Deck 21: RNA Synthesis, Processing, and Gene Silencing

Question 1

Which protein-synthesizing RNA molecule carries an amino acid to the ribosome active site?

A) rRNA
B) tRNA
C) mRNA
D) siRNA

Answer 1

rRNA

Question 2

RNA is a dynamic biomolecule because it can

A) be a component in protein synthesis, regulate protein synthesis, and be synthesized and function in cell nucleus.
B) catalyze its own synthesis.
C) contain a ribose sugar backbone.
D) be stable to hydrolysis.

Answer 2

be a component in protein synthesis, regulate protein synthesis, and be synthesized and function in cell nucleus.

Question 3

Which class of RNA molecules is unique to eukaryotic organisms?

A) transfer RNA
B) ribosomal RNA
C) small nuclear RNA
D) messenger RNA

Answer 3

small nuclear RNA

Question 4

A 7-methylguanylate cap and poly(A) tail is added to mRNA to

A) differentiate the mRNA from the tRNA.
B) facilitate binding and translation by the ribosome.
C) increase mRNA splicing efficiency.
D) signify the start and end of the gene sequence.

Question 5

Of the following protein synthesizing RNA molecules, which codes for a protein?

A) tRNA
B) siRNA
C) mRNA
D) rRNA

Question 6

RNA is typically more susceptible to backbone hydrolysis than DNA because of the

A) presence of simpler nucleotides.
B) presence of a 2 ^' OH group.
C) presence of a 3 ^' OH group.
D) lack of thymine nucleotides.

Question 7

Which enzyme is important in the processing of tRNA and mRNA from prokaryotes?

A) RNaseP
B) snRNA
C) reverse transcriptase
D) ribozyme

Question 8

How are RNA structures different from protein structures?

A) RNA is single stranded, whereas proteins are not.
B) RNA can H-bond with itself, whereas proteins cannot.
C) RNA mutations can lead to nonfunctioning proteins, whereas protein mutations do not.
D) RNA adopts less defined tertiary structures than proteins.

Question 9

RNA is a highly dynamic biomolecule in that it

A) can fold and hydrogen bond with itself, DNA, proteins, or small molecules to adopt largely modified tertiary structures.
B) is less capable of forming stable H-bonds than DNA.
C) is often shorter than DNA.
D) is largely composed of a phosphate backbone.

Question 10

The most significant influence on why mRNA is processed differently in prokaryotes than eukaryotes is the fact that

A) eukaryotes separate transcription and translation with a nucleus.
B) prokaryotes are often polycistronic.
C) eukaryotes are multicellular organisms.
D) prokaryotes do not add a poly(A) tail.

Question 11

It has been estimated that as much as % of the human genome is transcribed into noncoding RNA, whereas % of the E. coli genome is noncoding RNA.

A) 10; 90
B) 90; 10
C) 50; 10
D) 25; 2

Question 12

Which is often removed from eukaryotic mRNA before translation?

A) poly(A) tails
B) exons
C) polycistrons
D) introns

Question 13

Prokaryotic mRNA is commonly processed through

A) splicing by RNaseP enzymes.
B) immediate translation during transcription.
C) addition of 7-methylguanylate cap.
D) removal of exons.

Question 14

Long noncoding RNA (lncRNA) is generated from

A) the tips of chromosomes.
B) the transcription of genomic DNA.
C) the splicing of used mRNA.
D) an infection of viral RNA.

Question 15

Which of the following is a coding RNA molecule?

A) short interfering RNA.
B) TERC RNA.
C) small nucleolar RNA.
D) messenger RNA.

Question 16

Which of the following RNA molecules has the LEAST number of different sequences in a given organism?

A) tRNA
B) rRNA
C) mRNA
D) snRNA

Question 17

Which class of RNA molecule is typically the shortest in length?

A) transfer RNA
B) messenger RNA
C) small nuclear RNA
D) micro RNA

Question 18

The RNA type directly involved in protein synthesis is

A) small nuclear RNA.
B) short interfering RNA.
C) ribosomal RNA.
D) long nc RNA.

Question 19

A knockout mutation in the X-inactive specific transcript (XIST) lncRNA of mice would result in

A) one inactivated X chromosome in female mice.
B) the inhibited transcription and translation of X-linked proteins.
C) two inactive X chromosomes in female mice.
D) two active X chromosomes in female mice.

Question 20

Which RNA molecule does NOT bind to the ribosome?

A) tRNA
B) rRNA
C) mRNA
D) snRNA

Question 21

Long noncoding RNAs (lncRNAs) are found on

A) exons of protein-coding genes.
B) introns of protein-coding genes.
C) non-functional rRNA.
D) protein-coding mRNA.

Question 22

In which direction is mRNA synthesized by RNA polymerase?

A) in the 3 ^' to 5 ^' direction
B) with 5 ^' to 3 ^' phosphodiester linkages
C) in the 5 ^' to 3 ^' direction
D) It depends on whether the sense or antisense strand is transcribed.

Question 23

What are $\sigma$ factors in RNA synthesis?

A) DNA promoter regions
B) RNA polymerases
C) transcription factors
D) receptor proteins

Question 24

Eukaryotic promoters, but NOT prokaryotic promoters,

A) are located before the transcription start site.
B) bind transcription factors.
C) are located after the transcription start site.
D) assist in activating transcription.

Question 25

Which biochemical lab technique is used in the DNA footprinting technique?

A) gel electrophoresis
B) polymerase chain reaction
C) plasmid ligation
D) cloning

Question 26

Weak prokaryotic promoters

A) can bind to different transcription factors.
B) have a DNA sequence that is significantly different from that of other common promotors.
C) can be easily bound to $\sigma$ factors.
D) give weak DNA footprinting signals.

Question 27

Which is true of RNA polymerases in both prokaryotic and eukaryotic organisms?

A) They are composed of an analogous $\alpha$ ₂ $\beta$$\beta$ ^' $\omega$ core.
B) There is a single enzyme type per organism.
C) They make copies of RNA from either DNA or RNA templates.
D) They have the same number of cofactors in prokaryotes and eukaryotes.

Question 28

Approximately how many different types of RNA promotors are needed in eukaryotic systems?

A) 1
B) 2
C) 3
D) 4

Question 29

Which is NOT required in the prokaryotic transcription initiation complex?

A) a primer
B) RNA polymerase
C) initiation factor
D) a ribonucleotide triphosphate (NTP)

Question 30

Eukaryotic transcription promoters

A) are typically found after the transcription start site.
B) have a single sequence and bind one RNA polymerase type.
C) may bind to both transcription factors and RNA polymerases.
D) are all controlled by a ubiquitous $\sigma$ factor.

Question 31

What do $\sigma$ factors bind to in RNA synthesis?

A) DNA promoters and RNA polymerase
B) RNA promoters and DNA
C) DNA and RNA
D) transcription factors

Question 32

Using the DNA footprinting technique, which of the following were/was identified as binding site(s) for $\sigma$ factors?

A) -35 box
B) -5 and -35 box
C) -10 and -35 box
D) -10 box

Question 33

Strong prokaryotic promoters

A) bind tightly to the transcription factors.
B) have $\sigma$ factors that are larger, more stable proteins.
C) generally result in a higher rate of transcription.
D) are less common in prokaryotes.

Question 34

The information gained from the DNA footprinting technique is the

A) DNA sequence.
B) promotor region of a gene.
C) location of a gene in DNA.
D) location of a DNA binding protein on DNA.

Question 35

The strand of DNA is transcribed into mRNA.

A) leading
B) coding
C) lagging
D) template

Question 36

Eukaryotic transcription promoters

A) require multiple DNA binding regions.
B) are largely conserved across the genome.
C) can stimulate DNA polymerases by direct binding.
D) control translational as well as transcriptional events.

Question 37

The function of DNase I is that it

A) cuts DNA whenever DNA binding proteins are present.
B) cuts double-stranded DNA by cutting phosphodiester bonds.
C) cuts DNA binding proteins.
D) makes an RNA copy of DNA.

Question 38

Eukaryotic RNA polymerase

A) is a ribozyme.
B) contains as many as five protein subunits in the final functional enzyme.
C) synthesizes all RNA types.
D) has a common core structure resembling that of prokaryotic RNA polymerase.

Question 39

What prokaryotic promoter would most likely control a housekeeping gene?

A) weak promoter
B) -10 and -35 box
C) TATA box
D) strong promoter

Question 40

The DNA sequence of prokaryotic gene promotors were found to be

A) largely conserved.
B) distinct for each gene.
C) capable of binding different promoters.
D) strong binders of DNA polymerase.

Question 41

Group I and group II introns are similar in their

A) requirement for metal ion cofactors.
B) requirement for exogenous nucleoside binding.
C) DNA composition.
D) intron lariat structure.

Question 42

Prokaryotic transcription could terminate by

A) association of a $\sigma$ factor with the DNA.
B) RNA with GC stem loop structures.
C) a G-rich region on the DNA.
D) RNA polymerase without the elongation factor.

Question 43

Most post-transcriptional RNA processing reactions are catalyzed by

A) DNAzymes.
B) ribozymes.
C) ligases.
D) transferases.

Question 44

What best describes the composition of the spliceosome?

A) small nuclear ribonucleoprotein
B) RNA only
C) protein
D) mRNA

Question 45

At what point during transcription does the F $\sigma$ factor dissociate from the RNA polymerase?

A) in the initiation phase
B) in the termination phase
C) before the elongation phase
D) during the elongation phase

Question 46

Which is true of ribozymes?

A) They have conserved primary sequences.
B) They are not true catalysts.
C) They are transcription factors.
D) They have conserved secondary and tertiary structures.

Question 47

The following is referred to as the ribozyme.

A) stem-loop
B) hairpin
C) hammerhead
D) cloverleaf

Question 48

The spliceosome

A) is a cis-acting ribozyme.
B) resembles group II introns in its mechanism and product.
C) performs the same function in prokaryotes and eukaryotes.
D) is a protein enzyme.

Question 49

Eukaryotic RNA polymerase II facilitates the

A) removal of exons.
B) addition of 7-methylguanylate cap.
C) addition of a poly(A) tail.
D) translation of the RNA transcript.

Question 50

The C-terminal domain (CTD) of the eukaryotic RNA polymerase II is involved in the transcriptional process of

A) addition of a poly(A) tail.
B) removal of exons.
C) directing RNA to the cytoplasm.
D) product phosphorylation.

Question 51

Trans activity refers to the __________ for a ribozyme.

A) cleavage of another identical RNA molecule
B) intermolecular cleavage of substrate
C) intramolecular cleavage
D) conserved activity of all enzymes

Question 52

What is a difference between group I and group II introns?

A) intron cleaving versus exon ligating abilities
B) cis versus trans cleaving capabilities
C) linear versus lariat intron products
D) nucleophilic versus electrophilic hydroxyl attacks

Question 53

A difference between transcription in prokaryotes and eukaryotes is the

A) lack of need for a primer.
B) presence of a transcription bubble.
C) addition of a poly(A) tail.
D) direction of transcription on the DNA template.

Question 54

In E. coli, RNA-DNA base pairs are maintained and about base pairs of single-stranded DNA are maintained in the transcription bubble.

A) 20; 80
B) 8; 17
C) 17; 20
D) 200; 1000

Question 55

Cis-acting enzymes are

A) self-operating enzymes.
B) enzymes that operate on a target molecule.
C) intermolecular-operating enzymes.
D) enzymes that operate on other enzymes.

Question 56

Identify the location of action of the spliceosome.

A) nuclear pore
B) nucleus
C) rough endoplasmic reticulum
D) cytoplasm

Question 57

The group I and group II introns catalyze which class of reaction?

A) transferase
B) cleavage
C) hydrolysis
D) transesterification

Question 58

The initiation, elongation, and termination of eukaryotic transcription is controlled by the

A) extent of phosphorylation and dephosphorylation of the RNA polymerase.
B) presence of initiation, elongation, and termination factors binding to RNA polymerase.
C) unwinding the double-stranded DNA.
D) length of the RNA transcript.

Question 59

What do group I introns require that group II introns do not?

A) ATP hydrolysis
B) metal ion cofactors
C) guanosine cofactor binding
D) external RNA substrate

Question 60

The initiation of transcription in eukaryotes

A) occurs in the same manner as prokaryotic transcription.
B) requires the complete unfolding of the gene into single-stranded DNA.
C) requires many more transcription factors than prokaryotic transcription.
D) uses RNA polymerase as well as helicase and primase.

Question 61

List the classes and types of noncoding RNAs that are found typically in eukaryotic organisms.

Question 62

What is the biggest difference between miRNA and siRNA?

A) One is derived from the nucleus and one is derived from double-stranded RNA.
B) One regulates gene expression, whereas the other regulates protein synthesis.
C) One binds to mRNA and suppresses its translation and one binds to mRNA and signals degradation.
D) One binds to the DNA gene and inhibits transcription and one binds to the mRNA and signals degradation.

Question 63

Which enzyme degrades the poly(A) tail in the degradation of mRNA?

A) poly(A) binding protein
B) exosome
C) CCR4
D) DCP1 and DCP2

Question 64

Which is central to the addition of the 7-methylguanosine cap to mRNA?

A) RNA polymerase 1
B) guanine-N7 methyltransferase
C) GMP
D) snoRNA

Question 65

The enzyme responsible for making siRNA is

A) RISC.
B) snoRNA.
C) exosome.
D) dicer.

Question 66

Which RNA molecule is expressed in the genome to regulate gene expression?

A) RNAi
B) snoRNA
C) miRNA
D) siRNA

Question 67

The roles of U1, U2, U4, U5, and U6 in the spliceosome complex are to

A) bind mRNA and facilitate the splicing reaction.
B) bind the small nuclear RNA.
C) carry the products from the nucleus to the cytoplasm.
D) bind proteins and hold the complex together.

Question 68

Antisense RNA binds to and sense RNA binds to .

A) template DNA; coding DNA
B) tRNA; mRNA
C) coding DNA; template DNA
D) mRNA; coding DNA

Question 69

More than 100 different RNA base modifications have been identified, and most of those are found in

A) mRNA.
B) rRNA.
C) snRNA.
D) tRNA.

Question 70

miRNA is

A) involved in stimulating gene expression.
B) derived from degraded mRNA.
C) expressed in the nucleus and is involved in regulating gene expression.
D) derived from degraded virus RNA strands.

Question 71

Many noncoding RNAs are involved in gene silencing. Gene silencing refers to

A) the splicing of mRNA into alternative transcripts.
B) defense mechanisms against RNA viruses.
C) mechanisms inhibiting gene expression.
D) the modification of genes through RNA-mediated mutation.

Question 72

Which type of RNA facilitates RNA interference by resulting in degraded mRNA?

A) snoRNA
B) siRNA
C) miRNA
D) rRNA

Question 73

Which is the correct order of mRNA degradation?

A) (1) poly(A) tail removal; (2) 7-methylguanosine cap removal; (3) RNA hydrolysis
B) (1) 7-methylguanosine cap removal; (2) RNA hydrolysis; (3) poly(A) tail removal
C) (1) 7-methylguanosine cap removal; (2) poly(A) tail removal; (3) RNA hydrolysis
D) (1) RNA hydrolysis; (2) Poly(A) tail removal; (3) 7-methylguanosine cap removal

Question 74

Using the picture below, describe the three ways that RNA is a highly dynamic biomolecule.

Question 75

A common RNA base modification is

A) methylation.
B) amination.
C) carboxylation.
D) hydroxylation.

Question 76

Different mRNAs can be obtained from the same gene by

A) terminating transcription at different stop codons.
B) splicing the mRNA with different exons.
C) adding the 7-methylguanosine cap at different sites.
D) alternate folding of mRNA.

Question 77

Which enzyme is responsible for adding the poly(A) tail to mRNA?

A) cleavage stimulatory factor (CStF)
B) poly(A) polymerase
C) cleavage and polyadenylation specificity factor (CPSF)
D) poly(A) binding protein

Question 78

List the four ways that long noncoding RNAs are thought to function.

Question 79

List the three main ways that eukaryotic mRNA molecules are processed before translation, which prokaryotic organisms to do not require.

Question 80

Name the RNA molecules involved in protein expression and synthesis that are found in both prokaryotic and eukaryotic organisms, and name the RNA molecules involved in protein expression and synthesis only in eukaryotic organisms.