Deck 8: RNA Synthesis and Processing

Question 1

The prokaryotic cells most commonly used to study transcription and translation are from

A) E. coli.
B) B. subtilis.
C) S. cerevisiae.
D) D. discoideum.

Answer 1

A

Question 2

RNA polymerase differs from DNA polymerase in that it

A) synthesizes new strands of RNA in a 3ʹ to 5ʹ direction.
B) is a monomeric protein.
C) can synthesize a complementary strand without the two strands of DNA being separated.
D) does not require a primer to initiate synthesis of RNA.

Answer 2

D

Question 3

The DNA sequence to which an RNA polymerase binds to initiate transcription of a gene is called a(n)

A) enhancer.
B) promoter.
C) polymerase-binding element.
D) origin of transcription.

Answer 3

B

Question 4

The regions of the DNA where RNA polymerase binds can be identified by

A) restriction mapping.
B) PCR.
C) inhibited transcription following mutagenesis in the -35 and -10 promoter regions.
D) polymerase mapping.

Question 5

The role of the sigma ( $\sigma$ ) factor in prokaryote transcription is to

A) unwind the DNA during transcription.
B) direct RNA polymerases to bind to different promoter regions.
C) recognize the transcription initiation site.
D) terminate transcription.

Question 6

Transcription of a bacterial gene is initiated

A) with RNA polymerase in the closed-promoter complex.
B) after release of the sigma ( $\sigma$ ) factor.
C) with RNA polymerase in the open-promoter complex.
D) Both b and c

Question 7

The sigma ( $\sigma$ ) subunit of bacterial RNA polymerase remains associated for the addition of _______ during transcription.

A) the first ten nucleotides
B) the first half of the nucleotides
C) all of the nucleotides
D) the last ten nucleotides

Question 8

Transcription is _______-dependent _______ synthesis.

A) DNA; DNA
B) DNA; RNA
C) RNA; DNA
D) RNA; protein

Question 9

Termination of transcription in E. coli is signaled by

A) formation of a stem-loop structure in the RNA.
B) binding of Rho protein to the end of the mRNA.
C) binding of a sigma ( $\sigma$ ) factor to the end of the mRNA.
D) an inverted GC-rich sequence followed by seven A residues.

Question 10

Eukaryotic RNA polymerase I genes code for

A) mRNAs.
B) tRNAs.
C) small nuclear RNAs and small cytoplasmic RNAs.
D) ribosomal RNAs.

Question 11

Mitochondrial genes are transcribed by

A) RNA polymerase I.
B) RNA polymerase II.
C) RNA polymerase III.
D) a separate mitochondrial RNA polymerase.

Question 12

The large multi-subunit complex that links the general transcription factors to the gene-specific transcription factors is called

A) the transcription complex.
B) Mediator.
C) the operator.
D) TBP.

Question 13

A major difference between eukaryotic and prokaryotic RNA polymerases is that eukaryotic polymerases

A) use a set of transcription factors to bind to and initiate transcription.
B) use sigma ( $\sigma$ ) factors to initiate transcription.
C) start from promoters.
D) start from origins of replication.

Question 14

The TATA box is similar to the _______ in E. coli.

A) -35 promoter sequence
B) -10 promoter sequence
C) +1 transcription start site
D) None of the above

Question 15

The first step in the formation of a transcription complex for mRNA transcription is the binding of _______ to the TATA box.

A) TFIA
B) TFIIA
C) TFIIIA
D) TFIID

Question 16

Release of RNA polymerase II to initiate transcription appears to be the direct result of the

A) binding of TAFs to the polymerase.
B) unwinding of the DNA by helicases.
C) phosphorylation of RNA polymerase by a protein kinase.
D) removal of the nucleosome occupying the promoter site.

Question 17

All of the following are required for eukaryotic transcription in vitro except

A) TAF.
B) TFIIE.
C) TBP.
D) Mediator.

Question 18

Processing of pre-tRNAs to produce tRNAs involves

A) cleavage of the pre-tRNA.
B) CCA addition to the 5ʹ end.
C) phosphodiesterase activity to cleave the base and deoxyribose.
D) the removal of one intron.

Question 19

Processing of RNA transcripts occurs

A) only in eukaryotic cells.
B) only with mRNA transcripts.
C) only with rRNA and mRNA transcripts.
D) with tRNA, rRNA, and mRNA transcripts.

Question 20

Self-splicing was discovered in studies of the

A) pre-mRNAs of Tetrahymena.
B) pre-mRNAs of E. coli.
C) pre-rRNA of Tetrahymena.
D) pre-rRNA of E. coli.

Question 21

rRNA modifications are mediated by

A) general transcription factors.
B) miRNAs.
C) snoRNPs.
D) Mediator.

Question 22

Eukaryote mRNA processing occurs in

A) the cytoplasm.
B) the nucleus after completion of transcription.
C) a complex with RNA polymerase.
D) the Golgi apparatus.

Question 23

Fertilization stimulates

A) addition of 7-methylguanosine caps to pre-mRNAs.
B) the lengthening of poly-A sequences to stored mRNAs in eggs.
C) removal of introns from pre-mRNAs.
D) the degradation of early developmental mRNAs.

Question 24

The 7-methylguanosine cap on mNRA is required for

A) protecting an mRNA from exonuclease attack.
B) protecting an mRNA from endonuclease attack.
C) initiation of translation of the mRNA.
D) the addition of the poly-A tail.

Question 25

A poly-A tail is added to an mRNA by

A) RNA polymerase, which reads a string of complementary dTs at the end of the gene.
B) poly-A polymerase, which adds A's sequentially to the end of the transcript.
C) poly-A transferase, which adds a pre-made poly-A sequence to the end of the transcript.
D) poly-A correctase, which recognizes an AAUAAA signal at the end of the message and changes the U to an A.

Question 26

The signal for the addition of a poly-A tail to pre-mRNA is

A) UUUUUUU.
B) TTTTTTTT.
C) AAUAAA.
D) GCGCUGC.

Question 27

During splicing, pre-mRNAs go through an intermediate stage when they are shaped like

A) a lariat.
B) a circle.
C) the Greek letter theta ( $\sigma$ ).
D) a cross.

Question 28

Spliced mRNAs have protective mechanisms, but introns are rapidly degraded in the

A) nucleus.
B) cytoplasm.
C) lysosomes.
D) nucleoli.

Question 29

The RNA components of the spliceosome are five different

A) small cytoplasmic RNAs.
B) small nuclear RNAs.
C) microRNAs.
D) siRNAs.

Question 30

Which is not part of the spliceosome?

A) U1
B) U2
C) U3
D) U5

Question 31

Which snRNA is responsible for recognition of the 5′ splice site consensus sequence in mRNA splicing?

A) U1
B) U4
C) U5
D) U6

Question 32

A process called alternative splicing of mRNA transcripts can produce mRNAs with _______ from the same gene.

A) one different exon
B) more or fewer exons
C) completely different exons
D) All of the above

Question 33

The form of apolipoprotein B (Apo-B) produced by the intestine is shorter than the Apo-B produced by the liver. The intestine produces a smaller protein by

A) proteolytic cleavage of the forming polypeptide chain.
B) a base alteration that changes a codon for glutamine to a termination codon.
C) shortening the mRNA from the 3' end after translation.
D) including fewer exons in the mRNA by alternative splicing.

Question 34

The structure that is formed during termination of transcription due to an inverted GC-rich inverted repeat is known as a _______.

Question 35

The predominant RNA synthesized by eukaryotic RNA polymerase II is _______.

Question 36

Eukaryotic RNA polymerase III synthesizes _______.

Question 37

A core promotion element located just upstream from the transcription start site in eukaryotic genes is an A- and T-rich region called the _______.

Question 38

The subunit of TFIID that is responsible for binding specifically to the TATA box is known as _______.

Question 39

During transcriptional initiation in eukaryotes, _______ is responsible for phosphorylating RNA polymerase II C-terminal domain (CTD).

Question 40

When Tetrahymena 28S rRNA is incubated in the absence of proteins, it undergoes _______.

Question 41

Processing of the 5′ end of pre-tRNAs involves cleavage by an enzyme called _______.

Question 42

RNA splicing takes place in large complexes called _______.

Question 43

The RNA components of spliceosomes are five types of _______.

Question 44

Through the process of _______, cells can produce different proteins from the same gene.

Question 45

RNA processing events (other than splicing) that alter the protein-coding sequences of some RNAs are called _______.

Question 46

Unstable mRNAs with very short half-lives are frequently _______ proteins.

Question 47

Cytoplasmic degradation of most eukaryotic mRNA is initiated by shortening of their _______.

Question 48

Sigma ( $\sigma$ ) subunits of bacterial RNA polymerase initiate binding to the DNA and are released from the polymerase at the end of transcription.

Question 49

The $\sigma$ subunit of E. coli RNA polymerase is necessary for transcriptional elongation.

Question 50

An internal channel between the $\beta$ and $\beta$ ' subunits contains the bacterial RNA polymerase active site.

Question 51

In eukaryotes, transcription of mitochondrial genes uses typical nuclear RNA polymerases.

Question 52

tRNA genes are transcribed by RNA polymerase III.

Question 53

Nucleosomes are an impediment to transcription in eukaryotic cells.

Question 54

A minimum of six general transcription factors are required for the recruitment of RNA polymerase II.

Question 55

The genes for the 5S, 5.8S and 28S rRNAs are found in tandem and transcribed as a unit.

Question 56

The processing of pre-rRNA requires proteins and RNAs that are localized to the nucleolus.

Question 57

Processing of tRNAs involves addition of a CCA 5′ terminus.

Question 58

RNA editing refers to RNA processing events (other than splicing) that alter the protein-coding sequences of some mRNAs.

Question 59

Tissue-specific RNA editing can occur.

Question 60

Messenger RNAs have varying half-lives in the cytoplasm, and those differences are usually due to differences in the sequences near the 3ʹ end of the mRNA.

Question 61

What are the 5 subunits that make up bacterial RNA polymerase, and which one(s), if any, are weakly bound to the complex?

Question 62

What are two reasons why eukaryotic transcription is considered to be more complex than bacterial transcription?

Question 63

Identify two functions of capping and polyadenylation of mRNA.

Question 64

What are the two signals for polyadenylation of mRNA?

Question 65

What happens to the lariat-like structure that is excised during mRNA splicing?

Question 66

Why are some RNAs considered to be self-splicing?

Question 67

What two types of molecules make up snoRNPs?

Question 68

What are the five types of small nuclear RNAs that make up the spliceosome?

Question 69

Why is dystrophin absent in Duchenne muscular dystrophy?

Question 70

How was RNA editing first discovered?

Question 71

What is the most common form of nuclear RNA editing in mammals?

Question 72

What is the general mechanism for degrading mature mRNAs in the cytoplasm?

Question 73

Explain why bacterial mRNAs need to be very unstable, usually having half-lives of about 2 to 3 minutes.

Question 74

What feature is often found on rapidly degraded mRNAs?

Question 75

In prokaryotes, $\sigma$ factors are necessary for

A) specific binding to certain promoters.
B) low-affinity binding upstream from promoters.
C) elongation of the RNA strand to its end.
D) All of the above

Question 76

According to the central dogma of molecular biology, transcription of genetic information occurs via

A) DNA-dependent DNA synthesis.
B) DNA-dependent RNA synthesis.
C) RNA-dependent DNA synthesis.
D) RNA-dependent protein synthesis.

Question 77

Which statement about transcriptional termination in prokaryotes is false?

A) Termination is signaled by transcription of a GC-rich interval.
B) Transcription terminates when the RNA polymerase dissociates from its DNA template.
C) The ribosome comes to a UAA, UAG, or UGA stop codon, and transcription ceases.
D) A segment of RNA forms a stable stem-loop structure by complementary base pairing.

Question 78

Small nuclear RNAs (snRNAs) and small cytoplasmic RNAs (scRNAs) are transcribed by RNA polymerase

A) I.
B) II.
C) III.
D) II and III.

Question 79

Which of the following RNAs is RNA polymerase II not responsible for transcribing?

A) mRNA
B) miRNA
C) tRNA
D) lncRNA

Question 80

All of the following are general transcription factors used in eukaryotic transcription except

A) TFIIE
B) TFIIH
C) TBP
D) BRE