsenseAnswer: BSkill: Factual recall

19) The poly(A) tail of an mRNAA) helps transport the pre-mRNA to the cytoplasm.B) keeps the coding sequences from being degraded.C) is added without an RNA template.D) is important in initiation of translation.E) is removed from an mRNA after its maturation.Answer: BSkill: Factual recall

20) Self-cleaving RNAs that function catalytically are calledA) snRNPs.B) snRNAs.C) ribozymes.D) ribosomes.E) spliceosomes.Answer: CSkill: Factual recall

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21) Molecules of tRNA areA) 75 to 90 nucleotides in length.B) single-stranded with secondary structure.C) cloverleaf in shape.D) synthesized with modified bases.E) All of theseAnswer: ESkill: Factual recall

22) A prokaryotic mRNA transcript isA) transcribed completely before being translated.B) further processed before it is transcribed.C) transported from the nucleus before it is translated.D) modified before it is translated.E) translated as it is being transcribed.Answer: ESkill: Factual recall

23) Which parts of a eukaryotic gene are transcribed?A) Only the exonsB) Only the intronsC) Both the exons and intronsD) Exons, introns, promoter, and terminator sequenceE) It depends on the geneAnswer: CSkill: Factual recall

24) Posttranscriptional insertion or deletion of nucleotides that is absent in the DNA template is calledA) RNA splicing.B) RNA editing.C) RNA processing.D) RNA capping.E) RNA modification.Answer: BSkill: Factual recall

25) A rho-dependent terminatorA) forms a hairpin loop during termination.B) requires ATP to complete termination.C) is rich in AT nucleotides.D) Both A and BE) All of theseAnswer: BSkill: Factual recall

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TRUE/FALSE

26) A promoter is a coding portion of a gene.Answer: FALSEExplanation: A promoter is a noncoding, regulatory DNA sequence at the start of a gene.Skill: Factual recall

27) The number of initiations of transcription from a promoter that has the sequence 5'-TAGCAT-3' will be greater than the number of initiations from a wild-type promoter.Answer: FALSEExplanation: It will be fewer than the number of initiations from a wild-type promoter.Skill: Factual recall

28) All genes encode proteins.Answer: FALSEExplanation: Some genes encode specific kinds of RNAs that are not translated into proteins. Protein coding (or structural) genes, code for mRNA transcripts.Skill: Factual recall

29) Activators are cis-acting sequences that increase transcription from a promoter.Answer: FALSEExplanation: Activators are regulatory proteins that determine the efficiency of initiation of transcription.Skill: Factual recall

30) Before a prokaryotic mRNA can be translated, it must be modified by the addition of a polyA tail.Answer: FALSEExplanation: Prokaryotic mRNAs are not processed before translation.Skill: Factual recall

31) Termination is carried out by RNA polymerase in a rho-independent terminator.Answer: TRUESkill: Factual recall

32) The Rho protein is a topoisomerase that helps in untwisting the DNA template.Answer: FALSEExplanation: The Rho protein is a helicase.Skill: Factual recall

33) RNA polymerase has no proofreading activity during transcription.Answer: FALSEExplanation: RNA polymerase has two different proofreading activities for correcting incorrectly inserted nucleotides.Skill: Factual recall

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34) Unlike eukaryotic mRNA, prokaryotic mRNA is polycistronic.Answer: TRUESkill: Factual recall

35) Group I introns, such as those found in Tetrahymena, are unique in that they are excised from mRNA by a protein-driven catalytic reaction.Answer: FALSEExplanation: Group I introns are unique in that they are self-splicing.Skill: Factual recall

SHORT ANSWER

36) Outline the basic differences in function among RNA polymerases in both prokaryotes and eukaryotes.Answer: Only one type of RNA polymerase is found in prokaryotes, so all classes of genes are transcribed by it. Eukaryotes have three distinct RNA polymerases, each of which transcribes different gene types. RNA polymerase I transcribes the genes for the 28S, 18S, and 5.8S ribosomal RNAs; RNA polymerase II transcribes mRNA genes and some snRNA genes; and RNA polymerase III transcribes genes for the 5S rRNAs, the tRNAs, and the other snRNAs.Skill: Factual recall

37) What are the three basic steps of transcription?Answer: Initiation, elongation, and termination.Skill: Factual recall

38) What is the function of the inverted repeat in the termination sequence of a rho-independent terminator? What would happen if a mutation occurred in this region?Answer: RNA polymerase transcribes the inverted repeat into the RNA transcript. As a result, a hairpin loop structure forms because of the complementarity of the inverted repeat regions. This hairpin is believed to aid termination by affecting the ability of RNA polymerase to continue elongation. If a mutation occurred in this region, termination would not be successful.Skill: Factual recall, analytical reasoning

39) What was the significance of the 1978 finding by Philip Leder's research group that the 0.7 kb β-globin mRNA is not colinear with the gene that encodes it, but the nuclear 1.5 kb pre-mRNA is?Answer: This meant that the β-globin contains an intron, which is spliced out after pre-mRNA processing, and the exons are spliced together to make a mature mRNA. The significance was the realization that genes could be "in pieces."Skill: Conceptual understanding

40) What would be the advantage of having multiple sigma factors that each could be produced under different stress conditions in E. coli?Answer: Different sigma factors recognize different promoter region sequences. Therefore, they play a role in the regulation of gene expression. Sigma factors produced under a particular stress condition, such as excessive heat or infection by bacteriophage, bind to promoters that belong to genes that encode proteins required to cope with those stresses.Skill: Analytical reasoning

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41) What kind of experiment or analysis could you conduct to define the location of the promoter elements of protein-coding genes?Answer: You could examine the effect of mutations that delete or alter base pairs upstream from the starting point of transcription and to see whether those mutants affect transcription. Mutations that significantly affect transcription define important promoter elements. Alternatively, you could compare the DNA sequences upstream of a number of protein-coding genes to see whether there are any regions with similar sequences.Skill: Analytical reasoning

42) What is the difference between an intervening sequence and an untranslated region in a eukaryotic mRNA?Answer: Untranslated regions (UTRs) are found on either side of the protein-coding sequence of mRNAs and are part of the exons (and are thus not removed in pre-mRNA processing). Intervening sequences, also called introns, are found within the protein-coding sequence region and are removed in the processing of the pre-mRNA molecule to the mature mRNA.Skill: Factual recall

43) The sequence of a template strand of DNA is 3'-CATTACGCTT-5'. What is the sequence of the corresponding mRNA?Answer: 5'-GUAAUGCGAA-3'Skill: Problem-solving

44) What are the three regions of a prokaryotic gene?Answer: A promoter region, an RNA-coding region, and a terminator region.Skill: Factual recall

45) Describe the structure and organization of the rDNA repeat unit in eukaryotes.Answer: The rDNA repeat unit exists in tandem arrays of 100s to 1,000s of copies. Each unit consists of coding sequences for three rRNA genes (18S, 5.8S, and 28S) separated by two internal transcribed spacer (ITS) regions. The genes are flanked by external transcribed spacer (ETS) regions. These regions comprise the ribosomal DNA transcription unit. Upstream of the unit and separating from the previous repeat unit is a nontranscribed spacer (NTS) region that contains the promoter.Skill: Factual recall

46) What are the functions of the 5' cap and poly(A) tail of mature mRNAs in eukaryotes?Answer: Both protect the mRNA from degradation by exonucleases. The 5' cap is also important for the binding of the ribosome at the beginning of translation. The poly(A) tail is required for efficient export of the mRNA from the nucleus to the cytoplasm.Skill: Factual recall

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47) Cite at least three ways in which transcription differs from DNA replication.Answer: (1) In replication, both strands of the double-stranded DNA are copied, resulting in new double-stranded DNA molecules. In transcription, only one strand of the double-stranded DNA is transcribed into a single-stranded RNA molecule. (2) In eukaryotes, while DNA replication typically occurs during only part of the cell cycle, transcription generally occurs throughout the cycle. (3) No primer is needed in transcription because the RNA polymerase can initiate new polynucleotide chains, unlike DNA polymerase, which needs a primer to begin replication. Skill: Application of knowledge

48) In eukaryotes, what is the difference between promoter proximal elements in "housekeeping genes" vs. cell-specific genes, and how does this relate to gene expression?Answer: In genes that are expressed in all cell types for basic cellular functions ("housekeeping genes"), promoter proximal elements are recognized by regulatory activator proteins that are ubiquitous to all cell types. In cell-specific genes, the proximal elements are recognized by activators that are found only in those cells.Skill: Conceptual understanding

49) What is the advantage of having a promoter sequence upstream of a coding sequence?Answer: The promoter ensures that the initiation of every RNA occurs at the same site. Otherwise, the ensuing polypeptide might be missing amino acids, or it might contain extra amino acids.Skill: Analytical reasoning

50) How does the rate of initiation of transcription relate to the similarity of the promoter region to the consensus sequence?Answer: The ability of the sigma factor of the RNA polymerase holoenzyme to recognize and bind to a promoter sequence (i.e., the efficiency of RNA polymerase binding) is dependent on the similarity of the promoter to the consensus sequence (the sequence found most frequently at each position of the promoter). As a result, the rate at which transcription is initiated varies from gene to gene.Skill: Analytical reasoning

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