Deck 13: Transcription

Question 1

Over time, DNA replaced RNA as the primary carrier of genetic information, and the chemical stability of DNA is believed to be the key reason for this. Which attribute of DNA is the reason behind its chemical stability?

A) DNA lacks a free hydroxyl group on the 2'-carbon atom of its sugar.
B) Unlike RNA, DNA is usually double stranded.
C) DNA does not usually form hairpin loops.
D) One of the two pyrimidines found in DNA does not involve uracil.
E) DNA contains thymines, which make it more chemically stable.

Answer 1

DNA lacks a free hydroxyl group on the 2'-carbon atom of its sugar.

Question 2

Whereas the nucleotide strand used for transcription is termed the _____, the nontranscribed strand is called the _____.

A) promoter; terminator
B) terminator; promoter
C) transcription apparatus; TATA box
D) template strand; nontemplate strand
E) nontemplate strand; template strand

Answer 2

D

Question 3

The discovery of ribozymes led to the theory that the evolution of life on Earth began with an "RNA world." Describe the chemical properties and functions of RNA that would allow it to be the basis of the first self-replicating systems.

Answer 3

not answered

Question 4

In eukaryotes, tRNAs are transcribed in:

A) the nucleus and function in the nucleus
B) the nucleus but function in the cytoplasm
C) the cytoplasm and function in the cytoplasm
D) both the nucleus and the cytoplasm and function in the cytoplasm
E) the cytoplasm and function in the nucleus

Question 5

In a transcription reaction, two phosphate groups are cleaved from the incoming:

A) deoxyribonucleoside diphosphate.
B) deoxyribonucleoside triphosphate.
C) ribonucleoside diphosphate.
D) ribonucleoside triphosphate.
E) ribozyme.

Question 6

Where are promoters usually located?

A) upstream of the start site
B) downstream of the start site
C) near nucleotide +25
D) near the hairpin loop
E) downstream of the terminator

Question 7

Which of the following is a sequence of DNA where transcription is initiated?

A) hairpin loop
B) TBP
C) initiator
D) sigma factor
E) promoter

Question 8

Which of the following statements is NOT true?

A) Both DNA and RNA are synthesized in a 5' to 3' direction.
B) During RNA synthesis, the DNA template strand is read in a 3' to 5'direction.
C) During RNA synthesis, new nucleotides are added to the 3' end of the growing RNA molecule.
D) RNA polymerase has 5' to 3' polymerase activity.
E) RNA molecules have the same 5' to 3'orientation as the DNA template strands to which they are complementary.

Question 9

What types of bonds are created between nucleotides during the process of transcription?

A) ionic
B) oxygen
C) phosphodiester
D) hydrogen
E) both phosphodiester and hydrogen

Question 10

Which of the following types of RNA gets translated?

A) rRNA
B) mRNA
C) tRNA
D) miRNA
E) rRNA, mRNA, and tRNA all get translated

Question 11

_____ probably began the evolution of life on Earth.

A) DNA
B) RNA promoters
C) DNA polymerases
D) RNA polymerases
E) Ribozymes

Question 12

Which of the following RNA molecules is required for the process of translation?

A) crRNA
B) tRNA
C) snRNA
D) snoRNA
E) siRNA

Question 13

Which of the following molecules is synthesized using nucleotides containing the bases adenine, guanine, cytosine, and uracil?

A) RNA only
B) DNA only
C) both RNA and DNA
D) neither RNA nor DNA

Question 14

In transcription, to which end of the elongating strand are nucleotides always added?

A) 3'
B) 5'
C) 3' in prokaryotes and 5' in eukaryotes
D) It depends on which RNA polymerase is being used.
E) It depends on which DNA strand is being used as the template.

Question 15

If you were asked to isolate total RNA from two unknown samples and then were required to identify if the RNA was from prokaryotes or eukaryotes, what aspects regarding the classes of RNA present would help you distinguish one from the other?

Question 16

Which of the following statements is TRUE regarding transcription in most organisms?

A) All genes are transcribed from the same strand of DNA.
B) Both DNA strands are used to transcribe a single gene.
C) Different genes may be transcribed from different strands of DNA.
D) The DNA template strand is used to encode double-stranded RNA.
E) The DNA nontemplate strand is used to encode single-stranded RNA.

Question 17

The discovery of ribozymes led to the theory that the evolution of life on Earth began with an "RNA world." What properties of proteins and DNA make them more suitable than RNA as enzymes and the cell's genetic material?

Question 18

In eukaryotes, which RNA polymerase transcribes the genes that encode proteins?

A) RNA polymerase I
B) RNA polymerase II
C) RNA polymerase III
D) RNA polymerase IV
E) RNA polymerase V

Question 19

The discovery of ribozymes led to the theory that the evolution of life on Earth began with an "RNA world." Describe how the current cellular roles of RNA support this theory.

Question 20

The DNA replication enzyme that most closely resembles RNA polymerase is:

A) DNA polymerase I.
B) DNA polymerase III.
C) primase.
D) telomerase.
E) helicase.

Question 21

The following diagram represents the transcription unit and corresponding RNA transcripts as "Christmas-tree-like" structures captured in the electron micrograph.

- Which of the following statements CORRECTLY describes the reason as to why the transcription unit looks like a "Christmas tree" with different length of tree branches along the DNA "tree trunk"?

A) Depending on where the transcription begins on the DNA template, different lengths of transcripts get generated.
B) Each position on the DNA dictates the specific length of the RNA transcript generated from that particular position.
C) The transcript randomly grows from the DNA without any particular reason.
D) A single DNA can be transcribed many times continuously, and the RNA transcript gets longer as the transcription apparatus moves down the DNA.
E) There is no known reason for the transcription unit to assume the "Christmas-tree-like" shape.

Question 22

The following diagram represents the transcription unit and corresponding RNA transcripts as "Christmas-tree-like" structures captured in the electron micrograph.

- Which of the following statements CORRECTLY describes the orientation of the DNA and RNA transcript? (Select all that apply.)

A) A represents the 5? end while B represents the 3? end of the DNA template undergoing transcription.
B) A represents the 3? end while B represents the 5? end of the DNA template undergoing transcription.
C) C represents the 5? end while D represents the 3? end of the RNA transcript.
D) C represents the 3? end while D represents the 5? end of the RNA transcript.
E) The specific orientation of the DNA template and RNA transcript cannot be determined based on the given information.

Question 23

Mutations occurred in one of the inverted repeat sequences within the rho-independent terminator sequence of a bacterium. What would likely be the consequence of this mutation? (Select all that apply.)

A) The transcription may end prematurely.
B) The transcription may not be initiated at all.
C) The transcription may be delayed.
D) The RNA transcript may not be able to dissociate from the DNA template.
E) The transcription may not terminate and result in much longer RNA.

Question 24

Which of the following molecules is synthesized using triphosphate nucleotides as a substrate for a polymerase enzyme that forms phosphodiester bonds?

A) RNA only
B) DNA only
C) both RNA and DNA
D) neither RNA nor DNA

Question 25

What may be the consequence of a mutation in the gene that encodes eukaryotic Rat1 exonuclease for eukaryotic transcription mediated by RNA polymerase II?

A) The transcription may end prematurely, resulting in shorter mRNA transcript.
B) The transcription may not be properly terminated, and RNA polymerase II may not be released.
C) The transcription may be delayed indefinitely, which may kill the cell.
D) The RNA transcript may not be able to dissociate from the DNA template.
E) The transcription may not terminate and result in much longer RNA.

Question 26

What would be the consequence of a mutation in the gene that encodes sigma factor for bacterial transcription?

A) The initiation of transcription may begin at random points of the DNA template.
B) The RNA polymerase may not be released from the DNA template.
C) Transcription may be delayed indefinitely, which may kill the cell.
D) The RNA transcript may not be able to dissociate from the DNA template.
E) The transcription may end prematurely, resulting in shorter mRNA transcript.

Question 27

The following diagram represents a transcription unit. What would likely happen to transcription of this transcription unit if a certain consensus sequence within region A is removed via deletion?

A) The mutation in region A would result in truncated RNA transcript that is shorter than expected RNA.
B) The mutation in region A does not affect the transcription as the transcript is copied only from regions B and C.
C) The transcript may get copied in reverse direction as the orientation of region A is important for the direction of the transcription.
D) The transcript may not be produced as the consensus sequence within region A may be important for the initiation of the transcription.
E) The transcription occurs normally as there are other consensus sequences that would compensate for the loss of one.

Question 28

Which of the following is NOT required for transcription?

A) ribonucleotides
B) RNA primers
C) DNA template
D) RNA polymerase
E) promoter

Question 29

Which of the following molecules is made of nucleotides joined by phosphodiester bonds that connect the 2' OH to the 5' phosphate?

A) RNA only
B) DNA only
C) both RNA and DNA
D) neither RNA nor DNA

Question 30

Mutations in which of the following regions upstream of the RNA coding sequence are LEAST likely to affect the transcription of a gene?

A) -10 consensus sequence within the promoter region
B) -35 consensus sequence within the promoter region
C) the region between -10 and -35 consensus sequences
D) the upstream elements at -40 to -60 position
E) Any mutation on the upstream of a gene will definitely have deleterious effect on gene transcription.

Question 31

Which process is illustrated in the diagram below?

A) transcription
B) translation
C) RNA processing
D) peplication
E) nucleosome assembly

Question 32

Which of the following statements about RNA polymerase is NOT true?

A) RNA polymerase adds a ribonucleotide to the 3ʹ end of a growing RNA molecule.
B) RNA polymerase binds to a promoter to initiate transcription.
C) During transcription of a gene, RNA polymerase reads only one strand of DNA.
D) RNA polymerase reads a template strand of DNA 5ʹ to 3ʹ.
E) RNA polymerase has many subunits.

Question 33

If the DNA strand 5ʹ-GTACCGTC-3ʹ were used as a template, what would be the sequence of the transcribed RNA?

A) 5'-GUACCGUC-3'
B) 5'-GACGGTAC-3'
C) 5'-CAUGGCAG-3'
D) 5'-GACGGUAC-3'
E) 5'-GUCGGUAC-3'

Question 34

Both strands of a DNA molecule are used as a template when which of the following molecules is synthesized?

A) RNA only
B) DNA only
C) both RNA and DNA
D) neither RNA nor DNA

Question 35

What is the function of eukaryotic RNA polymerase I?

A) transcription of rRNA genes
B) transcription of mRNA genes
C) transcription of tRNA genes
D) transcription of snRNAs
E) initiation of transcription (but not elongation)

Question 36

The following diagram represents a transcription unit. Which region(s), A, B, and/or C, would be transcribed into an RNA transcript? (Select all that apply.)

A) A
B) B
C) C

Question 37

What is the RNA sequence transcribed from the DNA shown below?

A) 5ʹ-CCGTATAATGA-3ʹ
B) 3ʹ-GGCATATTACT-5ʹ
C) 5ʹ-GGCAUAUUACA-3ʹ
D) 5ʹ-CCGUAUAAUGA-3ʹ
E) 3ʹ-GGCAUAUUACU-5ʹ

Question 38

If the sequence of an RNA molecule is 5ʹ-GGCAUCGACG-3ʹ, what is the sequence of the nontemplate strand of DNA?

A) 5ʹ-GGCATCGACG-3ʹ
B) 3ʹ-GGCATCGACG-5ʹ
C) 5ʹ-CCGTAGCTGC-3ʹ
D) 3ʹ-CCGTAGCTGC-5ʹ
E) 3ʹ-CGTCGATGCC-5ʹ

Question 39

The polymerase that synthesizes which of the following molecules uses DNA as a template and synthesizes new strands from 5' to 3'?

A) RNA only
B) DNA only
C) both RNA and DNA
D) neither RNA nor DNA

Question 40

Choose the BEST consensus sequence for the following set of nucleotide sequences. TAAGACGCCATGA
AAAGTCGCAATCA
AAAGTTCCGTTCA
AGAGTTGCTATCA
AGAGTTGCAATCA

A) YACGTRGCATG/CA
B) AYTRTRGCATGA
C) AAAGTNGANTCA
D) ARAGTYGCNTCA
E) ACTNCGYTGARA

Question 41

On the DNA strands shown below, two RNA polymerase enzymes are using the top strand as a template. In the boxes, label the 5' and 3' ends of the DNA molecules and the RNA molecules being made. With arrows, indicate the directions, left to right or right to left, that the polymerases are moving.

Question 42

In prokaryotes, rho-independent transcription termination depends on a secondary structure formed in:

A) the RNA polymerase that is transcribing the gene.
B) the DNA template.
C) the RNA that is being transcribed.
D) a protein factor that binds to RNA polymerase.
E) a protein factor that binds to the RNA that is being transcribed.

Question 43

What are the three different RNA polymerases found in all eukaryotes and what types of genes do they transcribe?

Question 44

What would you add to an in vitro transcription system that contains an E. coli gene for glyceraldehyde 3-phosphate dehydrogenase, an enzyme in glycolysis, in order to get transcription that begins from the normal transcription start site?

Question 45

Which of the following is not necessary for RNA polymerase to recognize the promoter of a bacterial gene?

A) sigma factor
B) origin of replication
C) -10 consensus sequence
D) -35 consensus sequence

Question 46

In prokaryotes, a group of genes that are usually transcribed following a specific stimulus is organized as an "operon" under a single shared promoter (Chapter 16; see the figure below). The result of the transcription of the genes in the presence of a stimulus would generate a:

A) crRNA.
B) miRNA.
C) polycistronic mRNA.
D) rRNA.
E) siRNA.

Question 47

An in vitro transcription system transcribes a bacterial gene but terminates inefficiently. What is one possible problem?

A) There is a mutation in the -10 consensus sequence, which is required for efficient termination.
B) Rho factor has not been added.
C) Sigma factor has not been added.
D) A hairpin secondary structure has formed at the 3' end of the mRNA, interfering with termination.
E) Histones were added prematurely and interfered with termination.

Question 48

Prokaryotic promoters contain the sequence TATAAT at a position _____ from the transcription start.

A) +1
B) -1
C) -10
D) -25
E) -35

Question 49

In prokaryotic RNA polymerases, the holoenzyme consists of the core enzyme and the:

A) rho factor.
B) TFIID.
C) TBP.
D) omega subunit.
E) sigma factor.

Question 50

What is the RNA sequence transcribed from the DNA shown below?

Question 51

Compare rho-dependent and rho-independent transcription termination in terms of their use of RNA secondary structures.

Question 52

An RNA molecule has the following percentage of bases: A = 15%, U = 30%, C = 20%, and G = 35%.
a. Is this RNA single stranded or double stranded? How can you tell based on the base composition?
b. What would be the percentage of bases in the template strand of the DNA that encodes this RNA molecule?

Question 53

An in vitro transcription system that contains a bacterial gene does not initiate transcription. What is one possible problem?

A) Histones that were on the DNA when it was isolated from E. coli are blocking access to the template.
B) There is a mutation in the inverted repeat sequence that prevents a hairpin secondary structure from forming.
C) There is a mutation at -10, where a promoter consensus sequence is located.
D) Rho factor has not been added.
E) TATA-binding protein (TBP) has not been added.

Question 54

When does sigma factor normally dissociate from RNA polymerase?

A) after transcription has terminated
B) after the process of initiation
C) after the addition of nucleosomes
D) after the binding of rho
E) following the addition of nucleosomes

Question 55

An in vitro transcription system that contains a bacterial gene initiates transcription from random points on the DNA. Which of the following proteins MOST likely is missing from the reaction?

A) sigma factor
B) rho factor
C) RNA polymerase II
D) TATA-binding protein (TBP)
E) TFIID

Question 56

Two sequences of a prokaryotic promoter are shown below. Sequence 1 is the wild-type sequence, and sequence 2 is a mutant sequence (mutation shown in bold) that results in increased transcription of the gene. Explain why sequence 2 shows this phenotype.

Question 57

Diagram an active transcription unit as it would appear at high magnification. On the diagram indicate each of the following:
(a) the DNA molecule
(b) the RNA molecule that was initiated earliest
(c) the 5' end of an RNA molecule
(d) the 5' end of the template strand of DNA
(e) the approximate location of the promoter
(f) a molecule of RNA polymerase
(g) an arrow indicating the direction of transcription

Question 58

The following diagram represents DNA that is part of the RNA-coding sequence of a transcription unit. ATAGGCGATGCCA
TATCCGCTACGGT The sequence of the RNA product of transcription is 5'-UGGCAUCGCCUAU-3'. Label the diagram of the DNA molecule to indicate which strand serves as the template strand. Also label the 5' and 3' ends of both strands.

Question 59

Transcription of a gene using what is normally the nontemplate strand can be accomplished using standard genetic engineering techniques to move the promoter. The resulting RNA is called "antisense RNA." Antisense RNA is often used to prevent production of a protein. Explain how antisense RNA would interact with RNA normally made by the gene and how this would interfere with protein production.

Question 60

Which of the following features of the rho protein is primarily responsible for its ability to cause termination of transcription?

A) recognizing unstructured RNA
B) helicase activity
C) migrating behind RNA polymerase
D) RNA-binding activity
E) polymerase activity

Question 61

A new mutation in Saccharomyces cerevisiae, a eukaryotic yeast, causes the cells to be unable to produce the amino acid histidine. Specifically, they cannot catalyze the first reaction in the histidine biosynthesis pathway. When examined closely, they are producing a completely wild-type enzyme for this reaction but at greatly reduced levels. Explain the mutation.

Question 62

The TATA-binding protein (TBP) binds to the TATA box sequence in eukaryotic promoters. What is its function in transcriptional initiation?

A) It blocks access of RNA polymerase to the promoter until removed by general transcription factors.
B) It is the subunit of prokaryotic RNA polymerase that is required to recognize promoters.
C) It modifies histones so that nucleosomes can be removed from DNA for transcription.
D) It bends and partly unwinds DNA at a promoter.
E) It creates a phosphodiester bond between the nucleotides.

Question 63

Which of the following statements is FALSE regarding TFIID?

A) It contains a TATA-binding protein.
B) It aids in initiation of transcription.
C) It binds to the core promoter.
D) It binds to the TATA box.
E) It is a transcriptional activator protein.

Question 64

An in vitro system to detect transcription initiation functions in protein extracts from either eukaryotic or archaebacterial cells is added. Initiation does not occur if extracts from eubacterial cells are added. What does the protein extract contain? Explain the results using the different sources of protein extracts.

Question 65

Explain why eukaryotic transcripts from the same RNA-polymerase-II-transcribed gene may vary in the sequences at the 3' end.

Question 66

If you wanted to express a eukaryotic gene in E. coli, would the normal promoter be sufficient for transcription? Why or why not?

Question 67

What would you add to an in vitro transcription system that contains a Drosophila gene for glyceraldehyde 3-phosphate dehydrogenase, an enzyme in glycolysis, in order to get basal transcription?

Question 68

Histone acetyltransferases add acetyl groups to lysines, which are positively charged amino acids. How might this affect the association of a nucleosome with DNA?

Question 69

Compare and contrast the operation of promoters and enhancers in affecting transcription of genes in eukaryotes. Include a discussion of how they operate and from what positions with respect to the transcription initiation site and the roles of each in bringing about and regulating transcription.

Question 70

How are enhancers different from promoters?

Question 71

In eukaryotic cells, where does the basal transcription apparatus bind?

A) core promoter
B) regulatory promoter
C) terminator
D) enhancer
E) ribozyme

Question 72

Describe how the activities and requirements of prokaryotic RNA polymerase and eukaryotic RNA polymerase II are both similar and different.

Question 73

You analyze a newly cloned eukaryotic gene by comparing the DNA sequence of the gene to the sequence of the transcribed RNA and find that it does not contain recognizable promoter sequences upstream of its coding sequence. How can you explain this result, and how might you confirm your hypothesis?

Question 74

Which of the following statements is TRUE regarding the termination of transcription?

A) In some organisms, transcription terminates thousands of nucleotides past the coding sequence.
B) Transcription typically terminates precisely at the hairpin loop terminator sequence.
C) In prokaryotes, transcription terminates as soon as rho has bound to the RNA.
D) In yeast, transcription terminates as soon as Rat1 has bound to the RNA.

Question 75

Your goal is to achieve a high level of transcription-a level similar to its in vivo levels-of a eukaryotic gene in an in vitro transcription system. You add the DNA template for this gene, which contains the following, to the in vitro transcription system: a TATA box sequence located -25 to -30 bp upstream of the transcription start site, the sequence for the gene, and terminator sequences. How would you interpret the result if you do not get high levels of RNA transcription, and what corrective measures would you take to achieve your goal?

Question 76

Organisms belonging to the archaea group possess a TATA-binding protein (TBP), but they are structurally very similar to members of the eubacteria (i.e., contain no nucleus, are single celled). What does this conundrum mean regarding the evolutionary relationships among the archaea, eubacteria, and eukaryotes?

Question 77

What is the function of general transcription factors?

A) They are DNA sequences to which RNA polymerase binds.
B) They direct nucleosome assembly.
C) They bind to regulatory promoters to increase the rate of transcription.
D) They bind to enhancers to allow minimal levels of transcription.
E) They are a part of the basal transcription apparatus.

Question 78

Describe three ways that eukaryotic transcription initiation is different from prokaryotic transcription initiation.

Question 79

Which one of the following statements regarding eukaryotic transcription is NOT true?

A) Eukaryotic transcription involves a core promoter and a regulatory promoter.
B) There is no one generic promoter.
C) A group of genes is transcribed into a polycistronic RNA.
D) Chromatin remodeling is necessary before certain genes are transcribed.
E) There are several different types of RNA polymerase.

Question 80

If you remove the TATA box and place it immediately upstream of a transcription start site of a eukaryotic gene and subsequently transcription of the mRNA is assayed, will you still achieve transcription from the same start site?